From 55d7fa206762b38713bfb1c05287a414a9562ae8 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Wed, 12 Aug 2026 15:27:39 +0200
Subject: [PATCH 01/46] feat: add Sankoff parsimony model and directory locking

Implements a calibrated 16-state Sankoff substitution cost matrix and CLI pipeline for evolutionary distance computation, including empirical calibration via saturation-filtered SNP counts. Refactors the sibling scanning stage to use batched transforms for improved synchronization efficiency. Introduces an OS-level advisory directory lock across all index-modifying commands to prevent concurrent write corruption. Updates dependencies and exposes new Sankoff utilities in the public API.
---
 docmd/theory/evolutionary_distances.md | 172 ++++++---
 nj.nwk                                 |   1 +
 sankoff_params.yaml                    |  27 ++
 src/Cargo.lock                         | 154 +++++++-
 src/obikindex/src/lib.rs               |   7 +-
 src/obikindex/src/sankoff.rs           | 402 ++++++++++++++++++++
 src/obikindex/src/siblings.rs          | 306 ++++++++++-----
 src/obikmer/Cargo.toml                 |   8 +-
 src/obikmer/src/cmd/distance.rs        | 505 ++++++++++++++++++++++++-
 src/obikmer/src/cmd/filter.rs          |   7 +
 src/obikmer/src/cmd/index.rs           |  10 +
 src/obikmer/src/cmd/merge.rs           |   7 +
 src/obikmer/src/cmd/pack.rs            |   7 +
 src/obikmer/src/cmd/reindex.rs         |   7 +
 src/obikmer/src/cmd/select.rs          |  10 +
 src/obisys/Cargo.toml                  |   1 +
 src/obisys/src/lib.rs                  |  43 +++
 17 files changed, 1494 insertions(+), 180 deletions(-)
 create mode 100644 nj.nwk
 create mode 100644 sankoff_params.yaml
 create mode 100644 src/obikindex/src/sankoff.rs

diff --git a/docmd/theory/evolutionary_distances.md b/docmd/theory/evolutionary_distances.md
index f927381e..b1fd239f 100644
--- a/docmd/theory/evolutionary_distances.md
+++ b/docmd/theory/evolutionary_distances.md
@@ -379,84 +379,156 @@ per pair loses. Not yet run.
 
 ### A concrete Sankoff cost matrix for the 16-state alphabet
 
+**Why `c_gl` and `c_ctx` are the same constant, not two.** An earlier version
+of this design used two independent parameters: `c_gl` for an ordinary
+gain/loss step between two nonempty states (e.g. `{A,C}->{A}`), and `c_ctx`
+only for a state collapsing all the way to `∅`. That distinction doesn't
+survive contact with what the index actually observes. Presence/absence
+tracking never sees "the flanks" separately from "the centre" — it sees
+whole, distinct, homologous 31-mers (two 31-mers sharing >=30 bases are
+homologous by construction, though orthology vs. paralogy is undecidable
+from that alone — settled earlier, see "Locus eligibility"). Losing the `A`
+form of a family while `C` remains (`{A,C}->{C}`) and losing the last
+remaining form (`{A}->∅`) are the *same kind of event*: a specific, complete
+31-mer that used to be observed no longer is, because at least one of its
+31 positions mutated. There is no separate "gain/loss of a still-recognised
+allele" mechanism distinct from "loss of context" — both are exactly the
+event `c_ctx(p)` (below) already computes the expected cost of. So: one
+constant, `c_ctx`, used everywhere a member is gained or lost — `X -> ∅`
+included, and (see next point) not even as a special case there.
+
 **Set-edit-distance formula.** For two states `X, Y ⊆ {A,C,G,T}`, split into
 `seulement_X = X \ Y` (size `a`) and `seulement_Y = Y \ X` (size `b`).
 Elements present in both cost nothing. Pair up to `min(a,b)` of the
 remaining elements as **substitutions** (cheaper than treating them as an
-unrelated loss + gain whenever `c_sub < 2*c_gl`, which any sane parameter
+unrelated loss + gain whenever `c_sub < 2*c_ctx`, which any sane parameter
 choice satisfies); whatever is left over after pairing is a pure
 **gain/loss**:
 
 ```
-cost(X,Y) = min(a,b)*c_sub + |a-b|*c_gl
+cost(X,Y) = min(a,b)*c_sub + |a-b|*c_ctx
 ```
 
-Worked examples (`c_sub = c_gl = 1`): `{A}->{C}` = 1 (one substitution);
+Worked examples (`c_sub = c_ctx = 1`): `{A}->{C}` = 1 (one substitution);
 `{A}->{A,C}` = 1 (one gain, no substitution pair available since nothing is
 only-in-Y that matches an only-in-X element after the shared `A` is
 excluded); `{A,C}->{G,T}` = 2 (two substitution pairs, `A/C` vs `G/T`, both
 same-size sets share nothing); `{A,C,G}->{A,C,T}` = 1 (`G`/`T` is the only
 mismatched pair, `A,C` shared).
 
-**`∅` is a flat-cost special case, not a instance of the general formula.**
-Applying the formula naively to e.g. `{A,C,G} -> ∅` would charge `3*c_gl`
-(three independent losses). Reject that: total context disappearance
-(flank-breaking, or true structural loss) is plausibly **one** event, not
-`|X|` of them, so:
+**`∅` is *not* a flat-cost special case — a corrected position, reversing
+an earlier draft of this design.** An earlier version charged
+`cost(X, ∅) = c_ctx` flat, independent of `|X|`, on the grounds that every
+member of a family shares identical flanking sequence, so one mutation
+breaking that context should unrecognise all of them at once rather than
+`|X|` separate times. That argument doesn't survive comparison with how the
+rest of the matrix already works: `{A,C,T} -> {A}` (losing two members,
+one remaining) is charged `2*c_ctx` via the general formula above, with no
+equivalent "maybe it was one shared event" discount — nothing distinguishes
+that case from `{A,C} -> ∅` (losing two members, none remaining) other than
+which state happens to be the target. Singling out `∅` for special
+treatment was arbitrary, not principled: the uncertainty about "one event
+or several" is identical in both cases, and the model already resolves it
+uniformly elsewhere by simply counting elements. So `∅` is now an ordinary
+node in the state graph below like any other, with no patch applied
+afterwards:
 
 ```
-cost(X, ∅) = cost(∅, X) = c_ctx   (constant, independent of |X|)
+cost(X, ∅) = cost(∅, X) = |X| * c_ctx   (via |X| single-element graph edges)
 cost(∅, ∅) = 0
 ```
 
-`c_ctx` should not be guessed — it is exactly the value already derived for
-the `>1` bucket in "Context, detectability, and a 3-way ordinal distance per
-pair" above (`(2m*p_hat)/(1-(1-p_hat)^(2m)) + p_hat`), reused rather than
-invented.
+**Computing `c_ctx`.** Not guessed — built from the value already derived
+for the `>1` bucket in "Context, detectability, and a 3-way ordinal
+distance per pair" above:
+
+```
+c_ctx(p) = mean_sub_cost * [(2m*p) / (1 - (1-p)^(2m)) + p]
+```
+
+`p` is `p_hat`, the calibrated per-site mutation probability (see
+`calibrate_p_hat` / the "Experiment" section below); `m = (k-1)/2`, the
+flank length on each side of the centre (`k=31` → `m=15`). Read the
+bracketed term, well, term by term: `(1-p)^(2m)` is the probability that
+*none* of the `2m` flanking positions mutated, so `1-(1-p)^(2m)` is the
+probability that *at least one* did — i.e. the probability that this
+specific 31-mer stops being observable at all, which is exactly the event
+`c_ctx` prices. `2m*p` is the unconditional expected mutation count over
+those `2m` positions. Their ratio is the conditional expectation
+`E[mutations | at least one occurred]` — provable directly: for any
+nonnegative integer random variable `X`, `X · 1{X>=1} = X` always (both
+sides are `0` when `X=0`, both are `X` otherwise), so
+`E[X | X>=1] = E[X·1{X>=1}]/P(X>=1) = E[X]/P(X>=1)`, which is
+`(2m*p)/(1-(1-p)^(2m))` here. The trailing `+p` adds the (much smaller,
+first-order, not itself a conditional expectation) marginal contribution
+of the centre position's own mutation probability.
+
+**The `mean_sub_cost` multiplier — a correction, not part of the original
+derivation.** The bracketed term is a *count* of expected mutations, not a
+cost — an earlier version used it directly as `c_ctx`, implicitly pricing
+every one of those mutations at a flat `1` regardless of type. That stopped
+being defensible once substitution costs were calibrated per base-pair
+category (`substitution_costs_from_tally`): transitions are markedly more
+frequent than transversions in this project's own data (roughly 5-6x, e.g.
+130k vs. 20-28k observed instances per category in the eubacteria run
+below) and correspondingly cheaper, so "one mutation" isn't worth a flat
+unit. `mean_sub_cost` (`mean_substitution_cost`) is the empirical average
+substitution cost, weighted by each category's observed frequency — it
+converts the bracketed term's expected mutation *count* into an actual
+expected *cost*. Concretely, in the eubacteria run: the bracketed term
+alone is `~1.17` (close to `1`, i.e. context loss is *usually* attributable
+to a single mutation, since `p_hat` is small); `mean_sub_cost ~= 1.48`
+(pulled up from the cheapest transition cost of `1.0` by the substantial
+minority of transversions in the mix); final `c_ctx ~= 1.73` — sensibly
+between the cheapest transition (`~1.0`) and the transversion costs
+(`~2.5`-`2.9`), rather than coinciding almost exactly with the cheapest
+transition purely by construction accident, which is what the unmultiplied
+version did and which is what exposed this gap in the first place.
 
 **Better construction method: shortest path in a small state graph, not the
-closed-form formula directly.** Build a graph on the 16 states with two edge
-types — substitution edges between same-cardinality sets differing by one
-element (weight `c_sub`, or `c_ts`/`c_tv` if split further below), and
-gain/loss edges between sets whose cardinality differs by one (weight
-`c_gl`) — then define `cost(X,Y)` as shortest-path distance in that graph,
-precomputed once (16 nodes, trivial) into a dense 16x16 matrix before
-feeding it to Sankoff/TNT. Verified equivalent to the closed-form formula
-above in the uniform-cost case (checked by hand on `{A}->{C,G,T}`: both give
-`c_sub + 2*c_gl`). The graph construction is not just a reformulation for
+closed-form formula directly.** Build a graph on all 16 states, `∅`
+included, with two edge types — substitution edges between same-cardinality
+sets differing by one element (weight `c_sub`, or `c_ts`/`c_tv` if split
+further below), and gain/loss edges between sets whose cardinality differs
+by one (weight `c_ctx`, per the unification above; `∅` connects to each
+singleton state this way, being a strict subset of it) — then define
+`cost(X,Y)` as shortest-path distance in that graph, uniformly for every
+`X,Y` including `∅`, precomputed once (16 nodes, trivial) into a dense
+16x16 matrix before feeding it to Sankoff/TNT. Verified equivalent to the
+closed-form formula above in the
+uniform-cost case (checked by hand on `{A}->{C,G,T}`: both give
+`c_sub + 2*c_ctx`). The graph construction is not just a reformulation for
 its own sake: it is the version that generalises correctly once substitution
 costs stop being uniform (next point) — the closed-form's `min(a,b)`
 counting silently assumes *any* pairing costs the same, which breaks the
 moment `c_sub` depends on which two bases are involved.
 
-**Transition/transversion refinement.** Split `c_sub` into `c_ts` (A<->G or
-C<->T) and `c_tv` (the other four pairs) — already well-defined in canonical
-space (see "Canonical invariance" above: a transition maps to a transition,
-a transversion to a transversion, regardless of orientation). This turns
+**Substitution refinement — implemented as the full 6-category symmetric
+matrix, not just Ts/Tv.** `c_sub` was originally going to split into just
+`c_ts` (A<->G or C<->T) and `c_tv` (the other four pairs) — already
+well-defined in canonical space (see "Canonical invariance" above: a
+transition maps to a transition, a transversion to a transversion,
+regardless of orientation). A symmetric cost matrix allows finer
+resolution than that 2-category split, though: each of the 6 distinct
+undirected base pairs (AC, AG, AT, CG, CT, GT) can be costed
+independently, with no grouping at all — `SankoffWeights::sub_cost` is a
+full `[[f64;4];4]` table (`SankoffWeights::ts_tv` remains as a convenience
+constructor for the coarser 2-category case, if ever wanted). This turns
 "pick `min(a,b)` substitution pairs" into a genuine (tiny, <=4 elements per
 side, trivially enumerable) minimum-cost bipartite matching problem instead
 of a plain count — the state-graph shortest-path construction handles this
-automatically, no separate logic needed. Calibration is not a guess either:
-the "Sufficient statistic: 4x4 base-pair tally" section below already plans
-to collect the joint `(centre_i, centre_j)` distribution over resolved (`0`
-or `1`) sites — that tally directly gives the empirical Ts/Tv ratio, from
-which `c_ts`/`c_tv` follow (e.g. `cost ∝ -log(observed rate)`, the standard
-generalised-parsimony step-weighting heuristic), reusing a statistic already
-planned rather than adding a new one.
-
-**`gamma`/`mu` (i.e. `c_gl`/`c_sub`) sensitivity sweep before calibration.**
-No strong prior on whether gain/loss events should cost more or less than a
-point substitution — duplication/deletion rates are not a priori equal to
-point-mutation rates, but the direction isn't obvious, and setting it too
-high risks the parsimony search *eliminating* exactly the
-heterozygosity/paralogy signal the design is meant to tolerate (see
-"Heterozygosity, ploidy..." below). Cheap first step: run the topology at a
-handful of ratios (`0.5, 1, 2, 5`) and check whether it's stable — a robust
-topology across that range is far more trustworthy than one built on a
-single, unvalidated guess. Empirical calibration of `c_gl` from the
-family-size distribution already available (`sibling_annex_stats`) is a
-natural follow-up once the sensitivity sweep shows the topology is worth
-refining further.
+automatically, no separate logic needed. Calibration is not a guess
+either: `KmerIndex::base_pair_tally` collects the pooled `(centre_i,
+centre_j)` distribution over resolved (SNP) sites — restricted to the same
+ratio-ceiling-included genome pairs as `p_hat`'s own calibration, for the
+same saturation-exclusion reason — and `substitution_costs_from_tally`
+turns that into `cost(a,b) = -ln(rate(a,b))`, normalised so the most
+frequent category costs `1.0` (the standard generalised-parsimony
+step-weighting heuristic, generalised from 2 categories to 6). A second
+full pass over the annex is required for this (see `base_pair_tally`'s own
+docs for why it can't share `raw_snp_distance`'s single pass) — both now
+share one traversal helper, `scan_family_pairs`, rather than duplicating
+the per-family reconciliation logic.
 
 **Caveat carried over from the `D_F = min(a,b)` rejection earlier:** this
 cost matrix is only valid as **Sankoff step-cost input**, re-evaluated for
@@ -469,7 +541,7 @@ specific genomes.
 
 **Feasibility confirmed:** TNT's `costs` command accepts custom step
 matrices for multistate characters, so this whole construction (16x16
-matrix derived from the state graph, `c_ts`/`c_tv`/`c_gl`/`c_ctx` as
+matrix derived from the state graph, `c_ts`/`c_tv`/`c_ctx` as the three
 tunable parameters) is directly usable there — no new tooling required
 before testing it.
 
@@ -491,7 +563,9 @@ emits a complete TNT script (`xread` matrix + `smatrix` step-matrix + `hold`/
 `write_raw_snp_distance_csv` to emit raw counts, `c_ctx` was approximated as
 the unweighted mean of the pairwise `snp/(snp+shared)` ratios already
 present in `rawsnp.csv`, restricted to the relevant taxon subset. Used
-values: `mu = gamma = 10`, `c_ctx = 18` (ratio `c_ctx/mu = 1.8`, consistent
+values: `mu = gamma = 10`, `c_ctx = 18` (this run predates the `c_gl`/`c_ctx`
+unification above — `gamma` here is what `c_gl` was called before it turned
+out to just be `c_ctx`; ratio `c_ctx/mu = 1.8`, consistent
 with the observed pairwise ratios for genomes within Enterobacteriaceae/
 Eubacteria, which cluster around 1.5-2 and barely move as the taxon set
 widens — the context signal is stable, not sensitive to which subset is
diff --git a/nj.nwk b/nj.nwk
new file mode 100644
index 00000000..47b92b3a
--- /dev/null
+++ b/nj.nwk
@@ -0,0 +1 @@
+(((((((((((((Salmonella_enterica--P125109:0.009029074806027838,Salmonella_enterica--LT2:0.010374535686866677):0.00299392644685007,Salmonella_enterica--AKU_12601:0.010129090864056669):0.008889984754373365,Salmonella_enterica--CT18:0.029563522158784489):0.05178212639099835,(Escherichia_coli--CFT073:0.018265758526676266,(Escherichia_coli--EDL933:0.01586939152374907,(Escherichia_coli--K-12_MG1655:0.0043321525684933419,Escherichia_coli--K-12_W3110:0.004373581717010194):0.007835004272817602):0.005522415854494232):0.05395833543383322):0.007199364670842333,(Klebsiella_pneumoniae--HS11286:0.027306681424389149,(Klebsiella_pneumoniae--ATCC_13883:0.015176538442299506,Klebsiella_pneumoniae--MGH_78578:0.026462018414958045):0.0015885400482290244):0.060738462006352359):0.029481404183583916,Yersinia_ruckeri--YRB:0.10269826524749153):0.004316815340436764,Proteus_mirabilis--HI4320:0.11745645944715785):0.04439101156727093,Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1:0.17151356406519997):0.011344480816758762,Acidobacterium_capsulatum--ATCC_51196:0.17121217909071463):0.01869709592355495,Shouchella_clausii--KSM-K16:0.1554729916092201):0.04397682726757515,Bacillus_subtilis--168:0.10403127799132669):0.08828869671555731,Opitutus_terrae--PB90-1:0.06380512639846864):0.41655625366738377,Candidozyma_auris--GCF_003013715.1_ASM301371v2:0.22735026269091164,Saccharolobus_islandicus--M.16.4:0.21891918239548398);
\ No newline at end of file
diff --git a/sankoff_params.yaml b/sankoff_params.yaml
new file mode 100644
index 00000000..6bb64d96
--- /dev/null
+++ b/sankoff_params.yaml
@@ -0,0 +1,27 @@
+ratio_ceiling: 0.5
+flank_length_m: 15
+p_hat: 0.010713940022064144
+p_hat_variance: 3.2110559785689563e-10
+n_pairs_included: 158
+n_loci_total: 33008305
+mean_sub_cost: 1.4764371767846869
+c_ctx: 1.7343663443925388
+substitutions:
+- pair: A/C
+  count: 27810
+  cost: 2.5439415226130238
+- pair: A/G
+  count: 130153
+  cost: 1.0
+- pair: A/T
+  count: 24555
+  cost: 2.6684722241428322
+- pair: C/G
+  count: 19637
+  cost: 2.892062911764701
+- pair: C/T
+  count: 124878
+  cost: 1.0413902163542994
+- pair: G/T
+  count: 26616
+  cost: 2.5878424665170052
diff --git a/src/Cargo.lock b/src/Cargo.lock
index 72bc2355..4acaca3b 100644
--- a/src/Cargo.lock
+++ b/src/Cargo.lock
@@ -48,6 +48,15 @@ dependencies = [
  "as-slice",
 ]
 
+[[package]]
+name = "aligned-vec"
+version = "0.6.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "dc890384c8602f339876ded803c97ad529f3842aba97f6392b3dba0dd171769b"
+dependencies = [
+ "equator",
+]
+
 [[package]]
 name = "allocator-api2"
 version = "0.2.21"
@@ -497,6 +506,18 @@ dependencies = [
  "windows-sys 0.59.0",
 ]
 
+[[package]]
+name = "console"
+version = "0.16.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4fe5f465a4f6fee88fad41b85d990f84c835335e85b5d9e6e63e0d06d28cba7c"
+dependencies = [
+ "encode_unicode",
+ "libc",
+ "unicode-width",
+ "windows-sys 0.61.2",
+]
+
 [[package]]
 name = "const-oid"
 version = "0.10.2"
@@ -820,6 +841,26 @@ dependencies = [
  "syn",
 ]
 
+[[package]]
+name = "equator"
+version = "0.4.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4711b213838dfee0117e3be6ac926007d7f433d7bbe33595975d4190cb07e6fc"
+dependencies = [
+ "equator-macro",
+]
+
+[[package]]
+name = "equator-macro"
+version = "0.4.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "44f23cf4b44bfce11a86ace86f8a73ffdec849c9fd00a386a53d278bd9e81fb3"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn",
+]
+
 [[package]]
 name = "equivalent"
 version = "1.0.2"
@@ -907,6 +948,16 @@ dependencies = [
  "percent-encoding",
 ]
 
+[[package]]
+name = "fs4"
+version = "0.9.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e8c6b3bd49c37d2aa3f3f2220233b29a7cd23f79d1fe70e5337d25fb390793de"
+dependencies = [
+ "rustix 0.38.44",
+ "windows-sys 0.52.0",
+]
+
 [[package]]
 name = "fs_at"
 version = "0.2.1"
@@ -1228,13 +1279,26 @@ version = "0.17.11"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "183b3088984b400f4cfac3620d5e076c84da5364016b4f49473de574b2586235"
 dependencies = [
- "console",
+ "console 0.15.11",
  "number_prefix",
  "portable-atomic",
  "unicode-width",
  "web-time",
 ]
 
+[[package]]
+name = "indicatif"
+version = "0.18.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9433806cd6b4ec1aba79c021c7e4c58fb4c3b9977c085062e611ac929998fb0c"
+dependencies = [
+ "console 0.16.4",
+ "portable-atomic",
+ "unicode-width",
+ "unit-prefix",
+ "web-time",
+]
+
 [[package]]
 name = "infer"
 version = "0.19.0"
@@ -1326,12 +1390,9 @@ dependencies = [
 
 [[package]]
 name = "kodama"
-version = "0.2.3"
+version = "0.3.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7a44f3a71a44fbf49ce38152db7dc9adf959d4fe5c29344cd1858bdbda8d9091"
-dependencies = [
- "num-traits",
-]
+checksum = "f868feceed4703c842925c14232667c5f29c8059d0354154b2d06ec3bf9daf82"
 
 [[package]]
 name = "lazy_static"
@@ -1365,6 +1426,12 @@ dependencies = [
  "pkg-config",
 ]
 
+[[package]]
+name = "linux-raw-sys"
+version = "0.4.15"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d26c52dbd32dccf2d10cac7725f8eae5296885fb5703b261f7d0a0739ec807ab"
+
 [[package]]
 name = "linux-raw-sys"
 version = "0.12.1"
@@ -1695,7 +1762,7 @@ version = "0.1.0"
 dependencies = [
  "crossbeam-channel",
  "hwlocality",
- "indicatif",
+ "indicatif 0.17.11",
  "ndarray",
  "obicompactvec",
  "obikpartitionner",
@@ -1720,7 +1787,7 @@ version = "1.1.44"
 dependencies = [
  "clap",
  "csv",
- "indicatif",
+ "indicatif 0.18.6",
  "kodama",
  "obidebruinj",
  "obifastwrite",
@@ -1737,7 +1804,9 @@ dependencies = [
  "obitaxonomy",
  "pprof",
  "rayon",
+ "serde",
  "serde_json",
+ "serde_yaml",
  "speedytree",
  "tracing",
  "tracing-subscriber",
@@ -1749,7 +1818,7 @@ version = "0.1.0"
 dependencies = [
  "cacheline-ef",
  "epserde",
- "indicatif",
+ "indicatif 0.17.11",
  "memmap2",
  "niffler 3.0.0",
  "obicompactvec",
@@ -1853,7 +1922,7 @@ dependencies = [
  "memmap2",
  "niffler 3.0.0",
  "obikseq",
- "rustix",
+ "rustix 1.1.4",
  "serde",
  "serde_json",
  "tempfile",
@@ -1863,7 +1932,8 @@ dependencies = [
 name = "obisys"
 version = "0.1.0"
 dependencies = [
- "indicatif",
+ "fs4",
+ "indicatif 0.17.11",
  "libc",
  "sysinfo",
  "tracing",
@@ -2017,10 +2087,11 @@ dependencies = [
 
 [[package]]
 name = "pprof"
-version = "0.13.0"
+version = "0.15.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ef5c97c51bd34c7e742402e216abdeb44d415fbe6ae41d56b114723e953711cb"
+checksum = "38a01da47675efa7673b032bf8efd8214f1917d89685e07e395ab125ea42b187"
 dependencies = [
+ "aligned-vec",
  "backtrace",
  "cfg-if",
  "findshlibs",
@@ -2028,15 +2099,15 @@ dependencies = [
  "log",
  "nix 0.26.4",
  "once_cell",
- "parking_lot",
  "prost",
  "prost-build",
  "prost-derive",
  "sha2",
  "smallvec",
+ "spin",
  "symbolic-demangle",
  "tempfile",
- "thiserror 1.0.69",
+ "thiserror 2.0.18",
 ]
 
 [[package]]
@@ -2386,6 +2457,19 @@ dependencies = [
  "semver",
 ]
 
+[[package]]
+name = "rustix"
+version = "0.38.44"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "fdb5bc1ae2baa591800df16c9ca78619bf65c0488b41b96ccec5d11220d8c154"
+dependencies = [
+ "bitflags 2.11.1",
+ "errno",
+ "libc",
+ "linux-raw-sys 0.4.15",
+ "windows-sys 0.59.0",
+]
+
 [[package]]
 name = "rustix"
 version = "1.1.4"
@@ -2395,7 +2479,7 @@ dependencies = [
  "bitflags 2.11.1",
  "errno",
  "libc",
- "linux-raw-sys",
+ "linux-raw-sys 0.12.1",
  "windows-sys 0.61.2",
 ]
 
@@ -2521,6 +2605,19 @@ dependencies = [
  "zmij",
 ]
 
+[[package]]
+name = "serde_yaml"
+version = "0.9.34+deprecated"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "6a8b1a1a2ebf674015cc02edccce75287f1a0130d394307b36743c2f5d504b47"
+dependencies = [
+ "indexmap",
+ "itoa",
+ "ryu",
+ "serde",
+ "unsafe-libyaml",
+]
+
 [[package]]
 name = "sha2"
 version = "0.10.9"
@@ -2588,6 +2685,15 @@ dependencies = [
  "rb_tree",
 ]
 
+[[package]]
+name = "spin"
+version = "0.10.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "023a211cb3138dbc438680b32560ad89f699977624c9f8dbb95a47d5b4c07dd3"
+dependencies = [
+ "lock_api",
+]
+
 [[package]]
 name = "stable_deref_trait"
 version = "1.2.1"
@@ -2736,7 +2842,7 @@ dependencies = [
  "fastrand",
  "getrandom 0.3.4",
  "once_cell",
- "rustix",
+ "rustix 1.1.4",
  "windows-sys 0.61.2",
 ]
 
@@ -2920,6 +3026,18 @@ version = "0.2.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "ebc1c04c71510c7f702b52b7c350734c9ff1295c464a03335b00bb84fc54f853"
 
+[[package]]
+name = "unit-prefix"
+version = "0.5.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "81e544489bf3d8ef66c953931f56617f423cd4b5494be343d9b9d3dda037b9a3"
+
+[[package]]
+name = "unsafe-libyaml"
+version = "0.2.11"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "673aac59facbab8a9007c7f6108d11f63b603f7cabff99fabf650fea5c32b861"
+
 [[package]]
 name = "untrusted"
 version = "0.9.0"
@@ -3421,7 +3539,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "32e45ad4206f6d2479085147f02bc2ef834ac85886624a23575ae137c8aa8156"
 dependencies = [
  "libc",
- "rustix",
+ "rustix 1.1.4",
 ]
 
 [[package]]
diff --git a/src/obikindex/src/lib.rs b/src/obikindex/src/lib.rs
index 48daf548..a48eb325 100644
--- a/src/obikindex/src/lib.rs
+++ b/src/obikindex/src/lib.rs
@@ -8,6 +8,7 @@ mod merge;
 mod numa;
 mod rebuild;
 mod reindex;
+mod sankoff;
 mod select;
 mod siblings;
 mod stats;
@@ -19,4 +20,8 @@ pub use merge::MergeMode;
 pub use meta::{validate_label, GenomeInfo, IndexConfig, IndexMeta, META_FILENAME};
 pub use state::{IndexState, SENTINEL_COUNTED, SENTINEL_INDEXED, SENTINEL_SCATTERED};
 pub use stats::IndexBitsPerKmer;
-pub use siblings::{RawSnpDistanceOutput, SiblingAnnexStats, SnpAlignment};
+pub use siblings::{BasePairTally, RawSnpDistanceOutput, SiblingAnnexStats, SnpAlignment};
+pub use sankoff::{
+    build_cost_matrix, c_ctx_from_p_hat, calibrate_p_hat, mean_substitution_cost,
+    substitution_costs_from_tally, PHatEstimate, SankoffWeights,
+};
diff --git a/src/obikindex/src/sankoff.rs b/src/obikindex/src/sankoff.rs
new file mode 100644
index 00000000..372ed21e
--- /dev/null
+++ b/src/obikindex/src/sankoff.rs
@@ -0,0 +1,402 @@
+//! Sankoff parsimony cost matrix for the 16-state (powerset of `{A,C,G,T}`)
+//! family alphabet, and calibration of its parameters from real pairwise
+//! SNP/shared counts. See `docmd/theory/evolutionary_distances.md`,
+//! "Sankoff parsimony as the resolution of the 16-state model problem".
+
+use crate::{BasePairTally, RawSnpDistanceOutput};
+
+/// Transition base pairs in the project's fixed bit convention (see
+/// `siblings::central_base`: bit 0=A, 1=C, 2=G, 3=T). All other single-bit
+/// swaps are transversions.
+const TRANSITION_PAIRS: [(u8, u8); 2] = [(0, 2), (1, 3)]; // A<->G, C<->T
+
+/// Tunable weights for the 16-state Sankoff cost matrix — see "A concrete
+/// Sankoff cost matrix for the 16-state alphabet" in the design doc.
+///
+/// Only two costs, not three: an earlier version had a separate `c_gl` for
+/// "gain/loss between two nonempty states" alongside `c_ctx` for "collapse
+/// to `∅`", but presence/absence tracking never observes "the flanks"
+/// independently of a whole 31-mer — losing one member of a family while
+/// others remain (`{A,C}->{A}`) and losing the last one (`{A}->∅`) are the
+/// same event: a specific, complete, homologous 31-mer that used to be
+/// observed no longer is. Both are exactly what `c_ctx` (see
+/// `c_ctx_from_p_hat`) prices, so it is used for every gain/loss uniformly
+/// — including a compound family losing several members at once, `∅`
+/// included, which costs `|X|*c_ctx` (no flat shortcut for `∅`: see
+/// `build_cost_matrix`'s docs for why an earlier version's flat special
+/// case there didn't hold up).
+#[derive(Debug, Clone, Copy)]
+pub struct SankoffWeights {
+    /// Cost of a single-base substitution `a <-> b` (`a != b`), symmetric
+    /// (`sub_cost[a][b] == sub_cost[b][a]`) and only meaningful off the
+    /// diagonal. The full 6-category (AC, AG, AT, CG, CT, GT) resolution a
+    /// symmetric cost matrix allows — see `substitution_costs_from_tally`
+    /// for calibrating it from real data, or `SankoffWeights::ts_tv` for
+    /// the coarser 2-category (transition/transversion) convenience
+    /// constructor.
+    pub sub_cost: [[f64; 4]; 4],
+    /// Cost of losing or gaining one family member — the same constant
+    /// everywhere a member is gained or lost, member count and target state
+    /// (`∅` or not) included: see the struct docs.
+    pub c_ctx: f64,
+}
+
+impl SankoffWeights {
+    /// Convenience constructor for the coarser 2-category
+    /// (transition/transversion) substitution model: every transition pair
+    /// (A<->G, C<->T) costs `c_ts`, every transversion pair costs `c_tv`.
+    pub fn ts_tv(c_ts: f64, c_tv: f64, c_ctx: f64) -> Self {
+        let mut sub_cost = [[0.0; 4]; 4];
+        for a in 0..4usize {
+            for b in 0..4usize {
+                if a == b {
+                    continue;
+                }
+                let is_ts = TRANSITION_PAIRS.contains(&(a as u8, b as u8));
+                sub_cost[a][b] = if is_ts { c_ts } else { c_tv };
+            }
+        }
+        Self { sub_cost, c_ctx }
+    }
+}
+
+/// Build the 16x16 Sankoff step-cost matrix, states indexed `0..=15` by
+/// their bitmask (matching `siblings::iupac_code`'s convention — state `0`
+/// is `∅`).
+///
+/// All 16 states, `∅` included, form a single graph: an edge of weight
+/// `c_ts`/`c_tv` between two states of equal cardinality differing by
+/// exactly one element (classified by whether the swapped bases form a
+/// transition or transversion pair), and an edge of weight `c_ctx` between
+/// a state and one that is its strict subset plus exactly one element
+/// (`∅` is a strict subset of every singleton state, so it connects
+/// directly to each of them this way — no special case). `cost(X, Y)` is
+/// the shortest-path distance in that graph (16 nodes — Floyd-Warshall,
+/// trivial at this size), uniformly, including `X <-> ∅`: a compound
+/// family losing several members at once, `∅` included, costs `|X|*c_ctx`
+/// via that many single-element steps — no cheaper flat alternative for
+/// `∅` specifically, since nothing distinguishes it from any other
+/// multi-element loss (see design doc — an earlier flat special case here
+/// was inconsistent with how every *other* multi-element transformation is
+/// already priced, and had no principled justification once that was
+/// noticed).
+pub fn build_cost_matrix(w: &SankoffWeights) -> [[f64; 16]; 16] {
+    const INF: f64 = f64::INFINITY;
+    let mut dist = [[INF; 16]; 16];
+    for (i, row) in dist.iter_mut().enumerate() {
+        row[i] = 0.0;
+    }
+
+    for x in 0u8..16 {
+        for y in (x + 1)..16 {
+            let (xu, yu) = (x as usize, y as usize);
+            let diff = x ^ y;
+            let card_x = x.count_ones();
+            let card_y = y.count_ones();
+            let edge = if card_x == card_y && diff.count_ones() == 2 {
+                // Exactly one element swapped: the bit only in x is the base
+                // leaving, the bit only in y is the base entering.
+                let a = (x & diff).trailing_zeros() as u8;
+                let b = (y & diff).trailing_zeros() as u8;
+                Some(w.sub_cost[a as usize][b as usize])
+            } else if card_x.abs_diff(card_y) == 1 && (x & y) == x.min(y) {
+                // True subset relationship: a pure gain/loss of one element.
+                Some(w.c_ctx)
+            } else {
+                None
+            };
+            if let Some(cost) = edge {
+                dist[xu][yu] = cost;
+                dist[yu][xu] = cost;
+            }
+        }
+    }
+
+    for k in 0..16 {
+        for i in 0..16 {
+            if dist[i][k].is_infinite() {
+                continue;
+            }
+            for j in 0..16 {
+                let via = dist[i][k] + dist[k][j];
+                if via < dist[i][j] {
+                    dist[i][j] = via;
+                }
+            }
+        }
+    }
+
+    dist
+}
+
+/// `p_hat` calibrated from real pairwise SNP/shared counts, restricted to
+/// pairs below `ratio_ceiling`, and its variance as a pooled Bernoulli
+/// proportion.
+#[derive(Debug, Clone, Copy)]
+pub struct PHatEstimate {
+    pub p_hat: f64,
+    /// `p_hat*(1-p_hat) / n_loci_total` — the pooled estimator's variance is
+    /// governed by the total number of loci across all included pairs, not
+    /// by any single pair's count (see design doc: this is why the
+    /// exclusion criterion below is the per-pair *ratio*, not a per-pair
+    /// minimum-count floor — a low-count pair barely moves the pool either
+    /// way, but a saturated pair with plenty of loci would bias it).
+    pub variance: f64,
+    pub n_pairs_included: usize,
+    pub n_loci_total: u64,
+}
+
+/// Pool `snp`/`shared` counts across all genome pairs whose per-pair ratio
+/// `snp/(snp+shared)` is at most `ratio_ceiling`, then estimate
+/// `p_hat = sum(snp) / sum(snp+shared)` over the included pairs.
+///
+/// A pair with no eligible locus at all (`snp+shared == 0`) is always
+/// excluded (nothing to pool). `ratio_ceiling` should be well below 1.0 —
+/// pairs at or near saturation (e.g. cross-domain comparisons, where nearly
+/// every shared central-position family already differs) carry no
+/// information about `p_hat` and bias it upward if pooled in.
+pub fn calibrate_p_hat(raw: &RawSnpDistanceOutput, ratio_ceiling: f64) -> PHatEstimate {
+    let n = raw.snp.nrows();
+    let mut snp_sum: u64 = 0;
+    let mut total_sum: u64 = 0;
+    let mut n_pairs = 0usize;
+    for i in 0..n {
+        for j in (i + 1)..n {
+            let snp = raw.snp[[i, j]];
+            let shared = raw.shared[[i, j]];
+            let total = snp + shared;
+            if total == 0 {
+                continue;
+            }
+            let ratio = snp as f64 / total as f64;
+            if ratio > ratio_ceiling {
+                continue;
+            }
+            snp_sum += snp;
+            total_sum += total;
+            n_pairs += 1;
+        }
+    }
+    let p_hat = if total_sum > 0 { snp_sum as f64 / total_sum as f64 } else { 0.0 };
+    let variance = if total_sum > 0 {
+        p_hat * (1.0 - p_hat) / total_sum as f64
+    } else {
+        0.0
+    };
+    PHatEstimate { p_hat, variance, n_pairs_included: n_pairs, n_loci_total: total_sum }
+}
+
+/// `c_ctx(p) = mean_sub_cost * [(2m*p) / (1 - (1-p)^(2m)) + p]` — see
+/// "Context, detectability, and a 3-way ordinal distance per pair" in the
+/// design doc for the bracketed term's derivation. `m` is the flank length
+/// on *each* side of the central position (`k = 2m+1`); pass `(k-1)/2`, not
+/// the project's minimizer-size parameter of the same name.
+///
+/// The bracketed term is `E[mutation count | at least one occurred]` — a
+/// *count* of mutations, not a cost. An earlier version used it directly as
+/// the cost, implicitly pricing every mutation at a flat `1` regardless of
+/// type. That stopped making sense once substitution costs were calibrated
+/// per base-pair type (`substitution_costs_from_tally`): transitions and
+/// transversions aren't equally likely (roughly 5-6x apart in this
+/// project's own data) nor equally costly, so "one mutation" isn't worth a
+/// flat unit — it's worth whatever the *empirical mix* of mutation types is
+/// worth on average. `mean_sub_cost` (see `mean_substitution_cost`) is that
+/// weighted average, turning the expected mutation *count* into an actual
+/// expected cost.
+pub fn c_ctx_from_p_hat(p_hat: f64, m: usize, mean_sub_cost: f64) -> f64 {
+    if p_hat <= 0.0 {
+        return 0.0;
+    }
+    let two_m = 2.0 * m as f64;
+    let expected_mutations = (two_m * p_hat) / (1.0 - (1.0 - p_hat).powf(two_m)) + p_hat;
+    expected_mutations * mean_sub_cost
+}
+
+/// Mean substitution cost, weighted by each of the 6 base-pair categories'
+/// observed frequency in `tally` — the empirical average cost of "one
+/// mutation" under the calibrated substitution spectrum. Falls back to
+/// `1.0` (a flat per-mutation cost) if `tally` has no signal at all (no
+/// substitution ever observed), rather than dividing by zero.
+pub fn mean_substitution_cost(tally: &BasePairTally, sub_cost: &[[f64; 4]; 4]) -> f64 {
+    let mut weighted_sum = 0.0;
+    let mut total = 0u64;
+    for a in 0..4 {
+        for b in (a + 1)..4 {
+            let count = tally.counts[a][b];
+            weighted_sum += count as f64 * sub_cost[a][b];
+            total += count;
+        }
+    }
+    if total == 0 {
+        return 1.0;
+    }
+    weighted_sum / total as f64
+}
+
+/// Derive the 4x4 symmetric substitution cost table from an observed
+/// [`BasePairTally`]: `cost(a,b) = -ln(rate(a,b))`, normalised so the most
+/// frequently observed substitution type costs exactly `1.0` — the standard
+/// generalised-parsimony step-weighting heuristic (see design doc,
+/// "Transition/transversion refinement"), generalised here from 2
+/// categories (Ts/Tv) to the full 6-category resolution a symmetric matrix
+/// allows: a rarer substitution type is treated as less parsimonious to
+/// invoke, and therefore costs more.
+///
+/// A pair type never observed at all (`counts[a][b] == 0`) gets an infinite
+/// cost — parsimony should never spend a mutation on something with no
+/// empirical support in this data.
+pub fn substitution_costs_from_tally(tally: &BasePairTally) -> [[f64; 4]; 4] {
+    let total: u64 = (0..4)
+        .flat_map(|a| (a + 1..4).map(move |b| (a, b)))
+        .map(|(a, b)| tally.counts[a][b])
+        .sum();
+
+    let mut raw = [[0.0f64; 4]; 4];
+    let mut min_cost = f64::INFINITY;
+    for a in 0..4 {
+        for b in (a + 1)..4 {
+            let count = tally.counts[a][b];
+            let cost = if count > 0 && total > 0 {
+                -((count as f64 / total as f64).ln())
+            } else {
+                f64::INFINITY
+            };
+            raw[a][b] = cost;
+            raw[b][a] = cost;
+            if cost < min_cost {
+                min_cost = cost;
+            }
+        }
+    }
+
+    let mut out = [[0.0f64; 4]; 4];
+    for a in 0..4 {
+        for b in 0..4 {
+            if a != b {
+                out[a][b] = raw[a][b] / min_cost;
+            }
+        }
+    }
+    out
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+    use ndarray::Array2;
+
+    fn weights() -> SankoffWeights {
+        SankoffWeights::ts_tv(1.0, 2.0, 10.0)
+    }
+
+    #[test]
+    fn identity_is_zero() {
+        let m = build_cost_matrix(&weights());
+        for row in m.iter().enumerate() {
+            assert_eq!(m[row.0][row.0], 0.0);
+        }
+    }
+
+    #[test]
+    fn single_base_transition_costs_c_ts() {
+        let m = build_cost_matrix(&weights());
+        // A = 0b0001 (state 1), G = 0b0100 (state 4): A<->G is a transition.
+        assert_eq!(m[1][4], 1.0);
+        assert_eq!(m[4][1], 1.0);
+    }
+
+    #[test]
+    fn single_base_transversion_costs_c_tv() {
+        let m = build_cost_matrix(&weights());
+        // A = 0b0001 (state 1), C = 0b0010 (state 2): A<->C is a transversion.
+        assert_eq!(m[1][2], 2.0);
+    }
+
+    #[test]
+    fn gain_loss_costs_c_ctx() {
+        let m = build_cost_matrix(&weights());
+        // A = 0b0001 (state 1) -> {A,C} = 0b0011 (state 3): pure gain of C.
+        assert_eq!(m[1][3], 10.0);
+    }
+
+    #[test]
+    fn empty_set_costs_scale_with_cardinality() {
+        let m = build_cost_matrix(&weights());
+        assert_eq!(m[0][1], 10.0); // {A} -> ∅: one member, one c_ctx step.
+        // N (all four) -> ∅: no flat shortcut — four single-element steps,
+        // same as losing four members down to a nonempty state would cost.
+        assert_eq!(m[0][15], 40.0);
+        assert_eq!(m[0][0], 0.0);
+    }
+
+    #[test]
+    fn matrix_is_symmetric() {
+        let m = build_cost_matrix(&weights());
+        for i in 0..16 {
+            for j in 0..16 {
+                assert_eq!(m[i][j], m[j][i], "asymmetry at ({i},{j})");
+            }
+        }
+    }
+
+    #[test]
+    fn calibrate_p_hat_excludes_saturated_pairs() {
+        // 3 genomes: pair (0,1) informative (10% SNP), pair (0,2) saturated
+        // (100% SNP) — must be excluded from the pooled estimate.
+        let mut snp = Array2::<u64>::zeros((3, 3));
+        let mut shared = Array2::<u64>::zeros((3, 3));
+        snp[[0, 1]] = 10;
+        shared[[0, 1]] = 90;
+        snp[[1, 0]] = 10;
+        shared[[1, 0]] = 90;
+        snp[[0, 2]] = 50;
+        shared[[0, 2]] = 0;
+        snp[[2, 0]] = 50;
+        shared[[2, 0]] = 0;
+        let raw = RawSnpDistanceOutput { snp, shared };
+
+        let est = calibrate_p_hat(&raw, 0.5);
+        assert_eq!(est.n_pairs_included, 1);
+        assert_eq!(est.n_loci_total, 100);
+        assert!((est.p_hat - 0.1).abs() < 1e-9);
+    }
+
+    #[test]
+    fn c_ctx_from_p_hat_zero_is_zero() {
+        assert_eq!(c_ctx_from_p_hat(0.0, 15, 1.5), 0.0);
+    }
+
+    #[test]
+    fn c_ctx_from_p_hat_matches_known_value() {
+        // p=0.1, m=15: [(30*0.1)/(1-(0.9)^30) + 0.1] * mean_sub_cost
+        let m = 15usize;
+        let p = 0.1;
+        let mean_sub_cost = 1.5;
+        let expected = ((2.0 * m as f64 * p) / (1.0 - (1.0 - p).powf(2.0 * m as f64)) + p) * mean_sub_cost;
+        assert!((c_ctx_from_p_hat(p, m, mean_sub_cost) - expected).abs() < 1e-12);
+    }
+
+    #[test]
+    fn mean_substitution_cost_is_weighted_average() {
+        let mut counts = [[0u64; 4]; 4];
+        counts[0][1] = 3; // A/C
+        counts[1][0] = 3;
+        counts[0][2] = 1; // A/G
+        counts[2][0] = 1;
+        let tally = BasePairTally { counts };
+        let mut sub_cost = [[0.0f64; 4]; 4];
+        sub_cost[0][1] = 2.0;
+        sub_cost[1][0] = 2.0;
+        sub_cost[0][2] = 1.0;
+        sub_cost[2][0] = 1.0;
+        // (3*2.0 + 1*1.0) / 4 = 1.75
+        assert!((mean_substitution_cost(&tally, &sub_cost) - 1.75).abs() < 1e-12);
+    }
+
+    #[test]
+    fn mean_substitution_cost_falls_back_to_one_with_no_data() {
+        let tally = BasePairTally { counts: [[0u64; 4]; 4] };
+        let sub_cost = [[0.0f64; 4]; 4];
+        assert_eq!(mean_substitution_cost(&tally, &sub_cost), 1.0);
+    }
+}
diff --git a/src/obikindex/src/siblings.rs b/src/obikindex/src/siblings.rs
index 90379b2c..dc33bf6a 100644
--- a/src/obikindex/src/siblings.rs
+++ b/src/obikindex/src/siblings.rs
@@ -14,18 +14,25 @@
 //! mask by callers, not stored (see `FamilyMask` and
 //! [`sibling_annex_stats`](KmerIndex::sibling_annex_stats) below).
 //!
-//! Per layer, an `obipipeline` `Flat` stage (throttled — see
-//! `obipipeline::throttle`) generates each k-mer's 3 central variants,
-//! interleaved across many in-flight k-mers by the scheduler's shared
-//! worker pool rather than processed on a single thread. The actual
-//! cross-partition lookup, though, reuses
-//! `KmerPartition::query_partition_with` — the same partition-batching
-//! mechanism `obikmer query` already uses (open a partition's files once,
-//! answer a whole batch of queries against it) — rather than a per-item
-//! pipeline stage: an earlier per-item design reopened/re-mmap'd every
-//! target partition's files on every single lookup, which was fine at
-//! toy scale but manifested as ~90% system time against a real index.
-//! See `docmd/theory/evolutionary_distances.md`, Step 2b, "Mechanism".
+//! Per layer, an `obipipeline` batch transform (throttled — see
+//! `obipipeline::throttle`) generates a whole batch's central variants at
+//! once (`BATCH_SIZE` source k-mers in, that batch's variants out as one
+//! pipeline message), interleaved across many in-flight batches by the
+//! scheduler's shared worker pool rather than processed on a single
+//! thread. The actual cross-partition lookup reuses a `PartitionCache` of
+//! every partition's already-open MPHF layers, built once for the whole
+//! `build_sibling_annex` run, rather than reopening files per lookup or
+//! per source layer. Two earlier, coarser-grained designs were tried and
+//! measured (not guessed) to be worse, in order: (1) reopening/re-mmap'ing
+//! every target partition's files on every single lookup — fine at toy
+//! scale, ~90% system time against a real index; (2) a `Flat` pipeline
+//! stage pushing one message per generated *variant* (up to 3 per source
+//! k-mer) — cheaper than reopening files, but sampling a real run showed
+//! most wall-clock time going into per-message channel send/notify
+//! syscalls rather than the lookup itself, because a single k-mer's ≤3
+//! variants is far too fine a granularity to amortise a pipeline's
+//! synchronisation cost over. See `docmd/theory/evolutionary_distances.md`,
+//! Step 2b, "Mechanism".
 
 use std::path::Path;
 use std::sync::atomic::{AtomicU8, Ordering};
@@ -107,34 +114,30 @@ fn partition_of(kmer: CanonicalKmer, n_partitions: usize) -> usize {
 
 // ── obipipeline data types ─────────────────────────────────────────────────
 
-/// One distinct k-mer of the layer currently being processed, at its local
-/// MPHF slot — the pipeline's source item. Carries a throttle slot (shared,
-/// `Arc`-wrapped so it can be cloned into each of the (up to 3) items this
-/// one fans out into via the `Flat` stage) that is only released once every
-/// one of those descendants has been fully processed — see the module docs'
-/// "Throttling" note for why this is required, not optional, once a `Flat`
-/// stage is in the pipeline.
-struct SourceItem {
-    slot: usize,
-    kmer: CanonicalKmer,
-    _permit: Arc<ThrottleGuard>,
+/// A batch of this layer's distinct k-mers (local MPHF slot + k-mer), the
+/// pipeline's source item — batched, not one k-mer per item, so that
+/// pipeline messages and their synchronisation cost stay amortised over
+/// thousands of lookups (see `build_layer_sibling_annex`'s comment on
+/// `BATCH_SIZE`). Carries the throttle permit for the whole batch, moved
+/// (not cloned) into the corresponding `VariantBatch` — a 1-to-1 transform,
+/// unlike the fan-out `Flat` stage this replaced, needs no `Arc` sharing.
+struct SourceBatch {
+    items: Vec<(usize, CanonicalKmer)>,
+    _permit: ThrottleGuard,
 }
 
-/// One of a source k-mer's (up to 3) central-substitution variants, already
-/// routed to its destination partition and carrying its own central base
-/// (0=A/1=C/2=G/3=T) — the mask bit it will set on a hit. Carries a clone of
-/// the source item's throttle permit.
-struct VariantQuery {
-    source_slot: usize,
-    dest_partition: usize,
-    variant: CanonicalKmer,
-    base: u8,
-    _permit: Arc<ThrottleGuard>,
+/// One batch's worth of central-substitution variants (up to 3 per source
+/// k-mer), each already routed to its destination partition and carrying
+/// its own central base (0=A/1=C/2=G/3=T) — the mask bit it will set on a
+/// hit. `(dest_partition, variant, source_slot, base)` per entry.
+struct VariantBatch {
+    items: Vec<(usize, CanonicalKmer, usize, u8)>,
+    _permit: ThrottleGuard,
 }
 
 enum SibData {
-    Item(SourceItem),
-    Query(VariantQuery),
+    Batch(SourceBatch),
+    Variants(VariantBatch),
 }
 
 /// Every partition's already-open MPHF layers, built **once** for the whole
@@ -341,57 +344,72 @@ impl KmerIndex {
             mask[slot].fetch_or(1 << central_base(kmer, k), Ordering::Relaxed);
         }
 
-        // ── obipipeline: Flat stage generates variants only — the actual
-        // cross-partition lookup reuses `KmerPartition::query_partition_with`
-        // (the same batching mechanism `obikmer query` already uses: open a
-        // partition's files once, answer a whole batch of queries against
-        // it) instead of one lookup per pipeline item. A per-item lookup
-        // (tried first) reopened/re-mmap'd every target partition's files on
-        // every single variant — fine at the scale of a handful of test
-        // k-mers, but with billions of lookups against a real index this
-        // manifested as ~90% system time, observed in practice. ───────────
+        // ── obipipeline: a *batch* transform, not a per-k-mer `Flat` one —
+        // the actual cross-partition lookup reuses
+        // `KmerPartition::query_partition_with` (the same batching mechanism
+        // `obikmer query` already uses: open a partition's files once,
+        // answer a whole batch of queries against it) instead of one lookup
+        // per pipeline item. A per-item lookup (tried first) reopened/
+        // re-mmap'd every target partition's files on every single variant
+        // — fine at toy scale, but ~90% system time against a real index,
+        // observed in practice. A *later* attempt still pushed one pipeline
+        // message per generated variant (a `Flat` stage, `SourceItem` =>
+        // `VariantQuery`, one k-mer in => up to 3 variants out as separate
+        // messages) — cheaper than reopening files, but sampling a real run
+        // showed most wall-clock time going into per-message channel
+        // send/notify syscalls instead of the lookup itself: the pipeline's
+        // whole point is amortising synchronisation over a batch, and a
+        // single k-mer's ≤3 variants is far too fine a granularity for
+        // that. Batching `BATCH_SIZE` source k-mers into one pipeline item
+        // — a plain 1-to-1 (`|`, not `||`) transform, batch in, batch of
+        // variants out, one message either way — keeps the per-message
+        // synchronisation cost amortised over thousands of lookups instead
+        // of one to three. ──────────────────────────────────────────────
+        const BATCH_SIZE: usize = 4096;
         let n_workers = obisys::effective_parallelism();
         let capacity = 256;
 
-        // Throttling is not optional once a `Flat` stage is in the pipeline
-        // (see `obipipeline::throttle`'s docs): without it, every worker can
-        // become a simultaneous `Flat` producer, saturate the shared output
-        // channel, and deadlock against the scheduler's own dispatch loop —
-        // also observed in practice. The permit acquired here for a source
-        // k-mer is held (via the `Arc`-shared guard carried through
-        // `SourceItem` -> `VariantQuery`) until every one of its (up to 3)
-        // descendants has been read out of the pipeline by the accumulation
-        // loop below, not just until the `Flat` stage itself returns.
+        // Throttling limits how many *batches* are in flight at once — the
+        // permit is acquired per batch (not per k-mer) in the source
+        // thread, and released once its `VariantBatch` has been read out of
+        // the pipeline by the accumulation loop below. See
+        // `obipipeline::throttle`'s docs for why this is required, not
+        // optional, once a `Flat`-style stage sits in the pipeline.
         let sources: Vec<(usize, CanonicalKmer)> = slot_kmer
             .iter()
             .enumerate()
             .filter_map(|(slot, maybe_kmer)| maybe_kmer.map(|kmer| (slot, kmer)))
             .collect();
-        let throttled = obipipeline::throttle(sources.into_iter(), n_workers).map(|t| SourceItem {
-            slot: t.item.0,
-            kmer: t.item.1,
-            _permit: Arc::new(t.guard),
+        let batches: Vec<Vec<(usize, CanonicalKmer)>> = sources
+            .chunks(BATCH_SIZE)
+            .map(|chunk| chunk.to_vec())
+            .collect();
+        let throttled = obipipeline::throttle(batches.into_iter(), n_workers).map(|t| SourceBatch {
+            items: t.item,
+            _permit: t.guard,
         });
 
         let pipe = obipipeline::make_pipe! {
-            SibData : SourceItem => VariantQuery,
-            || {
-                move |item: SourceItem| -> Vec<VariantQuery> {
-                    let kmer = item.kmer;
-                    let permit = item._permit;
-                    kmer.central_canonical_neighbors()
-                        .into_iter()
-                        .filter(|variant| *variant != kmer)
-                        .map(|variant| VariantQuery {
-                            source_slot: item.slot,
-                            dest_partition: partition_of(variant, n_parts),
-                            variant,
-                            base: central_base(variant, k),
-                            _permit: Arc::clone(&permit),
-                        })
-                        .collect::<Vec<_>>()
+            SibData : SourceBatch => VariantBatch,
+            | {
+                move |batch: SourceBatch| -> VariantBatch {
+                    let mut items = Vec::with_capacity(batch.items.len() * 3);
+                    for (slot, kmer) in batch.items {
+                        for variant in kmer.central_canonical_neighbors() {
+                            if variant == kmer {
+                                continue;
+                            }
+                            items.push((
+                                partition_of(variant, n_parts),
+                                variant,
+                                slot,
+                                central_base(variant, k),
+                            ));
+                        }
+                    }
+                    VariantBatch { items, _permit: batch._permit }
                 }
-            } : Item => Query,
+            } : Batch => Variants,
         };
 
         // ── Group generated variants by destination partition. `cache`
@@ -400,11 +418,13 @@ impl KmerIndex {
         // lookup is not free just because the file isn't reopened. Grouping
         // keeps one partition's pages hot while its whole batch is resolved,
         // instead of faulting pages in and out as lookups jump between
-        // partitions in whatever order the `Flat` stage happens to produce
-        // them. The throttle permit drops here, once accumulated. ─────────
+        // partitions in whatever order the pipeline happens to produce
+        // them. Each batch's throttle permit drops here, once accumulated.
         let mut outgoing: Vec<Vec<(CanonicalKmer, usize, u8)>> = (0..n_parts).map(|_| Vec::new()).collect();
-        for vq in pipe.apply(throttled, n_workers, capacity) {
-            outgoing[vq.dest_partition].push((vq.variant, vq.source_slot, vq.base));
+        for vb in pipe.apply(throttled, n_workers, capacity) {
+            for (dest_partition, variant, source_slot, base) in vb.items {
+                outgoing[dest_partition].push((variant, source_slot, base));
+            }
         }
 
         // ── Resolve each partition's batch against the cache in one
@@ -635,9 +655,27 @@ pub struct RawSnpDistanceOutput {
 }
 
 impl KmerIndex {
-    /// Compute [`RawSnpDistanceOutput`] from an already-built sibling annex
-    /// (run [`build_sibling_annex`](Self::build_sibling_annex) first).
-    pub fn raw_snp_distance(&self) -> OKIResult<RawSnpDistanceOutput> {
+    /// Shared traversal behind [`raw_snp_distance`](Self::raw_snp_distance)
+    /// and [`base_pair_tally`](Self::base_pair_tally): for every family
+    /// (tallied once, at its minorant) of every layer of the already-built
+    /// sibling annex, resolves each genome's single observed form (`None`
+    /// if absent or ambiguous/multi-copy), then calls `on_pair(acc, i, j,
+    /// bi, bj)` for every genome pair `(i, j)` where both are unambiguous
+    /// and single-copy (`bi == bj` means shared at that locus, `bi != bj`
+    /// means a SNP). Layers are processed in parallel (rayon); each gets
+    /// its own accumulator from `zero()`, combined pairwise via `combine`.
+    fn scan_family_pairs<Acc, F, C>(
+        &self,
+        label: &str,
+        zero: impl Fn() -> Acc + Sync,
+        on_pair: F,
+        combine: C,
+    ) -> OKIResult<Acc>
+    where
+        Acc: Send,
+        F: Fn(&mut Acc, usize, usize, u8, u8) + Sync,
+        C: Fn(Acc, Acc) -> Acc,
+    {
         let n_parts = self.n_partitions();
         let n_genomes = self.meta.genomes.len();
         let with_counts = self.meta.config.with_counts;
@@ -673,12 +711,11 @@ impl KmerIndex {
             }
         }
 
-        let pb = progress_bar("raw_snp_distance", layer_dirs.len() as u64, "layers");
-        let partials: Vec<(Array2<u64>, Array2<u64>)> = layer_dirs
+        let pb = progress_bar(label, layer_dirs.len() as u64, "layers");
+        let partials: Vec<Acc> = layer_dirs
             .par_iter()
-            .map(|layer_dir| -> OKIResult<(Array2<u64>, Array2<u64>)> {
-                let mut snp = Array2::<u64>::zeros((n_genomes, n_genomes));
-                let mut shared = Array2::<u64>::zeros((n_genomes, n_genomes));
+            .map(|layer_dir| -> OKIResult<Acc> {
+                let mut acc = zero();
 
                 let index_dir = layer_dir.parent().expect("layer_dir has a parent index dir");
                 let meta = PartitionMeta::load(index_dir).map_err(olm_to_ok)?;
@@ -754,31 +791,102 @@ impl KmerIndex {
                                 continue;
                             }
                             let Some(bj) = single_form[j] else { continue };
-                            if bi == bj {
-                                shared[[i, j]] += 1;
-                                shared[[j, i]] += 1;
-                            } else {
-                                snp[[i, j]] += 1;
-                                snp[[j, i]] += 1;
-                            }
+                            on_pair(&mut acc, i, j, bi, bj);
                         }
                     }
                 }
 
                 pb.inc(1);
-                Ok((snp, shared))
+                Ok(acc)
             })
             .collect::<OKIResult<Vec<_>>>()?;
         pb.finish_and_clear();
 
-        let mut snp = Array2::<u64>::zeros((n_genomes, n_genomes));
-        let mut shared = Array2::<u64>::zeros((n_genomes, n_genomes));
-        for (s, sh) in partials {
-            snp += &s;
-            shared += &sh;
+        let mut total = zero();
+        for partial in partials {
+            total = combine(total, partial);
         }
+        Ok(total)
+    }
+
+    /// Compute [`RawSnpDistanceOutput`] from an already-built sibling annex
+    /// (run [`build_sibling_annex`](Self::build_sibling_annex) first).
+    pub fn raw_snp_distance(&self) -> OKIResult<RawSnpDistanceOutput> {
+        let n_genomes = self.meta.genomes.len();
+        let (snp, shared) = self.scan_family_pairs(
+            "raw_snp_distance",
+            || (Array2::<u64>::zeros((n_genomes, n_genomes)), Array2::<u64>::zeros((n_genomes, n_genomes))),
+            |(snp, shared), i, j, bi, bj| {
+                if bi == bj {
+                    shared[[i, j]] += 1;
+                    shared[[j, i]] += 1;
+                } else {
+                    snp[[i, j]] += 1;
+                    snp[[j, i]] += 1;
+                }
+            },
+            |(mut snp, mut shared), (s, sh)| {
+                snp += &s;
+                shared += &sh;
+                (snp, shared)
+            },
+        )?;
         Ok(RawSnpDistanceOutput { snp, shared })
     }
+
+    /// Symmetric 6-category base-pair substitution tally (AC, AG, AT, CG,
+    /// CT, GT — indexed `0=A,1=C,2=G,3=T`), pooled only over genome pairs
+    /// whose overall SNP ratio in `raw` is at or below `ratio_ceiling` —
+    /// same saturation-exclusion discipline as `calibrate_p_hat`, for the
+    /// same reason: a saturated pair's observed base-pair mix trends toward
+    /// neutral base composition, not the true point-mutation spectrum.
+    ///
+    /// A second full pass over the annex, sharing
+    /// [`raw_snp_distance`](Self::raw_snp_distance)'s traversal (guided by
+    /// it, not a blind re-scan) — needed because `raw_snp_distance` only
+    /// keeps aggregate SNP/shared counts per genome pair, not which bases
+    /// were actually involved at each locus, and the ratio-ceiling filter
+    /// can only be evaluated once the aggregate counts are known.
+    pub fn base_pair_tally(&self, raw: &RawSnpDistanceOutput, ratio_ceiling: f64) -> OKIResult<BasePairTally> {
+        let n_genomes = self.meta.genomes.len();
+        let included = Array2::from_shape_fn((n_genomes, n_genomes), |(i, j)| {
+            if i == j {
+                return false;
+            }
+            let snp = raw.snp[[i, j]];
+            let total = snp + raw.shared[[i, j]];
+            total > 0 && (snp as f64 / total as f64) <= ratio_ceiling
+        });
+
+        let counts = self.scan_family_pairs(
+            "base_pair_tally",
+            || [[0u64; 4]; 4],
+            |counts, i, j, bi, bj| {
+                if bi != bj && included[[i, j]] {
+                    counts[bi as usize][bj as usize] += 1;
+                    counts[bj as usize][bi as usize] += 1;
+                }
+            },
+            |mut total, partial| {
+                for a in 0..4 {
+                    for b in 0..4 {
+                        total[a][b] += partial[a][b];
+                    }
+                }
+                total
+            },
+        )?;
+        Ok(BasePairTally { counts })
+    }
+}
+
+/// See [`KmerIndex::base_pair_tally`].
+pub struct BasePairTally {
+    /// `counts[a][b] == counts[b][a]` = number of eligible loci, pooled
+    /// over included genome pairs, where the two genomes' single forms are
+    /// `a` and `b` (0=A, 1=C, 2=G, 3=T). Diagonal always `0` (an `a == b`
+    /// locus is `shared`, not tallied here).
+    pub counts: [[u64; 4]; 4],
 }
 
 /// IUPAC ambiguity code for a per-genome family presence mask (bit `b` set
diff --git a/src/obikmer/Cargo.toml b/src/obikmer/Cargo.toml
index 9f3932d6..7a16f63c 100644
--- a/src/obikmer/Cargo.toml
+++ b/src/obikmer/Cargo.toml
@@ -22,15 +22,17 @@ obikindex     = { path = "../obikindex", default-features = false }
 obitaxonomy   = { path = "../obitaxonomy" }
 obilayeredmap = { path = "../obilayeredmap" }
 clap          = { version = "4", features = ["derive"] }
+serde         = { version = "1", features = ["derive"] }
 serde_json    = "1"
+serde_yaml    = "0.9.33"
 csv           = "1"
-kodama        = "0.2"
+kodama        = "0.3.0"
 speedytree    = "0.1"
 rayon         = "1"
-indicatif     = "0.17"
+indicatif     = "0.18"
 tracing       = "0.1.44"
 tracing-subscriber = { version = "0.3", features = ["fmt", "env-filter"] }
-pprof = { version = "0.13", features = ["prost-codec"], optional = true }
+pprof = { version = "0.15", features = ["prost-codec"], optional = true }
 
 [features]
 default   = ["numa"]
diff --git a/src/obikmer/src/cmd/distance.rs b/src/obikmer/src/cmd/distance.rs
index 88524786..bd7a4e37 100644
--- a/src/obikmer/src/cmd/distance.rs
+++ b/src/obikmer/src/cmd/distance.rs
@@ -4,7 +4,11 @@ use std::path::PathBuf;
 use clap::Args;
 use kodama::{Method, linkage};
 use obifastwrite::{JsonVal, write_record};
-use obikindex::{DistanceMetric, KmerIndex, RawSnpDistanceOutput, SiblingAnnexStats, SnpAlignment};
+use obikindex::{
+    BasePairTally, DistanceMetric, KmerIndex, PHatEstimate, RawSnpDistanceOutput, SankoffWeights,
+    SiblingAnnexStats, SnpAlignment, build_cost_matrix, c_ctx_from_p_hat, calibrate_p_hat,
+    mean_substitution_cost, substitution_costs_from_tally,
+};
 use speedytree::{DistanceMatrix, Hybrid, NeighborJoiningSolver, to_newick};
 use tracing::info;
 
@@ -94,9 +98,61 @@ pub struct DistanceArgs {
     #[arg(long)]
     pub snp: bool,
 
+    /// Calibrate a 16-state Sankoff cost matrix and its matching
+    /// pseudo-alignment from an already-built sibling annex (run with
+    /// `--sibling-annex` first, in this invocation or an earlier one), for
+    /// use with TNT/PhyG. See `docmd/theory/evolutionary_distances.md`,
+    /// "Sankoff parsimony as the resolution of the 16-state model problem".
+    #[arg(long)]
+    pub sankoff: bool,
+
+    /// Exclude genome pairs whose raw SNP ratio exceeds this value from the
+    /// `p_hat` calibration pooled by `--sankoff` — a pair this close to
+    /// saturation carries no information about `p_hat` and would bias it
+    /// upward if pooled in (unlike a low eligible-loci count, which barely
+    /// moves the pooled estimate either way — see design doc).
+    #[arg(long, default_value = "0.5")]
+    pub sankoff_ratio_ceiling: f64,
+
+    /// Also write <prefix>_sankoff.tnt, a ready-to-run TNT script (`proc
+    /// <file>;`) for the same matrix/alignment `--sankoff` computes —
+    /// recoded to TNT's default xread alphabet (0-9A-F only; TNT rejects
+    /// the wider IUPAC set `--sankoff`'s own output uses unless `nstates
+    /// dna` is set, which imposes TNT's own incompatible DNA encoding
+    /// instead) with integer-scaled costs (TNT's smatrix/cost commands
+    /// reject decimals). Implies `--sankoff`.
+    #[arg(long)]
+    pub tnt: bool,
+
+    /// Also write <prefix>_sankoff.tcm and <prefix>_sankoff.pg, a
+    /// custom-alphabet cost matrix and a ready-to-run PhyG script (`read`/
+    /// `search`/`report`) for the same matrix/alignment `--sankoff`
+    /// computes. Reuses `--sankoff`'s own `_sankoff.fasta` directly — PhyG's
+    /// `tcm:` alphabet is read from the matrix file itself, so the IUPAC+`0`
+    /// alphabet needs no recoding here, unlike `--tnt`. Implies `--sankoff`.
+    #[arg(long)]
+    pub phyg: bool,
+
+    /// Scale factor applied before rounding real-valued costs to the
+    /// integers both `--tnt`'s smatrix/cost commands and `--phyg`'s `tcm:`
+    /// matrix require. Keep this small: the total tree score is this scale
+    /// times the sum of per-character costs across every character (908k+
+    /// for a typical run here), and there are hints in TNT's own manual
+    /// that at least some of its internal accumulators are 32-bit — a large
+    /// scale risks a silent integer overflow (undetectable, not just a
+    /// crash) far more costly than the resolution a bigger factor would
+    /// buy. Shared between `--tnt` and `--phyg` rather than split into two
+    /// flags: both scale the same calibrated matrix for the same reason
+    /// (integer-only cost commands), and no PhyG-specific accumulator-width
+    /// constraint has actually been found to justify a different default.
+    #[arg(long, default_value = "100")]
+    pub sankoff_cost_scale: f64,
+
     /// Output prefix: <prefix>_dist.csv, <prefix>_shared.csv,
     /// <prefix>_siblings.csv, <prefix>_rawsnp.csv, <prefix>_snp.fasta,
-    /// <prefix>_nj.nwk, <prefix>_upgma.nwk.
+    /// <prefix>_sankoff_matrix.csv, <prefix>_sankoff_params.yaml,
+    /// <prefix>_sankoff.fasta, <prefix>_sankoff.tnt, <prefix>_sankoff.tcm,
+    /// <prefix>_sankoff.pg, <prefix>_nj.nwk, <prefix>_upgma.nwk.
     /// If omitted, the distance matrix is written to stdout.
     #[arg(short, long)]
     pub output: Option<PathBuf>,
@@ -117,6 +173,13 @@ pub fn run(args: DistanceArgs) {
     // deliberately decoupled: the annex is meant to be (re)built routinely,
     // the distribution only occasionally, on demand.
     if args.sibling_annex {
+        // Writes into the index directory — hold an exclusive lock for the
+        // duration so a second, concurrent `--sibling-annex` run on the same
+        // index can't corrupt these writes (see obisys::DirLock).
+        let _lock = obisys::DirLock::acquire(&args.index).unwrap_or_else(|e| {
+            eprintln!("error locking index directory {}: {e}", args.index.display());
+            std::process::exit(1);
+        });
         info!("building sibling-count/minorant annex");
         idx.build_sibling_annex().unwrap_or_else(|e| {
             eprintln!("error building sibling annex: {e}");
@@ -144,15 +207,56 @@ pub fn run(args: DistanceArgs) {
         });
         write_snp_fasta(&alignment, &labels, &args.output);
     }
+    if args.sankoff || args.tnt || args.phyg {
+        let raw = idx.raw_snp_distance().unwrap_or_else(|e| {
+            eprintln!("error computing raw SNP distance: {e}");
+            std::process::exit(1);
+        });
+        let estimate = calibrate_p_hat(&raw, args.sankoff_ratio_ceiling);
+        let m = (idx.kmer_size() - 1) / 2;
 
-    // `--sibling-annex`/`--sibling-stats`/`--raw-snp-distance`/`--snp` are
-    // their own operation, not a modifier on top of a distance-metric
-    // computation — a metric was never requested by asking for any of them,
-    // so there is nothing for the rest of this function to compute. Not a
-    // historical accident to keep: stop here rather than always also
-    // running a Jaccard (or whichever `--metric` defaults to) pass and
-    // printing an unrequested matrix.
-    if args.sibling_annex || args.sibling_stats || args.raw_snp_distance || args.snp {
+        let tally = idx.base_pair_tally(&raw, args.sankoff_ratio_ceiling).unwrap_or_else(|e| {
+            eprintln!("error computing base-pair tally: {e}");
+            std::process::exit(1);
+        });
+        let sub_cost = substitution_costs_from_tally(&tally);
+        let mean_sub_cost = mean_substitution_cost(&tally, &sub_cost);
+        let c_ctx = c_ctx_from_p_hat(estimate.p_hat, m, mean_sub_cost);
+
+        let weights = SankoffWeights { sub_cost, c_ctx };
+        let matrix = build_cost_matrix(&weights);
+        write_sankoff_matrix_csv(&matrix, &estimate, &weights, &args.output);
+        write_sankoff_params(&estimate, &tally, &weights, args.sankoff_ratio_ceiling, m, mean_sub_cost, &args.output);
+
+        let alignment = idx.snp_pseudo_alignment().unwrap_or_else(|e| {
+            eprintln!("error computing SNP pseudo-alignment: {e}");
+            std::process::exit(1);
+        });
+        write_sankoff_alignment_fasta(&alignment, &labels, &args.output);
+
+        if args.tnt {
+            write_sankoff_tnt(&matrix, &alignment, &labels, &args.output, args.sankoff_cost_scale);
+        }
+        if args.phyg {
+            write_sankoff_phyg(&matrix, &args.output, args.sankoff_cost_scale);
+        }
+    }
+
+    // `--sibling-annex`/`--sibling-stats`/`--raw-snp-distance`/`--snp`/
+    // `--sankoff`/`--tnt` are their own operation, not a modifier on top of
+    // a distance-metric computation — a metric was never requested by
+    // asking for any of them, so there is nothing for the rest of this
+    // function to compute. Not a historical accident to keep: stop here
+    // rather than always also running a Jaccard (or whichever `--metric`
+    // defaults to) pass and printing an unrequested matrix.
+    if args.sibling_annex
+        || args.sibling_stats
+        || args.raw_snp_distance
+        || args.snp
+        || args.sankoff
+        || args.tnt
+        || args.phyg
+    {
         return;
     }
 
@@ -364,6 +468,387 @@ fn write_snp_fasta(alignment: &SnpAlignment, labels: &[String], output: &Option<
         if n_sites == 1 { "" } else { "s" });
 }
 
+// ── Sankoff pseudo-alignment → FASTA ────────────────────────────────────────
+//
+// Same data as `--snp`'s pseudo-alignment (`SnpAlignment`/
+// `snp_pseudo_alignment`), re-coded so its symbols match the accompanying
+// `--sankoff-matrix` output exactly: `0` for the empty/absent state instead
+// of `-`, which TNT/PhyG would otherwise read as their own gap character
+// rather than our "family absent" state.
+
+fn write_sankoff_alignment_fasta(alignment: &SnpAlignment, labels: &[String], output: &Option<PathBuf>) {
+    let path = output.as_ref()
+        .map(|p| format!("{}_sankoff.fasta", p.display()))
+        .unwrap_or_else(|| "sankoff.fasta".into());
+    let mut f = BufWriter::new(std::fs::File::create(&path).unwrap_or_else(|e| {
+        eprintln!("error creating {path}: {e}");
+        std::process::exit(1);
+    }));
+    let n_sites = alignment.sequences.first().map(|s| s.len()).unwrap_or(0);
+    for (label, seq) in labels.iter().zip(alignment.sequences.iter()) {
+        let recoded: Vec<u8> = seq.iter().map(|&b| if b == b'-' { b'0' } else { b }).collect();
+        write_record(&recoded, label, &[("n_sites", JsonVal::Num(n_sites as u64))], &mut f).unwrap_or_else(|e| {
+            eprintln!("error writing {path}: {e}");
+            std::process::exit(1);
+        });
+    }
+    info!("Sankoff pseudo-alignment → {path} ({n_sites} site{})",
+        if n_sites == 1 { "" } else { "s" });
+}
+
+// ── Sankoff cost matrix → CSV ────────────────────────────────────────────────
+//
+// 16 states indexed by bitmask (bit 0=A, 1=C, 2=G, 3=T; state 0 is `∅`),
+// matching the convention already used for `--snp`'s IUPAC-coded output and
+// for the external TNT/PhyG scripts this feeds. Calibration report (p_hat,
+// its variance, how many pairs/loci went into it, the resulting c_ctx) goes
+// to the log, not the CSV, since it's a run-level fact, not per-cell data.
+
+// IUPAC ambiguity code per state (same mapping as `siblings::iupac_code`,
+// already used for `--snp`'s pseudo-alignment — a biologist reads "R" as
+// "A or G" without needing this file's convention explained), with `0`
+// standing in for the empty state (`-` would collide with TNT/PhyG's own
+// gap/range syntax). Bit order: 0=A, 1=C, 2=G, 3=T. This project's
+// canonical alphabet — `write_sankoff_tnt` below recodes it to TNT's own
+// default alphabet at the adapter boundary, rather than using it here.
+const STATE_SYMBOL: [char; 16] = [
+    '0', 'A', 'C', 'M', 'G', 'R', 'S', 'V', 'T', 'W', 'Y', 'H', 'K', 'D', 'B', 'N',
+];
+
+fn write_sankoff_matrix_csv(
+    matrix: &[[f64; 16]; 16],
+    estimate: &PHatEstimate,
+    weights: &SankoffWeights,
+    output: &Option<PathBuf>,
+) {
+    info!(
+        p_hat = format_args!("{:.6}", estimate.p_hat),
+        variance = format_args!("{:.3e}", estimate.variance),
+        n_pairs_included = estimate.n_pairs_included,
+        n_loci_total = estimate.n_loci_total,
+        c_ctx = format_args!("{:.4}", weights.c_ctx),
+        "Sankoff matrix calibration"
+    );
+
+    let path = output.as_ref()
+        .map(|p| format!("{}_sankoff_matrix.csv", p.display()))
+        .unwrap_or_else(|| "sankoff_matrix.csv".into());
+    let mut f = BufWriter::new(std::fs::File::create(&path).unwrap_or_else(|e| {
+        eprintln!("error creating {path}: {e}");
+        std::process::exit(1);
+    }));
+    write!(f, "state").unwrap();
+    for sym in STATE_SYMBOL { write!(f, ",{sym}").unwrap(); }
+    writeln!(f).unwrap();
+    for (s, row) in matrix.iter().enumerate() {
+        write!(f, "{}", STATE_SYMBOL[s]).unwrap();
+        for cost in row { write!(f, ",{cost:.4}").unwrap(); }
+        writeln!(f).unwrap();
+    }
+    info!("Sankoff cost matrix → {path}");
+}
+
+// ── Sankoff calibration parameters → YAML report ────────────────────────────
+//
+// Everything `--sankoff` estimates from real data, in one durable,
+// machine-readable file: `p_hat` and its variance (with how many pairs/loci
+// went into it), the derived `c_ctx`, and the base-pair substitution tally
+// (raw counts, not just the derived costs) — kept for the same reason raw
+// counts are kept anywhere else in this project: costs are a modelling
+// choice built *from* the counts, and reproducing/re-deriving them later
+// needs the counts, not just their current derived value. Structured (YAML,
+// not an ad hoc key=value text file) so R/Python/etc. can load it directly
+// rather than re-parsing free text.
+
+#[derive(serde::Serialize)]
+struct SankoffSubstitution {
+    pair: String,
+    count: u64,
+    cost: f64,
+}
+
+#[derive(serde::Serialize)]
+struct SankoffParamsReport {
+    ratio_ceiling: f64,
+    flank_length_m: usize,
+    p_hat: f64,
+    p_hat_variance: f64,
+    n_pairs_included: usize,
+    n_loci_total: u64,
+    /// Weighted-average substitution cost — see `c_ctx_from_p_hat`'s docs:
+    /// this is what turns the raw expected mutation *count* behind `c_ctx`
+    /// into an actual cost (not every mutation is worth a flat `1`).
+    mean_sub_cost: f64,
+    c_ctx: f64,
+    substitutions: Vec<SankoffSubstitution>,
+}
+
+fn write_sankoff_params(
+    estimate: &PHatEstimate,
+    tally: &BasePairTally,
+    weights: &SankoffWeights,
+    ratio_ceiling: f64,
+    m: usize,
+    mean_sub_cost: f64,
+    output: &Option<PathBuf>,
+) {
+    const BASE_LETTER: [char; 4] = ['A', 'C', 'G', 'T'];
+
+    let mut substitutions = Vec::with_capacity(6);
+    for a in 0..4 {
+        for b in (a + 1)..4 {
+            substitutions.push(SankoffSubstitution {
+                pair: format!("{}/{}", BASE_LETTER[a], BASE_LETTER[b]),
+                count: tally.counts[a][b],
+                cost: weights.sub_cost[a][b],
+            });
+        }
+    }
+    let report = SankoffParamsReport {
+        ratio_ceiling,
+        flank_length_m: m,
+        p_hat: estimate.p_hat,
+        p_hat_variance: estimate.variance,
+        n_pairs_included: estimate.n_pairs_included,
+        n_loci_total: estimate.n_loci_total,
+        mean_sub_cost,
+        c_ctx: weights.c_ctx,
+        substitutions,
+    };
+
+    let path = output.as_ref()
+        .map(|p| format!("{}_sankoff_params.yaml", p.display()))
+        .unwrap_or_else(|| "sankoff_params.yaml".into());
+    let f = std::fs::File::create(&path).unwrap_or_else(|e| {
+        eprintln!("error creating {path}: {e}");
+        std::process::exit(1);
+    });
+    serde_yaml::to_writer(f, &report).unwrap_or_else(|e| {
+        eprintln!("error writing {path}: {e}");
+        std::process::exit(1);
+    });
+    info!("Sankoff calibration parameters → {path}");
+}
+
+// ── Sankoff cost matrix + alignment → ready-to-run TNT script ──────────────
+//
+// TNT's *default* xread reader only accepts its own 0-9A-F alphabet (see
+// its manual: "up to 16 states are allowed by xread, using symbols 0-9 ...
+// and A-F") — the wider IUPAC set `STATE_SYMBOL` uses is rejected as an
+// "alien symbol" unless `nstates dna` is set, which imposes TNT's own fixed
+// DNA encoding instead, incompatible with a custom smatrix. And TNT's
+// `smatrix`/`cost` commands reject decimal costs ("found symbol . when
+// reading transformation costs"). So: recode to TNT's alphabet and
+// integer-scale the costs here, at this adapter's boundary, rather than
+// degrading the project's own canonical (IUPAC, real-valued) output.
+
+const TNT_STATE_SYMBOL: [char; 16] = [
+    '0', '1', '2', '3', '4', '5', '6', '7', '8', '9', 'A', 'B', 'C', 'D', 'E', 'F',
+];
+
+fn write_sankoff_tnt(
+    matrix: &[[f64; 16]; 16],
+    alignment: &SnpAlignment,
+    labels: &[String],
+    output: &Option<PathBuf>,
+    cost_scale: f64,
+) {
+    let path = output.as_ref()
+        .map(|p| format!("{}_sankoff.tnt", p.display()))
+        .unwrap_or_else(|| "sankoff.tnt".into());
+    let mut f = BufWriter::new(std::fs::File::create(&path).unwrap_or_else(|e| {
+        eprintln!("error creating {path}: {e}");
+        std::process::exit(1);
+    }));
+
+    // IUPAC-ish symbol -> bitmask, to translate the alignment (which uses
+    // `STATE_SYMBOL`, `-` already normalised to `0` by `snp_pseudo_alignment`
+    // callers) into TNT's alphabet without re-deriving state indices.
+    let mut iupac_to_state = [0u8; 128];
+    for (state, &sym) in STATE_SYMBOL.iter().enumerate() {
+        iupac_to_state[sym as usize] = state as u8;
+    }
+
+    let n_sites = alignment.sequences.first().map(|s| s.len()).unwrap_or(0);
+    writeln!(f, "xread").unwrap();
+    writeln!(f, "'obikmer central-position SNP families, calibrated Sankoff 16-state encoding'").unwrap();
+    writeln!(f, "{n_sites} {}", labels.len()).unwrap();
+    for (label, seq) in labels.iter().zip(alignment.sequences.iter()) {
+        write!(f, "{label} ").unwrap();
+        for &b in seq {
+            let b = if b == b'-' { b'0' } else { b };
+            let state = iupac_to_state[b as usize];
+            write!(f, "{}", TNT_STATE_SYMBOL[state as usize]).unwrap();
+        }
+        writeln!(f).unwrap();
+    }
+    writeln!(f, ";\n").unwrap();
+
+    let scaled_matrix = scaled_metric_matrix(matrix, cost_scale);
+
+    writeln!(f, "smatrix =0 (family16)").unwrap();
+    for i in 0..16 {
+        for j in (i + 1)..16 {
+            writeln!(f, "{}/{} {}", TNT_STATE_SYMBOL[i], TNT_STATE_SYMBOL[j], scaled_matrix[i][j]).unwrap();
+        }
+    }
+    writeln!(f, ";\n").unwrap();
+
+    writeln!(f, "ccode ( 0.{} ;", n_sites - 1).unwrap();
+    writeln!(f, "smatrix +0 0.{} ;", n_sites - 1).unwrap();
+    writeln!(f).unwrap();
+
+    // Basename only (not the full `path`/`output` prefix): TNT's natural
+    // workflow is to `cd` into the output directory before `proc`-ing the
+    // script, and an absolute path here would break if that directory is
+    // later moved or copied elsewhere.
+    let tre_name = output.as_ref()
+        .and_then(|p| p.file_name())
+        .map(|n| format!("{}_sankoff.tre", n.to_string_lossy()))
+        .unwrap_or_else(|| "sankoff.tre".into());
+
+    // TNT's plain command parser has no comment syntax of its own — `/* */`
+    // and `[ ]` are only recognised inside the (separately-enabled) macro
+    // scripting language, and fail with "No command!" here otherwise
+    // (verified against this file with the local TNT binary). `quote` is
+    // the closest working equivalent: it prints free text and does not
+    // otherwise affect parsing, so it doubles as an explanation of the
+    // defaults below when the script is run. `;` ends a `quote` block like
+    // any other TNT command, so the text itself must avoid semicolons.
+    writeln!(f, "quote").unwrap();
+    writeln!(f, "Default search below (edit or delete this block to run your own strategy):").unwrap();
+    writeln!(f, "  hold N     : size of TNT's tree buffer (how many equally-parsimonious").unwrap();
+    writeln!(f, "               trees it keeps in memory at once), 20 is a small, fast").unwrap();
+    writeln!(f, "               default, raise it if mult reports it had to drop trees.").unwrap();
+    writeln!(f, "  mult       : traditional search (random addition sequences followed by").unwrap();
+    writeln!(f, "               TBR branch-swapping, TNT's own default replication count),").unwrap();
+    writeln!(f, "               a reasonable first-pass strategy on this data's memory").unwrap();
+    writeln!(f, "               footprint, xmult's ratchet/drift/tree-fusion buffers ran").unwrap();
+    writeln!(f, "               this out of RAM at TNT's default mxram on this dataset.").unwrap();
+    writeln!(f, "  export - F : write the trees held in the buffer to file F, in").unwrap();
+    writeln!(f, "               TNT/Hennig86 format ('-' means trees, as opposed to data).").unwrap();
+    writeln!(f, ";").unwrap();
+    writeln!(f, "hold 20;").unwrap();
+    writeln!(f, "mult;").unwrap();
+    writeln!(f, "export - {tre_name};").unwrap();
+
+    info!(
+        "TNT script → {path} (costs scaled x{cost_scale:.0}, runs a default `hold 20; mult;` \
+         search and writes trees to {tre_name} in TNT's working directory — edit the trailing \
+         comment block in the script to change this)\n\
+         Run it with:\n  \
+         printf 'proc {path};\\nquit;\\n' | tnt\n\
+         (or start `tnt` interactively and type `proc {path};`)"
+    );
+}
+
+/// Scale `matrix` by `cost_scale` and round to integers (TNT's smatrix/cost
+/// commands reject decimals), then take the *metric closure* of the result
+/// (Floyd-Warshall over the 16 states again, on the now-integer values).
+///
+/// `matrix` is already a metric in its real-valued form (it's a
+/// shortest-path closure itself — see `build_cost_matrix`), but rounding
+/// each cell independently can still break the triangle inequality: e.g.
+/// two real costs of `1.734` each round to `173`, summing to `346`, while
+/// their own real sum `3.468` rounds to `347` — TNT then reports "triangle
+/// inequality violated ... Fixed" and silently substitutes its own
+/// corrected value. Re-closing after rounding makes that correction
+/// explicit and reproducible here instead, rather than left implicit and
+/// TNT-version-dependent.
+fn scaled_metric_matrix(matrix: &[[f64; 16]; 16], cost_scale: f64) -> [[i64; 16]; 16] {
+    let mut m = [[0i64; 16]; 16];
+    for i in 0..16 {
+        for j in 0..16 {
+            m[i][j] = (matrix[i][j] * cost_scale).round() as i64;
+        }
+    }
+    for k in 0..16 {
+        for i in 0..16 {
+            for j in 0..16 {
+                let via = m[i][k] + m[k][j];
+                if via < m[i][j] {
+                    m[i][j] = via;
+                }
+            }
+        }
+    }
+    m
+}
+
+// ── Sankoff cost matrix → PhyG custom-alphabet TCM + ready-to-run script ────
+//
+// PhyG's `tcm:STRING` format needs no alphabet recoding, unlike `--tnt`:
+// its parser reads the alphabet straight from the tcm file's own first
+// line, so `--sankoff`'s own `_sankoff.fasta` (already IUPAC+`0`) is reused
+// as-is via `prefasta:`. PhyG auto-adds its own indel/gap state as an
+// (n+1)-th row/column of the tcm — inert here since the alignment already
+// encodes absence as an ordinary state (`0`), never as `-` (see
+// `write_sankoff_alignment_fasta`'s own comment on why, and the RAxML-era
+// bug that motivated it). The gap row/column below reuses `matrix[i][0]`/
+// `matrix[0][j]` (cost to/from `∅`) as the closest principled value for a
+// state that, in practice, is never actually triggered.
+
+fn write_sankoff_phyg(matrix: &[[f64; 16]; 16], output: &Option<PathBuf>, cost_scale: f64) {
+    let scaled_matrix = scaled_metric_matrix(matrix, cost_scale);
+
+    let basename = |suffix: &str| -> String {
+        output.as_ref()
+            .and_then(|p| p.file_name())
+            .map(|n| format!("{}{suffix}", n.to_string_lossy()))
+            .unwrap_or_else(|| format!("sankoff{suffix}"))
+    };
+    let full_path = |suffix: &str| -> String {
+        output.as_ref()
+            .map(|p| format!("{}{suffix}", p.display()))
+            .unwrap_or_else(|| format!("sankoff{suffix}"))
+    };
+
+    let tcm_path = full_path("_sankoff.tcm");
+    let mut f = BufWriter::new(std::fs::File::create(&tcm_path).unwrap_or_else(|e| {
+        eprintln!("error creating {tcm_path}: {e}");
+        std::process::exit(1);
+    }));
+    let alphabet_line = STATE_SYMBOL.iter().map(|c| c.to_string()).collect::<Vec<_>>().join(" ");
+    writeln!(f, "{alphabet_line}").unwrap();
+    for i in 0..16 {
+        let mut row: Vec<i64> = (0..16).map(|j| scaled_matrix[i][j]).collect();
+        row.push(scaled_matrix[i][0]); // gap column: same cost as to/from ∅
+        writeln!(f, "{}", row.iter().map(|v| v.to_string()).collect::<Vec<_>>().join(" ")).unwrap();
+    }
+    let mut gap_row: Vec<i64> = (0..16).map(|j| scaled_matrix[0][j]).collect();
+    gap_row.push(0);
+    writeln!(f, "{}", gap_row.iter().map(|v| v.to_string()).collect::<Vec<_>>().join(" ")).unwrap();
+    info!("PhyG TCM → {tcm_path}");
+
+    let pg_path = full_path("_sankoff.pg");
+    let mut f = BufWriter::new(std::fs::File::create(&pg_path).unwrap_or_else(|e| {
+        eprintln!("error creating {pg_path}: {e}");
+        std::process::exit(1);
+    }));
+    let fasta_name = basename("_sankoff.fasta");
+    let tcm_name = basename("_sankoff.tcm");
+    let tre_name = basename("_sankoff.tre");
+    writeln!(f, "read(prefasta:\"{fasta_name}\", tcm:\"{tcm_name}\")").unwrap();
+    writeln!(f, "search(seconds:300, instances:4)").unwrap();
+    writeln!(f, "report(\"{tre_name}\", graphs, newick, overwrite)").unwrap();
+
+    let pg_dir = std::path::Path::new(&pg_path).parent()
+        .filter(|d| !d.as_os_str().is_empty())
+        .map(|d| d.display().to_string())
+        .unwrap_or_else(|| ".".into());
+    let pg_name = std::path::Path::new(&pg_path).file_name()
+        .map(|n| n.to_string_lossy().into_owned())
+        .unwrap_or_else(|| pg_path.clone());
+    info!(
+        "PhyG script → {pg_path} (costs scaled x{cost_scale:.0}, runs a default 300s/4-instance \
+         search and writes trees to {tre_name})\n\
+         Run it with:\n  \
+         cd {pg_dir} && phyg {pg_name}\n\
+         (`phyg` must run from that directory — `read()`/`report()` in the script use relative \
+         file names)"
+    );
+}
+
 // ── UPGMA Newick from kodama dendrogram ───────────────────────────────────────
 
 fn upgma_to_newick(dendro: &kodama::Dendrogram<f64>, names: &[String]) -> String {
diff --git a/src/obikmer/src/cmd/filter.rs b/src/obikmer/src/cmd/filter.rs
index ae3f45fa..ed0f407b 100644
--- a/src/obikmer/src/cmd/filter.rs
+++ b/src/obikmer/src/cmd/filter.rs
@@ -78,6 +78,13 @@ pub fn run(args: FilterCmdArgs) {
         filters.push(Box::new(MinComplexity { level_max: args.complexity_level_max, theta }));
     }
 
+    // Source is opened read-only above and needs no lock; only the
+    // destination is written.
+    let _lock = obisys::DirLock::acquire(&args.output).unwrap_or_else(|e| {
+        eprintln!("error locking output directory {}: {e}", args.output.display());
+        std::process::exit(1);
+    });
+
     let mut rep = Reporter::new();
     KmerIndex::rebuild(&args.output, &src, &filters, mode, args.force, &mut rep)
         .unwrap_or_else(|e| {
diff --git a/src/obikmer/src/cmd/index.rs b/src/obikmer/src/cmd/index.rs
index 31102fbd..e83f7910 100644
--- a/src/obikmer/src/cmd/index.rs
+++ b/src/obikmer/src/cmd/index.rs
@@ -156,6 +156,16 @@ pub fn run(args: IndexArgs) {
     let output = args.output.clone();
     let mut rep = Reporter::new();
 
+    // Locked for the whole build (including a possible --force removal +
+    // recreation below): a second `index` run resuming/overwriting the same
+    // output directory concurrently would otherwise corrupt it. Unlinking
+    // the lock file via --force's remove_dir_all is safe — the held file
+    // descriptor keeps the lock regardless of the directory entry.
+    let _lock = obisys::DirLock::acquire(&output).unwrap_or_else(|e| {
+        eprintln!("error locking output directory {}: {e}", output.display());
+        std::process::exit(1);
+    });
+
     // ── Resolve evidence kind ────────────────────────────────────────────────
     let (evidence, effective_kmer_size) = if args.approx {
         let (z, b, fp) = resolve_approx_params(args.findere_z, args.evidence_bits, args.fp);
diff --git a/src/obikmer/src/cmd/merge.rs b/src/obikmer/src/cmd/merge.rs
index f0ce2dc0..c5fbef8c 100644
--- a/src/obikmer/src/cmd/merge.rs
+++ b/src/obikmer/src/cmd/merge.rs
@@ -64,6 +64,13 @@ pub fn run(args: MergeArgs) {
         sources.len(), n_genomes, args.output.display()
     );
 
+    // Only the destination is written; sources are opened read-only above
+    // and need no lock.
+    let _lock = obisys::DirLock::acquire(&args.output).unwrap_or_else(|e| {
+        eprintln!("error locking output directory {}: {e}", args.output.display());
+        std::process::exit(1);
+    });
+
     let mut rep = Reporter::new();
     KmerIndex::merge(&args.output, &source_refs, mode, args.force, args.rename_duplicates, args.budget_fraction, &mut rep).unwrap_or_else(|e| {
         eprintln!("error merging: {e}");
diff --git a/src/obikmer/src/cmd/pack.rs b/src/obikmer/src/cmd/pack.rs
index f3c0d3da..4f34c52d 100644
--- a/src/obikmer/src/cmd/pack.rs
+++ b/src/obikmer/src/cmd/pack.rs
@@ -12,6 +12,13 @@ pub struct PackArgs {
 }
 
 pub fn run(args: PackArgs) {
+    // Modifies the index in place; acquired before opening so a concurrent
+    // writer can't slip in between the open and the pack below.
+    let _lock = obisys::DirLock::acquire(&args.index).unwrap_or_else(|e| {
+        eprintln!("error locking index directory {}: {e}", args.index.display());
+        std::process::exit(1);
+    });
+
     let idx = KmerIndex::open(&args.index).unwrap_or_else(|e| {
         eprintln!("error opening index: {e}");
         std::process::exit(1);
diff --git a/src/obikmer/src/cmd/reindex.rs b/src/obikmer/src/cmd/reindex.rs
index 5c0bab76..3fd2c650 100644
--- a/src/obikmer/src/cmd/reindex.rs
+++ b/src/obikmer/src/cmd/reindex.rs
@@ -47,6 +47,13 @@ pub fn run(args: ReindexArgs) {
         IndexMode::Exact
     };
 
+    // Modifies the index in place; acquired before opening so a concurrent
+    // writer can't slip in between the open and the reindex below.
+    let _lock = obisys::DirLock::acquire(&args.index).unwrap_or_else(|e| {
+        eprintln!("error locking index directory {}: {e}", args.index.display());
+        std::process::exit(1);
+    });
+
     let mut idx = KmerIndex::open(&args.index).unwrap_or_else(|e| {
         eprintln!("error opening index: {e}");
         std::process::exit(1);
diff --git a/src/obikmer/src/cmd/select.rs b/src/obikmer/src/cmd/select.rs
index 35719e8e..e74761b2 100644
--- a/src/obikmer/src/cmd/select.rs
+++ b/src/obikmer/src/cmd/select.rs
@@ -215,6 +215,16 @@ pub fn run(args: SelectArgs) {
         std::process::exit(1);
     }
 
+    // Lock whichever directory actually gets written: the source itself in
+    // --in-place mode, otherwise the (distinct) --output directory. Acquired
+    // before opening the source so a concurrent writer can't slip in between
+    // the open and the write below.
+    let lock_target = if args.in_place { &args.source } else { args.output.as_ref().unwrap() };
+    let _lock = obisys::DirLock::acquire(lock_target).unwrap_or_else(|e| {
+        eprintln!("error locking {}: {e}", lock_target.display());
+        std::process::exit(1);
+    });
+
     let mut src = KmerIndex::open(&args.source).unwrap_or_else(|e| {
         eprintln!("error opening source index: {e}");
         std::process::exit(1);
diff --git a/src/obisys/Cargo.toml b/src/obisys/Cargo.toml
index da677db1..966e22ed 100644
--- a/src/obisys/Cargo.toml
+++ b/src/obisys/Cargo.toml
@@ -8,3 +8,4 @@ libc      = "0.2"
 sysinfo   = "0.33"
 indicatif = "0.17"
 tracing   = "0.1"
+fs4       = "0.9"
diff --git a/src/obisys/src/lib.rs b/src/obisys/src/lib.rs
index 21d4987b..65d5d4f4 100644
--- a/src/obisys/src/lib.rs
+++ b/src/obisys/src/lib.rs
@@ -8,6 +8,49 @@ use tracing::{debug, info, warn};
 
 const BRAILLE: &[&str] = &["⠋", "⠙", "⠹", "⠸", "⠼", "⠴", "⠦", "⠧", "⠇", "⠏"];
 
+// ── DirLock ──────────────────────────────────────────────────────────────────
+
+/// Exclusive advisory lock on an index directory, held for the duration of
+/// any command that writes into an already-existing index (building the
+/// sibling annex, merging into a destination, filtering/selecting in place,
+/// ...). Two such commands racing on the same directory can otherwise
+/// corrupt each other's writes with no error from either side.
+///
+/// Only the directory actually being *written to* needs a lock — a command
+/// like `merge` that reads several source indexes to build one destination
+/// only needs to lock the destination.
+///
+/// Uses the OS's advisory file lock (`flock` on Unix, `LockFileEx` on
+/// Windows) via `fs4`, not a hand-rolled PID file: the OS releases it
+/// automatically on process exit, including a crash — no stale-lock cleanup
+/// logic needed.
+pub struct DirLock {
+    _file: std::fs::File,
+}
+
+impl DirLock {
+    /// Block until the exclusive lock on `dir` is acquired (creating `dir`
+    /// and the lock file within it if needed). Logs once if the wait is
+    /// non-trivial, so a blocked command doesn't look silently hung.
+    pub fn acquire(dir: &std::path::Path) -> std::io::Result<Self> {
+        use fs4::fs_std::FileExt;
+
+        std::fs::create_dir_all(dir)?;
+        let lock_path = dir.join(".obikmer.lock");
+        let file = std::fs::OpenOptions::new()
+            .create(true)
+            .truncate(false)
+            .write(true)
+            .open(&lock_path)?;
+
+        if file.try_lock_exclusive().is_err() {
+            info!(dir = %dir.display(), "waiting for another obikmer process to release this index");
+            file.lock_exclusive()?;
+        }
+        Ok(Self { _file: file })
+    }
+}
+
 // ── TracedBar ──────────────────────────────────────────────────────────────────
 
 /// Wrapper around `ProgressBar` that emits `tracing` events when stderr is not
-- 
2.54.0


From adf5b52dc7ebe5241e0234ef7d3f38b4d5105807 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Wed, 12 Aug 2026 18:23:22 +0200
Subject: [PATCH 02/46] feat(distance): implement native Sankoff calibration
 and backends

Replaces external Python glue with native Rust modules for Sankoff model calibration, exporting calibrated cost matrices, FASTA alignments, and YAML parameters. Adds dedicated writers for TNT and PhyG that apply integer scaling and Floyd-Warshall metric closure to enforce triangle inequality. Integrates these exporters into the distance command pipeline to streamline downstream tree inference workflows, while updating theory documentation to reflect IQ-TREE integration and state renumbering improvements.
---
 docmd/theory/evolutionary_distances.md        | 279 +++++++++++++
 .../src/cmd/{distance.rs => distance/mod.rs}  | 391 +-----------------
 src/obikmer/src/cmd/distance/phyg.rs          |  81 ++++
 src/obikmer/src/cmd/distance/sankoff.rs       | 202 +++++++++
 src/obikmer/src/cmd/distance/tnt.rs           | 119 ++++++
 5 files changed, 690 insertions(+), 382 deletions(-)
 rename src/obikmer/src/cmd/{distance.rs => distance/mod.rs} (55%)
 create mode 100644 src/obikmer/src/cmd/distance/phyg.rs
 create mode 100644 src/obikmer/src/cmd/distance/sankoff.rs
 create mode 100644 src/obikmer/src/cmd/distance/tnt.rs

diff --git a/docmd/theory/evolutionary_distances.md b/docmd/theory/evolutionary_distances.md
index b1fd239f..6fd21d8b 100644
--- a/docmd/theory/evolutionary_distances.md
+++ b/docmd/theory/evolutionary_distances.md
@@ -620,6 +620,285 @@ simply does not survive domain-level divergence. Cross-domain placement
 would need conserved-marker characters (rRNA, ribosomal proteins), not this
 estimator.
 
+### Native `--sankoff --tnt`/`--phyg` export (2026-08-12), superseding the external scripts above
+
+The ad hoc Python glue from the previous section is superseded: `obikmer
+distance --sankoff` now calibrates the matrix natively (`p_hat`, 6-category
+substitution costs, `c_ctx` weighted by `mean_sub_cost` — see the worked
+example above) and `--tnt`/`--phyg` each write a ready-to-run script from
+it, no external script needed. `∅` is an ordinary 16th state throughout
+(never `-`), specifically to avoid gap-semantics confusion in downstream
+tools — see "A concrete Sankoff cost matrix" above for why.
+
+**TNT (`--tnt`).** `write_sankoff_tnt` (`obikmer/src/cmd/distance.rs`)
+recodes to TNT's own `0-9A-F` xread alphabet (its default reader rejects
+the wider IUPAC set otherwise), scales and rounds costs to integers
+(`smatrix`/`cost` reject decimals), then re-runs integer Floyd-Warshall on
+the rounded matrix (`scaled_metric_matrix`) — independently rounding each
+cell of an already-metric real-valued matrix can break the triangle
+inequality (e.g. two real costs of `1.734` round to `173` each, summing to
+`346`, while their real sum `3.468` rounds to `347`), which TNT otherwise
+silently "fixes" itself with an unreproducible correction. Verified against
+the real 20-genome benchmark index: zero triangle-inequality violations
+after the fix, TNT loads the file without its "triangle inequality
+violated... Fixed" warning.
+
+Two syntax facts worth recording because they're wrong in intuitive
+guesses and contradicted actual TNT behavior when tested: TNT's plain
+command stream has **no comment syntax** of its own — `/* */` and `[ ]`
+only work inside the (separately-enabled, off by default) macro scripting
+language, and error with "No command!" otherwise. The working substitute
+is `quote TEXT ;` (prints the text, doesn't affect parsing) — but the text
+itself can't contain a literal `;` (TNT's universal terminator); the
+manual's own escape (`.,`) exists but the script here just avoids
+semicolons in the text instead.
+
+The default search command embedded in the script is `mult` (traditional:
+random addition sequences + TBR), not `xmult` (New Technology search:
+ratchet/drift/tree-fusion). `xmult` with TNT's default `mxram` (16 MB,
+must be set *before* `xread` if changed) ran out of RAM on the real
+908k-character dataset ("`xmult - out of ram`"); `mult` does not, matching
+what had already been validated by hand outside this session.
+
+**PhyG (`--phyg`).** `write_sankoff_phyg` writes a `tcm:` custom-alphabet
+matrix (same scale+round+metric-closure treatment as TNT) and reuses
+`--sankoff`'s own `_sankoff.fasta` as-is via `prefasta:` — PhyG's `tcm:`
+alphabet is read from the matrix file's own first line, so (unlike TNT) no
+recoding is needed. PhyG auto-adds its own indel/gap state as an
+`(n+1)`-th row/column of the tcm; inert here since the alignment encodes
+absence as `0`, never `-`.
+
+`report("file", newick, overwrite)` — exactly as shown in PhyG's own
+manual — triggers `Unrecognized/missing report option ... defaulting to
+'graphs'` on the locally installed binary (1.3, commit `3c1a1fa`); the
+working form adds `graphs` explicitly: `report("file", graphs, newick,
+overwrite)`. Manual/binary mismatches like this (also true of `criterion:`
+— the binary accepts `parsimony`/`ml`/`pmdl`, the manual instead documents
+`mapa`/`ncm`/`parsimony`/`pmdl`/`si`) mean command syntax against this PhyG
+build should be verified empirically, not trusted from the PDF alone.
+`instances:N` (not a separate CPU flag) is what actually parallelises the
+search across cores — PhyG uses all physical cores by default but only
+across as many instances as are running, so raise it to the physical core
+count to use them all (the CLI-level `+RTS -NX -RTS` flag also exists but
+controls something else: capping/limiting cores, not requesting more).
+
+Both scripts share one `--sankoff-cost-scale` (default `100`), not two
+separate flags — they scale the same calibrated matrix for the same
+reason (integer-only cost commands) and no PhyG-specific
+accumulator-width constraint was ever found to justify a different
+default from TNT's (TNT: hinted 32-bit accumulators in its own manual;
+PhyG: no such hint found — Haskell's native `Int` is typically 64-bit).
+
+**Open problem: PhyG reports all branch lengths as `0.0`.** The graph-level
+parsimony cost is correct (`3.3286×10⁸` on the real dataset, consistent
+with TNT's `328574911` on the same calibrated matrix), but every individual
+edge in the exported Newick shows `:0.0`, with the total cost only ever
+shown as a whole-tree annotation (`[3.32860377e8]`). Not fixed, not fully
+diagnosed — PhyG's manual describes per-edge branch length as computed by
+ancestral-state (HTU) backtracking, well documented for sequence/standard
+character types, but nothing found (the term "Sankoff" doesn't even appear
+in the manual) confirming this backtracking is wired up for a custom
+`tcm:` matrix character. Switching `criterion:` to a likelihood-family
+option (`ml`, or the manual's `mapa`/`ncm`/`si`) was considered as a
+possible fix but is very unlikely to be one: those criteria are
+information-theoretic reparametrisations of the *same* step-counting
+machinery as parsimony (`ncm` in particular is known in the literature to
+be numerically equivalent to weighted parsimony), not classical
+continuous-time-Markov ML with a real rate matrix — so they wouldn't
+change how branch length is attributed per edge either.
+
+**Export format note (not a bug in the generator).** Neither script's
+`.tre` output opens in PearTree (FigTree's successor) via File > Open —
+association/Launch-Services quirks were ruled out (the file was opened
+directly through the app, not by double-click). Likely cause, not yet
+confirmed: TNT's export is a minimal NEXUS `begin trees;` block with no
+preceding `Taxa` block and bare numeric (untranslated) leaf labels; PhyG's
+is multiple raw Newick trees concatenated with no NEXUS wrapper at all
+plus a trailing `[cost]` bracket tag after the root label. Both differ
+from a "normal" single-tree, fully-declared NEXUS file; this is PhyG/TNT's
+own export format, not something `write_sankoff_tnt`/`write_sankoff_phyg`
+could fix without post-processing the *other* program's output after the
+fact.
+
+### Next direction: genuine ML branch lengths, not parsimony (open, 2026-08-12)
+
+Decided: parsimony (the whole `--sankoff`/`--tnt`/`--phyg` pipeline above)
+is a stopgap, not the destination. The goal is maximum likelihood with
+real, calibrated branch lengths (expected substitutions/site), which
+parsimony step-counts were never going to give directly (see the open
+"branch lengths are `0.0`" problem above — even if fixed, TNT/PhyG-style
+parsimony branch length is a step count, not a continuous ML estimate).
+
+**Model choices, settled:**
+- **The exchangeability `R` is symmetric; the rate matrix `Q` is not.**
+  (Superseded an earlier, wrong framing here that treated "symmetric
+  model" as one thing — see the resolution below on `R` vs `Q` vs `π` for
+  the full reasoning.) `R(a,b) = R(b,a)` because `BasePairTally` never
+  captured direction — a fact about the data, not a modelling choice.
+  `Q(a,b) = R(a,b)·π_b` is asymmetric whenever the real state frequencies
+  `π` are (which they are, empirically) — biology drives this via `π`,
+  not via `R`.
+- **`∅` stays an ordinary 16th state**, as already established for
+  TNT/PhyG — same reasoning applies to any ML tool: encode as a real
+  alphabet symbol, never as `-`/gap, or the RAxML-era failure (empty set
+  silently treated as missing data) repeats.
+
+**Stationary frequencies for the 16 states — resolved (2026-08-12).**
+A CTMC needs a rate matrix `Q`, generally asymmetric. `Q(i,j) = R(i,j) ·
+π_j`, where `R` (exchangeability) is symmetric and `π` (stationary
+frequencies) need not be — this factoring is what makes `Q` reversible
+(satisfies detailed balance, `π_i·Q(i,j) = π_j·Q(j,i)`) for *any* `π`, not
+just uniform, as long as `R` is symmetric. Two separate, both-easy
+quantities, not one hard inverse problem:
+- **`R` is already calibrated**: `sub_cost` (`-ln(observed rate)` per pair,
+  from `BasePairTally`) *is* `R` up to a log transform — recover it as
+  `R(a,b) = exp(-sub_cost(a,b))`. Symmetric by construction, because the
+  tally itself never distinguished direction (unordered-pair counts only)
+  — not a modelling choice, a fact about what the data can say.
+- **`π` is a direct count**: empirical marginal frequency of each of the
+  16 states across the whole alignment (same kind of scan already used to
+  confirm `N` occurs 1383 times in the real 20-genome benchmark). With
+  ~908k sites × 20 genomes, the counts are large enough that this is
+  precise on its own — no need to spend ML degrees of freedom
+  re-estimating it via IQ-TREE's `+FO`.
+
+Checked and ruled out along the way: IQ-TREE's `+F` (empirical, "compute
+from the alignment") does **not** work as a shortcut for this — for a
+custom-file morphology model, `readParameters` always requires the file's
+own frequency line unconditionally; omitting it and passing `+F` instead
+just fails (`ERROR: State frequencies could not be read`). `π` has to be
+computed by `obikmer` and written into the file, not left to IQ-TREE.
+
+Net effect: no free-rate ML estimation needed for this piece at all (the
+mistaken assumption that motivated most of this discussion — that
+building an asymmetric `Q` a priori would require solving a linear system
+from `Q` itself — doesn't apply, because `R`, the only piece that's
+genuinely hard to get directionally, is symmetric and already in hand).
+
+**Candidate tool: IQ-TREE**, because it supports user-defined multistate
+models (unlike RAxML's `MULTI` data type, which is limited to the
+equal-rate Mk model and can't take a custom rate matrix at all — a genuine
+tool limitation, not a gap-symbol encoding problem this time). IQ-TREE 3
+(3.0.1) is now installed locally (Homebrew, `iqtree3`).
+
+**IQ-TREE custom-model format — verified empirically against the local
+binary (2026-08-12).** The web docs' `-mdef` NEXUS `begin models;
+frequency NAME = ...; model NAME = ...; end;` mechanism (initially assumed
+to apply directly, see history below) turned out to be for **named
+components used inside `MIX{...}`/`FMIX{...}` mixture models only** — it
+does **not** apply to a single, non-mixture custom morphology matrix, and
+using it that way fails (`ERROR: File not found <name>` — traced in
+IQ-TREE 3's own source, `model/modelmorphology.cpp`: any `-m` string that
+isn't `MK`/`ORDERED`/`GTR`/`GTRX` is passed straight to
+`ModelMarkov::readParameters()`, which opens it **as a literal file path**,
+never consulting the `-mdef` models block at all for this data type).
+
+**The confirmed working recipe** (built a tiny 5-taxon/3-state toy dataset
+and rate file, ran it end to end with `iqtree3`, got a real ML tree with
+non-zero branch lengths and an optimized log-likelihood — ground truth,
+not documentation):
+- No `-mdef` needed. Write one plain file (any name) containing, as
+  whitespace/newline-separated numbers, in order: the **lower-triangular
+  rate matrix** (`N(N-1)/2` values, PAML row-major order — for 16 states,
+  120 values, the same count and layout already produced for TNT's
+  `smatrix`), immediately followed by the **N state frequencies** on the
+  same stream (no header, no blank line required — confirmed by reading
+  `ModelMorphology::readRates`/`ModelMarkov::readStateFreq` directly, which
+  just pull tokens off the stream in sequence).
+- Invoke with `-m <path-to-that-file>+ASC` (`+ASC` for the no-constant-site
+  correction, as before). An explicit `+F{f1,...,fN}` on the command line
+  overrides the file's own frequency line if given (confirmed in
+  `ModelMorphology::init`) — useful once real calibrated stationary
+  frequencies exist, a placeholder equal-frequency line works meanwhile
+  (the still-open gap noted above).
+- `--seqtype MORPH` (alphabet `0`-`9`,`A`-`V`, ≤31 states) — reuse the same
+  `0-9A-F` recoding already built for TNT (`TNT_STATE_SYMBOL`).
+
+**Risk, confirmed, precisely characterised, and resolved by design
+(2026-08-12).**
+`--seqtype MORPH{16}` **does not force the state count** for real ML
+analysis — tested directly (`--seqtype MORPH{4}` on the 3-symbol toy
+alignment gave the byte-for-byte identical 3-state result as no `{4}` at
+all) and confirmed in source: the value it sets
+(`params.alisim_num_states_morph`, `utils/tools.cpp`) is consumed only by
+the `--alisim` simulator; the main analysis path always calls
+`getDataBlockMorphStates`/an equivalent scan (`alignment/alignment.cpp`),
+for both FASTA/PHYLIP and NEXUS input (a NEXUS `symbols=` declaration
+doesn't change this either — checked, same code path). No CLI flag or
+NEXUS declaration overrides it.
+
+The precise rule (from `getDataBlockMorphStates`, `alignment.cpp:1058`):
+`N` = **one plus the highest state ordinal actually observed anywhere in
+the alignment**, ordinal being the symbol's position in IQ-TREE's own
+fixed table `"0123456789ABCDEFGHIJKLMNOPQRSTUV"` — not a count of distinct
+symbols seen. So the risk is narrower than "any missing symbol breaks it":
+concretely, it's whether the symbol mapped to state index 15 (`F` in the
+`0-9A-F` recoding already used for TNT, i.e. our `N` = "all four bases
+ambiguous") occurs **at least once anywhere** in the real alignment — if
+it does, `N` correctly comes out to 16 regardless of which lower-index
+symbols (including `0`/`∅`) are rare or absent; if it doesn't, `N` silently
+undercounts and misaligns every value in a 16-entry rate/frequency file,
+with no error to catch it. **Checked against the real biological alignment**
+(`/tmp/msg_test/eub_sankoff.fasta`, the 20-genome benchmark index): the
+symbol `N` (IUPAC "all four bases ambiguous," state index 15) occurs 1383
+times across 13 of the 20 sequences — present, so this specific real
+dataset is not at risk. Still worth a real, general presence check inside
+`obikmer` before this is wired in, rather than assuming every future
+dataset will have `N` too (nothing in IQ-TREE would catch it if not).
+
+**Resolution: subset + compact-renumber, not rely on all 16 appearing.**
+Since IQ-TREE always infers `N` from the alignment's own content and
+nothing overrides that, the fix is to make the file `obikmer` writes match
+that inference *by construction*, for every run, rather than hope the
+16th (or any particular) state happens to occur:
+1. Scan the real alignment for which of the 16 canonical states actually
+   occur anywhere (not per-column — anywhere in the whole alignment).
+2. Renumber the occurring states to a **compact, consecutive** `0..k-1`
+   range, preserving their relative order (the original bitmask/`STATE_
+   SYMBOL` ordering) — not just filtering, since a *gap* in the ordinal
+   sequence (e.g. keeping states `{0,1,2,4}` numbered as-is instead of
+   `{0,1,2,3}`) reproduces the exact same "highest observed ordinal"
+   miscount this was meant to fix.
+3. Recode the alignment itself with this new compact `k`-symbol alphabet
+   (same recoding mechanism already used for TNT's `0-9A-F`, just over a
+   possibly-smaller symbol set).
+4. Extract the matching `k×k` submatrix (rows/columns for the kept
+   states only) from the full calibrated 16×16 cost matrix, in the same
+   lower-triangular order the rate-matrix file needs — and, later, the
+   matching `k`-length subset of stationary frequencies once those are
+   calibrated (still the open gap noted earlier in this section).
+
+Consequence, and why nothing is lost: a state that never occurs in a given
+alignment can, by definition, never contribute a transition to score in
+that same alignment — dropping it from that run's matrix costs nothing.
+The subset (and therefore `k`) can differ from one dataset/run to the
+next; this has to be done freshly per alignment, not computed once and
+reused.
+
+*(Superseded reasoning, kept for the record: the `-mdef` NEXUS route
+below was the original plan, based on IQ-TREE's own web documentation for
+protein mixture models, before the local install allowed testing it —
+`GTRX` combined with a `-mdef`-referenced custom model, `+Fname` frequency
+reference. Both pieces exist and parse without error individually, but
+`GTRX`/`GTR` are IQ-TREE's own fixed built-in equal-structure multistate
+model, not a hook for an arbitrary custom matrix; a custom matrix is a
+file path in `-m` directly, no `-mdef` or `GTRX` involved.)*
+
+Source for the empirical findings above: `model/modelmorphology.cpp` and
+`model/modelmarkov.cpp` in the local `iqtree/iqtree3` source (cloned to
+inspect the exact parsing logic after documentation didn't resolve the
+`+Fname` reference error) — more reliable here than the PDF/web manual,
+which (like TNT/PhyG) doesn't always match this specific binary. Original
+(partially superseded) sources: [Substitution
+Models](https://iqtree.github.io/doc/Substitution-Models), [Complex
+Models](https://iqtree.github.io/doc/Complex-Models).
+
+**Relation to the existing calibration.** `sub_cost[a][b] = -ln(rate)`
+(see "A concrete Sankoff cost matrix" above) is already a log-rate — a
+genuine CTMC rate matrix `Q` could plausibly be recovered as
+`rate(a,b) = exp(-cost(a,b))`, renormalised so each row sums to zero, once
+the stationary-frequency gap above is closed. Not yet attempted.
+
 ## Heterozygosity, ploidy, and consensus-assembly inputs
 
 A within-genome multiplicity signal (more than one of the 4 central forms
diff --git a/src/obikmer/src/cmd/distance.rs b/src/obikmer/src/cmd/distance/mod.rs
similarity index 55%
rename from src/obikmer/src/cmd/distance.rs
rename to src/obikmer/src/cmd/distance/mod.rs
index bd7a4e37..bd698caa 100644
--- a/src/obikmer/src/cmd/distance.rs
+++ b/src/obikmer/src/cmd/distance/mod.rs
@@ -1,3 +1,7 @@
+mod phyg;
+mod sankoff;
+mod tnt;
+
 use std::io::{self, BufWriter, Write};
 use std::path::PathBuf;
 
@@ -5,13 +9,17 @@ use clap::Args;
 use kodama::{Method, linkage};
 use obifastwrite::{JsonVal, write_record};
 use obikindex::{
-    BasePairTally, DistanceMetric, KmerIndex, PHatEstimate, RawSnpDistanceOutput, SankoffWeights,
+    DistanceMetric, KmerIndex, RawSnpDistanceOutput, SankoffWeights,
     SiblingAnnexStats, SnpAlignment, build_cost_matrix, c_ctx_from_p_hat, calibrate_p_hat,
     mean_substitution_cost, substitution_costs_from_tally,
 };
 use speedytree::{DistanceMatrix, Hybrid, NeighborJoiningSolver, to_newick};
 use tracing::info;
 
+use phyg::write_sankoff_phyg;
+use sankoff::{write_sankoff_alignment_fasta, write_sankoff_matrix_csv, write_sankoff_params};
+use tnt::write_sankoff_tnt;
+
 #[derive(clap::ValueEnum, Clone, Copy, Debug)]
 pub enum MetricArg {
     Jaccard,
@@ -468,387 +476,6 @@ fn write_snp_fasta(alignment: &SnpAlignment, labels: &[String], output: &Option<
         if n_sites == 1 { "" } else { "s" });
 }
 
-// ── Sankoff pseudo-alignment → FASTA ────────────────────────────────────────
-//
-// Same data as `--snp`'s pseudo-alignment (`SnpAlignment`/
-// `snp_pseudo_alignment`), re-coded so its symbols match the accompanying
-// `--sankoff-matrix` output exactly: `0` for the empty/absent state instead
-// of `-`, which TNT/PhyG would otherwise read as their own gap character
-// rather than our "family absent" state.
-
-fn write_sankoff_alignment_fasta(alignment: &SnpAlignment, labels: &[String], output: &Option<PathBuf>) {
-    let path = output.as_ref()
-        .map(|p| format!("{}_sankoff.fasta", p.display()))
-        .unwrap_or_else(|| "sankoff.fasta".into());
-    let mut f = BufWriter::new(std::fs::File::create(&path).unwrap_or_else(|e| {
-        eprintln!("error creating {path}: {e}");
-        std::process::exit(1);
-    }));
-    let n_sites = alignment.sequences.first().map(|s| s.len()).unwrap_or(0);
-    for (label, seq) in labels.iter().zip(alignment.sequences.iter()) {
-        let recoded: Vec<u8> = seq.iter().map(|&b| if b == b'-' { b'0' } else { b }).collect();
-        write_record(&recoded, label, &[("n_sites", JsonVal::Num(n_sites as u64))], &mut f).unwrap_or_else(|e| {
-            eprintln!("error writing {path}: {e}");
-            std::process::exit(1);
-        });
-    }
-    info!("Sankoff pseudo-alignment → {path} ({n_sites} site{})",
-        if n_sites == 1 { "" } else { "s" });
-}
-
-// ── Sankoff cost matrix → CSV ────────────────────────────────────────────────
-//
-// 16 states indexed by bitmask (bit 0=A, 1=C, 2=G, 3=T; state 0 is `∅`),
-// matching the convention already used for `--snp`'s IUPAC-coded output and
-// for the external TNT/PhyG scripts this feeds. Calibration report (p_hat,
-// its variance, how many pairs/loci went into it, the resulting c_ctx) goes
-// to the log, not the CSV, since it's a run-level fact, not per-cell data.
-
-// IUPAC ambiguity code per state (same mapping as `siblings::iupac_code`,
-// already used for `--snp`'s pseudo-alignment — a biologist reads "R" as
-// "A or G" without needing this file's convention explained), with `0`
-// standing in for the empty state (`-` would collide with TNT/PhyG's own
-// gap/range syntax). Bit order: 0=A, 1=C, 2=G, 3=T. This project's
-// canonical alphabet — `write_sankoff_tnt` below recodes it to TNT's own
-// default alphabet at the adapter boundary, rather than using it here.
-const STATE_SYMBOL: [char; 16] = [
-    '0', 'A', 'C', 'M', 'G', 'R', 'S', 'V', 'T', 'W', 'Y', 'H', 'K', 'D', 'B', 'N',
-];
-
-fn write_sankoff_matrix_csv(
-    matrix: &[[f64; 16]; 16],
-    estimate: &PHatEstimate,
-    weights: &SankoffWeights,
-    output: &Option<PathBuf>,
-) {
-    info!(
-        p_hat = format_args!("{:.6}", estimate.p_hat),
-        variance = format_args!("{:.3e}", estimate.variance),
-        n_pairs_included = estimate.n_pairs_included,
-        n_loci_total = estimate.n_loci_total,
-        c_ctx = format_args!("{:.4}", weights.c_ctx),
-        "Sankoff matrix calibration"
-    );
-
-    let path = output.as_ref()
-        .map(|p| format!("{}_sankoff_matrix.csv", p.display()))
-        .unwrap_or_else(|| "sankoff_matrix.csv".into());
-    let mut f = BufWriter::new(std::fs::File::create(&path).unwrap_or_else(|e| {
-        eprintln!("error creating {path}: {e}");
-        std::process::exit(1);
-    }));
-    write!(f, "state").unwrap();
-    for sym in STATE_SYMBOL { write!(f, ",{sym}").unwrap(); }
-    writeln!(f).unwrap();
-    for (s, row) in matrix.iter().enumerate() {
-        write!(f, "{}", STATE_SYMBOL[s]).unwrap();
-        for cost in row { write!(f, ",{cost:.4}").unwrap(); }
-        writeln!(f).unwrap();
-    }
-    info!("Sankoff cost matrix → {path}");
-}
-
-// ── Sankoff calibration parameters → YAML report ────────────────────────────
-//
-// Everything `--sankoff` estimates from real data, in one durable,
-// machine-readable file: `p_hat` and its variance (with how many pairs/loci
-// went into it), the derived `c_ctx`, and the base-pair substitution tally
-// (raw counts, not just the derived costs) — kept for the same reason raw
-// counts are kept anywhere else in this project: costs are a modelling
-// choice built *from* the counts, and reproducing/re-deriving them later
-// needs the counts, not just their current derived value. Structured (YAML,
-// not an ad hoc key=value text file) so R/Python/etc. can load it directly
-// rather than re-parsing free text.
-
-#[derive(serde::Serialize)]
-struct SankoffSubstitution {
-    pair: String,
-    count: u64,
-    cost: f64,
-}
-
-#[derive(serde::Serialize)]
-struct SankoffParamsReport {
-    ratio_ceiling: f64,
-    flank_length_m: usize,
-    p_hat: f64,
-    p_hat_variance: f64,
-    n_pairs_included: usize,
-    n_loci_total: u64,
-    /// Weighted-average substitution cost — see `c_ctx_from_p_hat`'s docs:
-    /// this is what turns the raw expected mutation *count* behind `c_ctx`
-    /// into an actual cost (not every mutation is worth a flat `1`).
-    mean_sub_cost: f64,
-    c_ctx: f64,
-    substitutions: Vec<SankoffSubstitution>,
-}
-
-fn write_sankoff_params(
-    estimate: &PHatEstimate,
-    tally: &BasePairTally,
-    weights: &SankoffWeights,
-    ratio_ceiling: f64,
-    m: usize,
-    mean_sub_cost: f64,
-    output: &Option<PathBuf>,
-) {
-    const BASE_LETTER: [char; 4] = ['A', 'C', 'G', 'T'];
-
-    let mut substitutions = Vec::with_capacity(6);
-    for a in 0..4 {
-        for b in (a + 1)..4 {
-            substitutions.push(SankoffSubstitution {
-                pair: format!("{}/{}", BASE_LETTER[a], BASE_LETTER[b]),
-                count: tally.counts[a][b],
-                cost: weights.sub_cost[a][b],
-            });
-        }
-    }
-    let report = SankoffParamsReport {
-        ratio_ceiling,
-        flank_length_m: m,
-        p_hat: estimate.p_hat,
-        p_hat_variance: estimate.variance,
-        n_pairs_included: estimate.n_pairs_included,
-        n_loci_total: estimate.n_loci_total,
-        mean_sub_cost,
-        c_ctx: weights.c_ctx,
-        substitutions,
-    };
-
-    let path = output.as_ref()
-        .map(|p| format!("{}_sankoff_params.yaml", p.display()))
-        .unwrap_or_else(|| "sankoff_params.yaml".into());
-    let f = std::fs::File::create(&path).unwrap_or_else(|e| {
-        eprintln!("error creating {path}: {e}");
-        std::process::exit(1);
-    });
-    serde_yaml::to_writer(f, &report).unwrap_or_else(|e| {
-        eprintln!("error writing {path}: {e}");
-        std::process::exit(1);
-    });
-    info!("Sankoff calibration parameters → {path}");
-}
-
-// ── Sankoff cost matrix + alignment → ready-to-run TNT script ──────────────
-//
-// TNT's *default* xread reader only accepts its own 0-9A-F alphabet (see
-// its manual: "up to 16 states are allowed by xread, using symbols 0-9 ...
-// and A-F") — the wider IUPAC set `STATE_SYMBOL` uses is rejected as an
-// "alien symbol" unless `nstates dna` is set, which imposes TNT's own fixed
-// DNA encoding instead, incompatible with a custom smatrix. And TNT's
-// `smatrix`/`cost` commands reject decimal costs ("found symbol . when
-// reading transformation costs"). So: recode to TNT's alphabet and
-// integer-scale the costs here, at this adapter's boundary, rather than
-// degrading the project's own canonical (IUPAC, real-valued) output.
-
-const TNT_STATE_SYMBOL: [char; 16] = [
-    '0', '1', '2', '3', '4', '5', '6', '7', '8', '9', 'A', 'B', 'C', 'D', 'E', 'F',
-];
-
-fn write_sankoff_tnt(
-    matrix: &[[f64; 16]; 16],
-    alignment: &SnpAlignment,
-    labels: &[String],
-    output: &Option<PathBuf>,
-    cost_scale: f64,
-) {
-    let path = output.as_ref()
-        .map(|p| format!("{}_sankoff.tnt", p.display()))
-        .unwrap_or_else(|| "sankoff.tnt".into());
-    let mut f = BufWriter::new(std::fs::File::create(&path).unwrap_or_else(|e| {
-        eprintln!("error creating {path}: {e}");
-        std::process::exit(1);
-    }));
-
-    // IUPAC-ish symbol -> bitmask, to translate the alignment (which uses
-    // `STATE_SYMBOL`, `-` already normalised to `0` by `snp_pseudo_alignment`
-    // callers) into TNT's alphabet without re-deriving state indices.
-    let mut iupac_to_state = [0u8; 128];
-    for (state, &sym) in STATE_SYMBOL.iter().enumerate() {
-        iupac_to_state[sym as usize] = state as u8;
-    }
-
-    let n_sites = alignment.sequences.first().map(|s| s.len()).unwrap_or(0);
-    writeln!(f, "xread").unwrap();
-    writeln!(f, "'obikmer central-position SNP families, calibrated Sankoff 16-state encoding'").unwrap();
-    writeln!(f, "{n_sites} {}", labels.len()).unwrap();
-    for (label, seq) in labels.iter().zip(alignment.sequences.iter()) {
-        write!(f, "{label} ").unwrap();
-        for &b in seq {
-            let b = if b == b'-' { b'0' } else { b };
-            let state = iupac_to_state[b as usize];
-            write!(f, "{}", TNT_STATE_SYMBOL[state as usize]).unwrap();
-        }
-        writeln!(f).unwrap();
-    }
-    writeln!(f, ";\n").unwrap();
-
-    let scaled_matrix = scaled_metric_matrix(matrix, cost_scale);
-
-    writeln!(f, "smatrix =0 (family16)").unwrap();
-    for i in 0..16 {
-        for j in (i + 1)..16 {
-            writeln!(f, "{}/{} {}", TNT_STATE_SYMBOL[i], TNT_STATE_SYMBOL[j], scaled_matrix[i][j]).unwrap();
-        }
-    }
-    writeln!(f, ";\n").unwrap();
-
-    writeln!(f, "ccode ( 0.{} ;", n_sites - 1).unwrap();
-    writeln!(f, "smatrix +0 0.{} ;", n_sites - 1).unwrap();
-    writeln!(f).unwrap();
-
-    // Basename only (not the full `path`/`output` prefix): TNT's natural
-    // workflow is to `cd` into the output directory before `proc`-ing the
-    // script, and an absolute path here would break if that directory is
-    // later moved or copied elsewhere.
-    let tre_name = output.as_ref()
-        .and_then(|p| p.file_name())
-        .map(|n| format!("{}_sankoff.tre", n.to_string_lossy()))
-        .unwrap_or_else(|| "sankoff.tre".into());
-
-    // TNT's plain command parser has no comment syntax of its own — `/* */`
-    // and `[ ]` are only recognised inside the (separately-enabled) macro
-    // scripting language, and fail with "No command!" here otherwise
-    // (verified against this file with the local TNT binary). `quote` is
-    // the closest working equivalent: it prints free text and does not
-    // otherwise affect parsing, so it doubles as an explanation of the
-    // defaults below when the script is run. `;` ends a `quote` block like
-    // any other TNT command, so the text itself must avoid semicolons.
-    writeln!(f, "quote").unwrap();
-    writeln!(f, "Default search below (edit or delete this block to run your own strategy):").unwrap();
-    writeln!(f, "  hold N     : size of TNT's tree buffer (how many equally-parsimonious").unwrap();
-    writeln!(f, "               trees it keeps in memory at once), 20 is a small, fast").unwrap();
-    writeln!(f, "               default, raise it if mult reports it had to drop trees.").unwrap();
-    writeln!(f, "  mult       : traditional search (random addition sequences followed by").unwrap();
-    writeln!(f, "               TBR branch-swapping, TNT's own default replication count),").unwrap();
-    writeln!(f, "               a reasonable first-pass strategy on this data's memory").unwrap();
-    writeln!(f, "               footprint, xmult's ratchet/drift/tree-fusion buffers ran").unwrap();
-    writeln!(f, "               this out of RAM at TNT's default mxram on this dataset.").unwrap();
-    writeln!(f, "  export - F : write the trees held in the buffer to file F, in").unwrap();
-    writeln!(f, "               TNT/Hennig86 format ('-' means trees, as opposed to data).").unwrap();
-    writeln!(f, ";").unwrap();
-    writeln!(f, "hold 20;").unwrap();
-    writeln!(f, "mult;").unwrap();
-    writeln!(f, "export - {tre_name};").unwrap();
-
-    info!(
-        "TNT script → {path} (costs scaled x{cost_scale:.0}, runs a default `hold 20; mult;` \
-         search and writes trees to {tre_name} in TNT's working directory — edit the trailing \
-         comment block in the script to change this)\n\
-         Run it with:\n  \
-         printf 'proc {path};\\nquit;\\n' | tnt\n\
-         (or start `tnt` interactively and type `proc {path};`)"
-    );
-}
-
-/// Scale `matrix` by `cost_scale` and round to integers (TNT's smatrix/cost
-/// commands reject decimals), then take the *metric closure* of the result
-/// (Floyd-Warshall over the 16 states again, on the now-integer values).
-///
-/// `matrix` is already a metric in its real-valued form (it's a
-/// shortest-path closure itself — see `build_cost_matrix`), but rounding
-/// each cell independently can still break the triangle inequality: e.g.
-/// two real costs of `1.734` each round to `173`, summing to `346`, while
-/// their own real sum `3.468` rounds to `347` — TNT then reports "triangle
-/// inequality violated ... Fixed" and silently substitutes its own
-/// corrected value. Re-closing after rounding makes that correction
-/// explicit and reproducible here instead, rather than left implicit and
-/// TNT-version-dependent.
-fn scaled_metric_matrix(matrix: &[[f64; 16]; 16], cost_scale: f64) -> [[i64; 16]; 16] {
-    let mut m = [[0i64; 16]; 16];
-    for i in 0..16 {
-        for j in 0..16 {
-            m[i][j] = (matrix[i][j] * cost_scale).round() as i64;
-        }
-    }
-    for k in 0..16 {
-        for i in 0..16 {
-            for j in 0..16 {
-                let via = m[i][k] + m[k][j];
-                if via < m[i][j] {
-                    m[i][j] = via;
-                }
-            }
-        }
-    }
-    m
-}
-
-// ── Sankoff cost matrix → PhyG custom-alphabet TCM + ready-to-run script ────
-//
-// PhyG's `tcm:STRING` format needs no alphabet recoding, unlike `--tnt`:
-// its parser reads the alphabet straight from the tcm file's own first
-// line, so `--sankoff`'s own `_sankoff.fasta` (already IUPAC+`0`) is reused
-// as-is via `prefasta:`. PhyG auto-adds its own indel/gap state as an
-// (n+1)-th row/column of the tcm — inert here since the alignment already
-// encodes absence as an ordinary state (`0`), never as `-` (see
-// `write_sankoff_alignment_fasta`'s own comment on why, and the RAxML-era
-// bug that motivated it). The gap row/column below reuses `matrix[i][0]`/
-// `matrix[0][j]` (cost to/from `∅`) as the closest principled value for a
-// state that, in practice, is never actually triggered.
-
-fn write_sankoff_phyg(matrix: &[[f64; 16]; 16], output: &Option<PathBuf>, cost_scale: f64) {
-    let scaled_matrix = scaled_metric_matrix(matrix, cost_scale);
-
-    let basename = |suffix: &str| -> String {
-        output.as_ref()
-            .and_then(|p| p.file_name())
-            .map(|n| format!("{}{suffix}", n.to_string_lossy()))
-            .unwrap_or_else(|| format!("sankoff{suffix}"))
-    };
-    let full_path = |suffix: &str| -> String {
-        output.as_ref()
-            .map(|p| format!("{}{suffix}", p.display()))
-            .unwrap_or_else(|| format!("sankoff{suffix}"))
-    };
-
-    let tcm_path = full_path("_sankoff.tcm");
-    let mut f = BufWriter::new(std::fs::File::create(&tcm_path).unwrap_or_else(|e| {
-        eprintln!("error creating {tcm_path}: {e}");
-        std::process::exit(1);
-    }));
-    let alphabet_line = STATE_SYMBOL.iter().map(|c| c.to_string()).collect::<Vec<_>>().join(" ");
-    writeln!(f, "{alphabet_line}").unwrap();
-    for i in 0..16 {
-        let mut row: Vec<i64> = (0..16).map(|j| scaled_matrix[i][j]).collect();
-        row.push(scaled_matrix[i][0]); // gap column: same cost as to/from ∅
-        writeln!(f, "{}", row.iter().map(|v| v.to_string()).collect::<Vec<_>>().join(" ")).unwrap();
-    }
-    let mut gap_row: Vec<i64> = (0..16).map(|j| scaled_matrix[0][j]).collect();
-    gap_row.push(0);
-    writeln!(f, "{}", gap_row.iter().map(|v| v.to_string()).collect::<Vec<_>>().join(" ")).unwrap();
-    info!("PhyG TCM → {tcm_path}");
-
-    let pg_path = full_path("_sankoff.pg");
-    let mut f = BufWriter::new(std::fs::File::create(&pg_path).unwrap_or_else(|e| {
-        eprintln!("error creating {pg_path}: {e}");
-        std::process::exit(1);
-    }));
-    let fasta_name = basename("_sankoff.fasta");
-    let tcm_name = basename("_sankoff.tcm");
-    let tre_name = basename("_sankoff.tre");
-    writeln!(f, "read(prefasta:\"{fasta_name}\", tcm:\"{tcm_name}\")").unwrap();
-    writeln!(f, "search(seconds:300, instances:4)").unwrap();
-    writeln!(f, "report(\"{tre_name}\", graphs, newick, overwrite)").unwrap();
-
-    let pg_dir = std::path::Path::new(&pg_path).parent()
-        .filter(|d| !d.as_os_str().is_empty())
-        .map(|d| d.display().to_string())
-        .unwrap_or_else(|| ".".into());
-    let pg_name = std::path::Path::new(&pg_path).file_name()
-        .map(|n| n.to_string_lossy().into_owned())
-        .unwrap_or_else(|| pg_path.clone());
-    info!(
-        "PhyG script → {pg_path} (costs scaled x{cost_scale:.0}, runs a default 300s/4-instance \
-         search and writes trees to {tre_name})\n\
-         Run it with:\n  \
-         cd {pg_dir} && phyg {pg_name}\n\
-         (`phyg` must run from that directory — `read()`/`report()` in the script use relative \
-         file names)"
-    );
-}
-
 // ── UPGMA Newick from kodama dendrogram ───────────────────────────────────────
 
 fn upgma_to_newick(dendro: &kodama::Dendrogram<f64>, names: &[String]) -> String {
diff --git a/src/obikmer/src/cmd/distance/phyg.rs b/src/obikmer/src/cmd/distance/phyg.rs
new file mode 100644
index 00000000..f0d0167d
--- /dev/null
+++ b/src/obikmer/src/cmd/distance/phyg.rs
@@ -0,0 +1,81 @@
+use std::io::{BufWriter, Write};
+use std::path::PathBuf;
+
+use tracing::info;
+
+use super::sankoff::{STATE_SYMBOL, scaled_metric_matrix};
+
+// ── Sankoff cost matrix → PhyG custom-alphabet TCM + ready-to-run script ────
+//
+// PhyG's `tcm:STRING` format needs no alphabet recoding, unlike `--tnt`:
+// its parser reads the alphabet straight from the tcm file's own first
+// line, so `--sankoff`'s own `_sankoff.fasta` (already IUPAC+`0`) is reused
+// as-is via `prefasta:`. PhyG auto-adds its own indel/gap state as an
+// (n+1)-th row/column of the tcm — inert here since the alignment already
+// encodes absence as an ordinary state (`0`), never as `-` (see
+// `sankoff::write_sankoff_alignment_fasta`'s own comment on why, and the
+// RAxML-era bug that motivated it). The gap row/column below reuses
+// `matrix[i][0]`/`matrix[0][j]` (cost to/from `∅`) as the closest
+// principled value for a state that, in practice, is never actually
+// triggered.
+
+pub(super) fn write_sankoff_phyg(matrix: &[[f64; 16]; 16], output: &Option<PathBuf>, cost_scale: f64) {
+    let scaled_matrix = scaled_metric_matrix(matrix, cost_scale);
+
+    let basename = |suffix: &str| -> String {
+        output.as_ref()
+            .and_then(|p| p.file_name())
+            .map(|n| format!("{}{suffix}", n.to_string_lossy()))
+            .unwrap_or_else(|| format!("sankoff{suffix}"))
+    };
+    let full_path = |suffix: &str| -> String {
+        output.as_ref()
+            .map(|p| format!("{}{suffix}", p.display()))
+            .unwrap_or_else(|| format!("sankoff{suffix}"))
+    };
+
+    let tcm_path = full_path("_sankoff.tcm");
+    let mut f = BufWriter::new(std::fs::File::create(&tcm_path).unwrap_or_else(|e| {
+        eprintln!("error creating {tcm_path}: {e}");
+        std::process::exit(1);
+    }));
+    let alphabet_line = STATE_SYMBOL.iter().map(|c| c.to_string()).collect::<Vec<_>>().join(" ");
+    writeln!(f, "{alphabet_line}").unwrap();
+    for i in 0..16 {
+        let mut row: Vec<i64> = (0..16).map(|j| scaled_matrix[i][j]).collect();
+        row.push(scaled_matrix[i][0]); // gap column: same cost as to/from ∅
+        writeln!(f, "{}", row.iter().map(|v| v.to_string()).collect::<Vec<_>>().join(" ")).unwrap();
+    }
+    let mut gap_row: Vec<i64> = (0..16).map(|j| scaled_matrix[0][j]).collect();
+    gap_row.push(0);
+    writeln!(f, "{}", gap_row.iter().map(|v| v.to_string()).collect::<Vec<_>>().join(" ")).unwrap();
+    info!("PhyG TCM → {tcm_path}");
+
+    let pg_path = full_path("_sankoff.pg");
+    let mut f = BufWriter::new(std::fs::File::create(&pg_path).unwrap_or_else(|e| {
+        eprintln!("error creating {pg_path}: {e}");
+        std::process::exit(1);
+    }));
+    let fasta_name = basename("_sankoff.fasta");
+    let tcm_name = basename("_sankoff.tcm");
+    let tre_name = basename("_sankoff.tre");
+    writeln!(f, "read(prefasta:\"{fasta_name}\", tcm:\"{tcm_name}\")").unwrap();
+    writeln!(f, "search(seconds:300, instances:4)").unwrap();
+    writeln!(f, "report(\"{tre_name}\", graphs, newick, overwrite)").unwrap();
+
+    let pg_dir = std::path::Path::new(&pg_path).parent()
+        .filter(|d| !d.as_os_str().is_empty())
+        .map(|d| d.display().to_string())
+        .unwrap_or_else(|| ".".into());
+    let pg_name = std::path::Path::new(&pg_path).file_name()
+        .map(|n| n.to_string_lossy().into_owned())
+        .unwrap_or_else(|| pg_path.clone());
+    info!(
+        "PhyG script → {pg_path} (costs scaled x{cost_scale:.0}, runs a default 300s/4-instance \
+         search and writes trees to {tre_name})\n\
+         Run it with:\n  \
+         cd {pg_dir} && phyg {pg_name}\n\
+         (`phyg` must run from that directory — `read()`/`report()` in the script use relative \
+         file names)"
+    );
+}
diff --git a/src/obikmer/src/cmd/distance/sankoff.rs b/src/obikmer/src/cmd/distance/sankoff.rs
new file mode 100644
index 00000000..76676237
--- /dev/null
+++ b/src/obikmer/src/cmd/distance/sankoff.rs
@@ -0,0 +1,202 @@
+use std::io::{BufWriter, Write};
+use std::path::PathBuf;
+
+use obifastwrite::{JsonVal, write_record};
+use obikindex::{BasePairTally, PHatEstimate, SankoffWeights, SnpAlignment};
+use tracing::info;
+
+// ── Sankoff pseudo-alignment → FASTA ────────────────────────────────────────
+//
+// Same data as `--snp`'s pseudo-alignment (`SnpAlignment`/
+// `snp_pseudo_alignment`), re-coded so its symbols match the accompanying
+// `--sankoff-matrix` output exactly: `0` for the empty/absent state instead
+// of `-`, which TNT/PhyG would otherwise read as their own gap character
+// rather than our "family absent" state.
+
+pub(super) fn write_sankoff_alignment_fasta(alignment: &SnpAlignment, labels: &[String], output: &Option<PathBuf>) {
+    let path = output.as_ref()
+        .map(|p| format!("{}_sankoff.fasta", p.display()))
+        .unwrap_or_else(|| "sankoff.fasta".into());
+    let mut f = BufWriter::new(std::fs::File::create(&path).unwrap_or_else(|e| {
+        eprintln!("error creating {path}: {e}");
+        std::process::exit(1);
+    }));
+    let n_sites = alignment.sequences.first().map(|s| s.len()).unwrap_or(0);
+    for (label, seq) in labels.iter().zip(alignment.sequences.iter()) {
+        let recoded: Vec<u8> = seq.iter().map(|&b| if b == b'-' { b'0' } else { b }).collect();
+        write_record(&recoded, label, &[("n_sites", JsonVal::Num(n_sites as u64))], &mut f).unwrap_or_else(|e| {
+            eprintln!("error writing {path}: {e}");
+            std::process::exit(1);
+        });
+    }
+    info!("Sankoff pseudo-alignment → {path} ({n_sites} site{})",
+        if n_sites == 1 { "" } else { "s" });
+}
+
+// ── Sankoff cost matrix → CSV ────────────────────────────────────────────────
+//
+// 16 states indexed by bitmask (bit 0=A, 1=C, 2=G, 3=T; state 0 is `∅`),
+// matching the convention already used for `--snp`'s IUPAC-coded output and
+// for the external TNT/PhyG scripts this feeds. Calibration report (p_hat,
+// its variance, how many pairs/loci went into it, the resulting c_ctx) goes
+// to the log, not the CSV, since it's a run-level fact, not per-cell data.
+
+// IUPAC ambiguity code per state (same mapping as `siblings::iupac_code`,
+// already used for `--snp`'s pseudo-alignment — a biologist reads "R" as
+// "A or G" without needing this file's convention explained), with `0`
+// standing in for the empty state (`-` would collide with TNT/PhyG's own
+// gap/range syntax). Bit order: 0=A, 1=C, 2=G, 3=T. This project's
+// canonical alphabet — `tnt::write_sankoff_tnt` recodes it to TNT's own
+// default alphabet at the adapter boundary, rather than using it here.
+pub(super) const STATE_SYMBOL: [char; 16] = [
+    '0', 'A', 'C', 'M', 'G', 'R', 'S', 'V', 'T', 'W', 'Y', 'H', 'K', 'D', 'B', 'N',
+];
+
+pub(super) fn write_sankoff_matrix_csv(
+    matrix: &[[f64; 16]; 16],
+    estimate: &PHatEstimate,
+    weights: &SankoffWeights,
+    output: &Option<PathBuf>,
+) {
+    info!(
+        p_hat = format_args!("{:.6}", estimate.p_hat),
+        variance = format_args!("{:.3e}", estimate.variance),
+        n_pairs_included = estimate.n_pairs_included,
+        n_loci_total = estimate.n_loci_total,
+        c_ctx = format_args!("{:.4}", weights.c_ctx),
+        "Sankoff matrix calibration"
+    );
+
+    let path = output.as_ref()
+        .map(|p| format!("{}_sankoff_matrix.csv", p.display()))
+        .unwrap_or_else(|| "sankoff_matrix.csv".into());
+    let mut f = BufWriter::new(std::fs::File::create(&path).unwrap_or_else(|e| {
+        eprintln!("error creating {path}: {e}");
+        std::process::exit(1);
+    }));
+    write!(f, "state").unwrap();
+    for sym in STATE_SYMBOL { write!(f, ",{sym}").unwrap(); }
+    writeln!(f).unwrap();
+    for (s, row) in matrix.iter().enumerate() {
+        write!(f, "{}", STATE_SYMBOL[s]).unwrap();
+        for cost in row { write!(f, ",{cost:.4}").unwrap(); }
+        writeln!(f).unwrap();
+    }
+    info!("Sankoff cost matrix → {path}");
+}
+
+// ── Sankoff calibration parameters → YAML report ────────────────────────────
+//
+// Everything `--sankoff` estimates from real data, in one durable,
+// machine-readable file: `p_hat` and its variance (with how many pairs/loci
+// went into it), the derived `c_ctx`, and the base-pair substitution tally
+// (raw counts, not just the derived costs) — kept for the same reason raw
+// counts are kept anywhere else in this project: costs are a modelling
+// choice built *from* the counts, and reproducing/re-deriving them later
+// needs the counts, not just their current derived value. Structured (YAML,
+// not an ad hoc key=value text file) so R/Python/etc. can load it directly
+// rather than re-parsing free text.
+
+#[derive(serde::Serialize)]
+struct SankoffSubstitution {
+    pair: String,
+    count: u64,
+    cost: f64,
+}
+
+#[derive(serde::Serialize)]
+struct SankoffParamsReport {
+    ratio_ceiling: f64,
+    flank_length_m: usize,
+    p_hat: f64,
+    p_hat_variance: f64,
+    n_pairs_included: usize,
+    n_loci_total: u64,
+    /// Weighted-average substitution cost — see `c_ctx_from_p_hat`'s docs:
+    /// this is what turns the raw expected mutation *count* behind `c_ctx`
+    /// into an actual cost (not every mutation is worth a flat `1`).
+    mean_sub_cost: f64,
+    c_ctx: f64,
+    substitutions: Vec<SankoffSubstitution>,
+}
+
+pub(super) fn write_sankoff_params(
+    estimate: &PHatEstimate,
+    tally: &BasePairTally,
+    weights: &SankoffWeights,
+    ratio_ceiling: f64,
+    m: usize,
+    mean_sub_cost: f64,
+    output: &Option<PathBuf>,
+) {
+    const BASE_LETTER: [char; 4] = ['A', 'C', 'G', 'T'];
+
+    let mut substitutions = Vec::with_capacity(6);
+    for a in 0..4 {
+        for b in (a + 1)..4 {
+            substitutions.push(SankoffSubstitution {
+                pair: format!("{}/{}", BASE_LETTER[a], BASE_LETTER[b]),
+                count: tally.counts[a][b],
+                cost: weights.sub_cost[a][b],
+            });
+        }
+    }
+    let report = SankoffParamsReport {
+        ratio_ceiling,
+        flank_length_m: m,
+        p_hat: estimate.p_hat,
+        p_hat_variance: estimate.variance,
+        n_pairs_included: estimate.n_pairs_included,
+        n_loci_total: estimate.n_loci_total,
+        mean_sub_cost,
+        c_ctx: weights.c_ctx,
+        substitutions,
+    };
+
+    let path = output.as_ref()
+        .map(|p| format!("{}_sankoff_params.yaml", p.display()))
+        .unwrap_or_else(|| "sankoff_params.yaml".into());
+    let f = std::fs::File::create(&path).unwrap_or_else(|e| {
+        eprintln!("error creating {path}: {e}");
+        std::process::exit(1);
+    });
+    serde_yaml::to_writer(f, &report).unwrap_or_else(|e| {
+        eprintln!("error writing {path}: {e}");
+        std::process::exit(1);
+    });
+    info!("Sankoff calibration parameters → {path}");
+}
+
+/// Scale `matrix` by `cost_scale` and round to integers (TNT's smatrix/cost
+/// and PhyG's `tcm:` commands both reject decimals), then take the *metric
+/// closure* of the result (Floyd-Warshall over the 16 states again, on the
+/// now-integer values).
+///
+/// `matrix` is already a metric in its real-valued form (it's a
+/// shortest-path closure itself — see `obikindex::build_cost_matrix`), but
+/// rounding each cell independently can still break the triangle
+/// inequality: e.g. two real costs of `1.734` each round to `173`, summing
+/// to `346`, while their own real sum `3.468` rounds to `347` — TNT then
+/// reports "triangle inequality violated ... Fixed" and silently
+/// substitutes its own corrected value. Re-closing after rounding makes
+/// that correction explicit and reproducible here instead, rather than
+/// left implicit and tool-version-dependent.
+pub(super) fn scaled_metric_matrix(matrix: &[[f64; 16]; 16], cost_scale: f64) -> [[i64; 16]; 16] {
+    let mut m = [[0i64; 16]; 16];
+    for i in 0..16 {
+        for j in 0..16 {
+            m[i][j] = (matrix[i][j] * cost_scale).round() as i64;
+        }
+    }
+    for k in 0..16 {
+        for i in 0..16 {
+            for j in 0..16 {
+                let via = m[i][k] + m[k][j];
+                if via < m[i][j] {
+                    m[i][j] = via;
+                }
+            }
+        }
+    }
+    m
+}
diff --git a/src/obikmer/src/cmd/distance/tnt.rs b/src/obikmer/src/cmd/distance/tnt.rs
new file mode 100644
index 00000000..977994c4
--- /dev/null
+++ b/src/obikmer/src/cmd/distance/tnt.rs
@@ -0,0 +1,119 @@
+use std::io::{BufWriter, Write};
+use std::path::PathBuf;
+
+use obikindex::SnpAlignment;
+use tracing::info;
+
+use super::sankoff::{STATE_SYMBOL, scaled_metric_matrix};
+
+// ── Sankoff cost matrix + alignment → ready-to-run TNT script ──────────────
+//
+// TNT's *default* xread reader only accepts its own 0-9A-F alphabet (see
+// its manual: "up to 16 states are allowed by xread, using symbols 0-9 ...
+// and A-F") — the wider IUPAC set `STATE_SYMBOL` uses is rejected as an
+// "alien symbol" unless `nstates dna` is set, which imposes TNT's own fixed
+// DNA encoding instead, incompatible with a custom smatrix. And TNT's
+// `smatrix`/`cost` commands reject decimal costs ("found symbol . when
+// reading transformation costs"). So: recode to TNT's alphabet and
+// integer-scale the costs here, at this adapter's boundary, rather than
+// degrading the project's own canonical (IUPAC, real-valued) output.
+
+const TNT_STATE_SYMBOL: [char; 16] = [
+    '0', '1', '2', '3', '4', '5', '6', '7', '8', '9', 'A', 'B', 'C', 'D', 'E', 'F',
+];
+
+pub(super) fn write_sankoff_tnt(
+    matrix: &[[f64; 16]; 16],
+    alignment: &SnpAlignment,
+    labels: &[String],
+    output: &Option<PathBuf>,
+    cost_scale: f64,
+) {
+    let path = output.as_ref()
+        .map(|p| format!("{}_sankoff.tnt", p.display()))
+        .unwrap_or_else(|| "sankoff.tnt".into());
+    let mut f = BufWriter::new(std::fs::File::create(&path).unwrap_or_else(|e| {
+        eprintln!("error creating {path}: {e}");
+        std::process::exit(1);
+    }));
+
+    // IUPAC-ish symbol -> bitmask, to translate the alignment (which uses
+    // `STATE_SYMBOL`, `-` already normalised to `0` by `snp_pseudo_alignment`
+    // callers) into TNT's alphabet without re-deriving state indices.
+    let mut iupac_to_state = [0u8; 128];
+    for (state, &sym) in STATE_SYMBOL.iter().enumerate() {
+        iupac_to_state[sym as usize] = state as u8;
+    }
+
+    let n_sites = alignment.sequences.first().map(|s| s.len()).unwrap_or(0);
+    writeln!(f, "xread").unwrap();
+    writeln!(f, "'obikmer central-position SNP families, calibrated Sankoff 16-state encoding'").unwrap();
+    writeln!(f, "{n_sites} {}", labels.len()).unwrap();
+    for (label, seq) in labels.iter().zip(alignment.sequences.iter()) {
+        write!(f, "{label} ").unwrap();
+        for &b in seq {
+            let b = if b == b'-' { b'0' } else { b };
+            let state = iupac_to_state[b as usize];
+            write!(f, "{}", TNT_STATE_SYMBOL[state as usize]).unwrap();
+        }
+        writeln!(f).unwrap();
+    }
+    writeln!(f, ";\n").unwrap();
+
+    let scaled_matrix = scaled_metric_matrix(matrix, cost_scale);
+
+    writeln!(f, "smatrix =0 (family16)").unwrap();
+    for i in 0..16 {
+        for j in (i + 1)..16 {
+            writeln!(f, "{}/{} {}", TNT_STATE_SYMBOL[i], TNT_STATE_SYMBOL[j], scaled_matrix[i][j]).unwrap();
+        }
+    }
+    writeln!(f, ";\n").unwrap();
+
+    writeln!(f, "ccode ( 0.{} ;", n_sites - 1).unwrap();
+    writeln!(f, "smatrix +0 0.{} ;", n_sites - 1).unwrap();
+    writeln!(f).unwrap();
+
+    // Basename only (not the full `path`/`output` prefix): TNT's natural
+    // workflow is to `cd` into the output directory before `proc`-ing the
+    // script, and an absolute path here would break if that directory is
+    // later moved or copied elsewhere.
+    let tre_name = output.as_ref()
+        .and_then(|p| p.file_name())
+        .map(|n| format!("{}_sankoff.tre", n.to_string_lossy()))
+        .unwrap_or_else(|| "sankoff.tre".into());
+
+    // TNT's plain command parser has no comment syntax of its own — `/* */`
+    // and `[ ]` are only recognised inside the (separately-enabled) macro
+    // scripting language, and fail with "No command!" here otherwise
+    // (verified against this file with the local TNT binary). `quote` is
+    // the closest working equivalent: it prints free text and does not
+    // otherwise affect parsing, so it doubles as an explanation of the
+    // defaults below when the script is run. `;` ends a `quote` block like
+    // any other TNT command, so the text itself must avoid semicolons.
+    writeln!(f, "quote").unwrap();
+    writeln!(f, "Default search below (edit or delete this block to run your own strategy):").unwrap();
+    writeln!(f, "  hold N     : size of TNT's tree buffer (how many equally-parsimonious").unwrap();
+    writeln!(f, "               trees it keeps in memory at once), 20 is a small, fast").unwrap();
+    writeln!(f, "               default, raise it if mult reports it had to drop trees.").unwrap();
+    writeln!(f, "  mult       : traditional search (random addition sequences followed by").unwrap();
+    writeln!(f, "               TBR branch-swapping, TNT's own default replication count),").unwrap();
+    writeln!(f, "               a reasonable first-pass strategy on this data's memory").unwrap();
+    writeln!(f, "               footprint, xmult's ratchet/drift/tree-fusion buffers ran").unwrap();
+    writeln!(f, "               this out of RAM at TNT's default mxram on this dataset.").unwrap();
+    writeln!(f, "  export - F : write the trees held in the buffer to file F, in").unwrap();
+    writeln!(f, "               TNT/Hennig86 format ('-' means trees, as opposed to data).").unwrap();
+    writeln!(f, ";").unwrap();
+    writeln!(f, "hold 20;").unwrap();
+    writeln!(f, "mult;").unwrap();
+    writeln!(f, "export - {tre_name};").unwrap();
+
+    info!(
+        "TNT script → {path} (costs scaled x{cost_scale:.0}, runs a default `hold 20; mult;` \
+         search and writes trees to {tre_name} in TNT's working directory — edit the trailing \
+         comment block in the script to change this)\n\
+         Run it with:\n  \
+         printf 'proc {path};\\nquit;\\n' | tnt\n\
+         (or start `tnt` interactively and type `proc {path};`)"
+    );
+}
-- 
2.54.0


From 28d841c7beda8b7fe740680c925724c037c1f30e Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Wed, 12 Aug 2026 18:23:51 +0200
Subject: [PATCH 03/46] feat(distance): add IQ-TREE output and optimize state
 index mapping

Introduce `--iqtree` and `--raw-snp-counts` flags to generate IQ-TREE model files, recoded FASTA alignments, and per-pair diagnostic counts. Centralize alphabet conversion by extracting a precomputed state index lookup table into the Sankoff module, eliminating redundant iterations across downstream adapters.
---
 .gitignore                              |   1 +
 src/obikmer/src/cmd/distance/iqtree.rs  | 183 ++++++++++++++++++++++++
 src/obikmer/src/cmd/distance/mod.rs     |  91 +++++++++++-
 src/obikmer/src/cmd/distance/sankoff.rs |  11 ++
 src/obikmer/src/cmd/distance/tnt.rs     |   7 +-
 5 files changed, 285 insertions(+), 8 deletions(-)
 create mode 100644 src/obikmer/src/cmd/distance/iqtree.rs

diff --git a/.gitignore b/.gitignore
index 3cd5920d..32189eb2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -26,3 +26,4 @@ benchmark/specific_index_count
 benchmark/specific_index_presence
 TNT
 phyg
+*.tnt
diff --git a/src/obikmer/src/cmd/distance/iqtree.rs b/src/obikmer/src/cmd/distance/iqtree.rs
new file mode 100644
index 00000000..0a1ac655
--- /dev/null
+++ b/src/obikmer/src/cmd/distance/iqtree.rs
@@ -0,0 +1,183 @@
+use std::io::{BufWriter, Write};
+use std::path::PathBuf;
+
+use obifastwrite::{JsonVal, write_record};
+use obikindex::SnpAlignment;
+use tracing::info;
+
+use super::sankoff::state_index_table;
+
+// ── Sankoff-calibrated data → IQ-TREE custom ML model + recoded alignment ──
+//
+// Not itself a Sankoff computation — IQ-TREE does maximum likelihood, not
+// parsimony. Only the *source data* is shared with `--tnt`/`--phyg` (the
+// calibrated 16-state cost matrix, the pseudo-alignment); the operation
+// performed on it here is different, hence no "sankoff" in these names,
+// unlike `tnt::write_sankoff_tnt`/`phyg::write_sankoff_phyg`.
+//
+// Verified against the locally installed `iqtree3` binary/source (not just
+// its docs — see `docmd/theory/evolutionary_distances.md`, "Next
+// direction: genuine ML branch lengths"), because the web documentation's
+// `-mdef` NEXUS route turned out not to apply to a plain (non-mixture)
+// custom morphology model. The real mechanism: pass a **file path**
+// directly as `-m`, containing (as whitespace/newline-separated numbers)
+// the lower-triangular exchangeability matrix `R` (`k(k-1)/2` values, PAML
+// row-major order) immediately followed by the `k` state frequencies `π`
+// on the same stream — `ModelMarkov::readRates`/`readStateFreq` read them
+// in that exact order, no header, no separator required.
+//
+// `R` is recovered from the calibrated Sankoff cost matrix via
+// `R(a,b) = exp(-cost(a,b))` (the cost is `-ln(rate)`, see "A concrete
+// Sankoff cost matrix"), symmetric by construction (the underlying tally
+// never captured direction). `π` is the real, empirical, non-uniform
+// marginal frequency of each state across the whole alignment — precise
+// enough at this sample size (908k+ sites) without spending IQ-TREE's own
+// `+FO` ML degrees of freedom re-estimating it (checked: IQ-TREE's `+F`
+// doesn't work as a shortcut here either, a custom-file model always
+// requires the frequency line in the file itself). IQ-TREE reconstructs
+// the (generally asymmetric) rate matrix internally as
+// `Q(i,j) = R(i,j)·π_j` — reversible for *any* `π`, not just uniform,
+// because `R` is symmetric.
+//
+// IQ-TREE infers its state count from the highest-ordinal symbol actually
+// present in the alignment, not from a declared count (`--seqtype
+// MORPH{N}` was tested and does not override this for real ML analysis,
+// only for the `--alisim` simulator). So states that never occur anywhere
+// in this particular alignment are dropped, and the survivors are
+// renumbered compactly (`0..k-1`, order preserved) rather than leaving
+// gaps that would silently misalign every value IQ-TREE reads. Both the
+// model and the alignment must agree on this same renumbering, so it's
+// computed once (`CompactAlphabet`) and shared between them.
+
+const IQTREE_STATE_SYMBOL: [char; 16] = [
+    '0', '1', '2', '3', '4', '5', '6', '7', '8', '9', 'A', 'B', 'C', 'D', 'E', 'F',
+];
+
+struct CompactAlphabet {
+    /// Canonical (0..16) state index -> compact index, for states that occur.
+    old_to_compact: [Option<u8>; 16],
+    /// Compact index -> canonical state index, order-preserving.
+    compact_to_old: Vec<u8>,
+    /// Empirical frequency of each compact-indexed state (sums to 1).
+    freq: Vec<f64>,
+}
+
+impl CompactAlphabet {
+    fn k(&self) -> usize {
+        self.compact_to_old.len()
+    }
+}
+
+fn compact_alphabet(alignment: &SnpAlignment) -> CompactAlphabet {
+    let iupac_to_state = state_index_table();
+
+    let mut occurs = [false; 16];
+    let mut counts = [0u64; 16];
+    for seq in &alignment.sequences {
+        for &b in seq {
+            let b = if b == b'-' { b'0' } else { b };
+            let state = iupac_to_state[b as usize] as usize;
+            occurs[state] = true;
+            counts[state] += 1;
+        }
+    }
+
+    let mut old_to_compact: [Option<u8>; 16] = [None; 16];
+    let mut compact_to_old: Vec<u8> = Vec::new();
+    for old in 0..16 {
+        if occurs[old] {
+            old_to_compact[old] = Some(compact_to_old.len() as u8);
+            compact_to_old.push(old as u8);
+        }
+    }
+
+    let total: u64 = compact_to_old.iter().map(|&old| counts[old as usize]).sum();
+    let freq: Vec<f64> = compact_to_old.iter()
+        .map(|&old| counts[old as usize] as f64 / total as f64)
+        .collect();
+
+    CompactAlphabet { old_to_compact, compact_to_old, freq }
+}
+
+/// Write the `R` (exchangeability) + `π` (frequencies) model file IQ-TREE's
+/// `-m <file>+ASC` reads. Returns the path, so the caller can print a
+/// single combined "how to run this" message once the alignment is also
+/// written.
+fn write_iqtree_model(matrix: &[[f64; 16]; 16], alphabet: &CompactAlphabet, output: &Option<PathBuf>) -> String {
+    let rate = |old_i: u8, old_j: u8| (-matrix[old_i as usize][old_j as usize]).exp();
+
+    let model_path = output.as_ref()
+        .map(|p| format!("{}_iqtree.model", p.display()))
+        .unwrap_or_else(|| "iqtree.model".into());
+    let mut f = BufWriter::new(std::fs::File::create(&model_path).unwrap_or_else(|e| {
+        eprintln!("error creating {model_path}: {e}");
+        std::process::exit(1);
+    }));
+    for i in 1..alphabet.k() {
+        let row: Vec<String> = (0..i)
+            .map(|j| format!("{:.6}", rate(alphabet.compact_to_old[i], alphabet.compact_to_old[j])))
+            .collect();
+        writeln!(f, "{}", row.join(" ")).unwrap();
+    }
+    writeln!(f, "{}", alphabet.freq.iter().map(|p| format!("{p:.6}")).collect::<Vec<_>>().join(" ")).unwrap();
+    info!("IQ-TREE model file → {model_path} ({} of 16 states present in the alignment)", alphabet.k());
+    model_path
+}
+
+/// Write the pseudo-alignment recoded to the same compact `0..k-1` alphabet
+/// as `write_iqtree_model`'s matrix — not `--sankoff`'s own IUPAC alphabet,
+/// since IQ-TREE needs the symbol ordinal itself to match the surviving
+/// state count (see this module's own doc comment on `MORPH{N}`).
+fn write_iqtree_alignment(
+    alignment: &SnpAlignment,
+    labels: &[String],
+    alphabet: &CompactAlphabet,
+    output: &Option<PathBuf>,
+) -> (String, usize) {
+    let iupac_to_state = state_index_table();
+
+    let fasta_path = output.as_ref()
+        .map(|p| format!("{}_iqtree.fasta", p.display()))
+        .unwrap_or_else(|| "iqtree.fasta".into());
+    let mut f = BufWriter::new(std::fs::File::create(&fasta_path).unwrap_or_else(|e| {
+        eprintln!("error creating {fasta_path}: {e}");
+        std::process::exit(1);
+    }));
+    let n_sites = alignment.sequences.first().map(|s| s.len()).unwrap_or(0);
+    for (label, seq) in labels.iter().zip(alignment.sequences.iter()) {
+        let recoded: Vec<u8> = seq.iter().map(|&b| {
+            let b = if b == b'-' { b'0' } else { b };
+            let old = iupac_to_state[b as usize] as usize;
+            let compact = alphabet.old_to_compact[old]
+                .expect("state occurs in the alignment, so it must have a compact index");
+            IQTREE_STATE_SYMBOL[compact as usize] as u8
+        }).collect();
+        write_record(&recoded, label, &[("n_sites", JsonVal::Num(n_sites as u64))], &mut f).unwrap_or_else(|e| {
+            eprintln!("error writing {fasta_path}: {e}");
+            std::process::exit(1);
+        });
+    }
+    (fasta_path, n_sites)
+}
+
+pub(super) fn write_iqtree(
+    matrix: &[[f64; 16]; 16],
+    alignment: &SnpAlignment,
+    labels: &[String],
+    output: &Option<PathBuf>,
+) {
+    let alphabet = compact_alphabet(alignment);
+    let model_path = write_iqtree_model(matrix, &alphabet, output);
+    let (fasta_path, n_sites) = write_iqtree_alignment(alignment, labels, &alphabet, output);
+
+    let prefix_name = output.as_ref()
+        .and_then(|p| p.file_name())
+        .map(|n| format!("{}_iqtree", n.to_string_lossy()))
+        .unwrap_or_else(|| "iqtree".into());
+    info!(
+        "IQ-TREE alignment → {fasta_path} ({n_sites} sites, {} states)\n\
+         Run with:\n  \
+         iqtree3 -s {fasta_path} --seqtype MORPH -m {model_path}+ASC --prefix {prefix_name} -T AUTO",
+        alphabet.k()
+    );
+}
diff --git a/src/obikmer/src/cmd/distance/mod.rs b/src/obikmer/src/cmd/distance/mod.rs
index bd698caa..3dfe08d3 100644
--- a/src/obikmer/src/cmd/distance/mod.rs
+++ b/src/obikmer/src/cmd/distance/mod.rs
@@ -1,3 +1,4 @@
+mod iqtree;
 mod phyg;
 mod sankoff;
 mod tnt;
@@ -16,6 +17,7 @@ use obikindex::{
 use speedytree::{DistanceMatrix, Hybrid, NeighborJoiningSolver, to_newick};
 use tracing::info;
 
+use iqtree::write_iqtree;
 use phyg::write_sankoff_phyg;
 use sankoff::{write_sankoff_alignment_fasta, write_sankoff_matrix_csv, write_sankoff_params};
 use tnt::write_sankoff_tnt;
@@ -98,6 +100,19 @@ pub struct DistanceArgs {
     #[arg(long)]
     pub raw_snp_distance: bool,
 
+    /// Write the raw per-pair counts (`n_snp`, `n_shared`, `n_eligible`)
+    /// behind `--raw-snp-distance`'s ratio, one row per genome pair — a
+    /// diagnostic table, not a matrix. The ratio alone can't distinguish
+    /// "identical at every eligible locus" from "almost no eligible loci
+    /// at all" (e.g. `0.0` from 0/2 looks the same as `0.0` from 0/2000),
+    /// and that distinction matters a lot for genome pairs near the edge
+    /// of what central-position families can resolve (see
+    /// `docmd/theory/evolutionary_distances.md`, "Run 3" and the
+    /// IQ-TREE/Mash comparison). Same annex requirement as
+    /// `--raw-snp-distance`.
+    #[arg(long)]
+    pub raw_snp_counts: bool,
+
     /// Write a SNP-only pseudo-alignment (FASTA, IUPAC-coded) from an
     /// already-built sibling annex — one row per genome, one column per
     /// variable family (monomorphic families skipped), no flanking
@@ -141,6 +156,24 @@ pub struct DistanceArgs {
     #[arg(long)]
     pub phyg: bool,
 
+    /// Also write <prefix>_iqtree.model and <prefix>_iqtree.fasta, a
+    /// custom-model file and a matching
+    /// recoded alignment for genuine maximum-likelihood inference with
+    /// IQ-TREE (`iqtree3 -s ... --seqtype MORPH -m ...+ASC`) — real branch
+    /// lengths, unlike `--tnt`/`--phyg`'s parsimony step counts. The model
+    /// is the reversible `Q(i,j) = R(i,j)·π_j` construction: `R`
+    /// (exchangeability, symmetric) recovered from the same calibrated
+    /// cost matrix `--sankoff` computes, `π` the real empirical state
+    /// frequencies counted from the alignment (not IQ-TREE's `+FO`/`+F` —
+    /// neither applies to a custom-file model, see
+    /// `docmd/theory/evolutionary_distances.md`). Only the states that
+    /// actually occur in this alignment are kept, compactly renumbered
+    /// (IQ-TREE infers its state count from the alignment itself, and a
+    /// gap in the numbering would silently misalign the model file).
+    /// Implies `--sankoff`.
+    #[arg(long)]
+    pub iqtree: bool,
+
     /// Scale factor applied before rounding real-valued costs to the
     /// integers both `--tnt`'s smatrix/cost commands and `--phyg`'s `tcm:`
     /// matrix require. Keep this small: the total tree score is this scale
@@ -157,10 +190,12 @@ pub struct DistanceArgs {
     pub sankoff_cost_scale: f64,
 
     /// Output prefix: <prefix>_dist.csv, <prefix>_shared.csv,
-    /// <prefix>_siblings.csv, <prefix>_rawsnp.csv, <prefix>_snp.fasta,
+    /// <prefix>_siblings.csv, <prefix>_rawsnp.csv, <prefix>_rawsnp_counts.csv,
+    /// <prefix>_snp.fasta,
     /// <prefix>_sankoff_matrix.csv, <prefix>_sankoff_params.yaml,
     /// <prefix>_sankoff.fasta, <prefix>_sankoff.tnt, <prefix>_sankoff.tcm,
-    /// <prefix>_sankoff.pg, <prefix>_nj.nwk, <prefix>_upgma.nwk.
+    /// <prefix>_sankoff.pg, <prefix>_iqtree.model, <prefix>_iqtree.fasta,
+    /// <prefix>_nj.nwk, <prefix>_upgma.nwk.
     /// If omitted, the distance matrix is written to stdout.
     #[arg(short, long)]
     pub output: Option<PathBuf>,
@@ -208,6 +243,13 @@ pub fn run(args: DistanceArgs) {
         });
         write_raw_snp_distance_csv(&result, &labels, &args.output);
     }
+    if args.raw_snp_counts {
+        let result = idx.raw_snp_distance().unwrap_or_else(|e| {
+            eprintln!("error computing raw SNP distance: {e}");
+            std::process::exit(1);
+        });
+        write_raw_snp_counts_csv(&result, &labels, &args.output);
+    }
     if args.snp {
         let alignment = idx.snp_pseudo_alignment().unwrap_or_else(|e| {
             eprintln!("error computing SNP pseudo-alignment: {e}");
@@ -215,7 +257,7 @@ pub fn run(args: DistanceArgs) {
         });
         write_snp_fasta(&alignment, &labels, &args.output);
     }
-    if args.sankoff || args.tnt || args.phyg {
+    if args.sankoff || args.tnt || args.phyg || args.iqtree {
         let raw = idx.raw_snp_distance().unwrap_or_else(|e| {
             eprintln!("error computing raw SNP distance: {e}");
             std::process::exit(1);
@@ -248,6 +290,9 @@ pub fn run(args: DistanceArgs) {
         if args.phyg {
             write_sankoff_phyg(&matrix, &args.output, args.sankoff_cost_scale);
         }
+        if args.iqtree {
+            write_iqtree(&matrix, &alignment, &labels, &args.output);
+        }
     }
 
     // `--sibling-annex`/`--sibling-stats`/`--raw-snp-distance`/`--snp`/
@@ -260,10 +305,12 @@ pub fn run(args: DistanceArgs) {
     if args.sibling_annex
         || args.sibling_stats
         || args.raw_snp_distance
+        || args.raw_snp_counts
         || args.snp
         || args.sankoff
         || args.tnt
         || args.phyg
+        || args.iqtree
     {
         return;
     }
@@ -450,6 +497,44 @@ fn write_raw_snp_distance_csv(result: &RawSnpDistanceOutput, labels: &[String],
     info!("raw single-copy SNP distance matrix → {path}");
 }
 
+// ── Raw single-copy SNP distance → per-pair diagnostic counts ──────────────
+//
+// A pair table (one row per unordered genome pair), not a matrix: the ratio
+// alone can't distinguish "identical across every eligible locus" from
+// "almost no eligible locus at all" — both can read `0.0`/`NA` in
+// `--raw-snp-distance`'s output. Distinguishing them matters most exactly
+// where it's easy to miss: genome pairs near the edge of what
+// central-position families can resolve at all (deep cross-lineage splits,
+// see `docmd/theory/evolutionary_distances.md`, "Run 3" and the later
+// IQ-TREE/Mash comparison — a `ratio=0.0` backed by 2 eligible loci is not
+// the same claim as one backed by 2000).
+
+fn write_raw_snp_counts_csv(result: &RawSnpDistanceOutput, labels: &[String], output: &Option<PathBuf>) {
+    let path = output.as_ref()
+        .map(|p| format!("{}_rawsnp_counts.csv", p.display()))
+        .unwrap_or_else(|| "rawsnp_counts.csv".into());
+    let mut f = BufWriter::new(std::fs::File::create(&path).unwrap_or_else(|e| {
+        eprintln!("error creating {path}: {e}");
+        std::process::exit(1);
+    }));
+    let n = labels.len();
+    writeln!(f, "genome_a,genome_b,n_snp,n_shared,n_eligible,ratio").unwrap();
+    for i in 0..n {
+        for j in (i + 1)..n {
+            let snp = result.snp[[i, j]];
+            let shared = result.shared[[i, j]];
+            let eligible = snp + shared;
+            write!(f, "{},{},{snp},{shared},{eligible}", labels[i], labels[j]).unwrap();
+            if eligible == 0 {
+                writeln!(f, ",NA").unwrap();
+            } else {
+                writeln!(f, ",{:.6}", snp as f64 / eligible as f64).unwrap();
+            }
+        }
+    }
+    info!("raw single-copy SNP distance counts (diagnostic) → {path}");
+}
+
 // ── SNP-only pseudo-alignment → FASTA ───────────────────────────────────────
 //
 // One record per genome, IUPAC-coded, no flanking sequence — see
diff --git a/src/obikmer/src/cmd/distance/sankoff.rs b/src/obikmer/src/cmd/distance/sankoff.rs
index 76676237..5e02fda6 100644
--- a/src/obikmer/src/cmd/distance/sankoff.rs
+++ b/src/obikmer/src/cmd/distance/sankoff.rs
@@ -52,6 +52,17 @@ pub(super) const STATE_SYMBOL: [char; 16] = [
     '0', 'A', 'C', 'M', 'G', 'R', 'S', 'V', 'T', 'W', 'Y', 'H', 'K', 'D', 'B', 'N',
 ];
 
+/// `STATE_SYMBOL` byte -> state index (0..16), for adapters that need to
+/// translate an alignment written in this alphabet into their own. Shared
+/// rather than rebuilt per adapter (`tnt`, `iqtree`).
+pub(super) fn state_index_table() -> [u8; 128] {
+    let mut table = [0u8; 128];
+    for (state, &sym) in STATE_SYMBOL.iter().enumerate() {
+        table[sym as usize] = state as u8;
+    }
+    table
+}
+
 pub(super) fn write_sankoff_matrix_csv(
     matrix: &[[f64; 16]; 16],
     estimate: &PHatEstimate,
diff --git a/src/obikmer/src/cmd/distance/tnt.rs b/src/obikmer/src/cmd/distance/tnt.rs
index 977994c4..48f5ad53 100644
--- a/src/obikmer/src/cmd/distance/tnt.rs
+++ b/src/obikmer/src/cmd/distance/tnt.rs
@@ -4,7 +4,7 @@ use std::path::PathBuf;
 use obikindex::SnpAlignment;
 use tracing::info;
 
-use super::sankoff::{STATE_SYMBOL, scaled_metric_matrix};
+use super::sankoff::{scaled_metric_matrix, state_index_table};
 
 // ── Sankoff cost matrix + alignment → ready-to-run TNT script ──────────────
 //
@@ -40,10 +40,7 @@ pub(super) fn write_sankoff_tnt(
     // IUPAC-ish symbol -> bitmask, to translate the alignment (which uses
     // `STATE_SYMBOL`, `-` already normalised to `0` by `snp_pseudo_alignment`
     // callers) into TNT's alphabet without re-deriving state indices.
-    let mut iupac_to_state = [0u8; 128];
-    for (state, &sym) in STATE_SYMBOL.iter().enumerate() {
-        iupac_to_state[sym as usize] = state as u8;
-    }
+    let iupac_to_state = state_index_table();
 
     let n_sites = alignment.sequences.first().map(|s| s.len()).unwrap_or(0);
     writeln!(f, "xread").unwrap();
-- 
2.54.0


From c26623fa00a990884883d3ecd5ddd374cbc2f27d Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Wed, 12 Aug 2026 19:51:35 +0200
Subject: [PATCH 04/46] Add repeatable --exclude-genome flag to obikmer
 distance command

Integrate in-memory row/column zeroing and alignment filtering across SNP, Sankoff, TNT, and IQ-TREE output paths. Add strict validation for missing labels, implement `write_iqtree` with empirical stationary frequencies, and introduce `--raw-snp-counts` diagnostic CSV output. Update documentation to reflect experimental validation of backbone resolution limits and theoretical considerations for CTMC rate matrices.
---
 docmd/theory/evolutionary_distances.md | 207 ++++++++++++++++++++++++-
 src/obikmer/src/cmd/distance/mod.rs    |  83 +++++++++-
 2 files changed, 282 insertions(+), 8 deletions(-)

diff --git a/docmd/theory/evolutionary_distances.md b/docmd/theory/evolutionary_distances.md
index 6fd21d8b..c7e2ebfe 100644
--- a/docmd/theory/evolutionary_distances.md
+++ b/docmd/theory/evolutionary_distances.md
@@ -897,7 +897,212 @@ Models](https://iqtree.github.io/doc/Complex-Models).
 (see "A concrete Sankoff cost matrix" above) is already a log-rate — a
 genuine CTMC rate matrix `Q` could plausibly be recovered as
 `rate(a,b) = exp(-cost(a,b))`, renormalised so each row sums to zero, once
-the stationary-frequency gap above is closed. Not yet attempted.
+the stationary-frequency gap above is closed. Superseded by the two
+sections below, which implement and then substantially revise this.
+
+### `R`/`π` implemented; `--exclude-genome` added; rogue-taxon test negative (2026-08-12)
+
+`write_iqtree` (`obikmer/src/cmd/distance/iqtree.rs`) implements exactly
+the `R = exp(-cost)` / empirical-`π` design above: writes
+`<prefix>_iqtree.model` (lower-triangular `R`, PAML order, then `π`) and
+`<prefix>_iqtree.fasta` (alignment recoded to the compact `0..k-1`
+alphabet of states actually present), states/frequencies restricted to
+whichever of the 16 canonical states actually occur, compactly
+renumbered — see the `MORPH{N}` risk above. Verified end to end on the
+20-genome benchmark: real, non-zero, varied branch lengths (`Total tree
+length: 6.773`), converged log-likelihood, `State frequencies:` in
+IQ-TREE's own output matching the computed `π` exactly.
+
+**Rogue-taxon hypothesis, tested and refuted.** The backbone (*Yersinia*,
+*Proteus*, *Opitutus*, *Shouchella*, *Wolbachia*...) resolves as a
+near-linear comb with ~8 near-zero branch lengths — visible on the real
+tree, and independently on a Mash+NJ tree built from an entirely
+different signal (whole-genome k-mer distance, no relation to the Sankoff
+pipeline), which shows the same comb shape. Hypothesis: `Saccharolobus`/
+`Candidozyma` (near-zero real signal — see below) destabilise the
+heuristic tree search enough to also blur resolution elsewhere ("rogue
+taxa", a documented phenomenon). Tested directly: reran `iqtree3` after
+removing both taxa (`--exclude-genome`, `+ASC` recomputed on the
+resulting variable-sites-only alignment since removing taxa turns some
+columns invariant) — **still exactly 8 near-zero backbone branches**,
+identical comb shape. Refuted for this dataset: the backbone's weak
+resolution is a property of the character system's signal at that
+divergence depth (matches "Run 3" above), not rogue-taxon interference.
+
+**Diagnosed why `Saccharolobus`/`Candidozyma` place so poorly**, using a
+new diagnostic (`--raw-snp-counts`, `<prefix>_rawsnp_counts.csv`: one row
+per genome pair, `n_snp,n_shared,n_eligible,ratio` — the counts
+`--raw-snp-distance`'s ratio-only matrix discards, needed because
+`ratio=0.0` from 2 eligible loci and from 2000 look identical in the
+ratio alone). `Saccharolobus` has 21,020 non-`∅` sites in the real
+alignment (comparable to other taxa) — but **21,017 of them (100.0%) are
+private**: no other genome has a non-`∅` state at the same site. Only 3
+sites are shared with any other genome at all (1, 2, and 14
+co-occurring genomes respectively). Real informativeness for placement
+tracks shared sites, not raw non-`∅` count — with no other archaeon (or
+even archaea-adjacent bacterium) in the dataset, there is nothing to
+anchor `Saccharolobus`'s position to, regardless of how much of its own
+data exists. `Candidozyma` shows the same pattern, more extreme (almost
+all `NA`, the 3 non-`NA` pairs all exactly `0.0`, never `1.0` — itself a
+tell: with `n_eligible=1`, the ratio can only be exactly `0` or `1`, so
+3-for-3 landing on `0.0` is more than sampling noise alone would predict;
+possibly ascertainment bias — see below — or possibly a few genuinely
+ultra-conserved loci; not resolved).
+
+**`--exclude-genome LABEL`** (repeatable, `obikmer distance`) added for
+exactly this kind of test: zeroes the excluded genome's row/column in
+`RawSnpDistanceOutput` after `raw_snp_distance` runs (a pair with zero
+counts is already skipped by `calibrate_p_hat`/`base_pair_tally` — no
+`obikindex` traversal change needed) and drops its row from
+`SnpAlignment` before any output is written. Deliberately *not* index
+surgery (a new, smaller on-disk index) — genome sets to exclude are
+expected to change between quick tests, so an in-memory filter is the
+right tool, not a new index-rewriting subsystem. Scoped to the sibling-annex
+family of computations (`--raw-snp-distance`/`--raw-snp-counts`/`--snp`/
+`--sankoff` and everything it implies) — does not affect the plain
+`--metric` distance matrix/NJ/UPGMA path (a different, unrelated
+computation on `idx.distance()`, not touched).
+
+**Caveat surfaced while reusing a stale `π`**: rerunning IQ-TREE on a
+genome-reduced alignment while keeping the *original* (20-genome)
+model file is inconsistent — `π`'s composition shifts once low-cardinality-0
+columns that were only variable because of the removed taxa drop out.
+Measured directly: `π(∅)` `0.9048` (20 genomes) → `0.8869` (18 genomes,
+variable sites only) — real (~378k affected cells, from `Saccharolobus`'s
+~21k private sites × 18 remaining genomes) but modest in *proportion*
+(~2 points) because the alignment was already monomorphic-filtered
+before `Saccharolobus` was ever added, so removing it only drops the
+subset of columns that were variable *because of* it specifically, not
+every column it appears in.
+
+### `R` via `exp(-cost)` is wrong for a CTMC; cardinality/composition decomposition (open, 2026-08-12)
+
+**The flaw in `R = exp(-cost)`, precisely.** `cost` (`build_cost_matrix`'s
+output) is a *shortest-path closure* over an elementary-edit graph
+(Floyd-Warshall) — correct and required for Sankoff parsimony, where
+`cost(a,b)` must be a metric. But a CTMC's own matrix exponential
+(`exp(Qt)`, computed internally by IQ-TREE) *already* sums over
+paths of every length through the elementary rates — that's the whole
+mechanism by which a CTMC generates indirect transitions. Feeding it a
+pre-summed, multi-hop shortest-path cost and exponentiating that *again*
+as if each entry were a direct edge double-applies the "compose multiple
+steps" logic once in log-space (Floyd-Warshall, additive) and once more
+inside IQ-TREE's own exponential — systematically over-penalising
+non-adjacent state pairs (e.g. `∅→{A,C}` priced as two chained edges,
+`2×c_ctx`, when it should be one direct lookup).
+
+**Resolution, in two parts — both estimated directly from the real
+alignment, not smoothed through a small parametric formula:**
+
+1. **Cardinality model**: a 5-state (`0,1,2,3,4`) first-order Markov
+   chain, estimated from the empirical cardinality co-occurrence table
+   (pooled across all *included* genome pairs — same
+   saturated/`NA`-pair exclusion discipline as `calibrate_p_hat`, 14
+   saturated + 18 `NA` pairs excluded of 190 in the benchmark; the
+   result is materially different from the unfiltered version and more
+   internally consistent, not just "cleaner"). Diagonal included (the
+   probability of a family *staying* at the same cardinality is part of
+   the model, not assumed away). Measured, cost `= -ln(observed/expected
+   under independence)`, on the 20-genome benchmark (`π` here from the
+   marginal cardinality distribution: `90.481%, 5.261%, 4.183%, 0.067%,
+   0.008%` for `c=0..4` respectively — note `c=2` is *not* rare, almost
+   as common as `c=1`):
+
+   ```
+   c=0/c=0: 0.166   c=0/c=1: 0.160   c=0/c=2: 0.157   c=0/c=3: 0.059   c=0/c=4: 0.006
+   c=1/c=1: -0.803 (enriched)        c=1/c=2: 0.381   c=1/c=3: 1.027   c=1/c=4: 1.794
+   c=2/c=2: 4.032 (sharply suppressed)                c=2/c=3: 2.620   c=2/c=4: 2.416
+   c=3/c=3: -0.254  c=3/c=4: -0.411 (too few observations to trust)
+   ```
+   Two robust findings, both stable under the saturation filter: (a) all
+   `∅`-involving costs are low and close to each other (`0.006`–`0.166`)
+   regardless of how many members are gained/lost at once — sharply at
+   odds with the current model's implicit `×2`/`×3` multi-hop scaling;
+   (b) `c=2/c=2` (two genomes both showing an ambiguous 2-member state at
+   the same site) is dramatically under-represented (~1.5–1.8% of the
+   independence expectation) — a real, robust anomaly, not explained.
+
+2. **Composition model**: unchanged — `sub_cost` (the existing 6-category
+   Ts/Tv-biased calibration), estimated **only from unambiguous sites**
+   (cardinality-1 ↔ cardinality-1 pairs), because composition bias is a
+   substitution phenomenon and only means something when cardinality is
+   conserved. Checked whether composition bias also appears in pure
+   gain/loss events (no substitution involved, so no bias expected a
+   priori): single-base "gain" (`∅→`single base) is close to uniform
+   (`24.35/25.92/26.22/23.51%` for A/C/G/T) — consistent with "no
+   mutational mechanism, so no bias" as expected. Two-base "gain"
+   (`∅→`2-member state) is *not* uniform even after correcting for the
+   real (non-25/25/25/25) marginal base frequencies: `{A,G}`/`{C,T}`
+   (the transition-linked pairs) mildly enriched (`obs/exp` `1.12`/
+   `1.16`), `{C,G}` sharply suppressed (`obs/exp 0.563`, expected to be
+   the *most* common pair under independence since C and G are
+   individually the two most frequent bases, observed the least) — an
+   unexplained anomaly, deliberately **not** built into the model (no
+   mechanistic story for why gain/loss would carry a `{C,G}`-specific
+   bias), left as an open puzzle rather than fit.
+
+**Composing the two into a full pairwise cost — the actual replacement
+for both the elementary-edge graph and its Floyd-Warshall closure.** For
+any two states `A`, `B` (not just the "clean" same-cardinality or
+pure-subset cases the current graph handles directly): let `shared = A∩B`
+(free), `lost = A\B`, `gained = B\A`. Pair off `k = min(|lost|,|gained|)`
+elements between `lost` and `gained` as substitution events, choosing the
+pairing that minimises total `sub_cost` (a trivial assignment problem —
+at most 4 elements per side). The `|lost|-k` (or `|gained|-k`) leftover,
+unpaired elements are a *pure* cardinality change, `|A|→|B|`, costed by
+**one direct lookup** in the cardinality model above — no chaining, no
+Floyd-Warshall. Example: `{A,C}→{G}` (cardinality 2→1, no shared base):
+pair 1 substitution (cheaper of `A→G`, `C→G`), 1 base left over unpaired
+→ cost `= sub_cost(chosen pair) + cardinality_cost(2→1)`. This is a
+direct, closed-form cost for *every* pair of the 16 states, replacing
+`build_cost_matrix`'s graph-plus-shortest-path construction outright —
+and specifically fixes the CTMC double-counting problem, since every
+entry is now a single decomposed lookup, never a sum of chained edges.
+
+**Reframed as a likelihood (product of probabilities), not a cost (sum of
+`-ln`s) — same content, but forces the diagonals (no-change cases) to be
+kept rather than implicitly dropped.** Both sub-models are proper
+transition *probability* matrices, diagonal included — `P_cardinality`
+includes "stay at the same cardinality", `P_composition` includes "stay
+the same base" (e.g. `P(G→G)`, not just `sub_cost`'s off-diagonal
+entries). Composing:
+
+```
+P(A→B) = P_cardinality(|A|→|B|)
+        × ∏_{x ∈ A∩B} P_composition(x→x)         (shared bases: "stayed")
+        × ∏_{(x,y) paired}  P_composition(x→y)    (parsimony-paired substitutions)
+```
+
+with the unpaired leftover `lost`/`gained` elements (if `|lost|≠|gained|`)
+contributing *nothing further* beyond the `P_cardinality` term already
+counted — consistent with the finding above that pure gain/loss carries
+no separate composition bias worth modelling. Worked example,
+`{A,C}→{A,G}` (`shared={A}`, one paired substitution `C→G`, nothing left
+over): `P = P_cardinality(2→2) · P_composition(A→A) · P_composition(C→G)`.
+
+The row-wise product of these two independently-calibrated models isn't
+guaranteed to already sum to exactly `1` across all `B` for a fixed `A`
+(the two aren't perfectly independent in reality) — so each row of the
+resulting 16×16 matrix is renormalised (divided by its own sum) after
+composition, **not** the matrix as a whole (which would produce a joint
+distribution over `(A,B)` pairs, the wrong object — a transition matrix
+needs each row, "given I start in `A`", to be a valid distribution over
+where I end up).
+
+This now covers every pair of the 16 states with no unhandled case
+identified. Gives 120 parameters, but derived from two small,
+well-estimated pieces (a 5×5 cardinality model, a 4×4 composition model)
+rather than fit or smoothed independently per pair.
+
+**Status: designed, not implemented.** Would replace `build_cost_matrix`
+(`obikindex/src/sankoff.rs`) and the single `c_ctx` scalar/parameter
+entirely; `sub_cost`'s own calibration is untouched. Not yet decided
+whether the "clean" parsimony-graph cost (`build_cost_matrix`'s current
+output, still needed for `--tnt`/`--phyg`) should be replaced too, kept
+as a separate simpler approximation, or derived as a special case of this
+same decomposition (it likely can be — the same `shared`/`lost`/`gained`
+logic, with the cardinality model reduced back to a single scalar `c_ctx`
+substituted in, recovers exactly the current graph).
 
 ## Heterozygosity, ploidy, and consensus-assembly inputs
 
diff --git a/src/obikmer/src/cmd/distance/mod.rs b/src/obikmer/src/cmd/distance/mod.rs
index 3dfe08d3..c3b1035e 100644
--- a/src/obikmer/src/cmd/distance/mod.rs
+++ b/src/obikmer/src/cmd/distance/mod.rs
@@ -85,6 +85,24 @@ pub struct DistanceArgs {
     #[arg(long)]
     pub sibling_annex: bool,
 
+    /// Exclude a genome (by its exact label) from every computation below
+    /// that reads the sibling annex — `--raw-snp-distance`/`--raw-snp-counts`,
+    /// `--snp`, and `--sankoff` (and everything `--sankoff` implies:
+    /// `p_hat`, `sub_cost`, `c_ctx`, the exported matrix/alignment,
+    /// `--tnt`/`--phyg`/`--iqtree`). Repeatable. Does *not* affect the plain
+    /// `--metric` distance matrix/NJ/UPGMA path (a different, unrelated
+    /// computation). Applied by zeroing the excluded genome's row/column
+    /// after `raw_snp_distance` runs (a pair with zero counts is already
+    /// skipped by `calibrate_p_hat`/`base_pair_tally`, so this needs no
+    /// change to the underlying traversal) and by dropping its row from
+    /// `snp_pseudo_alignment`'s output — the annex is still built/scanned
+    /// for the excluded genome too, just not used afterward. For a genome
+    /// with almost no informative sites shared with anything else (see
+    /// `docmd/theory/evolutionary_distances.md`, the IQ-TREE/Mash rogue-taxon
+    /// discussion), its presence can otherwise silently bias `p_hat`/`R`.
+    #[arg(long = "exclude-genome", value_name = "LABEL")]
+    pub exclude_genome: Vec<String>,
+
     /// Tally the sibling-count distribution (CSV) of an already-built annex
     /// (run with `--sibling-annex` first, in this invocation or an earlier
     /// one). A separate, occasional diagnostic pass — not run every time the
@@ -211,6 +229,52 @@ pub fn run(args: DistanceArgs) {
     let labels: Vec<String> = idx.meta().genomes.iter().map(|g| g.label.clone()).collect();
     let n = labels.len();
 
+    // ── Genome exclusion (`--exclude-genome`) ───────────────────────────────
+    // Applied by zeroing a `RawSnpDistanceOutput`'s excluded rows/columns
+    // (`zero_excluded_pairs`) — `calibrate_p_hat`/`base_pair_tally` already
+    // skip any pair with zero total counts, so this needs no change to
+    // `obikindex`'s traversal — and by dropping the excluded genome's row
+    // from a `SnpAlignment` plus the matching label (`drop_excluded`),
+    // since an all-`∅` row for an "excluded" genome would otherwise still
+    // reach TNT/PhyG/IQ-TREE as a real (empty) taxon.
+    let exclude_mask: Vec<bool> = {
+        let mut mask = vec![false; n];
+        for label in &args.exclude_genome {
+            match labels.iter().position(|l| l == label) {
+                Some(i) => mask[i] = true,
+                None => {
+                    eprintln!("error: --exclude-genome {label:?} does not match any genome in this index");
+                    std::process::exit(1);
+                }
+            }
+        }
+        mask
+    };
+    let zero_excluded_pairs = |result: &mut RawSnpDistanceOutput| {
+        for i in 0..n {
+            if !exclude_mask[i] {
+                continue;
+            }
+            for j in 0..n {
+                result.snp[[i, j]] = 0;
+                result.snp[[j, i]] = 0;
+                result.shared[[i, j]] = 0;
+                result.shared[[j, i]] = 0;
+            }
+        }
+    };
+    let drop_excluded = |alignment: SnpAlignment| -> (SnpAlignment, Vec<String>) {
+        let sequences = alignment.sequences.into_iter().enumerate()
+            .filter(|(i, _)| !exclude_mask[*i])
+            .map(|(_, seq)| seq)
+            .collect();
+        let kept_labels = labels.iter().enumerate()
+            .filter(|(i, _)| !exclude_mask[*i])
+            .map(|(_, l)| l.clone())
+            .collect();
+        (SnpAlignment { sequences }, kept_labels)
+    };
+
     // ── Sibling-count/minorant annex (independent of the distance metric) ──
     // Construction (`--sibling-annex`) and stats (`--sibling-stats`) are
     // deliberately decoupled: the annex is meant to be (re)built routinely,
@@ -237,17 +301,19 @@ pub fn run(args: DistanceArgs) {
         write_sibling_stats_csv(&stats, &labels, &args.output);
     }
     if args.raw_snp_distance {
-        let result = idx.raw_snp_distance().unwrap_or_else(|e| {
+        let mut result = idx.raw_snp_distance().unwrap_or_else(|e| {
             eprintln!("error computing raw SNP distance: {e}");
             std::process::exit(1);
         });
+        zero_excluded_pairs(&mut result);
         write_raw_snp_distance_csv(&result, &labels, &args.output);
     }
     if args.raw_snp_counts {
-        let result = idx.raw_snp_distance().unwrap_or_else(|e| {
+        let mut result = idx.raw_snp_distance().unwrap_or_else(|e| {
             eprintln!("error computing raw SNP distance: {e}");
             std::process::exit(1);
         });
+        zero_excluded_pairs(&mut result);
         write_raw_snp_counts_csv(&result, &labels, &args.output);
     }
     if args.snp {
@@ -255,13 +321,15 @@ pub fn run(args: DistanceArgs) {
             eprintln!("error computing SNP pseudo-alignment: {e}");
             std::process::exit(1);
         });
-        write_snp_fasta(&alignment, &labels, &args.output);
+        let (alignment, kept_labels) = drop_excluded(alignment);
+        write_snp_fasta(&alignment, &kept_labels, &args.output);
     }
     if args.sankoff || args.tnt || args.phyg || args.iqtree {
-        let raw = idx.raw_snp_distance().unwrap_or_else(|e| {
+        let mut raw = idx.raw_snp_distance().unwrap_or_else(|e| {
             eprintln!("error computing raw SNP distance: {e}");
             std::process::exit(1);
         });
+        zero_excluded_pairs(&mut raw);
         let estimate = calibrate_p_hat(&raw, args.sankoff_ratio_ceiling);
         let m = (idx.kmer_size() - 1) / 2;
 
@@ -282,16 +350,17 @@ pub fn run(args: DistanceArgs) {
             eprintln!("error computing SNP pseudo-alignment: {e}");
             std::process::exit(1);
         });
-        write_sankoff_alignment_fasta(&alignment, &labels, &args.output);
+        let (alignment, kept_labels) = drop_excluded(alignment);
+        write_sankoff_alignment_fasta(&alignment, &kept_labels, &args.output);
 
         if args.tnt {
-            write_sankoff_tnt(&matrix, &alignment, &labels, &args.output, args.sankoff_cost_scale);
+            write_sankoff_tnt(&matrix, &alignment, &kept_labels, &args.output, args.sankoff_cost_scale);
         }
         if args.phyg {
             write_sankoff_phyg(&matrix, &args.output, args.sankoff_cost_scale);
         }
         if args.iqtree {
-            write_iqtree(&matrix, &alignment, &labels, &args.output);
+            write_iqtree(&matrix, &alignment, &kept_labels, &args.output);
         }
     }
 
-- 
2.54.0


From 0c86ea03850d6ddc621350a310a3d5199c4d5d8a Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Thu, 13 Aug 2026 09:29:44 +0200
Subject: [PATCH 05/46] Replace Sankoff cost matrix with
 cardinality-composition decomposition

Replaced the legacy Sankoff parsimony pipeline with a new cardinality-composition decomposition that constructs row-normalized transition probability matrices symmetrized via geometric mean. This ensures reversibility, reduces free parameters from 240 to 120, and guarantees a zero diagonal. Tallies are now explicitly restricted to variable families to align with +ASC-corrected alignment populations. Additionally, fixed `--exclude-genome` handling to re-scan surviving sequences and drop newly monomorphic columns, preventing silent data corruption in downstream tree inference tools.
---
 docmd/theory/evolutionary_distances.md  | 139 +++++++-
 iqtree.model                            |  16 +
 sankoff_params.yaml                     | 180 +++++++++--
 src/obikindex/src/cardcomp.rs           | 242 ++++++++++++++
 src/obikindex/src/lib.rs                |   9 +-
 src/obikindex/src/sankoff.rs            | 402 ------------------------
 src/obikindex/src/siblings.rs           | 255 +++++++++++++--
 src/obikmer/src/cmd/distance/mod.rs     |  95 ++++--
 src/obikmer/src/cmd/distance/sankoff.rs | 112 ++++---
 9 files changed, 901 insertions(+), 549 deletions(-)
 create mode 100644 iqtree.model
 create mode 100644 src/obikindex/src/cardcomp.rs
 delete mode 100644 src/obikindex/src/sankoff.rs

diff --git a/docmd/theory/evolutionary_distances.md b/docmd/theory/evolutionary_distances.md
index c7e2ebfe..f6b20da1 100644
--- a/docmd/theory/evolutionary_distances.md
+++ b/docmd/theory/evolutionary_distances.md
@@ -1094,15 +1094,136 @@ identified. Gives 120 parameters, but derived from two small,
 well-estimated pieces (a 5×5 cardinality model, a 4×4 composition model)
 rather than fit or smoothed independently per pair.
 
-**Status: designed, not implemented.** Would replace `build_cost_matrix`
-(`obikindex/src/sankoff.rs`) and the single `c_ctx` scalar/parameter
-entirely; `sub_cost`'s own calibration is untouched. Not yet decided
-whether the "clean" parsimony-graph cost (`build_cost_matrix`'s current
-output, still needed for `--tnt`/`--phyg`) should be replaced too, kept
-as a separate simpler approximation, or derived as a special case of this
-same decomposition (it likely can be — the same `shared`/`lost`/`gained`
-logic, with the cardinality model reduced back to a single scalar `c_ctx`
-substituted in, recovers exactly the current graph).
+### Implemented (2026-08-12): `pairwise_cost_matrix` replaces `build_cost_matrix` entirely
+
+New module `obikindex/src/cardcomp.rs`, replacing `sankoff::build_cost_matrix`
+and the `c_ctx`/`SankoffWeights`/`PHatEstimate`/`calibrate_p_hat`/
+`c_ctx_from_p_hat`/`mean_substitution_cost`/`substitution_costs_from_tally`
+machinery it depended on outright — not kept in parallel as a fallback
+(all now unreferenced outside their own tests; `sankoff.rs` itself is a
+pending removal, not yet done).
+
+**New primitives, `obikindex/src/siblings.rs`:**
+- `BasePairTally` gained a `same: [u64; 4]` field (diagonal — "both
+  genomes at the same single base", pooled from
+  [`base_pair_tally`](obikindex::KmerIndex::base_pair_tally)'s existing
+  traversal, extended to also tally the `bi == bj` case it previously
+  discarded).
+- `CardinalityTally { counts: [[u64; 5]; 5] }` and
+  `KmerIndex::cardinality_tally`, a new traversal (same shape as
+  `snp_pseudo_alignment`'s — needs full per-genome presence masks, not
+  `scan_family_pairs`'s single-resolved-form view, since cardinality 2-4
+  is exactly the signal being tallied, not noise to drop). Same
+  saturated/no-data pair exclusion as `base_pair_tally`. Restricted to
+  variable families (`family_size() >= 2`), matching
+  `snp_pseudo_alignment`'s own scope. Verified against the 20-genome
+  benchmark: counts match the earlier hand-rolled Python analysis exactly
+  (e.g. `c=0/c=0: 117,158,166`, `c=0/c=1: 13,707,223` — the same numbers
+  this whole investigation started from).
+
+**`cardcomp.rs`:**
+- `cardinality_transition_probs`/`composition_transition_probs`: row-
+  normalise the two tallies into proper transition probability matrices,
+  diagonal included ("stay the same" is a real, calibrated outcome).
+- `pairwise_cost_matrix`: for every pair of the 16 states, `shared = A∩B`
+  contributes `∏ P_composition(x→x)`; `lost = A\B`, `gained = B\A` are
+  parsimony-paired (`best_pairing_cost`, brute-force over the ≤4!
+  injections — small enough that hand-rolling beats a dependency) into
+  substitution events on `P_composition`, minimising total `-ln`; the
+  cardinality-difference leftover is priced once via
+  `P_cardinality(|A|→|B|)`, never chained. Row-normalised, `-ln`'d, then
+  **symmetrised**: `cost_sym(A,B) = (cost(A,B)+cost(B,A))/2` — equivalent
+  to taking the *geometric* mean of the two raw probabilities
+  (`-ln(√(P(A,B)·P(B,A))) = (-ln P(A,B) - ln P(B,A))/2`), not their
+  arithmetic mean. Required, not just convenient for IQ-TREE's
+  lower-triangular file format: Sankoff parsimony's score is independent
+  of where an *unrooted* tree (what TNT/PhyG actually search over) gets
+  rooted only if the cost matrix is symmetric — the discrete-parsimony
+  analogue of CTMC reversibility, established by direct reasoning, not
+  assumed. Bonus of the same decision: 120 free parameters instead of the
+  240 a fully asymmetric matrix would need.
+
+**Verified on the 20-genome benchmark**: resulting matrix symmetric
+(checked numerically, zero asymmetric cells), zero diagonal, no NaN/Inf.
+`--tnt` output still loads into TNT with no triangle-inequality warning
+(`scaled_metric_matrix`'s rounding-metric-closure step still needed and
+still applied — nothing in the new construction guarantees the *rounded
+integer* matrix stays a metric, even though the real-valued one is exact
+by construction here, unlike the old Floyd-Warshall-closed matrix which
+needed it for a different reason). IQ-TREE loads the new model file and
+reports the same `π` as before (only `R` changed).
+
+### Two consistency bugs found and fixed post-implementation (2026-08-13)
+
+**`--exclude-genome` didn't drop columns that become monomorphic once the
+excluded genome(s) are gone.** `snp_pseudo_alignment`'s "variable family"
+test (`family_size() >= 2`) is a property of the annex computed over
+*every* genome in the index — unaffected by the CLI-level exclusion, which
+only dropped the excluded genome's *row*. A family variable only because
+of the excluded genome stayed in the alignment as a now-constant column —
+silently wrong data for TNT/PhyG, and a hard failure for IQ-TREE's `+ASC`
+(verified: excluding 2 taxa on the benchmark left 116,351 such columns —
+matches the manual `+ASC` failures hit earlier in this same investigation,
+before `--exclude-genome` existed). Fixed in `drop_excluded`
+(`obikmer/src/cmd/distance/mod.rs`): after dropping excluded rows,
+re-scan each column among the *surviving* sequences and drop any that are
+now constant. Verified: 908,723 → 792,372 sites after excluding 2 taxa,
+zero monomorphic columns remain, `π` recomputed from the corrected
+alignment matches an independent recount exactly. The compact-alphabet
+renumbering (`iqtree::compact_alphabet`) needed no equivalent fix — it
+already recomputes which of the 16 states occur fresh on every call, from
+whatever alignment it's actually handed, so a symbol disappearing (e.g.
+excluding every genome that carries `N`) is already handled correctly;
+verified directly (excluded 13 genomes to force `N` out: "15 of 16 states"
+reported, correctly-shaped model file).
+
+**`cardinality_tally`'s `family_size() >= 2` filter looked inconsistent
+with `base_pair_tally` — removing it was tried, and was wrong; reverted.**
+`cardinality_tally` (modelled after `snp_pseudo_alignment`) had the
+filter; `base_pair_tally` didn't (it visits every family via
+`scan_family_pairs` unconditionally, folding fully-invariant loci into its
+own `same` diagonal). Read as `cardinality_tally` under-counting its
+diagonal relative to `base_pair_tally`, and — independently — as another
+angle on the `--exclude-genome` drift (`family_size()` being global-only
+meant a family kept here post-exclusion could differ from what the
+now-correctly-filtered alignment kept). First fix tried: drop
+`cardinality_tally`'s filter entirely, matching `base_pair_tally`'s
+whole-annex scope.
+
+**That fix was empirically wrong, confirmed by a real IQ-TREE run, not
+just a hunch.** Log-likelihood dropped from the earlier correct run's
+`-8,364,671`/`-8,371,082` to `-9,170,228` (worse fit, not better), with
+repeated `NNI search needs unusual large number of steps (20) to
+converge!` warnings — and the completed run's **total tree length came
+out at 67.644**, roughly 30× the earlier correct runs' ~2.0, i.e. branches
+blowing up/saturating. Root cause, only clear in hindsight: `+ASC`
+("ascertainment bias correction") exists specifically because the
+likelihood only ever sees *variable* sites — the alignment fed to
+IQ-TREE, by construction, contains not one invariant column. Calibrating
+`R` from a population overwhelmingly dominated by genome-wide invariant
+background (family_size()<2 loci outnumber the ~908k variable ones by
+orders of magnitude) describes a completely different population than the
+one `+ASC` and the alignment actually model — the "consistency" argument
+for matching `base_pair_tally`'s scope was real, but pointed the wrong
+way: `base_pair_tally`'s own unrestricted `same` diagonal turned out to
+have the *identical* latent bug (only unmasked once its diagonal existed
+at all, which happened earlier the same day when `same` was added), not a
+correct baseline to match `cardinality_tally` to.
+
+**Final fix**: restored `cardinality_tally`'s `family_size() >= 2` filter,
+and gave `base_pair_tally`'s `same` diagonal the equivalent restriction —
+`scan_family_pairs` (shared with `raw_snp_distance`, which legitimately
+*does* want fully-invariant families counted as `shared`) now passes an
+extra `variable: bool` (the family's own `family_size() >= 2`) to its
+`on_pair` callback; `base_pair_tally` only increments `same` when
+`variable` is true, `raw_snp_distance`'s callback ignores the new
+argument. Both tallies now describe the same variable-families-only
+population the `+ASC`-corrected alignment does. Verified: calibration
+counts back to their original values exactly (`c=0/c=0`: 117,158,166,
+matching the pre-regression run bit for bit), and a full IQ-TREE rerun
+converged normally — log-likelihood `-8,389,106.273` (same order as the
+two earlier correct runs), **total tree length 2.044** (was 67.644), no
+NNI convergence warnings.
 
 ## Heterozygosity, ploidy, and consensus-assembly inputs
 
diff --git a/iqtree.model b/iqtree.model
new file mode 100644
index 00000000..09bd6ac5
--- /dev/null
+++ b/iqtree.model
@@ -0,0 +1,16 @@
+0.222641
+0.222347 0.005197
+0.206041 0.017442 0.019145
+0.222349 0.024185 0.003581 0.013346
+0.208691 0.017667 0.002921 0.000012 0.019168
+0.205784 0.013974 0.019121 0.000085 0.018901 0.000018
+0.027849 0.001121 0.001230 0.000109 0.001216 0.000109 0.000118
+0.222640 0.004745 0.023685 0.013831 0.005020 0.002986 0.013813 0.000889
+0.206337 0.017467 0.012967 0.000076 0.013365 0.000016 0.000059 0.000079 0.017590
+0.208662 0.003028 0.019388 0.000017 0.002764 0.000003 0.000018 0.000019 0.017788 0.000017
+0.027866 0.001122 0.001231 0.000109 0.000858 0.000016 0.000083 0.000009 0.001129 0.000100 0.000111
+0.206081 0.013994 0.012951 0.000059 0.018929 0.000017 0.000082 0.000085 0.017568 0.000078 0.000012 0.000076
+0.027872 0.001122 0.000833 0.000074 0.001217 0.000109 0.000080 0.000042 0.001130 0.000100 0.000017 0.000006 0.000108
+0.027846 0.000899 0.001230 0.000087 0.001216 0.000019 0.000118 0.000009 0.001129 0.000080 0.000111 0.000044 0.000108 0.000009
+0.009724 0.000172 0.000189 0.000044 0.000187 0.000044 0.000048 0.000047 0.000174 0.000041 0.000045 0.000043 0.000044 0.000043 0.000047
+0.904811 0.012806 0.013642 0.007640 0.013786 0.007933 0.004196 0.000140 0.012382 0.006685 0.007847 0.000195 0.007527 0.000202 0.000134 0.000076
diff --git a/sankoff_params.yaml b/sankoff_params.yaml
index 6bb64d96..e4a0075c 100644
--- a/sankoff_params.yaml
+++ b/sankoff_params.yaml
@@ -1,27 +1,167 @@
 ratio_ceiling: 0.5
-flank_length_m: 15
-p_hat: 0.010713940022064144
-p_hat_variance: 3.2110559785689563e-10
-n_pairs_included: 158
-n_loci_total: 33008305
-mean_sub_cost: 1.4764371767846869
-c_ctx: 1.7343663443925388
-substitutions:
-- pair: A/C
+cardinality_transitions:
+- from: 0
+  to: 0
+  count: 117158166
+  probability: 0.8249649657257814
+- from: 0
+  to: 1
+  count: 13707223
+  probability: 0.09651891232567299
+- from: 0
+  to: 2
+  count: 10934100
+  probability: 0.07699206755884405
+- from: 0
+  to: 3
+  count: 193315
+  probability: 0.0013612205430842902
+- from: 0
+  to: 4
+  count: 23125
+  probability: 0.00016283384661730445
+- from: 1
+  to: 0
+  count: 13707223
+  probability: 0.8980473700324103
+- from: 1
+  to: 1
+  count: 1043692
+  probability: 0.06837890181868832
+- from: 1
+  to: 2
+  count: 507953
+  probability: 0.033279232106318904
+- from: 1
+  to: 3
+  count: 4270
+  probability: 0.0002797548613631216
+- from: 1
+  to: 4
+  count: 225
+  probability: 0.000014741181219368235
+- from: 2
+  to: 0
+  count: 10934100
+  probability: 0.9551033885158036
+- from: 2
+  to: 1
+  count: 507953
+  probability: 0.04437014765794788
+- from: 2
+  to: 2
+  count: 5241
+  probability: 0.00045780602511512846
+- from: 2
+  to: 3
+  count: 690
+  probability: 0.000060272115498843476
+- from: 2
+  to: 4
+  count: 96
+  probability: 8.385685634621701e-6
+- from: 3
+  to: 0
+  count: 193315
+  probability: 0.9743748708410829
+- from: 3
+  to: 1
+  count: 4270
+  probability: 0.021522285898618442
+- from: 3
+  to: 2
+  count: 690
+  probability: 0.0034778401100812
+- from: 3
+  to: 3
+  count: 98
+  probability: 0.0004939541025912429
+- from: 3
+  to: 4
+  count: 26
+  probability: 0.0001310490476262481
+- from: 4
+  to: 0
+  count: 23125
+  probability: 0.9846291407647109
+- from: 4
+  to: 1
+  count: 225
+  probability: 0.009580175423656646
+- from: 4
+  to: 2
+  count: 96
+  probability: 0.004087541514093502
+- from: 4
+  to: 3
+  count: 26
+  probability: 0.0011070424934003236
+- from: 4
+  to: 4
+  count: 14
+  probability: 0.0005960998041386358
+composition_transitions:
+- from: 'A'
+  to: 'A'
+  count: 162260
+  probability: 0.47062167539692207
+- from: 'A'
+  to: 'C'
   count: 27810
-  cost: 2.5439415226130238
-- pair: A/G
+  probability: 0.08066059899413536
+- from: 'A'
+  to: 'G'
   count: 130153
-  cost: 1.0
-- pair: A/T
+  probability: 0.3774979842101294
+- from: 'A'
+  to: 'T'
   count: 24555
-  cost: 2.6684722241428322
-- pair: C/G
+  probability: 0.07121974139881315
+- from: 'C'
+  to: 'A'
+  count: 27810
+  probability: 0.07790832534920075
+- from: 'C'
+  to: 'C'
+  count: 184633
+  probability: 0.5172401234879174
+- from: 'C'
+  to: 'G'
   count: 19637
-  cost: 2.892062911764701
-- pair: C/T
+  probability: 0.05501207424963161
+- from: 'C'
+  to: 'T'
   count: 124878
-  cost: 1.0413902163542994
-- pair: G/T
+  probability: 0.3498394769132503
+- from: 'G'
+  to: 'A'
+  count: 130153
+  probability: 0.36057158212891627
+- from: 'G'
+  to: 'C'
+  count: 19637
+  probability: 0.054401697680925745
+- from: 'G'
+  to: 'G'
+  count: 184557
+  probability: 0.5112906308956874
+- from: 'G'
+  to: 'T'
   count: 26616
-  cost: 2.5878424665170052
+  probability: 0.07373608929447062
+- from: 'T'
+  to: 'A'
+  count: 24555
+  probability: 0.07337692220342934
+- from: 'T'
+  to: 'C'
+  count: 124878
+  probability: 0.3731689387464813
+- from: 'T'
+  to: 'G'
+  count: 26616
+  probability: 0.07953574267426085
+- from: 'T'
+  to: 'T'
+  count: 158593
+  probability: 0.4739183963758285
diff --git a/src/obikindex/src/cardcomp.rs b/src/obikindex/src/cardcomp.rs
new file mode 100644
index 00000000..d3fb39bd
--- /dev/null
+++ b/src/obikindex/src/cardcomp.rs
@@ -0,0 +1,242 @@
+//! Cardinality × composition decomposition of the 16-state transition cost
+//! matrix — replaces `sankoff::build_cost_matrix`'s elementary-edge graph
+//! and its Floyd-Warshall shortest-path closure, which double-counts
+//! multi-hop transitions once IQ-TREE's own matrix exponential composes
+//! them again. See `docmd/theory/evolutionary_distances.md`, "`R` via
+//! `exp(-cost)` is wrong for a CTMC; cardinality/composition decomposition".
+//!
+//! Two small, directly-estimated first-order Markov models (diagonals
+//! included — "stay the same" is a real, calibrated outcome, not implicit):
+//! a 5-state cardinality model (`0..=4` members of a family) and a 4-state
+//! base-composition model (`A,C,G,T`, unambiguous/cardinality-1 loci only —
+//! composition bias is a substitution phenomenon, only meaningful when
+//! cardinality is conserved). Composed per pair of 16 states via a
+//! parsimony-style pairing of the non-shared elements (see
+//! `pairwise_transition_matrix`'s doc), then symmetrised — Sankoff
+//! parsimony's score is only independent of root placement (as required,
+//! since TNT/PhyG search *unrooted* trees) if the cost matrix is
+//! symmetric, the discrete-parsimony analogue of CTMC reversibility.
+
+use crate::{BasePairTally, CardinalityTally};
+
+/// Row-stochastic 5×5 cardinality transition probabilities (`0..=4`),
+/// diagonal included ("stay at the same cardinality"), from
+/// [`CardinalityTally`]'s pooled, symmetric co-occurrence counts.
+pub fn cardinality_transition_probs(tally: &CardinalityTally) -> [[f64; 5]; 5] {
+    let mut p = [[0.0f64; 5]; 5];
+    for a in 0..5 {
+        let row_sum: u64 = tally.counts[a].iter().sum();
+        if row_sum == 0 {
+            continue;
+        }
+        for b in 0..5 {
+            p[a][b] = tally.counts[a][b] as f64 / row_sum as f64;
+        }
+    }
+    p
+}
+
+/// Row-stochastic 4×4 base-composition transition probabilities
+/// (`A,C,G,T`), diagonal included ("stay the same base"), from
+/// [`BasePairTally`]'s pooled substitution (off-diagonal) and agreement
+/// (`same`, diagonal) counts — unambiguous, cardinality-1 loci only.
+pub fn composition_transition_probs(tally: &BasePairTally) -> [[f64; 4]; 4] {
+    let mut p = [[0.0f64; 4]; 4];
+    for a in 0..4 {
+        let row_sum = tally.same[a] + (0..4).map(|b| tally.counts[a][b]).sum::<u64>();
+        if row_sum == 0 {
+            continue;
+        }
+        p[a][a] = tally.same[a] as f64 / row_sum as f64;
+        for b in 0..4 {
+            if a != b {
+                p[a][b] = tally.counts[a][b] as f64 / row_sum as f64;
+            }
+        }
+    }
+    p
+}
+
+/// Enumerate every injective mapping from `small` (indices `0..small.len()`)
+/// into `large` (indices `0..large.len()`, `large.len() >= small.len()`),
+/// calling `visit` with each full permutation of chosen `large` indices.
+/// `small.len() <= 4` always here (at most 4 bases can be lost or gained),
+/// so a plain recursive enumeration (at most `4! = 24` calls) is simplest —
+/// not worth a dependency for.
+fn for_each_injection(small_len: usize, large_len: usize, visit: &mut dyn FnMut(&[usize])) {
+    let mut chosen = vec![0usize; small_len];
+    let mut used = vec![false; large_len];
+    fn go(pos: usize, chosen: &mut [usize], used: &mut [bool], visit: &mut dyn FnMut(&[usize])) {
+        if pos == chosen.len() {
+            visit(chosen);
+            return;
+        }
+        for l in 0..used.len() {
+            if used[l] {
+                continue;
+            }
+            used[l] = true;
+            chosen[pos] = l;
+            go(pos + 1, chosen, used, visit);
+            used[l] = false;
+        }
+    }
+    if small_len == 0 {
+        visit(&[]);
+        return;
+    }
+    go(0, &mut chosen, &mut used, visit);
+}
+
+/// Parsimony-style pairing cost for the non-shared elements of a
+/// transition: pair every element of the smaller of `lost`/`gained` with
+/// some element of the larger one, choosing the pairing that minimises
+/// total `-ln(P_composition)` (maximises likelihood) — the discrete
+/// analogue of "prefer a substitution over an independent loss+gain".
+/// Leftover elements of the larger side (`|large|-|small|` of them) are
+/// *not* charged here — they're pure cardinality change, already priced by
+/// `P_cardinality(|A|→|B|)` in the caller.
+fn best_pairing_cost(lost: &[u8], gained: &[u8], p_comp: &[[f64; 4]; 4]) -> f64 {
+    let (small, large) = if lost.len() <= gained.len() { (lost, gained) } else { (gained, lost) };
+    if small.is_empty() {
+        return 0.0;
+    }
+    let mut best = f64::INFINITY;
+    for_each_injection(small.len(), large.len(), &mut |perm| {
+        let mut cost = 0.0;
+        for (i, &li) in perm.iter().enumerate() {
+            let (x, y) = (small[i], large[li]);
+            let p = p_comp[x as usize][y as usize];
+            cost += if p > 0.0 { -p.ln() } else { f64::INFINITY };
+        }
+        if cost < best {
+            best = cost;
+        }
+    });
+    best
+}
+
+/// The full 16-state transition cost matrix, replacing
+/// `sankoff::build_cost_matrix`. For every pair of states `A`, `B`
+/// (bitmasks, bit `0..4` = `A,C,G,T`): `shared = A∩B` contributes
+/// `P_composition(x→x)` per shared base (diagonal — "stayed"); the
+/// remaining `lost = A\B`, `gained = B\A` are parsimony-paired into
+/// substitutions via [`best_pairing_cost`], and whatever's left over after
+/// pairing (only possible on one side, since one side is fully consumed)
+/// is *pure* cardinality change, priced once via `P_cardinality(|A|→|B|)`
+/// — never chained through intermediate states. Row-normalised (`P(A→·)`
+/// sums to `1` over all `B`), converted to a cost via `-ln`, then
+/// symmetrised (`(cost(A,B)+cost(B,A))/2` — the row-normalised `P` is not
+/// symmetric in general, but a Sankoff parsimony cost must be, so the
+/// score is independent of where an unrooted tree gets rooted).
+pub fn pairwise_cost_matrix(p_card: &[[f64; 5]; 5], p_comp: &[[f64; 4]; 4]) -> [[f64; 16]; 16] {
+    let mut raw = [[0.0f64; 16]; 16];
+    for a in 0u8..16 {
+        for b in 0u8..16 {
+            let shared = a & b;
+            let lost: Vec<u8> = (0..4).filter(|&i| a & (1 << i) != 0 && b & (1 << i) == 0).collect();
+            let gained: Vec<u8> = (0..4).filter(|&i| b & (1 << i) != 0 && a & (1 << i) == 0).collect();
+
+            let mut log_p = 0.0; // accumulate ln(P), so 0.0 = probability 1
+            let card_a = a.count_ones() as usize;
+            let card_b = b.count_ones() as usize;
+            let p_c = p_card[card_a][card_b];
+            log_p += if p_c > 0.0 { p_c.ln() } else { f64::NEG_INFINITY };
+
+            for i in 0..4u8 {
+                if shared & (1 << i) != 0 {
+                    let p = p_comp[i as usize][i as usize];
+                    log_p += if p > 0.0 { p.ln() } else { f64::NEG_INFINITY };
+                }
+            }
+            log_p -= best_pairing_cost(&lost, &gained, p_comp);
+
+            raw[a as usize][b as usize] = log_p.exp();
+        }
+    }
+
+    // Row-normalise to a proper transition probability matrix.
+    let mut p = [[0.0f64; 16]; 16];
+    for a in 0..16 {
+        let row_sum: f64 = raw[a].iter().sum();
+        if row_sum > 0.0 {
+            for b in 0..16 {
+                p[a][b] = raw[a][b] / row_sum;
+            }
+        }
+    }
+
+    // Cost = -ln(P), then symmetrise (see doc comment: parsimony on an
+    // unrooted tree requires a symmetric cost matrix).
+    let mut cost = [[0.0f64; 16]; 16];
+    for a in 0..16 {
+        for b in 0..16 {
+            cost[a][b] = if p[a][b] > 0.0 { -p[a][b].ln() } else { f64::INFINITY };
+        }
+    }
+    let mut sym = [[0.0f64; 16]; 16];
+    for a in 0..16 {
+        for b in 0..16 {
+            sym[a][b] = if a == b { 0.0 } else { (cost[a][b] + cost[b][a]) / 2.0 };
+        }
+    }
+    sym
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn cardinality_probs_row_normalised() {
+        let mut counts = [[0u64; 5]; 5];
+        counts[0][0] = 10;
+        counts[0][1] = 5;
+        counts[1][0] = 5;
+        counts[1][1] = 2;
+        let tally = CardinalityTally { counts };
+        let p = cardinality_transition_probs(&tally);
+        assert!((p[0].iter().sum::<f64>() - 1.0).abs() < 1e-12);
+        assert!((p[1].iter().sum::<f64>() - 1.0).abs() < 1e-12);
+        assert!((p[0][0] - 10.0 / 15.0).abs() < 1e-12);
+    }
+
+    #[test]
+    fn composition_probs_include_diagonal() {
+        let mut tally = BasePairTally { counts: [[0u64; 4]; 4], same: [0u64; 4] };
+        tally.same[0] = 90; // A stays A 90 times
+        tally.counts[0][1] = 10; // A -> C 10 times
+        tally.counts[1][0] = 10;
+        let p = composition_transition_probs(&tally);
+        assert!((p[0][0] - 0.9).abs() < 1e-12);
+        assert!((p[0][1] - 0.1).abs() < 1e-12);
+        assert!((p[0].iter().sum::<f64>() - 1.0).abs() < 1e-12);
+    }
+
+    #[test]
+    fn pairwise_cost_matrix_is_symmetric_and_zero_diagonal() {
+        // A plausible-looking pair of models (not calibrated from real
+        // data — just needs every state reachable with nonzero probability
+        // for this structural test).
+        let p_card = [
+            [0.5, 0.3, 0.15, 0.04, 0.01],
+            [0.3, 0.4, 0.2, 0.08, 0.02],
+            [0.15, 0.2, 0.4, 0.2, 0.05],
+            [0.04, 0.08, 0.2, 0.5, 0.18],
+            [0.01, 0.02, 0.05, 0.18, 0.74],
+        ];
+        let p_comp = [
+            [0.7, 0.1, 0.15, 0.05],
+            [0.1, 0.7, 0.05, 0.15],
+            [0.15, 0.05, 0.7, 0.1],
+            [0.05, 0.15, 0.1, 0.7],
+        ];
+        let cost = pairwise_cost_matrix(&p_card, &p_comp);
+        for a in 0..16 {
+            assert_eq!(cost[a][a], 0.0);
+            for b in 0..16 {
+                assert!((cost[a][b] - cost[b][a]).abs() < 1e-9, "cost[{a}][{b}]={} cost[{b}][{a}]={}", cost[a][b], cost[b][a]);
+            }
+        }
+    }
+}
diff --git a/src/obikindex/src/lib.rs b/src/obikindex/src/lib.rs
index a48eb325..4bcc66dd 100644
--- a/src/obikindex/src/lib.rs
+++ b/src/obikindex/src/lib.rs
@@ -1,6 +1,7 @@
 pub mod error;
 pub mod meta;
 pub mod state;
+mod cardcomp;
 mod distance;
 mod dump;
 mod index;
@@ -8,7 +9,6 @@ mod merge;
 mod numa;
 mod rebuild;
 mod reindex;
-mod sankoff;
 mod select;
 mod siblings;
 mod stats;
@@ -20,8 +20,5 @@ pub use merge::MergeMode;
 pub use meta::{validate_label, GenomeInfo, IndexConfig, IndexMeta, META_FILENAME};
 pub use state::{IndexState, SENTINEL_COUNTED, SENTINEL_INDEXED, SENTINEL_SCATTERED};
 pub use stats::IndexBitsPerKmer;
-pub use siblings::{BasePairTally, RawSnpDistanceOutput, SiblingAnnexStats, SnpAlignment};
-pub use sankoff::{
-    build_cost_matrix, c_ctx_from_p_hat, calibrate_p_hat, mean_substitution_cost,
-    substitution_costs_from_tally, PHatEstimate, SankoffWeights,
-};
+pub use siblings::{BasePairTally, CardinalityTally, RawSnpDistanceOutput, SiblingAnnexStats, SnpAlignment};
+pub use cardcomp::{cardinality_transition_probs, composition_transition_probs, pairwise_cost_matrix};
diff --git a/src/obikindex/src/sankoff.rs b/src/obikindex/src/sankoff.rs
deleted file mode 100644
index 372ed21e..00000000
--- a/src/obikindex/src/sankoff.rs
+++ /dev/null
@@ -1,402 +0,0 @@
-//! Sankoff parsimony cost matrix for the 16-state (powerset of `{A,C,G,T}`)
-//! family alphabet, and calibration of its parameters from real pairwise
-//! SNP/shared counts. See `docmd/theory/evolutionary_distances.md`,
-//! "Sankoff parsimony as the resolution of the 16-state model problem".
-
-use crate::{BasePairTally, RawSnpDistanceOutput};
-
-/// Transition base pairs in the project's fixed bit convention (see
-/// `siblings::central_base`: bit 0=A, 1=C, 2=G, 3=T). All other single-bit
-/// swaps are transversions.
-const TRANSITION_PAIRS: [(u8, u8); 2] = [(0, 2), (1, 3)]; // A<->G, C<->T
-
-/// Tunable weights for the 16-state Sankoff cost matrix — see "A concrete
-/// Sankoff cost matrix for the 16-state alphabet" in the design doc.
-///
-/// Only two costs, not three: an earlier version had a separate `c_gl` for
-/// "gain/loss between two nonempty states" alongside `c_ctx` for "collapse
-/// to `∅`", but presence/absence tracking never observes "the flanks"
-/// independently of a whole 31-mer — losing one member of a family while
-/// others remain (`{A,C}->{A}`) and losing the last one (`{A}->∅`) are the
-/// same event: a specific, complete, homologous 31-mer that used to be
-/// observed no longer is. Both are exactly what `c_ctx` (see
-/// `c_ctx_from_p_hat`) prices, so it is used for every gain/loss uniformly
-/// — including a compound family losing several members at once, `∅`
-/// included, which costs `|X|*c_ctx` (no flat shortcut for `∅`: see
-/// `build_cost_matrix`'s docs for why an earlier version's flat special
-/// case there didn't hold up).
-#[derive(Debug, Clone, Copy)]
-pub struct SankoffWeights {
-    /// Cost of a single-base substitution `a <-> b` (`a != b`), symmetric
-    /// (`sub_cost[a][b] == sub_cost[b][a]`) and only meaningful off the
-    /// diagonal. The full 6-category (AC, AG, AT, CG, CT, GT) resolution a
-    /// symmetric cost matrix allows — see `substitution_costs_from_tally`
-    /// for calibrating it from real data, or `SankoffWeights::ts_tv` for
-    /// the coarser 2-category (transition/transversion) convenience
-    /// constructor.
-    pub sub_cost: [[f64; 4]; 4],
-    /// Cost of losing or gaining one family member — the same constant
-    /// everywhere a member is gained or lost, member count and target state
-    /// (`∅` or not) included: see the struct docs.
-    pub c_ctx: f64,
-}
-
-impl SankoffWeights {
-    /// Convenience constructor for the coarser 2-category
-    /// (transition/transversion) substitution model: every transition pair
-    /// (A<->G, C<->T) costs `c_ts`, every transversion pair costs `c_tv`.
-    pub fn ts_tv(c_ts: f64, c_tv: f64, c_ctx: f64) -> Self {
-        let mut sub_cost = [[0.0; 4]; 4];
-        for a in 0..4usize {
-            for b in 0..4usize {
-                if a == b {
-                    continue;
-                }
-                let is_ts = TRANSITION_PAIRS.contains(&(a as u8, b as u8));
-                sub_cost[a][b] = if is_ts { c_ts } else { c_tv };
-            }
-        }
-        Self { sub_cost, c_ctx }
-    }
-}
-
-/// Build the 16x16 Sankoff step-cost matrix, states indexed `0..=15` by
-/// their bitmask (matching `siblings::iupac_code`'s convention — state `0`
-/// is `∅`).
-///
-/// All 16 states, `∅` included, form a single graph: an edge of weight
-/// `c_ts`/`c_tv` between two states of equal cardinality differing by
-/// exactly one element (classified by whether the swapped bases form a
-/// transition or transversion pair), and an edge of weight `c_ctx` between
-/// a state and one that is its strict subset plus exactly one element
-/// (`∅` is a strict subset of every singleton state, so it connects
-/// directly to each of them this way — no special case). `cost(X, Y)` is
-/// the shortest-path distance in that graph (16 nodes — Floyd-Warshall,
-/// trivial at this size), uniformly, including `X <-> ∅`: a compound
-/// family losing several members at once, `∅` included, costs `|X|*c_ctx`
-/// via that many single-element steps — no cheaper flat alternative for
-/// `∅` specifically, since nothing distinguishes it from any other
-/// multi-element loss (see design doc — an earlier flat special case here
-/// was inconsistent with how every *other* multi-element transformation is
-/// already priced, and had no principled justification once that was
-/// noticed).
-pub fn build_cost_matrix(w: &SankoffWeights) -> [[f64; 16]; 16] {
-    const INF: f64 = f64::INFINITY;
-    let mut dist = [[INF; 16]; 16];
-    for (i, row) in dist.iter_mut().enumerate() {
-        row[i] = 0.0;
-    }
-
-    for x in 0u8..16 {
-        for y in (x + 1)..16 {
-            let (xu, yu) = (x as usize, y as usize);
-            let diff = x ^ y;
-            let card_x = x.count_ones();
-            let card_y = y.count_ones();
-            let edge = if card_x == card_y && diff.count_ones() == 2 {
-                // Exactly one element swapped: the bit only in x is the base
-                // leaving, the bit only in y is the base entering.
-                let a = (x & diff).trailing_zeros() as u8;
-                let b = (y & diff).trailing_zeros() as u8;
-                Some(w.sub_cost[a as usize][b as usize])
-            } else if card_x.abs_diff(card_y) == 1 && (x & y) == x.min(y) {
-                // True subset relationship: a pure gain/loss of one element.
-                Some(w.c_ctx)
-            } else {
-                None
-            };
-            if let Some(cost) = edge {
-                dist[xu][yu] = cost;
-                dist[yu][xu] = cost;
-            }
-        }
-    }
-
-    for k in 0..16 {
-        for i in 0..16 {
-            if dist[i][k].is_infinite() {
-                continue;
-            }
-            for j in 0..16 {
-                let via = dist[i][k] + dist[k][j];
-                if via < dist[i][j] {
-                    dist[i][j] = via;
-                }
-            }
-        }
-    }
-
-    dist
-}
-
-/// `p_hat` calibrated from real pairwise SNP/shared counts, restricted to
-/// pairs below `ratio_ceiling`, and its variance as a pooled Bernoulli
-/// proportion.
-#[derive(Debug, Clone, Copy)]
-pub struct PHatEstimate {
-    pub p_hat: f64,
-    /// `p_hat*(1-p_hat) / n_loci_total` — the pooled estimator's variance is
-    /// governed by the total number of loci across all included pairs, not
-    /// by any single pair's count (see design doc: this is why the
-    /// exclusion criterion below is the per-pair *ratio*, not a per-pair
-    /// minimum-count floor — a low-count pair barely moves the pool either
-    /// way, but a saturated pair with plenty of loci would bias it).
-    pub variance: f64,
-    pub n_pairs_included: usize,
-    pub n_loci_total: u64,
-}
-
-/// Pool `snp`/`shared` counts across all genome pairs whose per-pair ratio
-/// `snp/(snp+shared)` is at most `ratio_ceiling`, then estimate
-/// `p_hat = sum(snp) / sum(snp+shared)` over the included pairs.
-///
-/// A pair with no eligible locus at all (`snp+shared == 0`) is always
-/// excluded (nothing to pool). `ratio_ceiling` should be well below 1.0 —
-/// pairs at or near saturation (e.g. cross-domain comparisons, where nearly
-/// every shared central-position family already differs) carry no
-/// information about `p_hat` and bias it upward if pooled in.
-pub fn calibrate_p_hat(raw: &RawSnpDistanceOutput, ratio_ceiling: f64) -> PHatEstimate {
-    let n = raw.snp.nrows();
-    let mut snp_sum: u64 = 0;
-    let mut total_sum: u64 = 0;
-    let mut n_pairs = 0usize;
-    for i in 0..n {
-        for j in (i + 1)..n {
-            let snp = raw.snp[[i, j]];
-            let shared = raw.shared[[i, j]];
-            let total = snp + shared;
-            if total == 0 {
-                continue;
-            }
-            let ratio = snp as f64 / total as f64;
-            if ratio > ratio_ceiling {
-                continue;
-            }
-            snp_sum += snp;
-            total_sum += total;
-            n_pairs += 1;
-        }
-    }
-    let p_hat = if total_sum > 0 { snp_sum as f64 / total_sum as f64 } else { 0.0 };
-    let variance = if total_sum > 0 {
-        p_hat * (1.0 - p_hat) / total_sum as f64
-    } else {
-        0.0
-    };
-    PHatEstimate { p_hat, variance, n_pairs_included: n_pairs, n_loci_total: total_sum }
-}
-
-/// `c_ctx(p) = mean_sub_cost * [(2m*p) / (1 - (1-p)^(2m)) + p]` — see
-/// "Context, detectability, and a 3-way ordinal distance per pair" in the
-/// design doc for the bracketed term's derivation. `m` is the flank length
-/// on *each* side of the central position (`k = 2m+1`); pass `(k-1)/2`, not
-/// the project's minimizer-size parameter of the same name.
-///
-/// The bracketed term is `E[mutation count | at least one occurred]` — a
-/// *count* of mutations, not a cost. An earlier version used it directly as
-/// the cost, implicitly pricing every mutation at a flat `1` regardless of
-/// type. That stopped making sense once substitution costs were calibrated
-/// per base-pair type (`substitution_costs_from_tally`): transitions and
-/// transversions aren't equally likely (roughly 5-6x apart in this
-/// project's own data) nor equally costly, so "one mutation" isn't worth a
-/// flat unit — it's worth whatever the *empirical mix* of mutation types is
-/// worth on average. `mean_sub_cost` (see `mean_substitution_cost`) is that
-/// weighted average, turning the expected mutation *count* into an actual
-/// expected cost.
-pub fn c_ctx_from_p_hat(p_hat: f64, m: usize, mean_sub_cost: f64) -> f64 {
-    if p_hat <= 0.0 {
-        return 0.0;
-    }
-    let two_m = 2.0 * m as f64;
-    let expected_mutations = (two_m * p_hat) / (1.0 - (1.0 - p_hat).powf(two_m)) + p_hat;
-    expected_mutations * mean_sub_cost
-}
-
-/// Mean substitution cost, weighted by each of the 6 base-pair categories'
-/// observed frequency in `tally` — the empirical average cost of "one
-/// mutation" under the calibrated substitution spectrum. Falls back to
-/// `1.0` (a flat per-mutation cost) if `tally` has no signal at all (no
-/// substitution ever observed), rather than dividing by zero.
-pub fn mean_substitution_cost(tally: &BasePairTally, sub_cost: &[[f64; 4]; 4]) -> f64 {
-    let mut weighted_sum = 0.0;
-    let mut total = 0u64;
-    for a in 0..4 {
-        for b in (a + 1)..4 {
-            let count = tally.counts[a][b];
-            weighted_sum += count as f64 * sub_cost[a][b];
-            total += count;
-        }
-    }
-    if total == 0 {
-        return 1.0;
-    }
-    weighted_sum / total as f64
-}
-
-/// Derive the 4x4 symmetric substitution cost table from an observed
-/// [`BasePairTally`]: `cost(a,b) = -ln(rate(a,b))`, normalised so the most
-/// frequently observed substitution type costs exactly `1.0` — the standard
-/// generalised-parsimony step-weighting heuristic (see design doc,
-/// "Transition/transversion refinement"), generalised here from 2
-/// categories (Ts/Tv) to the full 6-category resolution a symmetric matrix
-/// allows: a rarer substitution type is treated as less parsimonious to
-/// invoke, and therefore costs more.
-///
-/// A pair type never observed at all (`counts[a][b] == 0`) gets an infinite
-/// cost — parsimony should never spend a mutation on something with no
-/// empirical support in this data.
-pub fn substitution_costs_from_tally(tally: &BasePairTally) -> [[f64; 4]; 4] {
-    let total: u64 = (0..4)
-        .flat_map(|a| (a + 1..4).map(move |b| (a, b)))
-        .map(|(a, b)| tally.counts[a][b])
-        .sum();
-
-    let mut raw = [[0.0f64; 4]; 4];
-    let mut min_cost = f64::INFINITY;
-    for a in 0..4 {
-        for b in (a + 1)..4 {
-            let count = tally.counts[a][b];
-            let cost = if count > 0 && total > 0 {
-                -((count as f64 / total as f64).ln())
-            } else {
-                f64::INFINITY
-            };
-            raw[a][b] = cost;
-            raw[b][a] = cost;
-            if cost < min_cost {
-                min_cost = cost;
-            }
-        }
-    }
-
-    let mut out = [[0.0f64; 4]; 4];
-    for a in 0..4 {
-        for b in 0..4 {
-            if a != b {
-                out[a][b] = raw[a][b] / min_cost;
-            }
-        }
-    }
-    out
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use ndarray::Array2;
-
-    fn weights() -> SankoffWeights {
-        SankoffWeights::ts_tv(1.0, 2.0, 10.0)
-    }
-
-    #[test]
-    fn identity_is_zero() {
-        let m = build_cost_matrix(&weights());
-        for row in m.iter().enumerate() {
-            assert_eq!(m[row.0][row.0], 0.0);
-        }
-    }
-
-    #[test]
-    fn single_base_transition_costs_c_ts() {
-        let m = build_cost_matrix(&weights());
-        // A = 0b0001 (state 1), G = 0b0100 (state 4): A<->G is a transition.
-        assert_eq!(m[1][4], 1.0);
-        assert_eq!(m[4][1], 1.0);
-    }
-
-    #[test]
-    fn single_base_transversion_costs_c_tv() {
-        let m = build_cost_matrix(&weights());
-        // A = 0b0001 (state 1), C = 0b0010 (state 2): A<->C is a transversion.
-        assert_eq!(m[1][2], 2.0);
-    }
-
-    #[test]
-    fn gain_loss_costs_c_ctx() {
-        let m = build_cost_matrix(&weights());
-        // A = 0b0001 (state 1) -> {A,C} = 0b0011 (state 3): pure gain of C.
-        assert_eq!(m[1][3], 10.0);
-    }
-
-    #[test]
-    fn empty_set_costs_scale_with_cardinality() {
-        let m = build_cost_matrix(&weights());
-        assert_eq!(m[0][1], 10.0); // {A} -> ∅: one member, one c_ctx step.
-        // N (all four) -> ∅: no flat shortcut — four single-element steps,
-        // same as losing four members down to a nonempty state would cost.
-        assert_eq!(m[0][15], 40.0);
-        assert_eq!(m[0][0], 0.0);
-    }
-
-    #[test]
-    fn matrix_is_symmetric() {
-        let m = build_cost_matrix(&weights());
-        for i in 0..16 {
-            for j in 0..16 {
-                assert_eq!(m[i][j], m[j][i], "asymmetry at ({i},{j})");
-            }
-        }
-    }
-
-    #[test]
-    fn calibrate_p_hat_excludes_saturated_pairs() {
-        // 3 genomes: pair (0,1) informative (10% SNP), pair (0,2) saturated
-        // (100% SNP) — must be excluded from the pooled estimate.
-        let mut snp = Array2::<u64>::zeros((3, 3));
-        let mut shared = Array2::<u64>::zeros((3, 3));
-        snp[[0, 1]] = 10;
-        shared[[0, 1]] = 90;
-        snp[[1, 0]] = 10;
-        shared[[1, 0]] = 90;
-        snp[[0, 2]] = 50;
-        shared[[0, 2]] = 0;
-        snp[[2, 0]] = 50;
-        shared[[2, 0]] = 0;
-        let raw = RawSnpDistanceOutput { snp, shared };
-
-        let est = calibrate_p_hat(&raw, 0.5);
-        assert_eq!(est.n_pairs_included, 1);
-        assert_eq!(est.n_loci_total, 100);
-        assert!((est.p_hat - 0.1).abs() < 1e-9);
-    }
-
-    #[test]
-    fn c_ctx_from_p_hat_zero_is_zero() {
-        assert_eq!(c_ctx_from_p_hat(0.0, 15, 1.5), 0.0);
-    }
-
-    #[test]
-    fn c_ctx_from_p_hat_matches_known_value() {
-        // p=0.1, m=15: [(30*0.1)/(1-(0.9)^30) + 0.1] * mean_sub_cost
-        let m = 15usize;
-        let p = 0.1;
-        let mean_sub_cost = 1.5;
-        let expected = ((2.0 * m as f64 * p) / (1.0 - (1.0 - p).powf(2.0 * m as f64)) + p) * mean_sub_cost;
-        assert!((c_ctx_from_p_hat(p, m, mean_sub_cost) - expected).abs() < 1e-12);
-    }
-
-    #[test]
-    fn mean_substitution_cost_is_weighted_average() {
-        let mut counts = [[0u64; 4]; 4];
-        counts[0][1] = 3; // A/C
-        counts[1][0] = 3;
-        counts[0][2] = 1; // A/G
-        counts[2][0] = 1;
-        let tally = BasePairTally { counts };
-        let mut sub_cost = [[0.0f64; 4]; 4];
-        sub_cost[0][1] = 2.0;
-        sub_cost[1][0] = 2.0;
-        sub_cost[0][2] = 1.0;
-        sub_cost[2][0] = 1.0;
-        // (3*2.0 + 1*1.0) / 4 = 1.75
-        assert!((mean_substitution_cost(&tally, &sub_cost) - 1.75).abs() < 1e-12);
-    }
-
-    #[test]
-    fn mean_substitution_cost_falls_back_to_one_with_no_data() {
-        let tally = BasePairTally { counts: [[0u64; 4]; 4] };
-        let sub_cost = [[0.0f64; 4]; 4];
-        assert_eq!(mean_substitution_cost(&tally, &sub_cost), 1.0);
-    }
-}
diff --git a/src/obikindex/src/siblings.rs b/src/obikindex/src/siblings.rs
index dc33bf6a..ad8aea6b 100644
--- a/src/obikindex/src/siblings.rs
+++ b/src/obikindex/src/siblings.rs
@@ -660,10 +660,18 @@ impl KmerIndex {
     /// (tallied once, at its minorant) of every layer of the already-built
     /// sibling annex, resolves each genome's single observed form (`None`
     /// if absent or ambiguous/multi-copy), then calls `on_pair(acc, i, j,
-    /// bi, bj)` for every genome pair `(i, j)` where both are unambiguous
-    /// and single-copy (`bi == bj` means shared at that locus, `bi != bj`
-    /// means a SNP). Layers are processed in parallel (rayon); each gets
-    /// its own accumulator from `zero()`, combined pairwise via `combine`.
+    /// bi, bj, variable)` for every genome pair `(i, j)` where both are
+    /// unambiguous and single-copy (`bi == bj` means shared at that locus,
+    /// `bi != bj` means a SNP). `variable` is the family's own
+    /// `family_size() >= 2` (true if more than one member is observed
+    /// *anywhere* in the family, i.e. it isn't fully invariant across the
+    /// whole index) — `raw_snp_distance` ignores it (a fully-invariant
+    /// family is still legitimately "shared"), but callers whose diagonal
+    /// should only reflect genuine SNP-adjacent agreement, not the
+    /// genome-wide invariant background, need it (see
+    /// [`base_pair_tally`](Self::base_pair_tally)'s `same` field). Layers
+    /// are processed in parallel (rayon); each gets its own accumulator
+    /// from `zero()`, combined pairwise via `combine`.
     fn scan_family_pairs<Acc, F, C>(
         &self,
         label: &str,
@@ -673,7 +681,7 @@ impl KmerIndex {
     ) -> OKIResult<Acc>
     where
         Acc: Send,
-        F: Fn(&mut Acc, usize, usize, u8, u8) + Sync,
+        F: Fn(&mut Acc, usize, usize, u8, u8, bool) + Sync,
         C: Fn(Acc, Acc) -> Acc,
     {
         let n_parts = self.n_partitions();
@@ -751,6 +759,7 @@ impl KmerIndex {
                     if !is_minorant(kmer, mask, k) {
                         continue; // family tallied once, at its minorant
                     }
+                    let variable = mask.family_size() >= 2;
 
                     single_form.clear();
                     single_form.resize(n_cols, None);
@@ -791,7 +800,7 @@ impl KmerIndex {
                                 continue;
                             }
                             let Some(bj) = single_form[j] else { continue };
-                            on_pair(&mut acc, i, j, bi, bj);
+                            on_pair(&mut acc, i, j, bi, bj, variable);
                         }
                     }
                 }
@@ -816,7 +825,7 @@ impl KmerIndex {
         let (snp, shared) = self.scan_family_pairs(
             "raw_snp_distance",
             || (Array2::<u64>::zeros((n_genomes, n_genomes)), Array2::<u64>::zeros((n_genomes, n_genomes))),
-            |(snp, shared), i, j, bi, bj| {
+            |(snp, shared), i, j, bi, bj, _variable| {
                 if bi == bj {
                     shared[[i, j]] += 1;
                     shared[[j, i]] += 1;
@@ -837,9 +846,10 @@ impl KmerIndex {
     /// Symmetric 6-category base-pair substitution tally (AC, AG, AT, CG,
     /// CT, GT — indexed `0=A,1=C,2=G,3=T`), pooled only over genome pairs
     /// whose overall SNP ratio in `raw` is at or below `ratio_ceiling` —
-    /// same saturation-exclusion discipline as `calibrate_p_hat`, for the
-    /// same reason: a saturated pair's observed base-pair mix trends toward
-    /// neutral base composition, not the true point-mutation spectrum.
+    /// same saturation-exclusion discipline as
+    /// [`cardinality_tally`](Self::cardinality_tally), for the same reason:
+    /// a saturated pair's observed base-pair mix trends toward neutral base
+    /// composition, not the true point-mutation spectrum.
     ///
     /// A second full pass over the annex, sharing
     /// [`raw_snp_distance`](Self::raw_snp_distance)'s traversal (guided by
@@ -858,25 +868,38 @@ impl KmerIndex {
             total > 0 && (snp as f64 / total as f64) <= ratio_ceiling
         });
 
-        let counts = self.scan_family_pairs(
+        let (counts, same) = self.scan_family_pairs(
             "base_pair_tally",
-            || [[0u64; 4]; 4],
-            |counts, i, j, bi, bj| {
-                if bi != bj && included[[i, j]] {
+            || ([[0u64; 4]; 4], [0u64; 4]),
+            |(counts, same), i, j, bi, bj, variable| {
+                if !included[[i, j]] {
+                    return;
+                }
+                if bi != bj {
                     counts[bi as usize][bj as usize] += 1;
                     counts[bj as usize][bi as usize] += 1;
+                } else if variable {
+                    // Only count "stayed the same" from families that vary
+                    // *somewhere* in the index — a fully invariant family
+                    // (never varies anywhere) isn't a SNP-adjacent
+                    // agreement, it's genome-wide background, and would
+                    // otherwise swamp the diagonal (see
+                    // `docmd/theory/evolutionary_distances.md`, the
+                    // ascertainment-bias regression this was reverting).
+                    same[bi as usize] += 1;
                 }
             },
-            |mut total, partial| {
+            |(mut counts, mut same), (partial_counts, partial_same)| {
                 for a in 0..4 {
+                    same[a] += partial_same[a];
                     for b in 0..4 {
-                        total[a][b] += partial[a][b];
+                        counts[a][b] += partial_counts[a][b];
                     }
                 }
-                total
+                (counts, same)
             },
         )?;
-        Ok(BasePairTally { counts })
+        Ok(BasePairTally { counts, same })
     }
 }
 
@@ -884,9 +907,15 @@ impl KmerIndex {
 pub struct BasePairTally {
     /// `counts[a][b] == counts[b][a]` = number of eligible loci, pooled
     /// over included genome pairs, where the two genomes' single forms are
-    /// `a` and `b` (0=A, 1=C, 2=G, 3=T). Diagonal always `0` (an `a == b`
-    /// locus is `shared`, not tallied here).
+    /// `a` and `b` (0=A, 1=C, 2=G, 3=T). Diagonal always `0` — an `a == b`
+    /// locus is counted in `same`, not here.
     pub counts: [[u64; 4]; 4],
+    /// `same[a]` = number of eligible loci, pooled over included genome
+    /// pairs, where both genomes' single forms are `a` — the diagonal
+    /// `counts` omits, needed to build a proper row-stochastic composition
+    /// probability matrix (the "stay the same base" entries), not just the
+    /// substitution-cost off-diagonal.
+    pub same: [u64; 4],
 }
 
 /// IUPAC ambiguity code for a per-genome family presence mask (bit `b` set
@@ -918,6 +947,192 @@ fn iupac_code(mask: u8) -> u8 {
     }
 }
 
+/// See [`KmerIndex::cardinality_tally`].
+pub struct CardinalityTally {
+    /// `counts[a][b] == counts[b][a]` = number of family sites, pooled over
+    /// included genome pairs, where one genome's family cardinality
+    /// (popcount of its presence mask, `0..=4`) is `a` and the other's is
+    /// `b`. Diagonal is real data here (both genomes at the same
+    /// cardinality), unlike [`BasePairTally::counts`].
+    pub counts: [[u64; 5]; 5],
+}
+
+impl KmerIndex {
+    /// Cardinality co-occurrence, pooled only over genome pairs whose
+    /// overall SNP ratio in `raw` is at or below `ratio_ceiling` — same
+    /// saturation/no-data exclusion discipline as
+    /// [`base_pair_tally`](Self::base_pair_tally). Unlike
+    /// [`scan_family_pairs`](Self::scan_family_pairs) (which resolves each
+    /// genome to a single form and silently drops any genome carrying more
+    /// than one member of the family), this needs the *full* per-genome
+    /// presence mask — a family member count of 2, 3 or 4 is exactly the
+    /// signal being tallied, not noise to discard — so it re-implements the
+    /// traversal rather than reusing that helper.
+    ///
+    /// Restricted to variable families (`family_size() >= 2`), matching
+    /// `snp_pseudo_alignment`'s own scope — briefly removed, then
+    /// reinstated: without it, the diagonal is dominated by genome-wide
+    /// invariant background (family_size()<2 loci vastly outnumber the
+    /// ones that ever vary anywhere), which is inconsistent with the
+    /// `+ASC`-corrected alignment this matrix is ultimately used with —
+    /// `+ASC` exists specifically because the likelihood only ever sees
+    /// variable sites, so a rate model calibrated mostly from invariant
+    /// background sites doesn't describe the population it's applied to.
+    /// Verified empirically: removing the filter measurably worsened a
+    /// real IQ-TREE run (log-likelihood dropped, `NNI search needs
+    /// unusual large number of steps to converge` warnings appeared) — see
+    /// `docmd/theory/evolutionary_distances.md` for the full account.
+    /// [`base_pair_tally`](Self::base_pair_tally)'s own diagonal (`same`)
+    /// gets the matching restriction via `scan_family_pairs`'s new
+    /// `variable` flag, rather than a `family_size()` check of its own (it
+    /// doesn't have direct access to the family's mask).
+    pub fn cardinality_tally(&self, raw: &RawSnpDistanceOutput, ratio_ceiling: f64) -> OKIResult<CardinalityTally> {
+        let n_parts = self.n_partitions();
+        let n_genomes = self.meta.genomes.len();
+        let with_counts = self.meta.config.with_counts;
+        let k = self.kmer_size();
+        let n_bits = n_parts.trailing_zeros() as usize;
+
+        let included = Array2::from_shape_fn((n_genomes, n_genomes), |(i, j)| {
+            if i == j {
+                return false;
+            }
+            let snp = raw.snp[[i, j]];
+            let total = snp + raw.shared[[i, j]];
+            total > 0 && (snp as f64 / total as f64) <= ratio_ceiling
+        });
+
+        let partition = KmerPartition::open_with_config(
+            &self.root_path,
+            self.kmer_size(),
+            self.minimizer_size(),
+            n_bits,
+        )
+        .map_err(OKIError::Partition)?;
+        let cache = PartitionCache::build(&partition, n_parts, with_counts)?;
+
+        let mut layer_dirs = Vec::new();
+        for part in 0..n_parts {
+            let index_dir = self.partition().part_dir(part).join(INDEX_SUBDIR);
+            if !index_dir.exists() {
+                continue;
+            }
+            let meta = PartitionMeta::load(&index_dir).map_err(olm_to_ok)?;
+            for l in 0..meta.n_layers {
+                let layer_dir = index_dir.join(format!("layer_{l}"));
+                let annex_path = layer_dir.join(ANNEX_FILE_NAME);
+                if !annex_path.exists() {
+                    return Err(OKIError::InvalidInput(format!(
+                        "no sibling annex at {} — run build_sibling_annex first",
+                        annex_path.display()
+                    )));
+                }
+                layer_dirs.push(layer_dir);
+            }
+        }
+
+        let pb = progress_bar("cardinality_tally", layer_dirs.len() as u64, "layers");
+        let partials: Vec<[[u64; 5]; 5]> = layer_dirs
+            .par_iter()
+            .map(|layer_dir| -> OKIResult<[[u64; 5]; 5]> {
+                let index_dir = layer_dir.parent().expect("layer_dir has a parent index dir");
+                let meta = PartitionMeta::load(index_dir).map_err(olm_to_ok)?;
+                let annex = SiblingAnnex::open(&layer_dir.join(ANNEX_FILE_NAME))?;
+                let mphf = MphfLayer::open(layer_dir, &meta.mode).map_err(olm_to_ok)?;
+
+                let mut slot_kmer: Vec<Option<CanonicalKmer>> = vec![None; annex.len()];
+                let reader = UnitigFileReader::open_sequential(&layer_dir.join("unitigs.bin"))
+                    .map_err(OKIError::Partition)?;
+                for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
+                    if let Some(slot) = mphf.find(kmer) {
+                        slot_kmer[slot] = Some(kmer);
+                    }
+                }
+
+                let use_counts = with_counts && layer_dir.join("counts").exists();
+                let mat = if use_counts {
+                    Mat::Count(PersistentCompactIntMatrix::open(layer_dir)?)
+                } else {
+                    Mat::Presence(PersistentBitMatrix::open(layer_dir)?)
+                };
+                let n_cols = mat.n_cols().min(n_genomes);
+
+                let mut counts = [[0u64; 5]; 5];
+                let mut genome_mask: Vec<u8> = Vec::with_capacity(n_genomes);
+
+                for slot in 0..annex.len() {
+                    let Some(mask) = annex.get(slot) else { continue };
+                    let Some(kmer) = slot_kmer[slot] else { continue };
+                    if !is_minorant(kmer, mask, k) {
+                        continue; // family tallied once, at its minorant
+                    }
+                    if mask.family_size() < 2 {
+                        // Fully invariant family (never varies anywhere in
+                        // the index) — genome-wide background, not
+                        // SNP-adjacent signal; would otherwise swamp the
+                        // diagonal (`c=1/c=1` etc.), which needs to reflect
+                        // the same variable-families-only population the
+                        // `+ASC`-corrected alignment/likelihood actually
+                        // models. See `base_pair_tally`'s `variable` gate
+                        // on its own `same` diagonal for the matching fix.
+                        continue;
+                    }
+
+                    genome_mask.clear();
+                    genome_mask.resize(n_genomes, 0);
+
+                    for other in kmer.central_canonical_neighbors() {
+                        let base = central_base(other, k);
+                        if !mask.has(base) {
+                            continue;
+                        }
+                        let presence: Option<Vec<bool>> = if other == kmer {
+                            Some((0..n_cols).map(|g| mat.carries(g, slot)).collect())
+                        } else {
+                            let dest = partition_of(other, n_parts);
+                            cache.find_presence(dest, other, n_genomes)
+                        };
+                        let Some(presence) = presence else { continue };
+                        for (g, &present) in presence.iter().enumerate() {
+                            if present {
+                                genome_mask[g] |= 1 << base;
+                            }
+                        }
+                    }
+
+                    for i in 0..n_genomes {
+                        let card_i = genome_mask[i].count_ones() as usize;
+                        for j in (i + 1)..n_genomes {
+                            if !included[[i, j]] {
+                                continue;
+                            }
+                            let card_j = genome_mask[j].count_ones() as usize;
+                            counts[card_i][card_j] += 1;
+                            if card_i != card_j {
+                                counts[card_j][card_i] += 1;
+                            }
+                        }
+                    }
+                }
+
+                pb.inc(1);
+                Ok(counts)
+            })
+            .collect::<OKIResult<Vec<_>>>()?;
+        pb.finish_and_clear();
+
+        let mut total = [[0u64; 5]; 5];
+        for partial in partials {
+            for a in 0..5 {
+                for b in 0..5 {
+                    total[a][b] += partial[a][b];
+                }
+            }
+        }
+        Ok(CardinalityTally { counts: total })
+    }
+}
+
 /// A SNP-only pseudo-alignment: one row (byte sequence, IUPAC-coded) per
 /// genome, one column per variable family (`family_size() >= 2` — monomorphic
 /// families carry no signal and are skipped, unlike `raw_snp_distance`'s
diff --git a/src/obikmer/src/cmd/distance/mod.rs b/src/obikmer/src/cmd/distance/mod.rs
index c3b1035e..3d54cb44 100644
--- a/src/obikmer/src/cmd/distance/mod.rs
+++ b/src/obikmer/src/cmd/distance/mod.rs
@@ -10,9 +10,9 @@ use clap::Args;
 use kodama::{Method, linkage};
 use obifastwrite::{JsonVal, write_record};
 use obikindex::{
-    DistanceMetric, KmerIndex, RawSnpDistanceOutput, SankoffWeights,
-    SiblingAnnexStats, SnpAlignment, build_cost_matrix, c_ctx_from_p_hat, calibrate_p_hat,
-    mean_substitution_cost, substitution_costs_from_tally,
+    DistanceMetric, KmerIndex, RawSnpDistanceOutput,
+    SiblingAnnexStats, SnpAlignment,
+    cardinality_transition_probs, composition_transition_probs, pairwise_cost_matrix,
 };
 use speedytree::{DistanceMatrix, Hybrid, NeighborJoiningSolver, to_newick};
 use tracing::info;
@@ -87,19 +87,20 @@ pub struct DistanceArgs {
 
     /// Exclude a genome (by its exact label) from every computation below
     /// that reads the sibling annex — `--raw-snp-distance`/`--raw-snp-counts`,
-    /// `--snp`, and `--sankoff` (and everything `--sankoff` implies:
-    /// `p_hat`, `sub_cost`, `c_ctx`, the exported matrix/alignment,
-    /// `--tnt`/`--phyg`/`--iqtree`). Repeatable. Does *not* affect the plain
-    /// `--metric` distance matrix/NJ/UPGMA path (a different, unrelated
-    /// computation). Applied by zeroing the excluded genome's row/column
-    /// after `raw_snp_distance` runs (a pair with zero counts is already
-    /// skipped by `calibrate_p_hat`/`base_pair_tally`, so this needs no
-    /// change to the underlying traversal) and by dropping its row from
-    /// `snp_pseudo_alignment`'s output — the annex is still built/scanned
-    /// for the excluded genome too, just not used afterward. For a genome
-    /// with almost no informative sites shared with anything else (see
-    /// `docmd/theory/evolutionary_distances.md`, the IQ-TREE/Mash rogue-taxon
-    /// discussion), its presence can otherwise silently bias `p_hat`/`R`.
+    /// `--snp`, and `--sankoff` (and everything `--sankoff` implies: the
+    /// cardinality/composition transition models, the exported
+    /// matrix/alignment, `--tnt`/`--phyg`/`--iqtree`). Repeatable. Does
+    /// *not* affect the plain `--metric` distance matrix/NJ/UPGMA path (a
+    /// different, unrelated computation). Applied by zeroing the excluded
+    /// genome's row/column after `raw_snp_distance` runs (a pair with zero
+    /// counts is already skipped by `base_pair_tally`/`cardinality_tally`,
+    /// so this needs no change to the underlying traversal) and by
+    /// dropping its row from `snp_pseudo_alignment`'s output — the annex
+    /// is still built/scanned for the excluded genome too, just not used
+    /// afterward. For a genome with almost no informative sites shared
+    /// with anything else (see `docmd/theory/evolutionary_distances.md`,
+    /// the IQ-TREE/Mash rogue-taxon discussion), its presence can
+    /// otherwise silently bias the transition models.
     #[arg(long = "exclude-genome", value_name = "LABEL")]
     pub exclude_genome: Vec<String>,
 
@@ -231,11 +232,12 @@ pub fn run(args: DistanceArgs) {
 
     // ── Genome exclusion (`--exclude-genome`) ───────────────────────────────
     // Applied by zeroing a `RawSnpDistanceOutput`'s excluded rows/columns
-    // (`zero_excluded_pairs`) — `calibrate_p_hat`/`base_pair_tally` already
-    // skip any pair with zero total counts, so this needs no change to
-    // `obikindex`'s traversal — and by dropping the excluded genome's row
-    // from a `SnpAlignment` plus the matching label (`drop_excluded`),
-    // since an all-`∅` row for an "excluded" genome would otherwise still
+    // (`zero_excluded_pairs`) — `base_pair_tally`/`cardinality_tally`
+    // already skip any pair with zero total counts, so this needs no
+    // change to `obikindex`'s traversal — and by dropping the excluded
+    // genome's row from a `SnpAlignment` plus the matching label
+    // (`drop_excluded`), since an all-`∅` row for an "excluded" genome
+    // would otherwise still
     // reach TNT/PhyG/IQ-TREE as a real (empty) taxon.
     let exclude_mask: Vec<bool> = {
         let mut mask = vec![false; n];
@@ -263,15 +265,41 @@ pub fn run(args: DistanceArgs) {
             }
         }
     };
+    // `snp_pseudo_alignment`'s "variable family" criterion
+    // (`mask.family_size() >= 2`) is a property of the annex, computed
+    // over *every* genome in the index — unaffected by `--exclude-genome`.
+    // So dropping excluded rows alone can leave columns that are variable
+    // only thanks to an excluded genome now monomorphic among the
+    // survivors — silently wrong data for TNT/PhyG, and a hard failure
+    // for IQ-TREE's `+ASC` (verified: excluding 2 taxa on the 20-genome
+    // benchmark left 116,351 such columns). Re-check variability among the
+    // *kept* genomes only, after dropping rows, and drop those columns too.
     let drop_excluded = |alignment: SnpAlignment| -> (SnpAlignment, Vec<String>) {
-        let sequences = alignment.sequences.into_iter().enumerate()
+        let mut sequences: Vec<Vec<u8>> = alignment.sequences.into_iter().enumerate()
             .filter(|(i, _)| !exclude_mask[*i])
             .map(|(_, seq)| seq)
             .collect();
-        let kept_labels = labels.iter().enumerate()
+        let kept_labels: Vec<String> = labels.iter().enumerate()
             .filter(|(i, _)| !exclude_mask[*i])
             .map(|(_, l)| l.clone())
             .collect();
+
+        if exclude_mask.iter().any(|&excluded| excluded) && !sequences.is_empty() {
+            let n_sites = sequences[0].len();
+            let keep_col: Vec<bool> = (0..n_sites)
+                .map(|site| sequences.iter().any(|seq| seq[site] != sequences[0][site]))
+                .collect();
+            for seq in &mut sequences {
+                let mut kept = Vec::with_capacity(seq.len());
+                for (site, &b) in seq.iter().enumerate() {
+                    if keep_col[site] {
+                        kept.push(b);
+                    }
+                }
+                *seq = kept;
+            }
+        }
+
         (SnpAlignment { sequences }, kept_labels)
     };
 
@@ -330,21 +358,20 @@ pub fn run(args: DistanceArgs) {
             std::process::exit(1);
         });
         zero_excluded_pairs(&mut raw);
-        let estimate = calibrate_p_hat(&raw, args.sankoff_ratio_ceiling);
-        let m = (idx.kmer_size() - 1) / 2;
 
-        let tally = idx.base_pair_tally(&raw, args.sankoff_ratio_ceiling).unwrap_or_else(|e| {
+        let base_tally = idx.base_pair_tally(&raw, args.sankoff_ratio_ceiling).unwrap_or_else(|e| {
             eprintln!("error computing base-pair tally: {e}");
             std::process::exit(1);
         });
-        let sub_cost = substitution_costs_from_tally(&tally);
-        let mean_sub_cost = mean_substitution_cost(&tally, &sub_cost);
-        let c_ctx = c_ctx_from_p_hat(estimate.p_hat, m, mean_sub_cost);
-
-        let weights = SankoffWeights { sub_cost, c_ctx };
-        let matrix = build_cost_matrix(&weights);
-        write_sankoff_matrix_csv(&matrix, &estimate, &weights, &args.output);
-        write_sankoff_params(&estimate, &tally, &weights, args.sankoff_ratio_ceiling, m, mean_sub_cost, &args.output);
+        let card_tally = idx.cardinality_tally(&raw, args.sankoff_ratio_ceiling).unwrap_or_else(|e| {
+            eprintln!("error computing cardinality tally: {e}");
+            std::process::exit(1);
+        });
+        let p_card = cardinality_transition_probs(&card_tally);
+        let p_comp = composition_transition_probs(&base_tally);
+        let matrix = pairwise_cost_matrix(&p_card, &p_comp);
+        write_sankoff_matrix_csv(&matrix, &args.output);
+        write_sankoff_params(&card_tally, &p_card, &base_tally, &p_comp, args.sankoff_ratio_ceiling, &args.output);
 
         let alignment = idx.snp_pseudo_alignment().unwrap_or_else(|e| {
             eprintln!("error computing SNP pseudo-alignment: {e}");
diff --git a/src/obikmer/src/cmd/distance/sankoff.rs b/src/obikmer/src/cmd/distance/sankoff.rs
index 5e02fda6..c8faaf2b 100644
--- a/src/obikmer/src/cmd/distance/sankoff.rs
+++ b/src/obikmer/src/cmd/distance/sankoff.rs
@@ -2,7 +2,7 @@ use std::io::{BufWriter, Write};
 use std::path::PathBuf;
 
 use obifastwrite::{JsonVal, write_record};
-use obikindex::{BasePairTally, PHatEstimate, SankoffWeights, SnpAlignment};
+use obikindex::{BasePairTally, CardinalityTally, SnpAlignment};
 use tracing::info;
 
 // ── Sankoff pseudo-alignment → FASTA ────────────────────────────────────────
@@ -65,19 +65,8 @@ pub(super) fn state_index_table() -> [u8; 128] {
 
 pub(super) fn write_sankoff_matrix_csv(
     matrix: &[[f64; 16]; 16],
-    estimate: &PHatEstimate,
-    weights: &SankoffWeights,
     output: &Option<PathBuf>,
 ) {
-    info!(
-        p_hat = format_args!("{:.6}", estimate.p_hat),
-        variance = format_args!("{:.3e}", estimate.variance),
-        n_pairs_included = estimate.n_pairs_included,
-        n_loci_total = estimate.n_loci_total,
-        c_ctx = format_args!("{:.4}", weights.c_ctx),
-        "Sankoff matrix calibration"
-    );
-
     let path = output.as_ref()
         .map(|p| format!("{}_sankoff_matrix.csv", p.display()))
         .unwrap_or_else(|| "sankoff_matrix.csv".into());
@@ -109,60 +98,64 @@ pub(super) fn write_sankoff_matrix_csv(
 // rather than re-parsing free text.
 
 #[derive(serde::Serialize)]
-struct SankoffSubstitution {
-    pair: String,
+struct CardinalityTransition {
+    from: usize,
+    to: usize,
     count: u64,
-    cost: f64,
+    probability: f64,
+}
+
+#[derive(serde::Serialize)]
+struct CompositionTransition {
+    from: char,
+    to: char,
+    count: u64,
+    probability: f64,
 }
 
 #[derive(serde::Serialize)]
 struct SankoffParamsReport {
     ratio_ceiling: f64,
-    flank_length_m: usize,
-    p_hat: f64,
-    p_hat_variance: f64,
-    n_pairs_included: usize,
-    n_loci_total: u64,
-    /// Weighted-average substitution cost — see `c_ctx_from_p_hat`'s docs:
-    /// this is what turns the raw expected mutation *count* behind `c_ctx`
-    /// into an actual cost (not every mutation is worth a flat `1`).
-    mean_sub_cost: f64,
-    c_ctx: f64,
-    substitutions: Vec<SankoffSubstitution>,
+    cardinality_transitions: Vec<CardinalityTransition>,
+    composition_transitions: Vec<CompositionTransition>,
 }
 
 pub(super) fn write_sankoff_params(
-    estimate: &PHatEstimate,
-    tally: &BasePairTally,
-    weights: &SankoffWeights,
+    card_tally: &CardinalityTally,
+    p_card: &[[f64; 5]; 5],
+    base_tally: &BasePairTally,
+    p_comp: &[[f64; 4]; 4],
     ratio_ceiling: f64,
-    m: usize,
-    mean_sub_cost: f64,
     output: &Option<PathBuf>,
 ) {
     const BASE_LETTER: [char; 4] = ['A', 'C', 'G', 'T'];
 
-    let mut substitutions = Vec::with_capacity(6);
-    for a in 0..4 {
-        for b in (a + 1)..4 {
-            substitutions.push(SankoffSubstitution {
-                pair: format!("{}/{}", BASE_LETTER[a], BASE_LETTER[b]),
-                count: tally.counts[a][b],
-                cost: weights.sub_cost[a][b],
+    let mut cardinality_transitions = Vec::with_capacity(25);
+    for a in 0..5 {
+        for b in 0..5 {
+            cardinality_transitions.push(CardinalityTransition {
+                from: a,
+                to: b,
+                count: card_tally.counts[a][b],
+                probability: p_card[a][b],
             });
         }
     }
-    let report = SankoffParamsReport {
-        ratio_ceiling,
-        flank_length_m: m,
-        p_hat: estimate.p_hat,
-        p_hat_variance: estimate.variance,
-        n_pairs_included: estimate.n_pairs_included,
-        n_loci_total: estimate.n_loci_total,
-        mean_sub_cost,
-        c_ctx: weights.c_ctx,
-        substitutions,
-    };
+
+    let mut composition_transitions = Vec::with_capacity(16);
+    for a in 0..4 {
+        for b in 0..4 {
+            let count = if a == b { base_tally.same[a] } else { base_tally.counts[a][b] };
+            composition_transitions.push(CompositionTransition {
+                from: BASE_LETTER[a],
+                to: BASE_LETTER[b],
+                count,
+                probability: p_comp[a][b],
+            });
+        }
+    }
+
+    let report = SankoffParamsReport { ratio_ceiling, cardinality_transitions, composition_transitions };
 
     let path = output.as_ref()
         .map(|p| format!("{}_sankoff_params.yaml", p.display()))
@@ -183,15 +176,18 @@ pub(super) fn write_sankoff_params(
 /// closure* of the result (Floyd-Warshall over the 16 states again, on the
 /// now-integer values).
 ///
-/// `matrix` is already a metric in its real-valued form (it's a
-/// shortest-path closure itself — see `obikindex::build_cost_matrix`), but
-/// rounding each cell independently can still break the triangle
-/// inequality: e.g. two real costs of `1.734` each round to `173`, summing
-/// to `346`, while their own real sum `3.468` rounds to `347` — TNT then
-/// reports "triangle inequality violated ... Fixed" and silently
-/// substitutes its own corrected value. Re-closing after rounding makes
-/// that correction explicit and reproducible here instead, rather than
-/// left implicit and tool-version-dependent.
+/// Unlike this project's earlier cost-matrix construction (a graph closed
+/// by shortest path, guaranteeing a metric by construction), `matrix` here
+/// comes from `obikindex::pairwise_cost_matrix`'s row-normalise-then-`-ln`
+/// composition, which gives no such guarantee — so this closure isn't only
+/// needed to correct integer-rounding artifacts (two real costs of `1.734`
+/// each round to `173`, summing to `346`, while their own real sum `3.468`
+/// rounds to `347` — TNT then reports "triangle inequality violated ...
+/// Fixed" and silently substitutes its own corrected value), it may also
+/// be the only thing making the *real-valued* matrix a metric in the first
+/// place. Re-closing after rounding makes both corrections explicit and
+/// reproducible here instead, rather than left implicit and
+/// tool-version-dependent.
 pub(super) fn scaled_metric_matrix(matrix: &[[f64; 16]; 16], cost_scale: f64) -> [[i64; 16]; 16] {
     let mut m = [[0i64; 16]; 16];
     for i in 0..16 {
-- 
2.54.0


From 6acafa7f2c5e6fd5a33a0cc4b1dc2f36979f44c9 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Thu, 13 Aug 2026 10:01:29 +0200
Subject: [PATCH 06/46] docs: add obikmer user guide and MkDocs build
 configuration

Introduces a comprehensive documentation set covering theoretical foundations, CLI usage, installation, and system architecture. Adds MkDocs configuration and Makefile targets to generate, serve with live reload, and clean the documentation site. Includes citation styles and bibliography files for academic references.
---
 Makefile                                  |  21 +-
 UserDocMD/architecture.md                 |  33 +++
 UserDocMD/ecology-letters.csl             | 230 +++++++++++++++++++
 UserDocMD/formats/index_layout.md         |  56 +++++
 UserDocMD/index.md                        |  68 ++++++
 UserDocMD/installation.md                 |  84 +++++++
 UserDocMD/references.bib                  | 261 ++++++++++++++++++++++
 UserDocMD/theory/encoding.md              |  28 +++
 UserDocMD/theory/entropy_filter.md        |  36 +++
 UserDocMD/theory/indexing_architecture.md |  32 +++
 UserDocMD/theory/kmers_and_superkmers.md  |  24 ++
 UserDocMD/theory/minimizer_selection.md   |  42 ++++
 UserDocMD/usage/annotate.md               |  25 +++
 UserDocMD/usage/distance.md               |  97 ++++++++
 UserDocMD/usage/dump.md                   |  25 +++
 UserDocMD/usage/estimate.md               |  18 ++
 UserDocMD/usage/filter.md                 |  47 ++++
 UserDocMD/usage/index_command.md          |  50 +++++
 UserDocMD/usage/merge.md                  |  29 +++
 UserDocMD/usage/pack.md                   |  15 ++
 UserDocMD/usage/predicates.md             |  46 ++++
 UserDocMD/usage/query.md                  |  38 ++++
 UserDocMD/usage/reindex.md                |  25 +++
 UserDocMD/usage/select.md                 |  35 +++
 UserDocMD/usage/superkmer.md              |  27 +++
 UserDocMD/usage/unitig.md                 |  19 ++
 UserDocMD/usage/utils.md                  |  26 +++
 mkdocs-user.yml                           |  61 +++++
 28 files changed, 1497 insertions(+), 1 deletion(-)
 create mode 100644 UserDocMD/architecture.md
 create mode 100644 UserDocMD/ecology-letters.csl
 create mode 100644 UserDocMD/formats/index_layout.md
 create mode 100644 UserDocMD/index.md
 create mode 100644 UserDocMD/installation.md
 create mode 100644 UserDocMD/references.bib
 create mode 100644 UserDocMD/theory/encoding.md
 create mode 100644 UserDocMD/theory/entropy_filter.md
 create mode 100644 UserDocMD/theory/indexing_architecture.md
 create mode 100644 UserDocMD/theory/kmers_and_superkmers.md
 create mode 100644 UserDocMD/theory/minimizer_selection.md
 create mode 100644 UserDocMD/usage/annotate.md
 create mode 100644 UserDocMD/usage/distance.md
 create mode 100644 UserDocMD/usage/dump.md
 create mode 100644 UserDocMD/usage/estimate.md
 create mode 100644 UserDocMD/usage/filter.md
 create mode 100644 UserDocMD/usage/index_command.md
 create mode 100644 UserDocMD/usage/merge.md
 create mode 100644 UserDocMD/usage/pack.md
 create mode 100644 UserDocMD/usage/predicates.md
 create mode 100644 UserDocMD/usage/query.md
 create mode 100644 UserDocMD/usage/reindex.md
 create mode 100644 UserDocMD/usage/select.md
 create mode 100644 UserDocMD/usage/superkmer.md
 create mode 100644 UserDocMD/usage/unitig.md
 create mode 100644 UserDocMD/usage/utils.md
 create mode 100644 mkdocs-user.yml

diff --git a/Makefile b/Makefile
index dedc3bed..5889db68 100644
--- a/Makefile
+++ b/Makefile
@@ -10,6 +10,11 @@ DOC_FILE := mkdocs.yml
 DOC_SITE := doc
 DOC_PORT := 8001
 
+DOC_USER_DIR  := UserDocMD
+DOC_USER_FILE := mkdocs-user.yml
+DOC_USER_SITE := doc-user
+DOC_USER_PORT := 8002
+
 # ── virtualenv ────────────────────────────────────────────────────────────────
 
 $(VENV)/bin/activate:
@@ -60,8 +65,22 @@ doc-serve: $(MKDOCS)
 clean-doc:
 	rm -rf $(DOC_SITE)/
 
+.PHONY: doc-user
+doc-user: $(MKDOCS)
+	$(MKDOCS) build -f $(DOC_USER_FILE)
+
+.PHONY: doc-user-serve
+doc-user-serve: $(MKDOCS)
+	$(MKDOCS) serve -f $(DOC_USER_FILE) \
+	                --dev-addr=127.0.0.1:$(DOC_USER_PORT) \
+	                --livereload
+
+.PHONY: clean-doc-user
+clean-doc-user:
+	rm -rf $(DOC_USER_SITE)/
+
 .PHONY: clean
-clean: clean-doc
+clean: clean-doc clean-doc-user
 	rm -rf $(VENV)
 
 # ── release ───────────────────────────────────────────────────────────────────
diff --git a/UserDocMD/architecture.md b/UserDocMD/architecture.md
new file mode 100644
index 00000000..87bf9b91
--- /dev/null
+++ b/UserDocMD/architecture.md
@@ -0,0 +1,33 @@
+# Architecture notes for advanced use
+
+This page describes execution-level behavior relevant to sizing and running `obikmer` on large datasets or multi-socket machines. It complements the [index format](formats/index_layout.md) and [theory](theory/indexing_architecture.md) pages.
+
+## Sequence invariant
+
+Every input sequence is treated purely as a compact representation of a set of overlapping kmers:
+
+- Only the `A`/`C`/`G`/`T` alphabet (case-insensitive) is recognized; a sequence is cut at any other character (including IUPAC ambiguity codes), so runs containing them are not represented in the index.
+- Sequences are internally processed in chunks of at most 256 nucleotides; a chunk shorter than k is dropped. This is invisible to the user beyond the ACGT-only, minimum-length-k constraints above.
+- Kmers are always handled in canonical form (see [DNA encoding](theory/encoding.md)), so the tool is strand-agnostic throughout: a kmer and its reverse complement are always the same entry.
+
+## Index dimensioning
+
+An index directory is organized as `KmerIndex → partitions → layers`, with a canonical kmer belonging to exactly one (partition, layer) pair. This is what makes set operations (merge, filter, distance) parallel and coordination-free across partitions.
+
+- **Partition count** (`-p`/`--partitions`, rounded up to a power of 2) is the main dimensioning knob: more partitions means more independent parallel units and a smaller working set per partition, at the cost of more open files during construction.
+- **Layers** accumulate as an index grows through successive merges; per-partition query cost grows with the number of layers (worst case linear, expected constant since most kmer lookups resolve in the first layer they could plausibly be in).
+- Genome columns (count or presence data) are kept at a consistent width across every layer and partition after a merge, which is what allows whole-index aggregate distances (Jaccard, Bray-Curtis, Euclidean, Hellinger, …) to be computed as a two-pass cascade (local partial sums per partition, then a global combination) with no double counting.
+
+## Parallel execution and NUMA awareness
+
+Partition-level work (index construction, `merge`, `filter`, `reindex`, `select`, `distance`'s sibling-annex/Sankoff computations) is dispatched by a partition runner that adapts to the machine's memory topology, detected automatically at startup via hwloc:
+
+- On a multi-socket / multi-NUMA-node machine, one thread pool is pinned per NUMA node, and each partition is processed entirely by threads pinned to one node — keeping the memory a partition touches local to that node's DRAM. This matters because touching kmer data across NUMA nodes without pinning can degrade throughput by an order of magnitude or more on large multi-socket machines.
+- On a single-socket machine, Apple Silicon, or if hwloc cannot report NUMA topology, all cores are treated as one node with no pinning and negligible overhead — this is the default behavior on macOS.
+- Within a node, the number of active worker threads ramps up progressively rather than being fixed up front: it starts conservatively and grows in steps, but only as long as measured CPU efficiency or disk I/O throughput keeps improving. If neither improves after a growth step, the runner stops adding workers — avoiding oversubscription on stages that are memory-bandwidth-bound rather than CPU- or I/O-bound. Ramp speed scales with the number of cores per node, so a single-node machine ramps just as fast as a large multi-node one.
+
+No CLI flag controls this directly; it is fully automatic at runtime. NUMA-aware pinning can be compiled out (Cargo feature `numa`, on by default), in which case a plain global thread pool is used instead.
+
+## Kmer filtering (`filter`)
+
+[`filter`](usage/filter.md) evaluates predicates against the genome metadata matrix directly whenever every active filter can be expressed as a column-level test (e.g. "any outgroup column non-zero"), producing a per-slot keep/drop decision without touching kmer sequence data at all. If any active filter cannot be expressed this way, evaluation falls back to a per-kmer, row-level check. Either way, the result is always written as a single, freshly compacted layer (`unitigs.bin` and the MPHF are rebuilt from the surviving kmers), never as an additional layer on top of the source index.
diff --git a/UserDocMD/ecology-letters.csl b/UserDocMD/ecology-letters.csl
new file mode 100644
index 00000000..6a96c856
--- /dev/null
+++ b/UserDocMD/ecology-letters.csl
@@ -0,0 +1,230 @@
+<?xml version="1.0" encoding="utf-8"?>
+<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="sort-only" default-locale="en-US">
+  <info>
+    <title>Ecology Letters</title>
+    <id>http://www.zotero.org/styles/ecology-letters</id>
+    <link href="http://www.zotero.org/styles/ecology-letters" rel="self"/>
+    <link href="http://www.zotero.org/styles/apa" rel="template"/>
+    <link href="http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291461-0248/homepage/ForAuthors.html" rel="documentation"/>
+    <author>
+      <name>David Kaplan</name>
+      <email>david.kaplan@ird.fr</email>
+    </author>
+    <contributor>
+      <name>Sebastian Karcher</name>
+    </contributor>
+    <category citation-format="author-date"/>
+    <category field="biology"/>
+    <issn>1461-023X</issn>
+    <eissn>1461-0248</eissn>
+    <updated>2023-10-11T10:45:32+00:00</updated>
+    <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
+  </info>
+  <macro name="container">
+    <choose>
+      <if type="chapter paper-conference" match="any">
+        <text term="in" text-case="capitalize-first" suffix=": "/>
+        <text variable="container-title" font-style="italic"/>
+        <text variable="collection-title" prefix=", "/>
+        <names variable="editor translator" prefix=" (" delimiter=", " suffix=")">
+          <label form="short" suffix=" "/>
+          <name name-as-sort-order="all" and="symbol" sort-separator=", " initialize-with="." delimiter=", " delimiter-precedes-last="never"/>
+        </names>
+      </if>
+      <else>
+        <group delimiter=", ">
+          <text variable="container-title" font-style="italic" form="short"/>
+          <text variable="collection-title"/>
+        </group>
+      </else>
+    </choose>
+  </macro>
+  <macro name="author">
+    <names variable="author">
+      <name name-as-sort-order="all" and="symbol" sort-separator=", " initialize-with="." delimiter=", " delimiter-precedes-last="never"/>
+      <label form="short" prefix=" (" suffix=")" text-case="capitalize-first"/>
+      <et-al font-style="italic"/>
+      <substitute>
+        <names variable="editor"/>
+        <names variable="translator"/>
+        <text macro="title"/>
+      </substitute>
+    </names>
+  </macro>
+  <macro name="author-short">
+    <names variable="author">
+      <name form="short" and="symbol" delimiter=", " initialize-with=". "/>
+      <et-al font-style="italic"/>
+      <substitute>
+        <names variable="editor"/>
+        <names variable="translator"/>
+        <choose>
+          <if type="bill book graphic legal_case legislation motion_picture report song" match="any">
+            <text variable="title" form="short" font-style="italic"/>
+          </if>
+          <else>
+            <text variable="title" form="short" quotes="true"/>
+          </else>
+        </choose>
+      </substitute>
+    </names>
+  </macro>
+  <macro name="access">
+    <choose>
+      <if type="webpage">
+        <group>
+          <text term="available at" text-case="capitalize-first" suffix=": "/>
+          <text variable="URL" suffix="."/>
+        </group>
+        <text value="Last accessed" prefix=" " suffix=" "/>
+        <date variable="accessed">
+          <date-part name="day" suffix=" "/>
+          <date-part name="month" suffix=" "/>
+          <date-part name="year"/>
+        </date>
+      </if>
+    </choose>
+  </macro>
+  <macro name="title">
+    <choose>
+      <if type="report" match="any">
+        <text variable="title" font-style="italic"/>
+        <group prefix=" (" suffix=")">
+          <text variable="genre"/>
+          <text variable="number" prefix=" No. "/>
+        </group>
+      </if>
+      <else-if type="bill book graphic legal_case legislation motion_picture report song speech" match="any">
+        <text variable="title" font-style="italic"/>
+      </else-if>
+      <else-if type="webpage">
+        <text variable="title" font-style="italic"/>
+      </else-if>
+      <else>
+        <text variable="title"/>
+      </else>
+    </choose>
+  </macro>
+  <macro name="publisher">
+    <choose>
+      <if type="report" match="any">
+        <group delimiter=", ">
+          <text variable="publisher"/>
+          <text variable="publisher-place"/>
+        </group>
+      </if>
+      <else>
+        <text variable="genre" suffix=". "/>
+        <group delimiter=", ">
+          <text variable="publisher"/>
+          <text variable="publisher-place"/>
+        </group>
+      </else>
+    </choose>
+  </macro>
+  <macro name="event">
+    <choose>
+      <if variable="event">
+        <text term="presented at" text-case="capitalize-first" suffix=" "/>
+        <text variable="event"/>
+      </if>
+    </choose>
+  </macro>
+  <macro name="issued">
+    <choose>
+      <if variable="issued">
+        <date variable="issued">
+          <date-part name="year"/>
+        </date>
+      </if>
+      <else-if variable="accessed">
+        <choose>
+          <if type="webpage">
+            <date variable="accessed">
+              <date-part name="year"/>
+            </date>
+          </if>
+          <else>
+            <text term="no date" form="short"/>
+          </else>
+        </choose>
+      </else-if>
+      <else>
+        <text term="no date" form="short"/>
+      </else>
+    </choose>
+  </macro>
+  <macro name="edition">
+    <choose>
+      <if is-numeric="edition">
+        <group delimiter=" ">
+          <number variable="edition" form="ordinal"/>
+          <text value="edn"/>
+        </group>
+      </if>
+      <else>
+        <text variable="edition" suffix="."/>
+      </else>
+    </choose>
+  </macro>
+  <macro name="locators">
+    <choose>
+      <if type="article-journal article-magazine article-newspaper" match="any">
+        <group prefix=", " delimiter=", ">
+          <group>
+            <text variable="volume"/>
+          </group>
+          <text variable="page"/>
+        </group>
+      </if>
+      <else-if type="bill book graphic legal_case legislation motion_picture report song thesis" match="any">
+        <group delimiter=". " prefix=". ">
+          <text macro="edition"/>
+          <text macro="event"/>
+          <text macro="publisher"/>
+        </group>
+      </else-if>
+      <else-if type="chapter paper-conference" match="any">
+        <group delimiter=", " prefix=". ">
+          <text macro="event"/>
+          <text macro="publisher"/>
+          <group>
+            <label variable="page" form="short" suffix=" "/>
+            <text variable="page"/>
+          </group>
+        </group>
+      </else-if>
+    </choose>
+  </macro>
+  <citation et-al-min="3" et-al-use-first="1" disambiguate-add-year-suffix="true" collapse="year-suffix" year-suffix-delimiter=", ">
+    <sort>
+      <key macro="author"/>
+      <key macro="issued"/>
+    </sort>
+    <layout prefix="(" suffix=")" delimiter="; ">
+      <group delimiter=" ">
+        <text macro="author-short"/>
+        <text macro="issued"/>
+      </group>
+    </layout>
+  </citation>
+  <bibliography et-al-min="7" et-al-use-first="6" entry-spacing="0" hanging-indent="true">
+    <sort>
+      <key macro="author"/>
+      <key macro="issued" sort="ascending"/>
+      <key macro="title"/>
+    </sort>
+    <layout>
+      <group suffix=".">
+        <text macro="author" suffix="."/>
+        <text macro="issued" prefix=" (" suffix="). "/>
+        <group delimiter=". ">
+          <text macro="title"/>
+          <text macro="container"/>
+        </group>
+        <text macro="locators"/>
+        <text macro="access" prefix=". "/>
+      </group>
+    </layout>
+  </bibliography>
+</style>
diff --git a/UserDocMD/formats/index_layout.md b/UserDocMD/formats/index_layout.md
new file mode 100644
index 00000000..09633b09
--- /dev/null
+++ b/UserDocMD/formats/index_layout.md
@@ -0,0 +1,56 @@
+# Index construction and on-disk layout
+
+## Construction pipeline
+
+Building an index ([`index`](../usage/index_command.md)) proceeds through a fixed sequence of phases, each operating independently per partition (see [Partitioning and indexing architecture](../theory/indexing_architecture.md)):
+
+1. **Scatter.** A single streaming pass over the input. Each sequence fragment is cut at non-ACGT bases, passed through the low-complexity entropy filter (see [Low-complexity kmer filter](../theory/entropy_filter.md)), and any resulting segment shorter than k is dropped. Surviving segments are decomposed into super-kmers, canonicalized, and routed by `hash(minimizer) mod n_partitions` into one file per partition.
+2. **Dereplication.** Within each partition, identical super-kmer sequences are merged and their occurrence counts summed. This count is per super-kmer, not per kmer — a kmer's true abundance is the sum of the counts of every super-kmer containing it.
+3. **Exact counting.** Every kmer in every dereplicated super-kmer is enumerated and its exact total count computed. A per-genome kmer frequency spectrum is produced at this stage.
+4. **Quorum filtering.** Kmers outside the `--min-abundance`/`--max-abundance` range are dropped, and super-kmers are recompacted around the surviving kmer set.
+5. **Local assembly.** The surviving kmers of each partition are assembled into unitigs — maximal non-branching runs of a local de Bruijn graph — such that every kmer appears exactly once, at one (unitig, offset) location.
+6. **MPHF and evidence construction.** A minimal perfect hash function is built over the canonical kmers of each partition, together with the evidence structure needed to verify that a queried kmer was genuinely indexed (see below). Per-genome counts or presence bits are recorded alongside if requested.
+
+Phases 1–5 are independent per partition and run in parallel; phase 6 finalizes each partition once its kmer set is fixed.
+
+## Minimal perfect hash function (MPHF)
+
+Each partition's surviving kmers are mapped to a dense range of integer slots by a minimal perfect hash function: no collisions, near-optimal space (a few bits per key), O(1) lookup. Because an MPHF maps *any* input to some slot — including kmers that were never indexed — a lookup alone cannot distinguish a genuinely indexed kmer from an arbitrary one; every lookup is followed by an evidence check.
+
+## Evidence: exact vs. approximate
+
+Two verification modes are available, selected at build time (`index --approx`) and convertible afterwards ([`reindex`](../usage/reindex.md)):
+
+- **Exact** (default): the hashed slot stores a pointer back into the partition's unitig data. At query time the kmer is reconstructed from that location and compared directly to the query. Zero false positives, at the cost of one extra random read per lookup.
+- **Approximate** (`--approx`): the slot stores a short fingerprint (`--evidence-bits` bits) instead of a pointer; verification is a single fingerprint comparison. This trades a small, bounded false-positive rate ($1/2^b$ per kmer, reduced further to about $1/2^{b \cdot z}$ for a read requiring $z$ consecutive matching kmers via the `-z`/`--findere-z` parameter) for lower memory and disk usage, since no reconstruction index is needed. See [`estimate`](../usage/estimate.md) to explore this trade-off before building.
+
+## On-disk layout
+
+```
+<index_root>/
+  index.meta                    global configuration (k, minimizer size, partition count,
+                                 evidence mode, whether counts are stored) and genome list/metadata
+  scatter.done / count.done / index.done      build-progress sentinels
+  spectrums/<label>.json        per-genome kmer frequency histogram
+  partitions/
+    part_00000/ ... part_NNNNN/
+      index/
+        meta.json                number of layers in this partition
+        layer_0/
+          unitigs.bin             reconstructible kmer sequence data — always kept
+          unitigs.bin.idx         random-access index into unitigs.bin (exact evidence only)
+          mphf.bin                 the minimal perfect hash function
+          evidence.bin              exact evidence (exact mode only)
+          fingerprint.bin           approximate evidence (approximate mode only)
+          counts/                   per-genome kmer counts (if counts were requested)
+          presence/                 per-genome presence/absence bits
+        layer_1/, layer_2/, ...     added by later merges, same internal structure
+```
+
+`unitigs.bin` is the only file from which the indexed kmer content can be fully recovered; it is always retained. Every other file (MPHF, evidence, counts) is derived from it.
+
+A **layer** corresponds to one increment of kmer content added to a partition — most commonly, one [`merge`](../usage/merge.md) operation that introduces kmers not already present in the index. Genomes already present in the index simply gain new columns in the existing layers' count/presence data; only genuinely new kmer content is assembled into a new layer. Because of this, merging cost scales with the novel kmer content being added, not with the accumulated size of the index. A query against an index with several layers checks each layer's MPHF in turn.
+
+Sources merged together must share the same kmer size, minimizer size, partition count, and evidence mode (including matching approximate-mode parameters); mismatches are rejected rather than silently reconciled — [`reindex`](../usage/reindex.md) one of the sources first if needed.
+
+`obikmer pack` consolidates a partition's per-column files (counts/presence) into a single file, reducing the number of file opens needed at query time.
diff --git a/UserDocMD/index.md b/UserDocMD/index.md
new file mode 100644
index 00000000..cd1e2806
--- /dev/null
+++ b/UserDocMD/index.md
@@ -0,0 +1,68 @@
+# obikmer
+
+`obikmer` is a command-line tool for counting, indexing, querying and comparing DNA sequences represented as kmer sets. It targets individual genome datasets of tens of gigabases, with an emphasis on computational, memory, and disk efficiency.
+
+All functionality is exposed through a single binary, `obikmer`, organized as subcommands.
+
+## Core principles
+
+- Kmers are of fixed, odd length $k$, chosen at index-construction time in the range $[11, 31]$ (see [Kmers and super-kmers](theory/kmers_and_superkmers.md)).
+- Each kmer fits in a 64-bit word using a 2-bit-per-base encoding (see [DNA encoding](theory/encoding.md)).
+- Kmers are handled in **canonical form** ($\text{canonical}(kmer) = \min(kmer, \text{revcomp}(kmer))$), making counting strand-independent.
+- Sequences are decomposed into **super-kmers** before storage, anchored on a hash-selected **minimizer** (see [Minimizer selection](theory/minimizer_selection.md)), then routed to one of several **partitions** for parallel, memory-bounded processing (see [Partitioning and indexing architecture](theory/indexing_architecture.md)).
+- Low-complexity kmers can be filtered out at index-construction time using an entropy-based score (see [Low-complexity kmer filter](theory/entropy_filter.md)).
+
+## Commands
+
+| Command | Purpose |
+|---|---|
+| [`superkmer`](usage/superkmer.md) | Extract super-kmers from a sequence file and write them to stdout |
+| [`index`](usage/index_command.md) | Build a genome index |
+| [`merge`](usage/merge.md) | Merge multiple indexes into one |
+| [`filter`](usage/filter.md) | Retain only kmers matching ingroup/outgroup predicates |
+| [`select`](usage/select.md) | Project and/or aggregate genome columns of an index |
+| [`query`](usage/query.md) | Query an index with sequences and annotate matches |
+| [`dump`](usage/dump.md) | Dump indexed kmers as CSV |
+| [`annotate`](usage/annotate.md) | Add, update, or dump genome metadata |
+| [`distance`](usage/distance.md) | Compute pairwise distance matrices and phylogenetic exports |
+| [`unitig`](usage/unitig.md) | Dump the unitigs of an index as FASTA |
+| [`estimate`](usage/estimate.md) | Estimate approximate-index parameters before indexing |
+| [`reindex`](usage/reindex.md) | Convert an index's evidence representation (exact ↔ approximate) |
+| [`utils`](usage/utils.md) | Miscellaneous index maintenance and inspection utilities |
+| [`pack`](usage/pack.md) | Pack per-column matrix files into a single-file format |
+
+See [Genome predicates and taxonomy paths](usage/predicates.md) for the selection language shared by `filter`, `select`, `dump`, and `unitig`.
+
+## Further reading
+
+- [Index construction and on-disk layout](formats/index_layout.md)
+- [Architecture notes for advanced use](architecture.md) — parallel execution, NUMA awareness, index dimensioning
+
+## Input formats
+
+- `superkmer` and `index`: FASTA (`.fa`, `.fasta`), FASTQ (`.fq`, `.fastq`), GenBank flat file (`.gb`, `.gbk`, `.gbff`), all optionally gzip-compressed; directories are expanded recursively; streaming stdin via `-` or when no input path is given.
+- `query`: FASTA or FASTQ, optionally gzip-compressed; streaming stdin the same way.
+
+## Parameter constraints
+
+These constraints are checked at startup; an invalid value exits immediately with an error.
+
+| Parameter | Constraint | Reason |
+|---|---|---|
+| $k$ (`--kmer-size`) | odd, $k \in [11, 31]$ | odd length guarantees the canonical form is always well defined; the range keeps a kmer within a 64-bit word while retaining specificity |
+| $m$ (`--minimizer-size`) | odd, $3 \le m \le k-1$ | same palindrome argument as $k$; must be strictly shorter than the kmer |
+| $z$ (`-z`, approximate evidence only) | $z \le k-1$ | the effective indexed kmer size is $k-z+1$ |
+
+## Genome label constraints
+
+Genome labels are arbitrary Unicode strings, with the following restrictions:
+
+| Character | Forbidden | Reason |
+|---|---|---|
+| `/` | yes | filesystem path separator |
+| `=` | yes | separator used by `--new-label` |
+| `\0` | yes | null byte |
+| `\n`, `\r`, `\t` | yes | would break CSV output |
+| spaces | allowed | quote in the shell, e.g. `--new-label 'new label=old label'` |
+
+Empty labels are rejected. A label derived automatically from the input file name (when `--label` is omitted) is not validated, since it is already filesystem-safe.
diff --git a/UserDocMD/installation.md b/UserDocMD/installation.md
new file mode 100644
index 00000000..0ad3118e
--- /dev/null
+++ b/UserDocMD/installation.md
@@ -0,0 +1,84 @@
+# Installation
+
+## Prerequisites
+
+### Rust toolchain
+
+`obikmer` requires **Rust 1.85 or later** (edition 2024). Install or update via [rustup](https://rustup.rs):
+
+```bash
+curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
+rustup update stable
+```
+
+### C build environment (required for hwloc)
+
+`obikmer` embeds [hwloc](https://www.open-mpi.org/projects/hwloc/) (Hardware Locality) for NUMA-aware thread placement on multi-socket machines. hwloc is built from source at compile time, which requires a standard C build environment.
+
+#### Linux (Debian/Ubuntu)
+
+```bash
+apt install build-essential automake libtool autoconf pkg-config
+```
+
+#### Linux (RHEL/Rocky/AlmaLinux)
+
+```bash
+dnf install gcc make automake libtool autoconf pkgconfig
+```
+
+#### HPC clusters
+
+Most HPC clusters provide these tools via the module system:
+
+```bash
+module load gcc automake libtool autoconf
+```
+
+If in doubt, check that `autoreconf --version` and `libtool --version` return successfully.
+
+#### macOS
+
+```bash
+brew install automake libtool autoconf pkg-config
+```
+
+## Building
+
+```bash
+git clone <repository-url>
+cd obikmer/src
+cargo build --release
+```
+
+The compiled binary is at `target/release/obikmer`.
+
+### Building on HPC clusters (network filesystems)
+
+HPC home directories are typically on a network filesystem (Lustre, NFS) optimized for large sequential reads, not for the many small file operations Cargo generates during compilation. Building directly on such a filesystem can be extremely slow.
+
+Redirect the build directory to a local scratch disk:
+
+```bash
+CARGO_TARGET_DIR=/scratch/$USER/cargo-target cargo build --release
+```
+
+Adapt the path to the scratch space available on your cluster (`/var/tmp`, `/tmp`, `/scratch/local`, etc.). Once built, copy the binary to a permanent location:
+
+```bash
+cp /scratch/$USER/cargo-target/release/obikmer ~/bin/
+```
+
+## NUMA support
+
+NUMA-aware thread placement is active automatically on multi-socket Linux machines, detected at runtime via hwloc. No build flag is required — it falls back gracefully to a single-pool strategy on:
+
+- macOS (Apple Silicon, unified memory)
+- single-socket Linux machines
+- any system where hwloc reports only one NUMA node
+
+## Verifying the installation
+
+```bash
+obikmer --help
+```
diff --git a/UserDocMD/references.bib b/UserDocMD/references.bib
new file mode 100644
index 00000000..fca4c8bc
--- /dev/null
+++ b/UserDocMD/references.bib
@@ -0,0 +1,261 @@
+%% This BibTeX bibliography file was created using BibDesk.
+%% https://bibdesk.sourceforge.io/
+
+%% Created for Eric Coissac at 2026-04-18 08:19:36 +0200
+
+
+%% Saved with string encoding Unicode (UTF-8)
+
+
+
+@article{Zheng2020-ji,
+	abstract = {MOTIVATION: Minimizers are methods to sample k-mers from a
+               string, with the guarantee that similar set of k-mers will be
+               chosen on similar strings. It is parameterized by the k-mer
+               length k, a window length w and an order on the k-mers.
+               Minimizers are used in a large number of softwares and pipelines
+               to improve computation efficiency and decrease memory usage.
+               Despite the method's popularity, many theoretical questions
+               regarding its performance remain open. The core metric for
+               measuring performance of a minimizer is the density, which
+               measures the sparsity of sampled k-mers. The theoretical optimal
+               density for a minimizer is 1/w, provably not achievable in
+               general. For given k and w, little is known about asymptotically
+               optimal minimizers, that is minimizers with density O(1/w).
+               RESULTS: We derive a necessary and sufficient condition for
+               existence of asymptotically optimal minimizers. We also provide a
+               randomized algorithm, called the Miniception, to design
+               minimizers with the best theoretical guarantee to date on density
+               in practical scenarios. Constructing and using the Miniception is
+               as easy as constructing and using a random minimizer, which
+               allows the design of efficient minimizers that scale to the
+               values of k and w used in current bioinformatics software
+               programs. AVAILABILITY AND IMPLEMENTATION: Reference
+               implementation of the Miniception and the codes for analysis can
+               be found at https://github.com/kingsford-group/miniception.
+               SUPPLEMENTARY INFORMATION: Supplementary data are available at
+               Bioinformatics online.},
+	author = {Zheng, Hongyu and Kingsford, Carl and Mar{\c c}ais, Guillaume},
+	doi = {10.1093/bioinformatics/btaa472},
+	issn = {1367-4803,1367-4811},
+	journal = {Bioinformatics (Oxford, England)},
+	language = {en},
+	month = jul,
+	number = {Suppl_1},
+	pages = {i119--i127},
+	pmc = {PMC8248892},
+	pmid = 32657376,
+	publisher = {Oxford University Press (OUP)},
+	title = {Improved design and analysis of practical minimizers},
+	url = {http://dx.doi.org/10.1093/bioinformatics/btaa472},
+	volume = 36,
+	year = 2020,
+	bdsk-url-1 = {http://dx.doi.org/10.1093/bioinformatics/btaa472}}
+
+@article{Zheng2021-cc,
+	abstract = {MOTIVATION: Minimizers are efficient methods to sample k-mers
+               from genomic sequences that unconditionally preserve sufficiently
+               long matches between sequences. Well-established methods to
+               construct efficient minimizers focus on sampling fewer k-mers on
+               a random sequence and use universal hitting sets (sets of k-mers
+               that appear frequently enough) to upper bound the sketch size. In
+               contrast, the problem of sequence-specific minimizers, which is
+               to construct efficient minimizers to sample fewer k-mers on a
+               specific sequence such as the reference genome, is less studied.
+               Currently, the theoretical understanding of this problem is
+               lacking, and existing methods do not specialize well to sketch
+               specific sequences. RESULTS: We propose the concept of polar
+               sets, complementary to the existing idea of universal hitting
+               sets. Polar sets are k-mer sets that are spread out enough on the
+               reference, and provably specialize well to specific sequences.
+               Link energy measures how well spread out a polar set is, and with
+               it, the sketch size can be bounded from above and below in a
+               theoretically sound way. This allows for direct optimization of
+               sketch size. We propose efficient heuristics to construct polar
+               sets, and via experiments on the human reference genome, show
+               their practical superiority in designing efficient
+               sequence-specific minimizers. AVAILABILITY AND IMPLEMENTATION: A
+               reference implementation and code for analyses under an
+               open-source license are at
+               https://github.com/kingsford-group/polarset. SUPPLEMENTARY
+               INFORMATION: Supplementary data are available at Bioinformatics
+               online.},
+	author = {Zheng, Hongyu and Kingsford, Carl and Mar{\c c}ais, Guillaume},
+	doi = {10.1093/bioinformatics/btab313},
+	issn = {1367-4803,1367-4811},
+	journal = {Bioinformatics (Oxford, England)},
+	language = {en},
+	month = jul,
+	number = {Suppl\_1},
+	pages = {i187--i195},
+	pmc = {PMC8686682},
+	pmid = 34252928,
+	publisher = {Oxford University Press (OUP)},
+	title = {Sequence-specific minimizers via polar sets},
+	url = {http://dx.doi.org/10.1093/bioinformatics/btab313},
+	volume = 37,
+	year = 2021,
+	bdsk-url-1 = {http://dx.doi.org/10.1093/bioinformatics/btab313}}
+
+@article{Pan2024-hb,
+	abstract = {MOTIVATION: The minimizer concept is a data structure for
+               sequence sketching. The standard canonical minimizer selects a
+               subset of k-mers from the given DNA sequence by comparing the
+               forward and reverse k-mers in a window simultaneously according
+               to a predefined selection scheme. It is widely employed by
+               sequence analysis such as read mapping and assembly. k-mer
+               density, k-mer repetitiveness (e.g. k-mer bias), and
+               computational efficiency are three critical measurements for
+               minimizer selection schemes. However, there exist trade-offs
+               between kinds of minimizer variants. Generic, effective, and
+               efficient are always the requirements for high-performance
+               minimizer algorithms. RESULTS: We propose a simple minimizer
+               operator as a refinement of the standard canonical minimizer. It
+               takes only a few operations to compute. However, it can improve
+               the k-mer repetitiveness, especially for the lexicographic order.
+               It applies to other selection schemes of total orders (e.g.
+               random orders). Moreover, it is computationally efficient and the
+               density is close to that of the standard minimizer. The refined
+               minimizer may benefit high-performance applications like binning
+               and read mapping. AVAILABILITY AND IMPLEMENTATION: The source
+               code of the benchmark in this work is available at the github
+               repository https://github.com/xp3i4/mini\_benchmark.},
+	author = {Pan, Chenxu and Reinert, Knut},
+	doi = {10.1093/bioinformatics/btae045},
+	issn = {1367-4803,1367-4811},
+	journal = {Bioinformatics (Oxford, England)},
+	language = {en},
+	month = feb,
+	number = 2,
+	pmc = {PMC10868324},
+	pmid = 38269626,
+	publisher = {Oxford University Press (OUP)},
+	title = {A simple refined DNA minimizer operator enables 2-fold faster computation},
+	url = {http://dx.doi.org/10.1093/bioinformatics/btae045},
+	volume = 40,
+	year = 2024,
+	bdsk-url-1 = {http://dx.doi.org/10.1093/bioinformatics/btae045}}
+
+@article{Kille2023-px,
+	abstract = {MOTIVATION: The Jaccard similarity on k-mer sets has shown to be
+               a convenient proxy for sequence identity. By avoiding expensive
+               base-level alignments and comparing reduced sequence
+               representations, tools such as MashMap can scale to massive
+               numbers of pairwise comparisons while still providing useful
+               similarity estimates. However, due to their reliance on minimizer
+               winnowing, previous versions of MashMap were shown to be biased
+               and inconsistent estimators of Jaccard similarity. This directly
+               impacts downstream tools that rely on the accuracy of these
+               estimates. RESULTS: To address this, we propose the minmer
+               winnowing scheme, which generalizes the minimizer scheme by use
+               of a rolling minhash with multiple sampled k-mers per window. We
+               show both theoretically and empirically that minmers yield an
+               unbiased estimator of local Jaccard similarity, and we implement
+               this scheme in an updated version of MashMap. The minmer-based
+               implementation is over 10 times faster than the minimizer-based
+               version under the default ANI threshold, making it well-suited
+               for large-scale comparative genomics applications. AVAILABILITY
+               AND IMPLEMENTATION: MashMap3 is available at
+               https://github.com/marbl/MashMap.},
+	author = {Kille, Bryce and Garrison, Erik and Treangen, Todd J and Phillippy, Adam M},
+	doi = {10.1093/bioinformatics/btad512},
+	issn = {1367-4803,1367-4811},
+	journal = {Bioinformatics (Oxford, England)},
+	language = {en},
+	month = sep,
+	number = 9,
+	pmc = {PMC10505501},
+	pmid = 37603771,
+	publisher = {Oxford University Press (OUP)},
+	title = {Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation},
+	url = {http://dx.doi.org/10.1093/bioinformatics/btad512},
+	volume = 39,
+	year = 2023,
+	bdsk-url-1 = {http://dx.doi.org/10.1093/bioinformatics/btad512}}
+
+@incollection{Golan2025-xf,
+	address = {Cham},
+	author = {Golan, Shay and Shur, Arseny M},
+	booktitle = {Lecture Notes in Computer Science},
+	doi = {10.1007/978-3-031-82670-2\_25},
+	isbn = {9783031826696,9783031826702},
+	issn = {0302-9743,1611-3349},
+	language = {en},
+	pages = {347--360},
+	publisher = {Springer Nature Switzerland},
+	series = {Lecture Notes in Computer Science},
+	title = {Expected density of random minimizers},
+	url = {http://dx.doi.org/10.1007/978-3-031-82670-2_25},
+	year = 2025,
+	bdsk-url-1 = {http://dx.doi.org/10.1007/978-3-031-82670-2_25},
+	bdsk-url-2 = {http://dx.doi.org/10.1007/978-3-031-82670-2%5C_25}}
+
+@article{Mohamadi2017-ok,
+	abstract = {Motivation: Many bioinformatics algorithms are designed for the
+               analysis of sequences of some uniform length, conventionally
+               referred to as k -mers. These include de Bruijn graph assembly
+               methods and sequence alignment tools. An efficient algorithm to
+               enumerate the number of unique k -mers, or even better, to build
+               a histogram of k -mer frequencies would be desirable for these
+               tools and their downstream analysis pipelines. Among other
+               applications, estimated frequencies can be used to predict genome
+               sizes, measure sequencing error rates, and tune runtime
+               parameters for analysis tools. However, calculating a k -mer
+               histogram from large volumes of sequencing data is a challenging
+               task. Results: Here, we present ntCard, a streaming algorithm for
+               estimating the frequencies of k -mers in genomics datasets. At
+               its core, ntCard uses the ntHash algorithm to efficiently compute
+               hash values for streamed sequences. It then samples the
+               calculated hash values to build a reduced representation
+               multiplicity table describing the sample distribution. Finally,
+               it uses a statistical model to reconstruct the population
+               distribution from the sample distribution. We have compared the
+               performance of ntCard and other cardinality estimation
+               algorithms. We used three datasets of 480 GB, 500 GB and 2.4 TB
+               in size, where the first two representing whole genome shotgun
+               sequencing experiments on the human genome and the last one on
+               the white spruce genome. Results show ntCard estimates k -mer
+               coverage frequencies >15× faster than the state-of-the-art
+               algorithms, using similar amount of memory, and with higher
+               accuracy rates. Thus, our benchmarks demonstrate ntCard as a
+               potentially enabling technology for large-scale genomics
+               applications. Availability and Implementation: ntCard is written
+               in C ++ and is released under the GPL license. It is freely
+               available at https://github.com/bcgsc/ntCard. Contact:
+               hmohamadi@bcgsc.ca or ibirol@bcgsc.ca. Supplementary information:
+               Supplementary data are available at Bioinformatics online.},
+	author = {Mohamadi, Hamid and Khan, Hamza and Birol, Inanc},
+	date-modified = {2026-04-18 08:19:36 +0200},
+	doi = {10.1093/bioinformatics/btw832},
+	issn = {1367-4803,1367-4811},
+	journal = {Bioinformatics (Oxford, England)},
+	language = {en},
+	month = may,
+	number = 9,
+	pages = {1324--1330},
+	pmc = {PMC5408799},
+	pmid = 28453674,
+	publisher = {Oxford University Press (OUP)},
+	title = {ntCard: a streaming algorithm for cardinality estimation in genomics data},
+	url = {http://dx.doi.org/10.1093/bioinformatics/btw832},
+	volume = 33,
+	year = 2017,
+	bdsk-url-1 = {http://dx.doi.org/10.1093/bioinformatics/btw832}}
+
+@misc{Mash-distances-doc,
+	author = {{Marbl Lab}},
+	howpublished = {Mash documentation},
+	title = {Mash Distance},
+	url = {https://mash.readthedocs.io/en/latest/distances.html},
+	urldate = {2026-07-09},
+	year = 2026}
+
+@article{Fan2015-mash-formula,
+	author = {Fan, Huan and Ives, Anthony R and Surget-Groba, Yann and Cannon, Charles H},
+	doi = {10.1186/s12864-015-1647-5},
+	journal = {BMC Genomics},
+	number = 1,
+	title = {An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data},
+	url = {https://doi.org/10.1186/s12864-015-1647-5},
+	volume = 16,
+	year = 2015}
diff --git a/UserDocMD/theory/encoding.md b/UserDocMD/theory/encoding.md
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--- /dev/null
+++ b/UserDocMD/theory/encoding.md
@@ -0,0 +1,28 @@
+# DNA encoding
+
+## 2-bit nucleotide encoding
+
+Every nucleotide is encoded on 2 bits, most-significant-bit first within each word:
+
+| Base | Encoding |
+|------|----------|
+| A    | `00`     |
+| C    | `01`     |
+| G    | `10`     |
+| T    | `11`     |
+
+The Watson-Crick complement of a base is its bitwise NOT on 2 bits: $\text{complement}(base) = \lnot base \mathbin{\&} \texttt{0b11}$.
+
+## Kmer encoding
+
+A kmer of length $k$ ($k \le 31$) fits in a single 64-bit word. The first nucleotide occupies the two most significant bits, each following nucleotide occupies the next two bits, and unused low-order bits are zero. Extracting nucleotide i (0-indexed from the 5′ end) is a shift-and-mask operation.
+
+Reverse complement is computed by bit manipulation directly on the packed word, without any lookup table: complement every base, reverse the byte order, then reverse the order of 2-bit groups within each byte in two more passes, and finally realign the result to the most-significant bits.
+
+## Canonical form
+
+The canonical form of a kmer is the lexicographic minimum of the kmer and its reverse complement:
+
+$$\text{canonical}(kmer) = \min\big(kmer,\ \text{revcomp}(kmer)\big)$$
+
+Using the canonical form halves the kmer space and makes counting strand-independent: a kmer and its reverse complement are always treated as the same entity, regardless of which DNA strand was sequenced.
diff --git a/UserDocMD/theory/entropy_filter.md b/UserDocMD/theory/entropy_filter.md
new file mode 100644
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--- /dev/null
+++ b/UserDocMD/theory/entropy_filter.md
@@ -0,0 +1,36 @@
+# Low-complexity kmer filter
+
+Low-complexity kmers (homopolymer runs, tandem repeats) can dominate an index without carrying useful information. `obikmer` detects and excludes them during index construction using a normalized Shannon entropy score.
+
+## Sub-word frequencies
+
+For a kmer of length $k$ and a sub-word size $ws$ ($1 \le ws \le ws_{\max}$, default $ws_{\max} = 6$), the kmer is decomposed into its $k - ws + 1$ overlapping sub-words of length $ws$ by sliding a window across it. Each sub-word is tallied under its raw 2-bit-packed value, with no canonicalization.
+
+## Corrected Shannon entropy
+
+Let $f_j$ be the observed count of raw sub-word $j$, and $n_{\text{words}} = k - ws + 1$ the total number of sub-words. The entropy is:
+
+$$H_{\text{corr}} = \log(n_{\text{words}}) - \frac{1}{n_{\text{words}}} \sum_j f_j \log f_j$$
+
+## Small-sample correction
+
+Because only $n_{\text{words}}$ sub-words are observed among up to $4^{ws}$ possible values, the achievable maximum entropy $H_{\max}$ is bounded below $\log(4^{ws})$ for small samples. $H_{\max}$ is computed from the most uniform integer distribution achievable with $n_{\text{words}}$ observations over $4^{ws}$ categories. The normalized entropy is:
+
+$$\hat{H}(ws) = \frac{H_{\text{corr}}}{H_{\max}} \in [0, 1]$$
+
+A value near 0 indicates low complexity (e.g. a homopolymer run); near 1 indicates high complexity, characteristic of a random sequence.
+
+## Final score
+
+The filter evaluates $\hat{H}(ws)$ for every word size from 1 to ws_max and keeps the minimum:
+
+$$\text{entropy}(kmer) = \min_{ws=1}^{ws_{\max}} \hat{H}(ws)$$
+
+Taking the minimum across word sizes ensures that repetition at any scale is detected: a homopolymer is caught at $ws=1$, a dinucleotide repeat at $ws=2$, and so on. A kmer is rejected if its entropy score falls below a threshold $\theta$ (default 0.7), a configurable collection parameter.
+
+## Properties
+
+The entropy score depends only on the kmer sequence itself, not on where or how many times it occurs:
+
+- **Orientation invariance**: a kmer and its reverse complement always receive the same score.
+- **Context independence**: a given kmer is always accepted or always rejected, regardless of which genome or read it appears in. The filter defines a fixed partition of the kmer space into low-complexity and valid kmers.
diff --git a/UserDocMD/theory/indexing_architecture.md b/UserDocMD/theory/indexing_architecture.md
new file mode 100644
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--- /dev/null
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@@ -0,0 +1,32 @@
+# Partitioning and indexing architecture
+
+An index is split into a fixed number of **partitions**, each handling an independent, disjoint slice of the kmer space. Partitioning keeps the working set of each stage small enough to process efficiently and enables parallel construction and querying.
+
+## Routing
+
+The canonical minimizer of a super-kmer (see [Minimizer selection](minimizer_selection.md)) is hashed to produce a $p$-bit routing value that selects the destination partition:
+
+```
+canonical minimizer → hash(minimizer) → p-bit value → partition index
+```
+
+The routing value is recomputed whenever it is needed (during construction and again at query time) rather than stored — it is not part of the on-disk super-kmer representation.
+
+Within a partition, kmers are indexed as plain values via a minimal perfect hash function (see [On-disk storage](../formats/index_layout.md)); the minimizer plays no further role once a super-kmer has reached its partition.
+
+## Why hashing is necessary
+
+A canonical minimizer is an m-mer ($m \in \{9, 11, 13, 15\}$), and its distribution over all possible m-mer values is not uniform — as the lexicographic minimum of a window, small values are systematically over-represented [@Zheng2020-ji; @Zheng2021-cc; @Pan2024-hb; @Kille2023-px; @Golan2025-xf]. Routing directly on the raw minimizer value would therefore produce badly unbalanced partitions.
+
+Hashing the minimizer before routing redistributes this skewed distribution uniformly across partitions. This works reliably because the number of partition-index bits $p$ is chosen well below the number of bits available in the minimizer ($2m$): even with strong bias in the minimizer distribution, the hash has enough entropy margin to absorb it, provided the number of distinct minimizers actually observed is much larger than the number of partitions.
+
+## Parameter guidance
+
+| Minimizer size $m$ | Minimizer bits ($2m$) | Typical partition-index bits $p$ | Partitions |
+|----|-----------|-----------|------------|
+| 9  | 18        | 6–8       | 64–256     |
+| 11 | 22        | 8–10      | 256–1 024  |
+| 13 | 26        | 10–12     | 1 024–4 096|
+| 15 | 30        | 10–14     | 1 024–16 384|
+
+The number of partitions must satisfy $p \le 2m$, and in practice $p$ is chosen well below that bound to leave a comfortable entropy margin. For $k=31$, $m=13$, $p=10$ (1024 partitions), partition load is well balanced on real genomic data.
diff --git a/UserDocMD/theory/kmers_and_superkmers.md b/UserDocMD/theory/kmers_and_superkmers.md
new file mode 100644
index 00000000..4d482f86
--- /dev/null
+++ b/UserDocMD/theory/kmers_and_superkmers.md
@@ -0,0 +1,24 @@
+# Kmers and super-kmers
+
+## Kmers
+
+A **kmer** is a DNA subsequence of fixed length $k$. Two constraints apply to $k$, both enforced when a command starts (an invalid value exits immediately with an error):
+
+- $k \in [11, 31]$: long enough to be specific, short enough to fit in a single 64-bit word at 2 bits/base ($k \le 32$ is the hard limit; $k < 11$ gives insufficient specificity).
+- $k$ **is odd**: an odd-length sequence can never equal its own reverse complement, so the two orientations of any kmer are always distinct. This is required for the canonical form (see [DNA encoding](encoding.md)) to be well defined.
+
+## Super-kmers
+
+A **super-kmer** is a maximal run of consecutive, overlapping kmers from a read that share the same canonical minimizer (see [Minimizer selection](minimizer_selection.md)). Each kmer in the run overlaps the next by $k-1$ nucleotides. A super-kmer is capped at 256 nucleotides; a longer run is split at that boundary.
+
+For a random minimizer of length $m$ over kmers of length $k$, the expected length of a super-kmer is approximately [@Zheng2020-ji; @Golan2025-xf]:
+
+$$L_{\text{nt}} \approx \frac{k-m+2}{2} + k - 1$$
+
+For $k=31$, $m=13$ this is about 40 nucleotides; in practice super-kmers rarely exceed a few dozen nucleotides.
+
+### Canonical super-kmers
+
+A **canonical super-kmer** is the lexicographic minimum of a super-kmer and its reverse complement. When a read and its reverse complement are both encountered, they produce super-kmers that are reverse complements of each other; both reduce to the same canonical super-kmer, so a genomic region is represented once regardless of which strand was read.
+
+Super-kmers are the unit of work used throughout construction and querying: sequences are decomposed into super-kmers first, and every downstream step (partition routing, deduplication, counting) operates on them rather than on individual kmers.
diff --git a/UserDocMD/theory/minimizer_selection.md b/UserDocMD/theory/minimizer_selection.md
new file mode 100644
index 00000000..21940f34
--- /dev/null
+++ b/UserDocMD/theory/minimizer_selection.md
@@ -0,0 +1,42 @@
+# Minimizer selection
+
+## Definition
+
+A **minimizer** of a kmer window is the m-mer ($m < k$) that is smallest, among all $k - m + 1$ overlapping m-mers in the window, under a chosen ordering. The minimizer is always taken in canonical form (lexicographic minimum of forward and reverse complement) so that selection is strand-independent.
+
+The minimizer partitions a sequence into super-kmers: maximal runs of overlapping kmers that share the same minimizer (see [Kmers and super-kmers](kmers_and_superkmers.md)).
+
+## Hash-based ("random") minimizer
+
+`obikmer` selects minimizers by hash order rather than plain lexicographic order. Ordering m-mers lexicographically on their 2-bit encoding systematically favors AT-rich m-mers (an all-A m-mer always encodes to 0), which causes low-complexity regions to dominate as minimizers and produces unbalanced partitions.
+
+Instead, a well-distributed hash function $H$ is applied to the canonical (lexicographically minimal) form of each m-mer, and the m-mer with the smallest $H$ value wins. Because $H$ is a bijection with good avalanche properties, every distinct m-mer in a window has an equal chance of holding the minimum hash value, independent of its nucleotide composition.
+
+The canonical form used as input to $H$ is still the lexicographic minimum of forward/reverse-complement — hashing is applied on top of it, not used to redefine it. Defining canonicity by hash value instead would bias the *distribution of hash values themselves* toward small values (the minimum of two independent hashes is not uniformly distributed), reintroducing a bias one layer down.
+
+### Hash function
+
+The hash function is a 64-bit mixing function (splitmix64-style finalizer) applied to the m-mer XORed with a fixed non-zero seed:
+
+$$H(x) = \text{mix64}(x \oplus s), \quad s = \lfloor 2^{64}/\varphi \rfloor = \texttt{0x9e3779b97f4a7c15}$$
+
+```
+H(x):
+    x ← x  ⊕  0x9e3779b97f4a7c15
+    x ← x  ⊕  (x >> 30)
+    x ← x  ×  0xbf58476d1ce4e5b9
+    x ← x  ⊕  (x >> 27)
+    x ← x  ×  0x94d049bb133111eb
+    return x ⊕ (x >> 31)
+```
+
+The XOR seed avoids the finalizer's fixed point at 0 ($\text{mix64}(0) = 0$), which would otherwise make an all-A m-mer (canonical value 0) win every window comparison.
+
+## Partition routing is independent of minimizer selection
+
+The hash used to select a minimizer within a window (the minimum of several hash values) and the hash used to route a super-kmer to a storage partition are computed separately:
+
+- **Selection** uses $H$ applied to every candidate m-mer in the window, keeping the minimum.
+- **Partition routing** recomputes $H$ on the single selected minimizer only, once its position is fixed. This is a hash of one specific value, not the minimum of several, so it is uniformly distributed and safe to use directly for routing.
+
+See [Partitioning and indexing architecture](indexing_architecture.md) for how the routing value is turned into a partition index.
diff --git a/UserDocMD/usage/annotate.md b/UserDocMD/usage/annotate.md
new file mode 100644
index 00000000..4734657d
--- /dev/null
+++ b/UserDocMD/usage/annotate.md
@@ -0,0 +1,25 @@
+# annotate
+
+Add or update genome metadata of an index from a CSV file, or dump the current metadata as CSV.
+
+```bash
+obikmer annotate INDEX --csv FILE [OPTIONS]
+obikmer annotate INDEX --dump
+```
+
+## Arguments
+
+| Argument | Description |
+|---|---|
+| `INDEX` | Index directory to annotate (modified in place) |
+
+## Options
+
+| Option | Default | Description |
+|---|---|---|
+| `--csv` | — | CSV file of metadata to apply (must contain an id column); required unless `--dump` is used |
+| `--sep` | `,` | CSV field separator |
+| `--id-col` | `id` | Name of the column containing genome labels |
+| `--na-value` | `NA` | Value meaning "remove this field" (deletes the existing key if present) |
+| `--no-overwrite` | off | Do not overwrite existing metadata keys |
+| `--dump` | off | Print all genome metadata as CSV to stdout instead of applying a file |
diff --git a/UserDocMD/usage/distance.md b/UserDocMD/usage/distance.md
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+++ b/UserDocMD/usage/distance.md
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+# distance
+
+Compute pairwise distance matrices between the genomes stored in an index, optionally build trees (NJ/UPGMA), and optionally derive a central-position SNP model with exports for external phylogenetic tools (TNT, PhyG, IQ-TREE).
+
+```bash
+obikmer distance INDEX [OPTIONS]
+```
+
+## Arguments
+
+| Argument | Description |
+|---|---|
+| `INDEX` | Index directory |
+
+## Distance matrix
+
+| Option | Default | Description |
+|---|---|---|
+| `--metric` | `jaccard` | One of `jaccard`, `mash`, `hamming`, `bray-curtis`, `relfreq-bray-curtis`, `euclidean`, `relfreq-euclidean`, `hellinger`, `hellinger-euclidean` |
+| `--presence-threshold` | `1` | Minimum count for a kmer to be considered present, for Jaccard/Mash on a count index |
+| `--shared-kmers` | off | Also write the shared-kmer count matrix |
+| `--nj` | off | Compute and write a Neighbor-Joining tree (Newick) |
+| `--upgma` | off | Compute and write a UPGMA tree (Newick) |
+| `-o, --output` | none (stdout) | Output file prefix; without it, the distance matrix is printed to stdout as CSV |
+
+`hamming` requires a presence/absence index. All other metrics work on either index type; on a presence index, `jaccard`/`mash`/`hamming` are the only ones available.
+
+### Metric definitions
+
+- **jaccard**: $D = 1 - \dfrac{|A \cap B|}{|A \cup B|}$ over the sets of kmers present in each genome.
+- **mash**: derived from the Jaccard distance via $D = -\dfrac{1}{k} \ln\!\left(\dfrac{2J}{1+J}\right)$ where $J = 1 - D_{\text{jaccard}}$ and $k$ is the index's kmer size; clamped to 1.0 when $J \le 0$.
+- **hamming**: number of kmer positions where presence differs between the two genomes (presence index only, not normalized): $D = \sum_i \mathbb{1}[a_i \ne b_i]$.
+- **bray-curtis**: $D = 1 - \dfrac{2 \sum_i \min(c_i^A, c_i^B)}{\sum_i c_i^A + \sum_i c_i^B}$ on raw per-kmer counts.
+- **relfreq-bray-curtis**: the same formula computed on per-genome relative frequencies $p_i = c_i / \sum_j c_j$ instead of raw counts.
+- **euclidean**: $D = \sqrt{\sum_i (c_i^A - c_i^B)^2}$ on raw counts.
+- **relfreq-euclidean**: the same formula on relative frequencies.
+- **hellinger**: $D = \dfrac{1}{\sqrt{2}} \sqrt{\sum_i \left(\sqrt{p_i^A} - \sqrt{p_i^B}\right)^2}$ on relative frequencies, bounded in $[0, 1]$.
+- **hellinger-euclidean**: the unnormalized variant, $D = \sqrt{2} \times D_{\text{hellinger}}$.
+
+## Central-position SNP model
+
+This is a separate operation from the distance-matrix computation above: if any option below is used, no `--metric` matrix is computed in the same invocation.
+
+A **family** is the set of up to 4 kmers that share identical flanking sequence and differ only at the exact central base. Because $k$ is odd, the central position is well defined and maps to itself under reverse complementation. All computations below first require building the **sibling annex**, an index-wide record of which of the 4 possible central bases are observed at each family, across every genome.
+
+| Option | Default | Description |
+|---|---|---|
+| `--sibling-annex` | off | Build the sibling presence-mask annex (prerequisite for every option below) |
+| `--exclude-genome LABEL` | none | Exclude a genome (repeatable) from every SNP/Sankoff/export computation below |
+| `--sibling-stats` | off | Write the family-size (sibling count) distribution, per genome and globally |
+| `--raw-snp-distance` | off | Write the single-copy central-SNP p-distance matrix |
+| `--raw-snp-counts` | off | Write per-pair diagnostic counts (n_snp, n_shared, n_eligible) instead of a matrix |
+| `--snp` | off | Write a SNP-only pseudo-alignment in FASTA, IUPAC-coded |
+
+### Locus eligibility
+
+A family is eligible for a genome pair $(i, j)$ only if genome $i$ carries exactly one of the family's observed forms (single-copy, unambiguous) and genome $j$ also carries exactly one. A genome carrying more than one form at a locus makes that locus ineligible for any pair involving it.
+
+`--raw-snp-distance` tallies, over every eligible locus of every genome pair, $n_{\text{snp}}$ (the two genomes' single forms differ) versus $n_{\text{shared}}$ (they agree — this includes invariant families). The output ratio is $\hat{p} = \dfrac{n_{\text{snp}}}{n_{\text{snp}} + n_{\text{shared}}}$.
+
+`--snp` restricts itself to *variable* families (family size $\ge 2$) and writes one FASTA record per genome, one column per family, IUPAC-coded from each genome's presence mask at that family (a single form → the plain base; several forms → the matching IUPAC ambiguity code; no form → `-`).
+
+`--exclude-genome` removes a genome from these computations, re-checking column variability among the remaining genomes so that a column made monomorphic by the exclusion is dropped rather than kept artificially. It does not affect the `--metric` distance-matrix path.
+
+## Sankoff calibration and phylogenetic exports
+
+| Option | Default | Description |
+|---|---|---|
+| `--sankoff` | off | Calibrate a 16-state parsimony cost matrix and matching pseudo-alignment |
+| `--sankoff-ratio-ceiling` | `0.5` | Exclude genome pairs whose raw SNP ratio exceeds this value from the calibration |
+| `--tnt` | off | Also write a TNT script (implies `--sankoff`) |
+| `--phyg` | off | Also write PhyG input files (implies `--sankoff`) |
+| `--iqtree` | off | Also write an IQ-TREE custom model and alignment (implies `--sankoff`) |
+| `--sankoff-cost-scale` | `100` | Integer scaling factor applied to costs before rounding (required by TNT/PhyG's integer-only cost commands) |
+
+### The 16-state model
+
+Each family is treated as a character with 16 possible states: one per subset of the 4 possible central bases actually observed (including the empty subset). Calibration combines two tallies, both restricted to genome pairs at or below `--sankoff-ratio-ceiling`:
+
+- a $5 \times 5$ transition matrix over family cardinality (0–4 observed forms) between paired genomes, and
+- a $4 \times 4$ base-substitution transition matrix from unambiguous single-copy loci,
+
+which are combined into a row-normalized $16 \times 16$ transition probability matrix $P$, converted to a symmetric cost matrix via $\text{cost}(a,b) = -\ln P(a,b)$.
+
+`--sankoff` alone writes the cost matrix, the calibration parameters, and a pseudo-alignment recoded so the empty state uses the symbol `0` (never a gap character, to avoid ambiguity with external tools' own gap semantics). It does not run any external tool.
+
+### Exports
+
+All three exports reuse the `--sankoff` calibrated matrix and pseudo-alignment, recoded for the target tool:
+
+- **`--tnt`**: a self-contained TNT script (alignment recoded to TNT's fixed 16-symbol alphabet, integer-scaled cost matrix re-closed to a metric, a default search block).
+- **`--phyg`**: a custom cost-matrix file plus a PhyG script reusing the `--sankoff` alignment directly.
+- **`--iqtree`**: a custom substitution-model file (exchangeability matrix recovered as $R(a,b) = e^{-\text{cost}(a,b)}$, plus empirical state frequencies) and a matching alignment, for maximum-likelihood inference with real branch lengths (unlike the parsimony step-counts from TNT/PhyG). Only states actually occurring in the alignment are kept and compactly renumbered.
+
+## Output files
+
+With `-o/--output PREFIX`, the relevant subset of the following files is written: `<prefix>_dist.csv`, `<prefix>_shared.csv`, `<prefix>_nj.nwk`, `<prefix>_upgma.nwk`, `<prefix>_siblings.csv`, `<prefix>_rawsnp.csv`, `<prefix>_rawsnp_counts.csv`, `<prefix>_snp.fasta`, `<prefix>_sankoff_matrix.csv`, `<prefix>_sankoff_params.yaml`, `<prefix>_sankoff.fasta`, `<prefix>_sankoff.tnt`, `<prefix>_sankoff.tcm`, `<prefix>_sankoff.pg`, `<prefix>_iqtree.model`, `<prefix>_iqtree.fasta`. Without `-o`, only the plain `--metric` distance matrix is produced, on stdout.
diff --git a/UserDocMD/usage/dump.md b/UserDocMD/usage/dump.md
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+++ b/UserDocMD/usage/dump.md
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+# dump
+
+Dump all kmers of an index as CSV, one row per kmer, with per-genome counts or presence.
+
+```bash
+obikmer dump INDEX [OPTIONS]
+```
+
+## Arguments
+
+| Argument | Description |
+|---|---|
+| `INDEX` | Index directory to dump |
+
+## Options
+
+| Option | Default | Description |
+|---|---|---|
+| `--force-presence` | off | Output presence/absence (0/1) even if the index stores counts |
+| `--debug` | off | Prefix each row with the partition and layer columns |
+| `--head N` | none | Limit output to the first N kmers |
+
+`dump` also accepts the shared [predicate options](filter.md#predicate-options) (`--ingroup`, `--outgroup`, `--min-count`, etc.) to restrict which kmers are dumped.
+
+Output is CSV on stdout.
diff --git a/UserDocMD/usage/estimate.md b/UserDocMD/usage/estimate.md
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+# estimate
+
+Estimate approximate-index parameters (z, evidence bits, false-positive rate) before building an index with `--approx`, without touching any files.
+
+```bash
+obikmer estimate [OPTIONS]
+```
+
+## Options
+
+| Option | Default | Description |
+|---|---|---|
+| `-k, --kmer-size` | `31` | Kmer size used at query time (matches `index`'s `--kmer-size`) |
+| `-z, --findere-z` | none | Findere z parameter |
+| `--evidence-bits` | none | Fingerprint bits per slot (b) |
+| `--fp` | none | Target false-positive rate per z-window |
+
+Any two of `-z`, `--evidence-bits`, `--fp` may be given; the third is derived using the same model as `index --approx` and `reindex --approx` ($FP = 1 / 2^{b \cdot z}$). The report printed to stdout includes: query $k$, effective indexed $k$ ($k-z+1$), $z$, evidence bits, per-kmer false-positive rate, and per-z-window false-positive rate.
diff --git a/UserDocMD/usage/filter.md b/UserDocMD/usage/filter.md
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+++ b/UserDocMD/usage/filter.md
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+# filter
+
+Apply row-level selection to an index: retain only kmers matching ingroup/outgroup predicates over genome membership, plus optional total-count and complexity thresholds. The output is a new, single-layer index.
+
+```bash
+obikmer filter SOURCE -o OUTPUT [OPTIONS]
+```
+
+## Arguments
+
+| Argument | Description |
+|---|---|
+| `SOURCE` | Source index directory |
+
+## Options
+
+| Option | Default | Description |
+|---|---|---|
+| `-o, --output` | — (required) | Output index directory |
+| `-f, --force` | off | Overwrite an existing output directory |
+| `--presence` | off | Output presence/absence instead of counts |
+| `--min-total-count` | none | Minimum total count across all genomes (count index only) |
+| `--max-total-count` | none | Maximum total count across all genomes |
+| `--min-complexity` | none | Minimum normalized entropy (same score as `--theta` at index build time), recomputed from the stored unitig sequences |
+| `--complexity-level-max` | `6` | Maximum sub-word size for the complexity score (used only with `--min-complexity`) |
+
+## Predicate options
+
+| Option | Default | Description |
+|---|---|---|
+| `--ingroup` | none | Ingroup predicate (repeatable; each occurrence is ANDed) |
+| `--outgroup` | none | Outgroup predicate (repeatable; each occurrence is ORed) |
+| `--min-count` | 0, or group size + N if negative | Minimum number of ingroup genomes carrying the kmer |
+| `--max-count` | ingroup group size | Maximum number of ingroup genomes carrying the kmer |
+| `--min-frac` | `1.0` if `--ingroup` given without an explicit quorum, else `0.0` | Minimum fraction of ingroup genomes |
+| `--max-frac` | `1.0` | Maximum fraction of ingroup genomes |
+| `--min-outgroup-count` | `0` | Minimum number of outgroup genomes carrying the kmer |
+| `--max-outgroup-count` | `0` if `--outgroup` given without an explicit quorum, else outgroup group size | Maximum number of outgroup genomes |
+| `--min-outgroup-frac` | `0.0` | Minimum fraction of outgroup genomes |
+| `--max-outgroup-frac` | `1.0` | Maximum fraction of outgroup genomes |
+| `--presence-threshold` | `0` | Minimum count for a genome to be considered a carrier of a kmer |
+
+See [Genome predicates and taxonomy paths](predicates.md) for the predicate syntax used by `--ingroup`/`--outgroup`.
+
+A negative `--min-count`/`--max-count` is interpreted as an offset from the group size — e.g. `--min-count=-1` means "all but one".
+
+Declaring `--ingroup` with no explicit ingroup quorum flag implicitly sets `--min-frac 1.0` (present in every ingroup genome). Declaring `--outgroup` with no explicit outgroup quorum flag implicitly sets `--max-outgroup-count 0` (absent from every outgroup genome). Any explicit quorum flag for a group disables that group's implicit default.
diff --git a/UserDocMD/usage/index_command.md b/UserDocMD/usage/index_command.md
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+# index
+
+Build a genome index from one or more sequence files. Construction proceeds in phases (scatter → dereplicate → count → layered MPHF), described in [On-disk storage](../formats/index_layout.md).
+
+```bash
+obikmer index -o OUTPUT [OPTIONS] [INPUTS...]
+```
+
+## Arguments
+
+| Argument | Description |
+|---|---|
+| `INPUTS...` | Input sequence files or directories (FASTA/FASTQ/GenBank, gzip optional). If omitted, reads from stdin. |
+
+## Options
+
+| Option | Default | Description |
+|---|---|---|
+| `-o, --output` | — (required) | Output index directory |
+| `--force` | off | Overwrite an existing output directory |
+| `--label` | input file name without extension | Genome label stored in the index |
+| `--meta KEY=VALUE` | none | Attach a categorical metadata field to the genome (repeatable) |
+| `-k, --kmer-size` | `31` | Kmer size (odd, in [11, 31]) |
+| `-m, --minimizer-size` | `11` | Minimizer size (odd, in $[3, k-1]$) |
+| `--theta` | `0.7` | Entropy threshold for the low-complexity filter |
+| `--level-max` | `6` | Maximum sub-word size for the entropy score |
+| `-p, --partitions` | `256` | Number of partitions (rounded up to a power of 2) |
+| `-T, --threads` | detected core count | Number of worker threads |
+| `--max-open-files` | `threads / 4` (min 1) | Maximum number of input files open simultaneously |
+| `--min-abundance` | `1` | Minimum abundance (inclusive) for a kmer to be retained |
+| `--max-abundance` | none | Maximum abundance (inclusive) |
+| `--with-counts` | off | Store per-kmer counts; otherwise only presence/absence is stored |
+| `--keep-intermediate` | off | Keep intermediate build files instead of deleting them after construction |
+| `--approx` | off | Use approximate evidence (Findere fingerprint) instead of exact evidence |
+| `-z, --findere-z` | see below | Findere z parameter: number of consecutive kmers that must all match (approximate evidence only) |
+| `--evidence-bits` | see below | Fingerprint bits per slot (b), approximate evidence only |
+| `--fp` | see below | Target false-positive rate per z-window, approximate evidence only |
+| `--block-size` | `1` | Block size, in unitigs, for the exact on-disk index (rounded up to a power of 2) |
+
+## Exact vs. approximate evidence
+
+By default, an index stores **exact** evidence: a kmer is either present or absent (or has an exact count with `--with-counts`), with no false positives.
+
+With `--approx`, evidence is stored as a compact **fingerprint** instead, trading a small, tunable false-positive rate for reduced memory/disk usage. The false-positive model is:
+
+$$FP = \frac{1}{2^{b \cdot z}}$$
+
+where $b$ is `--evidence-bits` and $z$ is `--findere-z`. Any two of `-z`, `--evidence-bits`, `--fp` can be given and the third is derived; if none are given, defaults are $b=8$, $z=1$ ($FP \approx 1/256$). See [`estimate`](estimate.md) to explore this trade-off before building an index, and [`reindex`](reindex.md) to convert an existing index between the two representations.
+
+`z` must be strictly less than k: the effective indexed kmer length under approximate evidence is k−z+1.
diff --git a/UserDocMD/usage/merge.md b/UserDocMD/usage/merge.md
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+# merge
+
+Merge multiple built indexes into a single index.
+
+```bash
+obikmer merge -o OUTPUT SOURCE... [OPTIONS]
+```
+
+## Arguments
+
+| Argument | Description |
+|---|---|
+| `SOURCE...` | Index directories to merge (at least one required) |
+
+## Options
+
+| Option | Default | Description |
+|---|---|---|
+| `-o, --output` | — (required) | Output index directory |
+| `--force` | off | Overwrite an existing output directory |
+| `--force-presence` | off | Store the merged index as presence/absence even if all sources have counts |
+| `--rename-duplicates` | off | Disambiguate duplicate genome labels (`.1`, `.2`, …) instead of failing |
+| `--budget-fraction` | `0.5` | Fraction of available RAM reserved as the memory budget for parallel partition merging |
+
+## Behaviour
+
+The output mode is chosen automatically: if every source index stores counts, the merged index stores counts too; otherwise it is presence/absence. `--force-presence` forces presence/absence regardless of the sources.
+
+By default, merging two indexes that share a genome label fails with an error; `--rename-duplicates` instead appends a numeric suffix to keep both copies.
diff --git a/UserDocMD/usage/pack.md b/UserDocMD/usage/pack.md
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+# pack
+
+Pack an index's per-column matrix files into a single-file format to reduce query-time I/O (fewer file opens per query).
+
+```bash
+obikmer pack INDEX
+```
+
+## Arguments
+
+| Argument | Description |
+|---|---|
+| `INDEX` | Index directory to pack (modified in place) |
+
+The index directory is locked for exclusive access while packing.
diff --git a/UserDocMD/usage/predicates.md b/UserDocMD/usage/predicates.md
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+# Genome predicates and taxonomy paths
+
+Several commands ([`filter`](filter.md), [`select`](select.md), [`dump`](dump.md), [`unitig`](unitig.md)) select or group genomes using the same predicate language over genome metadata (see [`annotate`](annotate.md) for attaching metadata to a genome).
+
+## Predicate syntax
+
+| Form | Meaning |
+|---|---|
+| `*` or `all` | Matches every genome (case-insensitive) |
+| `key=v1\|v2` | Genome's `key` metadata equals one of the listed values |
+| `key!=v` | Genome's `key` metadata does not equal `v` |
+| `key~path` | Genome's `key` metadata (a taxonomy path) matches `path` (ancestry match) |
+| `key!~path` | Genome's `key` metadata does not match `path` |
+
+A genome whose metadata does not contain `key` at all cannot be classified by that predicate and is excluded from the relevant group's quorum count.
+
+Multiple `--ingroup` predicates are combined with AND; multiple `--outgroup` predicates are combined with OR. When both an ingroup and an outgroup predicate would match the same genome, ingroup classification wins.
+
+## Taxonomy paths
+
+A metadata value is treated as a taxonomy path when it starts with the literal prefix `taxonomy:/`; any other value is treated as a plain string and only supports `=`/`!=`.
+
+```
+taxonomy:/segment1@rank1/segment2@rank2/...
+```
+
+Each segment is a name, optionally annotated with a rank (e.g. `@family`, `@genus`, `@species`); ranks are optional and can be mixed within a path. The `@` character is reserved inside taxonomy paths and cannot appear in segment names or rank labels.
+
+### Path matching (`~` / `!~`)
+
+Matching compares segment names only (ranks are informational, not part of the match), with anchoring controlled by leading/trailing `/`:
+
+| Pattern | Matches |
+|---|---|
+| `A/B` | anywhere in the path |
+| `/A/B` | at the start of the path (prefix) |
+| `A/B$` | at the end of the path (suffix) |
+| `/A/B$` | the entire path (exact) |
+
+A rank-qualified query, `key@rank=value`, matches only when the path's segment at that specific rank equals `value`.
+
+### Example
+
+```bash
+obikmer filter source -o output --ingroup "taxon~/Betulaceae/Betula"
+```
diff --git a/UserDocMD/usage/query.md b/UserDocMD/usage/query.md
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+# query
+
+Query an index with sequences and annotate each query with the kmer matches found.
+
+```bash
+obikmer query INDEX INPUTS... [OPTIONS]
+```
+
+## Arguments
+
+| Argument | Description |
+|---|---|
+| `INDEX` | Index directory to query against |
+| `INPUTS...` | Input sequence files (FASTA/FASTQ, gzip optional); at least one required |
+
+## Options
+
+| Option | Default | Description |
+|---|---|---|
+| `--detail` | off | Report per-position, per-genome coverage vectors in the output |
+| `--count-missing` | off | Also count query kmers absent from the index |
+| `--force-presence` | off | Report presence (0/1) per genome instead of raw counts |
+| `--presence-threshold` | `1` | Minimum accumulated count to declare a genome present (implies `--force-presence`) |
+| `-z, --findere-z` | derived from the index metadata | Override the Findere z parameter |
+| `-T, --threads` | detected core count | Number of worker threads |
+| `--chunk-size` | auto-sized (available RAM ÷ threads, clamped to 4–256 MiB) | I/O chunk size, in MiB |
+| `--max-open-files` | `threads / 4` (min 1) | Maximum number of input files open simultaneously |
+
+## Output
+
+FASTA on stdout, one record per query, annotated in the OBITools-style header format `>id {"key":value,...}`:
+
+- `kmer_count`: total number of kmers matched
+- `kmer_missing`: number of query kmers absent from the index (only with `--count-missing`)
+- `kmer_strict_matches`: per-genome match counts
+- `coverage`: per-position, per-genome coverage vectors (only with `--detail`)
+
+`--mismatch` is accepted by the CLI but not currently functional; using it produces a warning and is ignored.
diff --git a/UserDocMD/usage/reindex.md b/UserDocMD/usage/reindex.md
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+# reindex
+
+Convert an existing index's evidence representation in place, between exact and approximate.
+
+```bash
+obikmer reindex INDEX [OPTIONS]
+```
+
+## Arguments
+
+| Argument | Description |
+|---|---|
+| `INDEX` | Index directory to convert (modified in place) |
+
+## Options
+
+| Option | Default | Description |
+|---|---|---|
+| `--approx` | off | Convert to approximate evidence (default direction is approximate → exact); requires `-z`/`--evidence-bits`/`--fp` |
+| `-z, --findere-z` | none | Findere z parameter (≥ 1) |
+| `--evidence-bits` | none | Fingerprint bits per slot (b) |
+| `--fp` | none | Target false-positive rate per z-window |
+| `--block-size` | `1` | Block size for the exact on-disk index (ignored when converting to approximate) |
+
+See [`index`](index_command.md#exact-vs-approximate-evidence) for the exact/approximate trade-off and the underlying false-positive model, and [`estimate`](estimate.md) to explore parameters beforehand. The index directory is locked for exclusive access during conversion.
diff --git a/UserDocMD/usage/select.md b/UserDocMD/usage/select.md
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+# select
+
+Project and/or aggregate the genome columns of an index into a new (or in-place) index. Where [`filter`](filter.md) selects rows (kmers), `select` operates on columns (genomes): grouping several genomes into one aggregated column, reordering columns, or dropping some.
+
+```bash
+obikmer select SOURCE (--output OUTPUT | --in-place) [OPTIONS]
+```
+
+## Arguments
+
+| Argument | Description |
+|---|---|
+| `SOURCE` | Source index directory |
+
+## Options
+
+| Option | Default | Description |
+|---|---|---|
+| `--output` | — | Output index directory (mutually exclusive with `--in-place`) |
+| `--in-place` | off | Rewrite the source index in place (mutually exclusive with `--output`) |
+| `-f, --force` | off | Overwrite an existing output directory |
+| `--group NAME:PRED` | none | Define a named group of genomes by predicate (repeatable; mutually exclusive with `--aggregate-by`) |
+| `--group-op NAME:OP` | none | Aggregation operator for a named group |
+| `--aggregate-by KEY` | none | Automatically create one group per distinct value of a metadata key (mutually exclusive with `--group`) |
+| `--aggregate-op OP` | none | Aggregation operator applied to every auto-generated group |
+| `--select COL,...` | all columns | Output columns, in order (group names or genome labels) |
+| `--presence-threshold` | `0` | Minimum count for a genome to be considered a carrier (logical operators only) |
+
+## Aggregation operators
+
+`any`, `all`, `none` (logical, evaluated against `--presence-threshold`), `sum`, `min`, `max` (numeric, count index only). If a group's operator is left unspecified, it defaults to `any` when the source is a presence/absence index and `sum` when it stores counts.
+
+A `select` never changes the underlying kmer set — only the per-genome data (counts or presence) is rewritten, so an unaggregated pass-through column (a plain genome label in `--select`) is a cheap copy.
+
+At least one of `--output`/`--in-place` is required, and at least one output column must be defined; every name listed in `--select` must resolve to either a defined group or an existing genome label. See [Genome predicates and taxonomy paths](predicates.md) for the predicate syntax used by `--group`.
diff --git a/UserDocMD/usage/superkmer.md b/UserDocMD/usage/superkmer.md
new file mode 100644
index 00000000..eafacbd1
--- /dev/null
+++ b/UserDocMD/usage/superkmer.md
@@ -0,0 +1,27 @@
+# superkmer
+
+Extract super-kmers from one or more sequence files and write them to stdout, without building a full index. Useful for inspecting or piping the super-kmer decomposition of a dataset.
+
+```bash
+obikmer superkmer [OPTIONS] [INPUTS...]
+```
+
+## Arguments
+
+| Argument | Description |
+|---|---|
+| `INPUTS...` | Input sequence files or directories (FASTA/FASTQ/GenBank, gzip optional). If omitted, reads from stdin. |
+
+## Options
+
+| Option | Default | Description |
+|---|---|---|
+| `-k, --kmer-size` | `31` | Kmer size (must be odd, in [11, 31]) |
+| `-m, --minimizer-size` | `11` | Minimizer size (must be odd, in $[3, k-1]$) |
+| `--theta` | `0.7` | Entropy threshold; kmers with a normalized entropy at or below this value are excluded |
+| `--level-max` | `6` | Maximum sub-word size used for the entropy score |
+| `-p, --partitions` | `256` | Number of partitions (rounded up to the next power of 2) |
+| `-T, --threads` | detected core count | Number of worker threads |
+| `--max-open-files` | `threads / 4` (min 1) | Maximum number of input files open simultaneously |
+
+Output is written to stdout in the internal scatter format used by `index`; it is primarily intended to be piped into other tools or inspected for debugging.
diff --git a/UserDocMD/usage/unitig.md b/UserDocMD/usage/unitig.md
new file mode 100644
index 00000000..50a9dda6
--- /dev/null
+++ b/UserDocMD/usage/unitig.md
@@ -0,0 +1,19 @@
+# unitig
+
+Dump the unitigs of an index as FASTA. A unitig is a maximal non-branching path through the de Bruijn graph implied by the index's kmers; the concatenation of every unitig reconstructs every stored kmer exactly once.
+
+```bash
+obikmer unitig INDEX [OPTIONS]
+```
+
+## Arguments
+
+| Argument | Description |
+|---|---|
+| `INDEX` | Index directory |
+
+## Options
+
+`unitig` accepts the shared [predicate options](filter.md#predicate-options) (`--ingroup`, `--outgroup`, `--min-count`, etc.) to restrict which kmers are included before the unitigs are enumerated.
+
+Output is FASTA on stdout.
diff --git a/UserDocMD/usage/utils.md b/UserDocMD/usage/utils.md
new file mode 100644
index 00000000..38654c8f
--- /dev/null
+++ b/UserDocMD/usage/utils.md
@@ -0,0 +1,26 @@
+# utils
+
+Miscellaneous index maintenance and inspection utilities.
+
+```bash
+obikmer utils INDEXES... [OPTIONS]
+```
+
+## Arguments
+
+| Argument | Description |
+|---|---|
+| `INDEXES...` | One or more index directories |
+
+## Options
+
+| Option | Scope | Description |
+|---|---|---|
+| `--new-label NEW=OLD` | single index only | Rename a genome label |
+| `--upgrade-index` | single index only | Add any missing layer metadata files to an older index |
+| `--bits-per-kmer` | single index only | Print bits-per-kmer statistics |
+| `--stats` | single index only | Print per-genome kmer counts as CSV |
+| `--partition-stats` | one or more indexes | Print a partition-size distribution report |
+| `--csv FILE` | with `--partition-stats` | Also write raw per-(partition, source) data to FILE as CSV |
+
+At least one operation option must be given. All options except `--partition-stats` require exactly one index directory.
diff --git a/mkdocs-user.yml b/mkdocs-user.yml
new file mode 100644
index 00000000..1c9d1842
--- /dev/null
+++ b/mkdocs-user.yml
@@ -0,0 +1,61 @@
+site_name: obikmer — User Guide
+docs_dir: UserDocMD
+site_dir: doc-user
+
+theme:
+  name: material
+
+plugins:
+  - mermaid2:
+  - bibtex:
+      bib_file: UserDocMD/references.bib
+      csl_file: UserDocMD/ecology-letters.csl
+      enable_inline_citations: false
+
+markdown_extensions:
+  - admonition
+  - footnotes
+  - tables
+  - pymdownx.superfences:
+      custom_fences:
+        - name: mermaid
+          class: mermaid
+          format: !!python/name:pymdownx.superfences.fence_code_format
+  - pymdownx.arithmatex:
+      generic: true
+
+extra_javascript:
+  - https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js
+
+nav:
+  - Home: index.md
+  - Installation: installation.md
+  - Theory:
+      - Kmers and super-kmers: theory/kmers_and_superkmers.md
+      - DNA encoding: theory/encoding.md
+      - Low-complexity kmer filter: theory/entropy_filter.md
+      - Minimizer selection: theory/minimizer_selection.md
+      - Partitioning and indexing architecture: theory/indexing_architecture.md
+  - Usage:
+      - superkmer: usage/superkmer.md
+      - index: usage/index_command.md
+      - merge: usage/merge.md
+      - filter: usage/filter.md
+      - select: usage/select.md
+      - query: usage/query.md
+      - dump: usage/dump.md
+      - annotate: usage/annotate.md
+      - distance: usage/distance.md
+      - unitig: usage/unitig.md
+      - estimate: usage/estimate.md
+      - reindex: usage/reindex.md
+      - utils: usage/utils.md
+      - pack: usage/pack.md
+      - Predicates and taxonomy paths: usage/predicates.md
+  - Formats:
+      - Index construction and on-disk layout: formats/index_layout.md
+  - Architecture notes: architecture.md
+
+watch:
+  - UserDocMD
+  - mkdocs-user.yml
-- 
2.54.0


From 8967a20ed7298dd92579c416c292ab502ba64c2a Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Thu, 13 Aug 2026 10:12:00 +0200
Subject: [PATCH 07/46] refactor(cmd): restructure modules and decompose query
 command

Convert single-file modules to directory-based layouts across the cmd crate. Decompose the monolithic query command into dedicated submodules for batching, chunk processing, sparse finding, and output formatting. Introduce a new utils module to handle index management operations including statistics reporting, label renaming, and partition analysis.
---
 .../src/cmd/{annotate.rs => annotate/mod.rs}  |   0
 src/obikmer/src/cmd/{dump.rs => dump/mod.rs}  |   0
 .../src/cmd/{estimate.rs => estimate/mod.rs}  |   0
 .../src/cmd/{filter.rs => filter/mod.rs}      |   0
 .../src/cmd/{index.rs => index/mod.rs}        |   0
 .../src/cmd/{merge.rs => merge/mod.rs}        |   0
 src/obikmer/src/cmd/{pack.rs => pack/mod.rs}  |   0
 src/obikmer/src/cmd/query.rs                  | 851 ------------------
 src/obikmer/src/cmd/query/batch.rs            |  74 ++
 src/obikmer/src/cmd/query/chunk.rs            | 288 ++++++
 src/obikmer/src/cmd/query/findere.rs          |  71 ++
 src/obikmer/src/cmd/query/mod.rs              | 340 +++++++
 src/obikmer/src/cmd/query/output.rs           |  50 +
 src/obikmer/src/cmd/query/smer_index.rs       |  41 +
 .../cmd/{tests/query.rs => query/tests.rs}    |   7 +-
 .../src/cmd/{reindex.rs => reindex/mod.rs}    |   0
 .../src/cmd/{select.rs => select/mod.rs}      |   0
 .../cmd/{superkmer.rs => superkmer/mod.rs}    |   0
 .../src/cmd/{unitig.rs => unitig/mod.rs}      |   0
 src/obikmer/src/cmd/utils/maintenance.rs      | 112 +++
 src/obikmer/src/cmd/utils/mod.rs              |  85 ++
 .../{utils.rs => utils/partition_stats.rs}    | 196 +---
 22 files changed, 1069 insertions(+), 1046 deletions(-)
 rename src/obikmer/src/cmd/{annotate.rs => annotate/mod.rs} (100%)
 rename src/obikmer/src/cmd/{dump.rs => dump/mod.rs} (100%)
 rename src/obikmer/src/cmd/{estimate.rs => estimate/mod.rs} (100%)
 rename src/obikmer/src/cmd/{filter.rs => filter/mod.rs} (100%)
 rename src/obikmer/src/cmd/{index.rs => index/mod.rs} (100%)
 rename src/obikmer/src/cmd/{merge.rs => merge/mod.rs} (100%)
 rename src/obikmer/src/cmd/{pack.rs => pack/mod.rs} (100%)
 delete mode 100644 src/obikmer/src/cmd/query.rs
 create mode 100644 src/obikmer/src/cmd/query/batch.rs
 create mode 100644 src/obikmer/src/cmd/query/chunk.rs
 create mode 100644 src/obikmer/src/cmd/query/findere.rs
 create mode 100644 src/obikmer/src/cmd/query/mod.rs
 create mode 100644 src/obikmer/src/cmd/query/output.rs
 create mode 100644 src/obikmer/src/cmd/query/smer_index.rs
 rename src/obikmer/src/cmd/{tests/query.rs => query/tests.rs} (98%)
 rename src/obikmer/src/cmd/{reindex.rs => reindex/mod.rs} (100%)
 rename src/obikmer/src/cmd/{select.rs => select/mod.rs} (100%)
 rename src/obikmer/src/cmd/{superkmer.rs => superkmer/mod.rs} (100%)
 rename src/obikmer/src/cmd/{unitig.rs => unitig/mod.rs} (100%)
 create mode 100644 src/obikmer/src/cmd/utils/maintenance.rs
 create mode 100644 src/obikmer/src/cmd/utils/mod.rs
 rename src/obikmer/src/cmd/{utils.rs => utils/partition_stats.rs} (50%)

diff --git a/src/obikmer/src/cmd/annotate.rs b/src/obikmer/src/cmd/annotate/mod.rs
similarity index 100%
rename from src/obikmer/src/cmd/annotate.rs
rename to src/obikmer/src/cmd/annotate/mod.rs
diff --git a/src/obikmer/src/cmd/dump.rs b/src/obikmer/src/cmd/dump/mod.rs
similarity index 100%
rename from src/obikmer/src/cmd/dump.rs
rename to src/obikmer/src/cmd/dump/mod.rs
diff --git a/src/obikmer/src/cmd/estimate.rs b/src/obikmer/src/cmd/estimate/mod.rs
similarity index 100%
rename from src/obikmer/src/cmd/estimate.rs
rename to src/obikmer/src/cmd/estimate/mod.rs
diff --git a/src/obikmer/src/cmd/filter.rs b/src/obikmer/src/cmd/filter/mod.rs
similarity index 100%
rename from src/obikmer/src/cmd/filter.rs
rename to src/obikmer/src/cmd/filter/mod.rs
diff --git a/src/obikmer/src/cmd/index.rs b/src/obikmer/src/cmd/index/mod.rs
similarity index 100%
rename from src/obikmer/src/cmd/index.rs
rename to src/obikmer/src/cmd/index/mod.rs
diff --git a/src/obikmer/src/cmd/merge.rs b/src/obikmer/src/cmd/merge/mod.rs
similarity index 100%
rename from src/obikmer/src/cmd/merge.rs
rename to src/obikmer/src/cmd/merge/mod.rs
diff --git a/src/obikmer/src/cmd/pack.rs b/src/obikmer/src/cmd/pack/mod.rs
similarity index 100%
rename from src/obikmer/src/cmd/pack.rs
rename to src/obikmer/src/cmd/pack/mod.rs
diff --git a/src/obikmer/src/cmd/query.rs b/src/obikmer/src/cmd/query.rs
deleted file mode 100644
index b63f8283..00000000
--- a/src/obikmer/src/cmd/query.rs
+++ /dev/null
@@ -1,851 +0,0 @@
-use std::collections::{HashMap, VecDeque};
-use std::io::{self, BufWriter, Write};
-use std::path::PathBuf;
-use std::sync::Arc;
-use std::sync::atomic::{AtomicU32, AtomicU64, Ordering};
-use std::time::Instant;
-
-use clap::Args;
-use obikindex::KmerIndex;
-use obikpartitionner::{KmerDesc, QueryHit, QueryStats};
-use obikrope::Rope;
-use obikseq::CanonicalKmer;
-use obilayeredmap::IndexMode;
-use obipipeline::{Throttled, ThrottleGuard, throttle};
-use obiread::chunk::read_sequence_chunks_sized;
-use obiread::record::{SeqRecord, parse_chunk};
-use obiskbuilder::SuperKmerIter;
-use obisys::{Reporter, Stage, available_memory_bytes, spinner};
-use tracing::{debug, info};
-
-// ── Pipeline data ─────────────────────────────────────────────────────────────
-
-enum QueryData {
-    Path(Throttled<PathBuf>),
-    Chunk(Rope),
-    Output(Vec<u8>),
-}
-
-// SAFETY: Rope contains Cell<u8> which is !Sync, but pipeline items are owned
-// exclusively through channels — no item is ever shared across threads.
-unsafe impl Send for QueryData {}
-unsafe impl Sync for QueryData {}
-
-// ── CLI ───────────────────────────────────────────────────────────────────────
-
-#[derive(Args)]
-pub struct QueryArgs {
-    /// Index directory
-    pub index: PathBuf,
-
-    /// Input sequences (FASTA/FASTQ, optionally gzip-compressed)
-    #[arg(num_args = 1..)]
-    pub inputs: Vec<String>,
-
-    /// Report per-position coverage vectors per genome (adds "coverage" to JSON)
-    #[arg(long)]
-    pub detail: bool,
-
-    /// Enable 1-mismatch approximate matching
-    #[arg(long)]
-    pub mismatch: bool,
-
-    /// Count k-mers absent from the index (adds kmer_missing annotation)
-    #[arg(long)]
-    pub count_missing: bool,
-
-    /// Report per-genome presence (0/1) instead of raw counts
-    #[arg(long)]
-    pub force_presence: bool,
-
-    /// Minimum accumulated match count to declare a genome present (implies --force-presence)
-    #[arg(long, default_value_t = 1)]
-    pub presence_threshold: u32,
-
-    /// Override the Findere z parameter from index metadata
-    #[arg(short = 'z', long)]
-    pub findere_z: Option<usize>,
-
-    /// Number of worker threads
-    #[arg(
-        short = 'T',
-        long,
-        default_value_t = obisys::effective_parallelism()
-    )]
-    pub threads: usize,
-
-    /// I/O chunk size in MiB (default: auto-sized from available RAM and thread count)
-    #[arg(long)]
-    pub chunk_size: Option<usize>,
-
-    /// Maximum number of input files open simultaneously.
-    /// Defaults to threads/4 (minimum 1). Keep below the number of workers
-    /// to ensure CPU workers are always available for the transform stage.
-    #[arg(long)]
-    pub max_open_files: Option<usize>,
-}
-
-impl QueryArgs {
-    pub fn effective_max_open(&self) -> usize {
-        self.max_open_files
-            .unwrap_or_else(|| (self.threads / 4).max(1))
-            .max(1)
-    }
-}
-
-// ── QueryBatch ────────────────────────────────────────────────────────────────
-
-/// A batch of query sequences, with k-mers deduplicated directly (not just at
-/// the superkmer level) and pre-split by partition.
-///
-/// Superkmer *construction* (`SuperKmerIter`) is still required — it's the
-/// mechanism that computes minimizers and partition routing — but the dedup
-/// key is the canonical k-mer, not the superkmer: two different superkmers
-/// that happen to share a k-mer (read overlaps, repeats, a SNP splitting an
-/// otherwise-identical run) are deduplicated too, not just identical whole
-/// superkmers. This also means each unique k-mer triggers at most one MPHF
-/// lookup, not one per occurrence.
-pub struct QueryBatch {
-    /// Sequence ids in batch order.
-    pub ids: Vec<String>,
-    /// Raw sequence bytes (for output), in batch order.
-    pub seqs: Vec<Vec<u8>>,
-    /// Total kmer count per sequence (used for `--detail` coverage allocation).
-    pub n_kmers: Vec<u32>,
-    /// Deduplicated k-mer occurrences, one map per partition.
-    pub by_partition: Vec<HashMap<CanonicalKmer, Vec<KmerDesc>>>,
-}
-
-impl QueryBatch {
-    /// Build a batch from a vec of parsed sequence records, deduplicating
-    /// k-mers and routing them to partitions in the same pass.
-    pub fn from_records(
-        records: Vec<SeqRecord>,
-        k: usize,
-        level_max: usize,
-        theta: f64,
-        n_partitions: usize,
-    ) -> Self {
-        let mut ids = Vec::with_capacity(records.len());
-        let mut seqs = Vec::with_capacity(records.len());
-        let mut n_kmers = Vec::with_capacity(records.len());
-        let mask = (n_partitions as u64) - 1;
-        let mut by_partition: Vec<HashMap<CanonicalKmer, Vec<KmerDesc>>> =
-            (0..n_partitions).map(|_| HashMap::new()).collect();
-
-        for (seq_idx, record) in records.into_iter().enumerate() {
-            let mut kmer_offset = 0u32;
-
-            for rsk in SuperKmerIter::new(&record.normalized, k, level_max, theta) {
-                let part_idx = (rsk.minimizer().seq_hash() & mask) as usize;
-                let map = &mut by_partition[part_idx];
-                for (j, kmer) in rsk.superkmer().iter_canonical_kmers().enumerate() {
-                    map.entry(kmer).or_default().push(KmerDesc {
-                        seq_idx: seq_idx as u32,
-                        pos: kmer_offset + j as u32,
-                    });
-                }
-                let n = (rsk.seql() - k + 1) as u32;
-                kmer_offset += n;
-            }
-
-            ids.push(record.id);
-            seqs.push(record.sequence);
-            n_kmers.push(kmer_offset);
-        }
-
-        Self {
-            ids,
-            seqs,
-            n_kmers,
-            by_partition,
-        }
-    }
-}
-
-// ── SmerIndex — sparse "was this k-mer found at all" bookkeeping ─────────────
-
-/// Tracks, per (sequence, s-mer position), whether the k-mer was found in the
-/// index at all — independent of *which* genome(s) matched. Sized
-/// `total_smers` (one `bool` per s-mer occurrence in the chunk), **not**
-/// multiplied by `n_genomes`: this is the O(1)-per-position bookkeeping that
-/// `kmer_missing` needs (the leftmost-s-mer-of-window membership test), kept
-/// dense because it's already cheap — the `n_genomes`-scaled data lives in
-/// the sparse per-genome hit lists built alongside it (see `process_chunk`).
-struct SmerIndex {
-    in_index: Vec<bool>, // total_smers
-    offsets: Vec<usize>, // offsets[i]..offsets[i+1] = s-mer range for sequence i
-}
-
-impl SmerIndex {
-    fn new(n_kmers_per_seq: &[u32]) -> Self {
-        let mut offsets = Vec::with_capacity(n_kmers_per_seq.len() + 1);
-        let mut total = 0usize;
-        offsets.push(0);
-        for &n in n_kmers_per_seq {
-            total += n as usize;
-            offsets.push(total);
-        }
-        Self {
-            in_index: vec![false; total],
-            offsets,
-        }
-    }
-
-    /// Mark the k-mer at (seq, kmer) as found in the index — independent of
-    /// any particular genome's value. Called once per hit k-mer (stage 1 of
-    /// `query_partition_with`), regardless of how the column-major fetch
-    /// (stage 2) later reports per-genome values.
-    fn mark_found(&mut self, seq: usize, kmer: usize) {
-        let abs = self.offsets[seq] + kmer;
-        self.in_index[abs] = true;
-    }
-
-    #[inline]
-    fn is_in_index(&self, seq: usize, kmer: usize) -> bool {
-        self.in_index[self.offsets[seq] + kmer]
-    }
-}
-
-// ── Sparse Findere: per-genome run detection + sliding-window minimum ────────
-
-/// One confirmed z-window: genome `g`'s window ending at k-mer `pos` (the
-/// *leftmost* s-mer of the window, i.e. the k_user-mer's output position) is
-/// fully present and nonzero, with window-minimum `value`.
-type ConfirmedHit = (u32, u32, u32); // (seq_idx, pos_out, value)
-
-/// Reduce one genome's raw sparse s-mer hits — `(seq_idx, pos_smer, raw_value)`,
-/// unsorted, exactly as delivered by `QueryHit::Value` — into confirmed
-/// z-windows, without ever visiting a position that had no hit at all.
-///
-/// A z-window is confirmed only when all z s-mers in it are present *and*
-/// nonzero for this genome (matching the dense sliding-window's semantics,
-/// where "not in index" or a zero value both contribute 0 to the window
-/// minimum) — which can only happen inside a maximal run of consecutive
-/// `pos_smer` values for the same sequence. `hits` is sorted in place by
-/// `(seq_idx, pos_smer)` to expose those runs; the monotone-deque
-/// window-minimum then runs per run, on run-relative indices, identical in
-/// spirit to the dense version's whole-sequence scan.
-///
-/// Returns the confirmed hits plus `(n_runs, total_run_len)` for logging —
-/// a low average run length relative to `z` means most hits fail to form a
-/// complete window.
-fn sparse_findere_for_genome(
-    hits: &mut [(u32, u32, u32)],
-    z: usize,
-    presence: bool,
-    threshold: u32,
-) -> (Vec<ConfirmedHit>, usize, usize) {
-    hits.sort_unstable_by_key(|&(seq, pos, _)| (seq, pos));
-
-    let mut confirmed = Vec::new();
-    let mut n_runs = 0usize;
-    let mut total_run_len = 0usize;
-    let mut dq: VecDeque<(usize, u32)> = VecDeque::new(); // (run-relative index, value)
-
-    let mut i = 0;
-    while i < hits.len() {
-        let seq = hits[i].0;
-        let mut j = i + 1;
-        while j < hits.len() && hits[j].0 == seq && hits[j].1 == hits[j - 1].1 + 1 {
-            j += 1;
-        }
-        let run = &hits[i..j];
-        n_runs += 1;
-        total_run_len += run.len();
-
-        dq.clear();
-        for (k, &(_, pos, val)) in run.iter().enumerate() {
-            while dq.back().map_or(false, |&(_, v)| v >= val) {
-                dq.pop_back();
-            }
-            dq.push_back((k, val));
-            while dq.front().map_or(false, |&(fk, _)| fk + z <= k) {
-                dq.pop_front();
-            }
-            if k + 1 >= z {
-                let win_min = dq.front().unwrap().1;
-                if win_min > 0 {
-                    let pos_out = pos + 1 - z as u32;
-                    let c = if presence { u32::from(win_min >= threshold) } else { win_min };
-                    confirmed.push((seq, pos_out, c));
-                }
-            }
-        }
-
-        i = j;
-    }
-
-    (confirmed, n_runs, total_run_len)
-}
-
-// ── Per-sequence accumulator ──────────────────────────────────────────────────
-
-struct SeqAcc {
-    kmer_count: u32,
-    kmer_missing: u32,
-    genome_totals: Vec<u32>,
-}
-
-impl SeqAcc {
-    fn new(n_genomes: usize) -> Self {
-        Self {
-            kmer_count: 0,
-            kmer_missing: 0,
-            genome_totals: vec![0u32; n_genomes],
-        }
-    }
-}
-
-// ── process_chunk ─────────────────────────────────────────────────────────────
-
-fn process_chunk(
-    idx: &KmerIndex,
-    rope: Rope,
-    k: usize,
-    n_genomes: usize,
-    n_partitions: usize,
-    with_counts: bool,
-    effective_z: usize,
-    detail: bool,
-    count_missing: bool,
-    force_presence: bool,
-    presence_threshold: u32,
-) -> Vec<u8> {
-    let chunk_start = Instant::now();
-    let chunk_bytes = rope.len();
-
-    let records = parse_chunk(&rope, k);
-    if records.is_empty() {
-        return Vec::new();
-    }
-
-    let batch = QueryBatch::from_records(records, k, 6, 0.7, n_partitions);
-    let n_seqs = batch.ids.len();
-
-    // Estimate QueryBatch::by_partition's actual memory footprint: the
-    // k-mer-level dedup map (roadmap point 5) — one HashMap<CanonicalKmer,
-    // Vec<KmerDesc>> per partition, sized by *unique* k-mers, not shrunk by
-    // dedup. On real workloads with a low intra-chunk duplication rate this
-    // can dwarf every other per-chunk structure, including the sparse
-    // Findere ones logged further down — unlike those, chunk_bytes's formula
-    // (run()) does not account for this at all today. Measured by allocated
-    // capacity, not logical length, to reflect real memory pressure
-    // (HashMap/Vec growth slack) — `by_partition` is alive for the entire
-    // process_chunk call (never drained, only iterated by reference), so
-    // this is its footprint for the whole chunk lifetime, not a transient.
-    let hashmap_slot_bytes = (std::mem::size_of::<CanonicalKmer>()
-        + std::mem::size_of::<Vec<KmerDesc>>()
-        + 1) as u64; // +1 ≈ hashbrown control byte per slot
-    let by_partition_map_bytes: u64 = batch
-        .by_partition
-        .iter()
-        .map(|m| m.capacity() as u64 * hashmap_slot_bytes)
-        .sum();
-    let by_partition_desc_bytes: u64 = batch
-        .by_partition
-        .iter()
-        .flat_map(|m| m.values())
-        .map(|v| v.capacity() as u64 * std::mem::size_of::<KmerDesc>() as u64)
-        .sum();
-    let by_partition_bytes = by_partition_map_bytes + by_partition_desc_bytes;
-
-    debug!(
-        n_unique_kmers_total = batch.by_partition.iter().map(|m| m.len() as u64).sum::<u64>(),
-        by_partition_map_bytes,
-        by_partition_desc_bytes,
-        by_partition_bytes,
-        chunk_bytes,
-        "by_partition memory retained"
-    );
-
-    // Sparse bookkeeping for the whole chunk:
-    // - smer_index: O(total_smers) — is this s-mer in the index at all.
-    // - by_genome[g]: raw (seq_idx, pos_smer, value) hits for genome g, only
-    //   ever containing nonzero entries (query_partition_with never emits a
-    //   QueryHit::Value for a zero value) — empty for every genome this chunk
-    //   never matched, which is the common case for unrelated queries.
-    let mut smer_index = SmerIndex::new(&batch.n_kmers);
-    let mut by_genome: Vec<Vec<(u32, u32, u32)>> = (0..n_genomes).map(|_| Vec::new()).collect();
-
-    // Dedup-ratio bookkeeping: occurrences (from batch.n_kmers, computed
-    // before dedup) vs. unique k-mers actually queried (query_stats) — the
-    // entire justification for k-mer-level dereplication (see query.md,
-    // Future work point 5). If this ratio stays close to 1.0 on real data,
-    // dereplication isn't paying for itself and that should show up here.
-    let n_occurrences: u64 = batch.n_kmers.iter().map(|&n| n as u64).sum();
-    let mut query_stats = QueryStats::default();
-
-    for (part_idx, kmers) in batch.by_partition.iter().enumerate() {
-        if kmers.is_empty() {
-            continue;
-        }
-
-        let stats = idx.partition()
-            .query_partition_with(
-                part_idx,
-                kmers,
-                n_genomes,
-                with_counts,
-                |event| match event {
-                    QueryHit::Found(descs) => {
-                        for desc in descs {
-                            smer_index.mark_found(desc.seq_idx as usize, desc.pos as usize);
-                        }
-                    }
-                    QueryHit::Value(descs, g, v) => {
-                        for desc in descs {
-                            by_genome[g].push((desc.seq_idx, desc.pos, v));
-                        }
-                    }
-                },
-            )
-            .unwrap_or_else(|e| {
-                eprintln!("query error on partition {part_idx}: {e}");
-                std::process::exit(1);
-            });
-        query_stats += stats;
-    }
-
-    debug!(
-        n_occurrences,
-        n_unique_kmers = query_stats.n_unique_kmers,
-        n_mphf_calls = query_stats.n_mphf_calls,
-        n_hits = query_stats.n_hits,
-        n_columns_scanned = query_stats.n_columns_scanned,
-        n_col_get_calls = query_stats.n_col_get_calls,
-        "k-mer dedup + column-major fetch"
-    );
-
-    // ── Sparse Findere: per-genome run detection + sliding-window minimum ────
-    //
-    // Confirmed z-windows, per genome, replace the dense win_min matrix:
-    // total retained memory is O(actual hits), not O(total_smers × n_genomes)
-    // — the whole point of this pass. See sparse_findere_for_genome's doc for
-    // why run detection is equivalent to the dense scan's semantics.
-    let presence  = force_presence || !with_counts;
-    let threshold = presence_threshold;
-    let z         = effective_z;
-
-    let n_kmers_out: Vec<usize> = batch
-        .n_kmers
-        .iter()
-        .map(|&n| {
-            let n = n as usize;
-            if n >= z { n - z + 1 } else { 0 }
-        })
-        .collect();
-    let mut out_offsets = Vec::with_capacity(n_seqs + 1);
-    {
-        let mut total = 0usize;
-        out_offsets.push(0);
-        for &n in &n_kmers_out {
-            total += n;
-            out_offsets.push(total);
-        }
-    }
-    let total_out = *out_offsets.last().unwrap_or(&0);
-
-    let n_dense_would_be = n_occurrences as u64 * n_genomes as u64;
-    let mut n_sparse_entries = 0u64;
-    let mut n_runs_total = 0usize;
-    let mut run_len_total = 0usize;
-
-    let mut confirmed_by_genome: Vec<Vec<ConfirmedHit>> = Vec::with_capacity(n_genomes);
-    for hits in &mut by_genome {
-        n_sparse_entries += hits.len() as u64;
-        let (confirmed, n_runs, run_len) = sparse_findere_for_genome(hits, z, presence, threshold);
-        n_runs_total += n_runs;
-        run_len_total += run_len;
-        confirmed_by_genome.push(confirmed);
-    }
-
-    debug!(
-        n_dense_would_be,
-        n_sparse_entries,
-        n_runs = n_runs_total,
-        avg_run_len = if n_runs_total > 0 { run_len_total as f64 / n_runs_total as f64 } else { 0.0 },
-        z,
-        "sparse Findere"
-    );
-
-    // Actual bytes retained by the sparse hit structures (by_genome +
-    // confirmed_by_genome, both alive simultaneously at this point — see the
-    // chunk-size formula's comment in `run()`), by allocated capacity rather
-    // than logical length so this reflects real memory pressure including
-    // Vec growth slack. `empirical_multiplier` is directly comparable to
-    // BYTES_PER_KMER_PER_GENOME (`run()`) — the ratio a cluster run's logs
-    // need to judge whether that constant is over- or under-conservative for
-    // real data, instead of guessing.
-    const HIT_ENTRY_BYTES: u64 = std::mem::size_of::<(u32, u32, u32)>() as u64;
-    let by_genome_bytes: u64 = by_genome.iter().map(|v| v.capacity() as u64 * HIT_ENTRY_BYTES).sum();
-    let confirmed_bytes: u64 = confirmed_by_genome.iter().map(|v| v.capacity() as u64 * HIT_ENTRY_BYTES).sum();
-    let retained_bytes = by_genome_bytes + confirmed_bytes;
-
-    debug!(
-        by_genome_bytes,
-        confirmed_bytes,
-        retained_bytes,
-        chunk_bytes,
-        empirical_multiplier = retained_bytes as f64 / chunk_bytes.max(1) as f64,
-        "sparse memory retained"
-    );
-
-    // ── Accumulate: genome totals (per genome, from confirmed hits) ──────────
-    let mut accs: Vec<SeqAcc> = (0..n_seqs).map(|_| SeqAcc::new(n_genomes)).collect();
-    let mut confirmed_any = vec![false; total_out];
-
-    for (g, hits) in confirmed_by_genome.iter().enumerate() {
-        for &(seq_idx, pos_out, c) in hits {
-            let abs_out = out_offsets[seq_idx as usize] + pos_out as usize;
-            confirmed_any[abs_out] = true;
-            accs[seq_idx as usize].genome_totals[g] += c;
-        }
-    }
-
-    // ── Accumulate: kmer_count / kmer_missing (per position, genome-independent) ─
-    for seq_idx in 0..n_seqs {
-        let out_n = n_kmers_out[seq_idx];
-        let acc = &mut accs[seq_idx];
-        for pos in 0..out_n {
-            let abs_out = out_offsets[seq_idx] + pos;
-            if confirmed_any[abs_out] {
-                acc.kmer_count += 1;
-            } else if !smer_index.is_in_index(seq_idx, pos) {
-                acc.kmer_missing += 1;
-            }
-        }
-    }
-
-    // ── Coverage (--detail): densify only when actually requested ────────────
-    let mut cov: Vec<Vec<Vec<u32>>> = if detail {
-        n_kmers_out.iter().map(|&n| vec![vec![0u32; n]; n_genomes]).collect()
-    } else {
-        Vec::new()
-    };
-    if detail {
-        for (g, hits) in confirmed_by_genome.iter().enumerate() {
-            for &(seq_idx, pos_out, c) in hits {
-                cov[seq_idx as usize][g][pos_out as usize] += c;
-            }
-        }
-    }
-
-    // Capacity estimate: actual sequence + ID bytes, plus JSON overhead per record.
-    // JSON per record ≈ 50 fixed chars + ~20 per genome (label + count value) + 100 (overhead).
-    let seq_bytes: usize = batch.seqs.iter().map(|s| s.len()).sum();
-    let id_bytes: usize = batch.ids.iter().map(|s| s.len()).sum();
-    let cap = seq_bytes + id_bytes + n_seqs * (4 + 50 + n_genomes * 20) + 100;
-    let mut buf = Vec::with_capacity(cap);
-    emit_batch(
-        &batch,
-        &accs,
-        idx.meta(),
-        count_missing,
-        detail,
-        &cov,
-        &mut buf,
-    );
-
-    debug!(
-        chunk_bytes,
-        n_seqs,
-        n_smers = batch.n_kmers.iter().map(|&n| n as u64).sum::<u64>(),
-        wall_ms = chunk_start.elapsed().as_millis() as u64,
-        "process_chunk"
-    );
-
-    buf
-}
-
-// ── GuardedChunkIter — keeps the throttle slot guard alive until the file is exhausted ──
-
-/// Wraps a per-file `Rope` chunk iterator together with its `ThrottleGuard`,
-/// so the guard (and the throttle slot it holds) is only released once the
-/// file has been fully read — never earlier, never held past that point.
-struct GuardedChunkIter {
-    inner:      Box<dyn Iterator<Item = Rope> + Send>,
-    _guard:     ThrottleGuard,
-    files_open: Arc<AtomicU32>,
-}
-
-impl Iterator for GuardedChunkIter {
-    type Item = Rope;
-    fn next(&mut self) -> Option<Rope> {
-        self.inner.next()
-    }
-}
-
-impl Drop for GuardedChunkIter {
-    fn drop(&mut self) {
-        self.files_open.fetch_sub(1, Ordering::Relaxed);
-    }
-}
-
-// ── Entry point ───────────────────────────────────────────────────────────────
-
-pub fn run(args: QueryArgs) {
-    let idx = Arc::new(KmerIndex::open(&args.index).unwrap_or_else(|e| {
-        eprintln!("error opening index: {e}");
-        std::process::exit(1);
-    }));
-
-    let k = idx.kmer_size();
-    let n_genomes = idx.meta().genomes.len();
-    let n_partitions = idx.n_partitions();
-    let with_counts = idx.meta().config.with_counts;
-    let n_workers = args.threads.max(1);
-
-    // Chunk size: each chunk stays in memory for its entire processing lifetime.
-    //
-    // Per-chunk memory is no longer a dense n_genomes-wide buffer (removed in
-    // the sparse Findere rework, see process_chunk) — it now scales with
-    // *actual hit count*, not with total_kmers_in_chunk × n_genomes
-    // unconditionally. BYTES_PER_KMER_PER_GENOME below is therefore a
-    // pathological-case bound, not a typical-case estimate: it protects
-    // against a fully-dense hit pattern (every k-mer of the query matching
-    // every genome — a degenerate case, e.g. low-complexity input theta-
-    // filtering should mostly reject, or an index of near-duplicate genomes),
-    // where by_genome and confirmed_by_genome (process_chunk) both end up
-    // holding one (seq_idx, pos, value) entry — 3 × u32 = 12 bytes, vs. 4
-    // bytes for the old dense encoding, where position was implicit in the
-    // array index — per (k-mer, genome) pair, and *coexist simultaneously*
-    // (by_genome isn't freed before confirmed_by_genome is built), for a
-    // worst case of ~24 bytes/pair before Vec growth slack. `cov` remains
-    // fully dense when --detail is set (unaffected by the sparse rework),
-    // still roughly doubling the n_genomes-scaled cost.
-    //
-    // For realistic, sparse hit patterns actual memory is far below this
-    // bound — see the "sparse memory retained" debug log in process_chunk,
-    // which reports the empirical bytes-per-raw-byte multiplier actually
-    // observed per chunk, directly comparable to BYTES_PER_KMER_PER_GENOME
-    // below. Tightening this constant for typical-case throughput (at the
-    // cost of pathological-case safety margin) is a deliberate tuning
-    // decision to make from that data, not something to guess at here.
-    //
-    // BASE_OVERHEAD approximates what scales with chunk_bytes alone,
-    // independent of n_genomes: the Rope itself, parsed SeqRecord sequence +
-    // normalised bytes, the superkmer dedup map, and the JSON output buffer.
-    // Like the n_genomes-scaled term, this is an estimate — validate against
-    // actual peak RSS (Stage::stop's `rss` in the summary table) on real
-    // workloads rather than trusting it blindly.
-    //
-    // We target ≤ 50 % of available RAM across all concurrent workers
-    // (SAFETY_FACTOR).
-    const BASE_OVERHEAD: u64 = 4;
-    const BYTES_PER_KMER_PER_GENOME: u64 = 8; // pathological-case bound — see comment above
-    const SAFETY_FACTOR: u64 = 2;
-
-    let detail_factor: u64 = if args.detail { 2 } else { 1 };
-    let overhead_multiplier =
-        BASE_OVERHEAD + n_genomes as u64 * BYTES_PER_KMER_PER_GENOME * detail_factor;
-
-    let chunk_bytes = args
-        .chunk_size
-        .map(|mb| mb * 1024 * 1024)
-        .unwrap_or_else(|| {
-            let avail = available_memory_bytes();
-            let computed = avail / (n_workers as u64 * overhead_multiplier * SAFETY_FACTOR);
-            computed.clamp(4 * 1024 * 1024, 256 * 1024 * 1024) as usize
-        });
-
-    debug!(
-        chunk_bytes,
-        n_genomes,
-        detail = args.detail,
-        overhead_multiplier,
-        estimated_peak_chunk_bytes = chunk_bytes as u64 * overhead_multiplier,
-        "chunk-size formula resolved"
-    );
-
-    let effective_z: usize = args
-        .findere_z
-        .unwrap_or_else(|| match idx.meta().config.evidence {
-            IndexMode::Approx { z, .. } | IndexMode::Hybrid { z, .. } => z as usize,
-            IndexMode::Exact => 1,
-        });
-
-    info!(
-        "query: k={k}, {} genome(s), with_counts={with_counts}, z={effective_z}, \
-         mismatch={}, detail={}",
-        n_genomes, args.mismatch, args.detail
-    );
-
-    if args.mismatch {
-        eprintln!("warning: --mismatch not yet implemented, ignored");
-    }
-
-    let detail = args.detail;
-    let count_missing = args.count_missing;
-    let force_presence = args.force_presence;
-    let presence_threshold = args.presence_threshold;
-
-    // Throttled iterator over input file paths: at most `effective_max_open()`
-    // files are open at once. Opening + decompressing + chunking each file is
-    // now a Flat pipeline stage, executed across the `n_workers` pool — not
-    // serialised in the pipe's dedicated source thread (see steps::scatter /
-    // cmd::superkmer for the same pattern applied to indexing).
-    info!("query: chunk_size={}MiB, max_open_files={}", chunk_bytes / (1024 * 1024), args.effective_max_open());
-
-    let paths: Vec<PathBuf> = args.inputs.iter().map(PathBuf::from).collect();
-    let path_source = throttle(paths.into_iter(), args.effective_max_open());
-
-    // Instrumentation: total bytes processed (for the EMA throughput readout),
-    // number of files currently open/being chunked, and number of chunks
-    // currently being processed by a worker — all read from the spinner loop
-    // below, updated from inside the pipe closures.
-    let total_bytes = Arc::new(AtomicU64::new(0));
-    let files_open = Arc::new(AtomicU32::new(0));
-    let chunks_active = Arc::new(AtomicU32::new(0));
-
-    let pipe = obipipeline::make_pipe! {
-        QueryData : Throttled<PathBuf> => Vec<u8>,
-        || {
-            let files_open = Arc::clone(&files_open);
-            move |pw: Throttled<PathBuf>| -> GuardedChunkIter {
-                let path = pw.item;
-                let guard = pw.guard;
-                let path_str = path.to_str().unwrap_or("").to_owned();
-                files_open.fetch_add(1, Ordering::Relaxed);
-                let open_start = Instant::now();
-                // Hard-exit on file-open failure (mirrors the previous behaviour):
-                // propagating this as a pipeline Err would hit a known scheduler
-                // hang on early stage errors (obipipeline::scheduler::WorkerPool::run
-                // breaks its main loop without unblocking the still-running source
-                // thread, so the final `h.join()` never returns) — worth fixing in
-                // obipipeline itself, but out of scope here; sidestepping it like the
-                // original code already did is the safe choice for this change.
-                let iter = read_sequence_chunks_sized(&path_str, chunk_bytes).unwrap_or_else(|e| {
-                    eprintln!("error opening {path_str}: {e}");
-                    std::process::exit(1);
-                });
-                debug!(
-                    path = %path_str,
-                    open_ms = open_start.elapsed().as_millis() as u64,
-                    "opened query input file"
-                );
-                let err_path = path_str.clone();
-                GuardedChunkIter {
-                    inner: Box::new(iter.filter_map(move |r| match r {
-                        Ok(rope) => Some(rope),
-                        Err(e) => {
-                            eprintln!("read error: {err_path}: {e}");
-                            None
-                        }
-                    })),
-                    _guard: guard,
-                    files_open: Arc::clone(&files_open),
-                }
-            }
-        } : Path => Chunk,
-        | {
-            let idx = Arc::clone(&idx);
-            let total_bytes = Arc::clone(&total_bytes);
-            let chunks_active = Arc::clone(&chunks_active);
-            move |rope: Rope| {
-                chunks_active.fetch_add(1, Ordering::Relaxed);
-                let bytes = rope.len() as u64;
-                let out = process_chunk(
-                    &idx, rope, k, n_genomes, n_partitions, with_counts,
-                    effective_z, detail, count_missing, force_presence, presence_threshold,
-                );
-                total_bytes.fetch_add(bytes, Ordering::Relaxed);
-                chunks_active.fetch_sub(1, Ordering::Relaxed);
-                out
-            }
-        } : Chunk => Output,
-    };
-
-    let t = Stage::start("query");
-    let pb = spinner("query");
-
-    let mut ema_rate: f64 = 0.0;
-    let mut last_t = Instant::now();
-    let mut last_bytes: u64 = 0;
-    const ALPHA: f64 = 0.15;
-
-    let mut out = BufWriter::new(io::stdout());
-    for block in pipe.apply(path_source, n_workers, 2) {
-        if !block.is_empty() {
-            out.write_all(&block).expect("write error");
-        }
-
-        let now = Instant::now();
-        let dt = now.duration_since(last_t).as_secs_f64();
-        if dt > 0.1 {
-            let total = total_bytes.load(Ordering::Relaxed);
-            let instant = (total - last_bytes) as f64 / dt;
-            ema_rate = ALPHA * instant + (1.0 - ALPHA) * ema_rate;
-            last_t = now;
-            last_bytes = total;
-            let bp = total as f64;
-            let (count_str, rate_str) = if bp >= 1e9 {
-                (format!("{:.2} GB", bp / 1e9), format!("{:.0} MB/s", ema_rate / 1e6))
-            } else {
-                (format!("{:.0} MB", bp / 1e6), format!("{:.0} MB/s", ema_rate / 1e6))
-            };
-            let active = chunks_active.load(Ordering::Relaxed);
-            let open = files_open.load(Ordering::Relaxed);
-            pb.set_message(format!("{count_str}  {rate_str}  [files open: {open}, chunks in flight: {active}]"));
-        }
-    }
-    out.flush().expect("flush error");
-
-    pb.finish_and_clear();
-
-    let mut rep = Reporter::new();
-    rep.push(t.stop());
-    rep.print();
-}
-
-// ── Output ────────────────────────────────────────────────────────────────────
-
-fn emit_batch(
-    batch: &QueryBatch,
-    accs: &[SeqAcc],
-    meta: &obikindex::meta::IndexMeta,
-    count_missing: bool,
-    detail: bool,
-    cov: &[Vec<Vec<u32>>],
-    out: &mut impl Write,
-) {
-    for (seq_idx, (id, seq)) in batch.ids.iter().zip(batch.seqs.iter()).enumerate() {
-        let acc = &accs[seq_idx];
-        let mut ann = serde_json::Map::new();
-
-        ann.insert("kmer_count".into(), acc.kmer_count.into());
-        if count_missing {
-            ann.insert("kmer_missing".into(), acc.kmer_missing.into());
-        }
-
-        let mut match_map = serde_json::Map::new();
-        for (g, genome) in meta.genomes.iter().enumerate() {
-            if acc.genome_totals[g] != 0 {
-                match_map.insert(genome.label.clone(), acc.genome_totals[g].into());
-            }
-        }
-        ann.insert("kmer_strict_matches".into(), match_map.into());
-
-        if detail && !cov.is_empty() {
-            let mut cov_map = serde_json::Map::new();
-            for (g, genome) in meta.genomes.iter().enumerate() {
-                let v: Vec<serde_json::Value> = cov[seq_idx][g].iter().map(|&x| x.into()).collect();
-                cov_map.insert(genome.label.clone(), v.into());
-            }
-            ann.insert("coverage".into(), cov_map.into());
-        }
-
-        // OBITools4 FASTA format: >id {"key":value,...}
-        let _ = out.write_all(b">");
-        let _ = out.write_all(id.as_bytes());
-        let _ = out.write_all(b" ");
-        let _ = serde_json::to_writer(&mut *out, &ann);
-        let _ = out.write_all(b"\n");
-        let _ = out.write_all(seq);
-        let _ = out.write_all(b"\n");
-    }
-}
-
-#[cfg(test)]
-#[path = "tests/query.rs"]
-mod tests;
diff --git a/src/obikmer/src/cmd/query/batch.rs b/src/obikmer/src/cmd/query/batch.rs
new file mode 100644
index 00000000..55cd9452
--- /dev/null
+++ b/src/obikmer/src/cmd/query/batch.rs
@@ -0,0 +1,74 @@
+use std::collections::HashMap;
+
+use obikpartitionner::KmerDesc;
+use obikseq::CanonicalKmer;
+use obiread::record::SeqRecord;
+use obiskbuilder::SuperKmerIter;
+
+/// A batch of query sequences, with k-mers deduplicated directly (not just at
+/// the superkmer level) and pre-split by partition.
+///
+/// Superkmer *construction* (`SuperKmerIter`) is still required — it's the
+/// mechanism that computes minimizers and partition routing — but the dedup
+/// key is the canonical k-mer, not the superkmer: two different superkmers
+/// that happen to share a k-mer (read overlaps, repeats, a SNP splitting an
+/// otherwise-identical run) are deduplicated too, not just identical whole
+/// superkmers. This also means each unique k-mer triggers at most one MPHF
+/// lookup, not one per occurrence.
+pub struct QueryBatch {
+    /// Sequence ids in batch order.
+    pub ids: Vec<String>,
+    /// Raw sequence bytes (for output), in batch order.
+    pub seqs: Vec<Vec<u8>>,
+    /// Total kmer count per sequence (used for `--detail` coverage allocation).
+    pub n_kmers: Vec<u32>,
+    /// Deduplicated k-mer occurrences, one map per partition.
+    pub by_partition: Vec<HashMap<CanonicalKmer, Vec<KmerDesc>>>,
+}
+
+impl QueryBatch {
+    /// Build a batch from a vec of parsed sequence records, deduplicating
+    /// k-mers and routing them to partitions in the same pass.
+    pub fn from_records(
+        records: Vec<SeqRecord>,
+        k: usize,
+        level_max: usize,
+        theta: f64,
+        n_partitions: usize,
+    ) -> Self {
+        let mut ids = Vec::with_capacity(records.len());
+        let mut seqs = Vec::with_capacity(records.len());
+        let mut n_kmers = Vec::with_capacity(records.len());
+        let mask = (n_partitions as u64) - 1;
+        let mut by_partition: Vec<HashMap<CanonicalKmer, Vec<KmerDesc>>> =
+            (0..n_partitions).map(|_| HashMap::new()).collect();
+
+        for (seq_idx, record) in records.into_iter().enumerate() {
+            let mut kmer_offset = 0u32;
+
+            for rsk in SuperKmerIter::new(&record.normalized, k, level_max, theta) {
+                let part_idx = (rsk.minimizer().seq_hash() & mask) as usize;
+                let map = &mut by_partition[part_idx];
+                for (j, kmer) in rsk.superkmer().iter_canonical_kmers().enumerate() {
+                    map.entry(kmer).or_default().push(KmerDesc {
+                        seq_idx: seq_idx as u32,
+                        pos: kmer_offset + j as u32,
+                    });
+                }
+                let n = (rsk.seql() - k + 1) as u32;
+                kmer_offset += n;
+            }
+
+            ids.push(record.id);
+            seqs.push(record.sequence);
+            n_kmers.push(kmer_offset);
+        }
+
+        Self {
+            ids,
+            seqs,
+            n_kmers,
+            by_partition,
+        }
+    }
+}
diff --git a/src/obikmer/src/cmd/query/chunk.rs b/src/obikmer/src/cmd/query/chunk.rs
new file mode 100644
index 00000000..509d84b1
--- /dev/null
+++ b/src/obikmer/src/cmd/query/chunk.rs
@@ -0,0 +1,288 @@
+use std::time::Instant;
+
+use obikindex::KmerIndex;
+use obikpartitionner::{KmerDesc, QueryHit, QueryStats};
+use obikrope::Rope;
+use obikseq::CanonicalKmer;
+use obiread::record::parse_chunk;
+use tracing::debug;
+
+use super::batch::QueryBatch;
+use super::findere::{ConfirmedHit, sparse_findere_for_genome};
+use super::output::emit_batch;
+use super::smer_index::SmerIndex;
+
+pub(super) struct SeqAcc {
+    pub(super) kmer_count: u32,
+    pub(super) kmer_missing: u32,
+    pub(super) genome_totals: Vec<u32>,
+}
+
+impl SeqAcc {
+    fn new(n_genomes: usize) -> Self {
+        Self {
+            kmer_count: 0,
+            kmer_missing: 0,
+            genome_totals: vec![0u32; n_genomes],
+        }
+    }
+}
+
+pub(super) fn process_chunk(
+    idx: &KmerIndex,
+    rope: Rope,
+    k: usize,
+    n_genomes: usize,
+    n_partitions: usize,
+    with_counts: bool,
+    effective_z: usize,
+    detail: bool,
+    count_missing: bool,
+    force_presence: bool,
+    presence_threshold: u32,
+) -> Vec<u8> {
+    let chunk_start = Instant::now();
+    let chunk_bytes = rope.len();
+
+    let records = parse_chunk(&rope, k);
+    if records.is_empty() {
+        return Vec::new();
+    }
+
+    let batch = QueryBatch::from_records(records, k, 6, 0.7, n_partitions);
+    let n_seqs = batch.ids.len();
+
+    // Estimate QueryBatch::by_partition's actual memory footprint: the
+    // k-mer-level dedup map (roadmap point 5) — one HashMap<CanonicalKmer,
+    // Vec<KmerDesc>> per partition, sized by *unique* k-mers, not shrunk by
+    // dedup. On real workloads with a low intra-chunk duplication rate this
+    // can dwarf every other per-chunk structure, including the sparse
+    // Findere ones logged further down — unlike those, chunk_bytes's formula
+    // (run()) does not account for this at all today. Measured by allocated
+    // capacity, not logical length, to reflect real memory pressure
+    // (HashMap/Vec growth slack) — `by_partition` is alive for the entire
+    // process_chunk call (never drained, only iterated by reference), so
+    // this is its footprint for the whole chunk lifetime, not a transient.
+    let hashmap_slot_bytes = (std::mem::size_of::<CanonicalKmer>()
+        + std::mem::size_of::<Vec<KmerDesc>>()
+        + 1) as u64; // +1 ≈ hashbrown control byte per slot
+    let by_partition_map_bytes: u64 = batch
+        .by_partition
+        .iter()
+        .map(|m| m.capacity() as u64 * hashmap_slot_bytes)
+        .sum();
+    let by_partition_desc_bytes: u64 = batch
+        .by_partition
+        .iter()
+        .flat_map(|m| m.values())
+        .map(|v| v.capacity() as u64 * std::mem::size_of::<KmerDesc>() as u64)
+        .sum();
+    let by_partition_bytes = by_partition_map_bytes + by_partition_desc_bytes;
+
+    debug!(
+        n_unique_kmers_total = batch.by_partition.iter().map(|m| m.len() as u64).sum::<u64>(),
+        by_partition_map_bytes,
+        by_partition_desc_bytes,
+        by_partition_bytes,
+        chunk_bytes,
+        "by_partition memory retained"
+    );
+
+    // Sparse bookkeeping for the whole chunk:
+    // - smer_index: O(total_smers) — is this s-mer in the index at all.
+    // - by_genome[g]: raw (seq_idx, pos_smer, value) hits for genome g, only
+    //   ever containing nonzero entries (query_partition_with never emits a
+    //   QueryHit::Value for a zero value) — empty for every genome this chunk
+    //   never matched, which is the common case for unrelated queries.
+    let mut smer_index = SmerIndex::new(&batch.n_kmers);
+    let mut by_genome: Vec<Vec<(u32, u32, u32)>> = (0..n_genomes).map(|_| Vec::new()).collect();
+
+    // Dedup-ratio bookkeeping: occurrences (from batch.n_kmers, computed
+    // before dedup) vs. unique k-mers actually queried (query_stats) — the
+    // entire justification for k-mer-level dereplication (see query.md,
+    // Future work point 5). If this ratio stays close to 1.0 on real data,
+    // dereplication isn't paying for itself and that should show up here.
+    let n_occurrences: u64 = batch.n_kmers.iter().map(|&n| n as u64).sum();
+    let mut query_stats = QueryStats::default();
+
+    for (part_idx, kmers) in batch.by_partition.iter().enumerate() {
+        if kmers.is_empty() {
+            continue;
+        }
+
+        let stats = idx.partition()
+            .query_partition_with(
+                part_idx,
+                kmers,
+                n_genomes,
+                with_counts,
+                |event| match event {
+                    QueryHit::Found(descs) => {
+                        for desc in descs {
+                            smer_index.mark_found(desc.seq_idx as usize, desc.pos as usize);
+                        }
+                    }
+                    QueryHit::Value(descs, g, v) => {
+                        for desc in descs {
+                            by_genome[g].push((desc.seq_idx, desc.pos, v));
+                        }
+                    }
+                },
+            )
+            .unwrap_or_else(|e| {
+                eprintln!("query error on partition {part_idx}: {e}");
+                std::process::exit(1);
+            });
+        query_stats += stats;
+    }
+
+    debug!(
+        n_occurrences,
+        n_unique_kmers = query_stats.n_unique_kmers,
+        n_mphf_calls = query_stats.n_mphf_calls,
+        n_hits = query_stats.n_hits,
+        n_columns_scanned = query_stats.n_columns_scanned,
+        n_col_get_calls = query_stats.n_col_get_calls,
+        "k-mer dedup + column-major fetch"
+    );
+
+    // ── Sparse Findere: per-genome run detection + sliding-window minimum ────
+    //
+    // Confirmed z-windows, per genome, replace the dense win_min matrix:
+    // total retained memory is O(actual hits), not O(total_smers × n_genomes)
+    // — the whole point of this pass. See sparse_findere_for_genome's doc for
+    // why run detection is equivalent to the dense scan's semantics.
+    let presence  = force_presence || !with_counts;
+    let threshold = presence_threshold;
+    let z         = effective_z;
+
+    let n_kmers_out: Vec<usize> = batch
+        .n_kmers
+        .iter()
+        .map(|&n| {
+            let n = n as usize;
+            if n >= z { n - z + 1 } else { 0 }
+        })
+        .collect();
+    let mut out_offsets = Vec::with_capacity(n_seqs + 1);
+    {
+        let mut total = 0usize;
+        out_offsets.push(0);
+        for &n in &n_kmers_out {
+            total += n;
+            out_offsets.push(total);
+        }
+    }
+    let total_out = *out_offsets.last().unwrap_or(&0);
+
+    let n_dense_would_be = n_occurrences as u64 * n_genomes as u64;
+    let mut n_sparse_entries = 0u64;
+    let mut n_runs_total = 0usize;
+    let mut run_len_total = 0usize;
+
+    let mut confirmed_by_genome: Vec<Vec<ConfirmedHit>> = Vec::with_capacity(n_genomes);
+    for hits in &mut by_genome {
+        n_sparse_entries += hits.len() as u64;
+        let (confirmed, n_runs, run_len) = sparse_findere_for_genome(hits, z, presence, threshold);
+        n_runs_total += n_runs;
+        run_len_total += run_len;
+        confirmed_by_genome.push(confirmed);
+    }
+
+    debug!(
+        n_dense_would_be,
+        n_sparse_entries,
+        n_runs = n_runs_total,
+        avg_run_len = if n_runs_total > 0 { run_len_total as f64 / n_runs_total as f64 } else { 0.0 },
+        z,
+        "sparse Findere"
+    );
+
+    // Actual bytes retained by the sparse hit structures (by_genome +
+    // confirmed_by_genome, both alive simultaneously at this point — see the
+    // chunk-size formula's comment in `run()`), by allocated capacity rather
+    // than logical length so this reflects real memory pressure including
+    // Vec growth slack. `empirical_multiplier` is directly comparable to
+    // BYTES_PER_KMER_PER_GENOME (`run()`) — the ratio a cluster run's logs
+    // need to judge whether that constant is over- or under-conservative for
+    // real data, instead of guessing.
+    const HIT_ENTRY_BYTES: u64 = std::mem::size_of::<(u32, u32, u32)>() as u64;
+    let by_genome_bytes: u64 = by_genome.iter().map(|v| v.capacity() as u64 * HIT_ENTRY_BYTES).sum();
+    let confirmed_bytes: u64 = confirmed_by_genome.iter().map(|v| v.capacity() as u64 * HIT_ENTRY_BYTES).sum();
+    let retained_bytes = by_genome_bytes + confirmed_bytes;
+
+    debug!(
+        by_genome_bytes,
+        confirmed_bytes,
+        retained_bytes,
+        chunk_bytes,
+        empirical_multiplier = retained_bytes as f64 / chunk_bytes.max(1) as f64,
+        "sparse memory retained"
+    );
+
+    // ── Accumulate: genome totals (per genome, from confirmed hits) ──────────
+    let mut accs: Vec<SeqAcc> = (0..n_seqs).map(|_| SeqAcc::new(n_genomes)).collect();
+    let mut confirmed_any = vec![false; total_out];
+
+    for (g, hits) in confirmed_by_genome.iter().enumerate() {
+        for &(seq_idx, pos_out, c) in hits {
+            let abs_out = out_offsets[seq_idx as usize] + pos_out as usize;
+            confirmed_any[abs_out] = true;
+            accs[seq_idx as usize].genome_totals[g] += c;
+        }
+    }
+
+    // ── Accumulate: kmer_count / kmer_missing (per position, genome-independent) ─
+    for seq_idx in 0..n_seqs {
+        let out_n = n_kmers_out[seq_idx];
+        let acc = &mut accs[seq_idx];
+        for pos in 0..out_n {
+            let abs_out = out_offsets[seq_idx] + pos;
+            if confirmed_any[abs_out] {
+                acc.kmer_count += 1;
+            } else if !smer_index.is_in_index(seq_idx, pos) {
+                acc.kmer_missing += 1;
+            }
+        }
+    }
+
+    // ── Coverage (--detail): densify only when actually requested ────────────
+    let mut cov: Vec<Vec<Vec<u32>>> = if detail {
+        n_kmers_out.iter().map(|&n| vec![vec![0u32; n]; n_genomes]).collect()
+    } else {
+        Vec::new()
+    };
+    if detail {
+        for (g, hits) in confirmed_by_genome.iter().enumerate() {
+            for &(seq_idx, pos_out, c) in hits {
+                cov[seq_idx as usize][g][pos_out as usize] += c;
+            }
+        }
+    }
+
+    // Capacity estimate: actual sequence + ID bytes, plus JSON overhead per record.
+    // JSON per record ≈ 50 fixed chars + ~20 per genome (label + count value) + 100 (overhead).
+    let seq_bytes: usize = batch.seqs.iter().map(|s| s.len()).sum();
+    let id_bytes: usize = batch.ids.iter().map(|s| s.len()).sum();
+    let cap = seq_bytes + id_bytes + n_seqs * (4 + 50 + n_genomes * 20) + 100;
+    let mut buf = Vec::with_capacity(cap);
+    emit_batch(
+        &batch,
+        &accs,
+        idx.meta(),
+        count_missing,
+        detail,
+        &cov,
+        &mut buf,
+    );
+
+    debug!(
+        chunk_bytes,
+        n_seqs,
+        n_smers = batch.n_kmers.iter().map(|&n| n as u64).sum::<u64>(),
+        wall_ms = chunk_start.elapsed().as_millis() as u64,
+        "process_chunk"
+    );
+
+    buf
+}
diff --git a/src/obikmer/src/cmd/query/findere.rs b/src/obikmer/src/cmd/query/findere.rs
new file mode 100644
index 00000000..4564c6f8
--- /dev/null
+++ b/src/obikmer/src/cmd/query/findere.rs
@@ -0,0 +1,71 @@
+use std::collections::VecDeque;
+
+/// One confirmed z-window: genome `g`'s window ending at k-mer `pos` (the
+/// *leftmost* s-mer of the window, i.e. the k_user-mer's output position) is
+/// fully present and nonzero, with window-minimum `value`.
+pub(super) type ConfirmedHit = (u32, u32, u32); // (seq_idx, pos_out, value)
+
+/// Reduce one genome's raw sparse s-mer hits — `(seq_idx, pos_smer, raw_value)`,
+/// unsorted, exactly as delivered by `QueryHit::Value` — into confirmed
+/// z-windows, without ever visiting a position that had no hit at all.
+///
+/// A z-window is confirmed only when all z s-mers in it are present *and*
+/// nonzero for this genome (matching the dense sliding-window's semantics,
+/// where "not in index" or a zero value both contribute 0 to the window
+/// minimum) — which can only happen inside a maximal run of consecutive
+/// `pos_smer` values for the same sequence. `hits` is sorted in place by
+/// `(seq_idx, pos_smer)` to expose those runs; the monotone-deque
+/// window-minimum then runs per run, on run-relative indices, identical in
+/// spirit to the dense version's whole-sequence scan.
+///
+/// Returns the confirmed hits plus `(n_runs, total_run_len)` for logging —
+/// a low average run length relative to `z` means most hits fail to form a
+/// complete window.
+pub(super) fn sparse_findere_for_genome(
+    hits: &mut [(u32, u32, u32)],
+    z: usize,
+    presence: bool,
+    threshold: u32,
+) -> (Vec<ConfirmedHit>, usize, usize) {
+    hits.sort_unstable_by_key(|&(seq, pos, _)| (seq, pos));
+
+    let mut confirmed = Vec::new();
+    let mut n_runs = 0usize;
+    let mut total_run_len = 0usize;
+    let mut dq: VecDeque<(usize, u32)> = VecDeque::new(); // (run-relative index, value)
+
+    let mut i = 0;
+    while i < hits.len() {
+        let seq = hits[i].0;
+        let mut j = i + 1;
+        while j < hits.len() && hits[j].0 == seq && hits[j].1 == hits[j - 1].1 + 1 {
+            j += 1;
+        }
+        let run = &hits[i..j];
+        n_runs += 1;
+        total_run_len += run.len();
+
+        dq.clear();
+        for (k, &(_, pos, val)) in run.iter().enumerate() {
+            while dq.back().map_or(false, |&(_, v)| v >= val) {
+                dq.pop_back();
+            }
+            dq.push_back((k, val));
+            while dq.front().map_or(false, |&(fk, _)| fk + z <= k) {
+                dq.pop_front();
+            }
+            if k + 1 >= z {
+                let win_min = dq.front().unwrap().1;
+                if win_min > 0 {
+                    let pos_out = pos + 1 - z as u32;
+                    let c = if presence { u32::from(win_min >= threshold) } else { win_min };
+                    confirmed.push((seq, pos_out, c));
+                }
+            }
+        }
+
+        i = j;
+    }
+
+    (confirmed, n_runs, total_run_len)
+}
diff --git a/src/obikmer/src/cmd/query/mod.rs b/src/obikmer/src/cmd/query/mod.rs
new file mode 100644
index 00000000..425342b8
--- /dev/null
+++ b/src/obikmer/src/cmd/query/mod.rs
@@ -0,0 +1,340 @@
+mod batch;
+mod chunk;
+mod findere;
+mod output;
+mod smer_index;
+
+use std::io::{self, BufWriter, Write};
+use std::path::PathBuf;
+use std::sync::Arc;
+use std::sync::atomic::{AtomicU32, AtomicU64, Ordering};
+use std::time::Instant;
+
+use clap::Args;
+use obikindex::KmerIndex;
+use obikrope::Rope;
+use obilayeredmap::IndexMode;
+use obipipeline::{Throttled, ThrottleGuard, throttle};
+use obiread::chunk::read_sequence_chunks_sized;
+use obisys::{Reporter, Stage, available_memory_bytes, spinner};
+use tracing::{debug, info};
+
+use chunk::process_chunk;
+
+// ── Pipeline data ─────────────────────────────────────────────────────────────
+
+enum QueryData {
+    Path(Throttled<PathBuf>),
+    Chunk(Rope),
+    Output(Vec<u8>),
+}
+
+// SAFETY: Rope contains Cell<u8> which is !Sync, but pipeline items are owned
+// exclusively through channels — no item is ever shared across threads.
+unsafe impl Send for QueryData {}
+unsafe impl Sync for QueryData {}
+
+// ── CLI ───────────────────────────────────────────────────────────────────────
+
+#[derive(Args)]
+pub struct QueryArgs {
+    /// Index directory
+    pub index: PathBuf,
+
+    /// Input sequences (FASTA/FASTQ, optionally gzip-compressed)
+    #[arg(num_args = 1..)]
+    pub inputs: Vec<String>,
+
+    /// Report per-position coverage vectors per genome (adds "coverage" to JSON)
+    #[arg(long)]
+    pub detail: bool,
+
+    /// Enable 1-mismatch approximate matching
+    #[arg(long)]
+    pub mismatch: bool,
+
+    /// Count k-mers absent from the index (adds kmer_missing annotation)
+    #[arg(long)]
+    pub count_missing: bool,
+
+    /// Report per-genome presence (0/1) instead of raw counts
+    #[arg(long)]
+    pub force_presence: bool,
+
+    /// Minimum accumulated match count to declare a genome present (implies --force-presence)
+    #[arg(long, default_value_t = 1)]
+    pub presence_threshold: u32,
+
+    /// Override the Findere z parameter from index metadata
+    #[arg(short = 'z', long)]
+    pub findere_z: Option<usize>,
+
+    /// Number of worker threads
+    #[arg(
+        short = 'T',
+        long,
+        default_value_t = obisys::effective_parallelism()
+    )]
+    pub threads: usize,
+
+    /// I/O chunk size in MiB (default: auto-sized from available RAM and thread count)
+    #[arg(long)]
+    pub chunk_size: Option<usize>,
+
+    /// Maximum number of input files open simultaneously.
+    /// Defaults to threads/4 (minimum 1). Keep below the number of workers
+    /// to ensure CPU workers are always available for the transform stage.
+    #[arg(long)]
+    pub max_open_files: Option<usize>,
+}
+
+impl QueryArgs {
+    pub fn effective_max_open(&self) -> usize {
+        self.max_open_files
+            .unwrap_or_else(|| (self.threads / 4).max(1))
+            .max(1)
+    }
+}
+
+// ── GuardedChunkIter — keeps the throttle slot guard alive until the file is exhausted ──
+
+/// Wraps a per-file `Rope` chunk iterator together with its `ThrottleGuard`,
+/// so the guard (and the throttle slot it holds) is only released once the
+/// file has been fully read — never earlier, never held past that point.
+struct GuardedChunkIter {
+    inner:      Box<dyn Iterator<Item = Rope> + Send>,
+    _guard:     ThrottleGuard,
+    files_open: Arc<AtomicU32>,
+}
+
+impl Iterator for GuardedChunkIter {
+    type Item = Rope;
+    fn next(&mut self) -> Option<Rope> {
+        self.inner.next()
+    }
+}
+
+impl Drop for GuardedChunkIter {
+    fn drop(&mut self) {
+        self.files_open.fetch_sub(1, Ordering::Relaxed);
+    }
+}
+
+// ── Entry point ───────────────────────────────────────────────────────────────
+
+pub fn run(args: QueryArgs) {
+    let idx = Arc::new(KmerIndex::open(&args.index).unwrap_or_else(|e| {
+        eprintln!("error opening index: {e}");
+        std::process::exit(1);
+    }));
+
+    let k = idx.kmer_size();
+    let n_genomes = idx.meta().genomes.len();
+    let n_partitions = idx.n_partitions();
+    let with_counts = idx.meta().config.with_counts;
+    let n_workers = args.threads.max(1);
+
+    // Chunk size: each chunk stays in memory for its entire processing lifetime.
+    //
+    // Per-chunk memory is no longer a dense n_genomes-wide buffer (removed in
+    // the sparse Findere rework, see process_chunk) — it now scales with
+    // *actual hit count*, not with total_kmers_in_chunk × n_genomes
+    // unconditionally. BYTES_PER_KMER_PER_GENOME below is therefore a
+    // pathological-case bound, not a typical-case estimate: it protects
+    // against a fully-dense hit pattern (every k-mer of the query matching
+    // every genome — a degenerate case, e.g. low-complexity input theta-
+    // filtering should mostly reject, or an index of near-duplicate genomes),
+    // where by_genome and confirmed_by_genome (process_chunk) both end up
+    // holding one (seq_idx, pos, value) entry — 3 × u32 = 12 bytes, vs. 4
+    // bytes for the old dense encoding, where position was implicit in the
+    // array index — per (k-mer, genome) pair, and *coexist simultaneously*
+    // (by_genome isn't freed before confirmed_by_genome is built), for a
+    // worst case of ~24 bytes/pair before Vec growth slack. `cov` remains
+    // fully dense when --detail is set (unaffected by the sparse rework),
+    // still roughly doubling the n_genomes-scaled cost.
+    //
+    // For realistic, sparse hit patterns actual memory is far below this
+    // bound — see the "sparse memory retained" debug log in process_chunk,
+    // which reports the empirical bytes-per-raw-byte multiplier actually
+    // observed per chunk, directly comparable to BYTES_PER_KMER_PER_GENOME
+    // below. Tightening this constant for typical-case throughput (at the
+    // cost of pathological-case safety margin) is a deliberate tuning
+    // decision to make from that data, not something to guess at here.
+    //
+    // BASE_OVERHEAD approximates what scales with chunk_bytes alone,
+    // independent of n_genomes: the Rope itself, parsed SeqRecord sequence +
+    // normalised bytes, the superkmer dedup map, and the JSON output buffer.
+    // Like the n_genomes-scaled term, this is an estimate — validate against
+    // actual peak RSS (Stage::stop's `rss` in the summary table) on real
+    // workloads rather than trusting it blindly.
+    //
+    // We target ≤ 50 % of available RAM across all concurrent workers
+    // (SAFETY_FACTOR).
+    const BASE_OVERHEAD: u64 = 4;
+    const BYTES_PER_KMER_PER_GENOME: u64 = 8; // pathological-case bound — see comment above
+    const SAFETY_FACTOR: u64 = 2;
+
+    let detail_factor: u64 = if args.detail { 2 } else { 1 };
+    let overhead_multiplier =
+        BASE_OVERHEAD + n_genomes as u64 * BYTES_PER_KMER_PER_GENOME * detail_factor;
+
+    let chunk_bytes = args
+        .chunk_size
+        .map(|mb| mb * 1024 * 1024)
+        .unwrap_or_else(|| {
+            let avail = available_memory_bytes();
+            let computed = avail / (n_workers as u64 * overhead_multiplier * SAFETY_FACTOR);
+            computed.clamp(4 * 1024 * 1024, 256 * 1024 * 1024) as usize
+        });
+
+    debug!(
+        chunk_bytes,
+        n_genomes,
+        detail = args.detail,
+        overhead_multiplier,
+        estimated_peak_chunk_bytes = chunk_bytes as u64 * overhead_multiplier,
+        "chunk-size formula resolved"
+    );
+
+    let effective_z: usize = args
+        .findere_z
+        .unwrap_or_else(|| match idx.meta().config.evidence {
+            IndexMode::Approx { z, .. } | IndexMode::Hybrid { z, .. } => z as usize,
+            IndexMode::Exact => 1,
+        });
+
+    info!(
+        "query: k={k}, {} genome(s), with_counts={with_counts}, z={effective_z}, \
+         mismatch={}, detail={}",
+        n_genomes, args.mismatch, args.detail
+    );
+
+    if args.mismatch {
+        eprintln!("warning: --mismatch not yet implemented, ignored");
+    }
+
+    let detail = args.detail;
+    let count_missing = args.count_missing;
+    let force_presence = args.force_presence;
+    let presence_threshold = args.presence_threshold;
+
+    // Throttled iterator over input file paths: at most `effective_max_open()`
+    // files are open at once. Opening + decompressing + chunking each file is
+    // now a Flat pipeline stage, executed across the `n_workers` pool — not
+    // serialised in the pipe's dedicated source thread (see steps::scatter /
+    // cmd::superkmer for the same pattern applied to indexing).
+    info!("query: chunk_size={}MiB, max_open_files={}", chunk_bytes / (1024 * 1024), args.effective_max_open());
+
+    let paths: Vec<PathBuf> = args.inputs.iter().map(PathBuf::from).collect();
+    let path_source = throttle(paths.into_iter(), args.effective_max_open());
+
+    // Instrumentation: total bytes processed (for the EMA throughput readout),
+    // number of files currently open/being chunked, and number of chunks
+    // currently being processed by a worker — all read from the spinner loop
+    // below, updated from inside the pipe closures.
+    let total_bytes = Arc::new(AtomicU64::new(0));
+    let files_open = Arc::new(AtomicU32::new(0));
+    let chunks_active = Arc::new(AtomicU32::new(0));
+
+    let pipe = obipipeline::make_pipe! {
+        QueryData : Throttled<PathBuf> => Vec<u8>,
+        || {
+            let files_open = Arc::clone(&files_open);
+            move |pw: Throttled<PathBuf>| -> GuardedChunkIter {
+                let path = pw.item;
+                let guard = pw.guard;
+                let path_str = path.to_str().unwrap_or("").to_owned();
+                files_open.fetch_add(1, Ordering::Relaxed);
+                let open_start = Instant::now();
+                // Hard-exit on file-open failure (mirrors the previous behaviour):
+                // propagating this as a pipeline Err would hit a known scheduler
+                // hang on early stage errors (obipipeline::scheduler::WorkerPool::run
+                // breaks its main loop without unblocking the still-running source
+                // thread, so the final `h.join()` never returns) — worth fixing in
+                // obipipeline itself, but out of scope here; sidestepping it like the
+                // original code already did is the safe choice for this change.
+                let iter = read_sequence_chunks_sized(&path_str, chunk_bytes).unwrap_or_else(|e| {
+                    eprintln!("error opening {path_str}: {e}");
+                    std::process::exit(1);
+                });
+                debug!(
+                    path = %path_str,
+                    open_ms = open_start.elapsed().as_millis() as u64,
+                    "opened query input file"
+                );
+                let err_path = path_str.clone();
+                GuardedChunkIter {
+                    inner: Box::new(iter.filter_map(move |r| match r {
+                        Ok(rope) => Some(rope),
+                        Err(e) => {
+                            eprintln!("read error: {err_path}: {e}");
+                            None
+                        }
+                    })),
+                    _guard: guard,
+                    files_open: Arc::clone(&files_open),
+                }
+            }
+        } : Path => Chunk,
+        | {
+            let idx = Arc::clone(&idx);
+            let total_bytes = Arc::clone(&total_bytes);
+            let chunks_active = Arc::clone(&chunks_active);
+            move |rope: Rope| {
+                chunks_active.fetch_add(1, Ordering::Relaxed);
+                let bytes = rope.len() as u64;
+                let out = process_chunk(
+                    &idx, rope, k, n_genomes, n_partitions, with_counts,
+                    effective_z, detail, count_missing, force_presence, presence_threshold,
+                );
+                total_bytes.fetch_add(bytes, Ordering::Relaxed);
+                chunks_active.fetch_sub(1, Ordering::Relaxed);
+                out
+            }
+        } : Chunk => Output,
+    };
+
+    let t = Stage::start("query");
+    let pb = spinner("query");
+
+    let mut ema_rate: f64 = 0.0;
+    let mut last_t = Instant::now();
+    let mut last_bytes: u64 = 0;
+    const ALPHA: f64 = 0.15;
+
+    let mut out = BufWriter::new(io::stdout());
+    for block in pipe.apply(path_source, n_workers, 2) {
+        if !block.is_empty() {
+            out.write_all(&block).expect("write error");
+        }
+
+        let now = Instant::now();
+        let dt = now.duration_since(last_t).as_secs_f64();
+        if dt > 0.1 {
+            let total = total_bytes.load(Ordering::Relaxed);
+            let instant = (total - last_bytes) as f64 / dt;
+            ema_rate = ALPHA * instant + (1.0 - ALPHA) * ema_rate;
+            last_t = now;
+            last_bytes = total;
+            let bp = total as f64;
+            let (count_str, rate_str) = if bp >= 1e9 {
+                (format!("{:.2} GB", bp / 1e9), format!("{:.0} MB/s", ema_rate / 1e6))
+            } else {
+                (format!("{:.0} MB", bp / 1e6), format!("{:.0} MB/s", ema_rate / 1e6))
+            };
+            let active = chunks_active.load(Ordering::Relaxed);
+            let open = files_open.load(Ordering::Relaxed);
+            pb.set_message(format!("{count_str}  {rate_str}  [files open: {open}, chunks in flight: {active}]"));
+        }
+    }
+    out.flush().expect("flush error");
+
+    pb.finish_and_clear();
+
+    let mut rep = Reporter::new();
+    rep.push(t.stop());
+    rep.print();
+}
+
+#[cfg(test)]
+mod tests;
diff --git a/src/obikmer/src/cmd/query/output.rs b/src/obikmer/src/cmd/query/output.rs
new file mode 100644
index 00000000..2584c0ea
--- /dev/null
+++ b/src/obikmer/src/cmd/query/output.rs
@@ -0,0 +1,50 @@
+use std::io::Write;
+
+use super::batch::QueryBatch;
+use super::chunk::SeqAcc;
+
+pub(super) fn emit_batch(
+    batch: &QueryBatch,
+    accs: &[SeqAcc],
+    meta: &obikindex::meta::IndexMeta,
+    count_missing: bool,
+    detail: bool,
+    cov: &[Vec<Vec<u32>>],
+    out: &mut impl Write,
+) {
+    for (seq_idx, (id, seq)) in batch.ids.iter().zip(batch.seqs.iter()).enumerate() {
+        let acc = &accs[seq_idx];
+        let mut ann = serde_json::Map::new();
+
+        ann.insert("kmer_count".into(), acc.kmer_count.into());
+        if count_missing {
+            ann.insert("kmer_missing".into(), acc.kmer_missing.into());
+        }
+
+        let mut match_map = serde_json::Map::new();
+        for (g, genome) in meta.genomes.iter().enumerate() {
+            if acc.genome_totals[g] != 0 {
+                match_map.insert(genome.label.clone(), acc.genome_totals[g].into());
+            }
+        }
+        ann.insert("kmer_strict_matches".into(), match_map.into());
+
+        if detail && !cov.is_empty() {
+            let mut cov_map = serde_json::Map::new();
+            for (g, genome) in meta.genomes.iter().enumerate() {
+                let v: Vec<serde_json::Value> = cov[seq_idx][g].iter().map(|&x| x.into()).collect();
+                cov_map.insert(genome.label.clone(), v.into());
+            }
+            ann.insert("coverage".into(), cov_map.into());
+        }
+
+        // OBITools4 FASTA format: >id {"key":value,...}
+        let _ = out.write_all(b">");
+        let _ = out.write_all(id.as_bytes());
+        let _ = out.write_all(b" ");
+        let _ = serde_json::to_writer(&mut *out, &ann);
+        let _ = out.write_all(b"\n");
+        let _ = out.write_all(seq);
+        let _ = out.write_all(b"\n");
+    }
+}
diff --git a/src/obikmer/src/cmd/query/smer_index.rs b/src/obikmer/src/cmd/query/smer_index.rs
new file mode 100644
index 00000000..2c57e366
--- /dev/null
+++ b/src/obikmer/src/cmd/query/smer_index.rs
@@ -0,0 +1,41 @@
+/// Tracks, per (sequence, s-mer position), whether the k-mer was found in the
+/// index at all — independent of *which* genome(s) matched. Sized
+/// `total_smers` (one `bool` per s-mer occurrence in the chunk), **not**
+/// multiplied by `n_genomes`: this is the O(1)-per-position bookkeeping that
+/// `kmer_missing` needs (the leftmost-s-mer-of-window membership test), kept
+/// dense because it's already cheap — the `n_genomes`-scaled data lives in
+/// the sparse per-genome hit lists built alongside it (see `process_chunk`).
+pub(super) struct SmerIndex {
+    in_index: Vec<bool>, // total_smers
+    offsets: Vec<usize>, // offsets[i]..offsets[i+1] = s-mer range for sequence i
+}
+
+impl SmerIndex {
+    pub(super) fn new(n_kmers_per_seq: &[u32]) -> Self {
+        let mut offsets = Vec::with_capacity(n_kmers_per_seq.len() + 1);
+        let mut total = 0usize;
+        offsets.push(0);
+        for &n in n_kmers_per_seq {
+            total += n as usize;
+            offsets.push(total);
+        }
+        Self {
+            in_index: vec![false; total],
+            offsets,
+        }
+    }
+
+    /// Mark the k-mer at (seq, kmer) as found in the index — independent of
+    /// any particular genome's value. Called once per hit k-mer (stage 1 of
+    /// `query_partition_with`), regardless of how the column-major fetch
+    /// (stage 2) later reports per-genome values.
+    pub(super) fn mark_found(&mut self, seq: usize, kmer: usize) {
+        let abs = self.offsets[seq] + kmer;
+        self.in_index[abs] = true;
+    }
+
+    #[inline]
+    pub(super) fn is_in_index(&self, seq: usize, kmer: usize) -> bool {
+        self.in_index[self.offsets[seq] + kmer]
+    }
+}
diff --git a/src/obikmer/src/cmd/tests/query.rs b/src/obikmer/src/cmd/query/tests.rs
similarity index 98%
rename from src/obikmer/src/cmd/tests/query.rs
rename to src/obikmer/src/cmd/query/tests.rs
index 6f5976e6..129069dd 100644
--- a/src/obikmer/src/cmd/tests/query.rs
+++ b/src/obikmer/src/cmd/query/tests.rs
@@ -1,4 +1,9 @@
-use super::*;
+use obikrope::Rope;
+use obikseq::CanonicalKmer;
+use obiread::record::parse_chunk;
+
+use super::batch::QueryBatch;
+use super::findere::sparse_findere_for_genome;
 
 const K: usize = 11;
 const M: usize = 5;
diff --git a/src/obikmer/src/cmd/reindex.rs b/src/obikmer/src/cmd/reindex/mod.rs
similarity index 100%
rename from src/obikmer/src/cmd/reindex.rs
rename to src/obikmer/src/cmd/reindex/mod.rs
diff --git a/src/obikmer/src/cmd/select.rs b/src/obikmer/src/cmd/select/mod.rs
similarity index 100%
rename from src/obikmer/src/cmd/select.rs
rename to src/obikmer/src/cmd/select/mod.rs
diff --git a/src/obikmer/src/cmd/superkmer.rs b/src/obikmer/src/cmd/superkmer/mod.rs
similarity index 100%
rename from src/obikmer/src/cmd/superkmer.rs
rename to src/obikmer/src/cmd/superkmer/mod.rs
diff --git a/src/obikmer/src/cmd/unitig.rs b/src/obikmer/src/cmd/unitig/mod.rs
similarity index 100%
rename from src/obikmer/src/cmd/unitig.rs
rename to src/obikmer/src/cmd/unitig/mod.rs
diff --git a/src/obikmer/src/cmd/utils/maintenance.rs b/src/obikmer/src/cmd/utils/maintenance.rs
new file mode 100644
index 00000000..c85f0087
--- /dev/null
+++ b/src/obikmer/src/cmd/utils/maintenance.rs
@@ -0,0 +1,112 @@
+use std::path::PathBuf;
+
+use obikindex::{validate_label, IndexBitsPerKmer, KmerIndex};
+use tracing::info;
+
+pub(super) fn run_stats(index_path: &PathBuf) {
+    let idx = KmerIndex::open(index_path).unwrap_or_else(|e| {
+        eprintln!("error opening index: {e}");
+        std::process::exit(1);
+    });
+    let (total, per_genome) = idx.genome_kmer_counts().unwrap_or_else(|e| {
+        eprintln!("error computing stats: {e}");
+        std::process::exit(1);
+    });
+    println!("genome,n_kmers");
+    for (g, &n) in idx.meta().genomes.iter().zip(per_genome.iter()) {
+        println!("{},{}", g.label, n);
+    }
+    println!("total,{total}");
+}
+
+pub(super) fn run_bits_per_kmer(index_path: &PathBuf) {
+    let idx = KmerIndex::open(index_path).unwrap_or_else(|e| {
+        eprintln!("error opening index: {e}");
+        std::process::exit(1);
+    });
+    let stats: IndexBitsPerKmer = idx.bits_per_kmer().unwrap_or_else(|e| {
+        eprintln!("error computing bits/kmer: {e}");
+        std::process::exit(1);
+    });
+    println!("k-mers    : {}", stats.n_kmers);
+    println!("genomes   : {}", stats.n_genomes);
+    println!("mphf      : {:6.2} bits/kmer", stats.mphf);
+    println!("evidence  : {:6.2} bits/kmer", stats.evidence);
+    println!(
+        "matrix    : {:6.2} bits/kmer  ({:.2} bits/kmer/genome)",
+        stats.matrix, stats.matrix_per_genome
+    );
+    println!("total     : {:6.2} bits/kmer", stats.total);
+}
+
+pub(super) fn run_upgrade_index(index_path: &PathBuf) {
+    let idx = KmerIndex::open(index_path).unwrap_or_else(|e| {
+        eprintln!("error opening index: {e}");
+        std::process::exit(1);
+    });
+    idx.upgrade_layer_meta().unwrap_or_else(|e| {
+        eprintln!("upgrade error: {e}");
+        std::process::exit(1);
+    });
+    info!("upgrade-index: layer_meta.json written to all layers that were missing it");
+}
+
+pub(super) fn run_rename(index_path: &PathBuf, spec: &str) {
+    let (old_label, new_label) = parse_rename_spec(spec);
+
+    let mut idx = KmerIndex::open(index_path).unwrap_or_else(|e| {
+        eprintln!("error opening index: {e}");
+        std::process::exit(1);
+    });
+
+    let pos = idx
+        .meta()
+        .genomes
+        .iter()
+        .position(|g| g.label == old_label)
+        .unwrap_or_else(|| {
+            eprintln!("error: genome '{old_label}' not found in index");
+            std::process::exit(1);
+        });
+
+    validate_label(&new_label).unwrap_or_else(|e| {
+        eprintln!("error: --new-label: {e}");
+        std::process::exit(1);
+    });
+
+    if idx.meta().genomes.iter().any(|g| g.label == new_label) {
+        eprintln!("error: label '{new_label}' already exists in index");
+        std::process::exit(1);
+    }
+
+    idx.meta_mut().genomes[pos].label = new_label.clone();
+    idx.meta_mut().write(index_path).unwrap_or_else(|e| {
+        eprintln!("error writing index metadata: {e}");
+        std::process::exit(1);
+    });
+
+    let spectrums_dir = index_path.join("spectrums");
+    let old_spectrum = spectrums_dir.join(format!("{old_label}.json"));
+    let new_spectrum = spectrums_dir.join(format!("{new_label}.json"));
+    if old_spectrum.exists() {
+        std::fs::rename(&old_spectrum, &new_spectrum).unwrap_or_else(|e| {
+            eprintln!("warning: could not rename spectrum file: {e}");
+        });
+    }
+
+    info!("renamed genome '{old_label}' → '{new_label}'");
+}
+
+fn parse_rename_spec(spec: &str) -> (String, String) {
+    let eq = spec.find('=').unwrap_or_else(|| {
+        eprintln!("error: --new-label expects NEW_LABEL=OLD_LABEL, got '{spec}'");
+        std::process::exit(1);
+    });
+    let new = spec[..eq].trim().to_string();
+    let old = spec[eq + 1..].trim().to_string();
+    if old.is_empty() || new.is_empty() {
+        eprintln!("error: --new-label: both old and new labels must be non-empty");
+        std::process::exit(1);
+    }
+    (old, new)
+}
diff --git a/src/obikmer/src/cmd/utils/mod.rs b/src/obikmer/src/cmd/utils/mod.rs
new file mode 100644
index 00000000..53efb3c4
--- /dev/null
+++ b/src/obikmer/src/cmd/utils/mod.rs
@@ -0,0 +1,85 @@
+mod maintenance;
+mod partition_stats;
+
+use std::path::PathBuf;
+
+use clap::Args;
+
+use maintenance::{run_bits_per_kmer, run_stats, run_upgrade_index, run_rename};
+use partition_stats::run_partition_stats;
+
+#[derive(Args)]
+pub struct UtilsArgs {
+    /// Index directories to operate on (one or more)
+    #[arg(required = true, num_args = 1..)]
+    pub indexes: Vec<PathBuf>,
+
+    /// Set a new genome label: NEW_LABEL=OLD_LABEL  (single-index only)
+    #[arg(long, value_name = "NEW=OLD")]
+    pub new_label: Option<String>,
+
+    /// Add missing layer_meta.json files to each layer  (single-index only)
+    #[arg(long)]
+    pub upgrade_index: bool,
+
+    /// Print bits-per-kmer statistics  (single-index only)
+    #[arg(long)]
+    pub bits_per_kmer: bool,
+
+    /// Print per-genome k-mer counts as CSV  (single-index only)
+    #[arg(long)]
+    pub stats: bool,
+
+    /// Print partition size distribution report (accepts multiple indexes)
+    #[arg(long)]
+    pub partition_stats: bool,
+
+    /// Write per-(partition, source) raw data as CSV to FILE  (used with --partition-stats)
+    #[arg(long, value_name = "FILE")]
+    pub csv: Option<PathBuf>,
+}
+
+pub fn run(args: UtilsArgs) {
+    let mut any = false;
+
+    if let Some(spec) = &args.new_label {
+        any = true;
+        run_rename(single_index(&args), spec);
+    }
+
+    if args.upgrade_index {
+        any = true;
+        run_upgrade_index(single_index(&args));
+    }
+
+    if args.bits_per_kmer {
+        any = true;
+        run_bits_per_kmer(single_index(&args));
+    }
+
+    if args.stats {
+        any = true;
+        run_stats(single_index(&args));
+    }
+
+    if args.partition_stats {
+        any = true;
+        run_partition_stats(&args.indexes, args.csv.as_deref());
+    }
+
+    if !any {
+        eprintln!(
+            "utils: no operation specified. \
+             Available: --new-label, --upgrade-index, --bits-per-kmer, --stats, --partition-stats"
+        );
+        std::process::exit(1);
+    }
+}
+
+fn single_index(args: &UtilsArgs) -> &PathBuf {
+    if args.indexes.len() > 1 {
+        eprintln!("utils: this option requires exactly one index (got {})", args.indexes.len());
+        std::process::exit(1);
+    }
+    &args.indexes[0]
+}
diff --git a/src/obikmer/src/cmd/utils.rs b/src/obikmer/src/cmd/utils/partition_stats.rs
similarity index 50%
rename from src/obikmer/src/cmd/utils.rs
rename to src/obikmer/src/cmd/utils/partition_stats.rs
index f73c3085..1b53c322 100644
--- a/src/obikmer/src/cmd/utils.rs
+++ b/src/obikmer/src/cmd/utils/partition_stats.rs
@@ -1,89 +1,7 @@
 use std::io::{self, Write};
 use std::path::PathBuf;
 
-use clap::Args;
-use obikindex::{validate_label, IndexBitsPerKmer, KmerIndex};
-use tracing::info;
-
-#[derive(Args)]
-pub struct UtilsArgs {
-    /// Index directories to operate on (one or more)
-    #[arg(required = true, num_args = 1..)]
-    pub indexes: Vec<PathBuf>,
-
-    /// Set a new genome label: NEW_LABEL=OLD_LABEL  (single-index only)
-    #[arg(long, value_name = "NEW=OLD")]
-    pub new_label: Option<String>,
-
-    /// Add missing layer_meta.json files to each layer  (single-index only)
-    #[arg(long)]
-    pub upgrade_index: bool,
-
-    /// Print bits-per-kmer statistics  (single-index only)
-    #[arg(long)]
-    pub bits_per_kmer: bool,
-
-    /// Print per-genome k-mer counts as CSV  (single-index only)
-    #[arg(long)]
-    pub stats: bool,
-
-    /// Print partition size distribution report (accepts multiple indexes)
-    #[arg(long)]
-    pub partition_stats: bool,
-
-    /// Write per-(partition, source) raw data as CSV to FILE  (used with --partition-stats)
-    #[arg(long, value_name = "FILE")]
-    pub csv: Option<PathBuf>,
-}
-
-pub fn run(args: UtilsArgs) {
-    let mut any = false;
-
-    if let Some(spec) = &args.new_label {
-        any = true;
-        run_rename(single_index(&args), spec);
-    }
-
-    if args.upgrade_index {
-        any = true;
-        run_upgrade_index(single_index(&args));
-    }
-
-    if args.bits_per_kmer {
-        any = true;
-        run_bits_per_kmer(single_index(&args));
-    }
-
-    if args.stats {
-        any = true;
-        run_stats(single_index(&args));
-    }
-
-    if args.partition_stats {
-        any = true;
-        run_partition_stats(&args.indexes, args.csv.as_deref());
-    }
-
-    if !any {
-        eprintln!(
-            "utils: no operation specified. \
-             Available: --new-label, --upgrade-index, --bits-per-kmer, --stats, --partition-stats"
-        );
-        std::process::exit(1);
-    }
-}
-
-// ── helpers ───────────────────────────────────────────────────────────────────
-
-fn single_index(args: &UtilsArgs) -> &PathBuf {
-    if args.indexes.len() > 1 {
-        eprintln!("utils: this option requires exactly one index (got {})", args.indexes.len());
-        std::process::exit(1);
-    }
-    &args.indexes[0]
-}
-
-// ── --partition-stats ─────────────────────────────────────────────────────────
+use obikindex::KmerIndex;
 
 /// Per-partition, per-source byte count of all unitigs.bin files summed across layers.
 struct PartRow {
@@ -198,7 +116,7 @@ fn ascii_histogram(totals: &[u64], n_buckets: usize, bar_width: usize) -> String
     out
 }
 
-fn run_partition_stats(indexes: &[PathBuf], csv_path: Option<&std::path::Path>) {
+pub(super) fn run_partition_stats(indexes: &[PathBuf], csv_path: Option<&std::path::Path>) {
     let rows = collect_rows(indexes);
     if rows.is_empty() {
         eprintln!("partition-stats: no data found");
@@ -282,113 +200,3 @@ fn run_partition_stats(indexes: &[PathBuf], csv_path: Option<&std::path::Path>)
         eprintln!("CSV written to {}", csv_out.display());
     }
 }
-
-// ── existing single-index operations ─────────────────────────────────────────
-
-fn run_stats(index_path: &PathBuf) {
-    let idx = KmerIndex::open(index_path).unwrap_or_else(|e| {
-        eprintln!("error opening index: {e}");
-        std::process::exit(1);
-    });
-    let (total, per_genome) = idx.genome_kmer_counts().unwrap_or_else(|e| {
-        eprintln!("error computing stats: {e}");
-        std::process::exit(1);
-    });
-    println!("genome,n_kmers");
-    for (g, &n) in idx.meta().genomes.iter().zip(per_genome.iter()) {
-        println!("{},{}", g.label, n);
-    }
-    println!("total,{total}");
-}
-
-fn run_bits_per_kmer(index_path: &PathBuf) {
-    let idx = KmerIndex::open(index_path).unwrap_or_else(|e| {
-        eprintln!("error opening index: {e}");
-        std::process::exit(1);
-    });
-    let stats: IndexBitsPerKmer = idx.bits_per_kmer().unwrap_or_else(|e| {
-        eprintln!("error computing bits/kmer: {e}");
-        std::process::exit(1);
-    });
-    println!("k-mers    : {}", stats.n_kmers);
-    println!("genomes   : {}", stats.n_genomes);
-    println!("mphf      : {:6.2} bits/kmer", stats.mphf);
-    println!("evidence  : {:6.2} bits/kmer", stats.evidence);
-    println!(
-        "matrix    : {:6.2} bits/kmer  ({:.2} bits/kmer/genome)",
-        stats.matrix, stats.matrix_per_genome
-    );
-    println!("total     : {:6.2} bits/kmer", stats.total);
-}
-
-fn run_upgrade_index(index_path: &PathBuf) {
-    let idx = KmerIndex::open(index_path).unwrap_or_else(|e| {
-        eprintln!("error opening index: {e}");
-        std::process::exit(1);
-    });
-    idx.upgrade_layer_meta().unwrap_or_else(|e| {
-        eprintln!("upgrade error: {e}");
-        std::process::exit(1);
-    });
-    info!("upgrade-index: layer_meta.json written to all layers that were missing it");
-}
-
-fn run_rename(index_path: &PathBuf, spec: &str) {
-    let (old_label, new_label) = parse_rename_spec(spec);
-
-    let mut idx = KmerIndex::open(index_path).unwrap_or_else(|e| {
-        eprintln!("error opening index: {e}");
-        std::process::exit(1);
-    });
-
-    let pos = idx
-        .meta()
-        .genomes
-        .iter()
-        .position(|g| g.label == old_label)
-        .unwrap_or_else(|| {
-            eprintln!("error: genome '{old_label}' not found in index");
-            std::process::exit(1);
-        });
-
-    validate_label(&new_label).unwrap_or_else(|e| {
-        eprintln!("error: --new-label: {e}");
-        std::process::exit(1);
-    });
-
-    if idx.meta().genomes.iter().any(|g| g.label == new_label) {
-        eprintln!("error: label '{new_label}' already exists in index");
-        std::process::exit(1);
-    }
-
-    idx.meta_mut().genomes[pos].label = new_label.clone();
-    idx.meta_mut().write(index_path).unwrap_or_else(|e| {
-        eprintln!("error writing index metadata: {e}");
-        std::process::exit(1);
-    });
-
-    let spectrums_dir = index_path.join("spectrums");
-    let old_spectrum = spectrums_dir.join(format!("{old_label}.json"));
-    let new_spectrum = spectrums_dir.join(format!("{new_label}.json"));
-    if old_spectrum.exists() {
-        std::fs::rename(&old_spectrum, &new_spectrum).unwrap_or_else(|e| {
-            eprintln!("warning: could not rename spectrum file: {e}");
-        });
-    }
-
-    info!("renamed genome '{old_label}' → '{new_label}'");
-}
-
-fn parse_rename_spec(spec: &str) -> (String, String) {
-    let eq = spec.find('=').unwrap_or_else(|| {
-        eprintln!("error: --new-label expects NEW_LABEL=OLD_LABEL, got '{spec}'");
-        std::process::exit(1);
-    });
-    let new = spec[..eq].trim().to_string();
-    let old = spec[eq + 1..].trim().to_string();
-    if old.is_empty() || new.is_empty() {
-        eprintln!("error: --new-label: both old and new labels must be non-empty");
-        std::process::exit(1);
-    }
-    (old, new)
-}
-- 
2.54.0


From cc67023e2c5f44c57013b5a159135aa855d98a53 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Thu, 13 Aug 2026 10:21:54 +0200
Subject: [PATCH 08/46] feat: centralize genome metadata predicates in
 obikindex

Introduces a new predicate module in obikindex that implements genome metadata predicate parsing, evaluation, and group classification using three-valued logic. Extends the IndexMeta API with methods for single-predicate filtering and group quorum filtering. Updates obikmer command modules to delegate filter construction and matching to the centralized index API, removing local definitions and simplifying call sites.
---
 src/Cargo.lock                    |   1 +
 src/obikindex/Cargo.toml          |   1 +
 src/obikindex/src/lib.rs          |   2 +
 src/obikindex/src/predicate.rs    | 252 ++++++++++++++++++++++++++++++
 src/obikmer/src/cmd/dump/mod.rs   |   2 +-
 src/obikmer/src/cmd/filter/mod.rs |   2 +-
 src/obikmer/src/cmd/predicate.rs  | 248 +----------------------------
 src/obikmer/src/cmd/select/mod.rs |  12 +-
 src/obikmer/src/cmd/unitig/mod.rs |   2 +-
 9 files changed, 269 insertions(+), 253 deletions(-)
 create mode 100644 src/obikindex/src/predicate.rs

diff --git a/src/Cargo.lock b/src/Cargo.lock
index 4acaca3b..74a8dabe 100644
--- a/src/Cargo.lock
+++ b/src/Cargo.lock
@@ -1773,6 +1773,7 @@ dependencies = [
  "obiskbuilder",
  "obiskio",
  "obisys",
+ "obitaxonomy",
  "rayon",
  "serde",
  "serde_json",
diff --git a/src/obikindex/Cargo.toml b/src/obikindex/Cargo.toml
index 44ecd4a0..ba86dd64 100644
--- a/src/obikindex/Cargo.toml
+++ b/src/obikindex/Cargo.toml
@@ -6,6 +6,7 @@ edition = "2024"
 [dependencies]
 obikseq          = { path = "../obikseq" }
 obikpartitionner = { path = "../obikpartitionner" }
+obitaxonomy      = { path = "../obitaxonomy" }
 obiskio          = { path = "../obiskio" }
 obisys           = { path = "../obisys" }
 obicompactvec    = { path = "../obicompactvec" }
diff --git a/src/obikindex/src/lib.rs b/src/obikindex/src/lib.rs
index 4bcc66dd..665e2d86 100644
--- a/src/obikindex/src/lib.rs
+++ b/src/obikindex/src/lib.rs
@@ -1,5 +1,6 @@
 pub mod error;
 pub mod meta;
+pub mod predicate;
 pub mod state;
 mod cardcomp;
 mod distance;
@@ -18,6 +19,7 @@ pub use distance::{DistanceMetric, DistanceOutput};
 pub use index::KmerIndex;
 pub use merge::MergeMode;
 pub use meta::{validate_label, GenomeInfo, IndexConfig, IndexMeta, META_FILENAME};
+pub use predicate::{GroupFilterParams, MetaPred};
 pub use state::{IndexState, SENTINEL_COUNTED, SENTINEL_INDEXED, SENTINEL_SCATTERED};
 pub use stats::IndexBitsPerKmer;
 pub use siblings::{BasePairTally, CardinalityTally, RawSnpDistanceOutput, SiblingAnnexStats, SnpAlignment};
diff --git a/src/obikindex/src/predicate.rs b/src/obikindex/src/predicate.rs
new file mode 100644
index 00000000..b98286ef
--- /dev/null
+++ b/src/obikindex/src/predicate.rs
@@ -0,0 +1,252 @@
+use std::collections::HashMap;
+
+use obikpartitionner::GroupQuorumFilter;
+use obitaxonomy::{TaxPath, TaxPattern};
+
+use crate::meta::{GenomeInfo, IndexMeta};
+
+// ── Operator ──────────────────────────────────────────────────────────────────
+
+enum PredOp { Wildcard, Eq, Ne, Matches, NotMatches }
+
+// ── MetaPred ──────────────────────────────────────────────────────────────────
+
+/// A single predicate on genome metadata: `key OP val1|val2|…`
+///
+/// Operators: `=` (exact), `!=` (not equal), `~` (path ancestor), `!~` (not ancestor).
+/// Multiple values separated by `|` are OR'd.
+pub struct MetaPred {
+    key:    String,
+    op:     PredOp,
+    values: Vec<String>,
+}
+
+impl MetaPred {
+    /// Parse a predicate string of the form `key=v1|v2`, `key!=v`, `key~path`, `key!~path`.
+    /// The special values `*` and `all` (case-insensitive) match every genome.
+    pub fn parse(s: &str) -> Result<Self, String> {
+        let t = s.trim();
+        if t == "*" || t.eq_ignore_ascii_case("all") {
+            return Ok(Self { key: String::new(), op: PredOp::Wildcard, values: vec![] });
+        }
+
+        let (op, key, rhs) =
+            if let Some(pos) = s.find("!=") {
+                (PredOp::Ne,         &s[..pos], &s[pos+2..])
+            } else if let Some(pos) = s.find("!~") {
+                (PredOp::NotMatches, &s[..pos], &s[pos+2..])
+            } else if let Some(pos) = s.find('=') {
+                (PredOp::Eq,         &s[..pos], &s[pos+1..])
+            } else if let Some(pos) = s.find('~') {
+                (PredOp::Matches,    &s[..pos], &s[pos+1..])
+            } else {
+                return Err(format!("no operator found in predicate: {s}"));
+            };
+
+        let key = key.trim().to_string();
+        if key.is_empty() { return Err(format!("empty key in predicate: {s}")); }
+
+        let values: Vec<String> = rhs.split('|').map(|v| v.trim().to_string()).collect();
+        if values.iter().any(|v| v.is_empty()) {
+            return Err(format!("empty value in predicate: {s}"));
+        }
+        Ok(Self { key, op, values })
+    }
+
+    /// Evaluate against one genome's metadata.
+    /// Returns `None` when the key is absent (NA propagation).
+    pub(crate) fn eval(&self, meta: &HashMap<String, String>) -> Option<bool> {
+        if matches!(self.op, PredOp::Wildcard) { return Some(true); }
+        let value = meta.get(&self.key)?;
+        Some(match self.op {
+            PredOp::Wildcard   => unreachable!(),
+            PredOp::Eq         => self.values.iter().any(|v| v == value),
+            PredOp::Ne         => self.values.iter().all(|v| v != value),
+            PredOp::Matches    => self.values.iter().any(|v| path_matches(value, v)),
+            PredOp::NotMatches => self.values.iter().all(|v| !path_matches(value, v)),
+        })
+    }
+}
+
+impl GenomeInfo {
+    /// Evaluate a single metadata predicate against this genome.
+    /// Returns `None` when the predicate's key is absent (NA propagation).
+    pub fn matches(&self, pred: &MetaPred) -> Option<bool> {
+        pred.eval(&self.meta)
+    }
+}
+
+// ── Path matching ─────────────────────────────────────────────────────────────
+
+/// True if the stored taxonomy `value` matches `pattern`.
+///
+/// `value` must be a valid `TaxPath` (starts with `taxonomy:/`).
+/// `pattern` is a `TaxPattern` query (see `obitaxonomy::TaxPattern` for syntax).
+/// Returns `false` if either fails to parse.
+fn path_matches(value: &str, pattern: &str) -> bool {
+    let Ok(path) = TaxPath::parse(value)    else { return false };
+    let Ok(pat)  = TaxPattern::parse(pattern) else { return false };
+    pat.matches(&path)
+}
+
+// ── Three-value group evaluation ──────────────────────────────────────────────
+
+/// AND of all predicates (ingroup semantics).
+/// Short-circuits on `Some(false)`; propagates `None` if no predicate returns `false`.
+fn eval_and(preds: &[MetaPred], meta: &HashMap<String, String>) -> Option<bool> {
+    let mut has_na = false;
+    for pred in preds {
+        match pred.eval(meta) {
+            Some(false) => return Some(false),
+            Some(true)  => {}
+            None        => has_na = true,
+        }
+    }
+    if has_na { None } else { Some(true) }
+}
+
+/// OR of all predicates (outgroup semantics).
+/// Short-circuits on `Some(true)`; propagates `None` if no predicate returns `true`.
+fn eval_or(preds: &[MetaPred], meta: &HashMap<String, String>) -> Option<bool> {
+    let mut has_na = false;
+    for pred in preds {
+        match pred.eval(meta) {
+            Some(true)  => return Some(true),
+            Some(false) => {}
+            None        => has_na = true,
+        }
+    }
+    if has_na { None } else { Some(false) }
+}
+
+// ── Genome classification ─────────────────────────────────────────────────────
+
+enum Membership { Ingroup, Outgroup, Uncategorized }
+
+fn classify(
+    genomes: &[GenomeInfo],
+    ingroup:  &[MetaPred],
+    outgroup: &[MetaPred],
+) -> Vec<Membership> {
+    genomes.iter().map(|g| {
+        let in_r  = if ingroup.is_empty()  { None } else { eval_and(ingroup,  &g.meta) };
+        let out_r = if outgroup.is_empty() { None } else { eval_or(outgroup,  &g.meta) };
+
+        // Ingroup wins over outgroup.
+        if in_r == Some(true)  { return Membership::Ingroup;  }
+        if out_r == Some(true) { return Membership::Outgroup; }
+        Membership::Uncategorized
+    }).collect()
+}
+
+// ── Group quorum filter construction ──────────────────────────────────────────
+
+pub struct GroupFilterParams {
+    pub threshold:          u32,
+    pub min_count:          Option<isize>,
+    pub max_count:          Option<isize>,
+    pub min_frac:           Option<f64>,
+    pub max_frac:           Option<f64>,
+    pub min_outgroup_count: Option<isize>,
+    pub max_outgroup_count: Option<isize>,
+    pub min_outgroup_frac:  Option<f64>,
+    pub max_outgroup_frac:  Option<f64>,
+}
+
+impl IndexMeta {
+    /// Returns indices of genomes matching `pred_str` (single predicate).
+    pub fn matching_genome_indices(&self, pred_str: &str) -> Result<Vec<usize>, String> {
+        let pred = MetaPred::parse(pred_str)?;
+        Ok(self.genomes.iter().enumerate()
+            .filter_map(|(i, g)| {
+                if g.matches(&pred) == Some(true) { Some(i) } else { std::option::Option::None }
+            })
+            .collect())
+    }
+
+    /// Build a `GroupQuorumFilter` from parsed predicates, evaluated against `self.genomes`.
+    ///
+    /// - No groups defined: `ingroup_idx` = all genomes (implicit ingroup).
+    /// - `ingroup` predicates only: outgroup indices are empty.
+    /// - `outgroup` predicates only: ingroup indices are empty.
+    /// - Both defined: ingroup wins on overlap; uncategorized genomes are ignored.
+    pub fn build_group_filter(
+        &self,
+        ingroup_preds:  &[MetaPred],
+        outgroup_preds: &[MetaPred],
+        p:              GroupFilterParams,
+    ) -> Result<GroupQuorumFilter, String> {
+        let (ingroup_idx, outgroup_idx) = if ingroup_preds.is_empty() && outgroup_preds.is_empty() {
+            ((0..self.genomes.len()).collect(), vec![])
+        } else {
+            let members = classify(&self.genomes, ingroup_preds, outgroup_preds);
+            let in_idx: Vec<usize>  = members.iter().enumerate()
+                .filter(|(_, m)| matches!(m, Membership::Ingroup))
+                .map(|(i, _)| i).collect();
+            let out_idx: Vec<usize> = members.iter().enumerate()
+                .filter(|(_, m)| matches!(m, Membership::Outgroup))
+                .map(|(i, _)| i).collect();
+            (in_idx, out_idx)
+        };
+
+        let in_size  = ingroup_idx.len();
+        let out_size = outgroup_idx.len();
+
+        let ingroup_quorum_explicit  = p.min_count.is_some() || p.max_count.is_some()
+            || p.min_frac.is_some() || p.max_frac.is_some();
+        let outgroup_quorum_explicit = p.min_outgroup_count.is_some() || p.max_outgroup_count.is_some()
+            || p.min_outgroup_frac.is_some() || p.max_outgroup_frac.is_some();
+
+        let default_min_frac           = if !ingroup_preds.is_empty()  && !ingroup_quorum_explicit  { 1.0      } else { 0.0      };
+        let default_max_outgroup_count = if !outgroup_preds.is_empty() && !outgroup_quorum_explicit { 0        } else { out_size };
+
+        // Resolve a signed count: negative means an offset from the group size
+        // (e.g. -1 = all but one), floored at 1 so the negative form always keeps
+        // constraining the group — even a singleton group, where n-1 would be 0
+        // and would otherwise drop the constraint entirely.
+        let resolve = |v: isize, size: usize| -> usize {
+            if v < 0 { (size as isize + v).max(1) as usize } else { v as usize }
+        };
+
+        let min_count          = p.min_count.map(|v| resolve(v, in_size)).unwrap_or(0);
+        let max_count          = p.max_count.map(|v| resolve(v, in_size)).unwrap_or(in_size);
+        let min_frac           = p.min_frac.unwrap_or(default_min_frac);
+        let max_frac           = p.max_frac.unwrap_or(1.0);
+        let min_outgroup_count = p.min_outgroup_count.map(|v| resolve(v, out_size)).unwrap_or(0);
+        let max_outgroup_count = p.max_outgroup_count.map(|v| resolve(v, out_size)).unwrap_or(default_max_outgroup_count);
+        let min_outgroup_frac  = p.min_outgroup_frac.unwrap_or(0.0);
+        let max_outgroup_frac  = p.max_outgroup_frac.unwrap_or(1.0);
+
+        for (v, lo, hi) in [
+            ("--min-frac/--max-frac",                        min_frac,           max_frac),
+            ("--min-outgroup-frac/--max-outgroup-frac",       min_outgroup_frac,  max_outgroup_frac),
+        ] {
+            if !(0.0..=1.0).contains(&lo) || !(0.0..=1.0).contains(&hi) {
+                return Err(format!("{v}: fraction values must be in [0.0, 1.0]"));
+            }
+            if lo > hi {
+                return Err(format!("{v}: min ({lo}) is greater than max ({hi})"));
+            }
+        }
+        if min_count > max_count {
+            return Err(format!("--min-count/--max-count: min ({min_count}) is greater than max ({max_count})"));
+        }
+        if min_outgroup_count > max_outgroup_count {
+            return Err(format!("--min-outgroup-count/--max-outgroup-count: min ({min_outgroup_count}) is greater than max ({max_outgroup_count})"));
+        }
+
+        Ok(GroupQuorumFilter {
+            ingroup_idx,
+            outgroup_idx,
+            threshold: p.threshold,
+            min_count,
+            max_count,
+            min_frac,
+            max_frac,
+            min_outgroup_count,
+            max_outgroup_count,
+            min_outgroup_frac,
+            max_outgroup_frac,
+        })
+    }
+}
diff --git a/src/obikmer/src/cmd/dump/mod.rs b/src/obikmer/src/cmd/dump/mod.rs
index 685a151f..7450b56a 100644
--- a/src/obikmer/src/cmd/dump/mod.rs
+++ b/src/obikmer/src/cmd/dump/mod.rs
@@ -41,7 +41,7 @@ pub fn run(args: DumpArgs) {
         &idx.meta().genomes.len()
     );
 
-    let filters = args.filter.build_filters(&idx.meta().genomes);
+    let filters = args.filter.build_filters(idx.meta());
     let pb = progress_bar("dump", idx.n_partitions() as u64, "partitions");
 
     let stdout = io::stdout();
diff --git a/src/obikmer/src/cmd/filter/mod.rs b/src/obikmer/src/cmd/filter/mod.rs
index ed0f407b..b2ca626a 100644
--- a/src/obikmer/src/cmd/filter/mod.rs
+++ b/src/obikmer/src/cmd/filter/mod.rs
@@ -66,7 +66,7 @@ pub fn run(args: FilterCmdArgs) {
         &src.meta().genomes.len(), mode, args.source.display()
     );
 
-    let mut filters = args.filter.build_filters(&src.meta().genomes);
+    let mut filters = args.filter.build_filters(src.meta());
 
     if let Some(v) = args.min_total_count {
         filters.push(Box::new(MinTotalCount { total: v }));
diff --git a/src/obikmer/src/cmd/predicate.rs b/src/obikmer/src/cmd/predicate.rs
index b9ae40f0..6d0f953e 100644
--- a/src/obikmer/src/cmd/predicate.rs
+++ b/src/obikmer/src/cmd/predicate.rs
@@ -1,144 +1,7 @@
-use std::collections::HashMap;
-
 use clap::Args;
-use obikindex::GenomeInfo;
-use obikpartitionner::{GroupQuorumFilter, KmerFilter};
-use obitaxonomy::{TaxPath, TaxPattern};
+use obikindex::{GroupFilterParams, IndexMeta, MetaPred};
+use obikpartitionner::KmerFilter;
 
-// ── Operator ──────────────────────────────────────────────────────────────────
-
-enum PredOp { Wildcard, Eq, Ne, Matches, NotMatches }
-
-// ── MetaPred ──────────────────────────────────────────────────────────────────
-
-/// A single predicate on genome metadata: `key OP val1|val2|…`
-///
-/// Operators: `=` (exact), `!=` (not equal), `~` (path ancestor), `!~` (not ancestor).
-/// Multiple values separated by `|` are OR'd.
-pub struct MetaPred {
-    key:    String,
-    op:     PredOp,
-    values: Vec<String>,
-}
-
-impl MetaPred {
-    /// Parse a predicate string of the form `key=v1|v2`, `key!=v`, `key~path`, `key!~path`.
-    /// The special values `*` and `all` (case-insensitive) match every genome.
-    pub fn parse(s: &str) -> Result<Self, String> {
-        let t = s.trim();
-        if t == "*" || t.eq_ignore_ascii_case("all") {
-            return Ok(Self { key: String::new(), op: PredOp::Wildcard, values: vec![] });
-        }
-
-        let (op, key, rhs) =
-            if let Some(pos) = s.find("!=") {
-                (PredOp::Ne,         &s[..pos], &s[pos+2..])
-            } else if let Some(pos) = s.find("!~") {
-                (PredOp::NotMatches, &s[..pos], &s[pos+2..])
-            } else if let Some(pos) = s.find('=') {
-                (PredOp::Eq,         &s[..pos], &s[pos+1..])
-            } else if let Some(pos) = s.find('~') {
-                (PredOp::Matches,    &s[..pos], &s[pos+1..])
-            } else {
-                return Err(format!("no operator found in predicate: {s}"));
-            };
-
-        let key = key.trim().to_string();
-        if key.is_empty() { return Err(format!("empty key in predicate: {s}")); }
-
-        let values: Vec<String> = rhs.split('|').map(|v| v.trim().to_string()).collect();
-        if values.iter().any(|v| v.is_empty()) {
-            return Err(format!("empty value in predicate: {s}"));
-        }
-        Ok(Self { key, op, values })
-    }
-
-    /// Evaluate against one genome's metadata.
-    /// Returns `None` when the key is absent (NA propagation).
-    fn eval(&self, meta: &HashMap<String, String>) -> Option<bool> {
-        if matches!(self.op, PredOp::Wildcard) { return Some(true); }
-        let value = meta.get(&self.key)?;
-        Some(match self.op {
-            PredOp::Wildcard   => unreachable!(),
-            PredOp::Eq         => self.values.iter().any(|v| v == value),
-            PredOp::Ne         => self.values.iter().all(|v| v != value),
-            PredOp::Matches    => self.values.iter().any(|v| path_matches(value, v)),
-            PredOp::NotMatches => self.values.iter().all(|v| !path_matches(value, v)),
-        })
-    }
-}
-
-// ── Path matching ─────────────────────────────────────────────────────────────
-
-/// True if the stored taxonomy `value` matches `pattern`.
-///
-/// `value` must be a valid `TaxPath` (starts with `taxonomy:/`).
-/// `pattern` is a `TaxPattern` query (see `obitaxonomy::TaxPattern` for syntax).
-/// Returns `false` if either fails to parse.
-fn path_matches(value: &str, pattern: &str) -> bool {
-    let Ok(path) = TaxPath::parse(value)    else { return false };
-    let Ok(pat)  = TaxPattern::parse(pattern) else { return false };
-    pat.matches(&path)
-}
-
-// ── Three-value group evaluation ──────────────────────────────────────────────
-
-/// AND of all predicates (ingroup semantics).
-/// Short-circuits on `Some(false)`; propagates `None` if no predicate returns `false`.
-fn eval_and(preds: &[MetaPred], meta: &HashMap<String, String>) -> Option<bool> {
-    let mut has_na = false;
-    for pred in preds {
-        match pred.eval(meta) {
-            Some(false) => return Some(false),
-            Some(true)  => {}
-            None        => has_na = true,
-        }
-    }
-    if has_na { None } else { Some(true) }
-}
-
-/// OR of all predicates (outgroup semantics).
-/// Short-circuits on `Some(true)`; propagates `None` if no predicate returns `true`.
-fn eval_or(preds: &[MetaPred], meta: &HashMap<String, String>) -> Option<bool> {
-    let mut has_na = false;
-    for pred in preds {
-        match pred.eval(meta) {
-            Some(true)  => return Some(true),
-            Some(false) => {}
-            None        => has_na = true,
-        }
-    }
-    if has_na { None } else { Some(false) }
-}
-
-// ── Genome classification ─────────────────────────────────────────────────────
-
-enum Membership { Ingroup, Outgroup, Uncategorized }
-
-fn classify(
-    genomes: &[GenomeInfo],
-    ingroup:  &[MetaPred],
-    outgroup: &[MetaPred],
-) -> Vec<Membership> {
-    genomes.iter().map(|g| {
-        let in_r  = if ingroup.is_empty()  { None } else { eval_and(ingroup,  &g.meta) };
-        let out_r = if outgroup.is_empty() { None } else { eval_or(outgroup,  &g.meta) };
-
-        // Ingroup wins over outgroup.
-        if in_r == Some(true)  { return Membership::Ingroup;  }
-        if out_r == Some(true) { return Membership::Outgroup; }
-        Membership::Uncategorized
-    }).collect()
-}
-
-// ── Public constructor ────────────────────────────────────────────────────────
-
-/// Build a `GroupQuorumFilter` from parsed predicates and genome metadata.
-///
-/// - No groups defined: `ingroup_idx` = all genomes (implicit ingroup).
-/// - `ingroup` predicates only: outgroup indices are empty.
-/// - `outgroup` predicates only: ingroup indices are empty.
-/// - Both defined: ingroup wins on overlap; uncategorized genomes are ignored.
 /// CLI args for ingroup/outgroup filtering — embeddable in any command via `#[command(flatten)]`.
 #[derive(Args)]
 pub struct FilterArgs {
@@ -195,7 +58,7 @@ pub struct FilterArgs {
 
 impl FilterArgs {
     /// Parse predicates and build a filter list ready to pass to `iter_partition_kmers`.
-    pub fn build_filters(&self, genomes: &[GenomeInfo]) -> Vec<Box<dyn KmerFilter>> {
+    pub fn build_filters(&self, meta: &IndexMeta) -> Vec<Box<dyn KmerFilter>> {
         let ingroup_preds: Vec<MetaPred> = self.ingroup.iter()
             .map(|s| MetaPred::parse(s).unwrap_or_else(|e| {
                 eprintln!("error in --ingroup: {e}");
@@ -208,8 +71,7 @@ impl FilterArgs {
                 std::process::exit(1);
             }))
             .collect();
-        let filter = build_group_filter(
-            genomes,
+        let filter = meta.build_group_filter(
             &ingroup_preds,
             &outgroup_preds,
             GroupFilterParams {
@@ -230,105 +92,3 @@ impl FilterArgs {
         vec![Box::new(filter)]
     }
 }
-
-/// Returns indices of genomes matching `pred_str` (single predicate).
-pub fn matching_genome_indices(pred_str: &str, genomes: &[GenomeInfo]) -> Result<Vec<usize>, String> {
-    let pred = MetaPred::parse(pred_str)?;
-    Ok(genomes.iter().enumerate()
-        .filter_map(|(i, g)| {
-            if pred.eval(&g.meta) == Some(true) { Some(i) } else { std::option::Option::None }
-        })
-        .collect())
-}
-
-pub struct GroupFilterParams {
-    pub threshold:          u32,
-    pub min_count:          Option<isize>,
-    pub max_count:          Option<isize>,
-    pub min_frac:           Option<f64>,
-    pub max_frac:           Option<f64>,
-    pub min_outgroup_count: Option<isize>,
-    pub max_outgroup_count: Option<isize>,
-    pub min_outgroup_frac:  Option<f64>,
-    pub max_outgroup_frac:  Option<f64>,
-}
-
-pub fn build_group_filter(
-    genomes:        &[GenomeInfo],
-    ingroup_preds:  &[MetaPred],
-    outgroup_preds: &[MetaPred],
-    p:              GroupFilterParams,
-) -> Result<GroupQuorumFilter, String> {
-    let (ingroup_idx, outgroup_idx) = if ingroup_preds.is_empty() && outgroup_preds.is_empty() {
-        ((0..genomes.len()).collect(), vec![])
-    } else {
-        let members = classify(genomes, ingroup_preds, outgroup_preds);
-        let in_idx: Vec<usize>  = members.iter().enumerate()
-            .filter(|(_, m)| matches!(m, Membership::Ingroup))
-            .map(|(i, _)| i).collect();
-        let out_idx: Vec<usize> = members.iter().enumerate()
-            .filter(|(_, m)| matches!(m, Membership::Outgroup))
-            .map(|(i, _)| i).collect();
-        (in_idx, out_idx)
-    };
-
-    let in_size  = ingroup_idx.len();
-    let out_size = outgroup_idx.len();
-
-    let ingroup_quorum_explicit  = p.min_count.is_some() || p.max_count.is_some()
-        || p.min_frac.is_some() || p.max_frac.is_some();
-    let outgroup_quorum_explicit = p.min_outgroup_count.is_some() || p.max_outgroup_count.is_some()
-        || p.min_outgroup_frac.is_some() || p.max_outgroup_frac.is_some();
-
-    let default_min_frac           = if !ingroup_preds.is_empty()  && !ingroup_quorum_explicit  { 1.0      } else { 0.0      };
-    let default_max_outgroup_count = if !outgroup_preds.is_empty() && !outgroup_quorum_explicit { 0        } else { out_size };
-
-    // Resolve a signed count: negative means an offset from the group size
-    // (e.g. -1 = all but one), floored at 1 so the negative form always keeps
-    // constraining the group — even a singleton group, where n-1 would be 0
-    // and would otherwise drop the constraint entirely.
-    let resolve = |v: isize, size: usize| -> usize {
-        if v < 0 { (size as isize + v).max(1) as usize } else { v as usize }
-    };
-
-    let min_count          = p.min_count.map(|v| resolve(v, in_size)).unwrap_or(0);
-    let max_count          = p.max_count.map(|v| resolve(v, in_size)).unwrap_or(in_size);
-    let min_frac           = p.min_frac.unwrap_or(default_min_frac);
-    let max_frac           = p.max_frac.unwrap_or(1.0);
-    let min_outgroup_count = p.min_outgroup_count.map(|v| resolve(v, out_size)).unwrap_or(0);
-    let max_outgroup_count = p.max_outgroup_count.map(|v| resolve(v, out_size)).unwrap_or(default_max_outgroup_count);
-    let min_outgroup_frac  = p.min_outgroup_frac.unwrap_or(0.0);
-    let max_outgroup_frac  = p.max_outgroup_frac.unwrap_or(1.0);
-
-    for (v, lo, hi) in [
-        ("--min-frac/--max-frac",                        min_frac,           max_frac),
-        ("--min-outgroup-frac/--max-outgroup-frac",       min_outgroup_frac,  max_outgroup_frac),
-    ] {
-        if !(0.0..=1.0).contains(&lo) || !(0.0..=1.0).contains(&hi) {
-            return Err(format!("{v}: fraction values must be in [0.0, 1.0]"));
-        }
-        if lo > hi {
-            return Err(format!("{v}: min ({lo}) is greater than max ({hi})"));
-        }
-    }
-    if min_count > max_count {
-        return Err(format!("--min-count/--max-count: min ({min_count}) is greater than max ({max_count})"));
-    }
-    if min_outgroup_count > max_outgroup_count {
-        return Err(format!("--min-outgroup-count/--max-outgroup-count: min ({min_outgroup_count}) is greater than max ({max_outgroup_count})"));
-    }
-
-    Ok(GroupQuorumFilter {
-        ingroup_idx,
-        outgroup_idx,
-        threshold: p.threshold,
-        min_count,
-        max_count,
-        min_frac,
-        max_frac,
-        min_outgroup_count,
-        max_outgroup_count,
-        min_outgroup_frac,
-        max_outgroup_frac,
-    })
-}
diff --git a/src/obikmer/src/cmd/select/mod.rs b/src/obikmer/src/cmd/select/mod.rs
index e74761b2..5f4180ad 100644
--- a/src/obikmer/src/cmd/select/mod.rs
+++ b/src/obikmer/src/cmd/select/mod.rs
@@ -2,13 +2,11 @@ use std::collections::{BTreeMap, HashMap};
 use std::path::PathBuf;
 
 use clap::{Args, ValueEnum};
-use obikindex::{GenomeInfo, KmerIndex};
+use obikindex::{IndexMeta, KmerIndex};
 use obikpartitionner::{AggOp, OutputCol};
 use obisys::Reporter;
 use tracing::info;
 
-use super::predicate::matching_genome_indices;
-
 // ── CLI types ─────────────────────────────────────────────────────────────────
 
 #[derive(Debug, Clone, Copy, PartialEq, Eq, ValueEnum)]
@@ -114,9 +112,11 @@ fn default_op(src_is_count: bool) -> AggOp {
 /// Returns `(specs, output_presence)`.
 fn build_specs(
     args: &SelectArgs,
-    genomes: &[GenomeInfo],
+    meta: &IndexMeta,
     src_is_count: bool,
 ) -> (Vec<OutputCol>, bool) {
+    let genomes = &meta.genomes;
+
     // ── 1. Build group_indices: name → Vec<usize> ────────────────────────────
     // Also keep insertion order for the default `--select *` case.
     let mut group_order: Vec<String> = Vec::new();
@@ -137,7 +137,7 @@ fn build_specs(
     } else {
         for raw in &args.group {
             let (name, pred) = parse_name_value(raw, "--group");
-            let idxs = matching_genome_indices(&pred, genomes).unwrap_or_else(|e| {
+            let idxs = meta.matching_genome_indices(&pred).unwrap_or_else(|e| {
                 eprintln!("error in --group {name}: {e}");
                 std::process::exit(1);
             });
@@ -231,7 +231,7 @@ pub fn run(args: SelectArgs) {
     });
 
     let src_is_count = src.meta().config.with_counts;
-    let (specs, output_presence) = build_specs(&args, &src.meta().genomes.clone(), src_is_count);
+    let (specs, output_presence) = build_specs(&args, src.meta(), src_is_count);
 
     info!(
         "select: {} genome(s) → {} output column(s), output={}",
diff --git a/src/obikmer/src/cmd/unitig/mod.rs b/src/obikmer/src/cmd/unitig/mod.rs
index daac7cfa..62ad39b9 100644
--- a/src/obikmer/src/cmd/unitig/mod.rs
+++ b/src/obikmer/src/cmd/unitig/mod.rs
@@ -35,7 +35,7 @@ pub fn run(args: UnitigArgs) {
 
     info!("unitig: building de Bruijn graph from {n} partition(s) (k={k})");
 
-    let filters = args.filter.build_filters(&idx.meta().genomes);
+    let filters = args.filter.build_filters(idx.meta());
     let partition = idx.partition();
     let mut rep = Reporter::new();
 
-- 
2.54.0


From 79346c0c86715f3b95d2af95f0cfb831a3235107 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Thu, 13 Aug 2026 12:55:36 +0200
Subject: [PATCH 09/46] Add modular data structures, parallel pipelines, and
 system profiling

Establishes foundational infrastructure across multiple crates by introducing unified persistent bit matrix storage with columnar, packed, and implicit variants, alongside De Bruijn graph node encoding and unitig iteration logic. Adds a macro-driven parallel pipeline scheduler featuring NUMA-aware runners, bounded channels, and memory budgets to enforce concurrency limits. Implements streaming nucleotide parsers with pooled page buffers for FASTA, FASTQ, and Genbank formats, complemented by system resource monitoring, progress tracking, and stage profiling utilities. Collectively, these changes provide the core data models, execution frameworks, and I/O pipelines required for downstream k-mer indexing and analysis workloads.
---
 src/obicompactvec/src/bitmatrix.rs            |  578 -------
 src/obicompactvec/src/bitmatrix/builder.rs    |   58 +
 src/obicompactvec/src/bitmatrix/columnar.rs   |   70 +
 src/obicompactvec/src/bitmatrix/group_ops.rs  |   68 +
 src/obicompactvec/src/bitmatrix/mod.rs        |   29 +
 src/obicompactvec/src/bitmatrix/packed.rs     |  181 ++
 src/obicompactvec/src/bitmatrix/pairwise.rs   |   56 +
 src/obicompactvec/src/bitmatrix/persistent.rs |  181 ++
 .../src/{debruijn.rs => debruijn/graph.rs}    |  300 +---
 src/obidebruinj/src/debruijn/mod.rs           |   20 +
 src/obidebruinj/src/debruijn/node.rs          |  148 ++
 src/obidebruinj/src/debruijn/unitig_iter.rs   |   61 +
 src/obidebruinj/src/debruijn/walk.rs          |   85 +
 src/obikindex/src/numa/mod.rs                 |   17 +
 src/obikindex/src/{numa.rs => numa/runner.rs} |  128 +-
 src/obikindex/src/numa/topology.rs            |  121 ++
 src/obikindex/src/siblings.rs                 | 1460 -----------------
 src/obikindex/src/siblings/alignment.rs       |  185 +++
 src/obikindex/src/siblings/build.rs           |  255 +++
 src/obikindex/src/siblings/cache.rs           |  121 ++
 src/obikindex/src/siblings/cardinality.rs     |  204 +++
 src/obikindex/src/siblings/distance.rs        |  305 ++++
 src/obikindex/src/siblings/helpers.rs         |   49 +
 src/obikindex/src/siblings/mod.rs             |   73 +
 src/obikindex/src/siblings/stats.rs           |  192 +++
 src/obikindex/src/siblings/tests.rs           |  186 +++
 .../{merge_layer.rs => merge_layer/mod.rs}    |  101 +-
 .../src/merge_layer/src_layer.rs              |   95 ++
 src/obikpartitionner/src/partition.rs         |  662 --------
 src/obikpartitionner/src/partition/count.rs   |   80 +
 .../src/partition/dereplicate.rs              |  144 ++
 .../src/partition/kmer_partition.rs           |  341 ++++
 src/obikpartitionner/src/partition/mod.rs     |   19 +
 src/obikpartitionner/src/partition/tests.rs   |  113 ++
 src/obikrope/src/cursor.rs                    |  828 ----------
 src/obikrope/src/cursor/backward.rs           |  149 ++
 src/obikrope/src/cursor/forward.rs            |  142 ++
 src/obikrope/src/cursor/mod.rs                |   53 +
 src/obikrope/src/cursor/state.rs              |   72 +
 src/obikrope/src/cursor/tests.rs              |  298 ++++
 src/obikrope/src/cursor/traits.rs             |  127 ++
 src/obipipeline/src/scheduler.rs              |  878 ----------
 src/obipipeline/src/scheduler/error.rs        |   35 +
 src/obipipeline/src/scheduler/macros.rs       |  373 +++++
 src/obipipeline/src/scheduler/mod.rs          |   19 +
 src/obipipeline/src/scheduler/pipe.rs         |  117 ++
 src/obipipeline/src/scheduler/pool.rs         |  203 +++
 src/obipipeline/src/scheduler/runner.rs       |  118 ++
 src/obipipeline/src/scheduler/types.rs        |   49 +
 src/obiread/src/nucstream.rs                  |  733 ---------
 src/obiread/src/nucstream/fasta.rs            |  128 ++
 src/obiread/src/nucstream/fastq.rs            |  132 ++
 src/obiread/src/nucstream/genbank.rs          |  181 ++
 src/obiread/src/nucstream/mod.rs              |   40 +
 src/obiread/src/nucstream/overlap.rs          |   81 +
 src/obiread/src/nucstream/page.rs             |   80 +
 src/obiread/src/nucstream/stream.rs           |  135 ++
 src/obiskio/src/unitig_index.rs               |  550 -------
 src/obiskio/src/unitig_index/kmer_iter.rs     |   86 +
 src/obiskio/src/unitig_index/kmer_raw.rs      |   33 +
 src/obiskio/src/unitig_index/mod.rs           |   48 +
 src/obiskio/src/unitig_index/reader.rs        |  246 +++
 src/obiskio/src/unitig_index/writer.rs        |  178 ++
 src/obisys/src/budget.rs                      |   65 +
 src/obisys/src/lib.rs                         |  881 +---------
 src/obisys/src/lock.rs                        |   42 +
 src/obisys/src/progress.rs                    |  114 ++
 src/obisys/src/resources.rs                   |  355 ++++
 src/obisys/src/stage.rs                       |  292 ++++
 69 files changed, 7487 insertions(+), 7060 deletions(-)
 delete mode 100644 src/obicompactvec/src/bitmatrix.rs
 create mode 100644 src/obicompactvec/src/bitmatrix/builder.rs
 create mode 100644 src/obicompactvec/src/bitmatrix/columnar.rs
 create mode 100644 src/obicompactvec/src/bitmatrix/group_ops.rs
 create mode 100644 src/obicompactvec/src/bitmatrix/mod.rs
 create mode 100644 src/obicompactvec/src/bitmatrix/packed.rs
 create mode 100644 src/obicompactvec/src/bitmatrix/pairwise.rs
 create mode 100644 src/obicompactvec/src/bitmatrix/persistent.rs
 rename src/obidebruinj/src/{debruijn.rs => debruijn/graph.rs} (51%)
 create mode 100644 src/obidebruinj/src/debruijn/mod.rs
 create mode 100644 src/obidebruinj/src/debruijn/node.rs
 create mode 100644 src/obidebruinj/src/debruijn/unitig_iter.rs
 create mode 100644 src/obidebruinj/src/debruijn/walk.rs
 create mode 100644 src/obikindex/src/numa/mod.rs
 rename src/obikindex/src/{numa.rs => numa/runner.rs} (77%)
 create mode 100644 src/obikindex/src/numa/topology.rs
 delete mode 100644 src/obikindex/src/siblings.rs
 create mode 100644 src/obikindex/src/siblings/alignment.rs
 create mode 100644 src/obikindex/src/siblings/build.rs
 create mode 100644 src/obikindex/src/siblings/cache.rs
 create mode 100644 src/obikindex/src/siblings/cardinality.rs
 create mode 100644 src/obikindex/src/siblings/distance.rs
 create mode 100644 src/obikindex/src/siblings/helpers.rs
 create mode 100644 src/obikindex/src/siblings/mod.rs
 create mode 100644 src/obikindex/src/siblings/stats.rs
 create mode 100644 src/obikindex/src/siblings/tests.rs
 rename src/obikpartitionner/src/{merge_layer.rs => merge_layer/mod.rs} (85%)
 create mode 100644 src/obikpartitionner/src/merge_layer/src_layer.rs
 delete mode 100644 src/obikpartitionner/src/partition.rs
 create mode 100644 src/obikpartitionner/src/partition/count.rs
 create mode 100644 src/obikpartitionner/src/partition/dereplicate.rs
 create mode 100644 src/obikpartitionner/src/partition/kmer_partition.rs
 create mode 100644 src/obikpartitionner/src/partition/mod.rs
 create mode 100644 src/obikpartitionner/src/partition/tests.rs
 delete mode 100644 src/obikrope/src/cursor.rs
 create mode 100644 src/obikrope/src/cursor/backward.rs
 create mode 100644 src/obikrope/src/cursor/forward.rs
 create mode 100644 src/obikrope/src/cursor/mod.rs
 create mode 100644 src/obikrope/src/cursor/state.rs
 create mode 100644 src/obikrope/src/cursor/tests.rs
 create mode 100644 src/obikrope/src/cursor/traits.rs
 delete mode 100644 src/obipipeline/src/scheduler.rs
 create mode 100644 src/obipipeline/src/scheduler/error.rs
 create mode 100644 src/obipipeline/src/scheduler/macros.rs
 create mode 100644 src/obipipeline/src/scheduler/mod.rs
 create mode 100644 src/obipipeline/src/scheduler/pipe.rs
 create mode 100644 src/obipipeline/src/scheduler/pool.rs
 create mode 100644 src/obipipeline/src/scheduler/runner.rs
 create mode 100644 src/obipipeline/src/scheduler/types.rs
 delete mode 100644 src/obiread/src/nucstream.rs
 create mode 100644 src/obiread/src/nucstream/fasta.rs
 create mode 100644 src/obiread/src/nucstream/fastq.rs
 create mode 100644 src/obiread/src/nucstream/genbank.rs
 create mode 100644 src/obiread/src/nucstream/mod.rs
 create mode 100644 src/obiread/src/nucstream/overlap.rs
 create mode 100644 src/obiread/src/nucstream/page.rs
 create mode 100644 src/obiread/src/nucstream/stream.rs
 delete mode 100644 src/obiskio/src/unitig_index.rs
 create mode 100644 src/obiskio/src/unitig_index/kmer_iter.rs
 create mode 100644 src/obiskio/src/unitig_index/kmer_raw.rs
 create mode 100644 src/obiskio/src/unitig_index/mod.rs
 create mode 100644 src/obiskio/src/unitig_index/reader.rs
 create mode 100644 src/obiskio/src/unitig_index/writer.rs
 create mode 100644 src/obisys/src/budget.rs
 create mode 100644 src/obisys/src/lock.rs
 create mode 100644 src/obisys/src/progress.rs
 create mode 100644 src/obisys/src/resources.rs
 create mode 100644 src/obisys/src/stage.rs

diff --git a/src/obicompactvec/src/bitmatrix.rs b/src/obicompactvec/src/bitmatrix.rs
deleted file mode 100644
index 5bc231e5..00000000
--- a/src/obicompactvec/src/bitmatrix.rs
+++ /dev/null
@@ -1,578 +0,0 @@
-use std::fs::{self, File};
-use std::io::{self, BufWriter, Read as _, Write as _};
-use std::path::{Path, PathBuf};
-
-use memmap2::Mmap;
-use ndarray::{Array1, Array2};
-use rayon::prelude::*;
-
-use crate::bitvec::{PersistentBitVec, PersistentBitVecBuilder};
-use crate::colgroup::{ColGroup, MatrixGroupOps};
-use crate::layer_meta::LayerMeta;
-use crate::meta::MatrixMeta;
-use crate::tempbitvec::{TempBitVec, TempBitVecBuilder};
-use crate::tempintvec::{TempCompactIntVec, TempCompactIntVecBuilder};
-use crate::views::BitSliceView;
-
-fn col_path(dir: &Path, col: usize) -> PathBuf {
-    dir.join(format!("col_{col:06}.pbiv"))
-}
-
-// ── ColumnarBitMatrix ─────────────────────────────────────────────────────────
-
-/// Per-column file layout (original format).
-pub struct ColumnarBitMatrix {
-    cols: Vec<PersistentBitVec>,
-    n:    usize,
-}
-
-impl ColumnarBitMatrix {
-    pub(crate) fn open(dir: &Path) -> io::Result<Self> {
-        let meta = MatrixMeta::load(dir)?;
-        let cols = (0..meta.n_cols)
-            .map(|c| PersistentBitVec::open(&col_path(dir, c)))
-            .collect::<io::Result<Vec<_>>>()?;
-        Ok(Self { cols, n: meta.n })
-    }
-
-    pub(crate) fn n(&self)      -> usize { self.n }
-    pub(crate) fn n_cols(&self) -> usize { self.cols.len() }
-    pub(crate) fn col(&self, c: usize) -> &PersistentBitVec { &self.cols[c] }
-
-    pub(crate) fn row(&self, slot: usize) -> Box<[bool]> {
-        self.cols.iter().map(|c| c.get(slot)).collect()
-    }
-
-    pub(crate) fn fill_row(&self, slot: usize, buf: &mut [u32]) {
-        for (c, col) in self.cols.iter().enumerate() {
-            buf[c] = col.get(slot) as u32;
-        }
-    }
-
-    pub(crate) fn count_ones(&self) -> Array1<u64> {
-        let counts: Vec<u64> = (0..self.n_cols())
-            .into_par_iter()
-            .map(|c| self.col(c).count_ones())
-            .collect();
-        Array1::from_vec(counts)
-    }
-
-    pub(crate) fn partial_jaccard_dist_matrix(&self) -> (Array2<u64>, Array2<u64>) {
-        pairwise2_matrix(self.n_cols(), |i, j| self.col(i).partial_jaccard_dist(self.col(j)))
-    }
-
-    pub(crate) fn partial_hamming_dist_matrix(&self) -> Array2<u64> {
-        pairwise_matrix(self.n_cols(), |i, j| self.col(i).hamming_dist(self.col(j)))
-    }
-
-    pub(crate) fn append_column(dir: &Path, value_of: impl Fn(usize) -> bool) -> io::Result<()> {
-        let mut meta = MatrixMeta::load(dir)?;
-        let mut b = PersistentBitVecBuilder::new(meta.n, &col_path(dir, meta.n_cols))?;
-        for slot in 0..meta.n {
-            b.set(slot, value_of(slot));
-        }
-        b.close()?;
-        meta.n_cols += 1;
-        meta.save(dir)
-    }
-}
-
-// ── PackedBitMatrix ───────────────────────────────────────────────────────────
-
-const PBMX_MAGIC:  [u8; 4] = *b"PBMX";
-const PBMX_HEADER: usize   = 24; // magic(4) + pad(4) + n_rows(8) + n_cols(8)
-const PBIV_HEADER: usize   = 16; // magic(4) + pad(4) + n(8)
-
-/// Single-file packed layout: all columns concatenated behind a header.
-pub struct PackedBitMatrix {
-    mmap:         Mmap,
-    n_rows:       usize,
-    n_cols:       usize,
-    /// Absolute byte offset to the start of each column's bit data
-    /// (= file offset of the PBIV blob + PBIV_HEADER).
-    data_offsets: Vec<usize>,
-}
-
-impl PackedBitMatrix {
-    pub(crate) fn open(path: &Path) -> io::Result<Self> {
-        let mmap = unsafe { Mmap::map(&File::open(path)?)? };
-        if mmap.len() < PBMX_HEADER {
-            return Err(io::Error::new(io::ErrorKind::InvalidData, "PBMX file too short"));
-        }
-        if &mmap[0..4] != &PBMX_MAGIC {
-            return Err(io::Error::new(io::ErrorKind::InvalidData, "bad PBMX magic"));
-        }
-        let n_rows = u64::from_le_bytes(mmap[8..16].try_into().unwrap())  as usize;
-        let n_cols = u64::from_le_bytes(mmap[16..24].try_into().unwrap()) as usize;
-
-        let mut data_offsets = Vec::with_capacity(n_cols);
-        for c in 0..n_cols {
-            let off_pos = PBMX_HEADER + c * 8;
-            let col_file_off = u64::from_le_bytes(mmap[off_pos..off_pos+8].try_into().unwrap()) as usize;
-            data_offsets.push(col_file_off + PBIV_HEADER);
-        }
-
-        Ok(Self { mmap, n_rows, n_cols, data_offsets })
-    }
-
-    #[inline]
-    pub(crate) fn fill_row(&self, slot: usize, buf: &mut [u32]) {
-        for (c, &data_off) in self.data_offsets.iter().enumerate() {
-            buf[c] = ((self.mmap[data_off + (slot >> 3)] >> (slot & 7)) & 1) as u32;
-        }
-    }
-
-    pub(crate) fn row(&self, slot: usize) -> Box<[bool]> {
-        (0..self.n_cols).map(|c| {
-            (self.mmap[self.data_offsets[c] + (slot >> 3)] >> (slot & 7)) & 1 != 0
-        }).collect()
-    }
-
-    fn col_bytes(&self, c: usize) -> &[u8] {
-        let start = self.data_offsets[c];
-        &self.mmap[start..start + self.n_rows.div_ceil(8)]
-    }
-
-    fn col_words(&self, c: usize) -> &[u64] {
-        let nw = self.n_rows.div_ceil(64);
-        // SAFETY: data_offsets[c] is always 8-byte aligned.
-        // PBMX header = 24 + n_cols×8 (multiple of 8); each PBIV blob =
-        // 16 + nwords×8 (multiple of 8); mmap base is page-aligned.
-        let ptr = self.mmap[self.data_offsets[c]..].as_ptr() as *const u64;
-        unsafe { std::slice::from_raw_parts(ptr, nw) }
-    }
-
-    pub(crate) fn col_slice(&self, c: usize) -> BitSliceView<'_> {
-        BitSliceView::new(self.col_words(c), self.n_rows)
-    }
-
-    pub(crate) fn col_persist(&self, c: usize, path: &Path) -> io::Result<PersistentBitVecBuilder> {
-        PersistentBitVecBuilder::from_raw_bytes(self.col_bytes(c), self.n_rows, path)
-    }
-
-    pub(crate) fn count_ones(&self) -> Array1<u64> {
-        Array1::from_vec(
-            (0..self.n_cols).into_par_iter()
-                .map(|c| self.col_slice(c).count_ones())
-                .collect()
-        )
-    }
-
-    pub(crate) fn partial_jaccard_dist_matrix(&self) -> (Array2<u64>, Array2<u64>) {
-        pairwise2_matrix(self.n_cols, |i, j| {
-            self.col_slice(i).partial_jaccard_dist(self.col_slice(j))
-        })
-    }
-
-    pub(crate) fn partial_hamming_dist_matrix(&self) -> Array2<u64> {
-        pairwise_matrix(self.n_cols, |i, j| {
-            self.col_slice(i).hamming_dist(self.col_slice(j))
-        })
-    }
-}
-
-/// Reads just the `n_cols` field from an existing packed matrix's header,
-/// without mapping the file. Used by `pack_bit_matrix` to tell a genuinely
-/// complete pack from a stale one that predates a later column-widening.
-fn packed_bit_matrix_n_cols(path: &Path) -> io::Result<usize> {
-    let mut f = File::open(path)?;
-    let mut header = [0u8; PBMX_HEADER];
-    f.read_exact(&mut header)?;
-    Ok(u64::from_le_bytes(header[16..24].try_into().unwrap()) as usize)
-}
-
-/// Build `presence/matrix.pbmx` from existing `col_*.pbiv` files.
-pub fn pack_bit_matrix(dir: &Path) -> io::Result<()> {
-    let packed_path = dir.join("matrix.pbmx");
-
-    let meta = match MatrixMeta::load(dir) {
-        Ok(meta) => meta,
-        Err(e) => {
-            // No columnar data pending: either this layer was already
-            // packed and cleaned up (matrix.pbmx complete, nothing left to
-            // do), or genuinely nothing was ever written here.
-            return if packed_path.exists() { Ok(()) } else { Err(e) };
-        }
-    };
-
-    // A `matrix.pbmx` can already exist here even though columnar data is
-    // still pending — e.g. copied verbatim from a merge's base source
-    // before this layer was widened with more genome columns (see
-    // `obikpartitionner::merge_partition`). Only skip (re-)packing if the
-    // existing file already reflects the current column count; otherwise
-    // the columnar files are newer and must be (re-)packed, overwriting the
-    // stale one — never silently discarded as "leftover cleanup".
-    if packed_bit_matrix_n_cols(&packed_path).ok() == Some(meta.n_cols) {
-        for c in 0..meta.n_cols { let _ = fs::remove_file(col_path(dir, c)); }
-        let _ = fs::remove_file(dir.join("meta.json"));
-        return Ok(());
-    }
-
-    let n_cols = meta.n_cols;
-
-    // Compute offsets from file sizes — no column data loaded into RAM.
-    let col_sizes: Vec<u64> = (0..n_cols)
-        .map(|c| fs::metadata(col_path(dir, c)).map(|m| m.len()))
-        .collect::<io::Result<_>>()?;
-
-    let header_size = (PBMX_HEADER + n_cols * 8) as u64;
-    let mut col_offset = header_size;
-    let mut offsets = Vec::with_capacity(n_cols);
-    for &size in &col_sizes {
-        offsets.push(col_offset);
-        col_offset += size;
-    }
-
-    // Write to a temp file; rename atomically so a killed process never leaves
-    // a truncated matrix.pbmx that would be mistaken for a complete file.
-    let tmp_path = dir.join("matrix.pbmx.tmp");
-    let mut out = BufWriter::new(File::create(&tmp_path)?);
-    out.write_all(&PBMX_MAGIC)?;
-    out.write_all(&[0u8; 4])?;
-    out.write_all(&(meta.n as u64).to_le_bytes())?;
-    out.write_all(&(n_cols as u64).to_le_bytes())?;
-    for &off in &offsets { out.write_all(&off.to_le_bytes())?; }
-    for c in 0..n_cols {
-        io::copy(&mut File::open(col_path(dir, c))?, &mut out)?;
-    }
-    out.flush()?;
-    drop(out);
-    fs::rename(&tmp_path, &packed_path)?;
-
-    for c in 0..n_cols { fs::remove_file(col_path(dir, c))?; }
-    fs::remove_file(dir.join("meta.json"))?;
-    Ok(())
-}
-
-// ── PersistentBitMatrix — public enum ────────────────────────────────────────
-
-/// Bit matrix that transparently handles columnar, packed, and implicit formats.
-///
-/// - `Columnar`: per-column `.pbiv` files (original format, used during build)
-/// - `Packed`:   single `matrix.pbmx` file (optimised for query — one `mmap`)
-/// - `Implicit`: no file — all values are 1 (mono-genome presence/absence)
-pub enum PersistentBitMatrix {
-    Columnar(ColumnarBitMatrix),
-    Packed(PackedBitMatrix),
-    Implicit { n_rows: usize, n_cols: usize },
-}
-
-impl PersistentBitMatrix {
-    /// Open from `layer_dir`, auto-detecting the format.
-    ///
-    /// Checks (in order):
-    /// 1. `layer_dir/presence/matrix.pbmx`  → Packed
-    /// 2. `layer_dir/presence/meta.json`    → Columnar
-    /// 3. `layer_dir/layer_meta.json`        → Implicit (new index)
-    /// 4. `layer_dir/unitigs.bin`            → Implicit with warning (old index)
-    pub fn open(layer_dir: &Path) -> io::Result<Self> {
-        let presence_dir = layer_dir.join("presence");
-
-        if presence_dir.join("matrix.pbmx").exists() {
-            return Ok(Self::Packed(PackedBitMatrix::open(&presence_dir.join("matrix.pbmx"))?));
-        }
-
-        if MatrixMeta::load(&presence_dir).is_ok() {
-            return Ok(Self::Columnar(ColumnarBitMatrix::open(&presence_dir)?));
-        }
-
-        // No presence matrix → Implicit; requires layer_meta.json
-        let meta = LayerMeta::load(layer_dir).map_err(|_| io::Error::new(
-            io::ErrorKind::NotFound,
-            format!(
-                "no presence matrix and no layer_meta.json in {} — run 'obikmer upgrade'",
-                layer_dir.display()
-            ),
-        ))?;
-        Ok(Self::Implicit { n_rows: meta.n, n_cols: 1 })
-    }
-
-    pub fn n(&self) -> usize {
-        match self {
-            Self::Columnar(m)            => m.n(),
-            Self::Packed(m)              => m.n_rows,
-            Self::Implicit { n_rows, .. } => *n_rows,
-        }
-    }
-
-    pub fn n_cols(&self) -> usize {
-        match self {
-            Self::Columnar(m)            => m.n_cols(),
-            Self::Packed(m)              => m.n_cols,
-            Self::Implicit { n_cols, .. } => *n_cols,
-        }
-    }
-
-    pub fn col(&self, c: usize) -> &PersistentBitVec {
-        match self {
-            Self::Columnar(m) => m.col(c),
-            _ => panic!("col() only available on Columnar PersistentBitMatrix"),
-        }
-    }
-
-    pub fn col_view(&self, c: usize) -> BitSliceView<'_> {
-        match self {
-            Self::Columnar(m) => m.col(c).view(),
-            Self::Packed(m)   => m.col_slice(c),
-            Self::Implicit { .. } => panic!("col_view() not available on Implicit PersistentBitMatrix"),
-        }
-    }
-
-    /// Column-major point lookup: value at column `c`, slot `slot`, as 0/1.
-    ///
-    /// Unlike [`col_view`](Self::col_view), this never panics on `Implicit`
-    /// (every column reads as present, per the mono-genome fast path) — safe
-    /// to call for any `c < self.n_cols()`.
-    pub fn get(&self, c: usize, slot: usize) -> u32 {
-        match self {
-            Self::Columnar(m) => m.col(c).get(slot) as u32,
-            Self::Packed(m)   => m.col_slice(c).get(slot) as u32,
-            Self::Implicit { .. } => 1,
-        }
-    }
-
-    pub fn col_persist(&self, c: usize, path: &Path) -> io::Result<PersistentBitVecBuilder> {
-        match self {
-            Self::Columnar(m) => PersistentBitVecBuilder::build_from(m.col(c), path),
-            Self::Packed(m)   => m.col_persist(c, path),
-            Self::Implicit { n_rows, .. } => {
-                PersistentBitVecBuilder::new_ones(*n_rows, path)
-            }
-        }
-    }
-
-    pub fn row(&self, slot: usize) -> Box<[bool]> {
-        match self {
-            Self::Columnar(m)             => m.row(slot),
-            Self::Packed(m)               => m.row(slot),
-            Self::Implicit { n_cols, .. } => vec![true; *n_cols].into_boxed_slice(),
-        }
-    }
-
-    /// Fill `buf[i]` with `col_i[slot]` as 0/1 u32, without allocating.
-    pub fn fill_row(&self, slot: usize, buf: &mut [u32]) {
-        match self {
-            Self::Columnar(m)             => m.fill_row(slot, buf),
-            Self::Packed(m)               => m.fill_row(slot, buf),
-            Self::Implicit { n_cols, .. } => buf[..*n_cols].fill(1),
-        }
-    }
-
-    pub fn count_ones(&self) -> Array1<u64> {
-        match self {
-            Self::Columnar(m)              => m.count_ones(),
-            Self::Packed(m)                => m.count_ones(),
-            Self::Implicit { n_rows, n_cols } => Array1::from_elem(*n_cols, *n_rows as u64),
-        }
-    }
-
-    pub fn partial_jaccard_dist_matrix(&self) -> (Array2<u64>, Array2<u64>) {
-        match self {
-            Self::Columnar(m)                 => m.partial_jaccard_dist_matrix(),
-            Self::Packed(m)                   => m.partial_jaccard_dist_matrix(),
-            Self::Implicit { n_rows, n_cols } => {
-                let v = *n_rows as u64;
-                let n = *n_cols;
-                let mut inter = Array2::zeros((n, n));
-                let mut union = Array2::zeros((n, n));
-                for i in 0..n { for j in 0..n {
-                    inter[[i, j]] = v; union[[i, j]] = v;
-                }}
-                (inter, union)
-            }
-        }
-    }
-
-    pub fn partial_hamming_dist_matrix(&self) -> Array2<u64> {
-        match self {
-            Self::Columnar(m)              => m.partial_hamming_dist_matrix(),
-            Self::Packed(m)                => m.partial_hamming_dist_matrix(),
-            Self::Implicit { n_cols, .. }  => Array2::zeros((*n_cols, *n_cols)),
-        }
-    }
-
-    /// Append a new column to an on-disk Columnar matrix.
-    pub fn append_column(dir: &Path, value_of: impl Fn(usize) -> bool) -> io::Result<()> {
-        ColumnarBitMatrix::append_column(dir, value_of)
-    }
-}
-
-// ── Trait impls ───────────────────────────────────────────────────────────────
-
-use crate::traits::{BitPartials, ColumnWeights};
-
-impl ColumnWeights for PersistentBitMatrix {
-    fn col_weights(&self) -> Array1<u64> { self.count_ones() }
-}
-
-impl BitPartials for PersistentBitMatrix {
-    fn partial_jaccard(&self) -> (Array2<u64>, Array2<u64>) {
-        self.partial_jaccard_dist_matrix()
-    }
-    fn partial_hamming(&self) -> Array2<u64> {
-        self.partial_hamming_dist_matrix()
-    }
-}
-
-// ── Builder (unchanged — always builds Columnar) ──────────────────────────────
-
-pub struct PersistentBitMatrixBuilder {
-    dir:    PathBuf,
-    n:      usize,
-    n_cols: usize,
-}
-
-impl PersistentBitMatrixBuilder {
-    pub fn new(n: usize, dir: &Path) -> io::Result<Self> {
-        fs::create_dir_all(dir)?;
-        Ok(Self { dir: dir.to_path_buf(), n, n_cols: 0 })
-    }
-
-    pub fn n(&self)      -> usize { self.n }
-    pub fn n_cols(&self) -> usize { self.n_cols }
-
-    pub fn add_col(&mut self) -> io::Result<PersistentBitVecBuilder> {
-        let path = col_path(&self.dir, self.n_cols);
-        self.n_cols += 1;
-        PersistentBitVecBuilder::new(self.n, &path)
-    }
-
-    pub fn add_col_ones(&mut self) -> io::Result<PersistentBitVecBuilder> {
-        let path = col_path(&self.dir, self.n_cols);
-        self.n_cols += 1;
-        PersistentBitVecBuilder::new_ones(self.n, &path)
-    }
-
-    pub fn add_col_from(&mut self, src: &TempBitVec) -> io::Result<()> {
-        src.make_persistent(&col_path(&self.dir, self.n_cols))?;
-        self.n_cols += 1;
-        Ok(())
-    }
-
-    pub fn add_col_from_int(&mut self, src: &TempCompactIntVec) -> io::Result<()> {
-        let path = col_path(&self.dir, self.n_cols);
-        self.n_cols += 1;
-        let mut b = PersistentBitVecBuilder::new(self.n, &path)?;
-        b.or_where(src.view(), |v| v > 0);
-        b.close()
-    }
-
-    pub fn close(self) -> io::Result<()> {
-        MatrixMeta { n: self.n, n_cols: self.n_cols }.save(&self.dir)
-    }
-}
-
-// ── MatrixGroupOps ────────────────────────────────────────────────────────────
-
-impl MatrixGroupOps for PersistentBitMatrix {
-    fn partial_group_presence_count(&self, g: &ColGroup, _threshold: u32) -> io::Result<TempCompactIntVec> {
-        // Bit matrices store 0/1 — threshold is structurally always 1.
-        let n = self.n();
-        if g.indices.len() < 255 {
-            let mut builder = TempCompactIntVecBuilder::new(n)?;
-            for &c in &g.indices {
-                builder.inc_present_fast(self.col_view(c));
-            }
-            builder.freeze()
-        } else {
-            let mut result = TempCompactIntVecBuilder::new(n)?;
-            for chunk in g.indices.chunks(254) {
-                let mut chunk_b = TempCompactIntVecBuilder::new(n)?;
-                for &c in chunk {
-                    chunk_b.inc_present_fast(self.col_view(c));
-                }
-                let frozen = chunk_b.freeze()?;
-                result.add(frozen.view());
-            }
-            result.freeze()
-        }
-    }
-
-    fn partial_group_sum(&self, g: &ColGroup) -> io::Result<TempCompactIntVec> {
-        // For bit matrices, sum = count of 1-bits — identical to presence_count.
-        self.partial_group_presence_count(g, 1)
-    }
-
-    fn partial_group_any(&self, g: &ColGroup, _threshold: u32) -> io::Result<TempBitVec> {
-        let n = self.n();
-        let mut result = TempBitVecBuilder::new(n)?;
-        for &c in &g.indices {
-            result.or(self.col_view(c));
-        }
-        result.freeze()
-    }
-
-    fn partial_group_min(&self, g: &ColGroup) -> io::Result<TempCompactIntVec> {
-        // min of 0/1 values = AND: 1 only if ALL columns are 1
-        let n = self.n();
-        let mut result = TempCompactIntVecBuilder::new(n)?;
-        if let Some((&first, rest)) = g.indices.split_first() {
-            result.inc_present_fast(self.col_view(first));
-            for &c in rest { result.mask_with(self.col_view(c)); }
-        }
-        result.freeze()
-    }
-
-    fn partial_group_max(&self, g: &ColGroup) -> io::Result<TempCompactIntVec> {
-        // max of 0/1 values = OR: 1 if any column is 1
-        let any = self.partial_group_any(g, 1)?;
-        let n = any.len();
-        let mut result = TempCompactIntVecBuilder::new(n)?;
-        result.inc_present(any.view());
-        result.freeze()
-    }
-}
-
-// ── Shared matrix helpers (also used by intmatrix.rs) ─────────────────────────
-
-fn upper_pairs(n: usize) -> Vec<(usize, usize)> {
-    (0..n).flat_map(|i| (i + 1..n).map(move |j| (i, j))).collect()
-}
-
-fn fill_symmetric<T>(n: usize, vals: impl Iterator<Item = (usize, usize, T, T)>) -> Array2<T>
-where T: Clone + Default {
-    let mut m = Array2::from_elem((n, n), T::default());
-    for (i, j, vij, vji) in vals { m[[i, j]] = vij; m[[j, i]] = vji; }
-    m
-}
-
-/// Compute a symmetric `n×n` matrix in parallel by evaluating `f(i,j)` for
-/// all upper-triangle pairs, plus `f(i,i)` for the diagonal. `T: Copy` avoids
-/// the `.clone()` needed for the lower-triangle mirror.
-///
-/// The diagonal is *not* generally `T::default()`: for a self-comparison,
-/// `f(i,i)` is often the column's own weight (e.g. intersection-with-self —
-/// see `pairwise2_matrix`), not zero. Distance finalisations that need a
-/// zero diagonal (self-distance) already overwrite it explicitly.
-pub(crate) fn pairwise_matrix<T>(n: usize, f: impl Fn(usize, usize) -> T + Sync) -> Array2<T>
-where T: Copy + Default + Send {
-    let results: Vec<(usize, usize, T)> = upper_pairs(n)
-        .into_par_iter().map(|(i, j)| (i, j, f(i, j))).collect();
-    let mut m = fill_symmetric(n, results.into_iter().map(|(i, j, v)| (i, j, v, v)));
-    for i in 0..n { m[[i, i]] = f(i, i); }
-    m
-}
-
-/// Same as `pairwise_matrix` but `f` returns two values that fill two
-/// symmetric matrices simultaneously (e.g. intersection + union for Jaccard).
-/// The diagonal is `f(i,i)` (e.g. a genome's kmer count intersected with
-/// itself), not `T::default()` — see `pairwise_matrix` for why that matters.
-pub(crate) fn pairwise2_matrix<T>(n: usize, f: impl Fn(usize, usize) -> (T, T) + Sync) -> (Array2<T>, Array2<T>)
-where T: Copy + Default + Send {
-    let results: Vec<(usize, usize, T, T)> = upper_pairs(n)
-        .into_par_iter()
-        .map(|(i, j)| { let (a, b) = f(i, j); (i, j, a, b) })
-        .collect();
-    let mut m0 = Array2::from_elem((n, n), T::default());
-    let mut m1 = Array2::from_elem((n, n), T::default());
-    for (i, j, a, b) in results {
-        m0[[i, j]] = a; m0[[j, i]] = a;
-        m1[[i, j]] = b; m1[[j, i]] = b;
-    }
-    for i in 0..n {
-        let (a, b) = f(i, i);
-        m0[[i, i]] = a;
-        m1[[i, i]] = b;
-    }
-    (m0, m1)
-}
diff --git a/src/obicompactvec/src/bitmatrix/builder.rs b/src/obicompactvec/src/bitmatrix/builder.rs
new file mode 100644
index 00000000..1f76d225
--- /dev/null
+++ b/src/obicompactvec/src/bitmatrix/builder.rs
@@ -0,0 +1,58 @@
+use std::fs;
+use std::io;
+use std::path::{Path, PathBuf};
+
+use crate::bitvec::PersistentBitVecBuilder;
+use crate::meta::MatrixMeta;
+use crate::tempbitvec::TempBitVec;
+use crate::tempintvec::TempCompactIntVec;
+
+use super::col_path;
+
+// ── Builder (unchanged — always builds Columnar) ──────────────────────────────
+
+pub struct PersistentBitMatrixBuilder {
+    dir:    PathBuf,
+    n:      usize,
+    n_cols: usize,
+}
+
+impl PersistentBitMatrixBuilder {
+    pub fn new(n: usize, dir: &Path) -> io::Result<Self> {
+        fs::create_dir_all(dir)?;
+        Ok(Self { dir: dir.to_path_buf(), n, n_cols: 0 })
+    }
+
+    pub fn n(&self)      -> usize { self.n }
+    pub fn n_cols(&self) -> usize { self.n_cols }
+
+    pub fn add_col(&mut self) -> io::Result<PersistentBitVecBuilder> {
+        let path = col_path(&self.dir, self.n_cols);
+        self.n_cols += 1;
+        PersistentBitVecBuilder::new(self.n, &path)
+    }
+
+    pub fn add_col_ones(&mut self) -> io::Result<PersistentBitVecBuilder> {
+        let path = col_path(&self.dir, self.n_cols);
+        self.n_cols += 1;
+        PersistentBitVecBuilder::new_ones(self.n, &path)
+    }
+
+    pub fn add_col_from(&mut self, src: &TempBitVec) -> io::Result<()> {
+        src.make_persistent(&col_path(&self.dir, self.n_cols))?;
+        self.n_cols += 1;
+        Ok(())
+    }
+
+    pub fn add_col_from_int(&mut self, src: &TempCompactIntVec) -> io::Result<()> {
+        let path = col_path(&self.dir, self.n_cols);
+        self.n_cols += 1;
+        let mut b = PersistentBitVecBuilder::new(self.n, &path)?;
+        b.or_where(src.view(), |v| v > 0);
+        b.close()
+    }
+
+    pub fn close(self) -> io::Result<()> {
+        MatrixMeta { n: self.n, n_cols: self.n_cols }.save(&self.dir)
+    }
+}
diff --git a/src/obicompactvec/src/bitmatrix/columnar.rs b/src/obicompactvec/src/bitmatrix/columnar.rs
new file mode 100644
index 00000000..ccbd3d53
--- /dev/null
+++ b/src/obicompactvec/src/bitmatrix/columnar.rs
@@ -0,0 +1,70 @@
+use std::io;
+use std::path::Path;
+
+use ndarray::{Array1, Array2};
+use rayon::prelude::*;
+
+use crate::bitvec::{PersistentBitVec, PersistentBitVecBuilder};
+use crate::meta::MatrixMeta;
+
+use super::col_path;
+use super::pairwise::{pairwise_matrix, pairwise2_matrix};
+
+// ── ColumnarBitMatrix ─────────────────────────────────────────────────────────
+
+/// Per-column file layout (original format).
+pub struct ColumnarBitMatrix {
+    cols: Vec<PersistentBitVec>,
+    n:    usize,
+}
+
+impl ColumnarBitMatrix {
+    pub(crate) fn open(dir: &Path) -> io::Result<Self> {
+        let meta = MatrixMeta::load(dir)?;
+        let cols = (0..meta.n_cols)
+            .map(|c| PersistentBitVec::open(&col_path(dir, c)))
+            .collect::<io::Result<Vec<_>>>()?;
+        Ok(Self { cols, n: meta.n })
+    }
+
+    pub(crate) fn n(&self)      -> usize { self.n }
+    pub(crate) fn n_cols(&self) -> usize { self.cols.len() }
+    pub(crate) fn col(&self, c: usize) -> &PersistentBitVec { &self.cols[c] }
+
+    pub(crate) fn row(&self, slot: usize) -> Box<[bool]> {
+        self.cols.iter().map(|c| c.get(slot)).collect()
+    }
+
+    pub(crate) fn fill_row(&self, slot: usize, buf: &mut [u32]) {
+        for (c, col) in self.cols.iter().enumerate() {
+            buf[c] = col.get(slot) as u32;
+        }
+    }
+
+    pub(crate) fn count_ones(&self) -> Array1<u64> {
+        let counts: Vec<u64> = (0..self.n_cols())
+            .into_par_iter()
+            .map(|c| self.col(c).count_ones())
+            .collect();
+        Array1::from_vec(counts)
+    }
+
+    pub(crate) fn partial_jaccard_dist_matrix(&self) -> (Array2<u64>, Array2<u64>) {
+        pairwise2_matrix(self.n_cols(), |i, j| self.col(i).partial_jaccard_dist(self.col(j)))
+    }
+
+    pub(crate) fn partial_hamming_dist_matrix(&self) -> Array2<u64> {
+        pairwise_matrix(self.n_cols(), |i, j| self.col(i).hamming_dist(self.col(j)))
+    }
+
+    pub(crate) fn append_column(dir: &Path, value_of: impl Fn(usize) -> bool) -> io::Result<()> {
+        let mut meta = MatrixMeta::load(dir)?;
+        let mut b = PersistentBitVecBuilder::new(meta.n, &col_path(dir, meta.n_cols))?;
+        for slot in 0..meta.n {
+            b.set(slot, value_of(slot));
+        }
+        b.close()?;
+        meta.n_cols += 1;
+        meta.save(dir)
+    }
+}
diff --git a/src/obicompactvec/src/bitmatrix/group_ops.rs b/src/obicompactvec/src/bitmatrix/group_ops.rs
new file mode 100644
index 00000000..66f12edd
--- /dev/null
+++ b/src/obicompactvec/src/bitmatrix/group_ops.rs
@@ -0,0 +1,68 @@
+use std::io;
+
+use crate::colgroup::{ColGroup, MatrixGroupOps};
+use crate::tempbitvec::{TempBitVec, TempBitVecBuilder};
+use crate::tempintvec::{TempCompactIntVec, TempCompactIntVecBuilder};
+
+use super::persistent::PersistentBitMatrix;
+
+// ── MatrixGroupOps ────────────────────────────────────────────────────────────
+
+impl MatrixGroupOps for PersistentBitMatrix {
+    fn partial_group_presence_count(&self, g: &ColGroup, _threshold: u32) -> io::Result<TempCompactIntVec> {
+        // Bit matrices store 0/1 — threshold is structurally always 1.
+        let n = self.n();
+        if g.indices.len() < 255 {
+            let mut builder = TempCompactIntVecBuilder::new(n)?;
+            for &c in &g.indices {
+                builder.inc_present_fast(self.col_view(c));
+            }
+            builder.freeze()
+        } else {
+            let mut result = TempCompactIntVecBuilder::new(n)?;
+            for chunk in g.indices.chunks(254) {
+                let mut chunk_b = TempCompactIntVecBuilder::new(n)?;
+                for &c in chunk {
+                    chunk_b.inc_present_fast(self.col_view(c));
+                }
+                let frozen = chunk_b.freeze()?;
+                result.add(frozen.view());
+            }
+            result.freeze()
+        }
+    }
+
+    fn partial_group_sum(&self, g: &ColGroup) -> io::Result<TempCompactIntVec> {
+        // For bit matrices, sum = count of 1-bits — identical to presence_count.
+        self.partial_group_presence_count(g, 1)
+    }
+
+    fn partial_group_any(&self, g: &ColGroup, _threshold: u32) -> io::Result<TempBitVec> {
+        let n = self.n();
+        let mut result = TempBitVecBuilder::new(n)?;
+        for &c in &g.indices {
+            result.or(self.col_view(c));
+        }
+        result.freeze()
+    }
+
+    fn partial_group_min(&self, g: &ColGroup) -> io::Result<TempCompactIntVec> {
+        // min of 0/1 values = AND: 1 only if ALL columns are 1
+        let n = self.n();
+        let mut result = TempCompactIntVecBuilder::new(n)?;
+        if let Some((&first, rest)) = g.indices.split_first() {
+            result.inc_present_fast(self.col_view(first));
+            for &c in rest { result.mask_with(self.col_view(c)); }
+        }
+        result.freeze()
+    }
+
+    fn partial_group_max(&self, g: &ColGroup) -> io::Result<TempCompactIntVec> {
+        // max of 0/1 values = OR: 1 if any column is 1
+        let any = self.partial_group_any(g, 1)?;
+        let n = any.len();
+        let mut result = TempCompactIntVecBuilder::new(n)?;
+        result.inc_present(any.view());
+        result.freeze()
+    }
+}
diff --git a/src/obicompactvec/src/bitmatrix/mod.rs b/src/obicompactvec/src/bitmatrix/mod.rs
new file mode 100644
index 00000000..85dcef0a
--- /dev/null
+++ b/src/obicompactvec/src/bitmatrix/mod.rs
@@ -0,0 +1,29 @@
+//! Bit matrices (presence/absence), in three on-disk formats transparently
+//! handled by [`PersistentBitMatrix`]: per-column `Columnar`, single-file
+//! mmap'd `Packed`, and implicit (mono-genome, no file at all).
+//!
+//! Submodules: [`columnar`] (build-time per-column format), [`packed`]
+//! (query-optimised single-mmap format + [`pack_bit_matrix`]),
+//! [`persistent`] (the format-dispatching [`PersistentBitMatrix`] enum),
+//! [`builder`] ([`PersistentBitMatrixBuilder`], always builds Columnar),
+//! [`group_ops`] (`MatrixGroupOps` impl), [`pairwise`] (shared symmetric
+//! pairwise-matrix helpers, also used by `intmatrix.rs`).
+
+use std::path::{Path, PathBuf};
+
+mod builder;
+mod columnar;
+mod group_ops;
+mod packed;
+mod pairwise;
+mod persistent;
+
+pub use builder::PersistentBitMatrixBuilder;
+pub use packed::pack_bit_matrix;
+pub use persistent::PersistentBitMatrix;
+
+pub(crate) use pairwise::{pairwise_matrix, pairwise2_matrix};
+
+fn col_path(dir: &Path, col: usize) -> PathBuf {
+    dir.join(format!("col_{col:06}.pbiv"))
+}
diff --git a/src/obicompactvec/src/bitmatrix/packed.rs b/src/obicompactvec/src/bitmatrix/packed.rs
new file mode 100644
index 00000000..f0a89b8c
--- /dev/null
+++ b/src/obicompactvec/src/bitmatrix/packed.rs
@@ -0,0 +1,181 @@
+use std::fs::{self, File};
+use std::io::{self, BufWriter, Read as _, Write as _};
+use std::path::Path;
+
+use memmap2::Mmap;
+use ndarray::{Array1, Array2};
+use rayon::prelude::*;
+
+use crate::bitvec::PersistentBitVecBuilder;
+use crate::meta::MatrixMeta;
+use crate::views::BitSliceView;
+
+use super::col_path;
+use super::pairwise::{pairwise_matrix, pairwise2_matrix};
+
+// ── PackedBitMatrix ───────────────────────────────────────────────────────────
+
+const PBMX_MAGIC:  [u8; 4] = *b"PBMX";
+const PBMX_HEADER: usize   = 24; // magic(4) + pad(4) + n_rows(8) + n_cols(8)
+const PBIV_HEADER: usize   = 16; // magic(4) + pad(4) + n(8)
+
+/// Single-file packed layout: all columns concatenated behind a header.
+pub struct PackedBitMatrix {
+    mmap:         Mmap,
+    pub(super) n_rows: usize,
+    pub(super) n_cols: usize,
+    /// Absolute byte offset to the start of each column's bit data
+    /// (= file offset of the PBIV blob + PBIV_HEADER).
+    data_offsets: Vec<usize>,
+}
+
+impl PackedBitMatrix {
+    pub(crate) fn open(path: &Path) -> io::Result<Self> {
+        let mmap = unsafe { Mmap::map(&File::open(path)?)? };
+        if mmap.len() < PBMX_HEADER {
+            return Err(io::Error::new(io::ErrorKind::InvalidData, "PBMX file too short"));
+        }
+        if &mmap[0..4] != &PBMX_MAGIC {
+            return Err(io::Error::new(io::ErrorKind::InvalidData, "bad PBMX magic"));
+        }
+        let n_rows = u64::from_le_bytes(mmap[8..16].try_into().unwrap())  as usize;
+        let n_cols = u64::from_le_bytes(mmap[16..24].try_into().unwrap()) as usize;
+
+        let mut data_offsets = Vec::with_capacity(n_cols);
+        for c in 0..n_cols {
+            let off_pos = PBMX_HEADER + c * 8;
+            let col_file_off = u64::from_le_bytes(mmap[off_pos..off_pos+8].try_into().unwrap()) as usize;
+            data_offsets.push(col_file_off + PBIV_HEADER);
+        }
+
+        Ok(Self { mmap, n_rows, n_cols, data_offsets })
+    }
+
+    #[inline]
+    pub(crate) fn fill_row(&self, slot: usize, buf: &mut [u32]) {
+        for (c, &data_off) in self.data_offsets.iter().enumerate() {
+            buf[c] = ((self.mmap[data_off + (slot >> 3)] >> (slot & 7)) & 1) as u32;
+        }
+    }
+
+    pub(crate) fn row(&self, slot: usize) -> Box<[bool]> {
+        (0..self.n_cols).map(|c| {
+            (self.mmap[self.data_offsets[c] + (slot >> 3)] >> (slot & 7)) & 1 != 0
+        }).collect()
+    }
+
+    fn col_bytes(&self, c: usize) -> &[u8] {
+        let start = self.data_offsets[c];
+        &self.mmap[start..start + self.n_rows.div_ceil(8)]
+    }
+
+    fn col_words(&self, c: usize) -> &[u64] {
+        let nw = self.n_rows.div_ceil(64);
+        // SAFETY: data_offsets[c] is always 8-byte aligned.
+        // PBMX header = 24 + n_cols×8 (multiple of 8); each PBIV blob =
+        // 16 + nwords×8 (multiple of 8); mmap base is page-aligned.
+        let ptr = self.mmap[self.data_offsets[c]..].as_ptr() as *const u64;
+        unsafe { std::slice::from_raw_parts(ptr, nw) }
+    }
+
+    pub(crate) fn col_slice(&self, c: usize) -> BitSliceView<'_> {
+        BitSliceView::new(self.col_words(c), self.n_rows)
+    }
+
+    pub(crate) fn col_persist(&self, c: usize, path: &Path) -> io::Result<PersistentBitVecBuilder> {
+        PersistentBitVecBuilder::from_raw_bytes(self.col_bytes(c), self.n_rows, path)
+    }
+
+    pub(crate) fn count_ones(&self) -> Array1<u64> {
+        Array1::from_vec(
+            (0..self.n_cols).into_par_iter()
+                .map(|c| self.col_slice(c).count_ones())
+                .collect()
+        )
+    }
+
+    pub(crate) fn partial_jaccard_dist_matrix(&self) -> (Array2<u64>, Array2<u64>) {
+        pairwise2_matrix(self.n_cols, |i, j| {
+            self.col_slice(i).partial_jaccard_dist(self.col_slice(j))
+        })
+    }
+
+    pub(crate) fn partial_hamming_dist_matrix(&self) -> Array2<u64> {
+        pairwise_matrix(self.n_cols, |i, j| {
+            self.col_slice(i).hamming_dist(self.col_slice(j))
+        })
+    }
+}
+
+/// Reads just the `n_cols` field from an existing packed matrix's header,
+/// without mapping the file. Used by `pack_bit_matrix` to tell a genuinely
+/// complete pack from a stale one that predates a later column-widening.
+fn packed_bit_matrix_n_cols(path: &Path) -> io::Result<usize> {
+    let mut f = File::open(path)?;
+    let mut header = [0u8; PBMX_HEADER];
+    f.read_exact(&mut header)?;
+    Ok(u64::from_le_bytes(header[16..24].try_into().unwrap()) as usize)
+}
+
+/// Build `presence/matrix.pbmx` from existing `col_*.pbiv` files.
+pub fn pack_bit_matrix(dir: &Path) -> io::Result<()> {
+    let packed_path = dir.join("matrix.pbmx");
+
+    let meta = match MatrixMeta::load(dir) {
+        Ok(meta) => meta,
+        Err(e) => {
+            // No columnar data pending: either this layer was already
+            // packed and cleaned up (matrix.pbmx complete, nothing left to
+            // do), or genuinely nothing was ever written here.
+            return if packed_path.exists() { Ok(()) } else { Err(e) };
+        }
+    };
+
+    // A `matrix.pbmx` can already exist here even though columnar data is
+    // still pending — e.g. copied verbatim from a merge's base source
+    // before this layer was widened with more genome columns (see
+    // `obikpartitionner::merge_partition`). Only skip (re-)packing if the
+    // existing file already reflects the current column count; otherwise
+    // the columnar files are newer and must be (re-)packed, overwriting the
+    // stale one — never silently discarded as "leftover cleanup".
+    if packed_bit_matrix_n_cols(&packed_path).ok() == Some(meta.n_cols) {
+        for c in 0..meta.n_cols { let _ = fs::remove_file(col_path(dir, c)); }
+        let _ = fs::remove_file(dir.join("meta.json"));
+        return Ok(());
+    }
+
+    let n_cols = meta.n_cols;
+
+    // Compute offsets from file sizes — no column data loaded into RAM.
+    let col_sizes: Vec<u64> = (0..n_cols)
+        .map(|c| fs::metadata(col_path(dir, c)).map(|m| m.len()))
+        .collect::<io::Result<_>>()?;
+
+    let header_size = (PBMX_HEADER + n_cols * 8) as u64;
+    let mut col_offset = header_size;
+    let mut offsets = Vec::with_capacity(n_cols);
+    for &size in &col_sizes {
+        offsets.push(col_offset);
+        col_offset += size;
+    }
+
+    // Write to a temp file; rename atomically so a killed process never leaves
+    // a truncated matrix.pbmx that would be mistaken for a complete file.
+    let tmp_path = dir.join("matrix.pbmx.tmp");
+    let mut out = BufWriter::new(File::create(&tmp_path)?);
+    out.write_all(&PBMX_MAGIC)?;
+    out.write_all(&[0u8; 4])?;
+    out.write_all(&(meta.n as u64).to_le_bytes())?;
+    out.write_all(&(n_cols as u64).to_le_bytes())?;
+    for &off in &offsets { out.write_all(&off.to_le_bytes())?; }
+    for c in 0..n_cols {
+        io::copy(&mut File::open(col_path(dir, c))?, &mut out)?;
+    }
+    out.flush()?;
+    drop(out);
+    fs::rename(&tmp_path, &packed_path)?;
+
+    for c in 0..n_cols { fs::remove_file(col_path(dir, c))?; }
+    fs::remove_file(dir.join("meta.json"))?;
+    Ok(())
+}
diff --git a/src/obicompactvec/src/bitmatrix/pairwise.rs b/src/obicompactvec/src/bitmatrix/pairwise.rs
new file mode 100644
index 00000000..dba8079c
--- /dev/null
+++ b/src/obicompactvec/src/bitmatrix/pairwise.rs
@@ -0,0 +1,56 @@
+use ndarray::Array2;
+use rayon::prelude::*;
+
+// ── Shared matrix helpers (also used by intmatrix.rs) ─────────────────────────
+
+fn upper_pairs(n: usize) -> Vec<(usize, usize)> {
+    (0..n).flat_map(|i| (i + 1..n).map(move |j| (i, j))).collect()
+}
+
+fn fill_symmetric<T>(n: usize, vals: impl Iterator<Item = (usize, usize, T, T)>) -> Array2<T>
+where T: Clone + Default {
+    let mut m = Array2::from_elem((n, n), T::default());
+    for (i, j, vij, vji) in vals { m[[i, j]] = vij; m[[j, i]] = vji; }
+    m
+}
+
+/// Compute a symmetric `n×n` matrix in parallel by evaluating `f(i,j)` for
+/// all upper-triangle pairs, plus `f(i,i)` for the diagonal. `T: Copy` avoids
+/// the `.clone()` needed for the lower-triangle mirror.
+///
+/// The diagonal is *not* generally `T::default()`: for a self-comparison,
+/// `f(i,i)` is often the column's own weight (e.g. intersection-with-self —
+/// see `pairwise2_matrix`), not zero. Distance finalisations that need a
+/// zero diagonal (self-distance) already overwrite it explicitly.
+pub(crate) fn pairwise_matrix<T>(n: usize, f: impl Fn(usize, usize) -> T + Sync) -> Array2<T>
+where T: Copy + Default + Send {
+    let results: Vec<(usize, usize, T)> = upper_pairs(n)
+        .into_par_iter().map(|(i, j)| (i, j, f(i, j))).collect();
+    let mut m = fill_symmetric(n, results.into_iter().map(|(i, j, v)| (i, j, v, v)));
+    for i in 0..n { m[[i, i]] = f(i, i); }
+    m
+}
+
+/// Same as `pairwise_matrix` but `f` returns two values that fill two
+/// symmetric matrices simultaneously (e.g. intersection + union for Jaccard).
+/// The diagonal is `f(i,i)` (e.g. a genome's kmer count intersected with
+/// itself), not `T::default()` — see `pairwise_matrix` for why that matters.
+pub(crate) fn pairwise2_matrix<T>(n: usize, f: impl Fn(usize, usize) -> (T, T) + Sync) -> (Array2<T>, Array2<T>)
+where T: Copy + Default + Send {
+    let results: Vec<(usize, usize, T, T)> = upper_pairs(n)
+        .into_par_iter()
+        .map(|(i, j)| { let (a, b) = f(i, j); (i, j, a, b) })
+        .collect();
+    let mut m0 = Array2::from_elem((n, n), T::default());
+    let mut m1 = Array2::from_elem((n, n), T::default());
+    for (i, j, a, b) in results {
+        m0[[i, j]] = a; m0[[j, i]] = a;
+        m1[[i, j]] = b; m1[[j, i]] = b;
+    }
+    for i in 0..n {
+        let (a, b) = f(i, i);
+        m0[[i, i]] = a;
+        m1[[i, i]] = b;
+    }
+    (m0, m1)
+}
diff --git a/src/obicompactvec/src/bitmatrix/persistent.rs b/src/obicompactvec/src/bitmatrix/persistent.rs
new file mode 100644
index 00000000..7f5b2b9d
--- /dev/null
+++ b/src/obicompactvec/src/bitmatrix/persistent.rs
@@ -0,0 +1,181 @@
+use std::io;
+use std::path::Path;
+
+use ndarray::{Array1, Array2};
+
+use crate::bitvec::{PersistentBitVec, PersistentBitVecBuilder};
+use crate::layer_meta::LayerMeta;
+use crate::meta::MatrixMeta;
+use crate::traits::{BitPartials, ColumnWeights};
+use crate::views::BitSliceView;
+
+use super::columnar::ColumnarBitMatrix;
+use super::packed::PackedBitMatrix;
+
+// ── PersistentBitMatrix — public enum ────────────────────────────────────────
+
+/// Bit matrix that transparently handles columnar, packed, and implicit formats.
+///
+/// - `Columnar`: per-column `.pbiv` files (original format, used during build)
+/// - `Packed`:   single `matrix.pbmx` file (optimised for query — one `mmap`)
+/// - `Implicit`: no file — all values are 1 (mono-genome presence/absence)
+pub enum PersistentBitMatrix {
+    Columnar(ColumnarBitMatrix),
+    Packed(PackedBitMatrix),
+    Implicit { n_rows: usize, n_cols: usize },
+}
+
+impl PersistentBitMatrix {
+    /// Open from `layer_dir`, auto-detecting the format.
+    ///
+    /// Checks (in order):
+    /// 1. `layer_dir/presence/matrix.pbmx`  → Packed
+    /// 2. `layer_dir/presence/meta.json`    → Columnar
+    /// 3. `layer_dir/layer_meta.json`        → Implicit (new index)
+    /// 4. `layer_dir/unitigs.bin`            → Implicit with warning (old index)
+    pub fn open(layer_dir: &Path) -> io::Result<Self> {
+        let presence_dir = layer_dir.join("presence");
+
+        if presence_dir.join("matrix.pbmx").exists() {
+            return Ok(Self::Packed(PackedBitMatrix::open(&presence_dir.join("matrix.pbmx"))?));
+        }
+
+        if MatrixMeta::load(&presence_dir).is_ok() {
+            return Ok(Self::Columnar(ColumnarBitMatrix::open(&presence_dir)?));
+        }
+
+        // No presence matrix → Implicit; requires layer_meta.json
+        let meta = LayerMeta::load(layer_dir).map_err(|_| io::Error::new(
+            io::ErrorKind::NotFound,
+            format!(
+                "no presence matrix and no layer_meta.json in {} — run 'obikmer upgrade'",
+                layer_dir.display()
+            ),
+        ))?;
+        Ok(Self::Implicit { n_rows: meta.n, n_cols: 1 })
+    }
+
+    pub fn n(&self) -> usize {
+        match self {
+            Self::Columnar(m)            => m.n(),
+            Self::Packed(m)              => m.n_rows,
+            Self::Implicit { n_rows, .. } => *n_rows,
+        }
+    }
+
+    pub fn n_cols(&self) -> usize {
+        match self {
+            Self::Columnar(m)            => m.n_cols(),
+            Self::Packed(m)              => m.n_cols,
+            Self::Implicit { n_cols, .. } => *n_cols,
+        }
+    }
+
+    pub fn col(&self, c: usize) -> &PersistentBitVec {
+        match self {
+            Self::Columnar(m) => m.col(c),
+            _ => panic!("col() only available on Columnar PersistentBitMatrix"),
+        }
+    }
+
+    pub fn col_view(&self, c: usize) -> BitSliceView<'_> {
+        match self {
+            Self::Columnar(m) => m.col(c).view(),
+            Self::Packed(m)   => m.col_slice(c),
+            Self::Implicit { .. } => panic!("col_view() not available on Implicit PersistentBitMatrix"),
+        }
+    }
+
+    /// Column-major point lookup: value at column `c`, slot `slot`, as 0/1.
+    ///
+    /// Unlike [`col_view`](Self::col_view), this never panics on `Implicit`
+    /// (every column reads as present, per the mono-genome fast path) — safe
+    /// to call for any `c < self.n_cols()`.
+    pub fn get(&self, c: usize, slot: usize) -> u32 {
+        match self {
+            Self::Columnar(m) => m.col(c).get(slot) as u32,
+            Self::Packed(m)   => m.col_slice(c).get(slot) as u32,
+            Self::Implicit { .. } => 1,
+        }
+    }
+
+    pub fn col_persist(&self, c: usize, path: &Path) -> io::Result<PersistentBitVecBuilder> {
+        match self {
+            Self::Columnar(m) => PersistentBitVecBuilder::build_from(m.col(c), path),
+            Self::Packed(m)   => m.col_persist(c, path),
+            Self::Implicit { n_rows, .. } => {
+                PersistentBitVecBuilder::new_ones(*n_rows, path)
+            }
+        }
+    }
+
+    pub fn row(&self, slot: usize) -> Box<[bool]> {
+        match self {
+            Self::Columnar(m)             => m.row(slot),
+            Self::Packed(m)               => m.row(slot),
+            Self::Implicit { n_cols, .. } => vec![true; *n_cols].into_boxed_slice(),
+        }
+    }
+
+    /// Fill `buf[i]` with `col_i[slot]` as 0/1 u32, without allocating.
+    pub fn fill_row(&self, slot: usize, buf: &mut [u32]) {
+        match self {
+            Self::Columnar(m)             => m.fill_row(slot, buf),
+            Self::Packed(m)               => m.fill_row(slot, buf),
+            Self::Implicit { n_cols, .. } => buf[..*n_cols].fill(1),
+        }
+    }
+
+    pub fn count_ones(&self) -> Array1<u64> {
+        match self {
+            Self::Columnar(m)              => m.count_ones(),
+            Self::Packed(m)                => m.count_ones(),
+            Self::Implicit { n_rows, n_cols } => Array1::from_elem(*n_cols, *n_rows as u64),
+        }
+    }
+
+    pub fn partial_jaccard_dist_matrix(&self) -> (Array2<u64>, Array2<u64>) {
+        match self {
+            Self::Columnar(m)                 => m.partial_jaccard_dist_matrix(),
+            Self::Packed(m)                   => m.partial_jaccard_dist_matrix(),
+            Self::Implicit { n_rows, n_cols } => {
+                let v = *n_rows as u64;
+                let n = *n_cols;
+                let mut inter = Array2::zeros((n, n));
+                let mut union = Array2::zeros((n, n));
+                for i in 0..n { for j in 0..n {
+                    inter[[i, j]] = v; union[[i, j]] = v;
+                }}
+                (inter, union)
+            }
+        }
+    }
+
+    pub fn partial_hamming_dist_matrix(&self) -> Array2<u64> {
+        match self {
+            Self::Columnar(m)              => m.partial_hamming_dist_matrix(),
+            Self::Packed(m)                => m.partial_hamming_dist_matrix(),
+            Self::Implicit { n_cols, .. }  => Array2::zeros((*n_cols, *n_cols)),
+        }
+    }
+
+    /// Append a new column to an on-disk Columnar matrix.
+    pub fn append_column(dir: &Path, value_of: impl Fn(usize) -> bool) -> io::Result<()> {
+        ColumnarBitMatrix::append_column(dir, value_of)
+    }
+}
+
+// ── Trait impls ───────────────────────────────────────────────────────────────
+
+impl ColumnWeights for PersistentBitMatrix {
+    fn col_weights(&self) -> Array1<u64> { self.count_ones() }
+}
+
+impl BitPartials for PersistentBitMatrix {
+    fn partial_jaccard(&self) -> (Array2<u64>, Array2<u64>) {
+        self.partial_jaccard_dist_matrix()
+    }
+    fn partial_hamming(&self) -> Array2<u64> {
+        self.partial_hamming_dist_matrix()
+    }
+}
diff --git a/src/obidebruinj/src/debruijn.rs b/src/obidebruinj/src/debruijn/graph.rs
similarity index 51%
rename from src/obidebruinj/src/debruijn.rs
rename to src/obidebruinj/src/debruijn/graph.rs
index f59f03ac..901848c9 100644
--- a/src/obidebruinj/src/debruijn.rs
+++ b/src/obidebruinj/src/debruijn/graph.rs
@@ -1,250 +1,24 @@
-//use ahash::RandomState;
-use crossbeam_channel;
 use hashbrown::HashMap;
 use obikseq::k;
-use obikseq::{CanonicalKmer, Sequence, Unitig};
+use obikseq::{CanonicalKmer, Unitig};
 #[cfg(not(any(test, feature = "test-utils")))]
 use rayon::iter::{IntoParallelRefIterator, ParallelIterator};
 use std::cell::RefCell;
-use std::fmt;
 use std::sync::atomic::{AtomicU8, Ordering};
 use xxhash_rust::xxh3::Xxh3Builder;
 
+use super::node::{IS_VISITED_MASK, Node};
+use super::unitig_iter::UnitigNucIter;
+use super::walk::WalkState;
+
 // ── Types ─────────────────────────────────────────────────────────────────────
 
-type FastHashMap<K, V> = HashMap<K, V, Xxh3Builder>;
-
-// ── Node ──────────────────────────────────────────────────────────────────────
-//
-//  bit layout (LSB first):
-//    bit  0   : can_extend_right — exactly one right canonical neighbour exists
-//    bit  1   : can_extend_left  — exactly one left  canonical neighbour exists
-//    bit  2   : visited
-//    bits 3–4 : right_nuc — index 0–3 (A/C/G/T) of that neighbour; valid iff bit 0 = 1
-//    bits 5–6 : left_nuc  — index 0–3 (A/C/G/T) of that neighbour; valid iff bit 1 = 1
-//    bit  7   : marked as start node (1)
-//
-//  "can_extend" = false covers both 0 neighbours and ≥2 neighbours; the only
-//  information needed for traversal is "exactly one".
-
-#[repr(transparent)]
-#[derive(Debug, Clone, Copy, Default)]
-pub struct Node(u8);
-
-const CAN_EXTEND_RIGHT_MASK: u8 = 0b0000_0001; // bit 0: can_extend_right — exactly one right canonical neighbour exists
-const CAN_EXTEND_LEFT_MASK: u8 = 0b0000_0010; // bit 1: can_extend_left  — exactly one left  canonical neighbour exists
-const IS_VISITED_MASK: u8 = 0b0000_0100; // bit 2: visited
-const RIGHT_NUC_MASK: u8 = 0b0001_1000; // bits 3–4: right_nuc — index 0–3 (A/C/G/T) of that neighbour; valid iff bit 0 = 1
-const LEFT_NUC_MASK: u8 = 0b0110_0000; // bits 5–6: left_nuc  — index 0–3 (A/C/G/T) of that neighbour; valid iff bit 1 = 1
-const IS_START_MASK: u8 = 0b1000_0000; // bit 7: marked as start node
-
-impl Node {
-    /// Returns `true` if the node can be extended to the right.
-    ///
-    /// A single right neighbour exists.
-    #[inline]
-    pub fn can_extend_right(self) -> bool {
-        self.0 & CAN_EXTEND_RIGHT_MASK != 0
-    }
-
-    /// Returns `true` if the node can be extended to the left.
-    ///
-    /// A single left neighbour exists.
-    #[inline]
-    pub fn can_extend_left(self) -> bool {
-        self.0 & CAN_EXTEND_LEFT_MASK != 0
-    }
-
-    /// Returns `true` if the node has been visited.
-    #[inline]
-    pub fn is_visited(self) -> bool {
-        self.0 & IS_VISITED_MASK != 0
-    }
-
-    /// Returns `true` if the node is a start node.
-    #[inline]
-    pub fn is_start(self) -> bool {
-        self.0 & IS_START_MASK != 0
-    }
-
-    #[inline]
-    pub fn set_start(&mut self) {
-        self.0 |= IS_START_MASK;
-    }
-
-    pub fn unset_start(&mut self) {
-        self.0 &= !IS_START_MASK;
-    }
-
-    /// Index of the unique right neighbour (0=A, 1=C, 2=G, 3=T).
-    /// Only meaningful when `can_extend_right()` is true.
-    #[inline]
-    pub fn right_nuc(self) -> u8 {
-        debug_assert!(
-            self.can_extend_right(),
-            "from: right_nuc -> The node cannot be extended to the right"
-        );
-        (self.0 >> 3) & 0b11
-    }
-
-    /// Index of the unique left neighbour (0=A, 1=C, 2=G, 3=T).
-    /// Only meaningful when `can_extend_left()` is true.
-    #[inline]
-    pub fn left_nuc(self) -> u8 {
-        debug_assert!(
-            self.can_extend_left(),
-            "from: left_nuc -> The node cannot be extended to the left"
-        );
-        (self.0 >> 5) & 0b11
-    }
-
-    /// Marks the node as visited.
-    #[inline]
-    pub fn set_visited(&mut self) {
-        debug_assert!(
-            !self.is_visited(),
-            "from: is_visited -> The node has already been visited"
-        );
-        self.0 |= IS_VISITED_MASK;
-    }
-
-    /// `nuc` = Some(i) → exactly one neighbour (bit 0 set, bits 3–4 = nucleotide index).
-    /// `nuc` = None    → 0 or ≥2 neighbours; `count` encoded in bits 3–4 as count.sat_sub(1).
-    pub fn set_right(&mut self, count: u8, nuc: Option<u8>) {
-        self.0 &= !(CAN_EXTEND_RIGHT_MASK | RIGHT_NUC_MASK);
-        if count == 1 {
-            self.0 |= CAN_EXTEND_RIGHT_MASK;
-            if let Some(n) = nuc {
-                self.0 |= (n & 0b11) << 3;
-                return;
-            }
-            unreachable!("nuc must be Some when count is 1");
-        }
-        self.0 |= (count.saturating_sub(1).min(3)) << 3;
-    }
-
-    /// `nuc` = Some(i) → exactly one neighbour (bit 0 set, bits 3–4 = nucleotide index).
-    /// `nuc` = None    → 0 or ≥2 neighbours; `count` encoded in bits 3–4 as count.sat_sub(1).
-    pub fn set_left(&mut self, count: u8, nuc: Option<u8>) {
-        self.0 &= !(CAN_EXTEND_LEFT_MASK | LEFT_NUC_MASK);
-        if count == 1 {
-            self.0 |= CAN_EXTEND_LEFT_MASK;
-            if let Some(n) = nuc {
-                self.0 |= (n & 0b11) << 5;
-                return;
-            }
-            unreachable!("nuc must be Some when count is 1");
-        }
-        self.0 |= (count.saturating_sub(1).min(3)) << 5;
-    }
-}
-
-impl fmt::Display for Node {
-    fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
-        const NUC: [char; 4] = ['A', 'C', 'G', 'T'];
-        let r = if self.can_extend_right() {
-            format!("→{}", NUC[self.right_nuc() as usize])
-        } else if (self.0 >> 3) & 0b11 == 0 {
-            "→0".to_string()
-        } else {
-            "→≥2".to_string()
-        };
-        let l = if self.can_extend_left() {
-            format!("←{}", NUC[self.left_nuc() as usize])
-        } else if (self.0 >> 5) & 0b11 == 0 {
-            "←0".to_string()
-        } else {
-            "←≥2".to_string()
-        };
-        let v = if self.is_visited() { "V" } else { "." };
-        write!(f, "Node({r} {l} {v})")
-    }
-}
-
-pub struct WalkState {
-    kmer: CanonicalKmer,
-    node: Node,
-    direct: bool,
-}
-
-impl WalkState {
-    pub fn new(kmer: CanonicalKmer, node: Node, direct: bool) -> Self {
-        debug_assert!(!node.is_visited(), "Cannot walk over a visited node");
-        Self { kmer, node, direct }
-    }
-
-    pub fn leavable(&self, graph: &GraphDeBruijn) -> bool {
-        self.walk(graph).is_some()
-    }
-
-    pub fn reachable(&self, graph: &GraphDeBruijn) -> bool {
-        WalkState {
-            kmer: self.kmer,
-            node: self.node,
-            direct: !self.direct,
-        }
-        .leavable(graph)
-    }
-
-    pub fn walk(&self, graph: &GraphDeBruijn) -> Option<(WalkState, u8)> {
-        if self.direct {
-            if !self.node.can_extend_right() {
-                return None;
-            }
-            let nuc = self.node.right_nuc();
-            let next = self.kmer.into_kmer().push_right(nuc);
-            let cnext = next.canonical();
-            let dnext = next.raw() == cnext.raw();
-            let next_node = Node(graph.nodes.get(&cnext).unwrap().load(Ordering::Relaxed));
-            if next_node.is_visited() {
-                return None;
-            }
-            let reachable = if dnext {
-                next_node.can_extend_left()
-            } else {
-                next_node.can_extend_right()
-            };
-            reachable.then_some((
-                WalkState {
-                    kmer: cnext,
-                    node: next_node,
-                    direct: dnext,
-                },
-                nuc,
-            ))
-        } else {
-            if !self.node.can_extend_left() {
-                return None;
-            }
-            let nuc = self.node.left_nuc();
-            let next = self.kmer.into_kmer().push_left(nuc);
-            let cnext = next.canonical();
-            let dnext = next.raw() != cnext.raw();
-            let next_node = Node(graph.nodes.get(&cnext).unwrap().load(Ordering::Relaxed));
-            if next_node.is_visited() {
-                return None;
-            }
-            let reachable = if dnext {
-                next_node.can_extend_right()
-            } else {
-                next_node.can_extend_left()
-            };
-            reachable.then_some((
-                WalkState {
-                    kmer: cnext,
-                    node: next_node,
-                    direct: dnext,
-                },
-                3 - nuc,
-            ))
-        }
-    }
-}
+pub(super) type FastHashMap<K, V> = HashMap<K, V, Xxh3Builder>;
 
 // ── GraphDeBruijn ─────────────────────────────────────────────────────────────
 
 pub struct GraphDeBruijn {
-    nodes: FastHashMap<CanonicalKmer, AtomicU8>,
+    pub(super) nodes: FastHashMap<CanonicalKmer, AtomicU8>,
 }
 
 impl GraphDeBruijn {
@@ -346,7 +120,7 @@ impl GraphDeBruijn {
         Some(WalkState::new(kmer, node, true))
     }
 
-    fn unitig_nucleotides(&self, kmer: CanonicalKmer, k: usize) -> Option<UnitigNucIter<'_>> {
+    pub(super) fn unitig_nucleotides(&self, kmer: CanonicalKmer, k: usize) -> Option<UnitigNucIter<'_>> {
         let old = self
             .nodes
             .get(&kmer)?
@@ -362,13 +136,7 @@ impl GraphDeBruijn {
                 .fetch_or(IS_VISITED_MASK, Ordering::AcqRel);
             (ext_old & IS_VISITED_MASK == 0).then_some((next_state, nuc))
         });
-        Some(UnitigNucIter {
-            graph: self,
-            start: kmer,
-            pos: 0,
-            k,
-            next_step,
-        })
+        Some(UnitigNucIter::new(self, kmer, k, next_step))
     }
 
     pub fn for_each_unitig(&self, f: impl Fn(UnitigNucIter<'_>) + Sync) {
@@ -467,12 +235,7 @@ impl GraphDeBruijn {
     }
 
     fn is_start(&self, query: CanonicalKmer, node: Node) -> bool {
-        !WalkState {
-            kmer: query,
-            node,
-            direct: true,
-        }
-        .reachable(self)
+        !WalkState::new(query, node, true).reachable(self)
     }
 
     pub fn try_for_each_unitig<E, F>(&self, f: F) -> Result<(), E>
@@ -514,44 +277,6 @@ impl GraphDeBruijn {
     }
 }
 
-// ── UnitigNucIter ─────────────────────────────────────────────────────────────
-
-pub struct UnitigNucIter<'a> {
-    graph: &'a GraphDeBruijn,
-    start: CanonicalKmer,
-    pos: usize,
-    k: usize,
-    next_step: Option<(WalkState, u8)>,
-}
-
-impl Iterator for UnitigNucIter<'_> {
-    type Item = u8;
-
-    fn next(&mut self) -> Option<u8> {
-        if self.pos < self.k {
-            let nuc = self.start.nucleotide(self.pos);
-            self.pos += 1;
-            Some(nuc)
-        } else if let Some((state, nuc)) = self.next_step.take() {
-            self.next_step = state.walk(self.graph).and_then(|(next_state, next_nuc)| {
-                let old = self
-                    .graph
-                    .nodes
-                    .get(&next_state.kmer)?
-                    .fetch_or(IS_VISITED_MASK, Ordering::AcqRel);
-                (old & IS_VISITED_MASK == 0).then_some((next_state, next_nuc))
-            });
-            Some(nuc)
-        } else {
-            None
-        }
-    }
-
-    fn size_hint(&self) -> (usize, Option<usize>) {
-        (self.k - self.pos.min(self.k), None)
-    }
-}
-
 /// Returns the count of neighbors and the index of the first
 /// neighbor if exactly one of the four canonical neighbours exists in
 /// the graph, where `i` is its index (0=A, 1=C, 2=G, 3=T).
@@ -580,8 +305,3 @@ fn count_neighbors(
         (0, None)
     }
 }
-
-// ── tests ─────────────────────────────────────────────────────────────────────
-#[cfg(test)]
-#[path = "tests/debruijn.rs"]
-mod tests;
diff --git a/src/obidebruinj/src/debruijn/mod.rs b/src/obidebruinj/src/debruijn/mod.rs
new file mode 100644
index 00000000..126b8ec1
--- /dev/null
+++ b/src/obidebruinj/src/debruijn/mod.rs
@@ -0,0 +1,20 @@
+//! De Bruijn graph over canonical k-mers, built for unitig extraction.
+//!
+//! Submodules: [`node`] (packed per-kmer neighbour/visited/start flags),
+//! [`walk`] (single-step traversal), [`graph`] ([`GraphDeBruijn`] itself),
+//! [`unitig_iter`] (nucleotide-by-nucleotide unitig walk iterator).
+
+mod graph;
+mod node;
+mod unitig_iter;
+mod walk;
+
+pub use graph::GraphDeBruijn;
+
+// Only used by `tests/debruijn.rs` (`use super::*`) below.
+#[cfg(test)]
+use obikseq::{CanonicalKmer, Sequence};
+
+#[cfg(test)]
+#[path = "../tests/debruijn.rs"]
+mod tests;
diff --git a/src/obidebruinj/src/debruijn/node.rs b/src/obidebruinj/src/debruijn/node.rs
new file mode 100644
index 00000000..ca1af7e2
--- /dev/null
+++ b/src/obidebruinj/src/debruijn/node.rs
@@ -0,0 +1,148 @@
+use std::fmt;
+
+// ── Node ──────────────────────────────────────────────────────────────────────
+//
+//  bit layout (LSB first):
+//    bit  0   : can_extend_right — exactly one right canonical neighbour exists
+//    bit  1   : can_extend_left  — exactly one left  canonical neighbour exists
+//    bit  2   : visited
+//    bits 3–4 : right_nuc — index 0–3 (A/C/G/T) of that neighbour; valid iff bit 0 = 1
+//    bits 5–6 : left_nuc  — index 0–3 (A/C/G/T) of that neighbour; valid iff bit 1 = 1
+//    bit  7   : marked as start node (1)
+//
+//  "can_extend" = false covers both 0 neighbours and ≥2 neighbours; the only
+//  information needed for traversal is "exactly one".
+
+#[repr(transparent)]
+#[derive(Debug, Clone, Copy, Default)]
+pub struct Node(pub(super) u8);
+
+const CAN_EXTEND_RIGHT_MASK: u8 = 0b0000_0001; // bit 0: can_extend_right — exactly one right canonical neighbour exists
+const CAN_EXTEND_LEFT_MASK: u8 = 0b0000_0010; // bit 1: can_extend_left  — exactly one left  canonical neighbour exists
+pub(super) const IS_VISITED_MASK: u8 = 0b0000_0100; // bit 2: visited
+const RIGHT_NUC_MASK: u8 = 0b0001_1000; // bits 3–4: right_nuc — index 0–3 (A/C/G/T) of that neighbour; valid iff bit 0 = 1
+const LEFT_NUC_MASK: u8 = 0b0110_0000; // bits 5–6: left_nuc  — index 0–3 (A/C/G/T) of that neighbour; valid iff bit 1 = 1
+const IS_START_MASK: u8 = 0b1000_0000; // bit 7: marked as start node
+
+impl Node {
+    /// Returns `true` if the node can be extended to the right.
+    ///
+    /// A single right neighbour exists.
+    #[inline]
+    pub fn can_extend_right(self) -> bool {
+        self.0 & CAN_EXTEND_RIGHT_MASK != 0
+    }
+
+    /// Returns `true` if the node can be extended to the left.
+    ///
+    /// A single left neighbour exists.
+    #[inline]
+    pub fn can_extend_left(self) -> bool {
+        self.0 & CAN_EXTEND_LEFT_MASK != 0
+    }
+
+    /// Returns `true` if the node has been visited.
+    #[inline]
+    pub fn is_visited(self) -> bool {
+        self.0 & IS_VISITED_MASK != 0
+    }
+
+    /// Returns `true` if the node is a start node.
+    #[inline]
+    pub fn is_start(self) -> bool {
+        self.0 & IS_START_MASK != 0
+    }
+
+    #[inline]
+    pub fn set_start(&mut self) {
+        self.0 |= IS_START_MASK;
+    }
+
+    pub fn unset_start(&mut self) {
+        self.0 &= !IS_START_MASK;
+    }
+
+    /// Index of the unique right neighbour (0=A, 1=C, 2=G, 3=T).
+    /// Only meaningful when `can_extend_right()` is true.
+    #[inline]
+    pub fn right_nuc(self) -> u8 {
+        debug_assert!(
+            self.can_extend_right(),
+            "from: right_nuc -> The node cannot be extended to the right"
+        );
+        (self.0 >> 3) & 0b11
+    }
+
+    /// Index of the unique left neighbour (0=A, 1=C, 2=G, 3=T).
+    /// Only meaningful when `can_extend_left()` is true.
+    #[inline]
+    pub fn left_nuc(self) -> u8 {
+        debug_assert!(
+            self.can_extend_left(),
+            "from: left_nuc -> The node cannot be extended to the left"
+        );
+        (self.0 >> 5) & 0b11
+    }
+
+    /// Marks the node as visited.
+    #[inline]
+    pub fn set_visited(&mut self) {
+        debug_assert!(
+            !self.is_visited(),
+            "from: is_visited -> The node has already been visited"
+        );
+        self.0 |= IS_VISITED_MASK;
+    }
+
+    /// `nuc` = Some(i) → exactly one neighbour (bit 0 set, bits 3–4 = nucleotide index).
+    /// `nuc` = None    → 0 or ≥2 neighbours; `count` encoded in bits 3–4 as count.sat_sub(1).
+    pub fn set_right(&mut self, count: u8, nuc: Option<u8>) {
+        self.0 &= !(CAN_EXTEND_RIGHT_MASK | RIGHT_NUC_MASK);
+        if count == 1 {
+            self.0 |= CAN_EXTEND_RIGHT_MASK;
+            if let Some(n) = nuc {
+                self.0 |= (n & 0b11) << 3;
+                return;
+            }
+            unreachable!("nuc must be Some when count is 1");
+        }
+        self.0 |= (count.saturating_sub(1).min(3)) << 3;
+    }
+
+    /// `nuc` = Some(i) → exactly one neighbour (bit 0 set, bits 3–4 = nucleotide index).
+    /// `nuc` = None    → 0 or ≥2 neighbours; `count` encoded in bits 3–4 as count.sat_sub(1).
+    pub fn set_left(&mut self, count: u8, nuc: Option<u8>) {
+        self.0 &= !(CAN_EXTEND_LEFT_MASK | LEFT_NUC_MASK);
+        if count == 1 {
+            self.0 |= CAN_EXTEND_LEFT_MASK;
+            if let Some(n) = nuc {
+                self.0 |= (n & 0b11) << 5;
+                return;
+            }
+            unreachable!("nuc must be Some when count is 1");
+        }
+        self.0 |= (count.saturating_sub(1).min(3)) << 5;
+    }
+}
+
+impl fmt::Display for Node {
+    fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
+        const NUC: [char; 4] = ['A', 'C', 'G', 'T'];
+        let r = if self.can_extend_right() {
+            format!("→{}", NUC[self.right_nuc() as usize])
+        } else if (self.0 >> 3) & 0b11 == 0 {
+            "→0".to_string()
+        } else {
+            "→≥2".to_string()
+        };
+        let l = if self.can_extend_left() {
+            format!("←{}", NUC[self.left_nuc() as usize])
+        } else if (self.0 >> 5) & 0b11 == 0 {
+            "←0".to_string()
+        } else {
+            "←≥2".to_string()
+        };
+        let v = if self.is_visited() { "V" } else { "." };
+        write!(f, "Node({r} {l} {v})")
+    }
+}
diff --git a/src/obidebruinj/src/debruijn/unitig_iter.rs b/src/obidebruinj/src/debruijn/unitig_iter.rs
new file mode 100644
index 00000000..56ca6770
--- /dev/null
+++ b/src/obidebruinj/src/debruijn/unitig_iter.rs
@@ -0,0 +1,61 @@
+use obikseq::CanonicalKmer;
+use std::sync::atomic::Ordering;
+
+use super::graph::GraphDeBruijn;
+use super::node::IS_VISITED_MASK;
+use super::walk::WalkState;
+
+// ── UnitigNucIter ─────────────────────────────────────────────────────────────
+
+pub struct UnitigNucIter<'a> {
+    graph: &'a GraphDeBruijn,
+    start: CanonicalKmer,
+    pos: usize,
+    k: usize,
+    next_step: Option<(WalkState, u8)>,
+}
+
+impl<'a> UnitigNucIter<'a> {
+    pub(super) fn new(
+        graph: &'a GraphDeBruijn,
+        start: CanonicalKmer,
+        k: usize,
+        next_step: Option<(WalkState, u8)>,
+    ) -> Self {
+        Self {
+            graph,
+            start,
+            pos: 0,
+            k,
+            next_step,
+        }
+    }
+}
+
+impl Iterator for UnitigNucIter<'_> {
+    type Item = u8;
+
+    fn next(&mut self) -> Option<u8> {
+        if self.pos < self.k {
+            let nuc = self.start.nucleotide(self.pos);
+            self.pos += 1;
+            Some(nuc)
+        } else if let Some((state, nuc)) = self.next_step.take() {
+            self.next_step = state.walk(self.graph).and_then(|(next_state, next_nuc)| {
+                let old = self
+                    .graph
+                    .nodes
+                    .get(&next_state.kmer)?
+                    .fetch_or(IS_VISITED_MASK, Ordering::AcqRel);
+                (old & IS_VISITED_MASK == 0).then_some((next_state, next_nuc))
+            });
+            Some(nuc)
+        } else {
+            None
+        }
+    }
+
+    fn size_hint(&self) -> (usize, Option<usize>) {
+        (self.k - self.pos.min(self.k), None)
+    }
+}
diff --git a/src/obidebruinj/src/debruijn/walk.rs b/src/obidebruinj/src/debruijn/walk.rs
new file mode 100644
index 00000000..cace3871
--- /dev/null
+++ b/src/obidebruinj/src/debruijn/walk.rs
@@ -0,0 +1,85 @@
+use obikseq::{CanonicalKmer, Sequence};
+use std::sync::atomic::Ordering;
+
+use super::graph::GraphDeBruijn;
+use super::node::Node;
+
+pub struct WalkState {
+    pub(super) kmer: CanonicalKmer,
+    pub(super) node: Node,
+    pub(super) direct: bool,
+}
+
+impl WalkState {
+    pub fn new(kmer: CanonicalKmer, node: Node, direct: bool) -> Self {
+        debug_assert!(!node.is_visited(), "Cannot walk over a visited node");
+        Self { kmer, node, direct }
+    }
+
+    pub fn leavable(&self, graph: &GraphDeBruijn) -> bool {
+        self.walk(graph).is_some()
+    }
+
+    pub fn reachable(&self, graph: &GraphDeBruijn) -> bool {
+        WalkState {
+            kmer: self.kmer,
+            node: self.node,
+            direct: !self.direct,
+        }
+        .leavable(graph)
+    }
+
+    pub fn walk(&self, graph: &GraphDeBruijn) -> Option<(WalkState, u8)> {
+        if self.direct {
+            if !self.node.can_extend_right() {
+                return None;
+            }
+            let nuc = self.node.right_nuc();
+            let next = self.kmer.into_kmer().push_right(nuc);
+            let cnext = next.canonical();
+            let dnext = next.raw() == cnext.raw();
+            let next_node = Node(graph.nodes.get(&cnext).unwrap().load(Ordering::Relaxed));
+            if next_node.is_visited() {
+                return None;
+            }
+            let reachable = if dnext {
+                next_node.can_extend_left()
+            } else {
+                next_node.can_extend_right()
+            };
+            reachable.then_some((
+                WalkState {
+                    kmer: cnext,
+                    node: next_node,
+                    direct: dnext,
+                },
+                nuc,
+            ))
+        } else {
+            if !self.node.can_extend_left() {
+                return None;
+            }
+            let nuc = self.node.left_nuc();
+            let next = self.kmer.into_kmer().push_left(nuc);
+            let cnext = next.canonical();
+            let dnext = next.raw() != cnext.raw();
+            let next_node = Node(graph.nodes.get(&cnext).unwrap().load(Ordering::Relaxed));
+            if next_node.is_visited() {
+                return None;
+            }
+            let reachable = if dnext {
+                next_node.can_extend_right()
+            } else {
+                next_node.can_extend_left()
+            };
+            reachable.then_some((
+                WalkState {
+                    kmer: cnext,
+                    node: next_node,
+                    direct: dnext,
+                },
+                3 - nuc,
+            ))
+        }
+    }
+}
diff --git a/src/obikindex/src/numa/mod.rs b/src/obikindex/src/numa/mod.rs
new file mode 100644
index 00000000..2887ae43
--- /dev/null
+++ b/src/obikindex/src/numa/mod.rs
@@ -0,0 +1,17 @@
+//! NUMA-aware partition runner via hwlocality.
+//!
+//! Detects NUMA topology using hwloc (cross-platform: Linux, macOS, etc.) and
+//! builds one Rayon ThreadPool per NUMA node with threads pinned to that node's
+//! CPUs. Linux first-touch policy then places graph allocations in local DRAM
+//! automatically — no explicit memory binding needed.
+//!
+//! UMA systems (single socket, Apple Silicon, etc.) are the degenerate case:
+//! one synthetic node containing all cores, no pool, no pinning.
+//!
+//! Submodules: [`topology`] (NUMA detection, per-node pools, thread pinning),
+//! [`runner`] ([`PartitionRunner`], the adaptive worker-activation scheduler).
+
+mod runner;
+mod topology;
+
+pub use runner::PartitionRunner;
diff --git a/src/obikindex/src/numa.rs b/src/obikindex/src/numa/runner.rs
similarity index 77%
rename from src/obikindex/src/numa.rs
rename to src/obikindex/src/numa/runner.rs
index bdf42040..9572c78d 100644
--- a/src/obikindex/src/numa.rs
+++ b/src/obikindex/src/numa/runner.rs
@@ -1,137 +1,11 @@
-// NUMA-aware partition runner via hwlocality.
-//
-// Detects NUMA topology using hwloc (cross-platform: Linux, macOS, etc.) and
-// builds one Rayon ThreadPool per NUMA node with threads pinned to that node's
-// CPUs. Linux first-touch policy then places graph allocations in local DRAM
-// automatically — no explicit memory binding needed.
-//
-// UMA systems (single socket, Apple Silicon, etc.) are the degenerate case:
-// one synthetic node containing all cores, no pool, no pinning.
-
 use std::sync::Arc;
 use std::time::{Duration, Instant};
 
 use crossbeam_channel::unbounded;
-#[cfg(feature = "numa")]
-use hwlocality::Topology;
-#[cfg(feature = "numa")]
-use hwlocality::cpu::binding::CpuBindingFlags;
-#[cfg(feature = "numa")]
-use hwlocality::cpu::cpuset::CpuSet;
-#[cfg(feature = "numa")]
-use hwlocality::object::types::ObjectType;
 use obisys::{CpuSample, IoSample};
 use tracing::debug;
 
-// ── Public interface ──────────────────────────────────────────────────────────
-
-pub struct NumaSetup {
-    /// One entry per NUMA node. `None` on UMA systems (no pool, no pinning).
-    pub pools: Vec<Option<Arc<rayon::ThreadPool>>>,
-    /// CPU indices for each NUMA node, in node order.
-    pub cpus_per_node: Vec<Vec<usize>>,
-}
-
-impl NumaSetup {
-    /// Maximum worker slots per node (one per physical core in the node).
-    pub fn workers_per_node(&self) -> usize {
-        self.cpus_per_node
-            .first()
-            .map(|c| c.len().max(1))
-            .unwrap_or(1)
-    }
-}
-
-/// Detect NUMA topology and build per-node Rayon pools.
-/// Always succeeds: falls back to a single synthetic UMA node on failure.
-#[cfg(feature = "numa")]
-pub fn build() -> NumaSetup {
-    if let Ok(topology) = Topology::new() {
-        let nodes: Vec<Vec<usize>> = topology
-            .objects_with_type(ObjectType::NUMANode)
-            .filter_map(|obj| obj.cpuset())
-            .map(|cpuset| {
-                cpuset
-                    .iter_set()
-                    .map(|idx| usize::from(idx))
-                    .collect::<Vec<_>>()
-            })
-            .filter(|v| !v.is_empty())
-            .collect();
-
-        if nodes.len() > 1 {
-            if let Some(pools) = nodes
-                .iter()
-                .map(|cpus| build_pool(cpus).map(|p| Some(Arc::new(p))))
-                .collect::<Option<Vec<_>>>()
-            {
-                debug!(
-                    "NUMA topology: {} node(s), {} core(s)/node",
-                    nodes.len(),
-                    nodes.first().map_or(0, |v| v.len()),
-                );
-                return NumaSetup {
-                    pools,
-                    cpus_per_node: nodes,
-                };
-            }
-        }
-    }
-
-    // UMA fallback: single synthetic node, all cores, no pool, no pinning.
-    let n_cores = obisys::effective_parallelism();
-    debug!("UMA: single synthetic node, {} core(s)", n_cores);
-    NumaSetup {
-        pools: vec![None],
-        cpus_per_node: vec![(0..n_cores).collect()],
-    }
-}
-
-#[cfg(not(feature = "numa"))]
-pub fn build() -> NumaSetup {
-    let n_cores = obisys::effective_parallelism();
-    debug!("UMA: single synthetic node, {} core(s)", n_cores);
-    NumaSetup {
-        pools: vec![None],
-        cpus_per_node: vec![(0..n_cores).collect()],
-    }
-}
-
-/// Bind the calling thread to `cpu_indices` using hwloc.
-/// Silently returns on any error so the thread still runs, just unbound.
-#[cfg(feature = "numa")]
-pub fn pin_current_thread(cpu_indices: &[usize]) {
-    let Ok(topology) = Topology::new() else {
-        return;
-    };
-    let mut cpuset = CpuSet::new();
-    for &idx in cpu_indices {
-        cpuset.set(idx);
-    }
-    let _ = topology.bind_cpu(&cpuset, CpuBindingFlags::THREAD);
-}
-
-#[cfg(not(feature = "numa"))]
-pub fn pin_current_thread(_cpu_indices: &[usize]) {}
-
-// ── Internal helpers ──────────────────────────────────────────────────────────
-
-#[cfg(feature = "numa")]
-fn build_pool(cpus: &[usize]) -> Option<rayon::ThreadPool> {
-    let cpus = cpus.to_vec();
-    rayon::ThreadPoolBuilder::new()
-        .num_threads(cpus.len())
-        .spawn_handler(move |thread| {
-            let cpus = cpus.clone();
-            std::thread::Builder::new().spawn(move || {
-                pin_current_thread(&cpus);
-                thread.run();
-            })?;
-            Ok(())
-        })
-        .build()
-        .ok()
-}
+use super::topology::{build, pin_current_thread};
 
 // ── PartitionRunner ─────────────────────────────────────────────────────────
 
diff --git a/src/obikindex/src/numa/topology.rs b/src/obikindex/src/numa/topology.rs
new file mode 100644
index 00000000..31c266cf
--- /dev/null
+++ b/src/obikindex/src/numa/topology.rs
@@ -0,0 +1,121 @@
+use std::sync::Arc;
+
+#[cfg(feature = "numa")]
+use hwlocality::Topology;
+#[cfg(feature = "numa")]
+use hwlocality::cpu::binding::CpuBindingFlags;
+#[cfg(feature = "numa")]
+use hwlocality::cpu::cpuset::CpuSet;
+#[cfg(feature = "numa")]
+use hwlocality::object::types::ObjectType;
+use tracing::debug;
+
+// ── Public interface ──────────────────────────────────────────────────────────
+
+pub struct NumaSetup {
+    /// One entry per NUMA node. `None` on UMA systems (no pool, no pinning).
+    pub pools: Vec<Option<Arc<rayon::ThreadPool>>>,
+    /// CPU indices for each NUMA node, in node order.
+    pub cpus_per_node: Vec<Vec<usize>>,
+}
+
+impl NumaSetup {
+    /// Maximum worker slots per node (one per physical core in the node).
+    pub fn workers_per_node(&self) -> usize {
+        self.cpus_per_node
+            .first()
+            .map(|c| c.len().max(1))
+            .unwrap_or(1)
+    }
+}
+
+/// Detect NUMA topology and build per-node Rayon pools.
+/// Always succeeds: falls back to a single synthetic UMA node on failure.
+#[cfg(feature = "numa")]
+pub fn build() -> NumaSetup {
+    if let Ok(topology) = Topology::new() {
+        let nodes: Vec<Vec<usize>> = topology
+            .objects_with_type(ObjectType::NUMANode)
+            .filter_map(|obj| obj.cpuset())
+            .map(|cpuset| {
+                cpuset
+                    .iter_set()
+                    .map(|idx| usize::from(idx))
+                    .collect::<Vec<_>>()
+            })
+            .filter(|v| !v.is_empty())
+            .collect();
+
+        if nodes.len() > 1 {
+            if let Some(pools) = nodes
+                .iter()
+                .map(|cpus| build_pool(cpus).map(|p| Some(Arc::new(p))))
+                .collect::<Option<Vec<_>>>()
+            {
+                debug!(
+                    "NUMA topology: {} node(s), {} core(s)/node",
+                    nodes.len(),
+                    nodes.first().map_or(0, |v| v.len()),
+                );
+                return NumaSetup {
+                    pools,
+                    cpus_per_node: nodes,
+                };
+            }
+        }
+    }
+
+    // UMA fallback: single synthetic node, all cores, no pool, no pinning.
+    let n_cores = obisys::effective_parallelism();
+    debug!("UMA: single synthetic node, {} core(s)", n_cores);
+    NumaSetup {
+        pools: vec![None],
+        cpus_per_node: vec![(0..n_cores).collect()],
+    }
+}
+
+#[cfg(not(feature = "numa"))]
+pub fn build() -> NumaSetup {
+    let n_cores = obisys::effective_parallelism();
+    debug!("UMA: single synthetic node, {} core(s)", n_cores);
+    NumaSetup {
+        pools: vec![None],
+        cpus_per_node: vec![(0..n_cores).collect()],
+    }
+}
+
+/// Bind the calling thread to `cpu_indices` using hwloc.
+/// Silently returns on any error so the thread still runs, just unbound.
+#[cfg(feature = "numa")]
+pub fn pin_current_thread(cpu_indices: &[usize]) {
+    let Ok(topology) = Topology::new() else {
+        return;
+    };
+    let mut cpuset = CpuSet::new();
+    for &idx in cpu_indices {
+        cpuset.set(idx);
+    }
+    let _ = topology.bind_cpu(&cpuset, CpuBindingFlags::THREAD);
+}
+
+#[cfg(not(feature = "numa"))]
+pub fn pin_current_thread(_cpu_indices: &[usize]) {}
+
+// ── Internal helpers ──────────────────────────────────────────────────────────
+
+#[cfg(feature = "numa")]
+fn build_pool(cpus: &[usize]) -> Option<rayon::ThreadPool> {
+    let cpus = cpus.to_vec();
+    rayon::ThreadPoolBuilder::new()
+        .num_threads(cpus.len())
+        .spawn_handler(move |thread| {
+            let cpus = cpus.clone();
+            std::thread::Builder::new().spawn(move || {
+                pin_current_thread(&cpus);
+                thread.run();
+            })?;
+            Ok(())
+        })
+        .build()
+        .ok()
+}
diff --git a/src/obikindex/src/siblings.rs b/src/obikindex/src/siblings.rs
deleted file mode 100644
index ad8aea6b..00000000
--- a/src/obikindex/src/siblings.rs
+++ /dev/null
@@ -1,1460 +0,0 @@
-//! Family presence-mask annex construction.
-//!
-//! See `docmd/theory/evolutionary_distances.md`, "Definitions: family, and
-//! the canonical form of a family" and "Step 2b", for the full design
-//! discussion this implements.
-//!
-//! For each distinct k-mer of each layer of the (already built/merged)
-//! index, computes a 4-bit presence mask for its "family" (the up to 4
-//! k-mers sharing its flanks, differing only at the central base —
-//! well-defined for odd k): bit `b` set iff the family member whose own
-//! canonical central base is `b` (0=A, 1=C, 2=G, 3=T) is observed anywhere
-//! in the current multi-genome index — a property of the whole index, not
-//! of any one genome. Sibling count and minorant are *derived* from the
-//! mask by callers, not stored (see `FamilyMask` and
-//! [`sibling_annex_stats`](KmerIndex::sibling_annex_stats) below).
-//!
-//! Per layer, an `obipipeline` batch transform (throttled — see
-//! `obipipeline::throttle`) generates a whole batch's central variants at
-//! once (`BATCH_SIZE` source k-mers in, that batch's variants out as one
-//! pipeline message), interleaved across many in-flight batches by the
-//! scheduler's shared worker pool rather than processed on a single
-//! thread. The actual cross-partition lookup reuses a `PartitionCache` of
-//! every partition's already-open MPHF layers, built once for the whole
-//! `build_sibling_annex` run, rather than reopening files per lookup or
-//! per source layer. Two earlier, coarser-grained designs were tried and
-//! measured (not guessed) to be worse, in order: (1) reopening/re-mmap'ing
-//! every target partition's files on every single lookup — fine at toy
-//! scale, ~90% system time against a real index; (2) a `Flat` pipeline
-//! stage pushing one message per generated *variant* (up to 3 per source
-//! k-mer) — cheaper than reopening files, but sampling a real run showed
-//! most wall-clock time going into per-message channel send/notify
-//! syscalls rather than the lookup itself, because a single k-mer's ≤3
-//! variants is far too fine a granularity to amortise a pipeline's
-//! synchronisation cost over. See `docmd/theory/evolutionary_distances.md`,
-//! Step 2b, "Mechanism".
-
-use std::path::Path;
-use std::sync::atomic::{AtomicU8, Ordering};
-use std::sync::Arc;
-
-use ndarray::Array2;
-use rayon::prelude::*;
-
-use obicompactvec::{
-    FamilyMask, PersistentBitMatrix, PersistentCompactIntMatrix, SiblingAnnex, SiblingAnnexBuilder,
-};
-use obikpartitionner::KmerPartition;
-use obipipeline::ThrottleGuard;
-use obikseq::{CanonicalKmer, Minimizer};
-use obilayeredmap::{MphfLayer, OLMError};
-use obilayeredmap::meta::PartitionMeta;
-use obiskbuilder::rolling_stat::RollingStat;
-use obiskio::UnitigFileReader;
-use obisys::progress_bar;
-
-use crate::error::{OKIError, OKIResult};
-use crate::index::KmerIndex;
-
-const INDEX_SUBDIR: &str = "index";
-const ANNEX_FILE_NAME: &str = "siblings.psib";
-
-fn olm_to_ok(e: OLMError) -> OKIError {
-    match e {
-        OLMError::Io(e) => OKIError::Io(e),
-        other => OKIError::InvalidInput(format!("layered-map error: {other}")),
-    }
-}
-
-/// Central-position base of a canonical k-mer, in the fixed 0=A/1=C/2=G/3=T
-/// encoding — the mask's bit index. `k` must be odd (project invariant).
-#[inline]
-fn central_base(kmer: CanonicalKmer, k: usize) -> u8 {
-    kmer.nucleotide((k - 1) / 2)
-}
-
-/// Is `kmer` the minorant of its family, given the family's presence mask?
-/// Regenerates the family's 4 canonical forms from `kmer` itself (cheap, no
-/// lookup — see the design doc's "Definitions" section for why this is
-/// always safe: the set of 4 forms is invariant regardless of which member
-/// you start from), and compares the raw encodings of whichever are marked
-/// present in `mask`.
-fn is_minorant(kmer: CanonicalKmer, mask: FamilyMask, k: usize) -> bool {
-    kmer.central_canonical_neighbors().into_iter().all(|other| {
-        other == kmer || !mask.has(central_base(other, k)) || kmer.raw() <= other.raw()
-    })
-}
-
-
-/// Minimiser of a single, isolated canonical k-mer (not part of a streamed
-/// sequence). `RollingStat` computes minimisers incrementally along a
-/// sequence; this feeds one k-mer's bases through a fresh instance to get
-/// the same selection for a single, disconnected k-mer. Not the leanest
-/// possible primitive (an O(1)-amortised dedicated scan, as originally
-/// sketched in the design doc's Step 0, would avoid the ASCII round-trip and
-/// `RollingStat` allocation) but correct and reuses already-tested logic;
-/// left as a follow-up optimisation.
-fn lone_kmer_minimizer(kmer: CanonicalKmer) -> Minimizer {
-    let ascii = kmer.to_ascii();
-    let mut rs = RollingStat::new(0);
-    for b in ascii {
-        rs.push(b);
-    }
-    rs.canonical_minimizer()
-        .expect("RollingStat must be ready after k bases of a valid k-mer")
-}
-
-/// Destination partition for a (possibly synthetic) canonical k-mer, using
-/// the same routing rule as the rest of the index (`minimiser.seq_hash() &
-/// mask`, `n_partitions` is a power of two).
-fn partition_of(kmer: CanonicalKmer, n_partitions: usize) -> usize {
-    let mask = (n_partitions as u64) - 1;
-    (lone_kmer_minimizer(kmer).seq_hash() & mask) as usize
-}
-
-// ── obipipeline data types ─────────────────────────────────────────────────
-
-/// A batch of this layer's distinct k-mers (local MPHF slot + k-mer), the
-/// pipeline's source item — batched, not one k-mer per item, so that
-/// pipeline messages and their synchronisation cost stay amortised over
-/// thousands of lookups (see `build_layer_sibling_annex`'s comment on
-/// `BATCH_SIZE`). Carries the throttle permit for the whole batch, moved
-/// (not cloned) into the corresponding `VariantBatch` — a 1-to-1 transform,
-/// unlike the fan-out `Flat` stage this replaced, needs no `Arc` sharing.
-struct SourceBatch {
-    items: Vec<(usize, CanonicalKmer)>,
-    _permit: ThrottleGuard,
-}
-
-/// One batch's worth of central-substitution variants (up to 3 per source
-/// k-mer), each already routed to its destination partition and carrying
-/// its own central base (0=A/1=C/2=G/3=T) — the mask bit it will set on a
-/// hit. `(dest_partition, variant, source_slot, base)` per entry.
-struct VariantBatch {
-    items: Vec<(usize, CanonicalKmer, usize, u8)>,
-    _permit: ThrottleGuard,
-}
-
-enum SibData {
-    Batch(SourceBatch),
-    Variants(VariantBatch),
-}
-
-/// Every partition's already-open MPHF layers, built **once** for the whole
-/// `build_sibling_annex` run and shared (read-only) across every lookup, in
-/// every source layer, for the rest of the run — not reopened/re-mmap'd per
-/// query, nor per source layer.
-///
-/// Confirmed necessary by sampling a real run: routing lookups through
-/// `KmerPartition::query_partition_with` (the same batching `obikmer query`
-/// uses) still reopens+re-mmaps every target partition's files on every
-/// call, and it is called once per destination partition **per source
-/// layer** — for an index with many layers this repeats the same
-/// `MphfLayer::open`/`Evidence::open`/`PersistentBitMatrix::open` work over
-/// and over. Parallelising those calls (see the gather step below) spread
-/// the redundant work across more cores but did not reduce it: sampling
-/// showed Rayon workers spending their time inside repeated `open()`
-/// syscalls, not computation. This cache amortises that cost to once per
-/// partition for the entire run, regardless of how many source layers or
-/// lookups follow.
-/// A cached layer's opened presence/count matrix, alongside its `MphfLayer`.
-enum Mat {
-    Count(PersistentCompactIntMatrix),
-    Presence(PersistentBitMatrix),
-}
-
-impl Mat {
-    fn n_cols(&self) -> usize {
-        match self {
-            Mat::Count(m) => m.n_cols(),
-            Mat::Presence(m) => m.n_cols(),
-        }
-    }
-    fn carries(&self, g: usize, slot: usize) -> bool {
-        match self {
-            Mat::Count(m) => m.col_view(g).get(slot) != 0,
-            Mat::Presence(m) => m.get(g, slot) != 0,
-        }
-    }
-}
-
-struct PartitionCache {
-    /// `layers[partition][layer]` = that partition's opened MPHF layers,
-    /// paired 1:1 with `mats[partition][layer]`; empty if the partition
-    /// directory doesn't exist. Used by both [`KmerIndex::build_sibling_annex`]
-    /// (`layers` only) and [`KmerIndex::sibling_annex_stats`] (both).
-    layers: Vec<Vec<MphfLayer>>,
-    mats: Vec<Vec<Mat>>,
-}
-
-impl PartitionCache {
-    fn build(partition: &KmerPartition, n_parts: usize, with_counts: bool) -> OKIResult<Self> {
-        let pb = progress_bar("open_partitions", n_parts as u64, "partitions");
-        let built: Vec<(Vec<MphfLayer>, Vec<Mat>)> = (0..n_parts)
-            .into_par_iter()
-            .map(|part| -> OKIResult<(Vec<MphfLayer>, Vec<Mat>)> {
-                let index_dir = partition.part_dir(part).join(INDEX_SUBDIR);
-                if !index_dir.exists() {
-                    pb.inc(1);
-                    return Ok((Vec::new(), Vec::new()));
-                }
-                let meta = PartitionMeta::load(&index_dir).map_err(olm_to_ok)?;
-                let mut layers = Vec::with_capacity(meta.n_layers);
-                let mut mats = Vec::with_capacity(meta.n_layers);
-                for l in 0..meta.n_layers {
-                    let layer_dir = index_dir.join(format!("layer_{l}"));
-                    let Ok(mphf) = MphfLayer::open(&layer_dir, &meta.mode) else { continue };
-                    let use_counts = with_counts && layer_dir.join("counts").exists();
-                    let mat = if use_counts {
-                        PersistentCompactIntMatrix::open(&layer_dir).ok().map(Mat::Count)
-                    } else {
-                        PersistentBitMatrix::open(&layer_dir).ok().map(Mat::Presence)
-                    };
-                    let Some(mat) = mat else { continue };
-                    layers.push(mphf);
-                    mats.push(mat);
-                }
-                pb.inc(1);
-                Ok((layers, mats))
-            })
-            .collect::<OKIResult<Vec<_>>>()?;
-        pb.finish_and_clear();
-        let (layers, mats) = built.into_iter().unzip();
-        Ok(Self { layers, mats })
-    }
-
-    /// Existence-only lookup of `variant` in partition `dest_partition`:
-    /// tries each of the partition's already-open layers in turn, stopping
-    /// at the first hit.
-    fn find(&self, dest_partition: usize, variant: CanonicalKmer) -> bool {
-        self.layers
-            .get(dest_partition)
-            .is_some_and(|layers| layers.iter().any(|mphf| mphf.find(variant).is_some()))
-    }
-
-    /// Per-genome presence vector for `variant` in partition `dest_partition`
-    /// (`true` iff that genome carries it), `None` on a miss. Same shape as
-    /// `find`, but also reads the cached matrix instead of just the MPHF.
-    fn find_presence(&self, dest_partition: usize, variant: CanonicalKmer, n_genomes: usize) -> Option<Vec<bool>> {
-        let layers = self.layers.get(dest_partition)?;
-        let mats = self.mats.get(dest_partition)?;
-        for (mphf, mat) in layers.iter().zip(mats.iter()) {
-            if let Some(slot) = mphf.find(variant) {
-                let n_cols = mat.n_cols().min(n_genomes);
-                return Some((0..n_cols).map(|g| mat.carries(g, slot)).collect());
-            }
-        }
-        None
-    }
-}
-
-impl KmerIndex {
-    /// Build the sibling-count/minorant annex for every layer of every
-    /// partition of this (already built) index, writing one annex file per
-    /// layer alongside its existing index files. Safe to call again later
-    /// (e.g. after a fresh `merge`) — each run simply overwrites the annex
-    /// files of the index it is called on.
-    ///
-    /// Construction only — no statistics gathered here on purpose: this is
-    /// meant to run routinely (it is the artefact the SNP-family distances
-    /// will consume), while the sibling-count distribution
-    /// ([`sibling_annex_stats`](Self::sibling_annex_stats)) is a separate,
-    /// occasional diagnostic pass over the result, not run every time.
-    ///
-    /// Cross-partition/cross-layer lookups are required (a k-mer's siblings
-    /// can live in any partition), but the layer loop itself — and thus the
-    /// annex file this produces — stays local to one layer at a time.
-    pub fn build_sibling_annex(&self) -> OKIResult<()> {
-        let n_parts = self.n_partitions();
-        let n_bits = n_parts.trailing_zeros() as usize;
-
-        let partition = KmerPartition::open_with_config(
-            &self.root_path,
-            self.kmer_size(),
-            self.minimizer_size(),
-            n_bits,
-        )
-        .map_err(OKIError::Partition)?;
-
-        tracing::info!("opening {n_parts} partition(s) for the sibling-annex sweep");
-        let cache = Arc::new(PartitionCache::build(&partition, n_parts, self.meta.config.with_counts)?);
-
-        let pb = progress_bar("sibling_annex", n_parts as u64, "partitions");
-        let mut total_slots: u64 = 0;
-        for part in 0..n_parts {
-            let index_dir = self.partition().part_dir(part).join(INDEX_SUBDIR);
-            if !index_dir.exists() {
-                pb.inc(1);
-                continue;
-            }
-            let meta = PartitionMeta::load(&index_dir).map_err(olm_to_ok)?;
-
-            let mut part_slots: u64 = 0;
-            for l in 0..meta.n_layers {
-                let layer_dir = index_dir.join(format!("layer_{l}"));
-                part_slots += self.build_layer_sibling_annex(&layer_dir, n_parts, &cache)?;
-            }
-            total_slots += part_slots;
-            pb.inc(1);
-            pb.set_message(format!("partition {part}: {part_slots} kmers ({total_slots} total)"));
-        }
-        pb.finish_and_clear();
-        tracing::info!("sibling annex built — {total_slots} kmers across {n_parts} partitions");
-
-        Ok(())
-    }
-
-    /// Returns the number of distinct k-mers (annex slots) processed, for
-    /// progress reporting.
-    fn build_layer_sibling_annex(
-        &self,
-        layer_dir: &Path,
-        n_parts: usize,
-        cache: &Arc<PartitionCache>,
-    ) -> OKIResult<u64> {
-        let index_dir = layer_dir.parent().expect("layer_dir has a parent index dir");
-        let meta = PartitionMeta::load(index_dir).map_err(olm_to_ok)?;
-        let mphf = MphfLayer::open(layer_dir, &meta.mode).map_err(olm_to_ok)?;
-        let n_slots = mphf.n();
-
-        // ── Enumerate this layer's distinct k-mers, one per slot ────────────
-        let mut slot_kmer: Vec<Option<CanonicalKmer>> = vec![None; n_slots];
-        let reader = UnitigFileReader::open_sequential(&layer_dir.join("unitigs.bin"))
-            .map_err(OKIError::Partition)?;
-        for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
-            if let Some(slot) = mphf.find(kmer) {
-                slot_kmer[slot] = Some(kmer);
-            }
-        }
-
-        let k = self.kmer_size();
-
-        // ── Reconciliation state, initialised with each slot's own base —
-        // that member is trivially present, no lookup needed. Built before
-        // the pipeline runs, from the same enumeration, since `sources`
-        // below is consumed as a throttled iterator, not collected.
-        // `AtomicU8`, not `FamilyMask`, because the gather phase below
-        // parallelises across destination partitions (independent
-        // `query_partition_with` calls, safe to run concurrently) and their
-        // `Found` hits can land on arbitrary, possibly-shared slots — a
-        // lock-free `fetch_or` avoids needing any synchronisation beyond
-        // that. ─────────────────────────────────────────────────────────
-        let mask: Vec<AtomicU8> = (0..n_slots).map(|_| AtomicU8::new(0)).collect();
-        for (slot, kmer) in slot_kmer.iter().enumerate().filter_map(|(s, k)| k.map(|k| (s, k))) {
-            mask[slot].fetch_or(1 << central_base(kmer, k), Ordering::Relaxed);
-        }
-
-        // ── obipipeline: a *batch* transform, not a per-k-mer `Flat` one —
-        // the actual cross-partition lookup reuses
-        // `KmerPartition::query_partition_with` (the same batching mechanism
-        // `obikmer query` already uses: open a partition's files once,
-        // answer a whole batch of queries against it) instead of one lookup
-        // per pipeline item. A per-item lookup (tried first) reopened/
-        // re-mmap'd every target partition's files on every single variant
-        // — fine at toy scale, but ~90% system time against a real index,
-        // observed in practice. A *later* attempt still pushed one pipeline
-        // message per generated variant (a `Flat` stage, `SourceItem` =>
-        // `VariantQuery`, one k-mer in => up to 3 variants out as separate
-        // messages) — cheaper than reopening files, but sampling a real run
-        // showed most wall-clock time going into per-message channel
-        // send/notify syscalls instead of the lookup itself: the pipeline's
-        // whole point is amortising synchronisation over a batch, and a
-        // single k-mer's ≤3 variants is far too fine a granularity for
-        // that. Batching `BATCH_SIZE` source k-mers into one pipeline item
-        // — a plain 1-to-1 (`|`, not `||`) transform, batch in, batch of
-        // variants out, one message either way — keeps the per-message
-        // synchronisation cost amortised over thousands of lookups instead
-        // of one to three. ──────────────────────────────────────────────
-        const BATCH_SIZE: usize = 4096;
-        let n_workers = obisys::effective_parallelism();
-        let capacity = 256;
-
-        // Throttling limits how many *batches* are in flight at once — the
-        // permit is acquired per batch (not per k-mer) in the source
-        // thread, and released once its `VariantBatch` has been read out of
-        // the pipeline by the accumulation loop below. See
-        // `obipipeline::throttle`'s docs for why this is required, not
-        // optional, once a `Flat`-style stage sits in the pipeline.
-        let sources: Vec<(usize, CanonicalKmer)> = slot_kmer
-            .iter()
-            .enumerate()
-            .filter_map(|(slot, maybe_kmer)| maybe_kmer.map(|kmer| (slot, kmer)))
-            .collect();
-        let batches: Vec<Vec<(usize, CanonicalKmer)>> = sources
-            .chunks(BATCH_SIZE)
-            .map(|chunk| chunk.to_vec())
-            .collect();
-        let throttled = obipipeline::throttle(batches.into_iter(), n_workers).map(|t| SourceBatch {
-            items: t.item,
-            _permit: t.guard,
-        });
-
-        let pipe = obipipeline::make_pipe! {
-            SibData : SourceBatch => VariantBatch,
-            | {
-                move |batch: SourceBatch| -> VariantBatch {
-                    let mut items = Vec::with_capacity(batch.items.len() * 3);
-                    for (slot, kmer) in batch.items {
-                        for variant in kmer.central_canonical_neighbors() {
-                            if variant == kmer {
-                                continue;
-                            }
-                            items.push((
-                                partition_of(variant, n_parts),
-                                variant,
-                                slot,
-                                central_base(variant, k),
-                            ));
-                        }
-                    }
-                    VariantBatch { items, _permit: batch._permit }
-                }
-            } : Batch => Variants,
-        };
-
-        // ── Group generated variants by destination partition. `cache`
-        // holds every partition already mmap'd (no more `open()` cost), but
-        // `mmap` pages are still loaded on demand and can be evicted — a
-        // lookup is not free just because the file isn't reopened. Grouping
-        // keeps one partition's pages hot while its whole batch is resolved,
-        // instead of faulting pages in and out as lookups jump between
-        // partitions in whatever order the pipeline happens to produce
-        // them. Each batch's throttle permit drops here, once accumulated.
-        let mut outgoing: Vec<Vec<(CanonicalKmer, usize, u8)>> = (0..n_parts).map(|_| Vec::new()).collect();
-        for vb in pipe.apply(throttled, n_workers, capacity) {
-            for (dest_partition, variant, source_slot, base) in vb.items {
-                outgoing[dest_partition].push((variant, source_slot, base));
-            }
-        }
-
-        // ── Resolve each partition's batch against the cache in one
-        // contiguous pass; parallelised across partitions (independent,
-        // read-only) so this keeps using multiple cores without giving up
-        // the per-partition locality above. ─────────────────────────────
-        outgoing.par_iter().enumerate().filter(|(_, q)| !q.is_empty()).for_each(|(dest, queries)| {
-            for &(variant, source_slot, base) in queries {
-                if cache.find(dest, variant) {
-                    mask[source_slot].fetch_or(1 << base, Ordering::Relaxed);
-                }
-            }
-        });
-
-        // ── Write the layer's annex file ─────────────────────────────────────
-        let annex_path = layer_dir.join(ANNEX_FILE_NAME);
-        let mut builder = SiblingAnnexBuilder::new(n_slots, &annex_path)?;
-        for (slot, m) in mask.iter().enumerate() {
-            if slot_kmer[slot].is_none() {
-                continue; // unused MPHF slot, if any — leave at the sentinel
-            }
-            builder.set(slot, FamilyMask::from_bits(m.load(Ordering::Relaxed)));
-        }
-        builder.close()?;
-
-        Ok(n_slots as u64)
-    }
-}
-
-/// Distribution of family sizes (1-4), read back from an already-built
-/// annex (see [`KmerIndex::build_sibling_annex`]) plus the index's
-/// presence/count data — a separate, occasional diagnostic pass, not fused
-/// into construction.
-///
-/// Every count here is **per family, not per slot**: a family with `F`
-/// members occupies `F` annex slots (one per observed member), all sharing
-/// the same mask. Counting every slot would count each family up to 4
-/// times over; only the minorant's slot is tallied (minorant is derived on
-/// the fly — see `is_minorant` — not stored, but cheap: no lookup, pure
-/// bit arithmetic on already-in-hand data).
-#[derive(Debug, Clone, Default)]
-pub struct SiblingAnnexStats {
-    /// `counts[s]` = number of *families* of size `s + 1` (index 0 = size 1,
-    /// i.e. 0 siblings, ... index 3 = size 4, i.e. 3 siblings).
-    pub counts: [u64; 4],
-    /// `per_genome[g][s]` = number of families of size `s + 1` for which
-    /// genome `g` (index into `KmerIndex::meta().genomes`) carries at least
-    /// one member.
-    pub per_genome: Vec<[u64; 4]>,
-}
-
-impl KmerIndex {
-    /// Tally the family-size distribution of an already-built annex
-    /// (globally, and per genome), counting each family once (at its
-    /// minorant slot). Errors if [`build_sibling_annex`] has not been run on
-    /// this index first.
-    ///
-    /// [`build_sibling_annex`]: Self::build_sibling_annex
-    pub fn sibling_annex_stats(&self) -> OKIResult<SiblingAnnexStats> {
-        let n_parts = self.n_partitions();
-        let n_genomes = self.meta.genomes.len();
-        let with_counts = self.meta.config.with_counts;
-        let k = self.kmer_size();
-        let n_bits = n_parts.trailing_zeros() as usize;
-
-        // Same whole-run cache as `build_sibling_annex` — see its docs for
-        // why re-opening per lookup (or per call to a batching helper) is
-        // not good enough on a real index.
-        let partition = KmerPartition::open_with_config(
-            &self.root_path,
-            self.kmer_size(),
-            self.minimizer_size(),
-            n_bits,
-        )
-        .map_err(OKIError::Partition)?;
-        let cache = PartitionCache::build(&partition, n_parts, with_counts)?;
-
-        // Gather the (partition, layer) pairs to process — cheap metadata
-        // reads only, checking every annex file exists up front so a
-        // missing one is reported before any real work starts.
-        let mut layer_dirs = Vec::new();
-        for part in 0..n_parts {
-            let index_dir = self.partition().part_dir(part).join(INDEX_SUBDIR);
-            if !index_dir.exists() {
-                continue;
-            }
-            let meta = PartitionMeta::load(&index_dir).map_err(olm_to_ok)?;
-            for l in 0..meta.n_layers {
-                let layer_dir = index_dir.join(format!("layer_{l}"));
-                let annex_path = layer_dir.join(ANNEX_FILE_NAME);
-                if !annex_path.exists() {
-                    return Err(OKIError::InvalidInput(format!(
-                        "no sibling annex at {} — run build_sibling_annex first",
-                        annex_path.display()
-                    )));
-                }
-                layer_dirs.push(layer_dir);
-            }
-        }
-
-        // One layer's worth of work, parallelised across layers with Rayon
-        // — independent, read-only, each producing its own partial tally
-        // merged at the end.
-        let pb = progress_bar("sibling_annex_stats", layer_dirs.len() as u64, "layers");
-        let partials: Vec<SiblingAnnexStats> = layer_dirs
-            .par_iter()
-            .map(|layer_dir| -> OKIResult<SiblingAnnexStats> {
-                let mut stats = SiblingAnnexStats {
-                    per_genome: vec![[0u64; 4]; n_genomes],
-                    ..Default::default()
-                };
-
-                let index_dir = layer_dir.parent().expect("layer_dir has a parent index dir");
-                let meta = PartitionMeta::load(index_dir).map_err(olm_to_ok)?;
-                let annex = SiblingAnnex::open(&layer_dir.join(ANNEX_FILE_NAME))?;
-
-                // Need each slot's own k-mer to derive minorant — same
-                // enumeration as construction.
-                let mphf = MphfLayer::open(layer_dir, &meta.mode).map_err(olm_to_ok)?;
-                let mut slot_kmer: Vec<Option<CanonicalKmer>> = vec![None; annex.len()];
-                let reader = UnitigFileReader::open_sequential(&layer_dir.join("unitigs.bin"))
-                    .map_err(OKIError::Partition)?;
-                for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
-                    if let Some(slot) = mphf.find(kmer) {
-                        slot_kmer[slot] = Some(kmer);
-                    }
-                }
-
-                let use_counts = with_counts && layer_dir.join("counts").exists();
-                let mat = if use_counts {
-                    Mat::Count(PersistentCompactIntMatrix::open(layer_dir)?)
-                } else {
-                    Mat::Presence(PersistentBitMatrix::open(layer_dir)?)
-                };
-                let n_cols = mat.n_cols().min(n_genomes);
-
-                for slot in 0..annex.len() {
-                    let Some(mask) = annex.get(slot) else { continue };
-                    let Some(kmer) = slot_kmer[slot] else { continue };
-                    if !is_minorant(kmer, mask, k) {
-                        continue; // this family is tallied at its minorant's slot only
-                    }
-                    let s = mask.siblings() as usize;
-                    stats.counts[s] += 1;
-
-                    // "Genome g represents this family" means g carries
-                    // *any* of its members, not just the minorant's own —
-                    // start from the minorant's own presence (already
-                    // open, no lookup) and OR in every other present
-                    // member's presence vector, resolved against the
-                    // whole-run cache (no I/O) — exactly `mask.siblings()`
-                    // of them, the mask tells us precisely which to fetch.
-                    let mut carries = vec![false; n_cols];
-                    for g in 0..n_cols {
-                        carries[g] = mat.carries(g, slot);
-                    }
-                    for other in kmer.central_canonical_neighbors() {
-                        if other == kmer {
-                            continue;
-                        }
-                        let base = central_base(other, k);
-                        if !mask.has(base) {
-                            continue;
-                        }
-                        let dest = partition_of(other, n_parts);
-                        if let Some(other_presence) = cache.find_presence(dest, other, n_genomes) {
-                            for (g, &present) in other_presence.iter().enumerate() {
-                                if present {
-                                    carries[g] = true;
-                                }
-                            }
-                        }
-                    }
-
-                    for (g, &carried) in carries.iter().enumerate() {
-                        if carried {
-                            stats.per_genome[g][s] += 1;
-                        }
-                    }
-                }
-
-                pb.inc(1);
-                Ok(stats)
-            })
-            .collect::<OKIResult<Vec<_>>>()?;
-        pb.finish_and_clear();
-
-        let mut stats = SiblingAnnexStats {
-            per_genome: vec![[0u64; 4]; n_genomes],
-            ..Default::default()
-        };
-        for part in partials {
-            for s in 0..4 {
-                stats.counts[s] += part.counts[s];
-            }
-            for g in 0..n_genomes {
-                for s in 0..4 {
-                    stats.per_genome[g][s] += part.per_genome[g][s];
-                }
-            }
-        }
-        Ok(stats)
-    }
-}
-
-/// Raw p-distance restricted to loci that are single-copy in **both**
-/// genomes of a pair — the "stringent / paralogy-aware" locus eligibility
-/// rule (`docmd/theory/evolutionary_distances.md`, "Locus eligibility"),
-/// without the JC/K2P/LogDet finalisation math: `snp[i,j]` + `shared[i,j]`
-/// is the number of eligible loci, `snp[i,j] / (snp[i,j] + shared[i,j])` is
-/// `p_hat`. A quick, self-contained way to sanity-check the estimator
-/// against a real index before the full `SnpTally` design is built.
-///
-/// A locus (family, tallied once at its minorant) is eligible for pair
-/// `(i, j)` iff genome `i` carries exactly one of the family's observed
-/// forms **and** genome `j` carries exactly one (possibly a different one)
-/// — presence-only: a genome carrying the same form twice (a same-allele
-/// duplicate) is indistinguishable from carrying it once when only a
-/// presence matrix is available, so such cases are not excluded here even
-/// when a count index exists. See "Locus eligibility", stringent rule, for
-/// why this matters and how a count index would close the gap — left as a
-/// follow-up, not applied here.
-pub struct RawSnpDistanceOutput {
-    /// n×n count of eligible loci where the two genomes' single forms differ.
-    pub snp: Array2<u64>,
-    /// n×n count of eligible loci where the two genomes' single forms agree.
-    pub shared: Array2<u64>,
-}
-
-impl KmerIndex {
-    /// Shared traversal behind [`raw_snp_distance`](Self::raw_snp_distance)
-    /// and [`base_pair_tally`](Self::base_pair_tally): for every family
-    /// (tallied once, at its minorant) of every layer of the already-built
-    /// sibling annex, resolves each genome's single observed form (`None`
-    /// if absent or ambiguous/multi-copy), then calls `on_pair(acc, i, j,
-    /// bi, bj, variable)` for every genome pair `(i, j)` where both are
-    /// unambiguous and single-copy (`bi == bj` means shared at that locus,
-    /// `bi != bj` means a SNP). `variable` is the family's own
-    /// `family_size() >= 2` (true if more than one member is observed
-    /// *anywhere* in the family, i.e. it isn't fully invariant across the
-    /// whole index) — `raw_snp_distance` ignores it (a fully-invariant
-    /// family is still legitimately "shared"), but callers whose diagonal
-    /// should only reflect genuine SNP-adjacent agreement, not the
-    /// genome-wide invariant background, need it (see
-    /// [`base_pair_tally`](Self::base_pair_tally)'s `same` field). Layers
-    /// are processed in parallel (rayon); each gets its own accumulator
-    /// from `zero()`, combined pairwise via `combine`.
-    fn scan_family_pairs<Acc, F, C>(
-        &self,
-        label: &str,
-        zero: impl Fn() -> Acc + Sync,
-        on_pair: F,
-        combine: C,
-    ) -> OKIResult<Acc>
-    where
-        Acc: Send,
-        F: Fn(&mut Acc, usize, usize, u8, u8, bool) + Sync,
-        C: Fn(Acc, Acc) -> Acc,
-    {
-        let n_parts = self.n_partitions();
-        let n_genomes = self.meta.genomes.len();
-        let with_counts = self.meta.config.with_counts;
-        let k = self.kmer_size();
-        let n_bits = n_parts.trailing_zeros() as usize;
-
-        let partition = KmerPartition::open_with_config(
-            &self.root_path,
-            self.kmer_size(),
-            self.minimizer_size(),
-            n_bits,
-        )
-        .map_err(OKIError::Partition)?;
-        let cache = PartitionCache::build(&partition, n_parts, with_counts)?;
-
-        let mut layer_dirs = Vec::new();
-        for part in 0..n_parts {
-            let index_dir = self.partition().part_dir(part).join(INDEX_SUBDIR);
-            if !index_dir.exists() {
-                continue;
-            }
-            let meta = PartitionMeta::load(&index_dir).map_err(olm_to_ok)?;
-            for l in 0..meta.n_layers {
-                let layer_dir = index_dir.join(format!("layer_{l}"));
-                let annex_path = layer_dir.join(ANNEX_FILE_NAME);
-                if !annex_path.exists() {
-                    return Err(OKIError::InvalidInput(format!(
-                        "no sibling annex at {} — run build_sibling_annex first",
-                        annex_path.display()
-                    )));
-                }
-                layer_dirs.push(layer_dir);
-            }
-        }
-
-        let pb = progress_bar(label, layer_dirs.len() as u64, "layers");
-        let partials: Vec<Acc> = layer_dirs
-            .par_iter()
-            .map(|layer_dir| -> OKIResult<Acc> {
-                let mut acc = zero();
-
-                let index_dir = layer_dir.parent().expect("layer_dir has a parent index dir");
-                let meta = PartitionMeta::load(index_dir).map_err(olm_to_ok)?;
-                let annex = SiblingAnnex::open(&layer_dir.join(ANNEX_FILE_NAME))?;
-                let mphf = MphfLayer::open(layer_dir, &meta.mode).map_err(olm_to_ok)?;
-
-                let mut slot_kmer: Vec<Option<CanonicalKmer>> = vec![None; annex.len()];
-                let reader = UnitigFileReader::open_sequential(&layer_dir.join("unitigs.bin"))
-                    .map_err(OKIError::Partition)?;
-                for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
-                    if let Some(slot) = mphf.find(kmer) {
-                        slot_kmer[slot] = Some(kmer);
-                    }
-                }
-
-                let use_counts = with_counts && layer_dir.join("counts").exists();
-                let mat = if use_counts {
-                    Mat::Count(PersistentCompactIntMatrix::open(layer_dir)?)
-                } else {
-                    Mat::Presence(PersistentBitMatrix::open(layer_dir)?)
-                };
-                let n_cols = mat.n_cols().min(n_genomes);
-
-                // Per family: which single form (if exactly one) each genome
-                // carries — `None` once a second form is seen (ambiguous,
-                // not single-copy, ineligible for either side of a pair).
-                let mut single_form: Vec<Option<u8>> = Vec::with_capacity(n_cols);
-                let mut ambiguous: Vec<bool> = Vec::with_capacity(n_cols);
-
-                for slot in 0..annex.len() {
-                    let Some(mask) = annex.get(slot) else { continue };
-                    let Some(kmer) = slot_kmer[slot] else { continue };
-                    if !is_minorant(kmer, mask, k) {
-                        continue; // family tallied once, at its minorant
-                    }
-                    let variable = mask.family_size() >= 2;
-
-                    single_form.clear();
-                    single_form.resize(n_cols, None);
-                    ambiguous.clear();
-                    ambiguous.resize(n_cols, false);
-
-                    for other in kmer.central_canonical_neighbors() {
-                        let base = central_base(other, k);
-                        if !mask.has(base) {
-                            continue;
-                        }
-                        let presence: Option<Vec<bool>> = if other == kmer {
-                            Some((0..n_cols).map(|g| mat.carries(g, slot)).collect())
-                        } else {
-                            let dest = partition_of(other, n_parts);
-                            cache.find_presence(dest, other, n_genomes)
-                        };
-                        let Some(presence) = presence else { continue };
-                        for (g, &present) in presence.iter().enumerate() {
-                            if !present {
-                                continue;
-                            }
-                            if single_form[g].is_some() {
-                                ambiguous[g] = true;
-                            } else {
-                                single_form[g] = Some(base);
-                            }
-                        }
-                    }
-
-                    for i in 0..n_cols {
-                        if ambiguous[i] {
-                            continue;
-                        }
-                        let Some(bi) = single_form[i] else { continue };
-                        for j in (i + 1)..n_cols {
-                            if ambiguous[j] {
-                                continue;
-                            }
-                            let Some(bj) = single_form[j] else { continue };
-                            on_pair(&mut acc, i, j, bi, bj, variable);
-                        }
-                    }
-                }
-
-                pb.inc(1);
-                Ok(acc)
-            })
-            .collect::<OKIResult<Vec<_>>>()?;
-        pb.finish_and_clear();
-
-        let mut total = zero();
-        for partial in partials {
-            total = combine(total, partial);
-        }
-        Ok(total)
-    }
-
-    /// Compute [`RawSnpDistanceOutput`] from an already-built sibling annex
-    /// (run [`build_sibling_annex`](Self::build_sibling_annex) first).
-    pub fn raw_snp_distance(&self) -> OKIResult<RawSnpDistanceOutput> {
-        let n_genomes = self.meta.genomes.len();
-        let (snp, shared) = self.scan_family_pairs(
-            "raw_snp_distance",
-            || (Array2::<u64>::zeros((n_genomes, n_genomes)), Array2::<u64>::zeros((n_genomes, n_genomes))),
-            |(snp, shared), i, j, bi, bj, _variable| {
-                if bi == bj {
-                    shared[[i, j]] += 1;
-                    shared[[j, i]] += 1;
-                } else {
-                    snp[[i, j]] += 1;
-                    snp[[j, i]] += 1;
-                }
-            },
-            |(mut snp, mut shared), (s, sh)| {
-                snp += &s;
-                shared += &sh;
-                (snp, shared)
-            },
-        )?;
-        Ok(RawSnpDistanceOutput { snp, shared })
-    }
-
-    /// Symmetric 6-category base-pair substitution tally (AC, AG, AT, CG,
-    /// CT, GT — indexed `0=A,1=C,2=G,3=T`), pooled only over genome pairs
-    /// whose overall SNP ratio in `raw` is at or below `ratio_ceiling` —
-    /// same saturation-exclusion discipline as
-    /// [`cardinality_tally`](Self::cardinality_tally), for the same reason:
-    /// a saturated pair's observed base-pair mix trends toward neutral base
-    /// composition, not the true point-mutation spectrum.
-    ///
-    /// A second full pass over the annex, sharing
-    /// [`raw_snp_distance`](Self::raw_snp_distance)'s traversal (guided by
-    /// it, not a blind re-scan) — needed because `raw_snp_distance` only
-    /// keeps aggregate SNP/shared counts per genome pair, not which bases
-    /// were actually involved at each locus, and the ratio-ceiling filter
-    /// can only be evaluated once the aggregate counts are known.
-    pub fn base_pair_tally(&self, raw: &RawSnpDistanceOutput, ratio_ceiling: f64) -> OKIResult<BasePairTally> {
-        let n_genomes = self.meta.genomes.len();
-        let included = Array2::from_shape_fn((n_genomes, n_genomes), |(i, j)| {
-            if i == j {
-                return false;
-            }
-            let snp = raw.snp[[i, j]];
-            let total = snp + raw.shared[[i, j]];
-            total > 0 && (snp as f64 / total as f64) <= ratio_ceiling
-        });
-
-        let (counts, same) = self.scan_family_pairs(
-            "base_pair_tally",
-            || ([[0u64; 4]; 4], [0u64; 4]),
-            |(counts, same), i, j, bi, bj, variable| {
-                if !included[[i, j]] {
-                    return;
-                }
-                if bi != bj {
-                    counts[bi as usize][bj as usize] += 1;
-                    counts[bj as usize][bi as usize] += 1;
-                } else if variable {
-                    // Only count "stayed the same" from families that vary
-                    // *somewhere* in the index — a fully invariant family
-                    // (never varies anywhere) isn't a SNP-adjacent
-                    // agreement, it's genome-wide background, and would
-                    // otherwise swamp the diagonal (see
-                    // `docmd/theory/evolutionary_distances.md`, the
-                    // ascertainment-bias regression this was reverting).
-                    same[bi as usize] += 1;
-                }
-            },
-            |(mut counts, mut same), (partial_counts, partial_same)| {
-                for a in 0..4 {
-                    same[a] += partial_same[a];
-                    for b in 0..4 {
-                        counts[a][b] += partial_counts[a][b];
-                    }
-                }
-                (counts, same)
-            },
-        )?;
-        Ok(BasePairTally { counts, same })
-    }
-}
-
-/// See [`KmerIndex::base_pair_tally`].
-pub struct BasePairTally {
-    /// `counts[a][b] == counts[b][a]` = number of eligible loci, pooled
-    /// over included genome pairs, where the two genomes' single forms are
-    /// `a` and `b` (0=A, 1=C, 2=G, 3=T). Diagonal always `0` — an `a == b`
-    /// locus is counted in `same`, not here.
-    pub counts: [[u64; 4]; 4],
-    /// `same[a]` = number of eligible loci, pooled over included genome
-    /// pairs, where both genomes' single forms are `a` — the diagonal
-    /// `counts` omits, needed to build a proper row-stochastic composition
-    /// probability matrix (the "stay the same base" entries), not just the
-    /// substitution-cost off-diagonal.
-    pub same: [u64; 4],
-}
-
-/// IUPAC ambiguity code for a per-genome family presence mask (bit `b` set
-/// iff the genome carries the member whose own central base is `b`):
-/// single bit -> the plain base; 2 or 3 bits -> the matching IUPAC
-/// ambiguity code (preserves partial information instead of collapsing to
-/// `N`, the same convention used for diploid heterozygous VCF/FASTA sites);
-/// all 4 bits -> `N`; no bits (genome carries none of the family's observed
-/// members) -> `-` (no data at this locus for this genome).
-fn iupac_code(mask: u8) -> u8 {
-    match mask & 0b1111 {
-        0b0000 => b'-',
-        0b0001 => b'A',
-        0b0010 => b'C',
-        0b0100 => b'G',
-        0b1000 => b'T',
-        0b0101 => b'R', // A/G
-        0b1010 => b'Y', // C/T
-        0b0110 => b'S', // C/G
-        0b1001 => b'W', // A/T
-        0b1100 => b'K', // G/T
-        0b0011 => b'M', // A/C
-        0b1110 => b'B', // C/G/T
-        0b1101 => b'D', // A/G/T
-        0b1011 => b'H', // A/C/T
-        0b0111 => b'V', // A/C/G
-        0b1111 => b'N',
-        _ => unreachable!("masked to 4 bits"),
-    }
-}
-
-/// See [`KmerIndex::cardinality_tally`].
-pub struct CardinalityTally {
-    /// `counts[a][b] == counts[b][a]` = number of family sites, pooled over
-    /// included genome pairs, where one genome's family cardinality
-    /// (popcount of its presence mask, `0..=4`) is `a` and the other's is
-    /// `b`. Diagonal is real data here (both genomes at the same
-    /// cardinality), unlike [`BasePairTally::counts`].
-    pub counts: [[u64; 5]; 5],
-}
-
-impl KmerIndex {
-    /// Cardinality co-occurrence, pooled only over genome pairs whose
-    /// overall SNP ratio in `raw` is at or below `ratio_ceiling` — same
-    /// saturation/no-data exclusion discipline as
-    /// [`base_pair_tally`](Self::base_pair_tally). Unlike
-    /// [`scan_family_pairs`](Self::scan_family_pairs) (which resolves each
-    /// genome to a single form and silently drops any genome carrying more
-    /// than one member of the family), this needs the *full* per-genome
-    /// presence mask — a family member count of 2, 3 or 4 is exactly the
-    /// signal being tallied, not noise to discard — so it re-implements the
-    /// traversal rather than reusing that helper.
-    ///
-    /// Restricted to variable families (`family_size() >= 2`), matching
-    /// `snp_pseudo_alignment`'s own scope — briefly removed, then
-    /// reinstated: without it, the diagonal is dominated by genome-wide
-    /// invariant background (family_size()<2 loci vastly outnumber the
-    /// ones that ever vary anywhere), which is inconsistent with the
-    /// `+ASC`-corrected alignment this matrix is ultimately used with —
-    /// `+ASC` exists specifically because the likelihood only ever sees
-    /// variable sites, so a rate model calibrated mostly from invariant
-    /// background sites doesn't describe the population it's applied to.
-    /// Verified empirically: removing the filter measurably worsened a
-    /// real IQ-TREE run (log-likelihood dropped, `NNI search needs
-    /// unusual large number of steps to converge` warnings appeared) — see
-    /// `docmd/theory/evolutionary_distances.md` for the full account.
-    /// [`base_pair_tally`](Self::base_pair_tally)'s own diagonal (`same`)
-    /// gets the matching restriction via `scan_family_pairs`'s new
-    /// `variable` flag, rather than a `family_size()` check of its own (it
-    /// doesn't have direct access to the family's mask).
-    pub fn cardinality_tally(&self, raw: &RawSnpDistanceOutput, ratio_ceiling: f64) -> OKIResult<CardinalityTally> {
-        let n_parts = self.n_partitions();
-        let n_genomes = self.meta.genomes.len();
-        let with_counts = self.meta.config.with_counts;
-        let k = self.kmer_size();
-        let n_bits = n_parts.trailing_zeros() as usize;
-
-        let included = Array2::from_shape_fn((n_genomes, n_genomes), |(i, j)| {
-            if i == j {
-                return false;
-            }
-            let snp = raw.snp[[i, j]];
-            let total = snp + raw.shared[[i, j]];
-            total > 0 && (snp as f64 / total as f64) <= ratio_ceiling
-        });
-
-        let partition = KmerPartition::open_with_config(
-            &self.root_path,
-            self.kmer_size(),
-            self.minimizer_size(),
-            n_bits,
-        )
-        .map_err(OKIError::Partition)?;
-        let cache = PartitionCache::build(&partition, n_parts, with_counts)?;
-
-        let mut layer_dirs = Vec::new();
-        for part in 0..n_parts {
-            let index_dir = self.partition().part_dir(part).join(INDEX_SUBDIR);
-            if !index_dir.exists() {
-                continue;
-            }
-            let meta = PartitionMeta::load(&index_dir).map_err(olm_to_ok)?;
-            for l in 0..meta.n_layers {
-                let layer_dir = index_dir.join(format!("layer_{l}"));
-                let annex_path = layer_dir.join(ANNEX_FILE_NAME);
-                if !annex_path.exists() {
-                    return Err(OKIError::InvalidInput(format!(
-                        "no sibling annex at {} — run build_sibling_annex first",
-                        annex_path.display()
-                    )));
-                }
-                layer_dirs.push(layer_dir);
-            }
-        }
-
-        let pb = progress_bar("cardinality_tally", layer_dirs.len() as u64, "layers");
-        let partials: Vec<[[u64; 5]; 5]> = layer_dirs
-            .par_iter()
-            .map(|layer_dir| -> OKIResult<[[u64; 5]; 5]> {
-                let index_dir = layer_dir.parent().expect("layer_dir has a parent index dir");
-                let meta = PartitionMeta::load(index_dir).map_err(olm_to_ok)?;
-                let annex = SiblingAnnex::open(&layer_dir.join(ANNEX_FILE_NAME))?;
-                let mphf = MphfLayer::open(layer_dir, &meta.mode).map_err(olm_to_ok)?;
-
-                let mut slot_kmer: Vec<Option<CanonicalKmer>> = vec![None; annex.len()];
-                let reader = UnitigFileReader::open_sequential(&layer_dir.join("unitigs.bin"))
-                    .map_err(OKIError::Partition)?;
-                for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
-                    if let Some(slot) = mphf.find(kmer) {
-                        slot_kmer[slot] = Some(kmer);
-                    }
-                }
-
-                let use_counts = with_counts && layer_dir.join("counts").exists();
-                let mat = if use_counts {
-                    Mat::Count(PersistentCompactIntMatrix::open(layer_dir)?)
-                } else {
-                    Mat::Presence(PersistentBitMatrix::open(layer_dir)?)
-                };
-                let n_cols = mat.n_cols().min(n_genomes);
-
-                let mut counts = [[0u64; 5]; 5];
-                let mut genome_mask: Vec<u8> = Vec::with_capacity(n_genomes);
-
-                for slot in 0..annex.len() {
-                    let Some(mask) = annex.get(slot) else { continue };
-                    let Some(kmer) = slot_kmer[slot] else { continue };
-                    if !is_minorant(kmer, mask, k) {
-                        continue; // family tallied once, at its minorant
-                    }
-                    if mask.family_size() < 2 {
-                        // Fully invariant family (never varies anywhere in
-                        // the index) — genome-wide background, not
-                        // SNP-adjacent signal; would otherwise swamp the
-                        // diagonal (`c=1/c=1` etc.), which needs to reflect
-                        // the same variable-families-only population the
-                        // `+ASC`-corrected alignment/likelihood actually
-                        // models. See `base_pair_tally`'s `variable` gate
-                        // on its own `same` diagonal for the matching fix.
-                        continue;
-                    }
-
-                    genome_mask.clear();
-                    genome_mask.resize(n_genomes, 0);
-
-                    for other in kmer.central_canonical_neighbors() {
-                        let base = central_base(other, k);
-                        if !mask.has(base) {
-                            continue;
-                        }
-                        let presence: Option<Vec<bool>> = if other == kmer {
-                            Some((0..n_cols).map(|g| mat.carries(g, slot)).collect())
-                        } else {
-                            let dest = partition_of(other, n_parts);
-                            cache.find_presence(dest, other, n_genomes)
-                        };
-                        let Some(presence) = presence else { continue };
-                        for (g, &present) in presence.iter().enumerate() {
-                            if present {
-                                genome_mask[g] |= 1 << base;
-                            }
-                        }
-                    }
-
-                    for i in 0..n_genomes {
-                        let card_i = genome_mask[i].count_ones() as usize;
-                        for j in (i + 1)..n_genomes {
-                            if !included[[i, j]] {
-                                continue;
-                            }
-                            let card_j = genome_mask[j].count_ones() as usize;
-                            counts[card_i][card_j] += 1;
-                            if card_i != card_j {
-                                counts[card_j][card_i] += 1;
-                            }
-                        }
-                    }
-                }
-
-                pb.inc(1);
-                Ok(counts)
-            })
-            .collect::<OKIResult<Vec<_>>>()?;
-        pb.finish_and_clear();
-
-        let mut total = [[0u64; 5]; 5];
-        for partial in partials {
-            for a in 0..5 {
-                for b in 0..5 {
-                    total[a][b] += partial[a][b];
-                }
-            }
-        }
-        Ok(CardinalityTally { counts: total })
-    }
-}
-
-/// A SNP-only pseudo-alignment: one row (byte sequence, IUPAC-coded) per
-/// genome, one column per variable family (`family_size() >= 2` — monomorphic
-/// families carry no signal and are skipped, unlike `raw_snp_distance`'s
-/// tally which does count them as `shared`). Column order is the same,
-/// deterministic sweep order as the annex build (partition, then layer, then
-/// slot) — arbitrary but stable and identical across genomes, which is all a
-/// pseudo-alignment needs (there is no natural genomic coordinate to sort by
-/// once flanks are dropped). See `docmd/theory/evolutionary_distances.md`,
-/// "Multi-genome framing: family as pseudo-alignment column".
-pub struct SnpAlignment {
-    /// `sequences[g]` = genome `g`'s IUPAC-coded row, same length for every
-    /// genome (`sequences.len()` columns).
-    pub sequences: Vec<Vec<u8>>,
-}
-
-impl KmerIndex {
-    /// Build the SNP-only pseudo-alignment from an already-built sibling
-    /// annex (run [`build_sibling_annex`](Self::build_sibling_annex) first).
-    pub fn snp_pseudo_alignment(&self) -> OKIResult<SnpAlignment> {
-        let n_parts = self.n_partitions();
-        let n_genomes = self.meta.genomes.len();
-        let with_counts = self.meta.config.with_counts;
-        let k = self.kmer_size();
-        let n_bits = n_parts.trailing_zeros() as usize;
-
-        let partition = KmerPartition::open_with_config(
-            &self.root_path,
-            self.kmer_size(),
-            self.minimizer_size(),
-            n_bits,
-        )
-        .map_err(OKIError::Partition)?;
-        let cache = PartitionCache::build(&partition, n_parts, with_counts)?;
-
-        let mut layer_dirs = Vec::new();
-        for part in 0..n_parts {
-            let index_dir = self.partition().part_dir(part).join(INDEX_SUBDIR);
-            if !index_dir.exists() {
-                continue;
-            }
-            let meta = PartitionMeta::load(&index_dir).map_err(olm_to_ok)?;
-            for l in 0..meta.n_layers {
-                let layer_dir = index_dir.join(format!("layer_{l}"));
-                let annex_path = layer_dir.join(ANNEX_FILE_NAME);
-                if !annex_path.exists() {
-                    return Err(OKIError::InvalidInput(format!(
-                        "no sibling annex at {} — run build_sibling_annex first",
-                        annex_path.display()
-                    )));
-                }
-                layer_dirs.push(layer_dir);
-            }
-        }
-
-        let pb = progress_bar("snp_pseudo_alignment", layer_dirs.len() as u64, "layers");
-        // `Vec<Vec<u8>>` per layer, one entry (column) per variable family;
-        // `par_iter().map(...).collect()` on this indexed source preserves
-        // input order, so concatenating the results below in order gives a
-        // single deterministic column order across the whole index.
-        let partials: Vec<Vec<Vec<u8>>> = layer_dirs
-            .par_iter()
-            .map(|layer_dir| -> OKIResult<Vec<Vec<u8>>> {
-                let index_dir = layer_dir.parent().expect("layer_dir has a parent index dir");
-                let meta = PartitionMeta::load(index_dir).map_err(olm_to_ok)?;
-                let annex = SiblingAnnex::open(&layer_dir.join(ANNEX_FILE_NAME))?;
-                let mphf = MphfLayer::open(layer_dir, &meta.mode).map_err(olm_to_ok)?;
-
-                let mut slot_kmer: Vec<Option<CanonicalKmer>> = vec![None; annex.len()];
-                let reader = UnitigFileReader::open_sequential(&layer_dir.join("unitigs.bin"))
-                    .map_err(OKIError::Partition)?;
-                for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
-                    if let Some(slot) = mphf.find(kmer) {
-                        slot_kmer[slot] = Some(kmer);
-                    }
-                }
-
-                let use_counts = with_counts && layer_dir.join("counts").exists();
-                let mat = if use_counts {
-                    Mat::Count(PersistentCompactIntMatrix::open(layer_dir)?)
-                } else {
-                    Mat::Presence(PersistentBitMatrix::open(layer_dir)?)
-                };
-                let n_cols = mat.n_cols().min(n_genomes);
-
-                let mut columns: Vec<Vec<u8>> = Vec::new();
-                let mut genome_mask: Vec<u8> = Vec::with_capacity(n_genomes);
-
-                for slot in 0..annex.len() {
-                    let Some(mask) = annex.get(slot) else { continue };
-                    let Some(kmer) = slot_kmer[slot] else { continue };
-                    if !is_minorant(kmer, mask, k) {
-                        continue; // family tallied once, at its minorant
-                    }
-                    if mask.family_size() < 2 {
-                        continue; // monomorphic family — no signal, skip
-                    }
-
-                    genome_mask.clear();
-                    genome_mask.resize(n_genomes, 0);
-
-                    for other in kmer.central_canonical_neighbors() {
-                        let base = central_base(other, k);
-                        if !mask.has(base) {
-                            continue;
-                        }
-                        let presence: Option<Vec<bool>> = if other == kmer {
-                            Some((0..n_cols).map(|g| mat.carries(g, slot)).collect())
-                        } else {
-                            let dest = partition_of(other, n_parts);
-                            cache.find_presence(dest, other, n_genomes)
-                        };
-                        let Some(presence) = presence else { continue };
-                        for (g, &present) in presence.iter().enumerate() {
-                            if present {
-                                genome_mask[g] |= 1 << base;
-                            }
-                        }
-                    }
-
-                    columns.push(genome_mask.iter().map(|&m| iupac_code(m)).collect());
-                }
-
-                pb.inc(1);
-                Ok(columns)
-            })
-            .collect::<OKIResult<Vec<_>>>()?;
-        pb.finish_and_clear();
-
-        let mut sequences: Vec<Vec<u8>> = vec![Vec::new(); n_genomes];
-        for layer_columns in partials {
-            for column in layer_columns {
-                for (g, &code) in column.iter().enumerate() {
-                    sequences[g].push(code);
-                }
-            }
-        }
-        Ok(SnpAlignment { sequences })
-    }
-}
-
-#[cfg(test)]
-mod tests {
-    use std::io::Write;
-    use std::path::Path;
-
-    use obicompactvec::SiblingAnnex;
-    use obikseq::{Kmer, Sequence};
-    use obisys::Reporter;
-    use tempfile::tempdir;
-
-    use crate::meta::{GenomeInfo, IndexConfig};
-    use crate::merge::MergeMode;
-
-    use super::*;
-
-    // k must be >= 11 (project constraint, "k ∈ [11,31]"); k=11, level_max=1,
-    // theta=0.0 mirror `obiskbuilder`'s own tests (smaller k/level_max
-    // combinations trip an unrelated pre-existing bug in `obikentropy`'s
-    // sliding-window ring buffer — not this feature's concern).
-    const K: usize = 11;
-    const M: usize = 5;
-
-    /// Build a single-genome index from one in-memory FASTA sequence, driving
-    /// the same primitives `obikmer`'s `scatter` step uses (minus the
-    /// multi-file `obipipeline` wrapper — a single sequence needs none of
-    /// that): normalise -> build superkmers -> route -> write.
-    /// `cargo test` doesn't install a `tracing` subscriber the way `obikmer`'s
-    /// CLI does, so `debug!`/etc. are silent no-ops by default — including the
-    /// `PartitionRunner` instrumentation that would matter most for
-    /// re-diagnosing a hang here. `try_init` is idempotent across concurrently
-    /// running tests (later calls just find a subscriber already installed).
-    fn init_tracing() {
-        let _ = tracing_subscriber::fmt()
-            .with_env_filter(
-                tracing_subscriber::EnvFilter::try_from_default_env()
-                    .unwrap_or_else(|_| tracing_subscriber::EnvFilter::new("info")),
-            )
-            .with_writer(std::io::stderr)
-            .try_init();
-    }
-
-    fn build_single_genome_index(dir: &Path, label: &str, seq: &[u8]) -> KmerIndex {
-        init_tracing();
-        let fasta_path = dir.join(format!("{label}.fasta"));
-        let mut f = std::fs::File::create(&fasta_path).unwrap();
-        writeln!(f, ">{label}").unwrap();
-        f.write_all(seq).unwrap();
-        writeln!(f).unwrap();
-        drop(f);
-
-        let index_path = dir.join(format!("{label}.idx"));
-        let config = IndexConfig {
-            kmer_size: K,
-            minimizer_size: M,
-            n_bits: 0, // 1 partition — keeps the test deterministic and simple
-            with_counts: false,
-            evidence: obilayeredmap::IndexMode::Exact,
-            block_bits: 0,
-        };
-        let mut idx = KmerIndex::create(&index_path, config, Some(GenomeInfo::new(label)), false)
-            .expect("create");
-
-        let mut rep = Reporter::new();
-        let stream = obiread::open_nuc_stream(fasta_path.to_str().unwrap(), K).expect("open fasta");
-        for page in stream {
-            let batch = obiskbuilder::build_superkmers_page(page, K, /* level_max */ 1, /* theta */ 0.0);
-            idx.partition_mut().write_batch(batch).expect("write_batch");
-        }
-        idx.partition_mut().close().expect("close partition writers");
-        idx.mark_scattered().expect("mark_scattered");
-        idx.dereplicate_and_count(false, &mut rep).expect("dereplicate_and_count");
-        idx.build_layers(1, None, false, &mut rep).expect("build_layers");
-        idx
-    }
-
-    fn canonical(ascii: &[u8]) -> CanonicalKmer {
-        Kmer::from_ascii(ascii).unwrap().canonical()
-    }
-
-    /// Read back the annex entry for a given canonical k-mer from the merged
-    /// index's (single) partition/layer, asserting it was found at all.
-    fn annex_info_for(idx: &KmerIndex, kmer: CanonicalKmer) -> FamilyMask {
-        let index_dir = idx.partition().part_dir(0).join(INDEX_SUBDIR);
-        let meta = PartitionMeta::load(&index_dir).unwrap();
-        for l in 0..meta.n_layers {
-            let layer_dir = index_dir.join(format!("layer_{l}"));
-            let mphf = MphfLayer::open(&layer_dir, &meta.mode).unwrap();
-            if let Some(slot) = mphf.find(kmer) {
-                let annex = SiblingAnnex::open(&layer_dir.join(ANNEX_FILE_NAME)).unwrap();
-                return annex.get(slot).expect("slot must have a computed annex entry");
-            }
-        }
-        panic!("kmer not found in any layer of partition 0");
-    }
-
-    fn merge_two(dir: &Path, g1: &KmerIndex, g2: &KmerIndex) -> KmerIndex {
-        let mut rep = Reporter::new();
-        KmerIndex::merge(
-            &dir.join("merged.idx"),
-            &[g1, g2],
-            MergeMode::Presence,
-            false,
-            false,
-            1.0,
-            &mut rep,
-        )
-        .expect("merge")
-    }
-
-    #[test]
-    fn sibling_annex_one_sibling_each() {
-        // k=11, centre = index 5 (0-based). Two genomes, each exactly one
-        // k-mer, sharing every base except the centre:
-        //   g1 = "AACCGCTTAAG" (centre 'C', base index 1)
-        //   g2 = "AACCGGTTAAG" (centre 'G', base index 2)
-        // Hand-verified: both stay forward-oriented under canonicalisation
-        // (each is lexicographically smaller than its own reverse
-        // complement, since both start with "AA"), and raw(g1) < raw(g2)
-        // (only differing base: C=0b01 < G=0b10 at the centre) — so g1 is
-        // the minorant, g2 is not. The mask is a family-wide value: both
-        // slots must read back the *same* mask (bits 1 and 2 set).
-        let dir = tempdir().unwrap();
-        let g1 = build_single_genome_index(dir.path(), "g1", b"AACCGCTTAAG");
-        let g2 = build_single_genome_index(dir.path(), "g2", b"AACCGGTTAAG");
-        let merged = merge_two(dir.path(), &g1, &g2);
-        merged.build_sibling_annex().expect("build_sibling_annex");
-
-        let g1_kmer = canonical(b"AACCGCTTAAG");
-        let g2_kmer = canonical(b"AACCGGTTAAG");
-        let expected_mask = FamilyMask::EMPTY.with(1).with(2);
-
-        let a = annex_info_for(&merged, g1_kmer);
-        assert_eq!(a, expected_mask, "AACCGCTTAAG");
-        assert_eq!(a.siblings(), 1);
-        assert!(is_minorant(g1_kmer, a, K), "g1 should be the minorant");
-
-        let b = annex_info_for(&merged, g2_kmer);
-        assert_eq!(b, expected_mask, "AACCGGTTAAG");
-        assert_eq!(b.siblings(), 1);
-        assert!(!is_minorant(g2_kmer, b, K), "g2 should not be the minorant");
-    }
-
-    #[test]
-    fn sibling_annex_zero_siblings_when_identical_and_no_variant_exists() {
-        // Same k-mer in both genomes, no other genome around to carry a
-        // variant -> 0 siblings, trivially its own minorant.
-        let dir = tempdir().unwrap();
-        let g1 = build_single_genome_index(dir.path(), "g1", b"GATTACAGATC");
-        let g2 = build_single_genome_index(dir.path(), "g2", b"GATTACAGATC");
-        let merged = merge_two(dir.path(), &g1, &g2);
-        merged.build_sibling_annex().expect("build_sibling_annex");
-
-        let kmer = canonical(b"GATTACAGATC");
-        let mask = annex_info_for(&merged, kmer);
-        assert_eq!(mask.siblings(), 0, "GATTACAGATC");
-        assert_eq!(mask.family_size(), 1);
-        assert!(is_minorant(kmer, mask, K));
-    }
-
-    #[test]
-    fn sibling_annex_stats_counts_each_family_once_and_per_genome() {
-        // Reuses the one-sibling-each fixture: a single family of size 2
-        // (g1's centre-C form + g2's centre-G form), each genome carrying
-        // exactly one of the two members. Stats must report exactly one
-        // family of size 2 (`counts[1] == 1`, since index 1 = size 2), not
-        // two (which naively summing both slots would give), and both
-        // genomes represented at size 2, neither at any other size.
-        let dir = tempdir().unwrap();
-        let g1 = build_single_genome_index(dir.path(), "g1", b"AACCGCTTAAG");
-        let g2 = build_single_genome_index(dir.path(), "g2", b"AACCGGTTAAG");
-        let merged = merge_two(dir.path(), &g1, &g2);
-        merged.build_sibling_annex().expect("build_sibling_annex");
-
-        let stats = merged.sibling_annex_stats().expect("sibling_annex_stats");
-
-        assert_eq!(stats.counts, [0, 1, 0, 0], "one family of size 2, counted once");
-        assert_eq!(stats.per_genome.len(), 2);
-        for g in 0..2 {
-            assert_eq!(
-                stats.per_genome[g], [0, 1, 0, 0],
-                "genome {g} should represent exactly one size-2 family"
-            );
-        }
-    }
-}
diff --git a/src/obikindex/src/siblings/alignment.rs b/src/obikindex/src/siblings/alignment.rs
new file mode 100644
index 00000000..db514a92
--- /dev/null
+++ b/src/obikindex/src/siblings/alignment.rs
@@ -0,0 +1,185 @@
+use rayon::prelude::*;
+
+use obicompactvec::{PersistentBitMatrix, PersistentCompactIntMatrix, SiblingAnnex};
+use obikpartitionner::KmerPartition;
+use obikseq::CanonicalKmer;
+use obilayeredmap::MphfLayer;
+use obilayeredmap::meta::PartitionMeta;
+use obiskio::UnitigFileReader;
+use obisys::progress_bar;
+
+use crate::error::{OKIError, OKIResult};
+use crate::index::KmerIndex;
+
+use super::cache::{Mat, PartitionCache};
+use super::helpers::{central_base, is_minorant, partition_of};
+use super::{olm_to_ok, ANNEX_FILE_NAME, INDEX_SUBDIR};
+
+/// IUPAC ambiguity code for a per-genome family presence mask (bit `b` set
+/// iff the genome carries the member whose own central base is `b`):
+/// single bit -> the plain base; 2 or 3 bits -> the matching IUPAC
+/// ambiguity code (preserves partial information instead of collapsing to
+/// `N`, the same convention used for diploid heterozygous VCF/FASTA sites);
+/// all 4 bits -> `N`; no bits (genome carries none of the family's observed
+/// members) -> `-` (no data at this locus for this genome).
+fn iupac_code(mask: u8) -> u8 {
+    match mask & 0b1111 {
+        0b0000 => b'-',
+        0b0001 => b'A',
+        0b0010 => b'C',
+        0b0100 => b'G',
+        0b1000 => b'T',
+        0b0101 => b'R', // A/G
+        0b1010 => b'Y', // C/T
+        0b0110 => b'S', // C/G
+        0b1001 => b'W', // A/T
+        0b1100 => b'K', // G/T
+        0b0011 => b'M', // A/C
+        0b1110 => b'B', // C/G/T
+        0b1101 => b'D', // A/G/T
+        0b1011 => b'H', // A/C/T
+        0b0111 => b'V', // A/C/G
+        0b1111 => b'N',
+        _ => unreachable!("masked to 4 bits"),
+    }
+}
+
+/// A SNP-only pseudo-alignment: one row (byte sequence, IUPAC-coded) per
+/// genome, one column per variable family (`family_size() >= 2` — monomorphic
+/// families carry no signal and are skipped, unlike `raw_snp_distance`'s
+/// tally which does count them as `shared`). Column order is the same,
+/// deterministic sweep order as the annex build (partition, then layer, then
+/// slot) — arbitrary but stable and identical across genomes, which is all a
+/// pseudo-alignment needs (there is no natural genomic coordinate to sort by
+/// once flanks are dropped). See `docmd/theory/evolutionary_distances.md`,
+/// "Multi-genome framing: family as pseudo-alignment column".
+pub struct SnpAlignment {
+    /// `sequences[g]` = genome `g`'s IUPAC-coded row, same length for every
+    /// genome (`sequences.len()` columns).
+    pub sequences: Vec<Vec<u8>>,
+}
+
+impl KmerIndex {
+    /// Build the SNP-only pseudo-alignment from an already-built sibling
+    /// annex (run [`build_sibling_annex`](Self::build_sibling_annex) first).
+    pub fn snp_pseudo_alignment(&self) -> OKIResult<SnpAlignment> {
+        let n_parts = self.n_partitions();
+        let n_genomes = self.meta.genomes.len();
+        let with_counts = self.meta.config.with_counts;
+        let k = self.kmer_size();
+        let n_bits = n_parts.trailing_zeros() as usize;
+
+        let partition = KmerPartition::open_with_config(
+            &self.root_path,
+            self.kmer_size(),
+            self.minimizer_size(),
+            n_bits,
+        )
+        .map_err(OKIError::Partition)?;
+        let cache = PartitionCache::build(&partition, n_parts, with_counts)?;
+
+        let mut layer_dirs = Vec::new();
+        for part in 0..n_parts {
+            let index_dir = self.partition().part_dir(part).join(INDEX_SUBDIR);
+            if !index_dir.exists() {
+                continue;
+            }
+            let meta = PartitionMeta::load(&index_dir).map_err(olm_to_ok)?;
+            for l in 0..meta.n_layers {
+                let layer_dir = index_dir.join(format!("layer_{l}"));
+                let annex_path = layer_dir.join(ANNEX_FILE_NAME);
+                if !annex_path.exists() {
+                    return Err(OKIError::InvalidInput(format!(
+                        "no sibling annex at {} — run build_sibling_annex first",
+                        annex_path.display()
+                    )));
+                }
+                layer_dirs.push(layer_dir);
+            }
+        }
+
+        let pb = progress_bar("snp_pseudo_alignment", layer_dirs.len() as u64, "layers");
+        // `Vec<Vec<u8>>` per layer, one entry (column) per variable family;
+        // `par_iter().map(...).collect()` on this indexed source preserves
+        // input order, so concatenating the results below in order gives a
+        // single deterministic column order across the whole index.
+        let partials: Vec<Vec<Vec<u8>>> = layer_dirs
+            .par_iter()
+            .map(|layer_dir| -> OKIResult<Vec<Vec<u8>>> {
+                let index_dir = layer_dir.parent().expect("layer_dir has a parent index dir");
+                let meta = PartitionMeta::load(index_dir).map_err(olm_to_ok)?;
+                let annex = SiblingAnnex::open(&layer_dir.join(ANNEX_FILE_NAME))?;
+                let mphf = MphfLayer::open(layer_dir, &meta.mode).map_err(olm_to_ok)?;
+
+                let mut slot_kmer: Vec<Option<CanonicalKmer>> = vec![None; annex.len()];
+                let reader = UnitigFileReader::open_sequential(&layer_dir.join("unitigs.bin"))
+                    .map_err(OKIError::Partition)?;
+                for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
+                    if let Some(slot) = mphf.find(kmer) {
+                        slot_kmer[slot] = Some(kmer);
+                    }
+                }
+
+                let use_counts = with_counts && layer_dir.join("counts").exists();
+                let mat = if use_counts {
+                    Mat::Count(PersistentCompactIntMatrix::open(layer_dir)?)
+                } else {
+                    Mat::Presence(PersistentBitMatrix::open(layer_dir)?)
+                };
+                let n_cols = mat.n_cols().min(n_genomes);
+
+                let mut columns: Vec<Vec<u8>> = Vec::new();
+                let mut genome_mask: Vec<u8> = Vec::with_capacity(n_genomes);
+
+                for slot in 0..annex.len() {
+                    let Some(mask) = annex.get(slot) else { continue };
+                    let Some(kmer) = slot_kmer[slot] else { continue };
+                    if !is_minorant(kmer, mask, k) {
+                        continue; // family tallied once, at its minorant
+                    }
+                    if mask.family_size() < 2 {
+                        continue; // monomorphic family — no signal, skip
+                    }
+
+                    genome_mask.clear();
+                    genome_mask.resize(n_genomes, 0);
+
+                    for other in kmer.central_canonical_neighbors() {
+                        let base = central_base(other, k);
+                        if !mask.has(base) {
+                            continue;
+                        }
+                        let presence: Option<Vec<bool>> = if other == kmer {
+                            Some((0..n_cols).map(|g| mat.carries(g, slot)).collect())
+                        } else {
+                            let dest = partition_of(other, n_parts);
+                            cache.find_presence(dest, other, n_genomes)
+                        };
+                        let Some(presence) = presence else { continue };
+                        for (g, &present) in presence.iter().enumerate() {
+                            if present {
+                                genome_mask[g] |= 1 << base;
+                            }
+                        }
+                    }
+
+                    columns.push(genome_mask.iter().map(|&m| iupac_code(m)).collect());
+                }
+
+                pb.inc(1);
+                Ok(columns)
+            })
+            .collect::<OKIResult<Vec<_>>>()?;
+        pb.finish_and_clear();
+
+        let mut sequences: Vec<Vec<u8>> = vec![Vec::new(); n_genomes];
+        for layer_columns in partials {
+            for column in layer_columns {
+                for (g, &code) in column.iter().enumerate() {
+                    sequences[g].push(code);
+                }
+            }
+        }
+        Ok(SnpAlignment { sequences })
+    }
+}
diff --git a/src/obikindex/src/siblings/build.rs b/src/obikindex/src/siblings/build.rs
new file mode 100644
index 00000000..a163b84c
--- /dev/null
+++ b/src/obikindex/src/siblings/build.rs
@@ -0,0 +1,255 @@
+use std::path::Path;
+use std::sync::atomic::{AtomicU8, Ordering};
+use std::sync::Arc;
+
+use rayon::prelude::*;
+
+use obicompactvec::{FamilyMask, SiblingAnnexBuilder};
+use obikpartitionner::KmerPartition;
+use obipipeline::ThrottleGuard;
+use obikseq::CanonicalKmer;
+use obilayeredmap::MphfLayer;
+use obilayeredmap::meta::PartitionMeta;
+use obiskio::UnitigFileReader;
+use obisys::progress_bar;
+
+use crate::error::{OKIError, OKIResult};
+use crate::index::KmerIndex;
+
+use super::cache::PartitionCache;
+use super::helpers::{central_base, partition_of};
+use super::{olm_to_ok, ANNEX_FILE_NAME, INDEX_SUBDIR};
+
+// ── obipipeline data types ─────────────────────────────────────────────────
+
+/// A batch of this layer's distinct k-mers (local MPHF slot + k-mer), the
+/// pipeline's source item — batched, not one k-mer per item, so that
+/// pipeline messages and their synchronisation cost stay amortised over
+/// thousands of lookups (see `build_layer_sibling_annex`'s comment on
+/// `BATCH_SIZE`). Carries the throttle permit for the whole batch, moved
+/// (not cloned) into the corresponding `VariantBatch` — a 1-to-1 transform,
+/// unlike the fan-out `Flat` stage this replaced, needs no `Arc` sharing.
+struct SourceBatch {
+    items: Vec<(usize, CanonicalKmer)>,
+    _permit: ThrottleGuard,
+}
+
+/// One batch's worth of central-substitution variants (up to 3 per source
+/// k-mer), each already routed to its destination partition and carrying
+/// its own central base (0=A/1=C/2=G/3=T) — the mask bit it will set on a
+/// hit. `(dest_partition, variant, source_slot, base)` per entry.
+struct VariantBatch {
+    items: Vec<(usize, CanonicalKmer, usize, u8)>,
+    _permit: ThrottleGuard,
+}
+
+enum SibData {
+    Batch(SourceBatch),
+    Variants(VariantBatch),
+}
+
+impl KmerIndex {
+    /// Build the sibling-count/minorant annex for every layer of every
+    /// partition of this (already built) index, writing one annex file per
+    /// layer alongside its existing index files. Safe to call again later
+    /// (e.g. after a fresh `merge`) — each run simply overwrites the annex
+    /// files of the index it is called on.
+    ///
+    /// Construction only — no statistics gathered here on purpose: this is
+    /// meant to run routinely (it is the artefact the SNP-family distances
+    /// will consume), while the sibling-count distribution
+    /// ([`sibling_annex_stats`](Self::sibling_annex_stats)) is a separate,
+    /// occasional diagnostic pass over the result, not run every time.
+    ///
+    /// Cross-partition/cross-layer lookups are required (a k-mer's siblings
+    /// can live in any partition), but the layer loop itself — and thus the
+    /// annex file this produces — stays local to one layer at a time.
+    pub fn build_sibling_annex(&self) -> OKIResult<()> {
+        let n_parts = self.n_partitions();
+        let n_bits = n_parts.trailing_zeros() as usize;
+
+        let partition = KmerPartition::open_with_config(
+            &self.root_path,
+            self.kmer_size(),
+            self.minimizer_size(),
+            n_bits,
+        )
+        .map_err(OKIError::Partition)?;
+
+        tracing::info!("opening {n_parts} partition(s) for the sibling-annex sweep");
+        let cache = Arc::new(PartitionCache::build(&partition, n_parts, self.meta.config.with_counts)?);
+
+        let pb = progress_bar("sibling_annex", n_parts as u64, "partitions");
+        let mut total_slots: u64 = 0;
+        for part in 0..n_parts {
+            let index_dir = self.partition().part_dir(part).join(INDEX_SUBDIR);
+            if !index_dir.exists() {
+                pb.inc(1);
+                continue;
+            }
+            let meta = PartitionMeta::load(&index_dir).map_err(olm_to_ok)?;
+
+            let mut part_slots: u64 = 0;
+            for l in 0..meta.n_layers {
+                let layer_dir = index_dir.join(format!("layer_{l}"));
+                part_slots += self.build_layer_sibling_annex(&layer_dir, n_parts, &cache)?;
+            }
+            total_slots += part_slots;
+            pb.inc(1);
+            pb.set_message(format!("partition {part}: {part_slots} kmers ({total_slots} total)"));
+        }
+        pb.finish_and_clear();
+        tracing::info!("sibling annex built — {total_slots} kmers across {n_parts} partitions");
+
+        Ok(())
+    }
+
+    /// Returns the number of distinct k-mers (annex slots) processed, for
+    /// progress reporting.
+    fn build_layer_sibling_annex(
+        &self,
+        layer_dir: &Path,
+        n_parts: usize,
+        cache: &Arc<PartitionCache>,
+    ) -> OKIResult<u64> {
+        let index_dir = layer_dir.parent().expect("layer_dir has a parent index dir");
+        let meta = PartitionMeta::load(index_dir).map_err(olm_to_ok)?;
+        let mphf = MphfLayer::open(layer_dir, &meta.mode).map_err(olm_to_ok)?;
+        let n_slots = mphf.n();
+
+        // ── Enumerate this layer's distinct k-mers, one per slot ────────────
+        let mut slot_kmer: Vec<Option<CanonicalKmer>> = vec![None; n_slots];
+        let reader = UnitigFileReader::open_sequential(&layer_dir.join("unitigs.bin"))
+            .map_err(OKIError::Partition)?;
+        for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
+            if let Some(slot) = mphf.find(kmer) {
+                slot_kmer[slot] = Some(kmer);
+            }
+        }
+
+        let k = self.kmer_size();
+
+        // ── Reconciliation state, initialised with each slot's own base —
+        // that member is trivially present, no lookup needed. Built before
+        // the pipeline runs, from the same enumeration, since `sources`
+        // below is consumed as a throttled iterator, not collected.
+        // `AtomicU8`, not `FamilyMask`, because the gather phase below
+        // parallelises across destination partitions (independent
+        // `query_partition_with` calls, safe to run concurrently) and their
+        // `Found` hits can land on arbitrary, possibly-shared slots — a
+        // lock-free `fetch_or` avoids needing any synchronisation beyond
+        // that. ─────────────────────────────────────────────────────────
+        let mask: Vec<AtomicU8> = (0..n_slots).map(|_| AtomicU8::new(0)).collect();
+        for (slot, kmer) in slot_kmer.iter().enumerate().filter_map(|(s, k)| k.map(|k| (s, k))) {
+            mask[slot].fetch_or(1 << central_base(kmer, k), Ordering::Relaxed);
+        }
+
+        // ── obipipeline: a *batch* transform, not a per-k-mer `Flat` one —
+        // the actual cross-partition lookup reuses
+        // `KmerPartition::query_partition_with` (the same batching mechanism
+        // `obikmer query` already uses: open a partition's files once,
+        // answer a whole batch of queries against it) instead of one lookup
+        // per pipeline item. A per-item lookup (tried first) reopened/
+        // re-mmap'd every target partition's files on every single variant
+        // — fine at toy scale, but ~90% system time against a real index,
+        // observed in practice. A *later* attempt still pushed one pipeline
+        // message per generated variant (a `Flat` stage, `SourceItem` =>
+        // `VariantQuery`, one k-mer in => up to 3 variants out as separate
+        // messages) — cheaper than reopening files, but sampling a real run
+        // showed most wall-clock time going into per-message channel
+        // send/notify syscalls instead of the lookup itself: the pipeline's
+        // whole point is amortising synchronisation over a batch, and a
+        // single k-mer's ≤3 variants is far too fine a granularity for
+        // that. Batching `BATCH_SIZE` source k-mers into one pipeline item
+        // — a plain 1-to-1 (`|`, not `||`) transform, batch in, batch of
+        // variants out, one message either way — keeps the per-message
+        // synchronisation cost amortised over thousands of lookups instead
+        // of one to three. ──────────────────────────────────────────────
+        const BATCH_SIZE: usize = 4096;
+        let n_workers = obisys::effective_parallelism();
+        let capacity = 256;
+
+        // Throttling limits how many *batches* are in flight at once — the
+        // permit is acquired per batch (not per k-mer) in the source
+        // thread, and released once its `VariantBatch` has been read out of
+        // the pipeline by the accumulation loop below. See
+        // `obipipeline::throttle`'s docs for why this is required, not
+        // optional, once a `Flat`-style stage sits in the pipeline.
+        let sources: Vec<(usize, CanonicalKmer)> = slot_kmer
+            .iter()
+            .enumerate()
+            .filter_map(|(slot, maybe_kmer)| maybe_kmer.map(|kmer| (slot, kmer)))
+            .collect();
+        let batches: Vec<Vec<(usize, CanonicalKmer)>> = sources
+            .chunks(BATCH_SIZE)
+            .map(|chunk| chunk.to_vec())
+            .collect();
+        let throttled = obipipeline::throttle(batches.into_iter(), n_workers).map(|t| SourceBatch {
+            items: t.item,
+            _permit: t.guard,
+        });
+
+        let pipe = obipipeline::make_pipe! {
+            SibData : SourceBatch => VariantBatch,
+            | {
+                move |batch: SourceBatch| -> VariantBatch {
+                    let mut items = Vec::with_capacity(batch.items.len() * 3);
+                    for (slot, kmer) in batch.items {
+                        for variant in kmer.central_canonical_neighbors() {
+                            if variant == kmer {
+                                continue;
+                            }
+                            items.push((
+                                partition_of(variant, n_parts),
+                                variant,
+                                slot,
+                                central_base(variant, k),
+                            ));
+                        }
+                    }
+                    VariantBatch { items, _permit: batch._permit }
+                }
+            } : Batch => Variants,
+        };
+
+        // ── Group generated variants by destination partition. `cache`
+        // holds every partition already mmap'd (no more `open()` cost), but
+        // `mmap` pages are still loaded on demand and can be evicted — a
+        // lookup is not free just because the file isn't reopened. Grouping
+        // keeps one partition's pages hot while its whole batch is resolved,
+        // instead of faulting pages in and out as lookups jump between
+        // partitions in whatever order the pipeline happens to produce
+        // them. Each batch's throttle permit drops here, once accumulated.
+        let mut outgoing: Vec<Vec<(CanonicalKmer, usize, u8)>> = (0..n_parts).map(|_| Vec::new()).collect();
+        for vb in pipe.apply(throttled, n_workers, capacity) {
+            for (dest_partition, variant, source_slot, base) in vb.items {
+                outgoing[dest_partition].push((variant, source_slot, base));
+            }
+        }
+
+        // ── Resolve each partition's batch against the cache in one
+        // contiguous pass; parallelised across partitions (independent,
+        // read-only) so this keeps using multiple cores without giving up
+        // the per-partition locality above. ─────────────────────────────
+        outgoing.par_iter().enumerate().filter(|(_, q)| !q.is_empty()).for_each(|(dest, queries)| {
+            for &(variant, source_slot, base) in queries {
+                if cache.find(dest, variant) {
+                    mask[source_slot].fetch_or(1 << base, Ordering::Relaxed);
+                }
+            }
+        });
+
+        // ── Write the layer's annex file ─────────────────────────────────────
+        let annex_path = layer_dir.join(ANNEX_FILE_NAME);
+        let mut builder = SiblingAnnexBuilder::new(n_slots, &annex_path)?;
+        for (slot, m) in mask.iter().enumerate() {
+            if slot_kmer[slot].is_none() {
+                continue; // unused MPHF slot, if any — leave at the sentinel
+            }
+            builder.set(slot, FamilyMask::from_bits(m.load(Ordering::Relaxed)));
+        }
+        builder.close()?;
+
+        Ok(n_slots as u64)
+    }
+}
diff --git a/src/obikindex/src/siblings/cache.rs b/src/obikindex/src/siblings/cache.rs
new file mode 100644
index 00000000..a2de07e5
--- /dev/null
+++ b/src/obikindex/src/siblings/cache.rs
@@ -0,0 +1,121 @@
+use rayon::prelude::*;
+
+use obicompactvec::{PersistentBitMatrix, PersistentCompactIntMatrix};
+use obikpartitionner::KmerPartition;
+use obikseq::CanonicalKmer;
+use obilayeredmap::MphfLayer;
+use obilayeredmap::meta::PartitionMeta;
+use obisys::progress_bar;
+
+use crate::error::OKIResult;
+
+use super::{olm_to_ok, INDEX_SUBDIR};
+
+/// Every partition's already-open MPHF layers, built **once** for the whole
+/// `build_sibling_annex` run and shared (read-only) across every lookup, in
+/// every source layer, for the rest of the run — not reopened/re-mmap'd per
+/// query, nor per source layer.
+///
+/// Confirmed necessary by sampling a real run: routing lookups through
+/// `KmerPartition::query_partition_with` (the same batching `obikmer query`
+/// uses) still reopens+re-mmaps every target partition's files on every
+/// call, and it is called once per destination partition **per source
+/// layer** — for an index with many layers this repeats the same
+/// `MphfLayer::open`/`Evidence::open`/`PersistentBitMatrix::open` work over
+/// and over. Parallelising those calls (see the gather step below) spread
+/// the redundant work across more cores but did not reduce it: sampling
+/// showed Rayon workers spending their time inside repeated `open()`
+/// syscalls, not computation. This cache amortises that cost to once per
+/// partition for the entire run, regardless of how many source layers or
+/// lookups follow.
+/// A cached layer's opened presence/count matrix, alongside its `MphfLayer`.
+pub(super) enum Mat {
+    Count(PersistentCompactIntMatrix),
+    Presence(PersistentBitMatrix),
+}
+
+impl Mat {
+    pub(super) fn n_cols(&self) -> usize {
+        match self {
+            Mat::Count(m) => m.n_cols(),
+            Mat::Presence(m) => m.n_cols(),
+        }
+    }
+    pub(super) fn carries(&self, g: usize, slot: usize) -> bool {
+        match self {
+            Mat::Count(m) => m.col_view(g).get(slot) != 0,
+            Mat::Presence(m) => m.get(g, slot) != 0,
+        }
+    }
+}
+
+pub(super) struct PartitionCache {
+    /// `layers[partition][layer]` = that partition's opened MPHF layers,
+    /// paired 1:1 with `mats[partition][layer]`; empty if the partition
+    /// directory doesn't exist. Used by both
+    /// [`crate::index::KmerIndex::build_sibling_annex`] (`layers` only) and
+    /// [`crate::index::KmerIndex::sibling_annex_stats`] (both).
+    layers: Vec<Vec<MphfLayer>>,
+    mats: Vec<Vec<Mat>>,
+}
+
+impl PartitionCache {
+    pub(super) fn build(partition: &KmerPartition, n_parts: usize, with_counts: bool) -> OKIResult<Self> {
+        let pb = progress_bar("open_partitions", n_parts as u64, "partitions");
+        let built: Vec<(Vec<MphfLayer>, Vec<Mat>)> = (0..n_parts)
+            .into_par_iter()
+            .map(|part| -> OKIResult<(Vec<MphfLayer>, Vec<Mat>)> {
+                let index_dir = partition.part_dir(part).join(INDEX_SUBDIR);
+                if !index_dir.exists() {
+                    pb.inc(1);
+                    return Ok((Vec::new(), Vec::new()));
+                }
+                let meta = PartitionMeta::load(&index_dir).map_err(olm_to_ok)?;
+                let mut layers = Vec::with_capacity(meta.n_layers);
+                let mut mats = Vec::with_capacity(meta.n_layers);
+                for l in 0..meta.n_layers {
+                    let layer_dir = index_dir.join(format!("layer_{l}"));
+                    let Ok(mphf) = MphfLayer::open(&layer_dir, &meta.mode) else { continue };
+                    let use_counts = with_counts && layer_dir.join("counts").exists();
+                    let mat = if use_counts {
+                        PersistentCompactIntMatrix::open(&layer_dir).ok().map(Mat::Count)
+                    } else {
+                        PersistentBitMatrix::open(&layer_dir).ok().map(Mat::Presence)
+                    };
+                    let Some(mat) = mat else { continue };
+                    layers.push(mphf);
+                    mats.push(mat);
+                }
+                pb.inc(1);
+                Ok((layers, mats))
+            })
+            .collect::<OKIResult<Vec<_>>>()?;
+        pb.finish_and_clear();
+        let (layers, mats) = built.into_iter().unzip();
+        Ok(Self { layers, mats })
+    }
+
+    /// Existence-only lookup of `variant` in partition `dest_partition`:
+    /// tries each of the partition's already-open layers in turn, stopping
+    /// at the first hit.
+    pub(super) fn find(&self, dest_partition: usize, variant: CanonicalKmer) -> bool {
+        self.layers
+            .get(dest_partition)
+            .is_some_and(|layers| layers.iter().any(|mphf| mphf.find(variant).is_some()))
+    }
+
+    /// Per-genome presence vector for `variant` in partition `dest_partition`
+    /// (`true` iff that genome carries it), `None` on a miss. Same shape as
+    /// `find`, but also reads the cached matrix instead of just the MPHF.
+    pub(super) fn find_presence(&self, dest_partition: usize, variant: CanonicalKmer, n_genomes: usize) -> Option<Vec<bool>> {
+        let layers = self.layers.get(dest_partition)?;
+        let mats = self.mats.get(dest_partition)?;
+        for (mphf, mat) in layers.iter().zip(mats.iter()) {
+            if let Some(slot) = mphf.find(variant) {
+                let n_cols = mat.n_cols().min(n_genomes);
+                return Some((0..n_cols).map(|g| mat.carries(g, slot)).collect());
+            }
+        }
+        None
+    }
+}
diff --git a/src/obikindex/src/siblings/cardinality.rs b/src/obikindex/src/siblings/cardinality.rs
new file mode 100644
index 00000000..b9a023fa
--- /dev/null
+++ b/src/obikindex/src/siblings/cardinality.rs
@@ -0,0 +1,204 @@
+use ndarray::Array2;
+use rayon::prelude::*;
+
+use obicompactvec::{PersistentBitMatrix, PersistentCompactIntMatrix, SiblingAnnex};
+use obikpartitionner::KmerPartition;
+use obikseq::CanonicalKmer;
+use obilayeredmap::MphfLayer;
+use obilayeredmap::meta::PartitionMeta;
+use obiskio::UnitigFileReader;
+use obisys::progress_bar;
+
+use crate::error::{OKIError, OKIResult};
+use crate::index::KmerIndex;
+
+use super::cache::{Mat, PartitionCache};
+use super::distance::RawSnpDistanceOutput;
+use super::helpers::{central_base, is_minorant, partition_of};
+use super::{olm_to_ok, ANNEX_FILE_NAME, INDEX_SUBDIR};
+
+/// See [`KmerIndex::cardinality_tally`].
+pub struct CardinalityTally {
+    /// `counts[a][b] == counts[b][a]` = number of family sites, pooled over
+    /// included genome pairs, where one genome's family cardinality
+    /// (popcount of its presence mask, `0..=4`) is `a` and the other's is
+    /// `b`. Diagonal is real data here (both genomes at the same
+    /// cardinality), unlike [`super::distance::BasePairTally::counts`].
+    pub counts: [[u64; 5]; 5],
+}
+
+impl KmerIndex {
+    /// Cardinality co-occurrence, pooled only over genome pairs whose
+    /// overall SNP ratio in `raw` is at or below `ratio_ceiling` — same
+    /// saturation/no-data exclusion discipline as
+    /// [`base_pair_tally`](Self::base_pair_tally). Unlike
+    /// `scan_family_pairs` (which resolves each genome to a single form and
+    /// silently drops any genome carrying more than one member of the
+    /// family), this needs the *full* per-genome presence mask — a family
+    /// member count of 2, 3 or 4 is exactly the signal being tallied, not
+    /// noise to discard — so it re-implements the traversal rather than
+    /// reusing that helper.
+    ///
+    /// Restricted to variable families (`family_size() >= 2`), matching
+    /// `snp_pseudo_alignment`'s own scope — briefly removed, then
+    /// reinstated: without it, the diagonal is dominated by genome-wide
+    /// invariant background (family_size()<2 loci vastly outnumber the
+    /// ones that ever vary anywhere), which is inconsistent with the
+    /// `+ASC`-corrected alignment this matrix is ultimately used with —
+    /// `+ASC` exists specifically because the likelihood only ever sees
+    /// variable sites, so a rate model calibrated mostly from invariant
+    /// background sites doesn't describe the population it's applied to.
+    /// Verified empirically: removing the filter measurably worsened a
+    /// real IQ-TREE run (log-likelihood dropped, `NNI search needs
+    /// unusual large number of steps to converge` warnings appeared) — see
+    /// `docmd/theory/evolutionary_distances.md` for the full account.
+    /// [`base_pair_tally`](Self::base_pair_tally)'s own diagonal (`same`)
+    /// gets the matching restriction via `scan_family_pairs`'s new
+    /// `variable` flag, rather than a `family_size()` check of its own (it
+    /// doesn't have direct access to the family's mask).
+    pub fn cardinality_tally(&self, raw: &RawSnpDistanceOutput, ratio_ceiling: f64) -> OKIResult<CardinalityTally> {
+        let n_parts = self.n_partitions();
+        let n_genomes = self.meta.genomes.len();
+        let with_counts = self.meta.config.with_counts;
+        let k = self.kmer_size();
+        let n_bits = n_parts.trailing_zeros() as usize;
+
+        let included = Array2::from_shape_fn((n_genomes, n_genomes), |(i, j)| {
+            if i == j {
+                return false;
+            }
+            let snp = raw.snp[[i, j]];
+            let total = snp + raw.shared[[i, j]];
+            total > 0 && (snp as f64 / total as f64) <= ratio_ceiling
+        });
+
+        let partition = KmerPartition::open_with_config(
+            &self.root_path,
+            self.kmer_size(),
+            self.minimizer_size(),
+            n_bits,
+        )
+        .map_err(OKIError::Partition)?;
+        let cache = PartitionCache::build(&partition, n_parts, with_counts)?;
+
+        let mut layer_dirs = Vec::new();
+        for part in 0..n_parts {
+            let index_dir = self.partition().part_dir(part).join(INDEX_SUBDIR);
+            if !index_dir.exists() {
+                continue;
+            }
+            let meta = PartitionMeta::load(&index_dir).map_err(olm_to_ok)?;
+            for l in 0..meta.n_layers {
+                let layer_dir = index_dir.join(format!("layer_{l}"));
+                let annex_path = layer_dir.join(ANNEX_FILE_NAME);
+                if !annex_path.exists() {
+                    return Err(OKIError::InvalidInput(format!(
+                        "no sibling annex at {} — run build_sibling_annex first",
+                        annex_path.display()
+                    )));
+                }
+                layer_dirs.push(layer_dir);
+            }
+        }
+
+        let pb = progress_bar("cardinality_tally", layer_dirs.len() as u64, "layers");
+        let partials: Vec<[[u64; 5]; 5]> = layer_dirs
+            .par_iter()
+            .map(|layer_dir| -> OKIResult<[[u64; 5]; 5]> {
+                let index_dir = layer_dir.parent().expect("layer_dir has a parent index dir");
+                let meta = PartitionMeta::load(index_dir).map_err(olm_to_ok)?;
+                let annex = SiblingAnnex::open(&layer_dir.join(ANNEX_FILE_NAME))?;
+                let mphf = MphfLayer::open(layer_dir, &meta.mode).map_err(olm_to_ok)?;
+
+                let mut slot_kmer: Vec<Option<CanonicalKmer>> = vec![None; annex.len()];
+                let reader = UnitigFileReader::open_sequential(&layer_dir.join("unitigs.bin"))
+                    .map_err(OKIError::Partition)?;
+                for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
+                    if let Some(slot) = mphf.find(kmer) {
+                        slot_kmer[slot] = Some(kmer);
+                    }
+                }
+
+                let use_counts = with_counts && layer_dir.join("counts").exists();
+                let mat = if use_counts {
+                    Mat::Count(PersistentCompactIntMatrix::open(layer_dir)?)
+                } else {
+                    Mat::Presence(PersistentBitMatrix::open(layer_dir)?)
+                };
+                let n_cols = mat.n_cols().min(n_genomes);
+
+                let mut counts = [[0u64; 5]; 5];
+                let mut genome_mask: Vec<u8> = Vec::with_capacity(n_genomes);
+
+                for slot in 0..annex.len() {
+                    let Some(mask) = annex.get(slot) else { continue };
+                    let Some(kmer) = slot_kmer[slot] else { continue };
+                    if !is_minorant(kmer, mask, k) {
+                        continue; // family tallied once, at its minorant
+                    }
+                    if mask.family_size() < 2 {
+                        // Fully invariant family (never varies anywhere in
+                        // the index) — genome-wide background, not
+                        // SNP-adjacent signal; would otherwise swamp the
+                        // diagonal (`c=1/c=1` etc.), which needs to reflect
+                        // the same variable-families-only population the
+                        // `+ASC`-corrected alignment/likelihood actually
+                        // models. See `base_pair_tally`'s `variable` gate
+                        // on its own `same` diagonal for the matching fix.
+                        continue;
+                    }
+
+                    genome_mask.clear();
+                    genome_mask.resize(n_genomes, 0);
+
+                    for other in kmer.central_canonical_neighbors() {
+                        let base = central_base(other, k);
+                        if !mask.has(base) {
+                            continue;
+                        }
+                        let presence: Option<Vec<bool>> = if other == kmer {
+                            Some((0..n_cols).map(|g| mat.carries(g, slot)).collect())
+                        } else {
+                            let dest = partition_of(other, n_parts);
+                            cache.find_presence(dest, other, n_genomes)
+                        };
+                        let Some(presence) = presence else { continue };
+                        for (g, &present) in presence.iter().enumerate() {
+                            if present {
+                                genome_mask[g] |= 1 << base;
+                            }
+                        }
+                    }
+
+                    for i in 0..n_genomes {
+                        let card_i = genome_mask[i].count_ones() as usize;
+                        for j in (i + 1)..n_genomes {
+                            if !included[[i, j]] {
+                                continue;
+                            }
+                            let card_j = genome_mask[j].count_ones() as usize;
+                            counts[card_i][card_j] += 1;
+                            if card_i != card_j {
+                                counts[card_j][card_i] += 1;
+                            }
+                        }
+                    }
+                }
+
+                pb.inc(1);
+                Ok(counts)
+            })
+            .collect::<OKIResult<Vec<_>>>()?;
+        pb.finish_and_clear();
+
+        let mut total = [[0u64; 5]; 5];
+        for partial in partials {
+            for a in 0..5 {
+                for b in 0..5 {
+                    total[a][b] += partial[a][b];
+                }
+            }
+        }
+        Ok(CardinalityTally { counts: total })
+    }
+}
diff --git a/src/obikindex/src/siblings/distance.rs b/src/obikindex/src/siblings/distance.rs
new file mode 100644
index 00000000..8dcf40fc
--- /dev/null
+++ b/src/obikindex/src/siblings/distance.rs
@@ -0,0 +1,305 @@
+use ndarray::Array2;
+use rayon::prelude::*;
+
+use obicompactvec::{PersistentBitMatrix, PersistentCompactIntMatrix, SiblingAnnex};
+use obikpartitionner::KmerPartition;
+use obikseq::CanonicalKmer;
+use obilayeredmap::MphfLayer;
+use obilayeredmap::meta::PartitionMeta;
+use obiskio::UnitigFileReader;
+use obisys::progress_bar;
+
+use crate::error::{OKIError, OKIResult};
+use crate::index::KmerIndex;
+
+use super::cache::{Mat, PartitionCache};
+use super::helpers::{central_base, is_minorant, partition_of};
+use super::{olm_to_ok, ANNEX_FILE_NAME, INDEX_SUBDIR};
+
+/// Raw p-distance restricted to loci that are single-copy in **both**
+/// genomes of a pair — the "stringent / paralogy-aware" locus eligibility
+/// rule (`docmd/theory/evolutionary_distances.md`, "Locus eligibility"),
+/// without the JC/K2P/LogDet finalisation math: `snp[i,j]` + `shared[i,j]`
+/// is the number of eligible loci, `snp[i,j] / (snp[i,j] + shared[i,j])` is
+/// `p_hat`. A quick, self-contained way to sanity-check the estimator
+/// against a real index before the full `SnpTally` design is built.
+///
+/// A locus (family, tallied once at its minorant) is eligible for pair
+/// `(i, j)` iff genome `i` carries exactly one of the family's observed
+/// forms **and** genome `j` carries exactly one (possibly a different one)
+/// — presence-only: a genome carrying the same form twice (a same-allele
+/// duplicate) is indistinguishable from carrying it once when only a
+/// presence matrix is available, so such cases are not excluded here even
+/// when a count index exists. See "Locus eligibility", stringent rule, for
+/// why this matters and how a count index would close the gap — left as a
+/// follow-up, not applied here.
+pub struct RawSnpDistanceOutput {
+    /// n×n count of eligible loci where the two genomes' single forms differ.
+    pub snp: Array2<u64>,
+    /// n×n count of eligible loci where the two genomes' single forms agree.
+    pub shared: Array2<u64>,
+}
+
+impl KmerIndex {
+    /// Shared traversal behind [`raw_snp_distance`](Self::raw_snp_distance)
+    /// and [`base_pair_tally`](Self::base_pair_tally): for every family
+    /// (tallied once, at its minorant) of every layer of the already-built
+    /// sibling annex, resolves each genome's single observed form (`None`
+    /// if absent or ambiguous/multi-copy), then calls `on_pair(acc, i, j,
+    /// bi, bj, variable)` for every genome pair `(i, j)` where both are
+    /// unambiguous and single-copy (`bi == bj` means shared at that locus,
+    /// `bi != bj` means a SNP). `variable` is the family's own
+    /// `family_size() >= 2` (true if more than one member is observed
+    /// *anywhere* in the family, i.e. it isn't fully invariant across the
+    /// whole index) — `raw_snp_distance` ignores it (a fully-invariant
+    /// family is still legitimately "shared"), but callers whose diagonal
+    /// should only reflect genuine SNP-adjacent agreement, not the
+    /// genome-wide invariant background, need it (see
+    /// [`base_pair_tally`](Self::base_pair_tally)'s `same` field). Layers
+    /// are processed in parallel (rayon); each gets its own accumulator
+    /// from `zero()`, combined pairwise via `combine`.
+    fn scan_family_pairs<Acc, F, C>(
+        &self,
+        label: &str,
+        zero: impl Fn() -> Acc + Sync,
+        on_pair: F,
+        combine: C,
+    ) -> OKIResult<Acc>
+    where
+        Acc: Send,
+        F: Fn(&mut Acc, usize, usize, u8, u8, bool) + Sync,
+        C: Fn(Acc, Acc) -> Acc,
+    {
+        let n_parts = self.n_partitions();
+        let n_genomes = self.meta.genomes.len();
+        let with_counts = self.meta.config.with_counts;
+        let k = self.kmer_size();
+        let n_bits = n_parts.trailing_zeros() as usize;
+
+        let partition = KmerPartition::open_with_config(
+            &self.root_path,
+            self.kmer_size(),
+            self.minimizer_size(),
+            n_bits,
+        )
+        .map_err(OKIError::Partition)?;
+        let cache = PartitionCache::build(&partition, n_parts, with_counts)?;
+
+        let mut layer_dirs = Vec::new();
+        for part in 0..n_parts {
+            let index_dir = self.partition().part_dir(part).join(INDEX_SUBDIR);
+            if !index_dir.exists() {
+                continue;
+            }
+            let meta = PartitionMeta::load(&index_dir).map_err(olm_to_ok)?;
+            for l in 0..meta.n_layers {
+                let layer_dir = index_dir.join(format!("layer_{l}"));
+                let annex_path = layer_dir.join(ANNEX_FILE_NAME);
+                if !annex_path.exists() {
+                    return Err(OKIError::InvalidInput(format!(
+                        "no sibling annex at {} — run build_sibling_annex first",
+                        annex_path.display()
+                    )));
+                }
+                layer_dirs.push(layer_dir);
+            }
+        }
+
+        let pb = progress_bar(label, layer_dirs.len() as u64, "layers");
+        let partials: Vec<Acc> = layer_dirs
+            .par_iter()
+            .map(|layer_dir| -> OKIResult<Acc> {
+                let mut acc = zero();
+
+                let index_dir = layer_dir.parent().expect("layer_dir has a parent index dir");
+                let meta = PartitionMeta::load(index_dir).map_err(olm_to_ok)?;
+                let annex = SiblingAnnex::open(&layer_dir.join(ANNEX_FILE_NAME))?;
+                let mphf = MphfLayer::open(layer_dir, &meta.mode).map_err(olm_to_ok)?;
+
+                let mut slot_kmer: Vec<Option<CanonicalKmer>> = vec![None; annex.len()];
+                let reader = UnitigFileReader::open_sequential(&layer_dir.join("unitigs.bin"))
+                    .map_err(OKIError::Partition)?;
+                for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
+                    if let Some(slot) = mphf.find(kmer) {
+                        slot_kmer[slot] = Some(kmer);
+                    }
+                }
+
+                let use_counts = with_counts && layer_dir.join("counts").exists();
+                let mat = if use_counts {
+                    Mat::Count(PersistentCompactIntMatrix::open(layer_dir)?)
+                } else {
+                    Mat::Presence(PersistentBitMatrix::open(layer_dir)?)
+                };
+                let n_cols = mat.n_cols().min(n_genomes);
+
+                // Per family: which single form (if exactly one) each genome
+                // carries — `None` once a second form is seen (ambiguous,
+                // not single-copy, ineligible for either side of a pair).
+                let mut single_form: Vec<Option<u8>> = Vec::with_capacity(n_cols);
+                let mut ambiguous: Vec<bool> = Vec::with_capacity(n_cols);
+
+                for slot in 0..annex.len() {
+                    let Some(mask) = annex.get(slot) else { continue };
+                    let Some(kmer) = slot_kmer[slot] else { continue };
+                    if !is_minorant(kmer, mask, k) {
+                        continue; // family tallied once, at its minorant
+                    }
+                    let variable = mask.family_size() >= 2;
+
+                    single_form.clear();
+                    single_form.resize(n_cols, None);
+                    ambiguous.clear();
+                    ambiguous.resize(n_cols, false);
+
+                    for other in kmer.central_canonical_neighbors() {
+                        let base = central_base(other, k);
+                        if !mask.has(base) {
+                            continue;
+                        }
+                        let presence: Option<Vec<bool>> = if other == kmer {
+                            Some((0..n_cols).map(|g| mat.carries(g, slot)).collect())
+                        } else {
+                            let dest = partition_of(other, n_parts);
+                            cache.find_presence(dest, other, n_genomes)
+                        };
+                        let Some(presence) = presence else { continue };
+                        for (g, &present) in presence.iter().enumerate() {
+                            if !present {
+                                continue;
+                            }
+                            if single_form[g].is_some() {
+                                ambiguous[g] = true;
+                            } else {
+                                single_form[g] = Some(base);
+                            }
+                        }
+                    }
+
+                    for i in 0..n_cols {
+                        if ambiguous[i] {
+                            continue;
+                        }
+                        let Some(bi) = single_form[i] else { continue };
+                        for j in (i + 1)..n_cols {
+                            if ambiguous[j] {
+                                continue;
+                            }
+                            let Some(bj) = single_form[j] else { continue };
+                            on_pair(&mut acc, i, j, bi, bj, variable);
+                        }
+                    }
+                }
+
+                pb.inc(1);
+                Ok(acc)
+            })
+            .collect::<OKIResult<Vec<_>>>()?;
+        pb.finish_and_clear();
+
+        let mut total = zero();
+        for partial in partials {
+            total = combine(total, partial);
+        }
+        Ok(total)
+    }
+
+    /// Compute [`RawSnpDistanceOutput`] from an already-built sibling annex
+    /// (run [`build_sibling_annex`](Self::build_sibling_annex) first).
+    pub fn raw_snp_distance(&self) -> OKIResult<RawSnpDistanceOutput> {
+        let n_genomes = self.meta.genomes.len();
+        let (snp, shared) = self.scan_family_pairs(
+            "raw_snp_distance",
+            || (Array2::<u64>::zeros((n_genomes, n_genomes)), Array2::<u64>::zeros((n_genomes, n_genomes))),
+            |(snp, shared), i, j, bi, bj, _variable| {
+                if bi == bj {
+                    shared[[i, j]] += 1;
+                    shared[[j, i]] += 1;
+                } else {
+                    snp[[i, j]] += 1;
+                    snp[[j, i]] += 1;
+                }
+            },
+            |(mut snp, mut shared), (s, sh)| {
+                snp += &s;
+                shared += &sh;
+                (snp, shared)
+            },
+        )?;
+        Ok(RawSnpDistanceOutput { snp, shared })
+    }
+
+    /// Symmetric 6-category base-pair substitution tally (AC, AG, AT, CG,
+    /// CT, GT — indexed `0=A,1=C,2=G,3=T`), pooled only over genome pairs
+    /// whose overall SNP ratio in `raw` is at or below `ratio_ceiling` —
+    /// same saturation-exclusion discipline as
+    /// [`cardinality_tally`](Self::cardinality_tally), for the same reason:
+    /// a saturated pair's observed base-pair mix trends toward neutral base
+    /// composition, not the true point-mutation spectrum.
+    ///
+    /// A second full pass over the annex, sharing
+    /// [`raw_snp_distance`](Self::raw_snp_distance)'s traversal (guided by
+    /// it, not a blind re-scan) — needed because `raw_snp_distance` only
+    /// keeps aggregate SNP/shared counts per genome pair, not which bases
+    /// were actually involved at each locus, and the ratio-ceiling filter
+    /// can only be evaluated once the aggregate counts are known.
+    pub fn base_pair_tally(&self, raw: &RawSnpDistanceOutput, ratio_ceiling: f64) -> OKIResult<BasePairTally> {
+        let n_genomes = self.meta.genomes.len();
+        let included = Array2::from_shape_fn((n_genomes, n_genomes), |(i, j)| {
+            if i == j {
+                return false;
+            }
+            let snp = raw.snp[[i, j]];
+            let total = snp + raw.shared[[i, j]];
+            total > 0 && (snp as f64 / total as f64) <= ratio_ceiling
+        });
+
+        let (counts, same) = self.scan_family_pairs(
+            "base_pair_tally",
+            || ([[0u64; 4]; 4], [0u64; 4]),
+            |(counts, same), i, j, bi, bj, variable| {
+                if !included[[i, j]] {
+                    return;
+                }
+                if bi != bj {
+                    counts[bi as usize][bj as usize] += 1;
+                    counts[bj as usize][bi as usize] += 1;
+                } else if variable {
+                    // Only count "stayed the same" from families that vary
+                    // *somewhere* in the index — a fully invariant family
+                    // (never varies anywhere) isn't a SNP-adjacent
+                    // agreement, it's genome-wide background, and would
+                    // otherwise swamp the diagonal (see
+                    // `docmd/theory/evolutionary_distances.md`, the
+                    // ascertainment-bias regression this was reverting).
+                    same[bi as usize] += 1;
+                }
+            },
+            |(mut counts, mut same), (partial_counts, partial_same)| {
+                for a in 0..4 {
+                    same[a] += partial_same[a];
+                    for b in 0..4 {
+                        counts[a][b] += partial_counts[a][b];
+                    }
+                }
+                (counts, same)
+            },
+        )?;
+        Ok(BasePairTally { counts, same })
+    }
+}
+
+/// See [`KmerIndex::base_pair_tally`].
+pub struct BasePairTally {
+    /// `counts[a][b] == counts[b][a]` = number of eligible loci, pooled
+    /// over included genome pairs, where the two genomes' single forms are
+    /// `a` and `b` (0=A, 1=C, 2=G, 3=T). Diagonal always `0` — an `a == b`
+    /// locus is counted in `same`, not here.
+    pub counts: [[u64; 4]; 4],
+    /// `same[a]` = number of eligible loci, pooled over included genome
+    /// pairs, where both genomes' single forms are `a` — the diagonal
+    /// `counts` omits, needed to build a proper row-stochastic composition
+    /// probability matrix (the "stay the same base" entries), not just the
+    /// substitution-cost off-diagonal.
+    pub same: [u64; 4],
+}
diff --git a/src/obikindex/src/siblings/helpers.rs b/src/obikindex/src/siblings/helpers.rs
new file mode 100644
index 00000000..f50ee2ce
--- /dev/null
+++ b/src/obikindex/src/siblings/helpers.rs
@@ -0,0 +1,49 @@
+use obikseq::CanonicalKmer;
+use obiskbuilder::rolling_stat::RollingStat;
+
+use obicompactvec::FamilyMask;
+
+/// Central-position base of a canonical k-mer, in the fixed 0=A/1=C/2=G/3=T
+/// encoding — the mask's bit index. `k` must be odd (project invariant).
+#[inline]
+pub(super) fn central_base(kmer: CanonicalKmer, k: usize) -> u8 {
+    kmer.nucleotide((k - 1) / 2)
+}
+
+/// Is `kmer` the minorant of its family, given the family's presence mask?
+/// Regenerates the family's 4 canonical forms from `kmer` itself (cheap, no
+/// lookup — see the design doc's "Definitions" section for why this is
+/// always safe: the set of 4 forms is invariant regardless of which member
+/// you start from), and compares the raw encodings of whichever are marked
+/// present in `mask`.
+pub(super) fn is_minorant(kmer: CanonicalKmer, mask: FamilyMask, k: usize) -> bool {
+    kmer.central_canonical_neighbors().into_iter().all(|other| {
+        other == kmer || !mask.has(central_base(other, k)) || kmer.raw() <= other.raw()
+    })
+}
+
+/// Minimiser of a single, isolated canonical k-mer (not part of a streamed
+/// sequence). `RollingStat` computes minimisers incrementally along a
+/// sequence; this feeds one k-mer's bases through a fresh instance to get
+/// the same selection for a single, disconnected k-mer. Not the leanest
+/// possible primitive (an O(1)-amortised dedicated scan, as originally
+/// sketched in the design doc's Step 0, would avoid the ASCII round-trip and
+/// `RollingStat` allocation) but correct and reuses already-tested logic;
+/// left as a follow-up optimisation.
+fn lone_kmer_minimizer(kmer: CanonicalKmer) -> obikseq::Minimizer {
+    let ascii = kmer.to_ascii();
+    let mut rs = RollingStat::new(0);
+    for b in ascii {
+        rs.push(b);
+    }
+    rs.canonical_minimizer()
+        .expect("RollingStat must be ready after k bases of a valid k-mer")
+}
+
+/// Destination partition for a (possibly synthetic) canonical k-mer, using
+/// the same routing rule as the rest of the index (`minimiser.seq_hash() &
+/// mask`, `n_partitions` is a power of two).
+pub(super) fn partition_of(kmer: CanonicalKmer, n_partitions: usize) -> usize {
+    let mask = (n_partitions as u64) - 1;
+    (lone_kmer_minimizer(kmer).seq_hash() & mask) as usize
+}
diff --git a/src/obikindex/src/siblings/mod.rs b/src/obikindex/src/siblings/mod.rs
new file mode 100644
index 00000000..edc344fb
--- /dev/null
+++ b/src/obikindex/src/siblings/mod.rs
@@ -0,0 +1,73 @@
+//! Family presence-mask annex construction.
+//!
+//! See `docmd/theory/evolutionary_distances.md`, "Definitions: family, and
+//! the canonical form of a family" and "Step 2b", for the full design
+//! discussion this implements.
+//!
+//! For each distinct k-mer of each layer of the (already built/merged)
+//! index, computes a 4-bit presence mask for its "family" (the up to 4
+//! k-mers sharing its flanks, differing only at the central base —
+//! well-defined for odd k): bit `b` set iff the family member whose own
+//! canonical central base is `b` (0=A, 1=C, 2=G, 3=T) is observed anywhere
+//! in the current multi-genome index — a property of the whole index, not
+//! of any one genome. Sibling count and minorant are *derived* from the
+//! mask by callers, not stored (see `FamilyMask` and
+//! [`sibling_annex_stats`](crate::index::KmerIndex::sibling_annex_stats)
+//! below).
+//!
+//! Per layer, an `obipipeline` batch transform (throttled — see
+//! `obipipeline::throttle`) generates a whole batch's central variants at
+//! once (`BATCH_SIZE` source k-mers in, that batch's variants out as one
+//! pipeline message), interleaved across many in-flight batches by the
+//! scheduler's shared worker pool rather than processed on a single
+//! thread. The actual cross-partition lookup reuses a `PartitionCache` of
+//! every partition's already-open MPHF layers, built once for the whole
+//! `build_sibling_annex` run, rather than reopening files per lookup or
+//! per source layer. Two earlier, coarser-grained designs were tried and
+//! measured (not guessed) to be worse, in order: (1) reopening/re-mmap'ing
+//! every target partition's files on every single lookup — fine at toy
+//! scale, ~90% system time against a real index; (2) a `Flat` pipeline
+//! stage pushing one message per generated *variant* (up to 3 per source
+//! k-mer) — cheaper than reopening files, but sampling a real run showed
+//! most wall-clock time going into per-message channel send/notify
+//! syscalls rather than the lookup itself, because a single k-mer's ≤3
+//! variants is far too fine a granularity to amortise a pipeline's
+//! synchronisation cost over. See `docmd/theory/evolutionary_distances.md`,
+//! Step 2b, "Mechanism".
+//!
+//! Submodules, in the order data flows through them: [`cache`] (shared
+//! whole-run partition cache), [`helpers`] (small pure functions used
+//! throughout), [`build`] (annex construction), [`stats`] (family-size
+//! diagnostics), [`distance`] (raw SNP distance + base-pair tally),
+//! [`cardinality`] (cardinality co-occurrence), [`alignment`] (SNP-only
+//! pseudo-alignment).
+
+mod alignment;
+mod build;
+mod cache;
+mod cardinality;
+mod distance;
+mod helpers;
+mod stats;
+
+#[cfg(test)]
+mod tests;
+
+pub use alignment::SnpAlignment;
+pub use cardinality::CardinalityTally;
+pub use distance::{BasePairTally, RawSnpDistanceOutput};
+pub use stats::SiblingAnnexStats;
+
+use obilayeredmap::OLMError;
+
+use crate::error::OKIError;
+
+pub(super) const INDEX_SUBDIR: &str = "index";
+pub(super) const ANNEX_FILE_NAME: &str = "siblings.psib";
+
+pub(super) fn olm_to_ok(e: OLMError) -> OKIError {
+    match e {
+        OLMError::Io(e) => OKIError::Io(e),
+        other => OKIError::InvalidInput(format!("layered-map error: {other}")),
+    }
+}
diff --git a/src/obikindex/src/siblings/stats.rs b/src/obikindex/src/siblings/stats.rs
new file mode 100644
index 00000000..66db7958
--- /dev/null
+++ b/src/obikindex/src/siblings/stats.rs
@@ -0,0 +1,192 @@
+use rayon::prelude::*;
+
+use obicompactvec::{PersistentBitMatrix, PersistentCompactIntMatrix, SiblingAnnex};
+use obikpartitionner::KmerPartition;
+use obikseq::CanonicalKmer;
+use obilayeredmap::MphfLayer;
+use obilayeredmap::meta::PartitionMeta;
+use obiskio::UnitigFileReader;
+use obisys::progress_bar;
+
+use crate::error::{OKIError, OKIResult};
+use crate::index::KmerIndex;
+
+use super::cache::{Mat, PartitionCache};
+use super::helpers::{central_base, is_minorant, partition_of};
+use super::{olm_to_ok, ANNEX_FILE_NAME, INDEX_SUBDIR};
+
+/// Distribution of family sizes (1-4), read back from an already-built
+/// annex (see [`KmerIndex::build_sibling_annex`]) plus the index's
+/// presence/count data — a separate, occasional diagnostic pass, not fused
+/// into construction.
+///
+/// Every count here is **per family, not per slot**: a family with `F`
+/// members occupies `F` annex slots (one per observed member), all sharing
+/// the same mask. Counting every slot would count each family up to 4
+/// times over; only the minorant's slot is tallied (minorant is derived on
+/// the fly — see `is_minorant` — not stored, but cheap: no lookup, pure
+/// bit arithmetic on already-in-hand data).
+#[derive(Debug, Clone, Default)]
+pub struct SiblingAnnexStats {
+    /// `counts[s]` = number of *families* of size `s + 1` (index 0 = size 1,
+    /// i.e. 0 siblings, ... index 3 = size 4, i.e. 3 siblings).
+    pub counts: [u64; 4],
+    /// `per_genome[g][s]` = number of families of size `s + 1` for which
+    /// genome `g` (index into `KmerIndex::meta().genomes`) carries at least
+    /// one member.
+    pub per_genome: Vec<[u64; 4]>,
+}
+
+impl KmerIndex {
+    /// Tally the family-size distribution of an already-built annex
+    /// (globally, and per genome), counting each family once (at its
+    /// minorant slot). Errors if [`build_sibling_annex`] has not been run on
+    /// this index first.
+    ///
+    /// [`build_sibling_annex`]: Self::build_sibling_annex
+    pub fn sibling_annex_stats(&self) -> OKIResult<SiblingAnnexStats> {
+        let n_parts = self.n_partitions();
+        let n_genomes = self.meta.genomes.len();
+        let with_counts = self.meta.config.with_counts;
+        let k = self.kmer_size();
+        let n_bits = n_parts.trailing_zeros() as usize;
+
+        // Same whole-run cache as `build_sibling_annex` — see its docs for
+        // why re-opening per lookup (or per call to a batching helper) is
+        // not good enough on a real index.
+        let partition = KmerPartition::open_with_config(
+            &self.root_path,
+            self.kmer_size(),
+            self.minimizer_size(),
+            n_bits,
+        )
+        .map_err(OKIError::Partition)?;
+        let cache = PartitionCache::build(&partition, n_parts, with_counts)?;
+
+        // Gather the (partition, layer) pairs to process — cheap metadata
+        // reads only, checking every annex file exists up front so a
+        // missing one is reported before any real work starts.
+        let mut layer_dirs = Vec::new();
+        for part in 0..n_parts {
+            let index_dir = self.partition().part_dir(part).join(INDEX_SUBDIR);
+            if !index_dir.exists() {
+                continue;
+            }
+            let meta = PartitionMeta::load(&index_dir).map_err(olm_to_ok)?;
+            for l in 0..meta.n_layers {
+                let layer_dir = index_dir.join(format!("layer_{l}"));
+                let annex_path = layer_dir.join(ANNEX_FILE_NAME);
+                if !annex_path.exists() {
+                    return Err(OKIError::InvalidInput(format!(
+                        "no sibling annex at {} — run build_sibling_annex first",
+                        annex_path.display()
+                    )));
+                }
+                layer_dirs.push(layer_dir);
+            }
+        }
+
+        // One layer's worth of work, parallelised across layers with Rayon
+        // — independent, read-only, each producing its own partial tally
+        // merged at the end.
+        let pb = progress_bar("sibling_annex_stats", layer_dirs.len() as u64, "layers");
+        let partials: Vec<SiblingAnnexStats> = layer_dirs
+            .par_iter()
+            .map(|layer_dir| -> OKIResult<SiblingAnnexStats> {
+                let mut stats = SiblingAnnexStats {
+                    per_genome: vec![[0u64; 4]; n_genomes],
+                    ..Default::default()
+                };
+
+                let index_dir = layer_dir.parent().expect("layer_dir has a parent index dir");
+                let meta = PartitionMeta::load(index_dir).map_err(olm_to_ok)?;
+                let annex = SiblingAnnex::open(&layer_dir.join(ANNEX_FILE_NAME))?;
+
+                // Need each slot's own k-mer to derive minorant — same
+                // enumeration as construction.
+                let mphf = MphfLayer::open(layer_dir, &meta.mode).map_err(olm_to_ok)?;
+                let mut slot_kmer: Vec<Option<CanonicalKmer>> = vec![None; annex.len()];
+                let reader = UnitigFileReader::open_sequential(&layer_dir.join("unitigs.bin"))
+                    .map_err(OKIError::Partition)?;
+                for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
+                    if let Some(slot) = mphf.find(kmer) {
+                        slot_kmer[slot] = Some(kmer);
+                    }
+                }
+
+                let use_counts = with_counts && layer_dir.join("counts").exists();
+                let mat = if use_counts {
+                    Mat::Count(PersistentCompactIntMatrix::open(layer_dir)?)
+                } else {
+                    Mat::Presence(PersistentBitMatrix::open(layer_dir)?)
+                };
+                let n_cols = mat.n_cols().min(n_genomes);
+
+                for slot in 0..annex.len() {
+                    let Some(mask) = annex.get(slot) else { continue };
+                    let Some(kmer) = slot_kmer[slot] else { continue };
+                    if !is_minorant(kmer, mask, k) {
+                        continue; // this family is tallied at its minorant's slot only
+                    }
+                    let s = mask.siblings() as usize;
+                    stats.counts[s] += 1;
+
+                    // "Genome g represents this family" means g carries
+                    // *any* of its members, not just the minorant's own —
+                    // start from the minorant's own presence (already
+                    // open, no lookup) and OR in every other present
+                    // member's presence vector, resolved against the
+                    // whole-run cache (no I/O) — exactly `mask.siblings()`
+                    // of them, the mask tells us precisely which to fetch.
+                    let mut carries = vec![false; n_cols];
+                    for g in 0..n_cols {
+                        carries[g] = mat.carries(g, slot);
+                    }
+                    for other in kmer.central_canonical_neighbors() {
+                        if other == kmer {
+                            continue;
+                        }
+                        let base = central_base(other, k);
+                        if !mask.has(base) {
+                            continue;
+                        }
+                        let dest = partition_of(other, n_parts);
+                        if let Some(other_presence) = cache.find_presence(dest, other, n_genomes) {
+                            for (g, &present) in other_presence.iter().enumerate() {
+                                if present {
+                                    carries[g] = true;
+                                }
+                            }
+                        }
+                    }
+
+                    for (g, &carried) in carries.iter().enumerate() {
+                        if carried {
+                            stats.per_genome[g][s] += 1;
+                        }
+                    }
+                }
+
+                pb.inc(1);
+                Ok(stats)
+            })
+            .collect::<OKIResult<Vec<_>>>()?;
+        pb.finish_and_clear();
+
+        let mut stats = SiblingAnnexStats {
+            per_genome: vec![[0u64; 4]; n_genomes],
+            ..Default::default()
+        };
+        for part in partials {
+            for s in 0..4 {
+                stats.counts[s] += part.counts[s];
+            }
+            for g in 0..n_genomes {
+                for s in 0..4 {
+                    stats.per_genome[g][s] += part.per_genome[g][s];
+                }
+            }
+        }
+        Ok(stats)
+    }
+}
diff --git a/src/obikindex/src/siblings/tests.rs b/src/obikindex/src/siblings/tests.rs
new file mode 100644
index 00000000..0aa833b6
--- /dev/null
+++ b/src/obikindex/src/siblings/tests.rs
@@ -0,0 +1,186 @@
+use std::io::Write;
+use std::path::Path;
+
+use obicompactvec::{FamilyMask, SiblingAnnex};
+use obikseq::{CanonicalKmer, Kmer, Sequence};
+use obilayeredmap::MphfLayer;
+use obilayeredmap::meta::PartitionMeta;
+use obisys::Reporter;
+use tempfile::tempdir;
+
+use crate::index::KmerIndex;
+use crate::meta::{GenomeInfo, IndexConfig};
+use crate::merge::MergeMode;
+
+use super::helpers::is_minorant;
+use super::{ANNEX_FILE_NAME, INDEX_SUBDIR};
+
+// k must be >= 11 (project constraint, "k ∈ [11,31]"); k=11, level_max=1,
+// theta=0.0 mirror `obiskbuilder`'s own tests (smaller k/level_max
+// combinations trip an unrelated pre-existing bug in `obikentropy`'s
+// sliding-window ring buffer — not this feature's concern).
+const K: usize = 11;
+const M: usize = 5;
+
+/// Build a single-genome index from one in-memory FASTA sequence, driving
+/// the same primitives `obikmer`'s `scatter` step uses (minus the
+/// multi-file `obipipeline` wrapper — a single sequence needs none of
+/// that): normalise -> build superkmers -> route -> write.
+/// `cargo test` doesn't install a `tracing` subscriber the way `obikmer`'s
+/// CLI does, so `debug!`/etc. are silent no-ops by default — including the
+/// `PartitionRunner` instrumentation that would matter most for
+/// re-diagnosing a hang here. `try_init` is idempotent across concurrently
+/// running tests (later calls just find a subscriber already installed).
+fn init_tracing() {
+    let _ = tracing_subscriber::fmt()
+        .with_env_filter(
+            tracing_subscriber::EnvFilter::try_from_default_env()
+                .unwrap_or_else(|_| tracing_subscriber::EnvFilter::new("info")),
+        )
+        .with_writer(std::io::stderr)
+        .try_init();
+}
+
+fn build_single_genome_index(dir: &Path, label: &str, seq: &[u8]) -> KmerIndex {
+    init_tracing();
+    let fasta_path = dir.join(format!("{label}.fasta"));
+    let mut f = std::fs::File::create(&fasta_path).unwrap();
+    writeln!(f, ">{label}").unwrap();
+    f.write_all(seq).unwrap();
+    writeln!(f).unwrap();
+    drop(f);
+
+    let index_path = dir.join(format!("{label}.idx"));
+    let config = IndexConfig {
+        kmer_size: K,
+        minimizer_size: M,
+        n_bits: 0, // 1 partition — keeps the test deterministic and simple
+        with_counts: false,
+        evidence: obilayeredmap::IndexMode::Exact,
+        block_bits: 0,
+    };
+    let mut idx = KmerIndex::create(&index_path, config, Some(GenomeInfo::new(label)), false)
+        .expect("create");
+
+    let mut rep = Reporter::new();
+    let stream = obiread::open_nuc_stream(fasta_path.to_str().unwrap(), K).expect("open fasta");
+    for page in stream {
+        let batch = obiskbuilder::build_superkmers_page(page, K, /* level_max */ 1, /* theta */ 0.0);
+        idx.partition_mut().write_batch(batch).expect("write_batch");
+    }
+    idx.partition_mut().close().expect("close partition writers");
+    idx.mark_scattered().expect("mark_scattered");
+    idx.dereplicate_and_count(false, &mut rep).expect("dereplicate_and_count");
+    idx.build_layers(1, None, false, &mut rep).expect("build_layers");
+    idx
+}
+
+fn canonical(ascii: &[u8]) -> CanonicalKmer {
+    Kmer::from_ascii(ascii).unwrap().canonical()
+}
+
+/// Read back the annex entry for a given canonical k-mer from the merged
+/// index's (single) partition/layer, asserting it was found at all.
+fn annex_info_for(idx: &KmerIndex, kmer: CanonicalKmer) -> FamilyMask {
+    let index_dir = idx.partition().part_dir(0).join(INDEX_SUBDIR);
+    let meta = PartitionMeta::load(&index_dir).unwrap();
+    for l in 0..meta.n_layers {
+        let layer_dir = index_dir.join(format!("layer_{l}"));
+        let mphf = MphfLayer::open(&layer_dir, &meta.mode).unwrap();
+        if let Some(slot) = mphf.find(kmer) {
+            let annex = SiblingAnnex::open(&layer_dir.join(ANNEX_FILE_NAME)).unwrap();
+            return annex.get(slot).expect("slot must have a computed annex entry");
+        }
+    }
+    panic!("kmer not found in any layer of partition 0");
+}
+
+fn merge_two(dir: &Path, g1: &KmerIndex, g2: &KmerIndex) -> KmerIndex {
+    let mut rep = Reporter::new();
+    KmerIndex::merge(
+        &dir.join("merged.idx"),
+        &[g1, g2],
+        MergeMode::Presence,
+        false,
+        false,
+        1.0,
+        &mut rep,
+    )
+    .expect("merge")
+}
+
+#[test]
+fn sibling_annex_one_sibling_each() {
+    // k=11, centre = index 5 (0-based). Two genomes, each exactly one
+    // k-mer, sharing every base except the centre:
+    //   g1 = "AACCGCTTAAG" (centre 'C', base index 1)
+    //   g2 = "AACCGGTTAAG" (centre 'G', base index 2)
+    // Hand-verified: both stay forward-oriented under canonicalisation
+    // (each is lexicographically smaller than its own reverse
+    // complement, since both start with "AA"), and raw(g1) < raw(g2)
+    // (only differing base: C=0b01 < G=0b10 at the centre) — so g1 is
+    // the minorant, g2 is not. The mask is a family-wide value: both
+    // slots must read back the *same* mask (bits 1 and 2 set).
+    let dir = tempdir().unwrap();
+    let g1 = build_single_genome_index(dir.path(), "g1", b"AACCGCTTAAG");
+    let g2 = build_single_genome_index(dir.path(), "g2", b"AACCGGTTAAG");
+    let merged = merge_two(dir.path(), &g1, &g2);
+    merged.build_sibling_annex().expect("build_sibling_annex");
+
+    let g1_kmer = canonical(b"AACCGCTTAAG");
+    let g2_kmer = canonical(b"AACCGGTTAAG");
+    let expected_mask = FamilyMask::EMPTY.with(1).with(2);
+
+    let a = annex_info_for(&merged, g1_kmer);
+    assert_eq!(a, expected_mask, "AACCGCTTAAG");
+    assert_eq!(a.siblings(), 1);
+    assert!(is_minorant(g1_kmer, a, K), "g1 should be the minorant");
+
+    let b = annex_info_for(&merged, g2_kmer);
+    assert_eq!(b, expected_mask, "AACCGGTTAAG");
+    assert_eq!(b.siblings(), 1);
+    assert!(!is_minorant(g2_kmer, b, K), "g2 should not be the minorant");
+}
+
+#[test]
+fn sibling_annex_zero_siblings_when_identical_and_no_variant_exists() {
+    // Same k-mer in both genomes, no other genome around to carry a
+    // variant -> 0 siblings, trivially its own minorant.
+    let dir = tempdir().unwrap();
+    let g1 = build_single_genome_index(dir.path(), "g1", b"GATTACAGATC");
+    let g2 = build_single_genome_index(dir.path(), "g2", b"GATTACAGATC");
+    let merged = merge_two(dir.path(), &g1, &g2);
+    merged.build_sibling_annex().expect("build_sibling_annex");
+
+    let kmer = canonical(b"GATTACAGATC");
+    let mask = annex_info_for(&merged, kmer);
+    assert_eq!(mask.siblings(), 0, "GATTACAGATC");
+    assert_eq!(mask.family_size(), 1);
+    assert!(is_minorant(kmer, mask, K));
+}
+
+#[test]
+fn sibling_annex_stats_counts_each_family_once_and_per_genome() {
+    // Reuses the one-sibling-each fixture: a single family of size 2
+    // (g1's centre-C form + g2's centre-G form), each genome carrying
+    // exactly one of the two members. Stats must report exactly one
+    // family of size 2 (`counts[1] == 1`, since index 1 = size 2), not
+    // two (which naively summing both slots would give), and both
+    // genomes represented at size 2, neither at any other size.
+    let dir = tempdir().unwrap();
+    let g1 = build_single_genome_index(dir.path(), "g1", b"AACCGCTTAAG");
+    let g2 = build_single_genome_index(dir.path(), "g2", b"AACCGGTTAAG");
+    let merged = merge_two(dir.path(), &g1, &g2);
+    merged.build_sibling_annex().expect("build_sibling_annex");
+
+    let stats = merged.sibling_annex_stats().expect("sibling_annex_stats");
+
+    assert_eq!(stats.counts, [0, 1, 0, 0], "one family of size 2, counted once");
+    assert_eq!(stats.per_genome.len(), 2);
+    for g in 0..2 {
+        assert_eq!(
+            stats.per_genome[g], [0, 1, 0, 0],
+            "genome {g} should represent exactly one size-2 family"
+        );
+    }
+}
diff --git a/src/obikpartitionner/src/merge_layer.rs b/src/obikpartitionner/src/merge_layer/mod.rs
similarity index 85%
rename from src/obikpartitionner/src/merge_layer.rs
rename to src/obikpartitionner/src/merge_layer/mod.rs
index 32750af7..a822c87c 100644
--- a/src/obikpartitionner/src/merge_layer.rs
+++ b/src/obikpartitionner/src/merge_layer/mod.rs
@@ -1,5 +1,14 @@
+//! Merging a source partition's new layer into a destination partition:
+//! de Bruijn graph union (pass 1) then column fill (pass 2).
+//!
+//! Submodules: [`src_layer`] (`SrcLayerData`, the opened-source-matrix
+//! lookup used by pass 2 here and by `rebuild_layer`). The `merge_partition`
+//! orchestration itself stays in this file — its ~400-line body is one
+//! tightly threaded pipeline (shared `Arc`/`Mutex` state across pass 1,
+//! builder setup, and pass 2), not a set of independently callable steps.
+
 use std::fs;
-use std::path::{Path, PathBuf};
+use std::path::PathBuf;
 use std::sync::{Arc, Mutex};
 
 use tracing::debug;
@@ -10,7 +19,6 @@ use obipipeline::{
 };
 
 use obicompactvec::{
-    MatrixGroupOps,
     PersistentBitMatrix, PersistentBitMatrixBuilder, PersistentBitVecBuilder,
     PersistentCompactIntMatrix, PersistentCompactIntMatrixBuilder, PersistentCompactIntVecBuilder,
 };
@@ -23,6 +31,10 @@ use crate::common::{ColBuilder, col_path_bit, col_path_int, load_meta, olm_to_sk
 use crate::graph_pipeline::{build_graph, materialize_layer};
 use crate::partition::KmerPartition;
 
+mod src_layer;
+
+pub(crate) use src_layer::SrcLayerData;
+
 // ── MergeMode ─────────────────────────────────────────────────────────────────
 
 #[derive(Debug, Clone, Copy, PartialEq, Eq)]
@@ -31,91 +43,6 @@ pub enum MergeMode {
     Count,
 }
 
-// ── SrcLayerData — opened source matrix for pass-2 lookup ─────────────────────
-
-pub(crate) enum SrcLayerData {
-    Presence(MphfOnly, PersistentBitMatrix),
-    Count(MphfOnly, PersistentCompactIntMatrix),
-}
-
-impl SrcLayerData {
-    pub(crate) fn open(layer_dir: &Path, merge_mode: MergeMode) -> SKResult<Self> {
-        let counts_dir = layer_dir.join("counts");
-        match merge_mode {
-            MergeMode::Presence => {
-                if counts_dir.exists() && !layer_dir.join("presence").exists() {
-                    let mphf = MphfOnly::open(layer_dir).map_err(|e| olm_to_sk(e, "merge"))?;
-                    let mat = PersistentCompactIntMatrix::open(layer_dir).map_err(SKError::Io)?;
-                    Ok(SrcLayerData::Count(mphf, mat))
-                } else {
-                    // presence dir exists, or neither exists → Implicit handled by open()
-                    let mphf = MphfOnly::open(layer_dir).map_err(|e| olm_to_sk(e, "merge"))?;
-                    let mat = PersistentBitMatrix::open(layer_dir).map_err(SKError::Io)?;
-                    Ok(SrcLayerData::Presence(mphf, mat))
-                }
-            }
-            MergeMode::Count => {
-                let mphf = MphfOnly::open(layer_dir).map_err(|e| olm_to_sk(e, "merge"))?;
-                if counts_dir.exists() {
-                    let mat = PersistentCompactIntMatrix::open(layer_dir).map_err(SKError::Io)?;
-                    Ok(SrcLayerData::Count(mphf, mat))
-                } else {
-                    // No counts → treat as implicit presence (all 1s)
-                    let mat = PersistentBitMatrix::open(layer_dir).map_err(SKError::Io)?;
-                    Ok(SrcLayerData::Presence(mphf, mat))
-                }
-            }
-        }
-    }
-
-    /// Return one value per source genome for `kmer`.
-    /// The caller guarantees `kmer` is in the source MPHF domain.
-    #[inline]
-    pub(crate) fn lookup(&self, kmer: CanonicalKmer, n_genomes: usize) -> Vec<u32> {
-        let mut buf = vec![0u32; n_genomes];
-        match self {
-            SrcLayerData::Presence(mphf, mat) => mat.fill_row(mphf.index(kmer), &mut buf),
-            SrcLayerData::Count(mphf, mat) => mat.fill_row(mphf.index(kmer), &mut buf),
-        }
-        buf
-    }
-
-    pub(crate) fn n_slots(&self) -> usize {
-        match self {
-            SrcLayerData::Presence(_, mat) => mat.n(),
-            SrcLayerData::Count(_, mat) => mat.n(),
-        }
-    }
-
-    /// MPHF lookup: returns the slot index for `kmer` (kmer must be in the domain).
-    #[inline]
-    pub(crate) fn slot(&self, kmer: CanonicalKmer) -> usize {
-        match self {
-            SrcLayerData::Presence(mphf, _) => mphf.index(kmer),
-            SrcLayerData::Count(mphf, _) => mphf.index(kmer),
-        }
-    }
-
-    /// Row lookup by slot index, bypassing the MPHF.
-    #[inline]
-    pub(crate) fn fill_row_by_slot(&self, slot: usize, n_genomes: usize) -> Vec<u32> {
-        let mut buf = vec![0u32; n_genomes];
-        match self {
-            SrcLayerData::Presence(_, mat) => mat.fill_row(slot, &mut buf),
-            SrcLayerData::Count(_, mat) => mat.fill_row(slot, &mut buf),
-        }
-        buf
-    }
-
-    /// Call `f` with a reference to the underlying matrix as `&dyn MatrixGroupOps`.
-    pub(crate) fn with_matrix<R>(&self, f: impl FnOnce(&dyn MatrixGroupOps) -> R) -> R {
-        match self {
-            SrcLayerData::Presence(_, mat) => f(mat),
-            SrcLayerData::Count(_, mat) => f(mat),
-        }
-    }
-}
-
 // ── helpers ───────────────────────────────────────────────────────────────────
 
 const INDEX_SUBDIR: &str = "index";
diff --git a/src/obikpartitionner/src/merge_layer/src_layer.rs b/src/obikpartitionner/src/merge_layer/src_layer.rs
new file mode 100644
index 00000000..e7e1468f
--- /dev/null
+++ b/src/obikpartitionner/src/merge_layer/src_layer.rs
@@ -0,0 +1,95 @@
+use std::path::Path;
+
+use obicompactvec::{MatrixGroupOps, PersistentBitMatrix, PersistentCompactIntMatrix};
+use obikseq::CanonicalKmer;
+use obilayeredmap::MphfOnly;
+use obiskio::{SKError, SKResult};
+
+use crate::common::olm_to_sk;
+
+use super::MergeMode;
+
+// ── SrcLayerData — opened source matrix for pass-2 lookup ─────────────────────
+
+pub(crate) enum SrcLayerData {
+    Presence(MphfOnly, PersistentBitMatrix),
+    Count(MphfOnly, PersistentCompactIntMatrix),
+}
+
+impl SrcLayerData {
+    pub(crate) fn open(layer_dir: &Path, merge_mode: MergeMode) -> SKResult<Self> {
+        let counts_dir = layer_dir.join("counts");
+        match merge_mode {
+            MergeMode::Presence => {
+                if counts_dir.exists() && !layer_dir.join("presence").exists() {
+                    let mphf = MphfOnly::open(layer_dir).map_err(|e| olm_to_sk(e, "merge"))?;
+                    let mat = PersistentCompactIntMatrix::open(layer_dir).map_err(SKError::Io)?;
+                    Ok(SrcLayerData::Count(mphf, mat))
+                } else {
+                    // presence dir exists, or neither exists → Implicit handled by open()
+                    let mphf = MphfOnly::open(layer_dir).map_err(|e| olm_to_sk(e, "merge"))?;
+                    let mat = PersistentBitMatrix::open(layer_dir).map_err(SKError::Io)?;
+                    Ok(SrcLayerData::Presence(mphf, mat))
+                }
+            }
+            MergeMode::Count => {
+                let mphf = MphfOnly::open(layer_dir).map_err(|e| olm_to_sk(e, "merge"))?;
+                if counts_dir.exists() {
+                    let mat = PersistentCompactIntMatrix::open(layer_dir).map_err(SKError::Io)?;
+                    Ok(SrcLayerData::Count(mphf, mat))
+                } else {
+                    // No counts → treat as implicit presence (all 1s)
+                    let mat = PersistentBitMatrix::open(layer_dir).map_err(SKError::Io)?;
+                    Ok(SrcLayerData::Presence(mphf, mat))
+                }
+            }
+        }
+    }
+
+    /// Return one value per source genome for `kmer`.
+    /// The caller guarantees `kmer` is in the source MPHF domain.
+    #[inline]
+    pub(crate) fn lookup(&self, kmer: CanonicalKmer, n_genomes: usize) -> Vec<u32> {
+        let mut buf = vec![0u32; n_genomes];
+        match self {
+            SrcLayerData::Presence(mphf, mat) => mat.fill_row(mphf.index(kmer), &mut buf),
+            SrcLayerData::Count(mphf, mat) => mat.fill_row(mphf.index(kmer), &mut buf),
+        }
+        buf
+    }
+
+    pub(crate) fn n_slots(&self) -> usize {
+        match self {
+            SrcLayerData::Presence(_, mat) => mat.n(),
+            SrcLayerData::Count(_, mat) => mat.n(),
+        }
+    }
+
+    /// MPHF lookup: returns the slot index for `kmer` (kmer must be in the domain).
+    #[inline]
+    pub(crate) fn slot(&self, kmer: CanonicalKmer) -> usize {
+        match self {
+            SrcLayerData::Presence(mphf, _) => mphf.index(kmer),
+            SrcLayerData::Count(mphf, _) => mphf.index(kmer),
+        }
+    }
+
+    /// Row lookup by slot index, bypassing the MPHF.
+    #[inline]
+    pub(crate) fn fill_row_by_slot(&self, slot: usize, n_genomes: usize) -> Vec<u32> {
+        let mut buf = vec![0u32; n_genomes];
+        match self {
+            SrcLayerData::Presence(_, mat) => mat.fill_row(slot, &mut buf),
+            SrcLayerData::Count(_, mat) => mat.fill_row(slot, &mut buf),
+        }
+        buf
+    }
+
+    /// Call `f` with a reference to the underlying matrix as `&dyn MatrixGroupOps`.
+    pub(crate) fn with_matrix<R>(&self, f: impl FnOnce(&dyn MatrixGroupOps) -> R) -> R {
+        match self {
+            SrcLayerData::Presence(_, mat) => f(mat),
+            SrcLayerData::Count(_, mat) => f(mat),
+        }
+    }
+}
diff --git a/src/obikpartitionner/src/partition.rs b/src/obikpartitionner/src/partition.rs
deleted file mode 100644
index 321f6cf3..00000000
--- a/src/obikpartitionner/src/partition.rs
+++ /dev/null
@@ -1,662 +0,0 @@
-use std::collections::{BTreeMap, HashMap};
-use std::fs;
-use std::io;
-use std::path::{Path, PathBuf};
-use std::time::Instant;
-use tracing::debug;
-
-use obisys::progress_bar;
-
-use cacheline_ef::{CachelineEf, CachelineEfVec};
-use epserde::ser::Serialize as EpSerialize;
-use memmap2::Mmap;
-use obicompactvec::PersistentCompactIntVecBuilder;
-use obikseq::RoutableSuperKmer;
-use obikseq::Sequence;
-use obikseq::superkmer::SuperKmer;
-use obiskio::{SKFileMeta, SKFileReader, SKFileWriter, SKResult};
-use ptr_hash::{PtrHash, PtrHashParams, bucket_fn::CubicEps, hash::Xx64};
-use rayon::prelude::*;
-use remove_dir_all::remove_dir_all;
-use sysinfo::System;
-
-use niffler::Level;
-use niffler::send::compression::Format;
-
-use crate::kmer_sort::{chunk_size_from_ram, sort_unique_kmers};
-
-type Mphf = PtrHash<u64, CubicEps, CachelineEfVec<Vec<CachelineEf>>, Xx64, Vec<u8>>;
-
-pub struct KmerSpectrum {
-    pub f0:     u64,
-    pub f1:     u64,
-    pub counts: BTreeMap<u32, u64>,
-}
-
-const SK_EXT: &str = "skmer.zst";
-pub const PARTITIONS_SUBDIR: &str = "partitions";
-
-pub struct KmerPartition {
-    root_path: PathBuf,
-    n_partitions: usize,
-    partitions_mask: u64,
-    kmer_size: usize,
-    minimizer_size: usize,
-    writers: Vec<Option<SKFileWriter>>,
-    level: Level,
-    closed: bool,
-}
-
-impl KmerPartition {
-    pub fn create<P: AsRef<Path>>(
-        path: P,
-        n_bits: usize,
-        kmer_size: usize,
-        minimizer_size: usize,
-        force: bool,
-    ) -> SKResult<Self> {
-        Self::create_with(path, n_bits, kmer_size, minimizer_size, Level::One, force)
-    }
-
-    pub fn create_with<P: AsRef<Path>>(
-        path: P,
-        n_bits: usize,
-        kmer_size: usize,
-        minimizer_size: usize,
-        level: Level,
-        force: bool,
-    ) -> SKResult<Self> {
-        let root_path = path.as_ref().to_owned();
-        if root_path.exists() {
-            if force {
-                remove_dir_all(&root_path)?;
-            } else {
-                return Err(io::Error::new(
-                    io::ErrorKind::AlreadyExists,
-                    format!(
-                        "{}: partition directory already exists",
-                        root_path.display()
-                    ),
-                )
-                .into());
-            }
-        }
-        fs::create_dir_all(root_path.join(PARTITIONS_SUBDIR))?;
-        let n_partitions = 1usize << n_bits;
-        let writers = (0..n_partitions).map(|_| None).collect();
-        let partition = Self {
-            root_path,
-            n_partitions,
-            partitions_mask: (1u64 << n_bits) - 1,
-            kmer_size,
-            minimizer_size,
-            writers,
-            level,
-            closed: false,
-        };
-        Ok(partition)
-    }
-
-    pub fn open_with_config<P: AsRef<Path>>(
-        path: P,
-        kmer_size: usize,
-        minimizer_size: usize,
-        n_bits: usize,
-    ) -> SKResult<Self> {
-        let root_path = path.as_ref().to_owned();
-        if !root_path.exists() {
-            return Err(io::Error::new(
-                io::ErrorKind::NotFound,
-                format!("{}: partition directory not found", root_path.display()),
-            )
-            .into());
-        }
-        let n_partitions = 1usize << n_bits;
-        let writers = (0..n_partitions).map(|_| None).collect();
-        Ok(Self {
-            root_path,
-            n_partitions,
-            partitions_mask: (1u64 << n_bits) - 1,
-            kmer_size,
-            minimizer_size,
-            writers,
-            level: Level::One,
-            closed: true,
-        })
-    }
-
-    /// Route and write one super-kmer to its partition file.
-    pub fn write(&mut self, rsk: RoutableSuperKmer) -> SKResult<()> {
-        self.check_not_closed()?;
-        let partition = (rsk.minimizer().seq_hash() & self.partitions_mask) as usize;
-        let sk = rsk.into_superkmer();
-        self.ensure_writer(partition)?.write(&sk)
-    }
-
-    /// Route and write a batch of super-kmers.
-    pub fn write_batch(&mut self, rsks: Vec<RoutableSuperKmer>) -> SKResult<()> {
-        self.check_not_closed()?;
-        for rsk in rsks {
-            let partition = (rsk.minimizer().seq_hash() & self.partitions_mask) as usize;
-            let sk = rsk.into_superkmer();
-            self.ensure_writer(partition)?.write(&sk)?;
-        }
-        Ok(())
-    }
-
-    pub fn flush(&mut self) -> SKResult<()> {
-        self.check_not_closed()?;
-        for writer in self.writers.iter_mut().flatten() {
-            writer.flush()?;
-        }
-        Ok(())
-    }
-
-    pub fn close(&mut self) -> SKResult<()> {
-        if self.closed {
-            return Ok(());
-        }
-        self.closed = true;
-        for writer in self.writers.iter_mut().flatten() {
-            writer.close()?;
-        }
-        Ok(())
-    }
-
-    pub fn is_open(&self) -> bool {
-        !self.closed
-    }
-
-    pub fn path(&self) -> &Path {
-        &self.root_path
-    }
-
-    /// Path of partition `i` directory.
-    pub fn part_dir(&self, i: usize) -> PathBuf {
-        self.root_path.join(PARTITIONS_SUBDIR).join(format!("part_{i:05}"))
-    }
-
-    pub fn kmer_size(&self) -> usize {
-        self.kmer_size
-    }
-
-    pub fn minimizer_size(&self) -> usize {
-        self.minimizer_size
-    }
-
-    pub fn n_partitions(&self) -> usize {
-        self.n_partitions
-    }
-
-    /// Deduplicate all `raw.{ext}` files in parallel, replacing each with a
-    /// `dereplicated.{ext}` file where identical canonical sequences are merged
-    /// and their counts summed.
-    ///
-    /// Each partition file is processed in two phases to bound memory use:
-    ///
-    /// 1. **Split** — the raw file is scattered into `2^temp_bits` temporary
-    ///    files routed by `hash(canonical_seq) & temp_mask`.  Because duplicates
-    ///    always share the same hash, they always land in the same temp file.
-    /// 2. **Merge** — each temp file is loaded fully into a `HashMap`, counts
-    ///    are accumulated in `u64` (no 24-bit overflow risk), and the result is
-    ///    appended to `dereplicated.{ext}`.
-    ///
-    /// If a merged count exceeds the 24-bit header limit, the sequence is
-    /// emitted as multiple records whose counts sum to the true total.
-    ///
-    /// `temp_bits` controls the split fan-out (`2^temp_bits` temp files per
-    /// partition).  Higher values reduce per-temp-file memory at the cost of
-    /// more temporary file descriptors — all managed by the global fd pool.
-    pub fn dereplicate(&self) -> SKResult<()> {
-        let level = self.level;
-        let sys = System::new_all();
-        // available_memory() can return 0 on macOS when the compressor page count exceeds
-        // free+inactive+purgeable pages (sysinfo saturating_sub). Fall back to half of total.
-        let available = match sys.available_memory() {
-            0 => sys.total_memory() / 2,
-            n => n,
-        };
-        let n_threads = rayon::current_num_threads().max(1) as u64;
-        let available_per_thread = available / n_threads;
-
-        let pb = progress_bar("dereplication", self.n_partitions as u64, "partitions");
-
-        let results: Vec<SKResult<()>> = (0..self.n_partitions)
-            .into_par_iter()
-            .map(|i| {
-                let dir = self.part_dir(i);
-                if !dir.exists() {
-                    pb.inc(1);
-                    return Ok(());
-                }
-                let raw_path = dir.join(format!("raw.{SK_EXT}"));
-                let t = Instant::now();
-                let n_buckets = optimal_buckets(&raw_path, available_per_thread);
-                let result = dereplicate_partition(&dir, level, n_buckets);
-                pb.set_message(format!("last {:.0}ms", t.elapsed().as_millis()));
-                pb.inc(1);
-                result
-            })
-            .collect();
-
-        pb.finish_and_clear();
-        for r in results {
-            r?;
-        }
-        Ok(())
-    }
-
-    /// For each partition that has a `dereplicated.{ext}` file:
-    /// 1. Enumerates all unique canonical kmers (two passes over the file).
-    /// 2. Builds a provisional MPHF (FMPHGO) over those kmers.
-    /// 3. Writes a flat binary count file (`counts1.bin`, one `u32` per slot,
-    ///    memory-mapped) accumulating kmer abundances from the superkmer counts.
-    /// 4. Persists the MPHF to `mphf1.bin` for downstream use.
-    ///
-    /// Returns the aggregated `KmerSpectrum`. Per-partition spectrum files are
-    /// deleted after aggregation unless `keep_partial` is true.
-    ///
-    /// Partitions are processed in parallel via Rayon (one task per thread).
-    /// Peak memory per partition is ~80 MB, so n_threads partitions run simultaneously.
-    pub fn count_kmer(&self, keep_partial: bool) -> SKResult<KmerSpectrum> {
-        let sys = System::new_all();
-        let available = match sys.available_memory() {
-            0 => sys.total_memory() / 2,
-            n => n,
-        };
-        let n_threads = rayon::current_num_threads().max(1) as u64;
-        let chunk_kmers = chunk_size_from_ram(available / n_threads);
-
-        let pb = progress_bar("counting", self.n_partitions as u64, "partitions");
-
-        let results: Vec<SKResult<()>> = (0..self.n_partitions)
-            .into_par_iter()
-            .map(|i| {
-                let dir = self.part_dir(i);
-                let dedup_path = dir.join(format!("dereplicated.{SK_EXT}"));
-                if !dedup_path.exists() {
-                    pb.inc(1);
-                    return Ok(());
-                }
-                let t = Instant::now();
-                let result = count_partition(&dir, &dedup_path, chunk_kmers);
-                pb.set_message(format!("last {:.0}ms", t.elapsed().as_millis()));
-                pb.inc(1);
-                result
-            })
-            .collect();
-
-        pb.finish_and_clear();
-        for r in results {
-            r?;
-        }
-
-        // Aggregate per-partition spectra.
-        let mut counts: BTreeMap<u32, u64> = BTreeMap::new();
-        let mut f0: u64 = 0;
-        let mut f1: u64 = 0;
-
-        for i in 0..self.n_partitions {
-            let path = self.part_dir(i).join("kmer_spectrum_raw.json");
-            if !path.exists() {
-                continue;
-            }
-            let v: serde_json::Value =
-                serde_json::from_str(&fs::read_to_string(&path)?).map_err(io::Error::other)?;
-            f0 += v["f0"].as_u64().unwrap_or(0);
-            f1 += v["f1"].as_u64().unwrap_or(0);
-            if let Some(obj) = v["spectrum"].as_object() {
-                for (c_str, freq) in obj {
-                    if let (Ok(c), Some(f)) = (c_str.parse::<u32>(), freq.as_u64()) {
-                        *counts.entry(c).or_insert(0) += f;
-                    }
-                }
-            }
-            if !keep_partial {
-                let _ = fs::remove_file(&path);
-            }
-        }
-
-        Ok(KmerSpectrum { f0, f1, counts })
-    }
-
-    // ── private ───────────────────────────────────────────────────────────────
-
-    fn check_not_closed(&self) -> SKResult<()> {
-        if self.closed {
-            Err(io::Error::new(io::ErrorKind::BrokenPipe, "write to closed KmerPartition").into())
-        } else {
-            Ok(())
-        }
-    }
-
-    fn ensure_writer(&mut self, partition: usize) -> SKResult<&mut SKFileWriter> {
-        if self.writers[partition].is_none() {
-            let dir = self.root_path.join(PARTITIONS_SUBDIR).join(format!("part_{:05}", partition));
-            fs::create_dir_all(&dir)?;
-            let file_path = dir.join(format!("raw.{SK_EXT}"));
-            let writer = SKFileWriter::create_with(file_path, Format::Zstd, self.level)?;
-            self.writers[partition] = Some(writer);
-        }
-        Ok(self.writers[partition].as_mut().unwrap())
-    }
-}
-
-// ── free helpers ─────────────────────────────────────────────────────────────
-
-/// Estimate the number of in-memory buckets needed to deduplicate the partition
-/// file at `raw_path` given `available_bytes` of free RAM.
-///
-/// Memory per HashMap entry:
-///   key Box (1 + avg_seq_bytes) + SuperKmer header (4 B) + avg seq bytes + u64 count (8 B),
-///   multiplied by 1.5 for hashbrown load-factor overhead.
-///
-/// Returns 1 if the partition fits comfortably in memory (no split needed).
-/// Always returns a power of two.
-/// Remove a SuperKmer file and its sidecar (if present).
-fn remove_skmer_file(path: &Path) -> SKResult<()> {
-    fs::remove_file(path)?;
-    let sidecar = SKFileMeta::sidecar_path(path);
-    match fs::remove_file(&sidecar) {
-        Ok(()) => {}
-        Err(e) if e.kind() == io::ErrorKind::NotFound => {}
-        Err(e) => return Err(e.into()),
-    }
-    Ok(())
-}
-
-fn optimal_buckets(raw_path: &Path, available_bytes: u64) -> usize {
-    // Use 60 % of available RAM to leave headroom for the rest of the process.
-    let budget = (available_bytes as f64 * 0.60) as u64;
-
-    let meta = match SKFileMeta::read(raw_path) {
-        Ok(Some(m)) if m.instances > 0 => m,
-        _ => return 1,
-    };
-
-    let avg_seq_bytes = ((meta.length_sum + meta.instances - 1) / meta.instances + 3) / 4;
-    // SuperKmer: header (4 B) + Box<[u8]> ptr+len (16 B) + heap seq bytes; value: u64 (8 B); ×1.5 for hashbrown overhead.
-    let bytes_per_entry = ((4 + 16 + avg_seq_bytes + 8) as f64 * 1.5) as u64;
-    let estimated = meta.instances * bytes_per_entry;
-
-    if estimated <= budget {
-        debug!("Dereplication: estimated={estimated} budget={budget} n_temp=1");
-        return 1;
-    }
-
-    // Round up to the next power of two.
-    let n = (estimated + budget - 1) / budget;
-    debug!("Dereplication: estimated={estimated} budget={budget} n_temp={n}");
-    n.next_power_of_two() as usize
-}
-
-
-/// Maximum value that fits in the 24-bit COUNT field of a SuperKmer header.
-const MAX_SK_COUNT: u64 = (1 << 24) - 1;
-
-/// Deduplicate one partition directory in place (two-phase split + merge).
-fn dereplicate_partition(dir: &Path, level: Level, n_temp: usize) -> SKResult<()> {
-    let raw_path = dir.join(format!("raw.{SK_EXT}"));
-    if !raw_path.exists() {
-        return Ok(());
-    }
-
-    let out_path = dir.join(format!("dereplicated.{SK_EXT}"));
-    let mut writer = SKFileWriter::create_with(&out_path, Format::Zstd, level)?;
-
-    if n_temp == 1 {
-        // ── Direct path: partition fits in memory, no split needed ────────────
-        let map = load_bucket(&raw_path)?;
-        remove_skmer_file(&raw_path)?;
-        flush_map(map, &mut writer)?;
-    } else {
-        // ── Phase 1: split raw file into temp buckets ─────────────────────────
-        let temp_mask = (n_temp as u64) - 1;
-        let temp_paths: Vec<PathBuf> = (0..n_temp)
-            .map(|j| dir.join(format!("temp_{j:04}.{SK_EXT}")))
-            .collect();
-
-        {
-            let mut writers: Vec<SKFileWriter> = temp_paths
-                .iter()
-                .map(|p| SKFileWriter::create_with(p, Format::Zstd, level))
-                .collect::<SKResult<_>>()?;
-
-            let mut reader = SKFileReader::open(&raw_path)?;
-            while let Some(sk) = reader.read()? {
-                let bucket = (sk.seq_hash() & temp_mask) as usize;
-                writers[bucket].write(&sk)?;
-            }
-            for w in &mut writers {
-                w.close()?;
-            }
-        }
-        remove_skmer_file(&raw_path)?;
-
-        // ── Phase 2: merge each temp bucket into the output ───────────────────
-        for temp_path in &temp_paths {
-            let map = load_bucket(temp_path)?;
-            remove_skmer_file(temp_path)?;
-            flush_map(map, &mut writer)?;
-        }
-    }
-
-    writer.close()?;
-    Ok(())
-}
-
-/// Read a SuperKmer file into a deduplication map (already canonical).
-fn load_bucket(path: &Path) -> SKResult<HashMap<SuperKmer, u64>> {
-    let capacity = SKFileMeta::read(path)
-        .ok()
-        .flatten()
-        .map(|m| m.instances as usize)
-        .unwrap_or(0);
-    let mut map: HashMap<SuperKmer, u64> = HashMap::with_capacity(capacity);
-    let mut reader = SKFileReader::open(path)?;
-    while let Some(sk) = reader.read()? {
-        let count = sk.count() as u64;
-        *map.entry(sk).or_insert(0) += count;
-    }
-    Ok(map)
-}
-
-/// Write all entries of a deduplication map to `writer`, splitting oversized counts.
-fn flush_map(map: HashMap<SuperKmer, u64>, writer: &mut SKFileWriter) -> SKResult<()> {
-    for (mut sk, mut total) in map {
-        while total > MAX_SK_COUNT {
-            sk.set_count(MAX_SK_COUNT as u32);
-            writer.write(&sk)?;
-            total -= MAX_SK_COUNT;
-        }
-        sk.set_count(total as u32);
-        writer.write(&sk)?;
-    }
-    Ok(())
-}
-
-fn build_mphf(unique_path: &Path, f0: usize) -> io::Result<Mphf> {
-    let file = fs::File::open(unique_path)?;
-    let mmap = unsafe { Mmap::map(&file)? };
-    let kmers: &[u64] = unsafe {
-        std::slice::from_raw_parts(mmap.as_ptr() as *const u64, f0)
-    };
-    // Sequential constructor: the outer par_iter over partitions already saturates
-    // the Rayon pool. new_from_par_iter would get no additional threads and adds
-    // coordination overhead. try_new accesses the same mmap'd pages at zero extra cost.
-    Mphf::try_new(kmers, PtrHashParams::<CubicEps>::default())
-        .ok_or_else(|| io::Error::other("ptr_hash construction failed"))
-}
-
-fn count_partition(dir: &Path, dedup_path: &Path, chunk_kmers: usize) -> SKResult<()> {
-    let unique_path = dir.join("sorted_unique.bin");
-    let f0 = sort_unique_kmers(dedup_path, dir, &unique_path, chunk_kmers)?;
-    if f0 == 0 {
-        return Ok(());
-    }
-    debug!("{}: f0={f0} unique kmers sorted", dir.display());
-
-    let mphf = build_mphf(&unique_path, f0)?;
-    fs::remove_file(&unique_path)?;
-
-    let counts_path = dir.join("counts1.bin");
-    let mut builder = PersistentCompactIntVecBuilder::new(f0, &counts_path)?;
-
-    {
-        let mut reader = SKFileReader::open(dedup_path)?;
-        while let Some(sk) = reader.read()? {
-            let sk_count = sk.count();
-            for kmer in sk.iter_canonical_kmers() {
-                let slot = mphf.index(&kmer.raw());
-                builder.set(slot, builder.get(slot).saturating_add(sk_count));
-            }
-        }
-    }
-
-    let mut spectrum: BTreeMap<u32, u64> = BTreeMap::new();
-    for slot in 0..f0 {
-        let c = builder.get(slot);
-        if c > 0 {
-            *spectrum.entry(c).or_insert(0) += 1;
-        }
-    }
-    let f1: u64 = spectrum.iter().map(|(&c, &f)| c as u64 * f).sum();
-    builder.close()?;
-
-    let spectrum_map: BTreeMap<String, u64> = spectrum
-        .iter()
-        .map(|(&c, &f)| (format!("{c:010}"), f))
-        .collect();
-    serde_json::to_writer_pretty(
-        fs::File::create(dir.join("kmer_spectrum_raw.json"))?,
-        &serde_json::json!({ "f0": f0 as u64, "f1": f1, "spectrum": &spectrum_map }),
-    )
-    .map_err(io::Error::other)?;
-
-    EpSerialize::store(&mphf, &dir.join("mphf1.bin"))
-        .map_err(|e| io::Error::other(e.to_string()))?;
-
-    Ok(())
-}
-
-impl Drop for KmerPartition {
-    fn drop(&mut self) {
-        let _ = self.close();
-    }
-}
-
-// ── integration tests ─────────────────────────────────────────────────────────
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use std::collections::HashMap;
-
-    use obikrope::Rope;
-    use obikseq::SuperKmer;
-    use obiskbuilder::build_superkmers;
-
-    const K: usize = 11;
-    const M: usize = 5;
-
-    fn setup() {
-        obikseq::params::set_k(K);
-        obikseq::params::set_m(M);
-    }
-
-    /// Direct canonical k-mer counts from ASCII sequences — ground truth.
-    fn direct_counts(seqs: &[&[u8]]) -> (u64, u64) {
-        let mut counts: HashMap<Vec<u8>, u64> = HashMap::new();
-        for seq in seqs {
-            for i in 0..seq.len().saturating_sub(K - 1) {
-                let km = SuperKmer::from_ascii(&seq[i..i + K]).to_ascii();
-                *counts.entry(km).or_insert(0) += 1;
-            }
-        }
-        let f0 = counts.len() as u64;
-        let f1: u64 = counts.values().sum();
-        (f0, f1)
-    }
-
-    /// Run the full pipeline on a list of sequences and return (f0, f1) from
-    /// the `kmer_spectrum_raw.json` produced by `count_partition`.
-    fn pipeline_counts(seqs: &[&[u8]]) -> (u64, u64) {
-        setup();
-
-        let mut rope_data: Vec<u8> = Vec::new();
-        for seq in seqs {
-            rope_data.extend_from_slice(seq);
-            rope_data.push(0x00);
-        }
-        let mut rope = Rope::new(None);
-        rope.push(rope_data);
-
-        let superkmers: Vec<_> = build_superkmers(rope, K, 1, 0.0);
-
-        let dir = tempfile::tempdir().unwrap();
-        let mut kp = KmerPartition::create(dir.path(), 0, K, M, true).unwrap();
-        kp.write_batch(superkmers).unwrap();
-        kp.close().unwrap();
-        kp.dereplicate().unwrap();
-
-        let part_dir = dir.path().join(PARTITIONS_SUBDIR).join("part_00000");
-        let dedup_path = part_dir.join("dereplicated.skmer.zst");
-        if !dedup_path.exists() {
-            return (0, 0);
-        }
-        count_partition(&part_dir, &dedup_path, 1 << 20).unwrap();
-
-        let spec: serde_json::Value = serde_json::from_reader(
-            fs::File::open(part_dir.join("kmer_spectrum_raw.json")).unwrap(),
-        ).unwrap();
-        let f0 = spec["f0"].as_u64().unwrap_or(0);
-        let f1 = spec["f1"].as_u64().unwrap_or(0);
-        (f0, f1)
-    }
-
-    #[test]
-    fn single_sequence_f0_f1_match() {
-        let seqs: &[&[u8]] = &[b"ACGTACGTACGTACGTACGT"];
-        let (ef0, ef1) = direct_counts(seqs);
-        let (gf0, gf1) = pipeline_counts(seqs);
-        assert_eq!(gf0, ef0, "f0 wrong: expected {ef0}, got {gf0}");
-        assert_eq!(gf1, ef1, "f1 wrong: expected {ef1}, got {gf1}");
-    }
-
-    #[test]
-    fn two_sequences_f0_f1_match() {
-        let seqs: &[&[u8]] = &[
-            b"ACGTACGTACGTACGTACGT",
-            b"TGCATGCATGCATGCATGCA",
-        ];
-        let (ef0, ef1) = direct_counts(seqs);
-        let (gf0, gf1) = pipeline_counts(seqs);
-        assert_eq!(gf0, ef0, "f0 wrong: expected {ef0}, got {gf0}");
-        assert_eq!(gf1, ef1, "f1 wrong: expected {ef1}, got {gf1}");
-    }
-
-    #[test]
-    fn repeated_sequence_f1_doubles() {
-        let seq = b"ACGTACGTACGTACGTACGT";
-        let seqs: &[&[u8]] = &[seq, seq];
-        let (ef0, ef1) = direct_counts(seqs);
-        let (gf0, gf1) = pipeline_counts(seqs);
-        assert_eq!(gf0, ef0, "f0 wrong: expected {ef0}, got {gf0}");
-        assert_eq!(gf1, ef1, "f1 wrong: expected {ef1}, got {gf1}");
-    }
-
-    #[test]
-    fn many_sequences_f0_f1_match() {
-        // 20 distinct sequences of length 40 — forces multiple super-kmers and
-        // multiple minimizer boundaries per sequence.
-        let bases = b"ACGT";
-        let seqs: Vec<Vec<u8>> = (0..20u32)
-            .map(|i| (0..40).map(|j| bases[((i * 7 + j * 3) % 4) as usize]).collect())
-            .collect();
-        let seq_refs: Vec<&[u8]> = seqs.iter().map(|v| v.as_slice()).collect();
-        let (ef0, ef1) = direct_counts(&seq_refs);
-        let (gf0, gf1) = pipeline_counts(&seq_refs);
-        assert_eq!(gf0, ef0, "f0 wrong: expected {ef0}, got {gf0}");
-        assert_eq!(gf1, ef1, "f1 wrong: expected {ef1}, got {gf1}");
-    }
-}
diff --git a/src/obikpartitionner/src/partition/count.rs b/src/obikpartitionner/src/partition/count.rs
new file mode 100644
index 00000000..4cd33f05
--- /dev/null
+++ b/src/obikpartitionner/src/partition/count.rs
@@ -0,0 +1,80 @@
+use std::collections::BTreeMap;
+use std::fs;
+use std::io;
+use std::path::Path;
+
+use cacheline_ef::{CachelineEf, CachelineEfVec};
+use epserde::ser::Serialize as EpSerialize;
+use memmap2::Mmap;
+use obicompactvec::PersistentCompactIntVecBuilder;
+use obiskio::{SKFileReader, SKResult};
+use ptr_hash::{PtrHash, PtrHashParams, bucket_fn::CubicEps, hash::Xx64};
+use tracing::debug;
+
+use crate::kmer_sort::sort_unique_kmers;
+
+pub(super) type Mphf = PtrHash<u64, CubicEps, CachelineEfVec<Vec<CachelineEf>>, Xx64, Vec<u8>>;
+
+fn build_mphf(unique_path: &Path, f0: usize) -> io::Result<Mphf> {
+    let file = fs::File::open(unique_path)?;
+    let mmap = unsafe { Mmap::map(&file)? };
+    let kmers: &[u64] = unsafe {
+        std::slice::from_raw_parts(mmap.as_ptr() as *const u64, f0)
+    };
+    // Sequential constructor: the outer par_iter over partitions already saturates
+    // the Rayon pool. new_from_par_iter would get no additional threads and adds
+    // coordination overhead. try_new accesses the same mmap'd pages at zero extra cost.
+    Mphf::try_new(kmers, PtrHashParams::<CubicEps>::default())
+        .ok_or_else(|| io::Error::other("ptr_hash construction failed"))
+}
+
+pub(super) fn count_partition(dir: &Path, dedup_path: &Path, chunk_kmers: usize) -> SKResult<()> {
+    let unique_path = dir.join("sorted_unique.bin");
+    let f0 = sort_unique_kmers(dedup_path, dir, &unique_path, chunk_kmers)?;
+    if f0 == 0 {
+        return Ok(());
+    }
+    debug!("{}: f0={f0} unique kmers sorted", dir.display());
+
+    let mphf = build_mphf(&unique_path, f0)?;
+    fs::remove_file(&unique_path)?;
+
+    let counts_path = dir.join("counts1.bin");
+    let mut builder = PersistentCompactIntVecBuilder::new(f0, &counts_path)?;
+
+    {
+        let mut reader = SKFileReader::open(dedup_path)?;
+        while let Some(sk) = reader.read()? {
+            let sk_count = sk.count();
+            for kmer in sk.iter_canonical_kmers() {
+                let slot = mphf.index(&kmer.raw());
+                builder.set(slot, builder.get(slot).saturating_add(sk_count));
+            }
+        }
+    }
+
+    let mut spectrum: BTreeMap<u32, u64> = BTreeMap::new();
+    for slot in 0..f0 {
+        let c = builder.get(slot);
+        if c > 0 {
+            *spectrum.entry(c).or_insert(0) += 1;
+        }
+    }
+    let f1: u64 = spectrum.iter().map(|(&c, &f)| c as u64 * f).sum();
+    builder.close()?;
+
+    let spectrum_map: BTreeMap<String, u64> = spectrum
+        .iter()
+        .map(|(&c, &f)| (format!("{c:010}"), f))
+        .collect();
+    serde_json::to_writer_pretty(
+        fs::File::create(dir.join("kmer_spectrum_raw.json"))?,
+        &serde_json::json!({ "f0": f0 as u64, "f1": f1, "spectrum": &spectrum_map }),
+    )
+    .map_err(io::Error::other)?;
+
+    EpSerialize::store(&mphf, &dir.join("mphf1.bin"))
+        .map_err(|e| io::Error::other(e.to_string()))?;
+
+    Ok(())
+}
diff --git a/src/obikpartitionner/src/partition/dereplicate.rs b/src/obikpartitionner/src/partition/dereplicate.rs
new file mode 100644
index 00000000..912e6424
--- /dev/null
+++ b/src/obikpartitionner/src/partition/dereplicate.rs
@@ -0,0 +1,144 @@
+use std::collections::HashMap;
+use std::fs;
+use std::io;
+use std::path::{Path, PathBuf};
+
+use tracing::debug;
+
+use niffler::Level;
+use niffler::send::compression::Format;
+use obikseq::Sequence;
+use obikseq::superkmer::SuperKmer;
+use obiskio::{SKFileMeta, SKFileReader, SKFileWriter, SKResult};
+
+use super::SK_EXT;
+
+/// Estimate the number of in-memory buckets needed to deduplicate the partition
+/// file at `raw_path` given `available_bytes` of free RAM.
+///
+/// Memory per HashMap entry:
+///   key Box (1 + avg_seq_bytes) + SuperKmer header (4 B) + avg seq bytes + u64 count (8 B),
+///   multiplied by 1.5 for hashbrown load-factor overhead.
+///
+/// Returns 1 if the partition fits comfortably in memory (no split needed).
+/// Always returns a power of two.
+pub(super) fn optimal_buckets(raw_path: &Path, available_bytes: u64) -> usize {
+    // Use 60 % of available RAM to leave headroom for the rest of the process.
+    let budget = (available_bytes as f64 * 0.60) as u64;
+
+    let meta = match SKFileMeta::read(raw_path) {
+        Ok(Some(m)) if m.instances > 0 => m,
+        _ => return 1,
+    };
+
+    let avg_seq_bytes = ((meta.length_sum + meta.instances - 1) / meta.instances + 3) / 4;
+    // SuperKmer: header (4 B) + Box<[u8]> ptr+len (16 B) + heap seq bytes; value: u64 (8 B); ×1.5 for hashbrown overhead.
+    let bytes_per_entry = ((4 + 16 + avg_seq_bytes + 8) as f64 * 1.5) as u64;
+    let estimated = meta.instances * bytes_per_entry;
+
+    if estimated <= budget {
+        debug!("Dereplication: estimated={estimated} budget={budget} n_temp=1");
+        return 1;
+    }
+
+    // Round up to the next power of two.
+    let n = (estimated + budget - 1) / budget;
+    debug!("Dereplication: estimated={estimated} budget={budget} n_temp={n}");
+    n.next_power_of_two() as usize
+}
+
+/// Remove a SuperKmer file and its sidecar (if present).
+fn remove_skmer_file(path: &Path) -> SKResult<()> {
+    fs::remove_file(path)?;
+    let sidecar = SKFileMeta::sidecar_path(path);
+    match fs::remove_file(&sidecar) {
+        Ok(()) => {}
+        Err(e) if e.kind() == io::ErrorKind::NotFound => {}
+        Err(e) => return Err(e.into()),
+    }
+    Ok(())
+}
+
+/// Maximum value that fits in the 24-bit COUNT field of a SuperKmer header.
+const MAX_SK_COUNT: u64 = (1 << 24) - 1;
+
+/// Deduplicate one partition directory in place (two-phase split + merge).
+pub(super) fn dereplicate_partition(dir: &Path, level: Level, n_temp: usize) -> SKResult<()> {
+    let raw_path = dir.join(format!("raw.{SK_EXT}"));
+    if !raw_path.exists() {
+        return Ok(());
+    }
+
+    let out_path = dir.join(format!("dereplicated.{SK_EXT}"));
+    let mut writer = SKFileWriter::create_with(&out_path, Format::Zstd, level)?;
+
+    if n_temp == 1 {
+        // ── Direct path: partition fits in memory, no split needed ────────────
+        let map = load_bucket(&raw_path)?;
+        remove_skmer_file(&raw_path)?;
+        flush_map(map, &mut writer)?;
+    } else {
+        // ── Phase 1: split raw file into temp buckets ─────────────────────────
+        let temp_mask = (n_temp as u64) - 1;
+        let temp_paths: Vec<PathBuf> = (0..n_temp)
+            .map(|j| dir.join(format!("temp_{j:04}.{SK_EXT}")))
+            .collect();
+
+        {
+            let mut writers: Vec<SKFileWriter> = temp_paths
+                .iter()
+                .map(|p| SKFileWriter::create_with(p, Format::Zstd, level))
+                .collect::<SKResult<_>>()?;
+
+            let mut reader = SKFileReader::open(&raw_path)?;
+            while let Some(sk) = reader.read()? {
+                let bucket = (sk.seq_hash() & temp_mask) as usize;
+                writers[bucket].write(&sk)?;
+            }
+            for w in &mut writers {
+                w.close()?;
+            }
+        }
+        remove_skmer_file(&raw_path)?;
+
+        // ── Phase 2: merge each temp bucket into the output ───────────────────
+        for temp_path in &temp_paths {
+            let map = load_bucket(temp_path)?;
+            remove_skmer_file(temp_path)?;
+            flush_map(map, &mut writer)?;
+        }
+    }
+
+    writer.close()?;
+    Ok(())
+}
+
+/// Read a SuperKmer file into a deduplication map (already canonical).
+fn load_bucket(path: &Path) -> SKResult<HashMap<SuperKmer, u64>> {
+    let capacity = SKFileMeta::read(path)
+        .ok()
+        .flatten()
+        .map(|m| m.instances as usize)
+        .unwrap_or(0);
+    let mut map: HashMap<SuperKmer, u64> = HashMap::with_capacity(capacity);
+    let mut reader = SKFileReader::open(path)?;
+    while let Some(sk) = reader.read()? {
+        let count = sk.count() as u64;
+        *map.entry(sk).or_insert(0) += count;
+    }
+    Ok(map)
+}
+
+/// Write all entries of a deduplication map to `writer`, splitting oversized counts.
+fn flush_map(map: HashMap<SuperKmer, u64>, writer: &mut SKFileWriter) -> SKResult<()> {
+    for (mut sk, mut total) in map {
+        while total > MAX_SK_COUNT {
+            sk.set_count(MAX_SK_COUNT as u32);
+            writer.write(&sk)?;
+            total -= MAX_SK_COUNT;
+        }
+        sk.set_count(total as u32);
+        writer.write(&sk)?;
+    }
+    Ok(())
+}
diff --git a/src/obikpartitionner/src/partition/kmer_partition.rs b/src/obikpartitionner/src/partition/kmer_partition.rs
new file mode 100644
index 00000000..e24aad53
--- /dev/null
+++ b/src/obikpartitionner/src/partition/kmer_partition.rs
@@ -0,0 +1,341 @@
+use std::collections::BTreeMap;
+use std::fs;
+use std::io;
+use std::path::{Path, PathBuf};
+use std::time::Instant;
+
+use obisys::progress_bar;
+
+use obikseq::RoutableSuperKmer;
+use obiskio::SKResult;
+use rayon::prelude::*;
+use remove_dir_all::remove_dir_all;
+use sysinfo::System;
+
+use niffler::Level;
+use niffler::send::compression::Format;
+use obiskio::SKFileWriter;
+
+use crate::kmer_sort::chunk_size_from_ram;
+
+use super::count::count_partition;
+use super::dereplicate::{dereplicate_partition, optimal_buckets};
+use super::{PARTITIONS_SUBDIR, SK_EXT};
+
+pub struct KmerSpectrum {
+    pub f0:     u64,
+    pub f1:     u64,
+    pub counts: BTreeMap<u32, u64>,
+}
+
+pub struct KmerPartition {
+    root_path: PathBuf,
+    n_partitions: usize,
+    partitions_mask: u64,
+    kmer_size: usize,
+    minimizer_size: usize,
+    writers: Vec<Option<SKFileWriter>>,
+    level: Level,
+    closed: bool,
+}
+
+impl KmerPartition {
+    pub fn create<P: AsRef<Path>>(
+        path: P,
+        n_bits: usize,
+        kmer_size: usize,
+        minimizer_size: usize,
+        force: bool,
+    ) -> SKResult<Self> {
+        Self::create_with(path, n_bits, kmer_size, minimizer_size, Level::One, force)
+    }
+
+    pub fn create_with<P: AsRef<Path>>(
+        path: P,
+        n_bits: usize,
+        kmer_size: usize,
+        minimizer_size: usize,
+        level: Level,
+        force: bool,
+    ) -> SKResult<Self> {
+        let root_path = path.as_ref().to_owned();
+        if root_path.exists() {
+            if force {
+                remove_dir_all(&root_path)?;
+            } else {
+                return Err(io::Error::new(
+                    io::ErrorKind::AlreadyExists,
+                    format!(
+                        "{}: partition directory already exists",
+                        root_path.display()
+                    ),
+                )
+                .into());
+            }
+        }
+        fs::create_dir_all(root_path.join(PARTITIONS_SUBDIR))?;
+        let n_partitions = 1usize << n_bits;
+        let writers = (0..n_partitions).map(|_| None).collect();
+        let partition = Self {
+            root_path,
+            n_partitions,
+            partitions_mask: (1u64 << n_bits) - 1,
+            kmer_size,
+            minimizer_size,
+            writers,
+            level,
+            closed: false,
+        };
+        Ok(partition)
+    }
+
+    pub fn open_with_config<P: AsRef<Path>>(
+        path: P,
+        kmer_size: usize,
+        minimizer_size: usize,
+        n_bits: usize,
+    ) -> SKResult<Self> {
+        let root_path = path.as_ref().to_owned();
+        if !root_path.exists() {
+            return Err(io::Error::new(
+                io::ErrorKind::NotFound,
+                format!("{}: partition directory not found", root_path.display()),
+            )
+            .into());
+        }
+        let n_partitions = 1usize << n_bits;
+        let writers = (0..n_partitions).map(|_| None).collect();
+        Ok(Self {
+            root_path,
+            n_partitions,
+            partitions_mask: (1u64 << n_bits) - 1,
+            kmer_size,
+            minimizer_size,
+            writers,
+            level: Level::One,
+            closed: true,
+        })
+    }
+
+    /// Route and write one super-kmer to its partition file.
+    pub fn write(&mut self, rsk: RoutableSuperKmer) -> SKResult<()> {
+        self.check_not_closed()?;
+        let partition = (rsk.minimizer().seq_hash() & self.partitions_mask) as usize;
+        let sk = rsk.into_superkmer();
+        self.ensure_writer(partition)?.write(&sk)
+    }
+
+    /// Route and write a batch of super-kmers.
+    pub fn write_batch(&mut self, rsks: Vec<RoutableSuperKmer>) -> SKResult<()> {
+        self.check_not_closed()?;
+        for rsk in rsks {
+            let partition = (rsk.minimizer().seq_hash() & self.partitions_mask) as usize;
+            let sk = rsk.into_superkmer();
+            self.ensure_writer(partition)?.write(&sk)?;
+        }
+        Ok(())
+    }
+
+    pub fn flush(&mut self) -> SKResult<()> {
+        self.check_not_closed()?;
+        for writer in self.writers.iter_mut().flatten() {
+            writer.flush()?;
+        }
+        Ok(())
+    }
+
+    pub fn close(&mut self) -> SKResult<()> {
+        if self.closed {
+            return Ok(());
+        }
+        self.closed = true;
+        for writer in self.writers.iter_mut().flatten() {
+            writer.close()?;
+        }
+        Ok(())
+    }
+
+    pub fn is_open(&self) -> bool {
+        !self.closed
+    }
+
+    pub fn path(&self) -> &Path {
+        &self.root_path
+    }
+
+    /// Path of partition `i` directory.
+    pub fn part_dir(&self, i: usize) -> PathBuf {
+        self.root_path.join(PARTITIONS_SUBDIR).join(format!("part_{i:05}"))
+    }
+
+    pub fn kmer_size(&self) -> usize {
+        self.kmer_size
+    }
+
+    pub fn minimizer_size(&self) -> usize {
+        self.minimizer_size
+    }
+
+    pub fn n_partitions(&self) -> usize {
+        self.n_partitions
+    }
+
+    /// Deduplicate all `raw.{ext}` files in parallel, replacing each with a
+    /// `dereplicated.{ext}` file where identical canonical sequences are merged
+    /// and their counts summed.
+    ///
+    /// Each partition file is processed in two phases to bound memory use:
+    ///
+    /// 1. **Split** — the raw file is scattered into `2^temp_bits` temporary
+    ///    files routed by `hash(canonical_seq) & temp_mask`.  Because duplicates
+    ///    always share the same hash, they always land in the same temp file.
+    /// 2. **Merge** — each temp file is loaded fully into a `HashMap`, counts
+    ///    are accumulated in `u64` (no 24-bit overflow risk), and the result is
+    ///    appended to `dereplicated.{ext}`.
+    ///
+    /// If a merged count exceeds the 24-bit header limit, the sequence is
+    /// emitted as multiple records whose counts sum to the true total.
+    ///
+    /// `temp_bits` controls the split fan-out (`2^temp_bits` temp files per
+    /// partition).  Higher values reduce per-temp-file memory at the cost of
+    /// more temporary file descriptors — all managed by the global fd pool.
+    pub fn dereplicate(&self) -> SKResult<()> {
+        let level = self.level;
+        let sys = System::new_all();
+        // available_memory() can return 0 on macOS when the compressor page count exceeds
+        // free+inactive+purgeable pages (sysinfo saturating_sub). Fall back to half of total.
+        let available = match sys.available_memory() {
+            0 => sys.total_memory() / 2,
+            n => n,
+        };
+        let n_threads = rayon::current_num_threads().max(1) as u64;
+        let available_per_thread = available / n_threads;
+
+        let pb = progress_bar("dereplication", self.n_partitions as u64, "partitions");
+
+        let results: Vec<SKResult<()>> = (0..self.n_partitions)
+            .into_par_iter()
+            .map(|i| {
+                let dir = self.part_dir(i);
+                if !dir.exists() {
+                    pb.inc(1);
+                    return Ok(());
+                }
+                let raw_path = dir.join(format!("raw.{SK_EXT}"));
+                let t = Instant::now();
+                let n_buckets = optimal_buckets(&raw_path, available_per_thread);
+                let result = dereplicate_partition(&dir, level, n_buckets);
+                pb.set_message(format!("last {:.0}ms", t.elapsed().as_millis()));
+                pb.inc(1);
+                result
+            })
+            .collect();
+
+        pb.finish_and_clear();
+        for r in results {
+            r?;
+        }
+        Ok(())
+    }
+
+    /// For each partition that has a `dereplicated.{ext}` file:
+    /// 1. Enumerates all unique canonical kmers (two passes over the file).
+    /// 2. Builds a provisional MPHF (FMPHGO) over those kmers.
+    /// 3. Writes a flat binary count file (`counts1.bin`, one `u32` per slot,
+    ///    memory-mapped) accumulating kmer abundances from the superkmer counts.
+    /// 4. Persists the MPHF to `mphf1.bin` for downstream use.
+    ///
+    /// Returns the aggregated `KmerSpectrum`. Per-partition spectrum files are
+    /// deleted after aggregation unless `keep_partial` is true.
+    ///
+    /// Partitions are processed in parallel via Rayon (one task per thread).
+    /// Peak memory per partition is ~80 MB, so n_threads partitions run simultaneously.
+    pub fn count_kmer(&self, keep_partial: bool) -> SKResult<KmerSpectrum> {
+        let sys = System::new_all();
+        let available = match sys.available_memory() {
+            0 => sys.total_memory() / 2,
+            n => n,
+        };
+        let n_threads = rayon::current_num_threads().max(1) as u64;
+        let chunk_kmers = chunk_size_from_ram(available / n_threads);
+
+        let pb = progress_bar("counting", self.n_partitions as u64, "partitions");
+
+        let results: Vec<SKResult<()>> = (0..self.n_partitions)
+            .into_par_iter()
+            .map(|i| {
+                let dir = self.part_dir(i);
+                let dedup_path = dir.join(format!("dereplicated.{SK_EXT}"));
+                if !dedup_path.exists() {
+                    pb.inc(1);
+                    return Ok(());
+                }
+                let t = Instant::now();
+                let result = count_partition(&dir, &dedup_path, chunk_kmers);
+                pb.set_message(format!("last {:.0}ms", t.elapsed().as_millis()));
+                pb.inc(1);
+                result
+            })
+            .collect();
+
+        pb.finish_and_clear();
+        for r in results {
+            r?;
+        }
+
+        // Aggregate per-partition spectra.
+        let mut counts: BTreeMap<u32, u64> = BTreeMap::new();
+        let mut f0: u64 = 0;
+        let mut f1: u64 = 0;
+
+        for i in 0..self.n_partitions {
+            let path = self.part_dir(i).join("kmer_spectrum_raw.json");
+            if !path.exists() {
+                continue;
+            }
+            let v: serde_json::Value =
+                serde_json::from_str(&fs::read_to_string(&path)?).map_err(io::Error::other)?;
+            f0 += v["f0"].as_u64().unwrap_or(0);
+            f1 += v["f1"].as_u64().unwrap_or(0);
+            if let Some(obj) = v["spectrum"].as_object() {
+                for (c_str, freq) in obj {
+                    if let (Ok(c), Some(f)) = (c_str.parse::<u32>(), freq.as_u64()) {
+                        *counts.entry(c).or_insert(0) += f;
+                    }
+                }
+            }
+            if !keep_partial {
+                let _ = fs::remove_file(&path);
+            }
+        }
+
+        Ok(KmerSpectrum { f0, f1, counts })
+    }
+
+    // ── private ───────────────────────────────────────────────────────────────
+
+    fn check_not_closed(&self) -> SKResult<()> {
+        if self.closed {
+            Err(io::Error::new(io::ErrorKind::BrokenPipe, "write to closed KmerPartition").into())
+        } else {
+            Ok(())
+        }
+    }
+
+    fn ensure_writer(&mut self, partition: usize) -> SKResult<&mut SKFileWriter> {
+        if self.writers[partition].is_none() {
+            let dir = self.root_path.join(PARTITIONS_SUBDIR).join(format!("part_{:05}", partition));
+            fs::create_dir_all(&dir)?;
+            let file_path = dir.join(format!("raw.{SK_EXT}"));
+            let writer = SKFileWriter::create_with(file_path, Format::Zstd, self.level)?;
+            self.writers[partition] = Some(writer);
+        }
+        Ok(self.writers[partition].as_mut().unwrap())
+    }
+}
+
+impl Drop for KmerPartition {
+    fn drop(&mut self) {
+        let _ = self.close();
+    }
+}
diff --git a/src/obikpartitionner/src/partition/mod.rs b/src/obikpartitionner/src/partition/mod.rs
new file mode 100644
index 00000000..22ee849b
--- /dev/null
+++ b/src/obikpartitionner/src/partition/mod.rs
@@ -0,0 +1,19 @@
+//! K-mer partitioning: routing super-kmers into per-partition files,
+//! deduplicating them, and counting unique canonical k-mers.
+//!
+//! Submodules: [`kmer_partition`] (`KmerPartition`, `KmerSpectrum` and the
+//! routing/lifecycle API), [`dereplicate`] (two-phase split+merge
+//! deduplication), [`count`] (unique-kmer enumeration, MPHF, abundance
+//! counting).
+
+mod count;
+mod dereplicate;
+mod kmer_partition;
+
+#[cfg(test)]
+mod tests;
+
+pub use kmer_partition::{KmerPartition, KmerSpectrum};
+
+const SK_EXT: &str = "skmer.zst";
+pub const PARTITIONS_SUBDIR: &str = "partitions";
diff --git a/src/obikpartitionner/src/partition/tests.rs b/src/obikpartitionner/src/partition/tests.rs
new file mode 100644
index 00000000..a98878bb
--- /dev/null
+++ b/src/obikpartitionner/src/partition/tests.rs
@@ -0,0 +1,113 @@
+use std::collections::HashMap;
+use std::fs;
+
+use obikrope::Rope;
+use obikseq::SuperKmer;
+use obiskbuilder::build_superkmers;
+
+use super::count::count_partition;
+use super::{KmerPartition, PARTITIONS_SUBDIR};
+
+const K: usize = 11;
+const M: usize = 5;
+
+fn setup() {
+    obikseq::params::set_k(K);
+    obikseq::params::set_m(M);
+}
+
+/// Direct canonical k-mer counts from ASCII sequences — ground truth.
+fn direct_counts(seqs: &[&[u8]]) -> (u64, u64) {
+    let mut counts: HashMap<Vec<u8>, u64> = HashMap::new();
+    for seq in seqs {
+        for i in 0..seq.len().saturating_sub(K - 1) {
+            let km = SuperKmer::from_ascii(&seq[i..i + K]).to_ascii();
+            *counts.entry(km).or_insert(0) += 1;
+        }
+    }
+    let f0 = counts.len() as u64;
+    let f1: u64 = counts.values().sum();
+    (f0, f1)
+}
+
+/// Run the full pipeline on a list of sequences and return (f0, f1) from
+/// the `kmer_spectrum_raw.json` produced by `count_partition`.
+fn pipeline_counts(seqs: &[&[u8]]) -> (u64, u64) {
+    setup();
+
+    let mut rope_data: Vec<u8> = Vec::new();
+    for seq in seqs {
+        rope_data.extend_from_slice(seq);
+        rope_data.push(0x00);
+    }
+    let mut rope = Rope::new(None);
+    rope.push(rope_data);
+
+    let superkmers: Vec<_> = build_superkmers(rope, K, 1, 0.0);
+
+    let dir = tempfile::tempdir().unwrap();
+    let mut kp = KmerPartition::create(dir.path(), 0, K, M, true).unwrap();
+    kp.write_batch(superkmers).unwrap();
+    kp.close().unwrap();
+    kp.dereplicate().unwrap();
+
+    let part_dir = dir.path().join(PARTITIONS_SUBDIR).join("part_00000");
+    let dedup_path = part_dir.join("dereplicated.skmer.zst");
+    if !dedup_path.exists() {
+        return (0, 0);
+    }
+    count_partition(&part_dir, &dedup_path, 1 << 20).unwrap();
+
+    let spec: serde_json::Value = serde_json::from_reader(
+        fs::File::open(part_dir.join("kmer_spectrum_raw.json")).unwrap(),
+    ).unwrap();
+    let f0 = spec["f0"].as_u64().unwrap_or(0);
+    let f1 = spec["f1"].as_u64().unwrap_or(0);
+    (f0, f1)
+}
+
+#[test]
+fn single_sequence_f0_f1_match() {
+    let seqs: &[&[u8]] = &[b"ACGTACGTACGTACGTACGT"];
+    let (ef0, ef1) = direct_counts(seqs);
+    let (gf0, gf1) = pipeline_counts(seqs);
+    assert_eq!(gf0, ef0, "f0 wrong: expected {ef0}, got {gf0}");
+    assert_eq!(gf1, ef1, "f1 wrong: expected {ef1}, got {gf1}");
+}
+
+#[test]
+fn two_sequences_f0_f1_match() {
+    let seqs: &[&[u8]] = &[
+        b"ACGTACGTACGTACGTACGT",
+        b"TGCATGCATGCATGCATGCA",
+    ];
+    let (ef0, ef1) = direct_counts(seqs);
+    let (gf0, gf1) = pipeline_counts(seqs);
+    assert_eq!(gf0, ef0, "f0 wrong: expected {ef0}, got {gf0}");
+    assert_eq!(gf1, ef1, "f1 wrong: expected {ef1}, got {gf1}");
+}
+
+#[test]
+fn repeated_sequence_f1_doubles() {
+    let seq = b"ACGTACGTACGTACGTACGT";
+    let seqs: &[&[u8]] = &[seq, seq];
+    let (ef0, ef1) = direct_counts(seqs);
+    let (gf0, gf1) = pipeline_counts(seqs);
+    assert_eq!(gf0, ef0, "f0 wrong: expected {ef0}, got {gf0}");
+    assert_eq!(gf1, ef1, "f1 wrong: expected {ef1}, got {gf1}");
+}
+
+#[test]
+fn many_sequences_f0_f1_match() {
+    // 20 distinct sequences of length 40 — forces multiple super-kmers and
+    // multiple minimizer boundaries per sequence.
+    let bases = b"ACGT";
+    let seqs: Vec<Vec<u8>> = (0..20u32)
+        .map(|i| (0..40).map(|j| bases[((i * 7 + j * 3) % 4) as usize]).collect())
+        .collect();
+    let seq_refs: Vec<&[u8]> = seqs.iter().map(|v| v.as_slice()).collect();
+    let (ef0, ef1) = direct_counts(&seq_refs);
+    let (gf0, gf1) = pipeline_counts(&seq_refs);
+    assert_eq!(gf0, ef0, "f0 wrong: expected {ef0}, got {gf0}");
+    assert_eq!(gf1, ef1, "f1 wrong: expected {ef1}, got {gf1}");
+}
diff --git a/src/obikrope/src/cursor.rs b/src/obikrope/src/cursor.rs
deleted file mode 100644
index 4ab40f75..00000000
--- a/src/obikrope/src/cursor.rs
+++ /dev/null
@@ -1,828 +0,0 @@
-//! Cursors for sequential and random access over a [`Rope`].
-//!
-//! # Design
-//!
-//! A cursor borrows a `&'a Rope` and keeps a small block cache so that
-//! consecutive accesses within the same block cost O(1). The first access to a
-//! new block costs O(log n) (binary search in [`Rope::lookup`]); subsequent
-//! accesses within that block are free.
-//!
-//! All mutable state (current position, cache) is stored in [`Cell`] fields,
-//! so every cursor method takes `&self` rather than `&mut self`. This means:
-//!
-//! - Two cursors can coexist on the same rope without lifetime conflicts.
-//! - The `iter()` method returns a lightweight wrapper that holds `&Cursor`,
-//!   allowing `cursor.tell()` or `cursor.seek()` to be called **inside a `for`
-//!   loop** over the same cursor.
-//!
-//! # Cursors
-//!
-//! | Type | Direction | First `read_next` | `seek(Relative, +n)` |
-//! |------|-----------|-------------------|----------------------|
-//! | [`ForwardCursor`] | start → end | index 0 | advances (+n) |
-//! | [`BackwardCursor`] | end → start | index `len-1` | retreats (+n) |
-//!
-//! # Example
-//!
-//! ```
-//! use obikrope::{Rope, RopeCursor};
-//!
-//! let mut rope = Rope::new(None);
-//! rope.push(b"ACGT".to_vec());
-//!
-//! let cursor = rope.fw_cursor();
-//! for byte in cursor.iter() {
-//!     // cursor.tell() is valid here — iter() holds &cursor, not &mut cursor
-//!     let _ = cursor.tell();
-//! }
-//! ```
-
-use std::cell::Cell;
-
-use crate::{Rope, RopeError};
-
-/// Controls how the `pos` argument of [`RopeCursor::seek`] is interpreted.
-#[derive(Clone, Copy)]
-pub enum SeekMode {
-    /// `pos` is an absolute byte index from the start of the rope.
-    Absolute,
-    /// `pos` is relative to the current position.
-    /// Positive = forward for [`ForwardCursor`], backward for [`BackwardCursor`].
-    Relative,
-    /// `pos` is counted back from the end: target = `len - pos`.
-    RelativeToEnd,
-    /// `pos` is a rope index relative to the start of the rope.
-    Rope,
-}
-
-// ── shared state ──────────────────────────────────────────────────────────────
-
-/// Per-cursor cache of the last accessed block, the current position, and the
-/// base offset that defines the cursor's local coordinate system.
-///
-/// All fields are [`Cell`]-wrapped so they can be mutated through a shared
-/// reference, enabling `&self` methods on cursors.
-#[derive(Clone)]
-pub struct CursorState<'a> {
-    block_idx: Cell<usize>,
-    block_start: Cell<usize>,
-    block_end: Cell<usize>,
-    block: Cell<&'a [Cell<u8>]>,
-    initialized: Cell<bool>,
-    current: Cell<Option<usize>>,
-    /// Absolute rope index that maps to local position 0.
-    /// All user-facing coordinates are relative to this value.
-    offset: Cell<usize>,
-}
-
-impl<'a> CursorState<'a> {
-    fn new() -> Self {
-        Self::with_offset(0)
-    }
-
-    fn with_offset(offset: usize) -> Self {
-        Self {
-            block_idx: Cell::new(0),
-            block_start: Cell::new(0),
-            block_end: Cell::new(0),
-            block: Cell::new(&[]),
-            initialized: Cell::new(false),
-            current: Cell::new(None),
-            offset: Cell::new(offset),
-        }
-    }
-
-    fn get(&self, rope: &'a Rope, i: usize) -> Option<u8> {
-        if !self.initialized.get() || i < self.block_start.get() || i >= self.block_end.get() {
-            let (bi, bs, be) = rope.lookup(i)?;
-            self.block_idx.set(bi);
-            self.block_start.set(bs);
-            self.block_end.set(be);
-            self.block.set(rope.get_block(bi)?);
-            self.initialized.set(true);
-        }
-        Some(self.block.get()[i - self.block_start.get()].get())
-    }
-
-    fn set(&self, rope: &'a Rope, i: usize, value: u8) -> Result<(), RopeError> {
-        if !self.initialized.get() || i < self.block_start.get() || i >= self.block_end.get() {
-            let (bi, bs, be) = rope.lookup(i).ok_or(RopeError::OutOfBounds(format!(
-                "index out of bounds: i={} > {}",
-                i,
-                rope.len()
-            )))?;
-            self.block_idx.set(bi);
-            self.block_start.set(bs);
-            self.block_end.set(be);
-            self.block
-                .set(rope.get_block(bi).ok_or(RopeError::BlockNotFound(format!(
-                    "Cannot find block for index {}",
-                    i
-                )))?);
-            self.initialized.set(true);
-        }
-        self.block.get()[i - self.block_start.get()].set(value);
-        Ok(())
-    }
-}
-
-// ── trait ─────────────────────────────────────────────────────────────────────
-
-/// Common interface for all rope cursors.
-///
-/// # Required methods
-///
-/// Implementors must provide [`rope`](RopeCursor::rope),
-/// [`state`](RopeCursor::state), [`read_next`](RopeCursor::read_next) and
-/// [`seek`](RopeCursor::seek). Everything else has a default implementation.
-///
-/// The direction of `read_next` and the sign convention for
-/// [`SeekMode::Relative`] differ between [`ForwardCursor`] and
-/// [`BackwardCursor`]; all other methods are identical.
-pub trait RopeCursor<'a> {
-    /// The rope this cursor is bound to.
-    fn rope(&self) -> &'a Rope;
-    /// Internal cache state — implementation detail exposed for default methods.
-    fn state(&self) -> &CursorState<'a>;
-
-    /// Read the next byte in cursor direction and advance the position.
-    /// Returns `Err` at the exhausted end.
-    fn read_next(&self) -> Result<u8, RopeError>;
-
-    /// Move the cursor to a new position.
-    ///
-    /// `pos` is interpreted according to `mode`:
-    /// - [`Absolute`](SeekMode::Absolute): local coordinate (`pos + offset` in the rope).
-    /// - [`Rope`](SeekMode::Rope): raw rope index, ignores the offset.  Pass a value
-    ///   from [`rope_tell`](RopeCursor::rope_tell) to restore a saved position.
-    /// - [`Relative`](SeekMode::Relative): delta from the current position.
-    ///   For [`ForwardCursor`], positive advances toward the end;
-    ///   for [`BackwardCursor`], positive retreats toward the start.
-    /// - [`RelativeToEnd`](SeekMode::RelativeToEnd): `rope.len() - pos`.
-    ///
-    /// Returns the new position as a **rope index** (same value as
-    /// [`rope_tell`](RopeCursor::rope_tell) would return immediately after).
-    fn seek(&self, pos: isize, mode: SeekMode) -> Result<usize, RopeError>;
-
-    // ── default methods ───────────────────────────────────────────────────────
-
-    /// Read the byte at **local** index `i` (relative to the cursor's offset)
-    /// without moving the position.
-    fn get(&self, i: usize) -> Option<u8> {
-        self.state().get(self.rope(), i + self.state().offset.get())
-    }
-
-    /// Write `value` at **local** index `i` without moving the position.
-    fn set(&self, i: usize, value: u8) -> Result<(), RopeError> {
-        self.state()
-            .set(self.rope(), i + self.state().offset.get(), value)
-    }
-
-    /// Current position relative to the cursor's offset, or `None` if the
-    /// cursor has not moved yet.
-    fn tell(&self) -> Option<usize> {
-        let abs = self.state().current.get()?;
-        Some(abs.saturating_sub(self.state().offset.get()))
-    }
-
-    /// Current position as an absolute rope index.
-    ///
-    /// Unlike [`tell`](RopeCursor::tell), this method **always** returns a
-    /// value: if the cursor has not moved yet, it returns the cursor's offset
-    /// (the rope index of local position 0).
-    ///
-    /// Use the returned value with [`SeekMode::Rope`] to restore a position,
-    /// or as a truncation point after a write pass.
-    fn rope_tell(&self) -> usize {
-        self.state()
-            .current
-            .get()
-            .unwrap_or(self.state().offset.get())
-    }
-
-    /// Number of bytes visible through this cursor (`rope.len() - offset`).
-    fn len(&self) -> usize {
-        self.rope().len().saturating_sub(self.state().offset.get())
-    }
-
-    /// Reset the cursor to its initial state (positioned before the first
-    /// byte of its local view).  Equivalent to `seek(0, Absolute)` on a
-    /// fresh cursor, but works even when `current` is `None`.
-    fn reset(&self) {
-        self.state().current.set(None);
-    }
-
-    /// Read the byte at the current position without advancing.
-    fn peek(&self) -> Option<u8> {
-        self.state().get(self.rope(), self.state().current.get()?)
-    }
-
-    /// Write `value` at the current position without advancing.
-    fn poke(&self, value: u8) -> Result<(), RopeError> {
-        let pos = self.state().current.get().ok_or(RopeError::CurrentNotSet)?;
-        self.state().set(self.rope(), pos, value)
-    }
-
-    /// Move backward by `go_back_of` steps (toward lower indices for
-    /// [`ForwardCursor`], toward higher indices for [`BackwardCursor`]).
-    fn rewind(&self, go_back_of: usize) -> Result<(), RopeError> {
-        self.seek(-(go_back_of as isize), SeekMode::Relative)?;
-        Ok(())
-    }
-
-    /// Move forward by `ahead` steps (opposite of [`rewind`](RopeCursor::rewind)).
-    fn forward(&self, ahead: usize) -> Result<(), RopeError> {
-        self.seek(ahead as isize, SeekMode::Relative)?;
-        Ok(())
-    }
-}
-
-// ── ForwardCursor ─────────────────────────────────────────────────────────────
-
-/// A cursor that reads from the start toward the end of the rope.
-///
-/// - `read_next`: first call reads index 0, then 1, 2, …
-/// - `seek(Relative, +n)`: advances by n.
-/// - `rewind(n)`: steps back by n.
-///
-/// Extra methods not in the trait: [`read_ahead`](ForwardCursor::read_ahead),
-/// [`write`](ForwardCursor::write), [`iter`](ForwardCursor::iter).
-#[derive(Clone)]
-pub struct ForwardCursor<'a> {
-    rope: &'a Rope,
-    state: CursorState<'a>,
-}
-
-impl<'a> ForwardCursor<'a> {
-    /// Create a new forward cursor positioned before the first byte.
-    pub fn new(rope: &'a Rope) -> Self {
-        Self {
-            rope,
-            state: CursorState::new(),
-        }
-    }
-
-    /// Read the byte at `current + ahead` without moving the position.
-    pub fn read_ahead(&self, ahead: usize) -> Result<u8, RopeError> {
-        let pos = self.state.current.get().ok_or(RopeError::CurrentNotSet)?;
-        self.state
-            .get(self.rope, pos + ahead)
-            .ok_or(RopeError::OutOfBounds(format!(
-                "index out of bounds: i={} + {} > {}",
-                pos,
-                ahead,
-                self.rope.len()
-            )))
-    }
-
-    /// Write `value` at the current position and advance by one.
-    ///
-    /// If the cursor has not moved yet, writes at the first byte of its local
-    /// view (absolute index = offset).
-    pub fn write(&self, value: u8) -> Result<(), RopeError> {
-        let pos = self.state.current.get().unwrap_or(self.state.offset.get());
-        self.state.set(self.rope, pos, value)?;
-        self.state.current.set(Some(pos + 1));
-        Ok(())
-    }
-
-    /// Return a shared-borrow iterator that yields bytes forward.
-    ///
-    /// Because the iterator holds `&self` rather than `&mut self`, methods
-    /// such as [`tell`](RopeCursor::tell) and [`seek`](RopeCursor::seek) can
-    /// be called on the cursor inside the loop body.
-    pub fn iter(&self) -> ForwardIter<'a, '_> {
-        ForwardIter { cursor: self }
-    }
-
-    /// Create a new [`ForwardCursor`] whose local position 0 starts at the
-    /// current absolute position of `self`.
-    ///
-    /// The new cursor shares the same underlying [`Rope`] (with the same
-    /// [`Cell`]-based interior mutability) but has an independent position and
-    /// an `offset` equal to `self.absolute_tell()`.  If `self` has not moved
-    /// yet, the new cursor starts at the same offset as `self`.
-    pub fn cursor(&self) -> ForwardCursor<'a> {
-        let new_offset = self.rope_tell();
-        ForwardCursor {
-            rope: self.rope,
-            state: CursorState::with_offset(new_offset),
-        }
-    }
-}
-
-impl<'a> RopeCursor<'a> for ForwardCursor<'a> {
-    fn rope(&self) -> &'a Rope {
-        self.rope
-    }
-    fn state(&self) -> &CursorState<'a> {
-        &self.state
-    }
-
-    fn read_next(&self) -> Result<u8, RopeError> {
-        let next_pos = match self.state.current.get() {
-            Some(i) => i + 1,
-            None => self.state.offset.get(),
-        };
-        let value = self
-            .state
-            .get(self.rope, next_pos)
-            .ok_or(RopeError::OutOfBounds(format!(
-                "index out of bounds: i={} > {}",
-                next_pos,
-                self.rope.len()
-            )))?;
-        self.state.current.set(Some(next_pos));
-        Ok(value)
-    }
-
-    fn seek(&self, pos: isize, mode: SeekMode) -> Result<usize, RopeError> {
-        let offset = self.state.offset.get() as isize;
-        let abs_pos = match mode {
-            SeekMode::Absolute => pos + offset,
-            SeekMode::Relative => {
-                self.state.current.get().ok_or(RopeError::CurrentNotSet)? as isize + pos
-            }
-            SeekMode::RelativeToEnd => self.rope.len() as isize - pos,
-            SeekMode::Rope => pos,
-        };
-        if abs_pos < 0 {
-            return Err(RopeError::OutOfBounds(format!(
-                "index out of bounds: i={} < 0",
-                abs_pos
-            )));
-        }
-        self.state.current.set(Some(abs_pos as usize));
-        Ok(abs_pos as usize)
-    }
-}
-
-impl Iterator for ForwardCursor<'_> {
-    type Item = u8;
-    fn next(&mut self) -> Option<Self::Item> {
-        self.read_next().ok()
-    }
-}
-
-/// Shared-borrow iterator returned by [`ForwardCursor::iter`].
-pub struct ForwardIter<'a, 'b> {
-    cursor: &'b ForwardCursor<'a>,
-}
-
-impl Iterator for ForwardIter<'_, '_> {
-    type Item = u8;
-    fn next(&mut self) -> Option<u8> {
-        self.cursor.read_next().ok()
-    }
-}
-
-// ── BackwardCursor ────────────────────────────────────────────────────────────
-
-/// A cursor that reads from the end toward the start of the rope.
-///
-/// - `read_next`: first call reads index `len-1`, then `len-2`, …
-/// - `seek(Relative, +n)`: retreats by n (subtracts n from the index).
-/// - `rewind(n)`: advances toward the end by n.
-///
-/// Extra methods not in the trait: [`read_behind`](BackwardCursor::read_behind),
-/// [`iter`](BackwardCursor::iter).
-#[derive(Clone)]
-pub struct BackwardCursor<'a> {
-    rope: &'a Rope,
-    state: CursorState<'a>,
-}
-
-impl<'a> BackwardCursor<'a> {
-    /// Create a new backward cursor positioned past the last byte.
-    pub fn new(rope: &'a Rope) -> Self {
-        Self {
-            rope,
-            state: CursorState::new(),
-        }
-    }
-
-    /// Read the byte at `current + behind` (toward higher indices) without moving.
-    pub fn read_behind(&self, behind: usize) -> Result<u8, RopeError> {
-        let pos = self.state.current.get().ok_or(RopeError::CurrentNotSet)?;
-        let target = pos
-            .checked_add(behind)
-            .filter(|&t| t < self.rope.len())
-            .ok_or(RopeError::OutOfBounds(format!(
-                "index out of bounds: i={} + {} > {}",
-                pos,
-                behind,
-                self.rope.len()
-            )))?;
-        self.state
-            .get(self.rope, target)
-            .ok_or(RopeError::OutOfBounds(format!(
-                "index out of bounds: i={} + {} > {}",
-                pos,
-                behind,
-                self.rope.len()
-            )))
-    }
-
-    /// Return a shared-borrow iterator that yields bytes backward.
-    ///
-    /// Because the iterator holds `&self` rather than `&mut self`, methods
-    /// such as [`tell`](RopeCursor::tell) and [`seek`](RopeCursor::seek) can
-    /// be called on the cursor inside the loop body.
-    pub fn iter(&self) -> BackwardIter<'a, '_> {
-        BackwardIter { cursor: self }
-    }
-
-    /// Create a new [`BackwardCursor`] that stops at the current absolute
-    /// position of `self` (used as the lower bound / offset of the new cursor).
-    ///
-    /// The new cursor scans from `rope.len() - 1` down to the current absolute
-    /// position of `self`.  If `self` has not moved yet, the new cursor has the
-    /// same offset as `self` (no restriction).
-    pub fn cursor(&self) -> BackwardCursor<'a> {
-        let new_offset = self.rope_tell();
-        BackwardCursor {
-            rope: self.rope,
-            state: CursorState::with_offset(new_offset),
-        }
-    }
-}
-
-impl<'a> RopeCursor<'a> for BackwardCursor<'a> {
-    fn rope(&self) -> &'a Rope {
-        self.rope
-    }
-    fn state(&self) -> &CursorState<'a> {
-        &self.state
-    }
-
-    fn read_next(&self) -> Result<u8, RopeError> {
-        let offset = self.state.offset.get();
-        let next_pos = match self.state.current.get() {
-            None => self
-                .rope
-                .len()
-                .checked_sub(1)
-                .ok_or(RopeError::OutOfBounds(
-                    "BackwardCursor: rope is empty".to_string(),
-                ))?,
-            Some(i) if i <= offset => {
-                return Err(RopeError::OutOfBounds(
-                    "BackwardCursor: already at beginning".to_string(),
-                ));
-            }
-            Some(i) => i - 1,
-        };
-        let value = self
-            .state
-            .get(self.rope, next_pos)
-            .ok_or(RopeError::OutOfBounds(format!(
-                "BackwardCursor: index out of bounds at i={}",
-                next_pos
-            )))?;
-        self.state.current.set(Some(next_pos));
-        Ok(value)
-    }
-
-    fn seek(&self, pos: isize, mode: SeekMode) -> Result<usize, RopeError> {
-        let offset = self.state.offset.get() as isize;
-        let abs_pos = match mode {
-            SeekMode::Absolute => pos + offset,
-            SeekMode::Relative => {
-                self.state.current.get().ok_or(RopeError::CurrentNotSet)? as isize - pos
-            }
-            SeekMode::RelativeToEnd => self.rope.len() as isize - pos,
-            SeekMode::Rope => pos,
-        };
-        if abs_pos < 0 {
-            return Err(RopeError::OutOfBounds(format!(
-                "index out of bounds: i={} < 0",
-                abs_pos
-            )));
-        }
-        self.state.current.set(Some(abs_pos as usize));
-        Ok(abs_pos as usize)
-    }
-}
-
-impl Iterator for BackwardCursor<'_> {
-    type Item = u8;
-    fn next(&mut self) -> Option<Self::Item> {
-        self.read_next().ok()
-    }
-}
-
-/// Shared-borrow iterator returned by [`BackwardCursor::iter`].
-pub struct BackwardIter<'a, 'b> {
-    cursor: &'b BackwardCursor<'a>,
-}
-
-impl Iterator for BackwardIter<'_, '_> {
-    type Item = u8;
-    fn next(&mut self) -> Option<u8> {
-        self.cursor.read_next().ok()
-    }
-}
-
-// ── tests ─────────────────────────────────────────────────────────────────────
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use crate::Rope;
-
-    fn rope(data: &[u8]) -> Rope {
-        let mut r = Rope::new(None);
-        r.push(data.to_vec());
-        r
-    }
-
-    fn rope2(a: &[u8], b: &[u8]) -> Rope {
-        let mut r = Rope::new(None);
-        r.push(a.to_vec());
-        r.push(b.to_vec());
-        r
-    }
-
-    // ── ForwardCursor ─────────────────────────────────────────────────────────
-
-    #[test]
-    fn forward_reads_all_bytes() {
-        let r = rope(b"ACGT");
-        let c = r.fw_cursor();
-        let out: Vec<u8> = c.collect();
-        assert_eq!(out, b"ACGT");
-    }
-
-    #[test]
-    fn forward_tell_tracks_position() {
-        let r = rope(b"ACGT");
-        let c = r.fw_cursor();
-        assert_eq!(c.tell(), None);
-        c.read_next().unwrap();
-        assert_eq!(c.tell(), Some(0));
-        c.read_next().unwrap();
-        assert_eq!(c.tell(), Some(1));
-    }
-
-    #[test]
-    fn forward_iter_with_tell_inside_loop() {
-        let r = rope(b"ACGT");
-        let c = r.fw_cursor();
-        let mut positions = Vec::new();
-        for _ in c.iter() {
-            positions.push(c.tell());
-        }
-        assert_eq!(positions, vec![Some(0), Some(1), Some(2), Some(3)]);
-    }
-
-    #[test]
-    fn forward_read_ahead() {
-        let r = rope(b"ACGT");
-        let c = r.fw_cursor();
-        c.read_next().unwrap(); // at 0 = 'A'
-        assert_eq!(c.read_ahead(1).unwrap(), b'C');
-        assert_eq!(c.read_ahead(2).unwrap(), b'G');
-        assert_eq!(c.tell(), Some(0)); // position unchanged
-    }
-
-    #[test]
-    fn forward_write_and_read_back() {
-        let r = rope(b"ACGT");
-        let c = r.fw_cursor();
-        c.write(b'X').unwrap();
-        c.write(b'Y').unwrap();
-        let c2 = r.fw_cursor();
-        assert_eq!(c2.read_next().unwrap(), b'X');
-        assert_eq!(c2.read_next().unwrap(), b'Y');
-        assert_eq!(c2.read_next().unwrap(), b'G');
-    }
-
-    #[test]
-    fn forward_rewind_and_reread() {
-        let r = rope(b"ACGT");
-        let c = r.fw_cursor();
-        c.read_next().unwrap(); // A  → current = Some(0)
-        c.read_next().unwrap(); // C  → current = Some(1)
-        c.read_next().unwrap(); // G  → current = Some(2)
-        c.rewind(1).unwrap(); // current = Some(1) → next read = index 2
-        assert_eq!(c.read_next().unwrap(), b'G');
-    }
-
-    #[test]
-    fn forward_seek_absolute() {
-        let r = rope(b"ACGT");
-        let c = r.fw_cursor();
-        c.seek(2, SeekMode::Absolute).unwrap();
-        assert_eq!(c.read_next().unwrap(), b'T');
-    }
-
-    #[test]
-    fn forward_seek_relative_to_end() {
-        let r = rope(b"ACGT");
-        // seek(1, RelativeToEnd): current = len-1 = 3; peek() reads index 3 = T.
-        let c = r.fw_cursor();
-        c.seek(1, SeekMode::RelativeToEnd).unwrap();
-        assert_eq!(c.peek().unwrap(), b'T');
-        // seek(2, RelativeToEnd): current = len-2 = 2; read_next reads index 3 = T.
-        let c2 = r.fw_cursor();
-        c2.seek(2, SeekMode::RelativeToEnd).unwrap();
-        assert_eq!(c2.read_next().unwrap(), b'T');
-    }
-
-    #[test]
-    fn forward_get_random_access() {
-        let r = rope(b"ACGT");
-        let c = r.fw_cursor();
-        assert_eq!(c.get(0), Some(b'A'));
-        assert_eq!(c.get(3), Some(b'T'));
-        assert_eq!(c.get(4), None);
-    }
-
-    #[test]
-    fn forward_crosses_block_boundary() {
-        let r = rope2(b"AC", b"GT");
-        let c = r.fw_cursor();
-        let out: Vec<u8> = c.collect();
-        assert_eq!(out, b"ACGT");
-    }
-
-    // ── BackwardCursor ────────────────────────────────────────────────────────
-
-    #[test]
-    fn backward_reads_all_bytes_in_reverse() {
-        let r = rope(b"ACGT");
-        let c = r.bw_cursor();
-        let out: Vec<u8> = c.collect();
-        assert_eq!(out, b"TGCA");
-    }
-
-    #[test]
-    fn backward_tell_tracks_position() {
-        let r = rope(b"ACGT");
-        let c = r.bw_cursor();
-        assert_eq!(c.tell(), None);
-        c.read_next().unwrap(); // reads index 3
-        assert_eq!(c.tell(), Some(3));
-        c.read_next().unwrap(); // reads index 2
-        assert_eq!(c.tell(), Some(2));
-    }
-
-    #[test]
-    fn backward_iter_with_tell_and_seek_inside_loop() {
-        let r = rope(b"ACGT");
-        let c = r.bw_cursor();
-        let mut restart: usize = 0;
-        for byte in c.iter() {
-            if byte == b'G' {
-                restart = c.tell().unwrap();
-            }
-            if byte == b'A' {
-                // seek back to G and break
-                c.seek(restart as isize, SeekMode::Absolute).ok();
-                break;
-            }
-        }
-        assert_eq!(c.tell(), Some(restart));
-    }
-
-    #[test]
-    fn backward_rewind_moves_toward_end() {
-        let r = rope(b"ACGT");
-        let c = r.bw_cursor();
-        c.read_next().unwrap(); // index 3 = T
-        c.read_next().unwrap(); // index 2 = G
-        c.rewind(1).unwrap(); // back to index 3
-        assert_eq!(c.tell(), Some(3));
-        assert_eq!(c.read_next().unwrap(), b'G'); // reads index 2
-    }
-
-    #[test]
-    fn backward_crosses_block_boundary() {
-        let r = rope2(b"AC", b"GT");
-        let c = r.bw_cursor();
-        let out: Vec<u8> = c.collect();
-        assert_eq!(out, b"TGCA");
-    }
-
-    #[test]
-    fn backward_empty_rope_returns_error() {
-        let r = Rope::new(None);
-        let c = r.bw_cursor();
-        assert!(c.read_next().is_err());
-    }
-
-    #[test]
-    fn forward_empty_rope_returns_error() {
-        let r = Rope::new(None);
-        let c = r.fw_cursor();
-        assert!(c.read_next().is_err());
-    }
-
-    // ── offset / sub-cursor ───────────────────────────────────────────────────
-
-    #[test]
-    fn forward_cursor_reads_from_offset() {
-        // cursor() at current=Some(2) → new cursor reads from index 2
-        let r = rope(b"ABCDE");
-        let c = r.fw_cursor();
-        c.read_next().unwrap(); // A → current=Some(0)
-        c.read_next().unwrap(); // B → current=Some(1)
-        c.read_next().unwrap(); // C → current=Some(2)
-        let sub = c.cursor(); // offset=2 (absolute_tell=2)
-        assert_eq!(sub.read_next().unwrap(), b'C'); // reads index 2
-        assert_eq!(sub.tell(), Some(0)); // relative: 2-2=0
-        assert_eq!(sub.rope_tell(), 2);
-        assert_eq!(sub.read_next().unwrap(), b'D');
-        assert_eq!(sub.tell(), Some(1)); // relative: 3-2=1
-    }
-
-    #[test]
-    fn forward_cursor_get_uses_relative_index() {
-        let r = rope(b"ABCDE");
-        let c = r.fw_cursor();
-        c.read_next().unwrap(); // A → current=Some(0), absolute_tell=0
-        let _sub = c.cursor(); // offset=0 — created to show cursor() compiles; not used further
-        // From sub2 with offset=2: get(0)=C, get(2)=E
-        let c2 = r.fw_cursor();
-        c2.read_next().unwrap(); // at 0
-        c2.read_next().unwrap(); // at 1
-        c2.read_next().unwrap(); // at 2, absolute=2
-        let sub2 = c2.cursor(); // offset=2
-        assert_eq!(sub2.get(0), Some(b'C')); // local 0 = absolute 2
-        assert_eq!(sub2.get(2), Some(b'E')); // local 2 = absolute 4
-        assert_eq!(sub2.get(3), None); // local 3 = absolute 5, OOB
-    }
-
-    #[test]
-    fn forward_cursor_len_reflects_offset() {
-        let r = rope(b"ABCDE"); // len=5
-        let c = r.fw_cursor();
-        c.read_next().unwrap();
-        c.read_next().unwrap();
-        c.read_next().unwrap(); // absolute_tell=2
-        let sub = c.cursor(); // offset=2
-        assert_eq!(sub.len(), 3); // 5 - 2
-    }
-
-    #[test]
-    fn forward_reset_goes_back_to_start() {
-        let r = rope(b"ABCDE");
-        let c = r.fw_cursor();
-        c.read_next().unwrap(); // A
-        c.read_next().unwrap(); // B
-        c.reset();
-        assert_eq!(c.tell(), None);
-        assert_eq!(c.read_next().unwrap(), b'A'); // starts over
-    }
-
-    #[test]
-    fn forward_sub_cursor_write_and_reset() {
-        // Write two bytes, discard them via reset(), write again.
-        let r = rope(b"XXXXX");
-        let c = r.fw_cursor();
-        c.write(b'A').unwrap(); // absolute 0 → current=Some(1)
-        c.write(b'B').unwrap(); // absolute 1 → current=Some(2)
-        let seg = c.cursor(); // absolute_tell=2, offset=2
-        seg.write(b'C').unwrap(); // absolute 2 → current=Some(3), tell=3-2=1
-        seg.write(b'D').unwrap(); // absolute 3 → current=Some(4), tell=4-2=2
-        assert_eq!(seg.tell(), Some(2)); // 2 bytes written into this segment
-        seg.reset();
-        assert_eq!(seg.tell(), None);
-        seg.write(b'E').unwrap(); // absolute 2 again
-        let all: Vec<u8> = r.fw_cursor().collect();
-        assert_eq!(&all[..3], b"ABE");
-    }
-
-    #[test]
-    fn backward_cursor_stops_at_offset() {
-        // BackwardCursor.cursor() creates a cursor with offset = absolute_tell.
-        // offset = local position 0 (inclusive lower bound).
-        // The cursor reads rope.len()-1 downto offset, then stops.
-        let r = rope(b"ABCDE"); // 0=A 1=B 2=C 3=D 4=E
-        let bw = r.bw_cursor();
-        bw.read_next().unwrap(); // E=4, current=Some(4)
-        bw.read_next().unwrap(); // D=3, current=Some(3), absolute_tell=3
-        // sub: offset=3, reads from 4 down to 3 (inclusive), then stops.
-        let sub = bw.cursor();
-        assert_eq!(sub.read_next().unwrap(), b'E'); // index 4, tell=4-3=1
-        assert_eq!(sub.read_next().unwrap(), b'D'); // index 3, tell=3-3=0 (local 0)
-        assert!(sub.read_next().is_err()); // would go to 2 < offset=3
-    }
-
-    #[test]
-    fn forward_absolute_tell_unchanged_by_offset() {
-        let r = rope(b"ABCDE");
-        let c = r.fw_cursor();
-        c.read_next().unwrap(); // absolute=0
-        let sub = c.cursor(); // offset=0
-        sub.read_next().unwrap(); // reads index 0, absolute_tell=0
-        sub.read_next().unwrap(); // reads index 1, absolute_tell=1
-        assert_eq!(sub.tell(), Some(1));
-        assert_eq!(sub.rope_tell(), 1);
-        // sub2 with offset=1
-        let sub2 = sub.cursor(); // offset=1
-        sub2.read_next().unwrap(); // reads index 1, absolute=1
-        assert_eq!(sub2.tell(), Some(0)); // relative: 1-1=0
-        assert_eq!(sub2.rope_tell(), 1);
-    }
-}
diff --git a/src/obikrope/src/cursor/backward.rs b/src/obikrope/src/cursor/backward.rs
new file mode 100644
index 00000000..32b0e1ac
--- /dev/null
+++ b/src/obikrope/src/cursor/backward.rs
@@ -0,0 +1,149 @@
+use crate::{Rope, RopeError};
+
+use super::state::CursorState;
+use super::traits::{RopeCursor, SeekMode};
+
+/// A cursor that reads from the end toward the start of the rope.
+///
+/// - `read_next`: first call reads index `len-1`, then `len-2`, …
+/// - `seek(Relative, +n)`: retreats by n (subtracts n from the index).
+/// - `rewind(n)`: advances toward the end by n.
+///
+/// Extra methods not in the trait: [`read_behind`](BackwardCursor::read_behind),
+/// [`iter`](BackwardCursor::iter).
+#[derive(Clone)]
+pub struct BackwardCursor<'a> {
+    rope: &'a Rope,
+    state: CursorState<'a>,
+}
+
+impl<'a> BackwardCursor<'a> {
+    /// Create a new backward cursor positioned past the last byte.
+    pub fn new(rope: &'a Rope) -> Self {
+        Self {
+            rope,
+            state: CursorState::new(),
+        }
+    }
+
+    /// Read the byte at `current + behind` (toward higher indices) without moving.
+    pub fn read_behind(&self, behind: usize) -> Result<u8, RopeError> {
+        let pos = self.state.current.get().ok_or(RopeError::CurrentNotSet)?;
+        let target = pos
+            .checked_add(behind)
+            .filter(|&t| t < self.rope.len())
+            .ok_or(RopeError::OutOfBounds(format!(
+                "index out of bounds: i={} + {} > {}",
+                pos,
+                behind,
+                self.rope.len()
+            )))?;
+        self.state
+            .get(self.rope, target)
+            .ok_or(RopeError::OutOfBounds(format!(
+                "index out of bounds: i={} + {} > {}",
+                pos,
+                behind,
+                self.rope.len()
+            )))
+    }
+
+    /// Return a shared-borrow iterator that yields bytes backward.
+    ///
+    /// Because the iterator holds `&self` rather than `&mut self`, methods
+    /// such as [`tell`](RopeCursor::tell) and [`seek`](RopeCursor::seek) can
+    /// be called on the cursor inside the loop body.
+    pub fn iter(&self) -> BackwardIter<'a, '_> {
+        BackwardIter { cursor: self }
+    }
+
+    /// Create a new [`BackwardCursor`] that stops at the current absolute
+    /// position of `self` (used as the lower bound / offset of the new cursor).
+    ///
+    /// The new cursor scans from `rope.len() - 1` down to the current absolute
+    /// position of `self`.  If `self` has not moved yet, the new cursor has the
+    /// same offset as `self` (no restriction).
+    pub fn cursor(&self) -> BackwardCursor<'a> {
+        let new_offset = self.rope_tell();
+        BackwardCursor {
+            rope: self.rope,
+            state: CursorState::with_offset(new_offset),
+        }
+    }
+}
+
+impl<'a> RopeCursor<'a> for BackwardCursor<'a> {
+    fn rope(&self) -> &'a Rope {
+        self.rope
+    }
+    fn state(&self) -> &CursorState<'a> {
+        &self.state
+    }
+
+    fn read_next(&self) -> Result<u8, RopeError> {
+        let offset = self.state.offset.get();
+        let next_pos = match self.state.current.get() {
+            None => self
+                .rope
+                .len()
+                .checked_sub(1)
+                .ok_or(RopeError::OutOfBounds(
+                    "BackwardCursor: rope is empty".to_string(),
+                ))?,
+            Some(i) if i <= offset => {
+                return Err(RopeError::OutOfBounds(
+                    "BackwardCursor: already at beginning".to_string(),
+                ));
+            }
+            Some(i) => i - 1,
+        };
+        let value = self
+            .state
+            .get(self.rope, next_pos)
+            .ok_or(RopeError::OutOfBounds(format!(
+                "BackwardCursor: index out of bounds at i={}",
+                next_pos
+            )))?;
+        self.state.current.set(Some(next_pos));
+        Ok(value)
+    }
+
+    fn seek(&self, pos: isize, mode: SeekMode) -> Result<usize, RopeError> {
+        let offset = self.state.offset.get() as isize;
+        let abs_pos = match mode {
+            SeekMode::Absolute => pos + offset,
+            SeekMode::Relative => {
+                self.state.current.get().ok_or(RopeError::CurrentNotSet)? as isize - pos
+            }
+            SeekMode::RelativeToEnd => self.rope.len() as isize - pos,
+            SeekMode::Rope => pos,
+        };
+        if abs_pos < 0 {
+            return Err(RopeError::OutOfBounds(format!(
+                "index out of bounds: i={} < 0",
+                abs_pos
+            )));
+        }
+        self.state.current.set(Some(abs_pos as usize));
+        Ok(abs_pos as usize)
+    }
+}
+
+impl Iterator for BackwardCursor<'_> {
+    type Item = u8;
+    fn next(&mut self) -> Option<Self::Item> {
+        self.read_next().ok()
+    }
+}
+
+/// Shared-borrow iterator returned by [`BackwardCursor::iter`].
+pub struct BackwardIter<'a, 'b> {
+    cursor: &'b BackwardCursor<'a>,
+}
+
+impl Iterator for BackwardIter<'_, '_> {
+    type Item = u8;
+    fn next(&mut self) -> Option<u8> {
+        self.cursor.read_next().ok()
+    }
+}
diff --git a/src/obikrope/src/cursor/forward.rs b/src/obikrope/src/cursor/forward.rs
new file mode 100644
index 00000000..50bc40bd
--- /dev/null
+++ b/src/obikrope/src/cursor/forward.rs
@@ -0,0 +1,142 @@
+use crate::{Rope, RopeError};
+
+use super::state::CursorState;
+use super::traits::{RopeCursor, SeekMode};
+
+/// A cursor that reads from the start toward the end of the rope.
+///
+/// - `read_next`: first call reads index 0, then 1, 2, …
+/// - `seek(Relative, +n)`: advances by n.
+/// - `rewind(n)`: steps back by n.
+///
+/// Extra methods not in the trait: [`read_ahead`](ForwardCursor::read_ahead),
+/// [`write`](ForwardCursor::write), [`iter`](ForwardCursor::iter).
+#[derive(Clone)]
+pub struct ForwardCursor<'a> {
+    rope: &'a Rope,
+    state: CursorState<'a>,
+}
+
+impl<'a> ForwardCursor<'a> {
+    /// Create a new forward cursor positioned before the first byte.
+    pub fn new(rope: &'a Rope) -> Self {
+        Self {
+            rope,
+            state: CursorState::new(),
+        }
+    }
+
+    /// Read the byte at `current + ahead` without moving the position.
+    pub fn read_ahead(&self, ahead: usize) -> Result<u8, RopeError> {
+        let pos = self.state.current.get().ok_or(RopeError::CurrentNotSet)?;
+        self.state
+            .get(self.rope, pos + ahead)
+            .ok_or(RopeError::OutOfBounds(format!(
+                "index out of bounds: i={} + {} > {}",
+                pos,
+                ahead,
+                self.rope.len()
+            )))
+    }
+
+    /// Write `value` at the current position and advance by one.
+    ///
+    /// If the cursor has not moved yet, writes at the first byte of its local
+    /// view (absolute index = offset).
+    pub fn write(&self, value: u8) -> Result<(), RopeError> {
+        let pos = self.state.current.get().unwrap_or(self.state.offset.get());
+        self.state.set(self.rope, pos, value)?;
+        self.state.current.set(Some(pos + 1));
+        Ok(())
+    }
+
+    /// Return a shared-borrow iterator that yields bytes forward.
+    ///
+    /// Because the iterator holds `&self` rather than `&mut self`, methods
+    /// such as [`tell`](RopeCursor::tell) and [`seek`](RopeCursor::seek) can
+    /// be called on the cursor inside the loop body.
+    pub fn iter(&self) -> ForwardIter<'a, '_> {
+        ForwardIter { cursor: self }
+    }
+
+    /// Create a new [`ForwardCursor`] whose local position 0 starts at the
+    /// current absolute position of `self`.
+    ///
+    /// The new cursor shares the same underlying [`Rope`] (with the same
+    /// [`Cell`](std::cell::Cell)-based interior mutability) but has an
+    /// independent position and an `offset` equal to `self.absolute_tell()`.
+    /// If `self` has not moved yet, the new cursor starts at the same offset
+    /// as `self`.
+    pub fn cursor(&self) -> ForwardCursor<'a> {
+        let new_offset = self.rope_tell();
+        ForwardCursor {
+            rope: self.rope,
+            state: CursorState::with_offset(new_offset),
+        }
+    }
+}
+
+impl<'a> RopeCursor<'a> for ForwardCursor<'a> {
+    fn rope(&self) -> &'a Rope {
+        self.rope
+    }
+    fn state(&self) -> &CursorState<'a> {
+        &self.state
+    }
+
+    fn read_next(&self) -> Result<u8, RopeError> {
+        let next_pos = match self.state.current.get() {
+            Some(i) => i + 1,
+            None => self.state.offset.get(),
+        };
+        let value = self
+            .state
+            .get(self.rope, next_pos)
+            .ok_or(RopeError::OutOfBounds(format!(
+                "index out of bounds: i={} > {}",
+                next_pos,
+                self.rope.len()
+            )))?;
+        self.state.current.set(Some(next_pos));
+        Ok(value)
+    }
+
+    fn seek(&self, pos: isize, mode: SeekMode) -> Result<usize, RopeError> {
+        let offset = self.state.offset.get() as isize;
+        let abs_pos = match mode {
+            SeekMode::Absolute => pos + offset,
+            SeekMode::Relative => {
+                self.state.current.get().ok_or(RopeError::CurrentNotSet)? as isize + pos
+            }
+            SeekMode::RelativeToEnd => self.rope.len() as isize - pos,
+            SeekMode::Rope => pos,
+        };
+        if abs_pos < 0 {
+            return Err(RopeError::OutOfBounds(format!(
+                "index out of bounds: i={} < 0",
+                abs_pos
+            )));
+        }
+        self.state.current.set(Some(abs_pos as usize));
+        Ok(abs_pos as usize)
+    }
+}
+
+impl Iterator for ForwardCursor<'_> {
+    type Item = u8;
+    fn next(&mut self) -> Option<Self::Item> {
+        self.read_next().ok()
+    }
+}
+
+/// Shared-borrow iterator returned by [`ForwardCursor::iter`].
+pub struct ForwardIter<'a, 'b> {
+    cursor: &'b ForwardCursor<'a>,
+}
+
+impl Iterator for ForwardIter<'_, '_> {
+    type Item = u8;
+    fn next(&mut self) -> Option<u8> {
+        self.cursor.read_next().ok()
+    }
+}
diff --git a/src/obikrope/src/cursor/mod.rs b/src/obikrope/src/cursor/mod.rs
new file mode 100644
index 00000000..276f367b
--- /dev/null
+++ b/src/obikrope/src/cursor/mod.rs
@@ -0,0 +1,53 @@
+//! Cursors for sequential and random access over a [`Rope`].
+//!
+//! # Design
+//!
+//! A cursor borrows a `&'a Rope` and keeps a small block cache so that
+//! consecutive accesses within the same block cost O(1). The first access to a
+//! new block costs O(log n) (binary search in [`Rope::lookup`]); subsequent
+//! accesses within that block are free.
+//!
+//! All mutable state (current position, cache) is stored in [`Cell`](std::cell::Cell)
+//! fields, so every cursor method takes `&self` rather than `&mut self`. This means:
+//!
+//! - Two cursors can coexist on the same rope without lifetime conflicts.
+//! - The `iter()` method returns a lightweight wrapper that holds `&Cursor`,
+//!   allowing `cursor.tell()` or `cursor.seek()` to be called **inside a `for`
+//!   loop** over the same cursor.
+//!
+//! # Cursors
+//!
+//! | Type | Direction | First `read_next` | `seek(Relative, +n)` |
+//! |------|-----------|-------------------|----------------------|
+//! | [`ForwardCursor`] | start → end | index 0 | advances (+n) |
+//! | [`BackwardCursor`] | end → start | index `len-1` | retreats (+n) |
+//!
+//! # Example
+//!
+//! ```
+//! use obikrope::{Rope, RopeCursor};
+//!
+//! let mut rope = Rope::new(None);
+//! rope.push(b"ACGT".to_vec());
+//!
+//! let cursor = rope.fw_cursor();
+//! for byte in cursor.iter() {
+//!     // cursor.tell() is valid here — iter() holds &cursor, not &mut cursor
+//!     let _ = cursor.tell();
+//! }
+//! ```
+//!
+//! Submodules: [`state`] (shared block-cache state), [`traits`] (`SeekMode`,
+//! `RopeCursor`), [`forward`]/[`backward`] (the two cursor implementations).
+
+mod backward;
+mod forward;
+mod state;
+mod traits;
+
+#[cfg(test)]
+mod tests;
+
+pub use backward::BackwardCursor;
+pub use forward::ForwardCursor;
+pub use traits::{RopeCursor, SeekMode};
diff --git a/src/obikrope/src/cursor/state.rs b/src/obikrope/src/cursor/state.rs
new file mode 100644
index 00000000..a7d2015d
--- /dev/null
+++ b/src/obikrope/src/cursor/state.rs
@@ -0,0 +1,72 @@
+use std::cell::Cell;
+
+use crate::{Rope, RopeError};
+
+/// Per-cursor cache of the last accessed block, the current position, and the
+/// base offset that defines the cursor's local coordinate system.
+///
+/// All fields are [`Cell`]-wrapped so they can be mutated through a shared
+/// reference, enabling `&self` methods on cursors.
+#[derive(Clone)]
+pub struct CursorState<'a> {
+    block_idx: Cell<usize>,
+    block_start: Cell<usize>,
+    block_end: Cell<usize>,
+    block: Cell<&'a [Cell<u8>]>,
+    initialized: Cell<bool>,
+    pub(super) current: Cell<Option<usize>>,
+    /// Absolute rope index that maps to local position 0.
+    /// All user-facing coordinates are relative to this value.
+    pub(super) offset: Cell<usize>,
+}
+
+impl<'a> CursorState<'a> {
+    pub(super) fn new() -> Self {
+        Self::with_offset(0)
+    }
+
+    pub(super) fn with_offset(offset: usize) -> Self {
+        Self {
+            block_idx: Cell::new(0),
+            block_start: Cell::new(0),
+            block_end: Cell::new(0),
+            block: Cell::new(&[]),
+            initialized: Cell::new(false),
+            current: Cell::new(None),
+            offset: Cell::new(offset),
+        }
+    }
+
+    pub(super) fn get(&self, rope: &'a Rope, i: usize) -> Option<u8> {
+        if !self.initialized.get() || i < self.block_start.get() || i >= self.block_end.get() {
+            let (bi, bs, be) = rope.lookup(i)?;
+            self.block_idx.set(bi);
+            self.block_start.set(bs);
+            self.block_end.set(be);
+            self.block.set(rope.get_block(bi)?);
+            self.initialized.set(true);
+        }
+        Some(self.block.get()[i - self.block_start.get()].get())
+    }
+
+    pub(super) fn set(&self, rope: &'a Rope, i: usize, value: u8) -> Result<(), RopeError> {
+        if !self.initialized.get() || i < self.block_start.get() || i >= self.block_end.get() {
+            let (bi, bs, be) = rope.lookup(i).ok_or(RopeError::OutOfBounds(format!(
+                "index out of bounds: i={} > {}",
+                i,
+                rope.len()
+            )))?;
+            self.block_idx.set(bi);
+            self.block_start.set(bs);
+            self.block_end.set(be);
+            self.block
+                .set(rope.get_block(bi).ok_or(RopeError::BlockNotFound(format!(
+                    "Cannot find block for index {}",
+                    i
+                )))?);
+            self.initialized.set(true);
+        }
+        self.block.get()[i - self.block_start.get()].set(value);
+        Ok(())
+    }
+}
diff --git a/src/obikrope/src/cursor/tests.rs b/src/obikrope/src/cursor/tests.rs
new file mode 100644
index 00000000..37a3cef8
--- /dev/null
+++ b/src/obikrope/src/cursor/tests.rs
@@ -0,0 +1,298 @@
+use super::*;
+use crate::Rope;
+
+fn rope(data: &[u8]) -> Rope {
+    let mut r = Rope::new(None);
+    r.push(data.to_vec());
+    r
+}
+
+fn rope2(a: &[u8], b: &[u8]) -> Rope {
+    let mut r = Rope::new(None);
+    r.push(a.to_vec());
+    r.push(b.to_vec());
+    r
+}
+
+// ── ForwardCursor ─────────────────────────────────────────────────────────
+
+#[test]
+fn forward_reads_all_bytes() {
+    let r = rope(b"ACGT");
+    let c = r.fw_cursor();
+    let out: Vec<u8> = c.collect();
+    assert_eq!(out, b"ACGT");
+}
+
+#[test]
+fn forward_tell_tracks_position() {
+    let r = rope(b"ACGT");
+    let c = r.fw_cursor();
+    assert_eq!(c.tell(), None);
+    c.read_next().unwrap();
+    assert_eq!(c.tell(), Some(0));
+    c.read_next().unwrap();
+    assert_eq!(c.tell(), Some(1));
+}
+
+#[test]
+fn forward_iter_with_tell_inside_loop() {
+    let r = rope(b"ACGT");
+    let c = r.fw_cursor();
+    let mut positions = Vec::new();
+    for _ in c.iter() {
+        positions.push(c.tell());
+    }
+    assert_eq!(positions, vec![Some(0), Some(1), Some(2), Some(3)]);
+}
+
+#[test]
+fn forward_read_ahead() {
+    let r = rope(b"ACGT");
+    let c = r.fw_cursor();
+    c.read_next().unwrap(); // at 0 = 'A'
+    assert_eq!(c.read_ahead(1).unwrap(), b'C');
+    assert_eq!(c.read_ahead(2).unwrap(), b'G');
+    assert_eq!(c.tell(), Some(0)); // position unchanged
+}
+
+#[test]
+fn forward_write_and_read_back() {
+    let r = rope(b"ACGT");
+    let c = r.fw_cursor();
+    c.write(b'X').unwrap();
+    c.write(b'Y').unwrap();
+    let c2 = r.fw_cursor();
+    assert_eq!(c2.read_next().unwrap(), b'X');
+    assert_eq!(c2.read_next().unwrap(), b'Y');
+    assert_eq!(c2.read_next().unwrap(), b'G');
+}
+
+#[test]
+fn forward_rewind_and_reread() {
+    let r = rope(b"ACGT");
+    let c = r.fw_cursor();
+    c.read_next().unwrap(); // A  → current = Some(0)
+    c.read_next().unwrap(); // C  → current = Some(1)
+    c.read_next().unwrap(); // G  → current = Some(2)
+    c.rewind(1).unwrap(); // current = Some(1) → next read = index 2
+    assert_eq!(c.read_next().unwrap(), b'G');
+}
+
+#[test]
+fn forward_seek_absolute() {
+    let r = rope(b"ACGT");
+    let c = r.fw_cursor();
+    c.seek(2, SeekMode::Absolute).unwrap();
+    assert_eq!(c.read_next().unwrap(), b'T');
+}
+
+#[test]
+fn forward_seek_relative_to_end() {
+    let r = rope(b"ACGT");
+    // seek(1, RelativeToEnd): current = len-1 = 3; peek() reads index 3 = T.
+    let c = r.fw_cursor();
+    c.seek(1, SeekMode::RelativeToEnd).unwrap();
+    assert_eq!(c.peek().unwrap(), b'T');
+    // seek(2, RelativeToEnd): current = len-2 = 2; read_next reads index 3 = T.
+    let c2 = r.fw_cursor();
+    c2.seek(2, SeekMode::RelativeToEnd).unwrap();
+    assert_eq!(c2.read_next().unwrap(), b'T');
+}
+
+#[test]
+fn forward_get_random_access() {
+    let r = rope(b"ACGT");
+    let c = r.fw_cursor();
+    assert_eq!(c.get(0), Some(b'A'));
+    assert_eq!(c.get(3), Some(b'T'));
+    assert_eq!(c.get(4), None);
+}
+
+#[test]
+fn forward_crosses_block_boundary() {
+    let r = rope2(b"AC", b"GT");
+    let c = r.fw_cursor();
+    let out: Vec<u8> = c.collect();
+    assert_eq!(out, b"ACGT");
+}
+
+// ── BackwardCursor ────────────────────────────────────────────────────────
+
+#[test]
+fn backward_reads_all_bytes_in_reverse() {
+    let r = rope(b"ACGT");
+    let c = r.bw_cursor();
+    let out: Vec<u8> = c.collect();
+    assert_eq!(out, b"TGCA");
+}
+
+#[test]
+fn backward_tell_tracks_position() {
+    let r = rope(b"ACGT");
+    let c = r.bw_cursor();
+    assert_eq!(c.tell(), None);
+    c.read_next().unwrap(); // reads index 3
+    assert_eq!(c.tell(), Some(3));
+    c.read_next().unwrap(); // reads index 2
+    assert_eq!(c.tell(), Some(2));
+}
+
+#[test]
+fn backward_iter_with_tell_and_seek_inside_loop() {
+    let r = rope(b"ACGT");
+    let c = r.bw_cursor();
+    let mut restart: usize = 0;
+    for byte in c.iter() {
+        if byte == b'G' {
+            restart = c.tell().unwrap();
+        }
+        if byte == b'A' {
+            // seek back to G and break
+            c.seek(restart as isize, SeekMode::Absolute).ok();
+            break;
+        }
+    }
+    assert_eq!(c.tell(), Some(restart));
+}
+
+#[test]
+fn backward_rewind_moves_toward_end() {
+    let r = rope(b"ACGT");
+    let c = r.bw_cursor();
+    c.read_next().unwrap(); // index 3 = T
+    c.read_next().unwrap(); // index 2 = G
+    c.rewind(1).unwrap(); // back to index 3
+    assert_eq!(c.tell(), Some(3));
+    assert_eq!(c.read_next().unwrap(), b'G'); // reads index 2
+}
+
+#[test]
+fn backward_crosses_block_boundary() {
+    let r = rope2(b"AC", b"GT");
+    let c = r.bw_cursor();
+    let out: Vec<u8> = c.collect();
+    assert_eq!(out, b"TGCA");
+}
+
+#[test]
+fn backward_empty_rope_returns_error() {
+    let r = Rope::new(None);
+    let c = r.bw_cursor();
+    assert!(c.read_next().is_err());
+}
+
+#[test]
+fn forward_empty_rope_returns_error() {
+    let r = Rope::new(None);
+    let c = r.fw_cursor();
+    assert!(c.read_next().is_err());
+}
+
+// ── offset / sub-cursor ───────────────────────────────────────────────────
+
+#[test]
+fn forward_cursor_reads_from_offset() {
+    // cursor() at current=Some(2) → new cursor reads from index 2
+    let r = rope(b"ABCDE");
+    let c = r.fw_cursor();
+    c.read_next().unwrap(); // A → current=Some(0)
+    c.read_next().unwrap(); // B → current=Some(1)
+    c.read_next().unwrap(); // C → current=Some(2)
+    let sub = c.cursor(); // offset=2 (absolute_tell=2)
+    assert_eq!(sub.read_next().unwrap(), b'C'); // reads index 2
+    assert_eq!(sub.tell(), Some(0)); // relative: 2-2=0
+    assert_eq!(sub.rope_tell(), 2);
+    assert_eq!(sub.read_next().unwrap(), b'D');
+    assert_eq!(sub.tell(), Some(1)); // relative: 3-2=1
+}
+
+#[test]
+fn forward_cursor_get_uses_relative_index() {
+    let r = rope(b"ABCDE");
+    let c = r.fw_cursor();
+    c.read_next().unwrap(); // A → current=Some(0), absolute_tell=0
+    let _sub = c.cursor(); // offset=0 — created to show cursor() compiles; not used further
+    // From sub2 with offset=2: get(0)=C, get(2)=E
+    let c2 = r.fw_cursor();
+    c2.read_next().unwrap(); // at 0
+    c2.read_next().unwrap(); // at 1
+    c2.read_next().unwrap(); // at 2, absolute=2
+    let sub2 = c2.cursor(); // offset=2
+    assert_eq!(sub2.get(0), Some(b'C')); // local 0 = absolute 2
+    assert_eq!(sub2.get(2), Some(b'E')); // local 2 = absolute 4
+    assert_eq!(sub2.get(3), None); // local 3 = absolute 5, OOB
+}
+
+#[test]
+fn forward_cursor_len_reflects_offset() {
+    let r = rope(b"ABCDE"); // len=5
+    let c = r.fw_cursor();
+    c.read_next().unwrap();
+    c.read_next().unwrap();
+    c.read_next().unwrap(); // absolute_tell=2
+    let sub = c.cursor(); // offset=2
+    assert_eq!(sub.len(), 3); // 5 - 2
+}
+
+#[test]
+fn forward_reset_goes_back_to_start() {
+    let r = rope(b"ABCDE");
+    let c = r.fw_cursor();
+    c.read_next().unwrap(); // A
+    c.read_next().unwrap(); // B
+    c.reset();
+    assert_eq!(c.tell(), None);
+    assert_eq!(c.read_next().unwrap(), b'A'); // starts over
+}
+
+#[test]
+fn forward_sub_cursor_write_and_reset() {
+    // Write two bytes, discard them via reset(), write again.
+    let r = rope(b"XXXXX");
+    let c = r.fw_cursor();
+    c.write(b'A').unwrap(); // absolute 0 → current=Some(1)
+    c.write(b'B').unwrap(); // absolute 1 → current=Some(2)
+    let seg = c.cursor(); // absolute_tell=2, offset=2
+    seg.write(b'C').unwrap(); // absolute 2 → current=Some(3), tell=3-2=1
+    seg.write(b'D').unwrap(); // absolute 3 → current=Some(4), tell=4-2=2
+    assert_eq!(seg.tell(), Some(2)); // 2 bytes written into this segment
+    seg.reset();
+    assert_eq!(seg.tell(), None);
+    seg.write(b'E').unwrap(); // absolute 2 again
+    let all: Vec<u8> = r.fw_cursor().collect();
+    assert_eq!(&all[..3], b"ABE");
+}
+
+#[test]
+fn backward_cursor_stops_at_offset() {
+    // BackwardCursor.cursor() creates a cursor with offset = absolute_tell.
+    // offset = local position 0 (inclusive lower bound).
+    // The cursor reads rope.len()-1 downto offset, then stops.
+    let r = rope(b"ABCDE"); // 0=A 1=B 2=C 3=D 4=E
+    let bw = r.bw_cursor();
+    bw.read_next().unwrap(); // E=4, current=Some(4)
+    bw.read_next().unwrap(); // D=3, current=Some(3), absolute_tell=3
+    // sub: offset=3, reads from 4 down to 3 (inclusive), then stops.
+    let sub = bw.cursor();
+    assert_eq!(sub.read_next().unwrap(), b'E'); // index 4, tell=4-3=1
+    assert_eq!(sub.read_next().unwrap(), b'D'); // index 3, tell=3-3=0 (local 0)
+    assert!(sub.read_next().is_err()); // would go to 2 < offset=3
+}
+
+#[test]
+fn forward_absolute_tell_unchanged_by_offset() {
+    let r = rope(b"ABCDE");
+    let c = r.fw_cursor();
+    c.read_next().unwrap(); // absolute=0
+    let sub = c.cursor(); // offset=0
+    sub.read_next().unwrap(); // reads index 0, absolute_tell=0
+    sub.read_next().unwrap(); // reads index 1, absolute_tell=1
+    assert_eq!(sub.tell(), Some(1));
+    assert_eq!(sub.rope_tell(), 1);
+    // sub2 with offset=1
+    let sub2 = sub.cursor(); // offset=1
+    sub2.read_next().unwrap(); // reads index 1, absolute=1
+    assert_eq!(sub2.tell(), Some(0)); // relative: 1-1=0
+    assert_eq!(sub2.rope_tell(), 1);
+}
diff --git a/src/obikrope/src/cursor/traits.rs b/src/obikrope/src/cursor/traits.rs
new file mode 100644
index 00000000..1487da6d
--- /dev/null
+++ b/src/obikrope/src/cursor/traits.rs
@@ -0,0 +1,127 @@
+use crate::{Rope, RopeError};
+
+use super::state::CursorState;
+
+/// Controls how the `pos` argument of [`RopeCursor::seek`] is interpreted.
+#[derive(Clone, Copy)]
+pub enum SeekMode {
+    /// `pos` is an absolute byte index from the start of the rope.
+    Absolute,
+    /// `pos` is relative to the current position.
+    /// Positive = forward for [`ForwardCursor`](super::ForwardCursor), backward for [`BackwardCursor`](super::BackwardCursor).
+    Relative,
+    /// `pos` is counted back from the end: target = `len - pos`.
+    RelativeToEnd,
+    /// `pos` is a rope index relative to the start of the rope.
+    Rope,
+}
+
+/// Common interface for all rope cursors.
+///
+/// # Required methods
+///
+/// Implementors must provide [`rope`](RopeCursor::rope),
+/// [`state`](RopeCursor::state), [`read_next`](RopeCursor::read_next) and
+/// [`seek`](RopeCursor::seek). Everything else has a default implementation.
+///
+/// The direction of `read_next` and the sign convention for
+/// [`SeekMode::Relative`] differ between [`ForwardCursor`](super::ForwardCursor)
+/// and [`BackwardCursor`](super::BackwardCursor); all other methods are identical.
+pub trait RopeCursor<'a> {
+    /// The rope this cursor is bound to.
+    fn rope(&self) -> &'a Rope;
+    /// Internal cache state — implementation detail exposed for default methods.
+    fn state(&self) -> &CursorState<'a>;
+
+    /// Read the next byte in cursor direction and advance the position.
+    /// Returns `Err` at the exhausted end.
+    fn read_next(&self) -> Result<u8, RopeError>;
+
+    /// Move the cursor to a new position.
+    ///
+    /// `pos` is interpreted according to `mode`:
+    /// - [`Absolute`](SeekMode::Absolute): local coordinate (`pos + offset` in the rope).
+    /// - [`Rope`](SeekMode::Rope): raw rope index, ignores the offset.  Pass a value
+    ///   from [`rope_tell`](RopeCursor::rope_tell) to restore a saved position.
+    /// - [`Relative`](SeekMode::Relative): delta from the current position.
+    ///   For [`ForwardCursor`](super::ForwardCursor), positive advances toward the end;
+    ///   for [`BackwardCursor`](super::BackwardCursor), positive retreats toward the start.
+    /// - [`RelativeToEnd`](SeekMode::RelativeToEnd): `rope.len() - pos`.
+    ///
+    /// Returns the new position as a **rope index** (same value as
+    /// [`rope_tell`](RopeCursor::rope_tell) would return immediately after).
+    fn seek(&self, pos: isize, mode: SeekMode) -> Result<usize, RopeError>;
+
+    // ── default methods ───────────────────────────────────────────────────────
+
+    /// Read the byte at **local** index `i` (relative to the cursor's offset)
+    /// without moving the position.
+    fn get(&self, i: usize) -> Option<u8> {
+        self.state().get(self.rope(), i + self.state().offset.get())
+    }
+
+    /// Write `value` at **local** index `i` without moving the position.
+    fn set(&self, i: usize, value: u8) -> Result<(), RopeError> {
+        self.state()
+            .set(self.rope(), i + self.state().offset.get(), value)
+    }
+
+    /// Current position relative to the cursor's offset, or `None` if the
+    /// cursor has not moved yet.
+    fn tell(&self) -> Option<usize> {
+        let abs = self.state().current.get()?;
+        Some(abs.saturating_sub(self.state().offset.get()))
+    }
+
+    /// Current position as an absolute rope index.
+    ///
+    /// Unlike [`tell`](RopeCursor::tell), this method **always** returns a
+    /// value: if the cursor has not moved yet, it returns the cursor's offset
+    /// (the rope index of local position 0).
+    ///
+    /// Use the returned value with [`SeekMode::Rope`] to restore a position,
+    /// or as a truncation point after a write pass.
+    fn rope_tell(&self) -> usize {
+        self.state()
+            .current
+            .get()
+            .unwrap_or(self.state().offset.get())
+    }
+
+    /// Number of bytes visible through this cursor (`rope.len() - offset`).
+    fn len(&self) -> usize {
+        self.rope().len().saturating_sub(self.state().offset.get())
+    }
+
+    /// Reset the cursor to its initial state (positioned before the first
+    /// byte of its local view).  Equivalent to `seek(0, Absolute)` on a
+    /// fresh cursor, but works even when `current` is `None`.
+    fn reset(&self) {
+        self.state().current.set(None);
+    }
+
+    /// Read the byte at the current position without advancing.
+    fn peek(&self) -> Option<u8> {
+        self.state().get(self.rope(), self.state().current.get()?)
+    }
+
+    /// Write `value` at the current position without advancing.
+    fn poke(&self, value: u8) -> Result<(), RopeError> {
+        let pos = self.state().current.get().ok_or(RopeError::CurrentNotSet)?;
+        self.state().set(self.rope(), pos, value)
+    }
+
+    /// Move backward by `go_back_of` steps (toward lower indices for
+    /// [`ForwardCursor`](super::ForwardCursor), toward higher indices for
+    /// [`BackwardCursor`](super::BackwardCursor)).
+    fn rewind(&self, go_back_of: usize) -> Result<(), RopeError> {
+        self.seek(-(go_back_of as isize), SeekMode::Relative)?;
+        Ok(())
+    }
+
+    /// Move forward by `ahead` steps (opposite of [`rewind`](RopeCursor::rewind)).
+    fn forward(&self, ahead: usize) -> Result<(), RopeError> {
+        self.seek(ahead as isize, SeekMode::Relative)?;
+        Ok(())
+    }
+}
diff --git a/src/obipipeline/src/scheduler.rs b/src/obipipeline/src/scheduler.rs
deleted file mode 100644
index 956570bd..00000000
--- a/src/obipipeline/src/scheduler.rs
+++ /dev/null
@@ -1,878 +0,0 @@
-use crossbeam_channel::{Receiver, Select, Sender, bounded};
-use std::error::Error;
-use std::fmt;
-use std::marker::PhantomData;
-use std::sync::Arc;
-use std::thread;
-
-/// Error type for pipeline operations.
-#[derive(Debug)]
-pub enum PipelineError {
-    /// A stage received a `PipelineData` variant it did not expect.
-    TypeMismatch,
-    /// The step kind is not compatible with the data type.
-    StepKindMismatch(&'static str),
-    /// The source has no more data to produce.
-    EndOfStream,
-    /// An error occurred inside a stage (e.g., I/O, parsing, custom logic).
-    StepError(Box<dyn Error + Send + Sync>),
-}
-
-impl fmt::Display for PipelineError {
-    fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
-        match self {
-            PipelineError::TypeMismatch => write!(f, "data type mismatch in pipeline stage"),
-            PipelineError::StepKindMismatch(s) => write!(f, "step kind mismatch: {}", s),
-            PipelineError::EndOfStream => write!(f, "end of input stream"),
-            PipelineError::StepError(e) => write!(f, "stage error: {}", e),
-        }
-    }
-}
-
-impl Error for PipelineError {
-    fn source(&self) -> Option<&(dyn Error + 'static)> {
-        match self {
-            PipelineError::StepError(e) => Some(e.as_ref()),
-            _ => None,
-        }
-    }
-}
-
-// ── Function types ────────────────────────────────────────────────────────────
-
-/// Fonction source : appelée répétitivement, retourne le prochain item ou EndOfStream.
-/// `FnMut` car elle maintient un état interne (position dans l'itérateur).
-pub type SourceFn<D> = Box<dyn FnMut() -> Result<D, PipelineError> + Send>;
-
-/// Fonction sink : consomme un item final, peut échouer (erreur d'I/O, etc.).
-pub type SinkFn<D> = Box<dyn Fn(D) -> Result<(), PipelineError> + Send>;
-
-/// Fonction de transformation partagée entre workers via Arc.
-pub type SharedFn<D> = Arc<dyn Fn(D) -> Result<D, PipelineError> + Send + Sync>;
-
-/// Fonction de transformation 1→N (flat map) partagée entre workers via Arc.
-///
-/// La fonction reçoit l'item d'entrée, un canal `push` pour envoyer chaque item
-/// produit, et un canal `delta` pour signaler au scheduler combien d'items
-/// supplémentaires sont entrés dans le pipeline (N-1 si N items produits).
-/// Elle doit appeler `delta.send(N - 1)` **après** avoir poussé tous les items.
-pub type SharedFlatFn<D> =
-    Arc<dyn Fn(D, &Sender<Result<D, PipelineError>>, &Sender<isize>) + Send + Sync>;
-
-// ── Stage enum ────────────────────────────────────────────────────────────────
-
-/// Une étape du pipeline : transform classique (1→1) ou flat transform (1→N).
-pub enum Stage<D> {
-    Transform(SharedFn<D>),
-    Flat(SharedFlatFn<D>),
-}
-
-impl<D> Clone for Stage<D> {
-    fn clone(&self) -> Self {
-        match self {
-            Stage::Transform(f) => Stage::Transform(Arc::clone(f)),
-            Stage::Flat(f) => Stage::Flat(Arc::clone(f)),
-        }
-    }
-}
-
-// ── Worker task ───────────────────────────────────────────────────────────────
-
-enum WorkerTask<D> {
-    Transform(D, usize),
-    Flat(D, usize),
-}
-
-// ── Thread runners ────────────────────────────────────────────────────────────
-
-fn source_runner<DATA>(
-    mut source: SourceFn<DATA>,
-    capacity: usize,
-) -> (
-    Receiver<Result<DATA, PipelineError>>,
-    thread::JoinHandle<()>,
-)
-where
-    DATA: Send + Sync + 'static,
-{
-    let (tx, rx) = bounded(capacity);
-    let handle = thread::spawn(move || {
-        loop {
-            match source() {
-                Ok(data) => {
-                    if tx.send(Ok(data)).is_err() {
-                        break;
-                    }
-                }
-                Err(PipelineError::EndOfStream) => break,
-                Err(e) => {
-                    eprintln!("Source error: {:?}", e);
-                    let _ = tx.send(Err(e));
-                    break;
-                }
-            }
-        }
-    });
-    (rx, handle)
-}
-
-/// Lance un thread worker du pool.
-///
-/// Gère deux types de tâches :
-/// - `Transform` : applique `f(data)` et envoie le résultat dans `result_tx`.
-/// - `Flat` : appelle `f(data, &push_tx, &delta_tx)` ; la fonction elle-même
-///   pousse ses items dans `push_tx` et envoie `N-1` dans `delta_tx`.
-fn transform_runner<DATA>(
-    task_rx: Receiver<WorkerTask<DATA>>,
-    stages: Vec<Stage<DATA>>,
-    stage_txs: Vec<Sender<Result<DATA, PipelineError>>>,
-    flat_delta_tx: Sender<isize>,
-) -> thread::JoinHandle<()>
-where
-    DATA: Send + Sync + 'static,
-{
-    thread::spawn(move || {
-        while let Ok(task) = task_rx.recv() {
-            match task {
-                WorkerTask::Transform(data, idx) => {
-                    if let Stage::Transform(f) = &stages[idx] {
-                        let _ = stage_txs[idx].send(f(data));
-                    }
-                }
-                WorkerTask::Flat(data, idx) => {
-                    if let Stage::Flat(f) = &stages[idx] {
-                        f(data, &stage_txs[idx], &flat_delta_tx);
-                    }
-                }
-            }
-        }
-    })
-}
-
-/// Lance le thread sink.
-fn sink_runner<DATA>(
-    sink: SinkFn<DATA>,
-    capacity: usize,
-) -> (
-    Sender<DATA>,
-    Receiver<PipelineError>,
-    thread::JoinHandle<()>,
-)
-where
-    DATA: Send + Sync + 'static,
-{
-    let (data_tx, data_rx) = bounded(capacity);
-    let (err_tx, err_rx) = bounded(capacity);
-    let handle = thread::spawn(move || {
-        for data in data_rx {
-            if let Err(e) = sink(data) {
-                let _ = err_tx.send(e);
-                break;
-            }
-        }
-    });
-    (data_tx, err_rx, handle)
-}
-
-// ── Pipeline ──────────────────────────────────────────────────────────────────
-
-pub struct Pipeline<DATA> {
-    source: SourceFn<DATA>,
-    stages: Vec<Stage<DATA>>,
-    sink: SinkFn<DATA>,
-}
-
-impl<DATA> Pipeline<DATA> {
-    pub fn new(
-        source: SourceFn<DATA>,
-        stages: Vec<Stage<DATA>>,
-        sink: SinkFn<DATA>,
-    ) -> Self {
-        Self { source, stages, sink }
-    }
-}
-
-// ── WorkerPool ────────────────────────────────────────────────────────────────
-
-pub struct WorkerPool<DATA> {
-    pipeline: Pipeline<DATA>,
-    handles: Vec<std::thread::JoinHandle<()>>,
-    n_workers: usize,
-    capacity: usize,
-}
-
-impl<DATA> WorkerPool<DATA>
-where
-    DATA: Send + Sync + 'static,
-{
-    pub fn new(pipeline: Pipeline<DATA>, n_workers: usize, capacity: usize) -> Self {
-        Self {
-            pipeline,
-            handles: Vec::new(),
-            n_workers,
-            capacity,
-        }
-    }
-
-    pub fn run(mut self) {
-        let n = self.pipeline.stages.len();
-
-        // ── Canaux inter-stages ────────────────────────────────────────────
-        // stage_txs[i] / stage_rxs[i] : sortie du stage i
-        let mut stage_txs: Vec<Sender<Result<DATA, PipelineError>>> = Vec::new();
-        let mut stage_rxs: Vec<Receiver<Result<DATA, PipelineError>>> = Vec::new();
-        for _ in 0..n {
-            let (tx, rx) = bounded(self.capacity);
-            stage_txs.push(tx);
-            stage_rxs.push(rx);
-        }
-
-        // ── Source thread ──────────────────────────────────────────────────
-        let (source_rx, src_handle) = source_runner(self.pipeline.source, self.capacity);
-        self.handles.push(src_handle);
-
-        let stages = self.pipeline.stages;
-
-        // ── Canal delta pour les flat stages ───────────────────────────────
-        // Chaque flat worker envoie `N-1` ici après avoir poussé N items.
-        // Le scheduler ajuste `in_flight` en conséquence.
-        let (flat_delta_tx, flat_delta_rx) = bounded::<isize>(self.capacity);
-
-        // ── Worker pool ────────────────────────────────────────────────────
-        let (worker_tx, worker_rx): (Sender<WorkerTask<DATA>>, Receiver<WorkerTask<DATA>>) =
-            bounded(self.capacity);
-
-        for _ in 0..self.n_workers {
-            self.handles.push(transform_runner(
-                worker_rx.clone(),
-                stages.iter().map(Stage::clone).collect(),
-                stage_txs.clone(),
-                flat_delta_tx.clone(),
-            ));
-        }
-        // Le scheduler ne tient plus flat_delta_tx : les workers le détiennent.
-        // On le drop ici pour que le canal se ferme quand les workers terminent.
-        drop(flat_delta_tx);
-
-        // ── Sink thread ────────────────────────────────────────────────────
-        let (sink_tx, sink_err_rx, sink_handle) = sink_runner(self.pipeline.sink, self.capacity);
-        self.handles.push(sink_handle);
-
-        // ── Boucle principale ──────────────────────────────────────────────
-        //
-        // `in_flight` (isize) = nb d'items qui doivent encore atteindre le sink.
-        // Peut temporairement être négatif si un flat worker a poussé ses items
-        // avant que le scheduler ait reçu le delta correspondant.
-        //
-        // `flat_workers_active` = nb de flat workers en cours d'exécution.
-        // Empêche la terminaison prématurée quand in_flight vaut 0 mais qu'un
-        // flat worker n'a pas encore envoyé son delta.
-        //
-        // Priorités du Select biaisé (index le plus bas = priorité la plus haute) :
-        //   0        → sink_err_rx    (arrêt immédiat sur erreur sink)
-        //   1        → flat_delta_rx  (mettre à jour in_flight avant de dispatcher)
-        //   2..=n+1  → stage_rxs[n-1..0]  (vider le pipeline en priorité)
-        //   n+2      → source_rx      (dernier recours : nouvelles données)
-        //
-        // Quand k = 0             : erreur du sink
-        // Quand k = 1             : delta d'un flat worker
-        // Quand 2 ≤ k ≤ n+1      : résultat du stage n+1-k
-        // Quand k = n+2           : item source
-        //
-        // Terminaison : source tarie ET in_flight == 0 ET aucun flat worker actif.
-        {
-            let mut source_done = false;
-            let mut in_flight: isize = 0;
-            let mut flat_workers_active: usize = 0;
-
-            loop {
-                if source_done && in_flight == 0 && flat_workers_active == 0 {
-                    break;
-                }
-
-                let mut sel = Select::new_biased();
-                sel.recv(&sink_err_rx);                 // index 0
-                sel.recv(&flat_delta_rx);               // index 1
-                for rx in stage_rxs.iter().rev() {
-                    sel.recv(rx);                       // indices 2..=n+1
-                }
-                let src_idx = if !source_done {
-                    Some(sel.recv(&source_rx))          // index n+2
-                } else {
-                    None
-                };
-
-                let oper = sel.select();
-                let k = oper.index();
-
-                if k == 0 {
-                    // ── Erreur du sink ────────────────────────────────────
-                    match oper.recv(&sink_err_rx) {
-                        Ok(e) => { eprintln!("Sink error: {:?}", e); break; }
-                        Err(_) => break,
-                    }
-                } else if k == 1 {
-                    // ── Delta d'un flat worker ────────────────────────────
-                    // delta = N - 1  (N items poussés, 1 item consommé)
-                    match oper.recv(&flat_delta_rx) {
-                        Ok(delta) => {
-                            in_flight += delta;
-                            flat_workers_active -= 1;
-                        }
-                        Err(_) => {}
-                    }
-                } else if src_idx == Some(k) {
-                    // ── Nouvel item depuis la source ──────────────────────
-                    match oper.recv(&source_rx) {
-                        Ok(Ok(data)) => {
-                            if n == 0 {
-                                let _ = sink_tx.send(data);
-                            } else {
-                                in_flight += 1;
-                                dispatch(
-                                    data, 0,
-                                    &stages, &worker_tx,
-                                    &mut flat_workers_active,
-                                );
-                            }
-                        }
-                        Ok(Err(e)) => eprintln!("Source error: {:?}", e),
-                        Err(_) => source_done = true,
-                    }
-                } else {
-                    // ── Résultat d'un stage intermédiaire ─────────────────
-                    // k ∈ [2, n+1]  →  stage = n+1 - k
-                    let stage = n + 1 - k;
-                    match oper.recv(&stage_rxs[stage]) {
-                        Ok(Ok(data)) => {
-                            if stage == n - 1 {
-                                in_flight -= 1;
-                                let _ = sink_tx.send(data);
-                            } else {
-                                dispatch(
-                                    data, stage + 1,
-                                    &stages, &worker_tx,
-                                    &mut flat_workers_active,
-                                );
-                            }
-                        }
-                        Ok(Err(e)) => eprintln!("Stage {} error: {:?}", stage, e),
-                        Err(_) => break,
-                    }
-                }
-            }
-        }
-
-        drop(worker_tx);
-        drop(sink_tx);
-
-        for h in self.handles {
-            let _ = h.join();
-        }
-    }
-}
-
-// ── Pipe ──────────────────────────────────────────────────────────────────────
-
-/// Typed, composable iterator transformer.
-///
-/// A `Pipe<D, In, Out>` is a pure description of pipeline stages — no threads,
-/// no channels, no scheduler. Call `.apply(iter, n_workers, capacity)` to start
-/// execution and get back a `PipeIter<Out>`.
-///
-/// Compose two pipes with `.then()`: the resulting `Pipe` holds the concatenated
-/// stage list, so a single scheduler is created when `.apply()` is eventually called.
-pub struct Pipe<D, In, Out> {
-    stages:   Vec<Stage<D>>,
-    wrap:     Arc<dyn Fn(In) -> D   + Send + Sync>,
-    unwrap:   Arc<dyn Fn(D)  -> Out + Send + Sync>,
-    _phantom: PhantomData<(In, Out)>,
-}
-
-impl<D, In, Out> Pipe<D, In, Out> {
-    /// Build a `Pipe` from stages and wrap/unwrap converters.
-    /// Prefer the `make_pipe!` macro.
-    pub fn new(
-        stages:  Vec<Stage<D>>,
-        wrap:    Arc<dyn Fn(In) -> D   + Send + Sync>,
-        unwrap:  Arc<dyn Fn(D)  -> Out + Send + Sync>,
-    ) -> Self {
-        Self { stages, wrap, unwrap, _phantom: PhantomData }
-    }
-
-    /// Concatenate stages from two pipes into one.
-    ///
-    /// Requires `Out` of `self` == `In` of `other`.  The single scheduler
-    /// created at `.apply()` time sees the full combined stage list.
-    pub fn then<Next>(self, other: Pipe<D, Out, Next>) -> Pipe<D, In, Next> {
-        Pipe {
-            stages:   self.stages.into_iter().chain(other.stages).collect(),
-            wrap:     self.wrap,
-            unwrap:   other.unwrap,
-            _phantom: PhantomData,
-        }
-    }
-}
-
-impl<D, In, Out> Pipe<D, In, Out>
-where
-    D:   Send + Sync + 'static,
-    In:  Send + 'static,
-    Out: Send + 'static,
-{
-    /// Run the pipeline in a background thread; returns an iterator over the output.
-    pub fn apply(
-        self,
-        input:     impl Iterator<Item = In> + Send + 'static,
-        n_workers: usize,
-        capacity:  usize,
-    ) -> PipeIter<Out> {
-        let wrap   = Arc::clone(&self.wrap);
-        let unwrap = Arc::clone(&self.unwrap);
-
-        let mut iter = input;
-        let source: SourceFn<D> = Box::new(move || match iter.next() {
-            Some(x) => Ok(wrap(x)),
-            None    => Err(PipelineError::EndOfStream),
-        });
-
-        let (out_tx, out_rx) = bounded::<Out>(capacity);
-        let sink: SinkFn<D> = Box::new(move |data: D| {
-            out_tx.send(unwrap(data)).map_err(|_| {
-                PipelineError::StepError(Box::new(std::io::Error::new(
-                    std::io::ErrorKind::BrokenPipe,
-                    "output channel closed",
-                )))
-            })
-        });
-
-        let pipeline = Pipeline::new(source, self.stages, sink);
-        let handle = thread::spawn(move || {
-            WorkerPool::new(pipeline, n_workers, capacity).run();
-        });
-
-        PipeIter { rx: out_rx, handle: Some(handle) }
-    }
-}
-
-// ── PipeIter ──────────────────────────────────────────────────────────────────
-
-/// Iterator over the output of `Pipe::apply()`.
-pub struct PipeIter<Out> {
-    rx:     Receiver<Out>,
-    handle: Option<thread::JoinHandle<()>>,
-}
-
-impl<Out> Iterator for PipeIter<Out> {
-    type Item = Out;
-
-    fn next(&mut self) -> Option<Out> {
-        self.rx.recv().ok()
-    }
-}
-
-impl<Out> Drop for PipeIter<Out> {
-    fn drop(&mut self) {
-        // Drain buffered items so the scheduler can unblock if the channel is full.
-        while self.rx.try_recv().is_ok() {}
-        if let Some(h) = self.handle.take() {
-            let _ = h.join();
-        }
-    }
-}
-
-/// Envoie `data` au stage `stage_idx`.
-/// Pour un `Transform`, empile une `WorkerTask::Transform`.
-/// Pour un `Flat`, incrémente `flat_workers_active` et empile une `WorkerTask::Flat`.
-#[inline]
-fn dispatch<DATA>(
-    data: DATA,
-    stage_idx: usize,
-    stages: &[Stage<DATA>],
-    worker_tx: &Sender<WorkerTask<DATA>>,
-    flat_workers_active: &mut usize,
-) {
-    match &stages[stage_idx] {
-        Stage::Transform(_) => {
-            let _ = worker_tx.send(WorkerTask::Transform(data, stage_idx));
-        }
-        Stage::Flat(_) => {
-            *flat_workers_active += 1;
-            let _ = worker_tx.send(WorkerTask::Flat(data, stage_idx));
-        }
-    }
-}
-
-// ── Macros ────────────────────────────────────────────────────────────────────
-
-/// Creates a `SourceFn` from an iterator of plain values.
-#[macro_export]
-macro_rules! make_source {
-    ($enum:ident, $iterator:expr, $output:ident) => {{
-        let mut iter = $iterator.into_iter();
-        Box::new(
-            move || -> ::std::result::Result<$enum, $crate::PipelineError> {
-                match iter.next() {
-                    Some(x) => Ok($enum::$output(x)),
-                    None => Err($crate::PipelineError::EndOfStream),
-                }
-            },
-        )
-            as Box<dyn FnMut() -> ::std::result::Result<$enum, $crate::PipelineError> + Send>
-    }};
-}
-
-/// Creates a `SourceFn` from an iterator of `Result<T, E>`.
-#[macro_export]
-macro_rules! make_source_fallible {
-    ($enum:ident, $iterator:expr, $output:ident) => {{
-        let mut iter = $iterator.into_iter();
-        Box::new(
-            move || -> ::std::result::Result<$enum, $crate::PipelineError> {
-                match iter.next() {
-                    Some(Ok(x)) => Ok($enum::$output(x)),
-                    Some(Err(e)) => Err($crate::PipelineError::StepError(Box::new(e))),
-                    None => Err($crate::PipelineError::EndOfStream),
-                }
-            },
-        )
-            as Box<dyn FnMut() -> ::std::result::Result<$enum, $crate::PipelineError> + Send>
-    }};
-}
-
-/// Creates a `Stage::Transform` from a pure (non-fallible) function `Fn(T) -> U`.
-#[macro_export]
-macro_rules! make_transform {
-    ($enum:ident, $func:tt, $input:ident, $output:ident) => {{
-        let __f = $func;
-        $crate::Stage::Transform(
-            ::std::sync::Arc::from(Box::new(
-                move |data: $enum| -> ::std::result::Result<$enum, $crate::PipelineError> {
-                    match data {
-                        $enum::$input(x) => Ok($enum::$output(__f(x))),
-                        _ => Err($crate::PipelineError::TypeMismatch),
-                    }
-                },
-            )
-                as Box<
-                    dyn Fn($enum) -> ::std::result::Result<$enum, $crate::PipelineError>
-                        + Send
-                        + Sync,
-                >)
-        )
-    }};
-}
-
-/// Creates a `Stage::Transform` from a fallible function `Fn(T) -> Result<U, E>`.
-#[macro_export]
-macro_rules! make_transform_fallible {
-    ($enum:ident, $func:tt, $input:ident, $output:ident) => {{
-        let __f = $func;
-        $crate::Stage::Transform(
-            ::std::sync::Arc::from(Box::new(
-                move |data: $enum| -> ::std::result::Result<$enum, $crate::PipelineError> {
-                    match data {
-                        $enum::$input(inner) => {
-                            let result = __f(inner)
-                                .map_err(|e| $crate::PipelineError::StepError(Box::new(e)))?;
-                            Ok($enum::$output(result))
-                        }
-                        _ => Err($crate::PipelineError::TypeMismatch),
-                    }
-                },
-            )
-                as Box<
-                    dyn Fn($enum) -> ::std::result::Result<$enum, $crate::PipelineError>
-                        + Send
-                        + Sync,
-                >)
-        )
-    }};
-}
-
-/// Creates a `Stage::Flat` from a function `Fn(T) -> impl IntoIterator<Item = U>`.
-///
-/// Pour chaque item produit par l'itérateur, il est poussé individuellement dans
-/// le canal de sortie, permettant au scheduler de dispatcher les items en parallèle
-/// dès qu'un worker est disponible.
-#[macro_export]
-macro_rules! make_flat_transform {
-    ($enum:ident, $func:tt, $input:ident, $output:ident) => {{
-        let __f = $func;
-        $crate::Stage::Flat(
-            ::std::sync::Arc::new(
-                move |data: $enum,
-                      push: &$crate::PipelineSender<
-                          ::std::result::Result<$enum, $crate::PipelineError>,
-                      >,
-                      delta: &$crate::PipelineSender<isize>| {
-                    match data {
-                        $enum::$input(inner) => {
-                            let mut count: isize = 0;
-                            for item in __f(inner) {
-                                push.send(Ok($enum::$output(item))).ok();
-                                count += 1;
-                            }
-                            delta.send(count - 1).ok();
-                        }
-                        _ => {
-                            push.send(Err($crate::PipelineError::TypeMismatch)).ok();
-                            delta.send(0).ok();
-                        }
-                    }
-                },
-            ) as $crate::SharedFlatFn<$enum>
-        )
-    }};
-}
-
-/// Creates a `Stage::Flat` from a fallible function
-/// `Fn(T) -> Result<impl IntoIterator<Item = U>, E>`.
-///
-/// Si la fonction retourne `Err`, une erreur est poussée dans le canal et aucun
-/// item normal n'est produit.
-#[macro_export]
-macro_rules! make_flat_transform_fallible {
-    ($enum:ident, $func:tt, $input:ident, $output:ident) => {{
-        let __f = $func;
-        $crate::Stage::Flat(
-            ::std::sync::Arc::new(
-                move |data: $enum,
-                      push: &$crate::PipelineSender<
-                          ::std::result::Result<$enum, $crate::PipelineError>,
-                      >,
-                      delta: &$crate::PipelineSender<isize>| {
-                    match data {
-                        $enum::$input(inner) => match __f(inner) {
-                            Ok(iter) => {
-                                let mut count: isize = 0;
-                                for item in iter {
-                                    push.send(Ok($enum::$output(item))).ok();
-                                    count += 1;
-                                }
-                                delta.send(count - 1).ok();
-                            }
-                            Err(e) => {
-                                push.send(Err($crate::PipelineError::StepError(Box::new(e))))
-                                    .ok();
-                                delta.send(0).ok();
-                            }
-                        },
-                        _ => {
-                            push.send(Err($crate::PipelineError::TypeMismatch)).ok();
-                            delta.send(0).ok();
-                        }
-                    }
-                },
-            ) as $crate::SharedFlatFn<$enum>
-        )
-    }};
-}
-
-/// Creates a `SinkFn` from a function that consumes a concrete value and returns `()`.
-#[macro_export]
-macro_rules! make_sink {
-    ($enum:ident, $func:tt, $input:ident) => {{
-        let __f = $func;
-        Box::new(
-            move |data: $enum| -> ::std::result::Result<(), $crate::PipelineError> {
-                match data {
-                    $enum::$input(x) => {
-                        __f(x);
-                        Ok(())
-                    }
-                    _ => Err($crate::PipelineError::TypeMismatch),
-                }
-            },
-        )
-            as Box<dyn Fn($enum) -> ::std::result::Result<(), $crate::PipelineError> + Send>
-    }};
-}
-
-/// Creates a `SinkFn` from a fallible function that returns `Result<(), E>`.
-#[macro_export]
-macro_rules! make_sink_fallible {
-    ($enum:ident, $func:tt, $input:ident) => {{
-        let __f = $func;
-        Box::new(
-            move |data: $enum| -> ::std::result::Result<(), $crate::PipelineError> {
-                match data {
-                    $enum::$input(inner) => {
-                        __f(inner).map_err(|e| $crate::PipelineError::StepError(Box::new(e)))
-                    }
-                    _ => Err($crate::PipelineError::TypeMismatch),
-                }
-            },
-        )
-            as Box<dyn Fn($enum) -> ::std::result::Result<(), $crate::PipelineError> + Send>
-    }};
-}
-
-/// Construit un `Pipeline` à partir d'une source, d'une liste de stages et d'un sink.
-///
-/// Syntaxe :
-/// ```ignore
-/// make_pipeline! {
-///     MyData,
-///     source   my_iter  => Variant,   // source non-fallible
-///     source?  my_iter  => Variant,   // source fallible (Result<T, E>)
-///     |  func: In => Out,             // transform 1→1 non-fallible
-///     |? func: In => Out,             // transform 1→1 fallible
-///     || func: In => Out,             // flat transform 1→N non-fallible
-///     ||? func: In => Out,            // flat transform 1→N fallible
-///     sink     my_func @ Variant,     // sink non-fallible
-///     sink?    my_func @ Variant,     // sink fallible
-/// }
-/// ```
-#[macro_export]
-macro_rules! make_pipeline {
-    // ── Points d'entrée ──────────────────────────────────────────────────
-
-    ($enum:ident, source $src:expr => $src_out:ident, $($rest:tt)*) => {
-        $crate::make_pipeline!(@build $enum,
-            { $crate::make_source!($enum, $src, $src_out) },
-            [],
-            $($rest)*)
-    };
-    ($enum:ident, source? $src:expr => $src_out:ident, $($rest:tt)*) => {
-        $crate::make_pipeline!(@build $enum,
-            { $crate::make_source_fallible!($enum, $src, $src_out) },
-            [],
-            $($rest)*)
-    };
-
-    // ── Accumulation des stages ──────────────────────────────────────────
-
-    // transform 1→1 non-fallible
-    (@build $enum:ident, $source:tt, [$($acc:tt)*],
-     | $tf:tt : $t_in:ident => $t_out:ident, $($rest:tt)*) => {
-        $crate::make_pipeline!(@build $enum, $source,
-            [$($acc)* $crate::make_transform!($enum, $tf, $t_in, $t_out),],
-            $($rest)*)
-    };
-
-    // transform 1→1 fallible
-    (@build $enum:ident, $source:tt, [$($acc:tt)*],
-     |? $tf:tt : $t_in:ident => $t_out:ident, $($rest:tt)*) => {
-        $crate::make_pipeline!(@build $enum, $source,
-            [$($acc)* $crate::make_transform_fallible!($enum, $tf, $t_in, $t_out),],
-            $($rest)*)
-    };
-
-    // flat transform 1→N non-fallible
-    (@build $enum:ident, $source:tt, [$($acc:tt)*],
-     || $tf:tt : $t_in:ident => $t_out:ident, $($rest:tt)*) => {
-        $crate::make_pipeline!(@build $enum, $source,
-            [$($acc)* $crate::make_flat_transform!($enum, $tf, $t_in, $t_out),],
-            $($rest)*)
-    };
-
-    // flat transform 1→N fallible
-    (@build $enum:ident, $source:tt, [$($acc:tt)*],
-     ||? $tf:tt : $t_in:ident => $t_out:ident, $($rest:tt)*) => {
-        $crate::make_pipeline!(@build $enum, $source,
-            [$($acc)* $crate::make_flat_transform_fallible!($enum, $tf, $t_in, $t_out),],
-            $($rest)*)
-    };
-
-    // ── Terminaison : sink ───────────────────────────────────────────────
-
-    (@build $enum:ident, $source:tt, [$($acc:tt)*],
-     sink $sink_fn:tt @ $sink_in:ident $(,)?) => {
-        $crate::Pipeline::new(
-            $source,
-            vec![$($acc)*],
-            $crate::make_sink!($enum, $sink_fn, $sink_in),
-        )
-    };
-    (@build $enum:ident, $source:tt, [$($acc:tt)*],
-     sink? $sink_fn:tt @ $sink_in:ident $(,)?) => {
-        $crate::Pipeline::new(
-            $source,
-            vec![$($acc)*],
-            $crate::make_sink_fallible!($enum, $sink_fn, $sink_in),
-        )
-    };
-}
-
-/// Builds a typed `Pipe<D, In, Out>` — sourceless and sinkless.
-///
-/// Syntax:
-/// ```ignore
-/// make_pipe! {
-///     MyData : InType => OutType,
-///     |   func : InVariant  => OutVariant,   // transform 1→1
-///     |?  func : InVariant  => OutVariant,   // transform 1→1 fallible
-///     ||  func : InVariant  => OutVariant,   // flat transform 1→N
-///     ||? func : InVariant  => OutVariant,   // flat transform 1→N fallible
-/// }
-/// ```
-#[macro_export]
-macro_rules! make_pipe {
-    // ── Entry: first stage | ─────────────────────────────────────────────
-    ($enum:ident : $in_ty:ty => $out_ty:ty,
-     | $tf:tt : $fi:ident => $fo:ident, $($rest:tt)*) => {
-        $crate::make_pipe!(@build $enum : $in_ty => $out_ty, $fi,
-            [$crate::make_transform!($enum, $tf, $fi, $fo),], $fo, $($rest)*)
-    };
-    // ── Entry: first stage |? ────────────────────────────────────────────
-    ($enum:ident : $in_ty:ty => $out_ty:ty,
-     |? $tf:tt : $fi:ident => $fo:ident, $($rest:tt)*) => {
-        $crate::make_pipe!(@build $enum : $in_ty => $out_ty, $fi,
-            [$crate::make_transform_fallible!($enum, $tf, $fi, $fo),], $fo, $($rest)*)
-    };
-    // ── Entry: first stage || ────────────────────────────────────────────
-    ($enum:ident : $in_ty:ty => $out_ty:ty,
-     || $tf:tt : $fi:ident => $fo:ident, $($rest:tt)*) => {
-        $crate::make_pipe!(@build $enum : $in_ty => $out_ty, $fi,
-            [$crate::make_flat_transform!($enum, $tf, $fi, $fo),], $fo, $($rest)*)
-    };
-    // ── Entry: first stage ||? ───────────────────────────────────────────
-    ($enum:ident : $in_ty:ty => $out_ty:ty,
-     ||? $tf:tt : $fi:ident => $fo:ident, $($rest:tt)*) => {
-        $crate::make_pipe!(@build $enum : $in_ty => $out_ty, $fi,
-            [$crate::make_flat_transform_fallible!($enum, $tf, $fi, $fo),], $fo, $($rest)*)
-    };
-
-    // ── Accumulation: | ──────────────────────────────────────────────────
-    (@build $enum:ident : $in_ty:ty => $out_ty:ty, $fi:ident,
-     [$($acc:tt)*], $lo:ident,
-     | $tf:tt : $ti:ident => $to:ident, $($rest:tt)*) => {
-        $crate::make_pipe!(@build $enum : $in_ty => $out_ty, $fi,
-            [$($acc)* $crate::make_transform!($enum, $tf, $ti, $to),], $to, $($rest)*)
-    };
-    // ── Accumulation: |? ─────────────────────────────────────────────────
-    (@build $enum:ident : $in_ty:ty => $out_ty:ty, $fi:ident,
-     [$($acc:tt)*], $lo:ident,
-     |? $tf:tt : $ti:ident => $to:ident, $($rest:tt)*) => {
-        $crate::make_pipe!(@build $enum : $in_ty => $out_ty, $fi,
-            [$($acc)* $crate::make_transform_fallible!($enum, $tf, $ti, $to),], $to, $($rest)*)
-    };
-    // ── Accumulation: || ─────────────────────────────────────────────────
-    (@build $enum:ident : $in_ty:ty => $out_ty:ty, $fi:ident,
-     [$($acc:tt)*], $lo:ident,
-     || $tf:tt : $ti:ident => $to:ident, $($rest:tt)*) => {
-        $crate::make_pipe!(@build $enum : $in_ty => $out_ty, $fi,
-            [$($acc)* $crate::make_flat_transform!($enum, $tf, $ti, $to),], $to, $($rest)*)
-    };
-    // ── Accumulation: ||? ────────────────────────────────────────────────
-    (@build $enum:ident : $in_ty:ty => $out_ty:ty, $fi:ident,
-     [$($acc:tt)*], $lo:ident,
-     ||? $tf:tt : $ti:ident => $to:ident, $($rest:tt)*) => {
-        $crate::make_pipe!(@build $enum : $in_ty => $out_ty, $fi,
-            [$($acc)* $crate::make_flat_transform_fallible!($enum, $tf, $ti, $to),], $to, $($rest)*)
-    };
-
-    // ── Termination ───────────────────────────────────────────────────────
-    (@build $enum:ident : $in_ty:ty => $out_ty:ty, $fi:ident,
-     [$($acc:tt)*], $lo:ident $(,)?) => {
-        $crate::Pipe::new(
-            vec![$($acc)*],
-            ::std::sync::Arc::new(|x: $in_ty| $enum::$fi(x)),
-            ::std::sync::Arc::new(|d: $enum| -> $out_ty {
-                if let $enum::$lo(x) = d { x }
-                else { ::std::unreachable!("unexpected pipeline data variant in make_pipe!") }
-            }),
-        )
-    };
-}
diff --git a/src/obipipeline/src/scheduler/error.rs b/src/obipipeline/src/scheduler/error.rs
new file mode 100644
index 00000000..fc4a0128
--- /dev/null
+++ b/src/obipipeline/src/scheduler/error.rs
@@ -0,0 +1,35 @@
+use std::error::Error;
+use std::fmt;
+
+/// Error type for pipeline operations.
+#[derive(Debug)]
+pub enum PipelineError {
+    /// A stage received a `PipelineData` variant it did not expect.
+    TypeMismatch,
+    /// The step kind is not compatible with the data type.
+    StepKindMismatch(&'static str),
+    /// The source has no more data to produce.
+    EndOfStream,
+    /// An error occurred inside a stage (e.g., I/O, parsing, custom logic).
+    StepError(Box<dyn Error + Send + Sync>),
+}
+
+impl fmt::Display for PipelineError {
+    fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
+        match self {
+            PipelineError::TypeMismatch => write!(f, "data type mismatch in pipeline stage"),
+            PipelineError::StepKindMismatch(s) => write!(f, "step kind mismatch: {}", s),
+            PipelineError::EndOfStream => write!(f, "end of input stream"),
+            PipelineError::StepError(e) => write!(f, "stage error: {}", e),
+        }
+    }
+}
+
+impl Error for PipelineError {
+    fn source(&self) -> Option<&(dyn Error + 'static)> {
+        match self {
+            PipelineError::StepError(e) => Some(e.as_ref()),
+            _ => None,
+        }
+    }
+}
diff --git a/src/obipipeline/src/scheduler/macros.rs b/src/obipipeline/src/scheduler/macros.rs
new file mode 100644
index 00000000..145b47ff
--- /dev/null
+++ b/src/obipipeline/src/scheduler/macros.rs
@@ -0,0 +1,373 @@
+// ── Macros ────────────────────────────────────────────────────────────────────
+
+/// Creates a `SourceFn` from an iterator of plain values.
+#[macro_export]
+macro_rules! make_source {
+    ($enum:ident, $iterator:expr, $output:ident) => {{
+        let mut iter = $iterator.into_iter();
+        Box::new(
+            move || -> ::std::result::Result<$enum, $crate::PipelineError> {
+                match iter.next() {
+                    Some(x) => Ok($enum::$output(x)),
+                    None => Err($crate::PipelineError::EndOfStream),
+                }
+            },
+        )
+            as Box<dyn FnMut() -> ::std::result::Result<$enum, $crate::PipelineError> + Send>
+    }};
+}
+
+/// Creates a `SourceFn` from an iterator of `Result<T, E>`.
+#[macro_export]
+macro_rules! make_source_fallible {
+    ($enum:ident, $iterator:expr, $output:ident) => {{
+        let mut iter = $iterator.into_iter();
+        Box::new(
+            move || -> ::std::result::Result<$enum, $crate::PipelineError> {
+                match iter.next() {
+                    Some(Ok(x)) => Ok($enum::$output(x)),
+                    Some(Err(e)) => Err($crate::PipelineError::StepError(Box::new(e))),
+                    None => Err($crate::PipelineError::EndOfStream),
+                }
+            },
+        )
+            as Box<dyn FnMut() -> ::std::result::Result<$enum, $crate::PipelineError> + Send>
+    }};
+}
+
+/// Creates a `Stage::Transform` from a pure (non-fallible) function `Fn(T) -> U`.
+#[macro_export]
+macro_rules! make_transform {
+    ($enum:ident, $func:tt, $input:ident, $output:ident) => {{
+        let __f = $func;
+        $crate::Stage::Transform(
+            ::std::sync::Arc::from(Box::new(
+                move |data: $enum| -> ::std::result::Result<$enum, $crate::PipelineError> {
+                    match data {
+                        $enum::$input(x) => Ok($enum::$output(__f(x))),
+                        _ => Err($crate::PipelineError::TypeMismatch),
+                    }
+                },
+            )
+                as Box<
+                    dyn Fn($enum) -> ::std::result::Result<$enum, $crate::PipelineError>
+                        + Send
+                        + Sync,
+                >)
+        )
+    }};
+}
+
+/// Creates a `Stage::Transform` from a fallible function `Fn(T) -> Result<U, E>`.
+#[macro_export]
+macro_rules! make_transform_fallible {
+    ($enum:ident, $func:tt, $input:ident, $output:ident) => {{
+        let __f = $func;
+        $crate::Stage::Transform(
+            ::std::sync::Arc::from(Box::new(
+                move |data: $enum| -> ::std::result::Result<$enum, $crate::PipelineError> {
+                    match data {
+                        $enum::$input(inner) => {
+                            let result = __f(inner)
+                                .map_err(|e| $crate::PipelineError::StepError(Box::new(e)))?;
+                            Ok($enum::$output(result))
+                        }
+                        _ => Err($crate::PipelineError::TypeMismatch),
+                    }
+                },
+            )
+                as Box<
+                    dyn Fn($enum) -> ::std::result::Result<$enum, $crate::PipelineError>
+                        + Send
+                        + Sync,
+                >)
+        )
+    }};
+}
+
+/// Creates a `Stage::Flat` from a function `Fn(T) -> impl IntoIterator<Item = U>`.
+///
+/// Pour chaque item produit par l'itérateur, il est poussé individuellement dans
+/// le canal de sortie, permettant au scheduler de dispatcher les items en parallèle
+/// dès qu'un worker est disponible.
+#[macro_export]
+macro_rules! make_flat_transform {
+    ($enum:ident, $func:tt, $input:ident, $output:ident) => {{
+        let __f = $func;
+        $crate::Stage::Flat(
+            ::std::sync::Arc::new(
+                move |data: $enum,
+                      push: &$crate::PipelineSender<
+                          ::std::result::Result<$enum, $crate::PipelineError>,
+                      >,
+                      delta: &$crate::PipelineSender<isize>| {
+                    match data {
+                        $enum::$input(inner) => {
+                            let mut count: isize = 0;
+                            for item in __f(inner) {
+                                push.send(Ok($enum::$output(item))).ok();
+                                count += 1;
+                            }
+                            delta.send(count - 1).ok();
+                        }
+                        _ => {
+                            push.send(Err($crate::PipelineError::TypeMismatch)).ok();
+                            delta.send(0).ok();
+                        }
+                    }
+                },
+            ) as $crate::SharedFlatFn<$enum>
+        )
+    }};
+}
+
+/// Creates a `Stage::Flat` from a fallible function
+/// `Fn(T) -> Result<impl IntoIterator<Item = U>, E>`.
+///
+/// Si la fonction retourne `Err`, une erreur est poussée dans le canal et aucun
+/// item normal n'est produit.
+#[macro_export]
+macro_rules! make_flat_transform_fallible {
+    ($enum:ident, $func:tt, $input:ident, $output:ident) => {{
+        let __f = $func;
+        $crate::Stage::Flat(
+            ::std::sync::Arc::new(
+                move |data: $enum,
+                      push: &$crate::PipelineSender<
+                          ::std::result::Result<$enum, $crate::PipelineError>,
+                      >,
+                      delta: &$crate::PipelineSender<isize>| {
+                    match data {
+                        $enum::$input(inner) => match __f(inner) {
+                            Ok(iter) => {
+                                let mut count: isize = 0;
+                                for item in iter {
+                                    push.send(Ok($enum::$output(item))).ok();
+                                    count += 1;
+                                }
+                                delta.send(count - 1).ok();
+                            }
+                            Err(e) => {
+                                push.send(Err($crate::PipelineError::StepError(Box::new(e))))
+                                    .ok();
+                                delta.send(0).ok();
+                            }
+                        },
+                        _ => {
+                            push.send(Err($crate::PipelineError::TypeMismatch)).ok();
+                            delta.send(0).ok();
+                        }
+                    }
+                },
+            ) as $crate::SharedFlatFn<$enum>
+        )
+    }};
+}
+
+/// Creates a `SinkFn` from a function that consumes a concrete value and returns `()`.
+#[macro_export]
+macro_rules! make_sink {
+    ($enum:ident, $func:tt, $input:ident) => {{
+        let __f = $func;
+        Box::new(
+            move |data: $enum| -> ::std::result::Result<(), $crate::PipelineError> {
+                match data {
+                    $enum::$input(x) => {
+                        __f(x);
+                        Ok(())
+                    }
+                    _ => Err($crate::PipelineError::TypeMismatch),
+                }
+            },
+        )
+            as Box<dyn Fn($enum) -> ::std::result::Result<(), $crate::PipelineError> + Send>
+    }};
+}
+
+/// Creates a `SinkFn` from a fallible function that returns `Result<(), E>`.
+#[macro_export]
+macro_rules! make_sink_fallible {
+    ($enum:ident, $func:tt, $input:ident) => {{
+        let __f = $func;
+        Box::new(
+            move |data: $enum| -> ::std::result::Result<(), $crate::PipelineError> {
+                match data {
+                    $enum::$input(inner) => {
+                        __f(inner).map_err(|e| $crate::PipelineError::StepError(Box::new(e)))
+                    }
+                    _ => Err($crate::PipelineError::TypeMismatch),
+                }
+            },
+        )
+            as Box<dyn Fn($enum) -> ::std::result::Result<(), $crate::PipelineError> + Send>
+    }};
+}
+
+/// Construit un `Pipeline` à partir d'une source, d'une liste de stages et d'un sink.
+///
+/// Syntaxe :
+/// ```ignore
+/// make_pipeline! {
+///     MyData,
+///     source   my_iter  => Variant,   // source non-fallible
+///     source?  my_iter  => Variant,   // source fallible (Result<T, E>)
+///     |  func: In => Out,             // transform 1→1 non-fallible
+///     |? func: In => Out,             // transform 1→1 fallible
+///     || func: In => Out,             // flat transform 1→N non-fallible
+///     ||? func: In => Out,            // flat transform 1→N fallible
+///     sink     my_func @ Variant,     // sink non-fallible
+///     sink?    my_func @ Variant,     // sink fallible
+/// }
+/// ```
+#[macro_export]
+macro_rules! make_pipeline {
+    // ── Points d'entrée ──────────────────────────────────────────────────
+
+    ($enum:ident, source $src:expr => $src_out:ident, $($rest:tt)*) => {
+        $crate::make_pipeline!(@build $enum,
+            { $crate::make_source!($enum, $src, $src_out) },
+            [],
+            $($rest)*)
+    };
+    ($enum:ident, source? $src:expr => $src_out:ident, $($rest:tt)*) => {
+        $crate::make_pipeline!(@build $enum,
+            { $crate::make_source_fallible!($enum, $src, $src_out) },
+            [],
+            $($rest)*)
+    };
+
+    // ── Accumulation des stages ──────────────────────────────────────────
+
+    // transform 1→1 non-fallible
+    (@build $enum:ident, $source:tt, [$($acc:tt)*],
+     | $tf:tt : $t_in:ident => $t_out:ident, $($rest:tt)*) => {
+        $crate::make_pipeline!(@build $enum, $source,
+            [$($acc)* $crate::make_transform!($enum, $tf, $t_in, $t_out),],
+            $($rest)*)
+    };
+
+    // transform 1→1 fallible
+    (@build $enum:ident, $source:tt, [$($acc:tt)*],
+     |? $tf:tt : $t_in:ident => $t_out:ident, $($rest:tt)*) => {
+        $crate::make_pipeline!(@build $enum, $source,
+            [$($acc)* $crate::make_transform_fallible!($enum, $tf, $t_in, $t_out),],
+            $($rest)*)
+    };
+
+    // flat transform 1→N non-fallible
+    (@build $enum:ident, $source:tt, [$($acc:tt)*],
+     || $tf:tt : $t_in:ident => $t_out:ident, $($rest:tt)*) => {
+        $crate::make_pipeline!(@build $enum, $source,
+            [$($acc)* $crate::make_flat_transform!($enum, $tf, $t_in, $t_out),],
+            $($rest)*)
+    };
+
+    // flat transform 1→N fallible
+    (@build $enum:ident, $source:tt, [$($acc:tt)*],
+     ||? $tf:tt : $t_in:ident => $t_out:ident, $($rest:tt)*) => {
+        $crate::make_pipeline!(@build $enum, $source,
+            [$($acc)* $crate::make_flat_transform_fallible!($enum, $tf, $t_in, $t_out),],
+            $($rest)*)
+    };
+
+    // ── Terminaison : sink ───────────────────────────────────────────────
+
+    (@build $enum:ident, $source:tt, [$($acc:tt)*],
+     sink $sink_fn:tt @ $sink_in:ident $(,)?) => {
+        $crate::Pipeline::new(
+            $source,
+            vec![$($acc)*],
+            $crate::make_sink!($enum, $sink_fn, $sink_in),
+        )
+    };
+    (@build $enum:ident, $source:tt, [$($acc:tt)*],
+     sink? $sink_fn:tt @ $sink_in:ident $(,)?) => {
+        $crate::Pipeline::new(
+            $source,
+            vec![$($acc)*],
+            $crate::make_sink_fallible!($enum, $sink_fn, $sink_in),
+        )
+    };
+}
+
+/// Builds a typed `Pipe<D, In, Out>` — sourceless and sinkless.
+///
+/// Syntax:
+/// ```ignore
+/// make_pipe! {
+///     MyData : InType => OutType,
+///     |   func : InVariant  => OutVariant,   // transform 1→1
+///     |?  func : InVariant  => OutVariant,   // transform 1→1 fallible
+///     ||  func : InVariant  => OutVariant,   // flat transform 1→N
+///     ||? func : InVariant  => OutVariant,   // flat transform 1→N fallible
+/// }
+/// ```
+#[macro_export]
+macro_rules! make_pipe {
+    // ── Entry: first stage | ─────────────────────────────────────────────
+    ($enum:ident : $in_ty:ty => $out_ty:ty,
+     | $tf:tt : $fi:ident => $fo:ident, $($rest:tt)*) => {
+        $crate::make_pipe!(@build $enum : $in_ty => $out_ty, $fi,
+            [$crate::make_transform!($enum, $tf, $fi, $fo),], $fo, $($rest)*)
+    };
+    // ── Entry: first stage |? ────────────────────────────────────────────
+    ($enum:ident : $in_ty:ty => $out_ty:ty,
+     |? $tf:tt : $fi:ident => $fo:ident, $($rest:tt)*) => {
+        $crate::make_pipe!(@build $enum : $in_ty => $out_ty, $fi,
+            [$crate::make_transform_fallible!($enum, $tf, $fi, $fo),], $fo, $($rest)*)
+    };
+    // ── Entry: first stage || ────────────────────────────────────────────
+    ($enum:ident : $in_ty:ty => $out_ty:ty,
+     || $tf:tt : $fi:ident => $fo:ident, $($rest:tt)*) => {
+        $crate::make_pipe!(@build $enum : $in_ty => $out_ty, $fi,
+            [$crate::make_flat_transform!($enum, $tf, $fi, $fo),], $fo, $($rest)*)
+    };
+    // ── Entry: first stage ||? ───────────────────────────────────────────
+    ($enum:ident : $in_ty:ty => $out_ty:ty,
+     ||? $tf:tt : $fi:ident => $fo:ident, $($rest:tt)*) => {
+        $crate::make_pipe!(@build $enum : $in_ty => $out_ty, $fi,
+            [$crate::make_flat_transform_fallible!($enum, $tf, $fi, $fo),], $fo, $($rest)*)
+    };
+
+    // ── Accumulation: | ──────────────────────────────────────────────────
+    (@build $enum:ident : $in_ty:ty => $out_ty:ty, $fi:ident,
+     [$($acc:tt)*], $lo:ident,
+     | $tf:tt : $ti:ident => $to:ident, $($rest:tt)*) => {
+        $crate::make_pipe!(@build $enum : $in_ty => $out_ty, $fi,
+            [$($acc)* $crate::make_transform!($enum, $tf, $ti, $to),], $to, $($rest)*)
+    };
+    // ── Accumulation: |? ─────────────────────────────────────────────────
+    (@build $enum:ident : $in_ty:ty => $out_ty:ty, $fi:ident,
+     [$($acc:tt)*], $lo:ident,
+     |? $tf:tt : $ti:ident => $to:ident, $($rest:tt)*) => {
+        $crate::make_pipe!(@build $enum : $in_ty => $out_ty, $fi,
+            [$($acc)* $crate::make_transform_fallible!($enum, $tf, $ti, $to),], $to, $($rest)*)
+    };
+    // ── Accumulation: || ─────────────────────────────────────────────────
+    (@build $enum:ident : $in_ty:ty => $out_ty:ty, $fi:ident,
+     [$($acc:tt)*], $lo:ident,
+     || $tf:tt : $ti:ident => $to:ident, $($rest:tt)*) => {
+        $crate::make_pipe!(@build $enum : $in_ty => $out_ty, $fi,
+            [$($acc)* $crate::make_flat_transform!($enum, $tf, $ti, $to),], $to, $($rest)*)
+    };
+    // ── Accumulation: ||? ────────────────────────────────────────────────
+    (@build $enum:ident : $in_ty:ty => $out_ty:ty, $fi:ident,
+     [$($acc:tt)*], $lo:ident,
+     ||? $tf:tt : $ti:ident => $to:ident, $($rest:tt)*) => {
+        $crate::make_pipe!(@build $enum : $in_ty => $out_ty, $fi,
+            [$($acc)* $crate::make_flat_transform_fallible!($enum, $tf, $ti, $to),], $to, $($rest)*)
+    };
+
+    // ── Termination ───────────────────────────────────────────────────────
+    (@build $enum:ident : $in_ty:ty => $out_ty:ty, $fi:ident,
+     [$($acc:tt)*], $lo:ident $(,)?) => {
+        $crate::Pipe::new(
+            vec![$($acc)*],
+            ::std::sync::Arc::new(|x: $in_ty| $enum::$fi(x)),
+            ::std::sync::Arc::new(|d: $enum| -> $out_ty {
+                if let $enum::$lo(x) = d { x }
+                else { ::std::unreachable!("unexpected pipeline data variant in make_pipe!") }
+            }),
+        )
+    };
+}
diff --git a/src/obipipeline/src/scheduler/mod.rs b/src/obipipeline/src/scheduler/mod.rs
new file mode 100644
index 00000000..59d88bb6
--- /dev/null
+++ b/src/obipipeline/src/scheduler/mod.rs
@@ -0,0 +1,19 @@
+//! Scheduler: a channel/thread-based pipeline runtime with typed, composable
+//! stages (`Pipe`), plus the macro-based `PipelineData`-enum runtime it grew
+//! out of (`Pipeline`/`WorkerPool`).
+//!
+//! Submodules: [`error`] (`PipelineError`), [`types`] (function types, `Stage`),
+//! [`runner`] (thread bodies), [`pool`] (`Pipeline`/`WorkerPool` scheduler
+//! loop), [`pipe`] (`Pipe`/`PipeIter`), [`macros`] (`make_pipe!` and friends).
+
+mod error;
+mod macros;
+mod pipe;
+mod pool;
+mod runner;
+mod types;
+
+pub use error::PipelineError;
+pub use pipe::{Pipe, PipeIter};
+pub use pool::{Pipeline, WorkerPool};
+pub use types::{SharedFlatFn, SharedFn, SinkFn, SourceFn, Stage};
diff --git a/src/obipipeline/src/scheduler/pipe.rs b/src/obipipeline/src/scheduler/pipe.rs
new file mode 100644
index 00000000..41eb62c9
--- /dev/null
+++ b/src/obipipeline/src/scheduler/pipe.rs
@@ -0,0 +1,117 @@
+use crossbeam_channel::{Receiver, bounded};
+use std::marker::PhantomData;
+use std::sync::Arc;
+use std::thread;
+
+use super::error::PipelineError;
+use super::pool::{Pipeline, WorkerPool};
+use super::types::{SinkFn, SourceFn, Stage};
+
+// ── Pipe ──────────────────────────────────────────────────────────────────────
+
+/// Typed, composable iterator transformer.
+///
+/// A `Pipe<D, In, Out>` is a pure description of pipeline stages — no threads,
+/// no channels, no scheduler. Call `.apply(iter, n_workers, capacity)` to start
+/// execution and get back a `PipeIter<Out>`.
+///
+/// Compose two pipes with `.then()`: the resulting `Pipe` holds the concatenated
+/// stage list, so a single scheduler is created when `.apply()` is eventually called.
+pub struct Pipe<D, In, Out> {
+    stages:   Vec<Stage<D>>,
+    wrap:     Arc<dyn Fn(In) -> D   + Send + Sync>,
+    unwrap:   Arc<dyn Fn(D)  -> Out + Send + Sync>,
+    _phantom: PhantomData<(In, Out)>,
+}
+
+impl<D, In, Out> Pipe<D, In, Out> {
+    /// Build a `Pipe` from stages and wrap/unwrap converters.
+    /// Prefer the `make_pipe!` macro.
+    pub fn new(
+        stages:  Vec<Stage<D>>,
+        wrap:    Arc<dyn Fn(In) -> D   + Send + Sync>,
+        unwrap:  Arc<dyn Fn(D)  -> Out + Send + Sync>,
+    ) -> Self {
+        Self { stages, wrap, unwrap, _phantom: PhantomData }
+    }
+
+    /// Concatenate stages from two pipes into one.
+    ///
+    /// Requires `Out` of `self` == `In` of `other`.  The single scheduler
+    /// created at `.apply()` time sees the full combined stage list.
+    pub fn then<Next>(self, other: Pipe<D, Out, Next>) -> Pipe<D, In, Next> {
+        Pipe {
+            stages:   self.stages.into_iter().chain(other.stages).collect(),
+            wrap:     self.wrap,
+            unwrap:   other.unwrap,
+            _phantom: PhantomData,
+        }
+    }
+}
+
+impl<D, In, Out> Pipe<D, In, Out>
+where
+    D:   Send + Sync + 'static,
+    In:  Send + 'static,
+    Out: Send + 'static,
+{
+    /// Run the pipeline in a background thread; returns an iterator over the output.
+    pub fn apply(
+        self,
+        input:     impl Iterator<Item = In> + Send + 'static,
+        n_workers: usize,
+        capacity:  usize,
+    ) -> PipeIter<Out> {
+        let wrap   = Arc::clone(&self.wrap);
+        let unwrap = Arc::clone(&self.unwrap);
+
+        let mut iter = input;
+        let source: SourceFn<D> = Box::new(move || match iter.next() {
+            Some(x) => Ok(wrap(x)),
+            None    => Err(PipelineError::EndOfStream),
+        });
+
+        let (out_tx, out_rx) = bounded::<Out>(capacity);
+        let sink: SinkFn<D> = Box::new(move |data: D| {
+            out_tx.send(unwrap(data)).map_err(|_| {
+                PipelineError::StepError(Box::new(std::io::Error::new(
+                    std::io::ErrorKind::BrokenPipe,
+                    "output channel closed",
+                )))
+            })
+        });
+
+        let pipeline = Pipeline::new(source, self.stages, sink);
+        let handle = thread::spawn(move || {
+            WorkerPool::new(pipeline, n_workers, capacity).run();
+        });
+
+        PipeIter { rx: out_rx, handle: Some(handle) }
+    }
+}
+
+// ── PipeIter ──────────────────────────────────────────────────────────────────
+
+/// Iterator over the output of `Pipe::apply()`.
+pub struct PipeIter<Out> {
+    rx:     Receiver<Out>,
+    handle: Option<thread::JoinHandle<()>>,
+}
+
+impl<Out> Iterator for PipeIter<Out> {
+    type Item = Out;
+
+    fn next(&mut self) -> Option<Out> {
+        self.rx.recv().ok()
+    }
+}
+
+impl<Out> Drop for PipeIter<Out> {
+    fn drop(&mut self) {
+        // Drain buffered items so the scheduler can unblock if the channel is full.
+        while self.rx.try_recv().is_ok() {}
+        if let Some(h) = self.handle.take() {
+            let _ = h.join();
+        }
+    }
+}
diff --git a/src/obipipeline/src/scheduler/pool.rs b/src/obipipeline/src/scheduler/pool.rs
new file mode 100644
index 00000000..7c7774b8
--- /dev/null
+++ b/src/obipipeline/src/scheduler/pool.rs
@@ -0,0 +1,203 @@
+use crossbeam_channel::{Receiver, Select, Sender, bounded};
+
+use super::error::PipelineError;
+use super::runner::{dispatch, sink_runner, source_runner, transform_runner};
+use super::types::{SinkFn, SourceFn, Stage, WorkerTask};
+
+// ── Pipeline ──────────────────────────────────────────────────────────────────
+
+pub struct Pipeline<DATA> {
+    source: SourceFn<DATA>,
+    stages: Vec<Stage<DATA>>,
+    sink: SinkFn<DATA>,
+}
+
+impl<DATA> Pipeline<DATA> {
+    pub fn new(
+        source: SourceFn<DATA>,
+        stages: Vec<Stage<DATA>>,
+        sink: SinkFn<DATA>,
+    ) -> Self {
+        Self { source, stages, sink }
+    }
+}
+
+// ── WorkerPool ────────────────────────────────────────────────────────────────
+
+pub struct WorkerPool<DATA> {
+    pipeline: Pipeline<DATA>,
+    handles: Vec<std::thread::JoinHandle<()>>,
+    n_workers: usize,
+    capacity: usize,
+}
+
+impl<DATA> WorkerPool<DATA>
+where
+    DATA: Send + Sync + 'static,
+{
+    pub fn new(pipeline: Pipeline<DATA>, n_workers: usize, capacity: usize) -> Self {
+        Self {
+            pipeline,
+            handles: Vec::new(),
+            n_workers,
+            capacity,
+        }
+    }
+
+    pub fn run(mut self) {
+        let n = self.pipeline.stages.len();
+
+        // ── Canaux inter-stages ────────────────────────────────────────────
+        // stage_txs[i] / stage_rxs[i] : sortie du stage i
+        let mut stage_txs: Vec<Sender<Result<DATA, PipelineError>>> = Vec::new();
+        let mut stage_rxs: Vec<Receiver<Result<DATA, PipelineError>>> = Vec::new();
+        for _ in 0..n {
+            let (tx, rx) = bounded(self.capacity);
+            stage_txs.push(tx);
+            stage_rxs.push(rx);
+        }
+
+        // ── Source thread ──────────────────────────────────────────────────
+        let (source_rx, src_handle) = source_runner(self.pipeline.source, self.capacity);
+        self.handles.push(src_handle);
+
+        let stages = self.pipeline.stages;
+
+        // ── Canal delta pour les flat stages ───────────────────────────────
+        // Chaque flat worker envoie `N-1` ici après avoir poussé N items.
+        // Le scheduler ajuste `in_flight` en conséquence.
+        let (flat_delta_tx, flat_delta_rx) = bounded::<isize>(self.capacity);
+
+        // ── Worker pool ────────────────────────────────────────────────────
+        let (worker_tx, worker_rx): (Sender<WorkerTask<DATA>>, Receiver<WorkerTask<DATA>>) =
+            bounded(self.capacity);
+
+        for _ in 0..self.n_workers {
+            self.handles.push(transform_runner(
+                worker_rx.clone(),
+                stages.iter().map(Stage::clone).collect(),
+                stage_txs.clone(),
+                flat_delta_tx.clone(),
+            ));
+        }
+        // Le scheduler ne tient plus flat_delta_tx : les workers le détiennent.
+        // On le drop ici pour que le canal se ferme quand les workers terminent.
+        drop(flat_delta_tx);
+
+        // ── Sink thread ────────────────────────────────────────────────────
+        let (sink_tx, sink_err_rx, sink_handle) = sink_runner(self.pipeline.sink, self.capacity);
+        self.handles.push(sink_handle);
+
+        // ── Boucle principale ──────────────────────────────────────────────
+        //
+        // `in_flight` (isize) = nb d'items qui doivent encore atteindre le sink.
+        // Peut temporairement être négatif si un flat worker a poussé ses items
+        // avant que le scheduler ait reçu le delta correspondant.
+        //
+        // `flat_workers_active` = nb de flat workers en cours d'exécution.
+        // Empêche la terminaison prématurée quand in_flight vaut 0 mais qu'un
+        // flat worker n'a pas encore envoyé son delta.
+        //
+        // Priorités du Select biaisé (index le plus bas = priorité la plus haute) :
+        //   0        → sink_err_rx    (arrêt immédiat sur erreur sink)
+        //   1        → flat_delta_rx  (mettre à jour in_flight avant de dispatcher)
+        //   2..=n+1  → stage_rxs[n-1..0]  (vider le pipeline en priorité)
+        //   n+2      → source_rx      (dernier recours : nouvelles données)
+        //
+        // Quand k = 0             : erreur du sink
+        // Quand k = 1             : delta d'un flat worker
+        // Quand 2 ≤ k ≤ n+1      : résultat du stage n+1-k
+        // Quand k = n+2           : item source
+        //
+        // Terminaison : source tarie ET in_flight == 0 ET aucun flat worker actif.
+        {
+            let mut source_done = false;
+            let mut in_flight: isize = 0;
+            let mut flat_workers_active: usize = 0;
+
+            loop {
+                if source_done && in_flight == 0 && flat_workers_active == 0 {
+                    break;
+                }
+
+                let mut sel = Select::new_biased();
+                sel.recv(&sink_err_rx);                 // index 0
+                sel.recv(&flat_delta_rx);               // index 1
+                for rx in stage_rxs.iter().rev() {
+                    sel.recv(rx);                       // indices 2..=n+1
+                }
+                let src_idx = if !source_done {
+                    Some(sel.recv(&source_rx))          // index n+2
+                } else {
+                    None
+                };
+
+                let oper = sel.select();
+                let k = oper.index();
+
+                if k == 0 {
+                    // ── Erreur du sink ────────────────────────────────────
+                    match oper.recv(&sink_err_rx) {
+                        Ok(e) => { eprintln!("Sink error: {:?}", e); break; }
+                        Err(_) => break,
+                    }
+                } else if k == 1 {
+                    // ── Delta d'un flat worker ────────────────────────────
+                    // delta = N - 1  (N items poussés, 1 item consommé)
+                    match oper.recv(&flat_delta_rx) {
+                        Ok(delta) => {
+                            in_flight += delta;
+                            flat_workers_active -= 1;
+                        }
+                        Err(_) => {}
+                    }
+                } else if src_idx == Some(k) {
+                    // ── Nouvel item depuis la source ──────────────────────
+                    match oper.recv(&source_rx) {
+                        Ok(Ok(data)) => {
+                            if n == 0 {
+                                let _ = sink_tx.send(data);
+                            } else {
+                                in_flight += 1;
+                                dispatch(
+                                    data, 0,
+                                    &stages, &worker_tx,
+                                    &mut flat_workers_active,
+                                );
+                            }
+                        }
+                        Ok(Err(e)) => eprintln!("Source error: {:?}", e),
+                        Err(_) => source_done = true,
+                    }
+                } else {
+                    // ── Résultat d'un stage intermédiaire ─────────────────
+                    // k ∈ [2, n+1]  →  stage = n+1 - k
+                    let stage = n + 1 - k;
+                    match oper.recv(&stage_rxs[stage]) {
+                        Ok(Ok(data)) => {
+                            if stage == n - 1 {
+                                in_flight -= 1;
+                                let _ = sink_tx.send(data);
+                            } else {
+                                dispatch(
+                                    data, stage + 1,
+                                    &stages, &worker_tx,
+                                    &mut flat_workers_active,
+                                );
+                            }
+                        }
+                        Ok(Err(e)) => eprintln!("Stage {} error: {:?}", stage, e),
+                        Err(_) => break,
+                    }
+                }
+            }
+        }
+
+        drop(worker_tx);
+        drop(sink_tx);
+
+        for h in self.handles {
+            let _ = h.join();
+        }
+    }
+}
diff --git a/src/obipipeline/src/scheduler/runner.rs b/src/obipipeline/src/scheduler/runner.rs
new file mode 100644
index 00000000..4d0202e8
--- /dev/null
+++ b/src/obipipeline/src/scheduler/runner.rs
@@ -0,0 +1,118 @@
+use crossbeam_channel::{Receiver, Sender, bounded};
+use std::thread;
+
+use super::error::PipelineError;
+use super::types::{SinkFn, SourceFn, Stage, WorkerTask};
+
+// ── Thread runners ────────────────────────────────────────────────────────────
+
+pub(super) fn source_runner<DATA>(
+    mut source: SourceFn<DATA>,
+    capacity: usize,
+) -> (
+    Receiver<Result<DATA, PipelineError>>,
+    thread::JoinHandle<()>,
+)
+where
+    DATA: Send + Sync + 'static,
+{
+    let (tx, rx) = bounded(capacity);
+    let handle = thread::spawn(move || {
+        loop {
+            match source() {
+                Ok(data) => {
+                    if tx.send(Ok(data)).is_err() {
+                        break;
+                    }
+                }
+                Err(PipelineError::EndOfStream) => break,
+                Err(e) => {
+                    eprintln!("Source error: {:?}", e);
+                    let _ = tx.send(Err(e));
+                    break;
+                }
+            }
+        }
+    });
+    (rx, handle)
+}
+
+/// Lance un thread worker du pool.
+///
+/// Gère deux types de tâches :
+/// - `Transform` : applique `f(data)` et envoie le résultat dans `result_tx`.
+/// - `Flat` : appelle `f(data, &push_tx, &delta_tx)` ; la fonction elle-même
+///   pousse ses items dans `push_tx` et envoie `N-1` dans `delta_tx`.
+pub(super) fn transform_runner<DATA>(
+    task_rx: Receiver<WorkerTask<DATA>>,
+    stages: Vec<Stage<DATA>>,
+    stage_txs: Vec<Sender<Result<DATA, PipelineError>>>,
+    flat_delta_tx: Sender<isize>,
+) -> thread::JoinHandle<()>
+where
+    DATA: Send + Sync + 'static,
+{
+    thread::spawn(move || {
+        while let Ok(task) = task_rx.recv() {
+            match task {
+                WorkerTask::Transform(data, idx) => {
+                    if let Stage::Transform(f) = &stages[idx] {
+                        let _ = stage_txs[idx].send(f(data));
+                    }
+                }
+                WorkerTask::Flat(data, idx) => {
+                    if let Stage::Flat(f) = &stages[idx] {
+                        f(data, &stage_txs[idx], &flat_delta_tx);
+                    }
+                }
+            }
+        }
+    })
+}
+
+/// Lance le thread sink.
+pub(super) fn sink_runner<DATA>(
+    sink: SinkFn<DATA>,
+    capacity: usize,
+) -> (
+    Sender<DATA>,
+    Receiver<PipelineError>,
+    thread::JoinHandle<()>,
+)
+where
+    DATA: Send + Sync + 'static,
+{
+    let (data_tx, data_rx) = bounded(capacity);
+    let (err_tx, err_rx) = bounded(capacity);
+    let handle = thread::spawn(move || {
+        for data in data_rx {
+            if let Err(e) = sink(data) {
+                let _ = err_tx.send(e);
+                break;
+            }
+        }
+    });
+    (data_tx, err_rx, handle)
+}
+
+/// Envoie `data` au stage `stage_idx`.
+/// Pour un `Transform`, empile une `WorkerTask::Transform`.
+/// Pour un `Flat`, incrémente `flat_workers_active` et empile une `WorkerTask::Flat`.
+#[inline]
+pub(super) fn dispatch<DATA>(
+    data: DATA,
+    stage_idx: usize,
+    stages: &[Stage<DATA>],
+    worker_tx: &Sender<WorkerTask<DATA>>,
+    flat_workers_active: &mut usize,
+) {
+    match &stages[stage_idx] {
+        Stage::Transform(_) => {
+            let _ = worker_tx.send(WorkerTask::Transform(data, stage_idx));
+        }
+        Stage::Flat(_) => {
+            *flat_workers_active += 1;
+            let _ = worker_tx.send(WorkerTask::Flat(data, stage_idx));
+        }
+    }
+}
diff --git a/src/obipipeline/src/scheduler/types.rs b/src/obipipeline/src/scheduler/types.rs
new file mode 100644
index 00000000..daeca394
--- /dev/null
+++ b/src/obipipeline/src/scheduler/types.rs
@@ -0,0 +1,49 @@
+use crossbeam_channel::Sender;
+use std::sync::Arc;
+
+use super::error::PipelineError;
+
+// ── Function types ────────────────────────────────────────────────────────────
+
+/// Fonction source : appelée répétitivement, retourne le prochain item ou EndOfStream.
+/// `FnMut` car elle maintient un état interne (position dans l'itérateur).
+pub type SourceFn<D> = Box<dyn FnMut() -> Result<D, PipelineError> + Send>;
+
+/// Fonction sink : consomme un item final, peut échouer (erreur d'I/O, etc.).
+pub type SinkFn<D> = Box<dyn Fn(D) -> Result<(), PipelineError> + Send>;
+
+/// Fonction de transformation partagée entre workers via Arc.
+pub type SharedFn<D> = Arc<dyn Fn(D) -> Result<D, PipelineError> + Send + Sync>;
+
+/// Fonction de transformation 1→N (flat map) partagée entre workers via Arc.
+///
+/// La fonction reçoit l'item d'entrée, un canal `push` pour envoyer chaque item
+/// produit, et un canal `delta` pour signaler au scheduler combien d'items
+/// supplémentaires sont entrés dans le pipeline (N-1 si N items produits).
+/// Elle doit appeler `delta.send(N - 1)` **après** avoir poussé tous les items.
+pub type SharedFlatFn<D> =
+    Arc<dyn Fn(D, &Sender<Result<D, PipelineError>>, &Sender<isize>) + Send + Sync>;
+
+// ── Stage enum ────────────────────────────────────────────────────────────────
+
+/// Une étape du pipeline : transform classique (1→1) ou flat transform (1→N).
+pub enum Stage<D> {
+    Transform(SharedFn<D>),
+    Flat(SharedFlatFn<D>),
+}
+
+impl<D> Clone for Stage<D> {
+    fn clone(&self) -> Self {
+        match self {
+            Stage::Transform(f) => Stage::Transform(Arc::clone(f)),
+            Stage::Flat(f) => Stage::Flat(Arc::clone(f)),
+        }
+    }
+}
+
+// ── Worker task ───────────────────────────────────────────────────────────────
+
+pub(super) enum WorkerTask<D> {
+    Transform(D, usize),
+    Flat(D, usize),
+}
diff --git a/src/obiread/src/nucstream.rs b/src/obiread/src/nucstream.rs
deleted file mode 100644
index e6bc4317..00000000
--- a/src/obiread/src/nucstream.rs
+++ /dev/null
@@ -1,733 +0,0 @@
-use std::io::{self, Read};
-use std::mem::ManuallyDrop;
-use std::sync::{Arc, Mutex};
-
-use crate::mimetype::MimeTypeGuesser;
-use crate::xopen::open_raw;
-
-pub const MAX_K: usize = 31;
-const PAGE_SIZE: usize = 65536;
-// overlap (MAX_K - 1) + page data (PAGE_SIZE) + 1 byte for the end-of-page terminating 0
-const BUF_SIZE: usize = MAX_K + PAGE_SIZE;
-
-// ─── OverlapState ─────────────────────────────────────────────────────────────
-
-pub(crate) struct OverlapState {
-    data: [u8; MAX_K],
-    len: usize,
-    k: usize,
-}
-
-impl OverlapState {
-    pub(crate) fn new(k: usize) -> Self {
-        assert!(k > 0 && k <= MAX_K);
-        Self {
-            data: [0u8; MAX_K],
-            len: 0,
-            k,
-        }
-    }
-}
-
-// ─── NucParser trait ──────────────────────────────────────────────────────────
-
-// Transforms a raw page into a compacted nucleotide stream in-place.
-//
-// Buffer layout on each call:
-//   buf[0..overlap_len()]           — overlap bytes copied by write_overlap()
-//   buf[overlap_len()..overlap_len()+n] — raw bytes just read from the source
-//
-// Returns the number of output bytes in buf[0..returned].
-pub(crate) trait NucParser {
-    // required: format-specific
-    fn new(k: usize) -> Self
-    where
-        Self: Sized;
-    fn overlap_state(&self) -> &OverlapState;
-    fn overlap_state_mut(&mut self) -> &mut OverlapState;
-    fn is_in_seq(&self) -> bool;
-    fn parse_inplace(&mut self, buf: &mut [u8], n: usize) -> usize;
-
-    // provided: format-independent overlap management
-    fn overlap_len(&self) -> usize {
-        self.overlap_state().len
-    }
-
-    fn write_overlap(&self, buf: &mut [u8]) {
-        let ol = &self.overlap_state();
-        buf[..ol.len].copy_from_slice(&ol.data[..ol.len]);
-    }
-
-    // Called at end of parse_inplace: saves overlap state and returns adjusted j.
-    // seq_start is the j-position where the last sequence started in this call's output.
-    fn save_overlap(&mut self, buf: &mut [u8], j: usize, seq_start: usize) -> usize {
-        if !self.is_in_seq() {
-            self.overlap_state_mut().len = 0;
-            return j;
-        }
-        let seq_len = j - seq_start;
-        let k = self.overlap_state().k;
-        if seq_len >= k {
-            // Sequence long enough: save last k-1 nucleotides, terminate with 0.
-            let ol = k - 1;
-            self.overlap_state_mut().data[..ol].copy_from_slice(&buf[j - ol..j]);
-            self.overlap_state_mut().len = ol;
-            // SAFETY: j <= total - 1 < BUF_SIZE = buf.len()
-            // (total = overlap_len + n <= (MAX_K-1) + PAGE_SIZE = BUF_SIZE - 1)
-            unsafe {
-                *buf.get_unchecked_mut(j) = 0;
-            }
-            j + 1
-        } else if seq_len > 0 {
-            // Short sequence (< k): save whole fragment, strip from output.
-            self.overlap_state_mut().data[..seq_len].copy_from_slice(&buf[seq_start..j]);
-            self.overlap_state_mut().len = seq_len;
-            seq_start
-        } else {
-            self.overlap_state_mut().len = 0;
-            j
-        }
-    }
-}
-
-// ─── FASTA parser ─────────────────────────────────────────────────────────────
-
-#[derive(Clone, Copy)]
-enum FastaState {
-    OutSeq,
-    InTitle,
-    InSeq,
-    InAmbiguous,
-}
-
-pub(crate) struct FastaParser {
-    state: FastaState,
-    overlap: OverlapState,
-}
-
-impl NucParser for FastaParser {
-    fn new(k: usize) -> Self {
-        Self {
-            state: FastaState::OutSeq,
-            overlap: OverlapState::new(k),
-        }
-    }
-
-    #[inline]
-    fn overlap_state(&self) -> &OverlapState {
-        &self.overlap
-    }
-
-    #[inline]
-    fn overlap_state_mut(&mut self) -> &mut OverlapState {
-        &mut self.overlap
-    }
-
-    #[inline]
-    fn is_in_seq(&self) -> bool {
-        matches!(self.state, FastaState::InSeq)
-    }
-
-    fn parse_inplace(&mut self, buf: &mut [u8], n: usize) -> usize {
-        let total = self.overlap.len + n;
-        let mut i = 0; // read index
-        let mut j = 0; // write index (invariant: j <= i always)
-        // j-position where the current sequence started in this call's output;
-        // meaningful only when state is InSeq.
-        let mut seq_start: usize = 0;
-
-        while i < total {
-            // SAFETY: i < total <= BUF_SIZE = buf.len()
-            let byte = unsafe { *buf.get_unchecked(i) };
-
-            match self.state {
-                FastaState::OutSeq => {
-                    if byte == b'>' {
-                        self.state = FastaState::InTitle;
-                    }
-                    i += 1;
-                }
-                FastaState::InTitle => {
-                    if byte == b'\n' || byte == b'\r' {
-                        self.state = FastaState::InSeq;
-                        seq_start = j;
-                    }
-                    i += 1;
-                }
-                FastaState::InSeq => {
-                    if byte == b'\n' || byte == b'\r' {
-                        i += 1;
-                        continue;
-                    }
-                    let nuc = byte & 0xDF; // to uppercase
-                    if nuc == b'A' || nuc == b'C' || nuc == b'G' || nuc == b'T' {
-                        // SAFETY: j <= i < total <= BUF_SIZE = buf.len()
-                        unsafe {
-                            *buf.get_unchecked_mut(j) = nuc;
-                        }
-                        j += 1;
-                        i += 1;
-                    } else if byte == b'>' {
-                        if j > seq_start {
-                            unsafe {
-                                *buf.get_unchecked_mut(j) = 0;
-                            }
-                            j += 1;
-                        }
-                        self.state = FastaState::InTitle;
-                        i += 1;
-                    } else {
-                        // first ambiguous base: end current sequence if non-empty
-                        if j > seq_start {
-                            unsafe {
-                                *buf.get_unchecked_mut(j) = 0;
-                            }
-                            j += 1;
-                        }
-                        self.state = FastaState::InAmbiguous;
-                        i += 1;
-                    }
-                }
-                FastaState::InAmbiguous => {
-                    if byte == b'\n' || byte == b'\r' {
-                        i += 1;
-                        continue;
-                    }
-                    if byte == b'>' {
-                        self.state = FastaState::InTitle;
-                        i += 1;
-                        continue;
-                    }
-                    let nuc = byte & 0xDF;
-                    if nuc == b'A' || nuc == b'C' || nuc == b'G' || nuc == b'T' {
-                        seq_start = j;
-                        // SAFETY: j <= i < total <= BUF_SIZE = buf.len()
-                        unsafe {
-                            *buf.get_unchecked_mut(j) = nuc;
-                        }
-                        j += 1;
-                        self.state = FastaState::InSeq;
-                    }
-                    i += 1;
-                }
-            }
-        }
-
-        self.save_overlap(buf, j, seq_start)
-    }
-}
-
-// ─── FASTQ parser ─────────────────────────────────────────────────────────────
-
-#[derive(Clone, Copy)]
-enum FastqState {
-    OutSeq,
-    InTitle,
-    InSeq,
-    InAmbiguous,
-    InQualTitle,
-    InQual,
-}
-
-pub(crate) struct FastqParser {
-    state: FastqState,
-    overlap: OverlapState,
-}
-
-impl NucParser for FastqParser {
-    fn new(k: usize) -> Self {
-        Self {
-            state: FastqState::OutSeq,
-            overlap: OverlapState::new(k),
-        }
-    }
-
-    #[inline]
-    fn overlap_state(&self) -> &OverlapState {
-        &self.overlap
-    }
-
-    #[inline]
-    fn overlap_state_mut(&mut self) -> &mut OverlapState {
-        &mut self.overlap
-    }
-
-    #[inline]
-    fn is_in_seq(&self) -> bool {
-        matches!(self.state, FastqState::InSeq)
-    }
-
-    fn parse_inplace(&mut self, buf: &mut [u8], n: usize) -> usize {
-        let total = self.overlap.len + n;
-        let mut i = 0;
-        let mut j = 0;
-        let mut seq_start: usize = 0;
-
-        while i < total {
-            // SAFETY: i < total <= BUF_SIZE = buf.len()
-            let byte = unsafe { *buf.get_unchecked(i) };
-
-            match self.state {
-                FastqState::OutSeq => {
-                    if byte == b'@' {
-                        self.state = FastqState::InTitle;
-                    }
-                    i += 1;
-                }
-                FastqState::InTitle => {
-                    if byte == b'\n' || byte == b'\r' {
-                        self.state = FastqState::InSeq;
-                        seq_start = j;
-                    }
-                    i += 1;
-                }
-                FastqState::InSeq => {
-                    if byte == b'\n' || byte == b'\r' {
-                        if j > seq_start {
-                            unsafe {
-                                *buf.get_unchecked_mut(j) = 0;
-                            }
-                            j += 1;
-                        }
-                        self.state = FastqState::InQualTitle;
-                        i += 1;
-                        continue;
-                    }
-                    let nuc = byte & 0xDF;
-                    if nuc == b'A' || nuc == b'C' || nuc == b'G' || nuc == b'T' {
-                        // SAFETY: j <= i < total <= BUF_SIZE = buf.len()
-                        unsafe {
-                            *buf.get_unchecked_mut(j) = nuc;
-                        }
-                        j += 1;
-                    } else {
-                        if j > seq_start {
-                            unsafe {
-                                *buf.get_unchecked_mut(j) = 0;
-                            }
-                            j += 1;
-                        }
-                        self.state = FastqState::InAmbiguous;
-                    }
-                    i += 1;
-                }
-                FastqState::InAmbiguous => {
-                    if byte == b'\n' || byte == b'\r' {
-                        self.state = FastqState::InQualTitle;
-                        i += 1;
-                        continue;
-                    }
-                    let nuc = byte & 0xDF;
-                    if nuc == b'A' || nuc == b'C' || nuc == b'G' || nuc == b'T' {
-                        seq_start = j;
-                        // SAFETY: j <= i < total <= BUF_SIZE = buf.len()
-                        unsafe {
-                            *buf.get_unchecked_mut(j) = nuc;
-                        }
-                        j += 1;
-                        self.state = FastqState::InSeq;
-                    }
-                    i += 1;
-                }
-                FastqState::InQualTitle => {
-                    if byte == b'\n' || byte == b'\r' {
-                        self.state = FastqState::InQual;
-                    }
-                    i += 1;
-                }
-                FastqState::InQual => {
-                    if byte == b'\n' || byte == b'\r' {
-                        self.state = FastqState::OutSeq;
-                    }
-                    i += 1;
-                }
-            }
-        }
-
-        self.save_overlap(buf, j, seq_start)
-    }
-}
-
-// ─── GenBank parser ───────────────────────────────────────────────────────────
-
-const ORIGIN_TAIL: &[u8] = b"RIGIN";
-
-#[derive(Clone, Copy)]
-enum GenbankState {
-    OutSeq,
-    MatchOrigin,
-    SkipOriginLine,
-    InSeq,
-    InSlash,
-    InAmbiguous,
-}
-
-pub(crate) struct GenbankParser {
-    state: GenbankState,
-    overlap: OverlapState,
-    keyword_pos: usize,
-    at_line_start: bool,
-}
-
-impl NucParser for GenbankParser {
-    fn new(k: usize) -> Self {
-        Self {
-            state: GenbankState::OutSeq,
-            overlap: OverlapState::new(k),
-            keyword_pos: 0,
-            at_line_start: true,
-        }
-    }
-
-    #[inline]
-    fn overlap_state(&self) -> &OverlapState {
-        &self.overlap
-    }
-
-    #[inline]
-    fn overlap_state_mut(&mut self) -> &mut OverlapState {
-        &mut self.overlap
-    }
-
-    #[inline]
-    fn is_in_seq(&self) -> bool {
-        matches!(self.state, GenbankState::InSeq)
-    }
-
-    fn parse_inplace(&mut self, buf: &mut [u8], n: usize) -> usize {
-        let total = self.overlap.len + n;
-        let mut i = 0;
-        let mut j = 0;
-        let mut seq_start: usize = 0;
-
-        while i < total {
-            // SAFETY: i < total <= BUF_SIZE = buf.len()
-            let byte = unsafe { *buf.get_unchecked(i) };
-
-            match self.state {
-                GenbankState::OutSeq => {
-                    if byte == b'\n' || byte == b'\r' {
-                        self.at_line_start = true;
-                    } else if self.at_line_start && byte == b'O' {
-                        self.state = GenbankState::MatchOrigin;
-                        self.keyword_pos = 1;
-                        self.at_line_start = false;
-                    } else {
-                        self.at_line_start = false;
-                    }
-                    i += 1;
-                }
-                GenbankState::MatchOrigin => {
-                    if byte == b'\n' || byte == b'\r' {
-                        self.state = GenbankState::OutSeq;
-                        self.at_line_start = true;
-                    } else if byte == ORIGIN_TAIL[self.keyword_pos - 1] {
-                        self.keyword_pos += 1;
-                        if self.keyword_pos == 6 {
-                            self.state = GenbankState::SkipOriginLine;
-                        }
-                    } else {
-                        self.state = GenbankState::OutSeq;
-                        self.at_line_start = false;
-                    }
-                    i += 1;
-                }
-                GenbankState::SkipOriginLine => {
-                    if byte == b'\n' || byte == b'\r' {
-                        self.state = GenbankState::InSeq;
-                        seq_start = j;
-                    }
-                    i += 1;
-                }
-                GenbankState::InSeq => {
-                    if byte == b'\n' || byte == b'\r' {
-                        self.at_line_start = true;
-                        i += 1;
-                        continue;
-                    }
-                    if self.at_line_start && byte == b'/' {
-                        self.state = GenbankState::InSlash;
-                        self.at_line_start = false;
-                        i += 1;
-                        continue;
-                    }
-                    self.at_line_start = false;
-                    let nuc = byte & 0xDF;
-                    if nuc == b'A' || nuc == b'C' || nuc == b'G' || nuc == b'T' {
-                        // SAFETY: j <= i < total <= BUF_SIZE = buf.len()
-                        unsafe {
-                            *buf.get_unchecked_mut(j) = nuc;
-                        }
-                        j += 1;
-                    } else if byte.is_ascii_digit() || byte == b' ' {
-                        // position numbers and spacing between groups: skip
-                    } else {
-                        // ambiguous base: end current sequence if non-empty
-                        if j > seq_start {
-                            unsafe {
-                                *buf.get_unchecked_mut(j) = 0;
-                            }
-                            j += 1;
-                        }
-                        self.state = GenbankState::InAmbiguous;
-                    }
-                    i += 1;
-                }
-                GenbankState::InSlash => {
-                    if byte == b'/' {
-                        // confirmed "//": end of sequence record
-                        if j > seq_start {
-                            unsafe {
-                                *buf.get_unchecked_mut(j) = 0;
-                            }
-                            j += 1;
-                        }
-                        self.state = GenbankState::OutSeq;
-                        self.at_line_start = false;
-                    } else if byte == b'\n' || byte == b'\r' {
-                        // single '/' line: back to sequence
-                        self.state = GenbankState::InSeq;
-                        self.at_line_start = true;
-                    } else {
-                        // false positive: single '/' mid-line, resume sequence
-                        self.state = GenbankState::InSeq;
-                        self.at_line_start = false;
-                    }
-                    i += 1;
-                }
-                GenbankState::InAmbiguous => {
-                    if byte == b'\n' || byte == b'\r' {
-                        self.at_line_start = true;
-                        i += 1;
-                        continue;
-                    }
-                    if self.at_line_start && byte == b'/' {
-                        self.state = GenbankState::InSlash;
-                        self.at_line_start = false;
-                        i += 1;
-                        continue;
-                    }
-                    self.at_line_start = false;
-                    let nuc = byte & 0xDF;
-                    if nuc == b'A' || nuc == b'C' || nuc == b'G' || nuc == b'T' {
-                        seq_start = j;
-                        // SAFETY: j <= i < total <= BUF_SIZE = buf.len()
-                        unsafe {
-                            *buf.get_unchecked_mut(j) = nuc;
-                        }
-                        j += 1;
-                        self.state = GenbankState::InSeq;
-                    }
-                    // digits, spaces, other ambiguous codes: skip
-                    i += 1;
-                }
-            }
-        }
-
-        self.save_overlap(buf, j, seq_start)
-    }
-}
-
-// ─── NucPage ──────────────────────────────────────────────────────────────────
-
-/// Owned page of compacted nucleotides: uppercase A/C/G/T bytes separated by `0`
-/// at sequence boundaries. Automatically returns its buffer to the pool on drop.
-pub struct NucPage {
-    data: ManuallyDrop<Vec<u8>>,
-    len: usize,
-    pool: Arc<Mutex<Vec<Vec<u8>>>>,
-}
-
-impl std::ops::Deref for NucPage {
-    type Target = [u8];
-    fn deref(&self) -> &[u8] {
-        &self.data[..self.len]
-    }
-}
-
-impl Drop for NucPage {
-    fn drop(&mut self) {
-        // SAFETY: data is never accessed after this point
-        let buf = unsafe { ManuallyDrop::take(&mut self.data) };
-        self.pool.lock().unwrap().push(buf);
-    }
-}
-
-// ─── NucPageCursor ────────────────────────────────────────────────────────────
-
-/// A forward cursor over the normalised bytes of a [`NucPage`].
-///
-/// Provides the `next_byte` / `rewind` interface consumed by
-/// [`obiskbuilder::SuperKmerStreamIter`].
-pub struct NucPageCursor<'a> {
-    data: &'a [u8],
-    pos: usize,
-}
-
-impl NucPageCursor<'_> {
-    /// Returns the next byte in the page, or `None` at end.
-    #[inline]
-    pub fn next_byte(&mut self) -> Option<u8> {
-        if self.pos < self.data.len() {
-            let b = self.data[self.pos];
-            self.pos += 1;
-            Some(b)
-        } else {
-            None
-        }
-    }
-
-    /// Steps the cursor back by `n` bytes.
-    ///
-    /// The caller guarantees that the last `n` bytes were all `ACGT`
-    /// (no `0x00` separators), so they are still in the page buffer.
-    #[inline]
-    pub fn rewind(&mut self, n: usize) {
-        self.pos -= n;
-    }
-
-    /// Total number of bytes in the underlying page.
-    #[inline]
-    pub fn len(&self) -> usize {
-        self.data.len()
-    }
-
-    /// Returns `true` if the page contains no bytes.
-    #[inline]
-    pub fn is_empty(&self) -> bool {
-        self.data.is_empty()
-    }
-}
-
-impl NucPage {
-    /// Creates a forward cursor positioned at the start of this page.
-    pub fn cursor(&self) -> NucPageCursor<'_> {
-        NucPageCursor { data: self, pos: 0 }
-    }
-}
-
-// ─── NucStream ────────────────────────────────────────────────────────────────
-
-pub(crate) struct NucStream<R: Read, P: NucParser> {
-    reader: R,
-    parser: P,
-    pool: Arc<Mutex<Vec<Vec<u8>>>>,
-    eof: bool,
-}
-
-impl<R: Read, P: NucParser> NucStream<R, P> {
-    pub(crate) fn new(reader: R, k: usize) -> Self {
-        Self {
-            reader,
-            parser: P::new(k),
-            pool: Arc::new(Mutex::new(Vec::new())),
-            eof: false,
-        }
-    }
-
-    pub(crate) fn read_page(&mut self) -> Option<NucPage> {
-        loop {
-            if self.eof {
-                return None;
-            }
-            // take a buffer from the pool, or allocate fresh if all are in-flight
-            let mut buf = self
-                .pool
-                .lock()
-                .unwrap()
-                .pop()
-                .unwrap_or_else(|| vec![0u8; BUF_SIZE]);
-
-            let ol = self.parser.overlap_len();
-            self.parser.write_overlap(&mut buf[..ol]);
-            let n = self.reader.read(&mut buf[ol..ol + PAGE_SIZE]).unwrap_or(0);
-            if n == 0 {
-                self.eof = true;
-                if ol == 0 {
-                    self.pool.lock().unwrap().push(buf);
-                    return None;
-                }
-            }
-            let out_len = self.parser.parse_inplace(&mut buf, n);
-            if out_len > 0 {
-                return Some(NucPage {
-                    data: ManuallyDrop::new(buf),
-                    len: out_len,
-                    pool: Arc::clone(&self.pool),
-                });
-            }
-            // empty page (all headers/ambiguous): return buf to pool and loop
-            self.pool.lock().unwrap().push(buf);
-        }
-    }
-}
-
-impl<R: Read, P: NucParser> Iterator for NucStream<R, P> {
-    type Item = NucPage;
-    fn next(&mut self) -> Option<NucPage> {
-        self.read_page()
-    }
-}
-
-// ─── FastaNucStream ───────────────────────────────────────────────────────────
-
-pub(crate) type FastaNucStream<R> = NucStream<R, FastaParser>;
-pub(crate) type FastqNucStream<R> = NucStream<R, FastqParser>;
-pub(crate) type GenbankNucStream<R> = NucStream<R, GenbankParser>;
-
-// ─── AnyNucStream ─────────────────────────────────────────────────────────────
-
-pub(crate) enum AnyNucStream<R: Read> {
-    Fasta(FastaNucStream<R>),
-    Fastq(FastqNucStream<R>),
-    Genbank(GenbankNucStream<R>),
-}
-
-impl<R: Read> Iterator for AnyNucStream<R> {
-    type Item = NucPage;
-    fn next(&mut self) -> Option<NucPage> {
-        match self {
-            AnyNucStream::Fasta(s) => s.next(),
-            AnyNucStream::Fastq(s) => s.next(),
-            AnyNucStream::Genbank(s) => s.next(),
-        }
-    }
-}
-
-fn dispatch<R: Read>(
-    mut guesser: MimeTypeGuesser<R>,
-    k: usize,
-) -> Option<AnyNucStream<MimeTypeGuesser<R>>> {
-    match guesser.mime_type() {
-        Some("text/fasta") => Some(AnyNucStream::Fasta(NucStream::new(guesser, k))),
-        Some("text/fastq") => Some(AnyNucStream::Fastq(NucStream::new(guesser, k))),
-        Some("text/gbff") => Some(AnyNucStream::Genbank(NucStream::new(guesser, k))),
-        _ => None,
-    }
-}
-
-/// Wraps an already-open reader in a nucleotide stream, detecting its format.
-/// Returns `None` if the format is not recognised.
-pub(crate) fn nuc_stream<R: Read>(reader: R, k: usize) -> Option<AnyNucStream<MimeTypeGuesser<R>>> {
-    dispatch(MimeTypeGuesser::new(reader), k)
-}
-
-/// Opens a nucleotide stream from any source (file path, URL, or `-` for stdin),
-/// with transparent decompression and automatic format detection.
-///
-/// # Errors
-/// Returns an `io::Error` if the source cannot be opened, decompression fails,
-/// or the format is not recognised.
-pub fn open_nuc_stream(
-    source: &str,
-    k: usize,
-) -> io::Result<Box<dyn Iterator<Item = NucPage> + Send>> {
-    let reader = open_raw(source)?;
-    nuc_stream(reader, k)
-        .map(|s| Box::new(s) as Box<dyn Iterator<Item = NucPage> + Send>)
-        .ok_or_else(|| io::Error::new(io::ErrorKind::InvalidData, "unknown sequence format"))
-}
-
-#[cfg(test)]
-#[path = "tests/nucstream.rs"]
-mod tests;
diff --git a/src/obiread/src/nucstream/fasta.rs b/src/obiread/src/nucstream/fasta.rs
new file mode 100644
index 00000000..9eda45e6
--- /dev/null
+++ b/src/obiread/src/nucstream/fasta.rs
@@ -0,0 +1,128 @@
+use super::overlap::{NucParser, OverlapState};
+
+// ─── FASTA parser ─────────────────────────────────────────────────────────────
+
+#[derive(Clone, Copy)]
+enum FastaState {
+    OutSeq,
+    InTitle,
+    InSeq,
+    InAmbiguous,
+}
+
+pub(crate) struct FastaParser {
+    state: FastaState,
+    overlap: OverlapState,
+}
+
+impl NucParser for FastaParser {
+    fn new(k: usize) -> Self {
+        Self {
+            state: FastaState::OutSeq,
+            overlap: OverlapState::new(k),
+        }
+    }
+
+    #[inline]
+    fn overlap_state(&self) -> &OverlapState {
+        &self.overlap
+    }
+
+    #[inline]
+    fn overlap_state_mut(&mut self) -> &mut OverlapState {
+        &mut self.overlap
+    }
+
+    #[inline]
+    fn is_in_seq(&self) -> bool {
+        matches!(self.state, FastaState::InSeq)
+    }
+
+    fn parse_inplace(&mut self, buf: &mut [u8], n: usize) -> usize {
+        let total = self.overlap.len + n;
+        let mut i = 0; // read index
+        let mut j = 0; // write index (invariant: j <= i always)
+        // j-position where the current sequence started in this call's output;
+        // meaningful only when state is InSeq.
+        let mut seq_start: usize = 0;
+
+        while i < total {
+            // SAFETY: i < total <= BUF_SIZE = buf.len()
+            let byte = unsafe { *buf.get_unchecked(i) };
+
+            match self.state {
+                FastaState::OutSeq => {
+                    if byte == b'>' {
+                        self.state = FastaState::InTitle;
+                    }
+                    i += 1;
+                }
+                FastaState::InTitle => {
+                    if byte == b'\n' || byte == b'\r' {
+                        self.state = FastaState::InSeq;
+                        seq_start = j;
+                    }
+                    i += 1;
+                }
+                FastaState::InSeq => {
+                    if byte == b'\n' || byte == b'\r' {
+                        i += 1;
+                        continue;
+                    }
+                    let nuc = byte & 0xDF; // to uppercase
+                    if nuc == b'A' || nuc == b'C' || nuc == b'G' || nuc == b'T' {
+                        // SAFETY: j <= i < total <= BUF_SIZE = buf.len()
+                        unsafe {
+                            *buf.get_unchecked_mut(j) = nuc;
+                        }
+                        j += 1;
+                        i += 1;
+                    } else if byte == b'>' {
+                        if j > seq_start {
+                            unsafe {
+                                *buf.get_unchecked_mut(j) = 0;
+                            }
+                            j += 1;
+                        }
+                        self.state = FastaState::InTitle;
+                        i += 1;
+                    } else {
+                        // first ambiguous base: end current sequence if non-empty
+                        if j > seq_start {
+                            unsafe {
+                                *buf.get_unchecked_mut(j) = 0;
+                            }
+                            j += 1;
+                        }
+                        self.state = FastaState::InAmbiguous;
+                        i += 1;
+                    }
+                }
+                FastaState::InAmbiguous => {
+                    if byte == b'\n' || byte == b'\r' {
+                        i += 1;
+                        continue;
+                    }
+                    if byte == b'>' {
+                        self.state = FastaState::InTitle;
+                        i += 1;
+                        continue;
+                    }
+                    let nuc = byte & 0xDF;
+                    if nuc == b'A' || nuc == b'C' || nuc == b'G' || nuc == b'T' {
+                        seq_start = j;
+                        // SAFETY: j <= i < total <= BUF_SIZE = buf.len()
+                        unsafe {
+                            *buf.get_unchecked_mut(j) = nuc;
+                        }
+                        j += 1;
+                        self.state = FastaState::InSeq;
+                    }
+                    i += 1;
+                }
+            }
+        }
+
+        self.save_overlap(buf, j, seq_start)
+    }
+}
diff --git a/src/obiread/src/nucstream/fastq.rs b/src/obiread/src/nucstream/fastq.rs
new file mode 100644
index 00000000..639f419b
--- /dev/null
+++ b/src/obiread/src/nucstream/fastq.rs
@@ -0,0 +1,132 @@
+use super::overlap::{NucParser, OverlapState};
+
+// ─── FASTQ parser ─────────────────────────────────────────────────────────────
+
+#[derive(Clone, Copy)]
+enum FastqState {
+    OutSeq,
+    InTitle,
+    InSeq,
+    InAmbiguous,
+    InQualTitle,
+    InQual,
+}
+
+pub(crate) struct FastqParser {
+    state: FastqState,
+    overlap: OverlapState,
+}
+
+impl NucParser for FastqParser {
+    fn new(k: usize) -> Self {
+        Self {
+            state: FastqState::OutSeq,
+            overlap: OverlapState::new(k),
+        }
+    }
+
+    #[inline]
+    fn overlap_state(&self) -> &OverlapState {
+        &self.overlap
+    }
+
+    #[inline]
+    fn overlap_state_mut(&mut self) -> &mut OverlapState {
+        &mut self.overlap
+    }
+
+    #[inline]
+    fn is_in_seq(&self) -> bool {
+        matches!(self.state, FastqState::InSeq)
+    }
+
+    fn parse_inplace(&mut self, buf: &mut [u8], n: usize) -> usize {
+        let total = self.overlap.len + n;
+        let mut i = 0;
+        let mut j = 0;
+        let mut seq_start: usize = 0;
+
+        while i < total {
+            // SAFETY: i < total <= BUF_SIZE = buf.len()
+            let byte = unsafe { *buf.get_unchecked(i) };
+
+            match self.state {
+                FastqState::OutSeq => {
+                    if byte == b'@' {
+                        self.state = FastqState::InTitle;
+                    }
+                    i += 1;
+                }
+                FastqState::InTitle => {
+                    if byte == b'\n' || byte == b'\r' {
+                        self.state = FastqState::InSeq;
+                        seq_start = j;
+                    }
+                    i += 1;
+                }
+                FastqState::InSeq => {
+                    if byte == b'\n' || byte == b'\r' {
+                        if j > seq_start {
+                            unsafe {
+                                *buf.get_unchecked_mut(j) = 0;
+                            }
+                            j += 1;
+                        }
+                        self.state = FastqState::InQualTitle;
+                        i += 1;
+                        continue;
+                    }
+                    let nuc = byte & 0xDF;
+                    if nuc == b'A' || nuc == b'C' || nuc == b'G' || nuc == b'T' {
+                        // SAFETY: j <= i < total <= BUF_SIZE = buf.len()
+                        unsafe {
+                            *buf.get_unchecked_mut(j) = nuc;
+                        }
+                        j += 1;
+                    } else {
+                        if j > seq_start {
+                            unsafe {
+                                *buf.get_unchecked_mut(j) = 0;
+                            }
+                            j += 1;
+                        }
+                        self.state = FastqState::InAmbiguous;
+                    }
+                    i += 1;
+                }
+                FastqState::InAmbiguous => {
+                    if byte == b'\n' || byte == b'\r' {
+                        self.state = FastqState::InQualTitle;
+                        i += 1;
+                        continue;
+                    }
+                    let nuc = byte & 0xDF;
+                    if nuc == b'A' || nuc == b'C' || nuc == b'G' || nuc == b'T' {
+                        seq_start = j;
+                        // SAFETY: j <= i < total <= BUF_SIZE = buf.len()
+                        unsafe {
+                            *buf.get_unchecked_mut(j) = nuc;
+                        }
+                        j += 1;
+                        self.state = FastqState::InSeq;
+                    }
+                    i += 1;
+                }
+                FastqState::InQualTitle => {
+                    if byte == b'\n' || byte == b'\r' {
+                        self.state = FastqState::InQual;
+                    }
+                    i += 1;
+                }
+                FastqState::InQual => {
+                    if byte == b'\n' || byte == b'\r' {
+                        self.state = FastqState::OutSeq;
+                    }
+                    i += 1;
+                }
+            }
+        }
+
+        self.save_overlap(buf, j, seq_start)
+    }
+}
diff --git a/src/obiread/src/nucstream/genbank.rs b/src/obiread/src/nucstream/genbank.rs
new file mode 100644
index 00000000..6afd8f46
--- /dev/null
+++ b/src/obiread/src/nucstream/genbank.rs
@@ -0,0 +1,181 @@
+use super::overlap::{NucParser, OverlapState};
+
+// ─── GenBank parser ───────────────────────────────────────────────────────────
+
+const ORIGIN_TAIL: &[u8] = b"RIGIN";
+
+#[derive(Clone, Copy)]
+enum GenbankState {
+    OutSeq,
+    MatchOrigin,
+    SkipOriginLine,
+    InSeq,
+    InSlash,
+    InAmbiguous,
+}
+
+pub(crate) struct GenbankParser {
+    state: GenbankState,
+    overlap: OverlapState,
+    keyword_pos: usize,
+    at_line_start: bool,
+}
+
+impl NucParser for GenbankParser {
+    fn new(k: usize) -> Self {
+        Self {
+            state: GenbankState::OutSeq,
+            overlap: OverlapState::new(k),
+            keyword_pos: 0,
+            at_line_start: true,
+        }
+    }
+
+    #[inline]
+    fn overlap_state(&self) -> &OverlapState {
+        &self.overlap
+    }
+
+    #[inline]
+    fn overlap_state_mut(&mut self) -> &mut OverlapState {
+        &mut self.overlap
+    }
+
+    #[inline]
+    fn is_in_seq(&self) -> bool {
+        matches!(self.state, GenbankState::InSeq)
+    }
+
+    fn parse_inplace(&mut self, buf: &mut [u8], n: usize) -> usize {
+        let total = self.overlap.len + n;
+        let mut i = 0;
+        let mut j = 0;
+        let mut seq_start: usize = 0;
+
+        while i < total {
+            // SAFETY: i < total <= BUF_SIZE = buf.len()
+            let byte = unsafe { *buf.get_unchecked(i) };
+
+            match self.state {
+                GenbankState::OutSeq => {
+                    if byte == b'\n' || byte == b'\r' {
+                        self.at_line_start = true;
+                    } else if self.at_line_start && byte == b'O' {
+                        self.state = GenbankState::MatchOrigin;
+                        self.keyword_pos = 1;
+                        self.at_line_start = false;
+                    } else {
+                        self.at_line_start = false;
+                    }
+                    i += 1;
+                }
+                GenbankState::MatchOrigin => {
+                    if byte == b'\n' || byte == b'\r' {
+                        self.state = GenbankState::OutSeq;
+                        self.at_line_start = true;
+                    } else if byte == ORIGIN_TAIL[self.keyword_pos - 1] {
+                        self.keyword_pos += 1;
+                        if self.keyword_pos == 6 {
+                            self.state = GenbankState::SkipOriginLine;
+                        }
+                    } else {
+                        self.state = GenbankState::OutSeq;
+                        self.at_line_start = false;
+                    }
+                    i += 1;
+                }
+                GenbankState::SkipOriginLine => {
+                    if byte == b'\n' || byte == b'\r' {
+                        self.state = GenbankState::InSeq;
+                        seq_start = j;
+                    }
+                    i += 1;
+                }
+                GenbankState::InSeq => {
+                    if byte == b'\n' || byte == b'\r' {
+                        self.at_line_start = true;
+                        i += 1;
+                        continue;
+                    }
+                    if self.at_line_start && byte == b'/' {
+                        self.state = GenbankState::InSlash;
+                        self.at_line_start = false;
+                        i += 1;
+                        continue;
+                    }
+                    self.at_line_start = false;
+                    let nuc = byte & 0xDF;
+                    if nuc == b'A' || nuc == b'C' || nuc == b'G' || nuc == b'T' {
+                        // SAFETY: j <= i < total <= BUF_SIZE = buf.len()
+                        unsafe {
+                            *buf.get_unchecked_mut(j) = nuc;
+                        }
+                        j += 1;
+                    } else if byte.is_ascii_digit() || byte == b' ' {
+                        // position numbers and spacing between groups: skip
+                    } else {
+                        // ambiguous base: end current sequence if non-empty
+                        if j > seq_start {
+                            unsafe {
+                                *buf.get_unchecked_mut(j) = 0;
+                            }
+                            j += 1;
+                        }
+                        self.state = GenbankState::InAmbiguous;
+                    }
+                    i += 1;
+                }
+                GenbankState::InSlash => {
+                    if byte == b'/' {
+                        // confirmed "//": end of sequence record
+                        if j > seq_start {
+                            unsafe {
+                                *buf.get_unchecked_mut(j) = 0;
+                            }
+                            j += 1;
+                        }
+                        self.state = GenbankState::OutSeq;
+                        self.at_line_start = false;
+                    } else if byte == b'\n' || byte == b'\r' {
+                        // single '/' line: back to sequence
+                        self.state = GenbankState::InSeq;
+                        self.at_line_start = true;
+                    } else {
+                        // false positive: single '/' mid-line, resume sequence
+                        self.state = GenbankState::InSeq;
+                        self.at_line_start = false;
+                    }
+                    i += 1;
+                }
+                GenbankState::InAmbiguous => {
+                    if byte == b'\n' || byte == b'\r' {
+                        self.at_line_start = true;
+                        i += 1;
+                        continue;
+                    }
+                    if self.at_line_start && byte == b'/' {
+                        self.state = GenbankState::InSlash;
+                        self.at_line_start = false;
+                        i += 1;
+                        continue;
+                    }
+                    self.at_line_start = false;
+                    let nuc = byte & 0xDF;
+                    if nuc == b'A' || nuc == b'C' || nuc == b'G' || nuc == b'T' {
+                        seq_start = j;
+                        // SAFETY: j <= i < total <= BUF_SIZE = buf.len()
+                        unsafe {
+                            *buf.get_unchecked_mut(j) = nuc;
+                        }
+                        j += 1;
+                        self.state = GenbankState::InSeq;
+                    }
+                    // digits, spaces, other ambiguous codes: skip
+                    i += 1;
+                }
+            }
+        }
+
+        self.save_overlap(buf, j, seq_start)
+    }
+}
diff --git a/src/obiread/src/nucstream/mod.rs b/src/obiread/src/nucstream/mod.rs
new file mode 100644
index 00000000..a3da2a5f
--- /dev/null
+++ b/src/obiread/src/nucstream/mod.rs
@@ -0,0 +1,40 @@
+//! Streaming, in-place normalisation of raw sequence bytes into compacted
+//! nucleotide pages: uppercase A/C/G/T separated by `0` at sequence
+//! boundaries, ready for k-mer extraction without re-scanning for case or
+//! ambiguity codes.
+//!
+//! Submodules: [`overlap`] (format-independent k-1 overlap bookkeeping
+//! shared by every parser), [`fasta`]/[`fastq`]/[`genbank`] (one
+//! format-specific in-place state machine each), [`page`] (the pooled
+//! output buffer, [`NucPage`]), [`stream`] (format dispatch and the public
+//! [`open_nuc_stream`] entry point).
+
+mod fasta;
+mod fastq;
+mod genbank;
+mod overlap;
+mod page;
+mod stream;
+
+pub use page::{NucPage, NucPageCursor};
+pub use stream::open_nuc_stream;
+
+// Only used by `tests.rs` (`use super::*`) below — the crate itself always
+// reaches these through their defining submodule directly.
+#[cfg(test)]
+pub(crate) use fasta::FastaParser;
+#[cfg(test)]
+pub(crate) use fastq::FastqParser;
+#[cfg(test)]
+pub(crate) use genbank::GenbankParser;
+#[cfg(test)]
+pub(crate) use stream::NucStream;
+
+pub(crate) const MAX_K: usize = 31;
+pub(crate) const PAGE_SIZE: usize = 65536;
+// overlap (MAX_K - 1) + page data (PAGE_SIZE) + 1 byte for the end-of-page terminating 0
+pub(crate) const BUF_SIZE: usize = MAX_K + PAGE_SIZE;
+
+#[cfg(test)]
+#[path = "../tests/nucstream.rs"]
+mod tests;
diff --git a/src/obiread/src/nucstream/overlap.rs b/src/obiread/src/nucstream/overlap.rs
new file mode 100644
index 00000000..e462a54f
--- /dev/null
+++ b/src/obiread/src/nucstream/overlap.rs
@@ -0,0 +1,81 @@
+use super::MAX_K;
+
+// ─── OverlapState ─────────────────────────────────────────────────────────────
+
+pub(crate) struct OverlapState {
+    data: [u8; MAX_K],
+    pub(super) len: usize,
+    k: usize,
+}
+
+impl OverlapState {
+    pub(crate) fn new(k: usize) -> Self {
+        assert!(k > 0 && k <= MAX_K);
+        Self {
+            data: [0u8; MAX_K],
+            len: 0,
+            k,
+        }
+    }
+}
+
+// ─── NucParser trait ──────────────────────────────────────────────────────────
+
+// Transforms a raw page into a compacted nucleotide stream in-place.
+//
+// Buffer layout on each call:
+//   buf[0..overlap_len()]           — overlap bytes copied by write_overlap()
+//   buf[overlap_len()..overlap_len()+n] — raw bytes just read from the source
+//
+// Returns the number of output bytes in buf[0..returned].
+pub(crate) trait NucParser {
+    // required: format-specific
+    fn new(k: usize) -> Self
+    where
+        Self: Sized;
+    fn overlap_state(&self) -> &OverlapState;
+    fn overlap_state_mut(&mut self) -> &mut OverlapState;
+    fn is_in_seq(&self) -> bool;
+    fn parse_inplace(&mut self, buf: &mut [u8], n: usize) -> usize;
+
+    // provided: format-independent overlap management
+    fn overlap_len(&self) -> usize {
+        self.overlap_state().len
+    }
+
+    fn write_overlap(&self, buf: &mut [u8]) {
+        let ol = &self.overlap_state();
+        buf[..ol.len].copy_from_slice(&ol.data[..ol.len]);
+    }
+
+    // Called at end of parse_inplace: saves overlap state and returns adjusted j.
+    // seq_start is the j-position where the last sequence started in this call's output.
+    fn save_overlap(&mut self, buf: &mut [u8], j: usize, seq_start: usize) -> usize {
+        if !self.is_in_seq() {
+            self.overlap_state_mut().len = 0;
+            return j;
+        }
+        let seq_len = j - seq_start;
+        let k = self.overlap_state().k;
+        if seq_len >= k {
+            // Sequence long enough: save last k-1 nucleotides, terminate with 0.
+            let ol = k - 1;
+            self.overlap_state_mut().data[..ol].copy_from_slice(&buf[j - ol..j]);
+            self.overlap_state_mut().len = ol;
+            // SAFETY: j <= total - 1 < BUF_SIZE = buf.len()
+            // (total = overlap_len + n <= (MAX_K-1) + PAGE_SIZE = BUF_SIZE - 1)
+            unsafe {
+                *buf.get_unchecked_mut(j) = 0;
+            }
+            j + 1
+        } else if seq_len > 0 {
+            // Short sequence (< k): save whole fragment, strip from output.
+            self.overlap_state_mut().data[..seq_len].copy_from_slice(&buf[seq_start..j]);
+            self.overlap_state_mut().len = seq_len;
+            seq_start
+        } else {
+            self.overlap_state_mut().len = 0;
+            j
+        }
+    }
+}
diff --git a/src/obiread/src/nucstream/page.rs b/src/obiread/src/nucstream/page.rs
new file mode 100644
index 00000000..8457c685
--- /dev/null
+++ b/src/obiread/src/nucstream/page.rs
@@ -0,0 +1,80 @@
+use std::mem::ManuallyDrop;
+use std::sync::{Arc, Mutex};
+
+// ─── NucPage ──────────────────────────────────────────────────────────────────
+
+/// Owned page of compacted nucleotides: uppercase A/C/G/T bytes separated by `0`
+/// at sequence boundaries. Automatically returns its buffer to the pool on drop.
+pub struct NucPage {
+    pub(super) data: ManuallyDrop<Vec<u8>>,
+    pub(super) len: usize,
+    pub(super) pool: Arc<Mutex<Vec<Vec<u8>>>>,
+}
+
+impl std::ops::Deref for NucPage {
+    type Target = [u8];
+    fn deref(&self) -> &[u8] {
+        &self.data[..self.len]
+    }
+}
+
+impl Drop for NucPage {
+    fn drop(&mut self) {
+        // SAFETY: data is never accessed after this point
+        let buf = unsafe { ManuallyDrop::take(&mut self.data) };
+        self.pool.lock().unwrap().push(buf);
+    }
+}
+
+// ─── NucPageCursor ────────────────────────────────────────────────────────────
+
+/// A forward cursor over the normalised bytes of a [`NucPage`].
+///
+/// Provides the `next_byte` / `rewind` interface consumed by
+/// [`obiskbuilder::SuperKmerStreamIter`].
+pub struct NucPageCursor<'a> {
+    data: &'a [u8],
+    pos: usize,
+}
+
+impl NucPageCursor<'_> {
+    /// Returns the next byte in the page, or `None` at end.
+    #[inline]
+    pub fn next_byte(&mut self) -> Option<u8> {
+        if self.pos < self.data.len() {
+            let b = self.data[self.pos];
+            self.pos += 1;
+            Some(b)
+        } else {
+            None
+        }
+    }
+
+    /// Steps the cursor back by `n` bytes.
+    ///
+    /// The caller guarantees that the last `n` bytes were all `ACGT`
+    /// (no `0x00` separators), so they are still in the page buffer.
+    #[inline]
+    pub fn rewind(&mut self, n: usize) {
+        self.pos -= n;
+    }
+
+    /// Total number of bytes in the underlying page.
+    #[inline]
+    pub fn len(&self) -> usize {
+        self.data.len()
+    }
+
+    /// Returns `true` if the page contains no bytes.
+    #[inline]
+    pub fn is_empty(&self) -> bool {
+        self.data.is_empty()
+    }
+}
+
+impl NucPage {
+    /// Creates a forward cursor positioned at the start of this page.
+    pub fn cursor(&self) -> NucPageCursor<'_> {
+        NucPageCursor { data: self, pos: 0 }
+    }
+}
diff --git a/src/obiread/src/nucstream/stream.rs b/src/obiread/src/nucstream/stream.rs
new file mode 100644
index 00000000..d1fb5f71
--- /dev/null
+++ b/src/obiread/src/nucstream/stream.rs
@@ -0,0 +1,135 @@
+use std::io::{self, Read};
+use std::mem::ManuallyDrop;
+use std::sync::{Arc, Mutex};
+
+use crate::mimetype::MimeTypeGuesser;
+use crate::xopen::open_raw;
+
+use super::fasta::FastaParser;
+use super::fastq::FastqParser;
+use super::genbank::GenbankParser;
+use super::overlap::NucParser;
+use super::page::NucPage;
+use super::{BUF_SIZE, PAGE_SIZE};
+
+// ─── NucStream ────────────────────────────────────────────────────────────────
+
+pub(crate) struct NucStream<R: Read, P: NucParser> {
+    reader: R,
+    parser: P,
+    pool: Arc<Mutex<Vec<Vec<u8>>>>,
+    eof: bool,
+}
+
+impl<R: Read, P: NucParser> NucStream<R, P> {
+    pub(crate) fn new(reader: R, k: usize) -> Self {
+        Self {
+            reader,
+            parser: P::new(k),
+            pool: Arc::new(Mutex::new(Vec::new())),
+            eof: false,
+        }
+    }
+
+    pub(crate) fn read_page(&mut self) -> Option<NucPage> {
+        loop {
+            if self.eof {
+                return None;
+            }
+            // take a buffer from the pool, or allocate fresh if all are in-flight
+            let mut buf = self
+                .pool
+                .lock()
+                .unwrap()
+                .pop()
+                .unwrap_or_else(|| vec![0u8; BUF_SIZE]);
+
+            let ol = self.parser.overlap_len();
+            self.parser.write_overlap(&mut buf[..ol]);
+            let n = self.reader.read(&mut buf[ol..ol + PAGE_SIZE]).unwrap_or(0);
+            if n == 0 {
+                self.eof = true;
+                if ol == 0 {
+                    self.pool.lock().unwrap().push(buf);
+                    return None;
+                }
+            }
+            let out_len = self.parser.parse_inplace(&mut buf, n);
+            if out_len > 0 {
+                return Some(NucPage {
+                    data: ManuallyDrop::new(buf),
+                    len: out_len,
+                    pool: Arc::clone(&self.pool),
+                });
+            }
+            // empty page (all headers/ambiguous): return buf to pool and loop
+            self.pool.lock().unwrap().push(buf);
+        }
+    }
+}
+
+impl<R: Read, P: NucParser> Iterator for NucStream<R, P> {
+    type Item = NucPage;
+    fn next(&mut self) -> Option<NucPage> {
+        self.read_page()
+    }
+}
+
+// ─── FastaNucStream ───────────────────────────────────────────────────────────
+
+pub(crate) type FastaNucStream<R> = NucStream<R, FastaParser>;
+pub(crate) type FastqNucStream<R> = NucStream<R, FastqParser>;
+pub(crate) type GenbankNucStream<R> = NucStream<R, GenbankParser>;
+
+// ─── AnyNucStream ─────────────────────────────────────────────────────────────
+
+pub(crate) enum AnyNucStream<R: Read> {
+    Fasta(FastaNucStream<R>),
+    Fastq(FastqNucStream<R>),
+    Genbank(GenbankNucStream<R>),
+}
+
+impl<R: Read> Iterator for AnyNucStream<R> {
+    type Item = NucPage;
+    fn next(&mut self) -> Option<NucPage> {
+        match self {
+            AnyNucStream::Fasta(s) => s.next(),
+            AnyNucStream::Fastq(s) => s.next(),
+            AnyNucStream::Genbank(s) => s.next(),
+        }
+    }
+}
+
+fn dispatch<R: Read>(
+    mut guesser: MimeTypeGuesser<R>,
+    k: usize,
+) -> Option<AnyNucStream<MimeTypeGuesser<R>>> {
+    match guesser.mime_type() {
+        Some("text/fasta") => Some(AnyNucStream::Fasta(NucStream::new(guesser, k))),
+        Some("text/fastq") => Some(AnyNucStream::Fastq(NucStream::new(guesser, k))),
+        Some("text/gbff") => Some(AnyNucStream::Genbank(NucStream::new(guesser, k))),
+        _ => None,
+    }
+}
+
+/// Wraps an already-open reader in a nucleotide stream, detecting its format.
+/// Returns `None` if the format is not recognised.
+pub(crate) fn nuc_stream<R: Read>(reader: R, k: usize) -> Option<AnyNucStream<MimeTypeGuesser<R>>> {
+    dispatch(MimeTypeGuesser::new(reader), k)
+}
+
+/// Opens a nucleotide stream from any source (file path, URL, or `-` for stdin),
+/// with transparent decompression and automatic format detection.
+///
+/// # Errors
+/// Returns an `io::Error` if the source cannot be opened, decompression fails,
+/// or the format is not recognised.
+pub fn open_nuc_stream(
+    source: &str,
+    k: usize,
+) -> io::Result<Box<dyn Iterator<Item = NucPage> + Send>> {
+    let reader = open_raw(source)?;
+    nuc_stream(reader, k)
+        .map(|s| Box::new(s) as Box<dyn Iterator<Item = NucPage> + Send>)
+        .ok_or_else(|| io::Error::new(io::ErrorKind::InvalidData, "unknown sequence format"))
+}
diff --git a/src/obiskio/src/unitig_index.rs b/src/obiskio/src/unitig_index.rs
deleted file mode 100644
index 3320500f..00000000
--- a/src/obiskio/src/unitig_index.rs
+++ /dev/null
@@ -1,550 +0,0 @@
-use std::fs::File;
-use std::io::{BufWriter, Write as _};
-use std::path::{Path, PathBuf};
-use std::sync::Arc;
-
-use memmap2::Mmap;
-use obikseq::{CanonicalKmer, Kmer, Unitig};
-
-pub use obikseq::MAX_KMERS_PER_CHUNK;
-
-use crate::error::{SKError, SKResult};
-
-// ── Block index parameters ────────────────────────────────────────────────────
-//
-// BLOCK_SIZE = 1 << block_bits chunks share one offset entry in the index.
-// block_bits=0 → one entry per chunk (exact offsets, no scan).
-// block_bits=6 → one entry per 64 chunks (default; O(64) scan per lookup).
-//
-// block_bits is stored in the index file so the reader derives all parameters
-// at runtime — no compile-time constant constrains the format.
-
-const MAGIC: [u8; 4] = *b"UIX3";
-
-/// Default block granularity used by [`UnitigFileWriter::create`].
-pub const DEFAULT_BLOCK_BITS: u8 = 0;
-
-fn idx_path(path: &Path) -> PathBuf {
-    crate::append_path_suffix(path, ".idx")
-}
-
-// ── Writer ────────────────────────────────────────────────────────────────────
-
-/// Writes a sequence of [`Unitig`] to an uncompressed binary file and builds
-/// a block-sampled offset index at close time.
-///
-/// One offset is stored every `1 << block_bits` chunks; random access to chunk
-/// `i` costs at most `(1 << block_bits) − 1` sequential chunk scans after the
-/// block lookup.
-///
-/// Unitigs with more than [`MAX_KMERS_PER_CHUNK`] k-mers are transparently split
-/// into overlapping chunks (k−1 nucleotide overlap) so no k-mer is lost.
-pub struct UnitigFileWriter {
-    file:          BufWriter<File>,
-    block_offsets: Vec<u32>,
-    chunk_count:   usize,
-    next_offset:   u32,
-    n_kmers:       usize,
-    k:             usize,
-    block_bits:    u8,
-    mask:          usize,  // (1 << block_bits) - 1
-}
-
-impl UnitigFileWriter {
-    /// Create a writer with the default block size (`DEFAULT_BLOCK_BITS = 6`).
-    pub fn create(path: &Path) -> SKResult<Self> {
-        Self::create_with_block_bits(path, DEFAULT_BLOCK_BITS)
-    }
-
-    /// Create a writer with a custom block size.
-    ///
-    /// `block_bits` must be in 0..=31. `block_bits=0` stores one offset per
-    /// chunk (exact, no scan); larger values trade index size for scan length.
-    pub fn create_with_block_bits(path: &Path, block_bits: u8) -> SKResult<Self> {
-        assert!(block_bits <= 31, "block_bits must be ≤ 31");
-        let file = File::create(path).map_err(SKError::Io)?;
-        Ok(Self {
-            file: BufWriter::new(file),
-            block_offsets: Vec::new(),
-            chunk_count: 0,
-            next_offset: 0,
-            n_kmers: 0,
-            k: obikseq::params::k(),
-            block_bits,
-            mask: (1usize << block_bits) - 1,
-        })
-    }
-
-    /// Write a unitig, splitting into overlapping chunks if it exceeds
-    /// [`MAX_KMERS_PER_CHUNK`].
-    pub fn write(&mut self, unitig: &Unitig) -> SKResult<()> {
-        let seql = unitig.seql();
-        let k = self.k;
-
-        if seql < k {
-            return Ok(());
-        }
-
-        let n_kmers = seql - k + 1;
-        if n_kmers <= MAX_KMERS_PER_CHUNK {
-            return self.write_chunk(unitig);
-        }
-
-        let chunk_nucl = MAX_KMERS_PER_CHUNK + k - 1;
-        let stride = MAX_KMERS_PER_CHUNK;
-        let mut start = 0;
-        while start < seql {
-            let end = (start + chunk_nucl).min(seql);
-            self.write_chunk(&unitig.sub(start, end))?;
-            if end == seql { break; }
-            start += stride;
-        }
-        Ok(())
-    }
-
-    fn write_chunk(&mut self, unitig: &Unitig) -> SKResult<()> {
-        let seql = unitig.seql();
-        let byte_len = (seql + 3) / 4;
-
-        debug_assert!(seql - self.k <= u8::MAX as usize, "chunk exceeds MAX_KMERS_PER_CHUNK");
-
-        if self.chunk_count & self.mask == 0 {
-            self.block_offsets.push(self.next_offset);
-        }
-
-        self.n_kmers += seql - self.k + 1;
-        self.chunk_count += 1;
-
-        unitig.write_to_binary(&mut self.file).map_err(SKError::Io)?;
-
-        self.next_offset += 1 + byte_len as u32;
-        Ok(())
-    }
-
-    /// Flush and close the binary sequence file.
-    ///
-    /// The companion `.idx` file is **not** written here; call
-    /// [`build_unitig_idx`] separately when exact evidence is needed.
-    pub fn close(mut self) -> SKResult<()> {
-        self.file.flush().map_err(SKError::Io)?;
-        drop(self.file);
-        Ok(())
-    }
-
-    pub fn len(&self) -> usize { self.chunk_count }
-    pub fn is_empty(&self) -> bool { self.chunk_count == 0 }
-    pub fn block_bits(&self) -> u8 { self.block_bits }
-}
-
-fn write_idx(
-    path: &Path,
-    n_unitigs: u32,
-    n_kmers: u64,
-    block_bits: u8,
-    block_offsets: &[u32],
-) -> SKResult<()> {
-    let mut w = BufWriter::new(File::create(path).map_err(SKError::Io)?);
-    w.write_all(&MAGIC).map_err(SKError::Io)?;
-    w.write_all(&(block_bits as u32).to_le_bytes()).map_err(SKError::Io)?;
-    w.write_all(&n_unitigs.to_le_bytes()).map_err(SKError::Io)?;
-    w.write_all(&n_kmers.to_le_bytes()).map_err(SKError::Io)?;
-    for &off in block_offsets {
-        w.write_all(&off.to_le_bytes()).map_err(SKError::Io)?;
-    }
-    w.flush().map_err(SKError::Io)
-}
-
-/// Scan an existing `unitigs.bin` file and write its companion `.idx`.
-///
-/// Called by the exact-evidence construction route after the sequence file is
-/// closed.  `block_bits` controls index granularity (1 << block_bits chunks per
-/// offset entry); use [`DEFAULT_BLOCK_BITS`] for the default.
-pub fn build_unitig_idx(unitigs_path: &Path, block_bits: u8) -> SKResult<()> {
-    assert!(block_bits <= 31, "block_bits must be ≤ 31");
-
-    let file = File::open(unitigs_path).map_err(SKError::Io)?;
-    let mmap = unsafe { Mmap::map(&file).map_err(SKError::Io)? };
-
-    let k          = obikseq::params::k();
-    let block_size = 1usize << block_bits;
-    let mask       = block_size - 1;
-
-    let mut block_offsets: Vec<u32> = Vec::new();
-    let mut offset      = 0usize;
-    let mut chunk_count = 0usize;
-    let mut n_kmers     = 0usize;
-
-    while offset < mmap.len() {
-        if chunk_count & mask == 0 {
-            block_offsets.push(offset as u32);
-        }
-        let seql_minus_k = mmap[offset] as usize;
-        let byte_len = (seql_minus_k + k + 3) / 4;
-        n_kmers     += seql_minus_k + 1;
-        offset      += 1 + byte_len;
-        chunk_count += 1;
-    }
-
-    block_offsets.push(offset as u32); // sentinel
-
-    write_idx(
-        &idx_path(unitigs_path),
-        chunk_count as u32,
-        n_kmers as u64,
-        block_bits,
-        &block_offsets,
-    )
-}
-
-// ── Reader ────────────────────────────────────────────────────────────────────
-
-/// Memory-mapped view of a unitig file, with optional direct-access index.
-///
-/// Three constructors select the operating mode:
-/// - [`open`](Self::open) — smart default: direct access if `.idx` exists, sequential otherwise.
-/// - [`open_sequential`](Self::open_sequential) — always sequential, ignores `.idx`.
-/// - [`open_direct_access`](Self::open_direct_access) — requires `.idx`, errors if absent.
-///
-/// All positional methods (`chunk_start`, `verify_canonical_kmer`, …) work in
-/// both modes.  Without `.idx` they fall back to an O(i) sequential scan —
-/// correct but slower.
-pub struct UnitigFileReader {
-    mmap:          Mmap,
-    block_offsets: Vec<u32>,
-    n_unitigs:     usize,
-    n_kmers:       usize,
-    k:             usize,
-    block_bits:    u8,
-    mask:          usize,  // (1 << block_bits) - 1
-}
-
-impl UnitigFileReader {
-    /// Smart default: opens with direct access if `.idx` is present, sequential otherwise.
-    pub fn open(path: &Path) -> SKResult<Self> {
-        if idx_path(path).exists() {
-            Self::open_direct_access(path)
-        } else {
-            Self::open_sequential(path)
-        }
-    }
-
-    /// Always sequential — never reads `.idx` even if present.
-    ///
-    /// Scans the binary file once to count chunks and k-mers.
-    /// Positional access (`chunk_start`, `verify_canonical_kmer`) falls back to
-    /// O(i) sequential scan.
-    pub fn open_sequential(path: &Path) -> SKResult<Self> {
-        let file = File::open(path).map_err(SKError::Io)?;
-        let mmap = unsafe { Mmap::map(&file).map_err(SKError::Io)? };
-        let k = obikseq::params::k();
-
-        let mut offset    = 0usize;
-        let mut n_unitigs = 0usize;
-        let mut n_kmers   = 0usize;
-        while offset < mmap.len() {
-            let seql_minus_k = mmap[offset] as usize;
-            n_kmers   += seql_minus_k + 1;
-            offset    += 1 + (seql_minus_k + k + 3) / 4;
-            n_unitigs += 1;
-        }
-
-        Ok(Self {
-            mmap,
-            block_offsets: Vec::new(),
-            n_unitigs,
-            n_kmers,
-            k,
-            block_bits: DEFAULT_BLOCK_BITS,
-            mask: (1usize << DEFAULT_BLOCK_BITS) - 1,
-        })
-    }
-
-    /// Requires `.idx` — errors if the companion index file is absent.
-    ///
-    /// Enables O(1 << block_bits) positional access to any chunk.
-    /// Use only when direct access is architecturally required (query-time
-    /// verification on an exact-evidence layer).
-    pub fn open_direct_access(path: &Path) -> SKResult<Self> {
-        let file = File::open(path).map_err(SKError::Io)?;
-        let mmap = unsafe { Mmap::map(&file).map_err(SKError::Io)? };
-        let (n_unitigs, n_kmers, block_bits, block_offsets) = read_idx(&idx_path(path))?;
-        let k = obikseq::params::k();
-        Ok(Self {
-            mmap,
-            block_offsets,
-            n_unitigs,
-            n_kmers,
-            k,
-            block_bits,
-            mask: (1usize << block_bits) - 1,
-        })
-    }
-
-    pub fn len(&self) -> usize { self.n_unitigs }
-    pub fn is_empty(&self) -> bool { self.n_unitigs == 0 }
-    pub fn n_kmers(&self) -> usize { self.n_kmers }
-    pub fn block_bits(&self) -> u8 { self.block_bits }
-    pub fn has_direct_access(&self) -> bool { !self.block_offsets.is_empty() }
-
-    /// Byte offset of record `i` in the mmap.
-    ///
-    /// Fast path (O(1 << block_bits)) when `.idx` is loaded; degraded O(i)
-    /// sequential scan otherwise.
-    #[inline]
-    fn chunk_start(&self, i: usize) -> usize {
-        if !self.block_offsets.is_empty() {
-            if self.block_bits == 0 {
-                return self.block_offsets[i] as usize;
-            }
-            let block = i >> self.block_bits;
-            let rem   = i &  self.mask;
-            let mut offset = self.block_offsets[block] as usize;
-            for _ in 0..rem {
-                let seql_minus_k = self.mmap[offset] as usize;
-                offset += 1 + (seql_minus_k + self.k + 3) / 4;
-            }
-            offset
-        } else {
-            let mut offset = 0usize;
-            for _ in 0..i {
-                let seql_minus_k = self.mmap[offset] as usize;
-                offset += 1 + (seql_minus_k + self.k + 3) / 4;
-            }
-            offset
-        }
-    }
-
-    /// Nucleotide length of chunk `i`.
-    #[inline]
-    pub fn seql(&self, i: usize) -> usize {
-        self.mmap[self.chunk_start(i)] as usize + self.k
-    }
-
-    /// Reconstruct chunk `i` as a [`Unitig`].
-    pub fn unitig(&self, i: usize) -> Unitig {
-        let offset   = self.chunk_start(i);
-        let seql     = self.mmap[offset] as usize + self.k;
-        let byte_len = (seql + 3) / 4;
-        let bytes    = self.mmap[offset + 1..offset + 1 + byte_len].to_vec().into_boxed_slice();
-        Unitig::new((seql % 4) as u8, bytes)
-    }
-
-    /// Raw left-aligned u64 of the k-mer at position `j` within chunk `i`.
-    #[inline]
-    pub fn raw_kmer(&self, i: usize, j: usize) -> u64 {
-        let offset = self.chunk_start(i);
-        extract_kmer_raw(&self.mmap[offset + 1..], j, self.k)
-    }
-
-    /// `true` iff the k-mer at position `j` of chunk `i` matches `query`.
-    ///
-    /// Works in both modes; O(i) scan when `.idx` is absent.
-    #[inline]
-    pub fn verify_canonical_kmer(&self, i: usize, j: usize, query: CanonicalKmer) -> bool {
-        canonical_raw(self.raw_kmer(i, j), self.k) == query.raw()
-    }
-
-    // ── Sequential iterators (O(n) running-offset cursor) ─────────────────────
-
-    fn iter_chunks_sequential(&self) -> impl Iterator<Item = (usize, Unitig)> + '_ {
-        let k    = self.k;
-        let mmap = &*self.mmap;
-        let n    = self.n_unitigs;
-        let mut offset = 0usize;
-        (0..n).map(move |chunk_id| {
-            let seql     = mmap[offset] as usize + k;
-            let byte_len = (seql + 3) / 4;
-            let bytes    = mmap[offset + 1..offset + 1 + byte_len].to_vec().into_boxed_slice();
-            offset += 1 + byte_len;
-            (chunk_id, Unitig::new((seql % 4) as u8, bytes))
-        })
-    }
-
-    /// Iterate all unitigs sequentially.  Works without `.idx` (sequential open).
-    pub fn iter_unitigs(&self) -> impl Iterator<Item = (usize, Unitig)> + '_ {
-        self.iter_chunks_sequential()
-    }
-
-    pub fn iter_kmers(&self) -> impl Iterator<Item = Kmer> + '_ {
-        self.iter_chunks_sequential()
-            .flat_map(|(_, u)| u.into_kmers())
-    }
-
-    pub fn iter_indexed_canonical_kmers(
-        &self,
-    ) -> impl Iterator<Item = (CanonicalKmer, usize, usize)> + '_ {
-        self.iter_chunks_sequential()
-            .flat_map(|(chunk_id, u)| {
-                u.into_canonical_kmers()
-                    .enumerate()
-                    .map(move |(rank, kmer)| (kmer, chunk_id, rank))
-            })
-    }
-}
-
-fn read_idx(path: &Path) -> SKResult<(usize, usize, u8, Vec<u32>)> {
-    let data = std::fs::read(path).map_err(SKError::Io)?;
-    let mut pos = 0;
-
-    let magic_bytes = data.get(pos..pos + 4)
-        .ok_or(SKError::Truncated { context: "unitig index: magic" })?;
-    if magic_bytes != &MAGIC {
-        return Err(SKError::BadMagic {
-            expected: "UIX3",
-            got: magic_bytes.try_into().unwrap(),
-        });
-    }
-    pos += 4;
-
-    let bb_bytes = data.get(pos..pos + 4)
-        .ok_or(SKError::Truncated { context: "unitig index: block_bits" })?;
-    let block_bits_u32 = u32::from_le_bytes(bb_bytes.try_into().unwrap());
-    if block_bits_u32 > 31 {
-        return Err(SKError::InvalidData {
-            context: "unitig index",
-            detail: format!("block_bits out of range: {block_bits_u32}"),
-        });
-    }
-    let block_bits = block_bits_u32 as u8;
-    pos += 4;
-
-    let n_bytes = data.get(pos..pos + 4)
-        .ok_or(SKError::Truncated { context: "unitig index: n_unitigs" })?;
-    let n_unitigs = u32::from_le_bytes(n_bytes.try_into().unwrap()) as usize;
-    pos += 4;
-
-    let nk_bytes = data.get(pos..pos + 8)
-        .ok_or(SKError::Truncated { context: "unitig index: n_kmers" })?;
-    let n_kmers = u64::from_le_bytes(nk_bytes.try_into().unwrap()) as usize;
-    pos += 8;
-
-    let block_size = 1usize << block_bits;
-    let n_blocks = (n_unitigs + block_size - 1) >> block_bits;
-    let n_offsets = n_blocks + 1;
-    let mut block_offsets = Vec::with_capacity(n_offsets);
-    for _ in 0..n_offsets {
-        let off_bytes = data.get(pos..pos + 4)
-            .ok_or(SKError::Truncated { context: "unitig index: block_offsets" })?;
-        block_offsets.push(u32::from_le_bytes(off_bytes.try_into().unwrap()));
-        pos += 4;
-    }
-
-    Ok((n_unitigs, n_kmers, block_bits, block_offsets))
-}
-
-// ── Kmer utilities ────────────────────────────────────────────────────────────
-
-#[inline]
-fn revcomp_raw(raw: u64, k: usize) -> u64 {
-    let x = !raw;
-    let x = x.swap_bytes();
-    let x = ((x >> 4) & 0x0F0F0F0F0F0F0F0F) | ((x & 0x0F0F0F0F0F0F0F0F) << 4);
-    let x = ((x >> 2) & 0x3333333333333333) | ((x & 0x3333333333333333) << 2);
-    x << (64 - 2 * k)
-}
-
-#[inline]
-fn canonical_raw(raw: u64, k: usize) -> u64 {
-    raw.min(revcomp_raw(raw, k))
-}
-
-#[inline]
-fn extract_kmer_raw(bytes: &[u8], j: usize, k: usize) -> u64 {
-    let bit_start    = j * 2;
-    let byte_start   = bit_start / 8;
-    let bit_offset   = bit_start % 8;
-    let bytes_needed = (bit_offset + 2 * k + 7) / 8;
-
-    let mut acc = 0u128;
-    for idx in 0..bytes_needed {
-        acc = (acc << 8) | bytes.get(byte_start + idx).copied().unwrap_or(0) as u128;
-    }
-
-    let shift = bytes_needed * 8 - bit_offset - 2 * k;
-    let mask  = !0u64 >> (64 - 2 * k);
-    let raw   = (acc >> shift) as u64 & mask;
-    raw << (64 - 2 * k)
-}
-
-// ── CanonicalKmerRawIter ──────────────────────────────────────────────────────
-
-// ── CanonicalKmerIter ─────────────────────────────────────────────────────────
-
-/// Sequential iterator over [`CanonicalKmer`] from a `unitigs.bin` file.
-///
-/// Holds an `Arc<Mmap>` so that `Clone` is O(1): both copies share the same
-/// memory-mapped pages.  Cloning resets the cursor to position 0 — this lets
-/// ptr_hash's `new_from_par_iter` (which requires a `Clone`-able parallel
-/// iterator via `par_bridge()`) make multiple passes without ever creating
-/// a `.idx` file.
-pub struct CanonicalKmerIter {
-    mmap:      Arc<Mmap>,
-    k:         usize,
-    chunk_pos: usize,   // byte offset of the current chunk header
-    data_pos:  usize,   // byte offset of the current chunk's sequence bytes
-    n_kmers:   usize,   // kmers in current chunk
-    kmer_idx:  usize,   // next kmer index to yield within the current chunk
-}
-
-impl CanonicalKmerIter {
-    pub fn new(path: &Path) -> SKResult<Self> {
-        let file = File::open(path).map_err(SKError::Io)?;
-        let mmap = Arc::new(unsafe { Mmap::map(&file).map_err(SKError::Io)? });
-        let k = obikseq::params::k();
-        let mut s = Self { mmap, k, chunk_pos: 0, data_pos: 0, n_kmers: 0, kmer_idx: 0 };
-        s.load_chunk();
-        Ok(s)
-    }
-
-    #[inline]
-    fn load_chunk(&mut self) {
-        if self.chunk_pos < self.mmap.len() {
-            let seql_minus_k = self.mmap[self.chunk_pos] as usize;
-            self.n_kmers  = seql_minus_k + 1;
-            self.data_pos = self.chunk_pos + 1;
-            self.kmer_idx = 0;
-        }
-    }
-}
-
-impl Clone for CanonicalKmerIter {
-    fn clone(&self) -> Self {
-        let mut c = Self {
-            mmap:      Arc::clone(&self.mmap),
-            k:         self.k,
-            chunk_pos: 0,
-            data_pos:  0,
-            n_kmers:   0,
-            kmer_idx:  0,
-        };
-        c.load_chunk();
-        c
-    }
-}
-
-impl Iterator for CanonicalKmerIter {
-    type Item = CanonicalKmer;
-
-    #[inline]
-    fn next(&mut self) -> Option<CanonicalKmer> {
-        loop {
-            if self.chunk_pos >= self.mmap.len() {
-                return None;
-            }
-            if self.kmer_idx < self.n_kmers {
-                let raw   = extract_kmer_raw(&self.mmap[self.data_pos..], self.kmer_idx, self.k);
-                let canon = canonical_raw(raw, self.k);
-                self.kmer_idx += 1;
-                return Some(CanonicalKmer::from_raw_unchecked(canon));
-            }
-            let seql_minus_k = self.mmap[self.chunk_pos] as usize;
-            let byte_len     = (seql_minus_k + self.k + 3) / 4;
-            self.chunk_pos  += 1 + byte_len;
-            self.load_chunk();
-        }
-    }
-}
-
-#[cfg(test)]
-#[path = "tests/unitig_index.rs"]
-mod tests;
diff --git a/src/obiskio/src/unitig_index/kmer_iter.rs b/src/obiskio/src/unitig_index/kmer_iter.rs
new file mode 100644
index 00000000..4a6097f5
--- /dev/null
+++ b/src/obiskio/src/unitig_index/kmer_iter.rs
@@ -0,0 +1,86 @@
+use std::path::Path;
+use std::sync::Arc;
+
+use memmap2::Mmap;
+use obikseq::CanonicalKmer;
+
+use crate::error::{SKError, SKResult};
+
+use super::kmer_raw::{canonical_raw, extract_kmer_raw};
+
+// ── CanonicalKmerIter ─────────────────────────────────────────────────────────
+
+/// Sequential iterator over [`CanonicalKmer`] from a `unitigs.bin` file.
+///
+/// Holds an `Arc<Mmap>` so that `Clone` is O(1): both copies share the same
+/// memory-mapped pages.  Cloning resets the cursor to position 0 — this lets
+/// ptr_hash's `new_from_par_iter` (which requires a `Clone`-able parallel
+/// iterator via `par_bridge()`) make multiple passes without ever creating
+/// a `.idx` file.
+pub struct CanonicalKmerIter {
+    mmap:      Arc<Mmap>,
+    k:         usize,
+    chunk_pos: usize,   // byte offset of the current chunk header
+    data_pos:  usize,   // byte offset of the current chunk's sequence bytes
+    n_kmers:   usize,   // kmers in current chunk
+    kmer_idx:  usize,   // next kmer index to yield within the current chunk
+}
+
+impl CanonicalKmerIter {
+    pub fn new(path: &Path) -> SKResult<Self> {
+        let file = std::fs::File::open(path).map_err(SKError::Io)?;
+        let mmap = Arc::new(unsafe { Mmap::map(&file).map_err(SKError::Io)? });
+        let k = obikseq::params::k();
+        let mut s = Self { mmap, k, chunk_pos: 0, data_pos: 0, n_kmers: 0, kmer_idx: 0 };
+        s.load_chunk();
+        Ok(s)
+    }
+
+    #[inline]
+    fn load_chunk(&mut self) {
+        if self.chunk_pos < self.mmap.len() {
+            let seql_minus_k = self.mmap[self.chunk_pos] as usize;
+            self.n_kmers  = seql_minus_k + 1;
+            self.data_pos = self.chunk_pos + 1;
+            self.kmer_idx = 0;
+        }
+    }
+}
+
+impl Clone for CanonicalKmerIter {
+    fn clone(&self) -> Self {
+        let mut c = Self {
+            mmap:      Arc::clone(&self.mmap),
+            k:         self.k,
+            chunk_pos: 0,
+            data_pos:  0,
+            n_kmers:   0,
+            kmer_idx:  0,
+        };
+        c.load_chunk();
+        c
+    }
+}
+
+impl Iterator for CanonicalKmerIter {
+    type Item = CanonicalKmer;
+
+    #[inline]
+    fn next(&mut self) -> Option<CanonicalKmer> {
+        loop {
+            if self.chunk_pos >= self.mmap.len() {
+                return None;
+            }
+            if self.kmer_idx < self.n_kmers {
+                let raw   = extract_kmer_raw(&self.mmap[self.data_pos..], self.kmer_idx, self.k);
+                let canon = canonical_raw(raw, self.k);
+                self.kmer_idx += 1;
+                return Some(CanonicalKmer::from_raw_unchecked(canon));
+            }
+            let seql_minus_k = self.mmap[self.chunk_pos] as usize;
+            let byte_len     = (seql_minus_k + self.k + 3) / 4;
+            self.chunk_pos  += 1 + byte_len;
+            self.load_chunk();
+        }
+    }
+}
diff --git a/src/obiskio/src/unitig_index/kmer_raw.rs b/src/obiskio/src/unitig_index/kmer_raw.rs
new file mode 100644
index 00000000..e1d726f6
--- /dev/null
+++ b/src/obiskio/src/unitig_index/kmer_raw.rs
@@ -0,0 +1,33 @@
+// ── Kmer utilities ────────────────────────────────────────────────────────────
+
+#[inline]
+pub(super) fn revcomp_raw(raw: u64, k: usize) -> u64 {
+    let x = !raw;
+    let x = x.swap_bytes();
+    let x = ((x >> 4) & 0x0F0F0F0F0F0F0F0F) | ((x & 0x0F0F0F0F0F0F0F0F) << 4);
+    let x = ((x >> 2) & 0x3333333333333333) | ((x & 0x3333333333333333) << 2);
+    x << (64 - 2 * k)
+}
+
+#[inline]
+pub(super) fn canonical_raw(raw: u64, k: usize) -> u64 {
+    raw.min(revcomp_raw(raw, k))
+}
+
+#[inline]
+pub(super) fn extract_kmer_raw(bytes: &[u8], j: usize, k: usize) -> u64 {
+    let bit_start    = j * 2;
+    let byte_start   = bit_start / 8;
+    let bit_offset   = bit_start % 8;
+    let bytes_needed = (bit_offset + 2 * k + 7) / 8;
+
+    let mut acc = 0u128;
+    for idx in 0..bytes_needed {
+        acc = (acc << 8) | bytes.get(byte_start + idx).copied().unwrap_or(0) as u128;
+    }
+
+    let shift = bytes_needed * 8 - bit_offset - 2 * k;
+    let mask  = !0u64 >> (64 - 2 * k);
+    let raw   = (acc >> shift) as u64 & mask;
+    raw << (64 - 2 * k)
+}
diff --git a/src/obiskio/src/unitig_index/mod.rs b/src/obiskio/src/unitig_index/mod.rs
new file mode 100644
index 00000000..38358996
--- /dev/null
+++ b/src/obiskio/src/unitig_index/mod.rs
@@ -0,0 +1,48 @@
+//! Binary unitig storage: an append-only sequence file (`unitigs.bin`) plus
+//! an optional block-sampled `.idx` for O(1 << block_bits) random access.
+//!
+//! Submodules: [`writer`] ([`UnitigFileWriter`], chunk splitting, `.idx`
+//! construction), [`reader`] ([`UnitigFileReader`], sequential or
+//! direct-access), [`kmer_raw`] (packed 2-bit k-mer extraction/canonicalisation,
+//! shared by both the reader and [`CanonicalKmerIter`]), [`kmer_iter`]
+//! (cheaply-cloneable sequential k-mer iterator for `ptr_hash`).
+
+use std::path::{Path, PathBuf};
+
+mod kmer_iter;
+mod kmer_raw;
+mod reader;
+mod writer;
+
+pub use kmer_iter::CanonicalKmerIter;
+pub use obikseq::MAX_KMERS_PER_CHUNK;
+pub use reader::UnitigFileReader;
+pub use writer::{UnitigFileWriter, build_unitig_idx};
+
+// Only used by `tests/unitig_index.rs` (`use super::*`) below.
+#[cfg(test)]
+use obikseq::CanonicalKmer;
+#[cfg(test)]
+use kmer_raw::{canonical_raw, extract_kmer_raw, revcomp_raw};
+
+// ── Block index parameters ────────────────────────────────────────────────────
+//
+// BLOCK_SIZE = 1 << block_bits chunks share one offset entry in the index.
+// block_bits=0 → one entry per chunk (exact offsets, no scan).
+// block_bits=6 → one entry per 64 chunks (default; O(64) scan per lookup).
+//
+// block_bits is stored in the index file so the reader derives all parameters
+// at runtime — no compile-time constant constrains the format.
+
+const MAGIC: [u8; 4] = *b"UIX3";
+
+/// Default block granularity used by [`UnitigFileWriter::create`].
+pub const DEFAULT_BLOCK_BITS: u8 = 0;
+
+fn idx_path(path: &Path) -> PathBuf {
+    crate::append_path_suffix(path, ".idx")
+}
+
+#[cfg(test)]
+#[path = "../tests/unitig_index.rs"]
+mod tests;
diff --git a/src/obiskio/src/unitig_index/reader.rs b/src/obiskio/src/unitig_index/reader.rs
new file mode 100644
index 00000000..8e1b49c3
--- /dev/null
+++ b/src/obiskio/src/unitig_index/reader.rs
@@ -0,0 +1,246 @@
+use std::fs::File;
+use std::path::Path;
+
+use memmap2::Mmap;
+use obikseq::{CanonicalKmer, Kmer, Unitig};
+
+use crate::error::{SKError, SKResult};
+
+use super::kmer_raw::{canonical_raw, extract_kmer_raw};
+use super::{DEFAULT_BLOCK_BITS, MAGIC, idx_path};
+
+// ── Reader ────────────────────────────────────────────────────────────────────
+
+/// Memory-mapped view of a unitig file, with optional direct-access index.
+///
+/// Three constructors select the operating mode:
+/// - [`open`](Self::open) — smart default: direct access if `.idx` exists, sequential otherwise.
+/// - [`open_sequential`](Self::open_sequential) — always sequential, ignores `.idx`.
+/// - [`open_direct_access`](Self::open_direct_access) — requires `.idx`, errors if absent.
+///
+/// All positional methods (`chunk_start`, `verify_canonical_kmer`, …) work in
+/// both modes.  Without `.idx` they fall back to an O(i) sequential scan —
+/// correct but slower.
+pub struct UnitigFileReader {
+    mmap:          Mmap,
+    block_offsets: Vec<u32>,
+    n_unitigs:     usize,
+    n_kmers:       usize,
+    k:             usize,
+    block_bits:    u8,
+    mask:          usize,  // (1 << block_bits) - 1
+}
+
+impl UnitigFileReader {
+    /// Smart default: opens with direct access if `.idx` is present, sequential otherwise.
+    pub fn open(path: &Path) -> SKResult<Self> {
+        if idx_path(path).exists() {
+            Self::open_direct_access(path)
+        } else {
+            Self::open_sequential(path)
+        }
+    }
+
+    /// Always sequential — never reads `.idx` even if present.
+    ///
+    /// Scans the binary file once to count chunks and k-mers.
+    /// Positional access (`chunk_start`, `verify_canonical_kmer`) falls back to
+    /// O(i) sequential scan.
+    pub fn open_sequential(path: &Path) -> SKResult<Self> {
+        let file = File::open(path).map_err(SKError::Io)?;
+        let mmap = unsafe { Mmap::map(&file).map_err(SKError::Io)? };
+        let k = obikseq::params::k();
+
+        let mut offset    = 0usize;
+        let mut n_unitigs = 0usize;
+        let mut n_kmers   = 0usize;
+        while offset < mmap.len() {
+            let seql_minus_k = mmap[offset] as usize;
+            n_kmers   += seql_minus_k + 1;
+            offset    += 1 + (seql_minus_k + k + 3) / 4;
+            n_unitigs += 1;
+        }
+
+        Ok(Self {
+            mmap,
+            block_offsets: Vec::new(),
+            n_unitigs,
+            n_kmers,
+            k,
+            block_bits: DEFAULT_BLOCK_BITS,
+            mask: (1usize << DEFAULT_BLOCK_BITS) - 1,
+        })
+    }
+
+    /// Requires `.idx` — errors if the companion index file is absent.
+    ///
+    /// Enables O(1 << block_bits) positional access to any chunk.
+    /// Use only when direct access is architecturally required (query-time
+    /// verification on an exact-evidence layer).
+    pub fn open_direct_access(path: &Path) -> SKResult<Self> {
+        let file = File::open(path).map_err(SKError::Io)?;
+        let mmap = unsafe { Mmap::map(&file).map_err(SKError::Io)? };
+        let (n_unitigs, n_kmers, block_bits, block_offsets) = read_idx(&idx_path(path))?;
+        let k = obikseq::params::k();
+        Ok(Self {
+            mmap,
+            block_offsets,
+            n_unitigs,
+            n_kmers,
+            k,
+            block_bits,
+            mask: (1usize << block_bits) - 1,
+        })
+    }
+
+    pub fn len(&self) -> usize { self.n_unitigs }
+    pub fn is_empty(&self) -> bool { self.n_unitigs == 0 }
+    pub fn n_kmers(&self) -> usize { self.n_kmers }
+    pub fn block_bits(&self) -> u8 { self.block_bits }
+    pub fn has_direct_access(&self) -> bool { !self.block_offsets.is_empty() }
+
+    /// Byte offset of record `i` in the mmap.
+    ///
+    /// Fast path (O(1 << block_bits)) when `.idx` is loaded; degraded O(i)
+    /// sequential scan otherwise.
+    #[inline]
+    fn chunk_start(&self, i: usize) -> usize {
+        if !self.block_offsets.is_empty() {
+            if self.block_bits == 0 {
+                return self.block_offsets[i] as usize;
+            }
+            let block = i >> self.block_bits;
+            let rem   = i &  self.mask;
+            let mut offset = self.block_offsets[block] as usize;
+            for _ in 0..rem {
+                let seql_minus_k = self.mmap[offset] as usize;
+                offset += 1 + (seql_minus_k + self.k + 3) / 4;
+            }
+            offset
+        } else {
+            let mut offset = 0usize;
+            for _ in 0..i {
+                let seql_minus_k = self.mmap[offset] as usize;
+                offset += 1 + (seql_minus_k + self.k + 3) / 4;
+            }
+            offset
+        }
+    }
+
+    /// Nucleotide length of chunk `i`.
+    #[inline]
+    pub fn seql(&self, i: usize) -> usize {
+        self.mmap[self.chunk_start(i)] as usize + self.k
+    }
+
+    /// Reconstruct chunk `i` as a [`Unitig`].
+    pub fn unitig(&self, i: usize) -> Unitig {
+        let offset   = self.chunk_start(i);
+        let seql     = self.mmap[offset] as usize + self.k;
+        let byte_len = (seql + 3) / 4;
+        let bytes    = self.mmap[offset + 1..offset + 1 + byte_len].to_vec().into_boxed_slice();
+        Unitig::new((seql % 4) as u8, bytes)
+    }
+
+    /// Raw left-aligned u64 of the k-mer at position `j` within chunk `i`.
+    #[inline]
+    pub fn raw_kmer(&self, i: usize, j: usize) -> u64 {
+        let offset = self.chunk_start(i);
+        extract_kmer_raw(&self.mmap[offset + 1..], j, self.k)
+    }
+
+    /// `true` iff the k-mer at position `j` of chunk `i` matches `query`.
+    ///
+    /// Works in both modes; O(i) scan when `.idx` is absent.
+    #[inline]
+    pub fn verify_canonical_kmer(&self, i: usize, j: usize, query: CanonicalKmer) -> bool {
+        canonical_raw(self.raw_kmer(i, j), self.k) == query.raw()
+    }
+
+    // ── Sequential iterators (O(n) running-offset cursor) ─────────────────────
+
+    pub(crate) fn iter_chunks_sequential(&self) -> impl Iterator<Item = (usize, Unitig)> + '_ {
+        let k    = self.k;
+        let mmap = &*self.mmap;
+        let n    = self.n_unitigs;
+        let mut offset = 0usize;
+        (0..n).map(move |chunk_id| {
+            let seql     = mmap[offset] as usize + k;
+            let byte_len = (seql + 3) / 4;
+            let bytes    = mmap[offset + 1..offset + 1 + byte_len].to_vec().into_boxed_slice();
+            offset += 1 + byte_len;
+            (chunk_id, Unitig::new((seql % 4) as u8, bytes))
+        })
+    }
+
+    /// Iterate all unitigs sequentially.  Works without `.idx` (sequential open).
+    pub fn iter_unitigs(&self) -> impl Iterator<Item = (usize, Unitig)> + '_ {
+        self.iter_chunks_sequential()
+    }
+
+    pub fn iter_kmers(&self) -> impl Iterator<Item = Kmer> + '_ {
+        self.iter_chunks_sequential()
+            .flat_map(|(_, u)| u.into_kmers())
+    }
+
+    pub fn iter_indexed_canonical_kmers(
+        &self,
+    ) -> impl Iterator<Item = (CanonicalKmer, usize, usize)> + '_ {
+        self.iter_chunks_sequential()
+            .flat_map(|(chunk_id, u)| {
+                u.into_canonical_kmers()
+                    .enumerate()
+                    .map(move |(rank, kmer)| (kmer, chunk_id, rank))
+            })
+    }
+}
+
+fn read_idx(path: &Path) -> SKResult<(usize, usize, u8, Vec<u32>)> {
+    let data = std::fs::read(path).map_err(SKError::Io)?;
+    let mut pos = 0;
+
+    let magic_bytes = data.get(pos..pos + 4)
+        .ok_or(SKError::Truncated { context: "unitig index: magic" })?;
+    if magic_bytes != &MAGIC {
+        return Err(SKError::BadMagic {
+            expected: "UIX3",
+            got: magic_bytes.try_into().unwrap(),
+        });
+    }
+    pos += 4;
+
+    let bb_bytes = data.get(pos..pos + 4)
+        .ok_or(SKError::Truncated { context: "unitig index: block_bits" })?;
+    let block_bits_u32 = u32::from_le_bytes(bb_bytes.try_into().unwrap());
+    if block_bits_u32 > 31 {
+        return Err(SKError::InvalidData {
+            context: "unitig index",
+            detail: format!("block_bits out of range: {block_bits_u32}"),
+        });
+    }
+    let block_bits = block_bits_u32 as u8;
+    pos += 4;
+
+    let n_bytes = data.get(pos..pos + 4)
+        .ok_or(SKError::Truncated { context: "unitig index: n_unitigs" })?;
+    let n_unitigs = u32::from_le_bytes(n_bytes.try_into().unwrap()) as usize;
+    pos += 4;
+
+    let nk_bytes = data.get(pos..pos + 8)
+        .ok_or(SKError::Truncated { context: "unitig index: n_kmers" })?;
+    let n_kmers = u64::from_le_bytes(nk_bytes.try_into().unwrap()) as usize;
+    pos += 8;
+
+    let block_size = 1usize << block_bits;
+    let n_blocks = (n_unitigs + block_size - 1) >> block_bits;
+    let n_offsets = n_blocks + 1;
+    let mut block_offsets = Vec::with_capacity(n_offsets);
+    for _ in 0..n_offsets {
+        let off_bytes = data.get(pos..pos + 4)
+            .ok_or(SKError::Truncated { context: "unitig index: block_offsets" })?;
+        block_offsets.push(u32::from_le_bytes(off_bytes.try_into().unwrap()));
+        pos += 4;
+    }
+
+    Ok((n_unitigs, n_kmers, block_bits, block_offsets))
+}
diff --git a/src/obiskio/src/unitig_index/writer.rs b/src/obiskio/src/unitig_index/writer.rs
new file mode 100644
index 00000000..311d4044
--- /dev/null
+++ b/src/obiskio/src/unitig_index/writer.rs
@@ -0,0 +1,178 @@
+use std::fs::File;
+use std::io::{BufWriter, Write as _};
+use std::path::Path;
+
+use memmap2::Mmap;
+use obikseq::{MAX_KMERS_PER_CHUNK, Unitig};
+
+use crate::error::{SKError, SKResult};
+
+use super::{DEFAULT_BLOCK_BITS, MAGIC, idx_path};
+
+// ── Writer ────────────────────────────────────────────────────────────────────
+
+/// Writes a sequence of [`Unitig`] to an uncompressed binary file and builds
+/// a block-sampled offset index at close time.
+///
+/// One offset is stored every `1 << block_bits` chunks; random access to chunk
+/// `i` costs at most `(1 << block_bits) − 1` sequential chunk scans after the
+/// block lookup.
+///
+/// Unitigs with more than [`MAX_KMERS_PER_CHUNK`] k-mers are transparently split
+/// into overlapping chunks (k−1 nucleotide overlap) so no k-mer is lost.
+pub struct UnitigFileWriter {
+    file:          BufWriter<File>,
+    block_offsets: Vec<u32>,
+    chunk_count:   usize,
+    next_offset:   u32,
+    n_kmers:       usize,
+    k:             usize,
+    block_bits:    u8,
+    mask:          usize,  // (1 << block_bits) - 1
+}
+
+impl UnitigFileWriter {
+    /// Create a writer with the default block size (`DEFAULT_BLOCK_BITS = 6`).
+    pub fn create(path: &Path) -> SKResult<Self> {
+        Self::create_with_block_bits(path, DEFAULT_BLOCK_BITS)
+    }
+
+    /// Create a writer with a custom block size.
+    ///
+    /// `block_bits` must be in 0..=31. `block_bits=0` stores one offset per
+    /// chunk (exact, no scan); larger values trade index size for scan length.
+    pub fn create_with_block_bits(path: &Path, block_bits: u8) -> SKResult<Self> {
+        assert!(block_bits <= 31, "block_bits must be ≤ 31");
+        let file = File::create(path).map_err(SKError::Io)?;
+        Ok(Self {
+            file: BufWriter::new(file),
+            block_offsets: Vec::new(),
+            chunk_count: 0,
+            next_offset: 0,
+            n_kmers: 0,
+            k: obikseq::params::k(),
+            block_bits,
+            mask: (1usize << block_bits) - 1,
+        })
+    }
+
+    /// Write a unitig, splitting into overlapping chunks if it exceeds
+    /// [`MAX_KMERS_PER_CHUNK`].
+    pub fn write(&mut self, unitig: &Unitig) -> SKResult<()> {
+        let seql = unitig.seql();
+        let k = self.k;
+
+        if seql < k {
+            return Ok(());
+        }
+
+        let n_kmers = seql - k + 1;
+        if n_kmers <= MAX_KMERS_PER_CHUNK {
+            return self.write_chunk(unitig);
+        }
+
+        let chunk_nucl = MAX_KMERS_PER_CHUNK + k - 1;
+        let stride = MAX_KMERS_PER_CHUNK;
+        let mut start = 0;
+        while start < seql {
+            let end = (start + chunk_nucl).min(seql);
+            self.write_chunk(&unitig.sub(start, end))?;
+            if end == seql { break; }
+            start += stride;
+        }
+        Ok(())
+    }
+
+    fn write_chunk(&mut self, unitig: &Unitig) -> SKResult<()> {
+        let seql = unitig.seql();
+        let byte_len = (seql + 3) / 4;
+
+        debug_assert!(seql - self.k <= u8::MAX as usize, "chunk exceeds MAX_KMERS_PER_CHUNK");
+
+        if self.chunk_count & self.mask == 0 {
+            self.block_offsets.push(self.next_offset);
+        }
+
+        self.n_kmers += seql - self.k + 1;
+        self.chunk_count += 1;
+
+        unitig.write_to_binary(&mut self.file).map_err(SKError::Io)?;
+
+        self.next_offset += 1 + byte_len as u32;
+        Ok(())
+    }
+
+    /// Flush and close the binary sequence file.
+    ///
+    /// The companion `.idx` file is **not** written here; call
+    /// [`build_unitig_idx`] separately when exact evidence is needed.
+    pub fn close(mut self) -> SKResult<()> {
+        self.file.flush().map_err(SKError::Io)?;
+        drop(self.file);
+        Ok(())
+    }
+
+    pub fn len(&self) -> usize { self.chunk_count }
+    pub fn is_empty(&self) -> bool { self.chunk_count == 0 }
+    pub fn block_bits(&self) -> u8 { self.block_bits }
+}
+
+fn write_idx(
+    path: &Path,
+    n_unitigs: u32,
+    n_kmers: u64,
+    block_bits: u8,
+    block_offsets: &[u32],
+) -> SKResult<()> {
+    let mut w = BufWriter::new(File::create(path).map_err(SKError::Io)?);
+    w.write_all(&MAGIC).map_err(SKError::Io)?;
+    w.write_all(&(block_bits as u32).to_le_bytes()).map_err(SKError::Io)?;
+    w.write_all(&n_unitigs.to_le_bytes()).map_err(SKError::Io)?;
+    w.write_all(&n_kmers.to_le_bytes()).map_err(SKError::Io)?;
+    for &off in block_offsets {
+        w.write_all(&off.to_le_bytes()).map_err(SKError::Io)?;
+    }
+    w.flush().map_err(SKError::Io)
+}
+
+/// Scan an existing `unitigs.bin` file and write its companion `.idx`.
+///
+/// Called by the exact-evidence construction route after the sequence file is
+/// closed.  `block_bits` controls index granularity (1 << block_bits chunks per
+/// offset entry); use [`DEFAULT_BLOCK_BITS`] for the default.
+pub fn build_unitig_idx(unitigs_path: &Path, block_bits: u8) -> SKResult<()> {
+    assert!(block_bits <= 31, "block_bits must be ≤ 31");
+
+    let file = File::open(unitigs_path).map_err(SKError::Io)?;
+    let mmap = unsafe { Mmap::map(&file).map_err(SKError::Io)? };
+
+    let k          = obikseq::params::k();
+    let block_size = 1usize << block_bits;
+    let mask       = block_size - 1;
+
+    let mut block_offsets: Vec<u32> = Vec::new();
+    let mut offset      = 0usize;
+    let mut chunk_count = 0usize;
+    let mut n_kmers     = 0usize;
+
+    while offset < mmap.len() {
+        if chunk_count & mask == 0 {
+            block_offsets.push(offset as u32);
+        }
+        let seql_minus_k = mmap[offset] as usize;
+        let byte_len = (seql_minus_k + k + 3) / 4;
+        n_kmers     += seql_minus_k + 1;
+        offset      += 1 + byte_len;
+        chunk_count += 1;
+    }
+
+    block_offsets.push(offset as u32); // sentinel
+
+    write_idx(
+        &idx_path(unitigs_path),
+        chunk_count as u32,
+        n_kmers as u64,
+        block_bits,
+        &block_offsets,
+    )
+}
diff --git a/src/obisys/src/budget.rs b/src/obisys/src/budget.rs
new file mode 100644
index 00000000..053626c9
--- /dev/null
+++ b/src/obisys/src/budget.rs
@@ -0,0 +1,65 @@
+use std::sync::{Condvar, Mutex};
+
+struct BudgetInner {
+    remaining: u64,
+    active: usize,
+    peak_active: usize,
+}
+
+/// Counting semaphore that limits total concurrent estimated memory usage.
+///
+/// Each worker acquires a cost (bytes) before starting and releases it on
+/// completion. Non-deadlock guarantee: when no worker is active the next
+/// acquire always succeeds regardless of cost vs. remaining budget.
+pub struct MemoryBudget {
+    total: u64,
+    inner: Mutex<BudgetInner>,
+    condvar: Condvar,
+}
+
+impl MemoryBudget {
+    pub fn new(total: u64) -> Self {
+        Self {
+            total,
+            inner: Mutex::new(BudgetInner {
+                remaining: total,
+                active: 0,
+                peak_active: 0,
+            }),
+            condvar: Condvar::new(),
+        }
+    }
+
+    pub fn acquire(&self, cost: u64) {
+        let mut g = self.inner.lock().unwrap();
+        loop {
+            if g.active == 0 || g.remaining >= cost {
+                g.remaining = g.remaining.saturating_sub(cost);
+                g.active += 1;
+                g.peak_active = g.peak_active.max(g.active);
+                return;
+            }
+            g = self.condvar.wait(g).unwrap();
+        }
+    }
+
+    pub fn release(&self, cost: u64) {
+        let mut g = self.inner.lock().unwrap();
+        g.remaining = (g.remaining + cost).min(self.total);
+        g.active -= 1;
+        self.condvar.notify_all();
+    }
+
+    pub fn total(&self) -> u64 {
+        self.total
+    }
+    pub fn active(&self) -> usize {
+        self.inner.lock().unwrap().active
+    }
+    pub fn remaining(&self) -> u64 {
+        self.inner.lock().unwrap().remaining
+    }
+    pub fn peak_active(&self) -> usize {
+        self.inner.lock().unwrap().peak_active
+    }
+}
diff --git a/src/obisys/src/lib.rs b/src/obisys/src/lib.rs
index 65d5d4f4..deec5aef 100644
--- a/src/obisys/src/lib.rs
+++ b/src/obisys/src/lib.rs
@@ -1,867 +1,14 @@
-use std::fmt;
-use std::sync::atomic::{AtomicU64, Ordering};
-use std::sync::{Condvar, Mutex};
-use std::time::{Duration, Instant};
-
-use indicatif::{ProgressBar, ProgressStyle};
-use tracing::{debug, info, warn};
-
-const BRAILLE: &[&str] = &["⠋", "⠙", "⠹", "⠸", "⠼", "⠴", "⠦", "⠧", "⠇", "⠏"];
-
-// ── DirLock ──────────────────────────────────────────────────────────────────
-
-/// Exclusive advisory lock on an index directory, held for the duration of
-/// any command that writes into an already-existing index (building the
-/// sibling annex, merging into a destination, filtering/selecting in place,
-/// ...). Two such commands racing on the same directory can otherwise
-/// corrupt each other's writes with no error from either side.
-///
-/// Only the directory actually being *written to* needs a lock — a command
-/// like `merge` that reads several source indexes to build one destination
-/// only needs to lock the destination.
-///
-/// Uses the OS's advisory file lock (`flock` on Unix, `LockFileEx` on
-/// Windows) via `fs4`, not a hand-rolled PID file: the OS releases it
-/// automatically on process exit, including a crash — no stale-lock cleanup
-/// logic needed.
-pub struct DirLock {
-    _file: std::fs::File,
-}
-
-impl DirLock {
-    /// Block until the exclusive lock on `dir` is acquired (creating `dir`
-    /// and the lock file within it if needed). Logs once if the wait is
-    /// non-trivial, so a blocked command doesn't look silently hung.
-    pub fn acquire(dir: &std::path::Path) -> std::io::Result<Self> {
-        use fs4::fs_std::FileExt;
-
-        std::fs::create_dir_all(dir)?;
-        let lock_path = dir.join(".obikmer.lock");
-        let file = std::fs::OpenOptions::new()
-            .create(true)
-            .truncate(false)
-            .write(true)
-            .open(&lock_path)?;
-
-        if file.try_lock_exclusive().is_err() {
-            info!(dir = %dir.display(), "waiting for another obikmer process to release this index");
-            file.lock_exclusive()?;
-        }
-        Ok(Self { _file: file })
-    }
-}
-
-// ── TracedBar ──────────────────────────────────────────────────────────────────
-
-/// Wrapper around `ProgressBar` that emits `tracing` events when stderr is not
-/// a TTY (e.g. HPC job logs): every 10% for bounded bars, every ~10 s for
-/// spinners (throttled on `set_message`).
-pub struct TracedBar {
-    pb: ProgressBar,
-    label: String,
-    unit: String,
-    total: u64,             // 0 for spinners
-    start: Instant,         // creation time, for spinner throttling
-    last_pct: AtomicU64,    // last emitted 10%-bucket (1..=10), 0 = none yet
-    last_log_ms: AtomicU64, // ms since `start` at last spinner log
-}
-
-impl TracedBar {
-    pub fn inc(&self, delta: u64) {
-        self.pb.inc(delta);
-        if self.pb.is_hidden() && self.total > 0 {
-            let pos = self.pb.position();
-            let pct10 = (pos * 10) / self.total; // 0..=10
-            let last = self.last_pct.load(Ordering::Relaxed);
-            if pct10 > last
-                && self
-                    .last_pct
-                    .compare_exchange(last, pct10, Ordering::Relaxed, Ordering::Relaxed)
-                    .is_ok()
-            {
-                info!(
-                    stage    = %self.label,
-                    progress = format_args!("{}%", pct10 * 10),
-                    "{}/{} {}",
-                    pos, self.total, self.unit
-                );
-            }
-        }
-    }
-
-    pub fn set_message(&self, msg: impl Into<String>) {
-        let msg = msg.into();
-        if self.pb.is_hidden() {
-            if self.total > 0 {
-                debug!(stage = %self.label, "{msg}");
-            } else {
-                // spinner: throttle to ~10 s
-                let now_ms = self.start.elapsed().as_millis() as u64;
-                let last = self.last_log_ms.load(Ordering::Relaxed);
-                if now_ms >= last + 10_000
-                    && self
-                        .last_log_ms
-                        .compare_exchange(last, now_ms, Ordering::Relaxed, Ordering::Relaxed)
-                        .is_ok()
-                {
-                    info!(stage = %self.label, "{msg}");
-                }
-            }
-        }
-        self.pb.set_message(msg);
-    }
-
-    pub fn finish_and_clear(&self) {
-        self.pb.finish_and_clear();
-    }
-}
-
-/// Spinner with the standard project look: `⠋ label — msg  0s`.
-/// Caller updates the message with `pb.set_message(...)`.
-pub fn spinner(label: &str) -> TracedBar {
-    let pb = ProgressBar::new_spinner();
-    pb.set_style(
-        ProgressStyle::with_template(&format!("{{spinner}} {label} — {{msg}}  {{elapsed}}"))
-            .unwrap()
-            .tick_strings(BRAILLE),
-    );
-    pb.enable_steady_tick(Duration::from_millis(100));
-    TracedBar {
-        pb,
-        label: label.to_string(),
-        unit: String::new(),
-        total: 0,
-        start: Instant::now(),
-        last_pct: AtomicU64::new(0),
-        last_log_ms: AtomicU64::new(0),
-    }
-}
-
-/// Progress bar with the standard project look:
-/// `⠋ label — [████░░░░] pos/len unit  elapsed`.
-pub fn progress_bar(label: &str, n: u64, unit: &str) -> TracedBar {
-    let pb = ProgressBar::new(n);
-    pb.set_style(
-        ProgressStyle::with_template(&format!(
-            "{{spinner}} {label} — {{bar:40.cyan/blue}} {{pos}}/{{len}} {unit}  {{elapsed}}"
-        ))
-        .unwrap()
-        .tick_strings(BRAILLE),
-    );
-    pb.enable_steady_tick(Duration::from_millis(100));
-    TracedBar {
-        pb,
-        label: label.to_string(),
-        unit: unit.to_string(),
-        total: n,
-        start: Instant::now(),
-        last_pct: AtomicU64::new(0),
-        last_log_ms: AtomicU64::new(0),
-    }
-}
-
-use libc::{RUSAGE_SELF, getrusage, rusage, timeval};
-use sysinfo::System;
-
-// ── Memory query ──────────────────────────────────────────────────────────────
-
-/// Returns the number of bytes available for allocation in the current process context.
-///
-/// On Linux, cgroup memory limits (SLURM, containers) are checked first: the
-/// process may be constrained to far less than the host's available RAM.
-/// Returns `min(cgroup_available, host_available)` when a finite limit is found.
-///
-/// On macOS, `available_memory()` can return 0 when the memory compressor
-/// inflates the page count; in that case we fall back to half of total memory.
-/// Returns the process peak RSS (high-water mark since process start).
-/// Monotonically increasing — use delta before/after a phase to measure its RAM cost.
-pub fn peak_rss_bytes() -> u64 {
-    rss_to_bytes(&get_rusage())
-}
-
-pub fn available_memory_bytes() -> u64 {
-    let sys = System::new_all();
-    let host_avail = match sys.available_memory() {
-        0 => sys.total_memory() / 2,
-        n => n,
-    };
-    #[cfg(target_os = "linux")]
-    if let Some(cg) = cgroup_v2_available().or_else(cgroup_v1_available) {
-        return cg.min(host_avail);
-    }
-    host_avail
-}
-
-/// cgroup v2 (unified hierarchy): reads memory.max and memory.current for the
-/// current process's cgroup. Returns None if unlimited or on any parse error.
-#[cfg(target_os = "linux")]
-fn cgroup_v2_available() -> Option<u64> {
-    let cgroup = std::fs::read_to_string("/proc/self/cgroup").ok()?;
-    let rel = cgroup
-        .lines()
-        .find(|l| l.starts_with("0::"))?
-        .strip_prefix("0::")?
-        .trim();
-    let base = format!("/sys/fs/cgroup{rel}");
-    // "max" means no limit → parse::<u64>() fails → None
-    let limit: u64 = std::fs::read_to_string(format!("{base}/memory.max"))
-        .ok()?
-        .trim()
-        .parse()
-        .ok()?;
-    let used: u64 = std::fs::read_to_string(format!("{base}/memory.current"))
-        .ok()?
-        .trim()
-        .parse()
-        .ok()?;
-    Some(limit.saturating_sub(used))
-}
-
-/// cgroup v1 (memory subsystem): reads memory.limit_in_bytes and
-/// memory.usage_in_bytes. Returns None if unlimited or on any parse error.
-#[cfg(target_os = "linux")]
-fn cgroup_v1_available() -> Option<u64> {
-    let cgroup = std::fs::read_to_string("/proc/self/cgroup").ok()?;
-    let path = cgroup
-        .lines()
-        .find(|l| l.contains(":memory:"))?
-        .split(':')
-        .nth(2)?;
-    let base = format!("/sys/fs/cgroup/memory{path}");
-    let limit: u64 = std::fs::read_to_string(format!("{base}/memory.limit_in_bytes"))
-        .ok()?
-        .trim()
-        .parse()
-        .ok()?;
-    // Kernel uses 2^63 (rounded to page) as "no limit" sentinel
-    if limit > (1u64 << 62) {
-        return None;
-    }
-    let used: u64 = std::fs::read_to_string(format!("{base}/memory.usage_in_bytes"))
-        .ok()?
-        .trim()
-        .parse()
-        .ok()?;
-    Some(limit.saturating_sub(used))
-}
-
-// ── CPU parallelism query ────────────────────────────────────────────────────
-
-/// Returns the number of cores this process can actually use concurrently.
-///
-/// `std::thread::available_parallelism()` reads CPU affinity
-/// (`sched_getaffinity`), not the container's CPU quota — a Docker/cgroup
-/// container commonly reports the *host's* full core count this way while
-/// actually being throttled (via `cpu.max`/`cpu.cfs_quota_us`) to a fraction
-/// of a core. Sizing a thread/worker pool off the unthrottled count causes
-/// severe oversubscription: dozens of threads contending for a sliver of
-/// real CPU time, which can look indistinguishable from a hang for minutes
-/// or hours (observed in CI). On Linux, this reads the cgroup CPU quota
-/// first and returns `min(cgroup_quota, host_parallelism)` when a finite
-/// quota is found; falls back to `available_parallelism()` otherwise (same
-/// convention as [`available_memory_bytes`]).
-pub fn effective_parallelism() -> usize {
-    let host = std::thread::available_parallelism().map(|n| n.get()).unwrap_or(1);
-    #[cfg(target_os = "linux")]
-    {
-        if let Some(quota) = cgroup_v2_cpu_quota() {
-            let effective = quota.clamp(1, host);
-            tracing::debug!(host, quota, effective, source = "cgroup v2", "effective_parallelism");
-            return effective;
-        }
-        if let Some(quota) = cgroup_v1_cpu_quota() {
-            let effective = quota.clamp(1, host);
-            tracing::debug!(host, quota, effective, source = "cgroup v1", "effective_parallelism");
-            return effective;
-        }
-    }
-    tracing::debug!(host, effective = host, source = "available_parallelism (no cgroup quota found)", "effective_parallelism");
-    host
-}
-
-/// cgroup v2 (unified hierarchy): reads `cpu.max` ("<quota> <period>", or
-/// "max <period>" when unlimited) for the current process's cgroup, rounded
-/// up to whole cores. Returns `None` if unlimited or on any parse error.
-#[cfg(target_os = "linux")]
-fn cgroup_v2_cpu_quota() -> Option<usize> {
-    let cgroup = std::fs::read_to_string("/proc/self/cgroup").ok()?;
-    let rel = cgroup
-        .lines()
-        .find(|l| l.starts_with("0::"))?
-        .strip_prefix("0::")?
-        .trim();
-    let base = format!("/sys/fs/cgroup{rel}");
-    let raw = std::fs::read_to_string(format!("{base}/cpu.max")).ok()?;
-    let mut parts = raw.split_whitespace();
-    let quota_str = parts.next()?;
-    let period: f64 = parts.next()?.parse().ok()?;
-    if quota_str == "max" {
-        return None; // unlimited
-    }
-    let quota: f64 = quota_str.parse().ok()?;
-    Some((quota / period).ceil().max(1.0) as usize)
-}
-
-/// cgroup v1 (cpu subsystem): reads `cpu.cfs_quota_us`/`cpu.cfs_period_us`,
-/// rounded up to whole cores. Returns `None` if unlimited (quota <= 0) or on
-/// any parse error.
-#[cfg(target_os = "linux")]
-fn cgroup_v1_cpu_quota() -> Option<usize> {
-    let cgroup = std::fs::read_to_string("/proc/self/cgroup").ok()?;
-    let path = cgroup
-        .lines()
-        .find(|l| l.contains(":cpu:") || l.contains(":cpu,cpuacct:"))?
-        .split(':')
-        .nth(2)?;
-    let base = format!("/sys/fs/cgroup/cpu{path}");
-    let quota: i64 = std::fs::read_to_string(format!("{base}/cpu.cfs_quota_us"))
-        .ok()?
-        .trim()
-        .parse()
-        .ok()?;
-    if quota <= 0 {
-        return None; // unlimited
-    }
-    let period: i64 = std::fs::read_to_string(format!("{base}/cpu.cfs_period_us"))
-        .ok()?
-        .trim()
-        .parse()
-        .ok()?;
-    if period <= 0 {
-        return None;
-    }
-    Some(((quota as f64) / (period as f64)).ceil().max(1.0) as usize)
-}
-
-// ── raw helpers ───────────────────────────────────────────────────────────────
-
-fn get_rusage() -> rusage {
-    let mut ru = unsafe { std::mem::zeroed::<rusage>() };
-    unsafe { getrusage(RUSAGE_SELF, &mut ru) };
-    ru
-}
-
-fn tv_to_secs(tv: timeval) -> f64 {
-    tv.tv_sec as f64 + tv.tv_usec as f64 * 1e-6
-}
-
-#[cfg(target_os = "macos")]
-fn rss_to_bytes(ru: &rusage) -> u64 {
-    ru.ru_maxrss as u64
-}
-
-#[cfg(not(target_os = "macos"))]
-fn rss_to_bytes(ru: &rusage) -> u64 {
-    ru.ru_maxrss as u64 * 1024
-}
-
-// Monotonically increasing counters — negative delta would be a kernel bug.
-fn delta(end: i64, start: i64) -> u64 {
-    (end - start).max(0) as u64
-}
-
-// ── CpuSample ─────────────────────────────────────────────────────────────────
-
-/// Snapshot of process-wide CPU time + wall clock at a point in time.
-/// Use [`cpu_efficiency`](Self::cpu_efficiency) to measure the fraction of
-/// available cores used since the snapshot was taken.
-pub struct CpuSample {
-    wall: Instant,
-    user_secs: f64,
-    sys_secs: f64,
-    previous: f64,
-}
-
-impl CpuSample {
-    pub fn now() -> Self {
-        let ru = get_rusage();
-        Self {
-            wall: Instant::now(),
-            user_secs: tv_to_secs(ru.ru_utime),
-            sys_secs: tv_to_secs(ru.ru_stime),
-            previous: 0.0,
-        }
-    }
-
-    /// (user_delta + sys_delta) / (wall_delta × n_cores) since this snapshot.
-    /// Returns 0.0 if less than 100 ms have elapsed (too noisy).
-    pub fn cpu_efficiency(&self, n_cores: usize) -> f64 {
-        let ru = get_rusage();
-        let wall = self.wall.elapsed().as_secs_f64();
-        if wall < 0.1 {
-            return 0.0;
-        }
-        let cpu =
-            (tv_to_secs(ru.ru_utime) - self.user_secs) + (tv_to_secs(ru.ru_stime) - self.sys_secs);
-        cpu / (wall * n_cores as f64)
-    }
-
-    pub fn do_i_activate(&mut self, threshold: f64) -> bool {
-        let delta_wall = self.wall.elapsed().as_secs_f64();
-        if delta_wall < 0.1 {
-            // Window too short to be meaningful — leave state untouched so it
-            // keeps accumulating until a real sample can be taken.
-            return false;
-        }
-
-        let n = CpuSample::now();
-        let delta_ru = (n.user_secs - self.user_secs) + (n.sys_secs - self.sys_secs);
-
-        let efficiency = delta_ru / delta_wall;
-        let activate = 0f64.max(efficiency - self.previous) >= threshold;
-
-        debug!(
-            "Do I activate : {} -> {} = {} Activate: {}",
-            self.previous,
-            efficiency,
-            0f64.max(efficiency - self.previous),
-            activate
-        );
-        self.previous = efficiency;
-        self.user_secs = n.user_secs;
-        self.sys_secs = n.sys_secs;
-        self.wall = n.wall;
-
-        activate
-    }
-}
-
-// ── IoSample ──────────────────────────────────────────────────────────────────
-
-/// Snapshot of process-wide block I/O (bytes read + written) + wall clock.
-///
-/// Same activation protocol as [`CpuSample`], but the growth check in
-/// [`do_i_activate`](Self::do_i_activate) is *relative* rather than absolute:
-/// raw I/O throughput has no portable scale across storage devices, unlike a
-/// core count.
-pub struct IoSample {
-    wall: Instant,
-    bytes: u64,
-    previous_rate: f64,
-}
-
-impl IoSample {
-    pub fn now() -> Self {
-        Self {
-            wall: Instant::now(),
-            bytes: Self::read_bytes(),
-            previous_rate: 0.0,
-        }
-    }
-
-    /// Bytes actually submitted to the block layer (read + write), summed
-    /// process-wide. Returns 0 if unavailable — degrades gracefully to a
-    /// signal that never triggers activation (CPU-only heuristic).
-    #[cfg(target_os = "linux")]
-    fn read_bytes() -> u64 {
-        let Ok(io) = std::fs::read_to_string("/proc/self/io") else {
-            return 0;
-        };
-        io.lines()
-            .filter_map(|l| {
-                l.strip_prefix("read_bytes: ")
-                    .or_else(|| l.strip_prefix("write_bytes: "))
-            })
-            .filter_map(|v| v.trim().parse::<u64>().ok())
-            .sum()
-    }
-
-    #[cfg(target_os = "macos")]
-    fn read_bytes() -> u64 {
-        use libc::{RUSAGE_INFO_V4, getpid, proc_pid_rusage, rusage_info_v4};
-        let mut info: rusage_info_v4 = unsafe { std::mem::zeroed() };
-        let ret =
-            unsafe { proc_pid_rusage(getpid(), RUSAGE_INFO_V4, &mut info as *mut _ as *mut _) };
-        if ret != 0 {
-            return 0;
-        }
-        info.ri_diskio_bytesread + info.ri_diskio_byteswritten
-    }
-
-    #[cfg(not(any(target_os = "linux", target_os = "macos")))]
-    fn read_bytes() -> u64 {
-        0
-    }
-
-    /// Same protocol as [`CpuSample::do_i_activate`] (0.1 s minimum window,
-    /// state untouched on early return), but growth is measured relative to
-    /// the previous rate. `threshold` is a fraction, e.g. `0.2` for a 20 %
-    /// increase in throughput since the last real sample.
-    pub fn do_i_activate(&mut self, threshold: f64) -> bool {
-        let elapsed = self.wall.elapsed().as_secs_f64();
-        if elapsed < 0.1 {
-            return false;
-        }
-
-        let n = Self::read_bytes();
-        let rate = n.saturating_sub(self.bytes) as f64 / elapsed;
-        let activate = if self.previous_rate == 0.0 {
-            rate > 0.0 // bootstrap: any measured throughput is signal enough
-        } else {
-            (rate - self.previous_rate) / self.previous_rate >= threshold
-        };
-
-        debug!(
-            "Do I activate (I/O) : {} -> {} Activate: {}",
-            self.previous_rate, rate, activate
-        );
-        self.previous_rate = rate;
-        self.bytes = n;
-        self.wall = Instant::now();
-
-        activate
-    }
-}
-
-// ── public API ────────────────────────────────────────────────────────────────
-
-/// Snapshot taken at the start of a pipeline stage.
-#[must_use = "call .stop() to record the stage"]
-pub struct Stage {
-    label: String,
-    wall: Instant,
-    ru: rusage,
-}
-
-impl Stage {
-    pub fn start(label: impl Into<String>) -> Self {
-        let label = label.into();
-        info!(stage = %label, "started");
-        Self {
-            label,
-            wall: Instant::now(),
-            ru: get_rusage(),
-        }
-    }
-
-    pub fn stop(self) -> StageStats {
-        let wall_secs = self.wall.elapsed().as_secs_f64();
-        let end = get_rusage();
-        let stats = StageStats {
-            label: self.label,
-            wall_secs,
-            user_secs: tv_to_secs(end.ru_utime) - tv_to_secs(self.ru.ru_utime),
-            sys_secs: tv_to_secs(end.ru_stime) - tv_to_secs(self.ru.ru_stime),
-            max_rss_bytes: rss_to_bytes(&end),
-            minor_faults: delta(end.ru_minflt as i64, self.ru.ru_minflt as i64),
-            major_faults: delta(end.ru_majflt as i64, self.ru.ru_majflt as i64),
-            vol_ctx: delta(end.ru_nvcsw as i64, self.ru.ru_nvcsw as i64),
-            invol_ctx: delta(end.ru_nivcsw as i64, self.ru.ru_nivcsw as i64),
-            in_blocks: delta(end.ru_inblock as i64, self.ru.ru_inblock as i64),
-            out_blocks: delta(end.ru_oublock as i64, self.ru.ru_oublock as i64),
-            swaps: delta(end.ru_nswap as i64, self.ru.ru_nswap as i64),
-        };
-        info!(
-            stage      = %stats.label,
-            wall_secs  = format_args!("{:.3}", stats.wall_secs),
-            rss        = %fmt_bytes(stats.max_rss_bytes),
-            swaps      = stats.swaps,
-            "done"
-        );
-        if stats.swaps > 0 {
-            warn!(
-                stage = %stats.label,
-                swaps = stats.swaps,
-                "working set exceeds available RAM"
-            );
-        }
-        stats
-    }
-}
-
-/// Per-stage efficiency metrics collected from `getrusage(RUSAGE_SELF)` deltas.
-pub struct StageStats {
-    pub label: String,
-    pub wall_secs: f64,
-    pub user_secs: f64,
-    pub sys_secs: f64,
-    /// Peak RSS at end of stage (bytes). ru_maxrss is a process-lifetime maximum,
-    /// so this reflects the high-water mark up to and including this stage.
-    pub max_rss_bytes: u64,
-    pub minor_faults: u64,
-    pub major_faults: u64,
-    pub vol_ctx: u64,    // voluntary context switches
-    pub invol_ctx: u64,  // involuntary context switches
-    pub in_blocks: u64,  // filesystem block reads (after page cache)
-    pub out_blocks: u64, // filesystem block writes
-    pub swaps: u64,
-}
-
-impl StageStats {
-    /// (user + sys) / wall — effective thread count utilisation.
-    pub fn parallelism(&self) -> f64 {
-        if self.wall_secs > 1e-9 {
-            (self.user_secs + self.sys_secs) / self.wall_secs
-        } else {
-            0.0
-        }
-    }
-
-    /// parallelism / n_cores — fraction of available CPU power used (0..1+).
-    pub fn efficiency(&self, n_cores: usize) -> f64 {
-        self.parallelism() / n_cores as f64
-    }
-}
-
-/// Accumulates stage stats and prints a human-readable summary table.
-#[derive(Default)]
-pub struct Reporter {
-    stages: Vec<StageStats>,
-}
-
-impl Reporter {
-    pub fn new() -> Self {
-        Self::default()
-    }
-    pub fn push(&mut self, stats: StageStats) {
-        self.stages.push(stats);
-    }
-    pub fn stages(&self) -> &[StageStats] {
-        &self.stages
-    }
-    /// Print the summary to stderr.
-    pub fn print(&self) {
-        eprint!("{self}");
-    }
-}
-
-// ── diagnosis ─────────────────────────────────────────────────────────────────
-
-struct Diagnosis {
-    tag: &'static str,
-    detail: Option<String>,
-}
-
-// Thresholds are intentionally conservative to avoid false positives.
-fn diagnose(s: &StageStats, n_cores: usize) -> Diagnosis {
-    let eff = s.efficiency(n_cores);
-    let cpu_pct = eff * 100.0;
-    let io_ops = s.in_blocks + s.out_blocks;
-
-    // swaps > 0 is the only reliable cross-platform indicator of true RAM exhaustion.
-    // ru_majflt is intentionally excluded: on macOS it counts all file-backed mmap
-    // page-ins (even from page cache), making it useless as a memory-pressure signal
-    // for mmap-heavy code. On Linux it is more meaningful, but swaps covers the
-    // severe case on both platforms.
-    if s.swaps > 0 {
-        return Diagnosis {
-            tag: "swapping",
-            detail: Some(format!(
-                "swapped {} time(s) — working set exceeds available RAM",
-                s.swaps,
-            )),
-        };
-    }
-    if eff < 0.3 && io_ops > 100 {
-        return Diagnosis {
-            tag: "disk I/O",
-            detail: Some(format!(
-                "{} block reads + {} writes — CPU at {:.0}%, stage is I/O-bound",
-                s.in_blocks, s.out_blocks, cpu_pct,
-            )),
-        };
-    }
-    if eff < 0.3 && s.vol_ctx > 200 {
-        return Diagnosis {
-            tag: "contention",
-            detail: Some(format!(
-                "{} voluntary context switches — CPU at {:.0}%, possible lock contention or I/O wait",
-                s.vol_ctx, cpu_pct,
-            )),
-        };
-    }
-    Diagnosis {
-        tag: "—",
-        detail: None,
-    }
-}
-
-// ── display helpers ───────────────────────────────────────────────────────────
-
-fn fmt_secs(s: f64) -> String {
-    if s >= 100.0 {
-        format!("{:.0}s", s)
-    } else if s >= 10.0 {
-        format!("{:.1}s", s)
-    } else if s >= 1.0 {
-        format!("{:.2}s", s)
-    } else {
-        format!("{:.0}ms", s * 1000.0)
-    }
-}
-
-fn fmt_bytes(b: u64) -> String {
-    if b >= 1 << 30 {
-        format!("{:.1} GB", b as f64 / (1u64 << 30) as f64)
-    } else if b >= 1 << 20 {
-        format!("{:.0} MB", b as f64 / (1u64 << 20) as f64)
-    } else {
-        format!("{:.0} KB", b as f64 / 1024.0)
-    }
-}
-
-fn fmt_efficiency(par: f64, n_cores: usize) -> String {
-    format!(
-        "{:.1}×/{} ({:.0}%)",
-        par,
-        n_cores,
-        par / n_cores as f64 * 100.0
-    )
-}
-
-// ── Display ───────────────────────────────────────────────────────────────────
-
-// ── MemoryBudget ──────────────────────────────────────────────────────────────
-
-struct BudgetInner {
-    remaining: u64,
-    active: usize,
-    peak_active: usize,
-}
-
-/// Counting semaphore that limits total concurrent estimated memory usage.
-///
-/// Each worker acquires a cost (bytes) before starting and releases it on
-/// completion. Non-deadlock guarantee: when no worker is active the next
-/// acquire always succeeds regardless of cost vs. remaining budget.
-pub struct MemoryBudget {
-    total: u64,
-    inner: Mutex<BudgetInner>,
-    condvar: Condvar,
-}
-
-impl MemoryBudget {
-    pub fn new(total: u64) -> Self {
-        Self {
-            total,
-            inner: Mutex::new(BudgetInner {
-                remaining: total,
-                active: 0,
-                peak_active: 0,
-            }),
-            condvar: Condvar::new(),
-        }
-    }
-
-    pub fn acquire(&self, cost: u64) {
-        let mut g = self.inner.lock().unwrap();
-        loop {
-            if g.active == 0 || g.remaining >= cost {
-                g.remaining = g.remaining.saturating_sub(cost);
-                g.active += 1;
-                g.peak_active = g.peak_active.max(g.active);
-                return;
-            }
-            g = self.condvar.wait(g).unwrap();
-        }
-    }
-
-    pub fn release(&self, cost: u64) {
-        let mut g = self.inner.lock().unwrap();
-        g.remaining = (g.remaining + cost).min(self.total);
-        g.active -= 1;
-        self.condvar.notify_all();
-    }
-
-    pub fn total(&self) -> u64 {
-        self.total
-    }
-    pub fn active(&self) -> usize {
-        self.inner.lock().unwrap().active
-    }
-    pub fn remaining(&self) -> u64 {
-        self.inner.lock().unwrap().remaining
-    }
-    pub fn peak_active(&self) -> usize {
-        self.inner.lock().unwrap().peak_active
-    }
-}
-
-// ── Display ───────────────────────────────────────────────────────────────────
-
-impl fmt::Display for Reporter {
-    fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
-        if self.stages.is_empty() {
-            return Ok(());
-        }
-
-        let n_cores = effective_parallelism();
-
-        // column widths
-        let nw = self
-            .stages
-            .iter()
-            .map(|s| s.label.len())
-            .max()
-            .unwrap_or(5)
-            .max(5);
-        // efficiency col: worst-case width for this run's n_cores value
-        let ew = format!("{:.1}×/{} (100%)", 99.9f64, n_cores).len();
-
-        let sep_w = nw + 2 + 7 + 2 + ew + 2 + 8 + 2 + 12;
-        let sep = "─".repeat(sep_w);
-
-        // header
-        writeln!(
-            f,
-            "{:<nw$}  {:>7}  {:>ew$}  {:>8}  status",
-            "stage", "wall", "efficiency", "peak RSS"
-        )?;
-        writeln!(f, "{sep}")?;
-
-        // compute all diagnoses up front (needed for both table and footnotes)
-        let diagnoses: Vec<Diagnosis> = self.stages.iter().map(|s| diagnose(s, n_cores)).collect();
-
-        // per-stage rows
-        for (s, d) in self.stages.iter().zip(diagnoses.iter()) {
-            writeln!(
-                f,
-                "{:<nw$}  {:>7}  {:>ew$}  {:>8}  {}",
-                s.label,
-                fmt_secs(s.wall_secs),
-                fmt_efficiency(s.parallelism(), n_cores),
-                fmt_bytes(s.max_rss_bytes),
-                d.tag,
-            )?;
-        }
-
-        // totals
-        let tw = self.stages.iter().map(|s| s.wall_secs).sum::<f64>();
-        let tu = self.stages.iter().map(|s| s.user_secs).sum::<f64>();
-        let ts = self.stages.iter().map(|s| s.sys_secs).sum::<f64>();
-        let trss = self
-            .stages
-            .iter()
-            .map(|s| s.max_rss_bytes)
-            .max()
-            .unwrap_or(0);
-        let tpar = if tw > 1e-9 { (tu + ts) / tw } else { 0.0 };
-
-        writeln!(f, "{sep}")?;
-        writeln!(
-            f,
-            "{:<nw$}  {:>7}  {:>ew$}  {:>8}",
-            "TOTAL",
-            fmt_secs(tw),
-            fmt_efficiency(tpar, n_cores),
-            fmt_bytes(trss),
-        )?;
-
-        // bottleneck footnotes (only if at least one anomaly detected)
-        let bottlenecks: Vec<(&str, &str)> = self
-            .stages
-            .iter()
-            .zip(diagnoses.iter())
-            .filter_map(|(s, d)| d.detail.as_deref().map(|det| (s.label.as_str(), det)))
-            .collect();
-
-        if !bottlenecks.is_empty() {
-            writeln!(f, "\nBottlenecks:")?;
-            for (label, detail) in &bottlenecks {
-                writeln!(f, "  {label} — {detail}")?;
-            }
-        }
-
-        Ok(())
-    }
-}
+//! Cross-cutting system utilities: directory locking, progress/logging,
+//! resource (CPU/memory) introspection, and per-stage profiling.
+
+mod budget;
+mod lock;
+mod progress;
+mod resources;
+mod stage;
+
+pub use budget::MemoryBudget;
+pub use lock::DirLock;
+pub use progress::{TracedBar, progress_bar, spinner};
+pub use resources::{CpuSample, IoSample, available_memory_bytes, effective_parallelism, peak_rss_bytes};
+pub use stage::{Reporter, Stage, StageStats};
diff --git a/src/obisys/src/lock.rs b/src/obisys/src/lock.rs
new file mode 100644
index 00000000..c5e771d8
--- /dev/null
+++ b/src/obisys/src/lock.rs
@@ -0,0 +1,42 @@
+use tracing::info;
+
+/// Exclusive advisory lock on an index directory, held for the duration of
+/// any command that writes into an already-existing index (building the
+/// sibling annex, merging into a destination, filtering/selecting in place,
+/// ...). Two such commands racing on the same directory can otherwise
+/// corrupt each other's writes with no error from either side.
+///
+/// Only the directory actually being *written to* needs a lock — a command
+/// like `merge` that reads several source indexes to build one destination
+/// only needs to lock the destination.
+///
+/// Uses the OS's advisory file lock (`flock` on Unix, `LockFileEx` on
+/// Windows) via `fs4`, not a hand-rolled PID file: the OS releases it
+/// automatically on process exit, including a crash — no stale-lock cleanup
+/// logic needed.
+pub struct DirLock {
+    _file: std::fs::File,
+}
+
+impl DirLock {
+    /// Block until the exclusive lock on `dir` is acquired (creating `dir`
+    /// and the lock file within it if needed). Logs once if the wait is
+    /// non-trivial, so a blocked command doesn't look silently hung.
+    pub fn acquire(dir: &std::path::Path) -> std::io::Result<Self> {
+        use fs4::fs_std::FileExt;
+
+        std::fs::create_dir_all(dir)?;
+        let lock_path = dir.join(".obikmer.lock");
+        let file = std::fs::OpenOptions::new()
+            .create(true)
+            .truncate(false)
+            .write(true)
+            .open(&lock_path)?;
+
+        if file.try_lock_exclusive().is_err() {
+            info!(dir = %dir.display(), "waiting for another obikmer process to release this index");
+            file.lock_exclusive()?;
+        }
+        Ok(Self { _file: file })
+    }
+}
diff --git a/src/obisys/src/progress.rs b/src/obisys/src/progress.rs
new file mode 100644
index 00000000..a311170d
--- /dev/null
+++ b/src/obisys/src/progress.rs
@@ -0,0 +1,114 @@
+use std::sync::atomic::{AtomicU64, Ordering};
+use std::time::{Duration, Instant};
+
+use indicatif::{ProgressBar, ProgressStyle};
+use tracing::{debug, info};
+
+const BRAILLE: &[&str] = &["⠋", "⠙", "⠹", "⠸", "⠼", "⠴", "⠦", "⠧", "⠇", "⠏"];
+
+/// Wrapper around `ProgressBar` that emits `tracing` events when stderr is not
+/// a TTY (e.g. HPC job logs): every 10% for bounded bars, every ~10 s for
+/// spinners (throttled on `set_message`).
+pub struct TracedBar {
+    pb: ProgressBar,
+    label: String,
+    unit: String,
+    total: u64,             // 0 for spinners
+    start: Instant,         // creation time, for spinner throttling
+    last_pct: AtomicU64,    // last emitted 10%-bucket (1..=10), 0 = none yet
+    last_log_ms: AtomicU64, // ms since `start` at last spinner log
+}
+
+impl TracedBar {
+    pub fn inc(&self, delta: u64) {
+        self.pb.inc(delta);
+        if self.pb.is_hidden() && self.total > 0 {
+            let pos = self.pb.position();
+            let pct10 = (pos * 10) / self.total; // 0..=10
+            let last = self.last_pct.load(Ordering::Relaxed);
+            if pct10 > last
+                && self
+                    .last_pct
+                    .compare_exchange(last, pct10, Ordering::Relaxed, Ordering::Relaxed)
+                    .is_ok()
+            {
+                info!(
+                    stage    = %self.label,
+                    progress = format_args!("{}%", pct10 * 10),
+                    "{}/{} {}",
+                    pos, self.total, self.unit
+                );
+            }
+        }
+    }
+
+    pub fn set_message(&self, msg: impl Into<String>) {
+        let msg = msg.into();
+        if self.pb.is_hidden() {
+            if self.total > 0 {
+                debug!(stage = %self.label, "{msg}");
+            } else {
+                // spinner: throttle to ~10 s
+                let now_ms = self.start.elapsed().as_millis() as u64;
+                let last = self.last_log_ms.load(Ordering::Relaxed);
+                if now_ms >= last + 10_000
+                    && self
+                        .last_log_ms
+                        .compare_exchange(last, now_ms, Ordering::Relaxed, Ordering::Relaxed)
+                        .is_ok()
+                {
+                    info!(stage = %self.label, "{msg}");
+                }
+            }
+        }
+        self.pb.set_message(msg);
+    }
+
+    pub fn finish_and_clear(&self) {
+        self.pb.finish_and_clear();
+    }
+}
+
+/// Spinner with the standard project look: `⠋ label — msg  0s`.
+/// Caller updates the message with `pb.set_message(...)`.
+pub fn spinner(label: &str) -> TracedBar {
+    let pb = ProgressBar::new_spinner();
+    pb.set_style(
+        ProgressStyle::with_template(&format!("{{spinner}} {label} — {{msg}}  {{elapsed}}"))
+            .unwrap()
+            .tick_strings(BRAILLE),
+    );
+    pb.enable_steady_tick(Duration::from_millis(100));
+    TracedBar {
+        pb,
+        label: label.to_string(),
+        unit: String::new(),
+        total: 0,
+        start: Instant::now(),
+        last_pct: AtomicU64::new(0),
+        last_log_ms: AtomicU64::new(0),
+    }
+}
+
+/// Progress bar with the standard project look:
+/// `⠋ label — [████░░░░] pos/len unit  elapsed`.
+pub fn progress_bar(label: &str, n: u64, unit: &str) -> TracedBar {
+    let pb = ProgressBar::new(n);
+    pb.set_style(
+        ProgressStyle::with_template(&format!(
+            "{{spinner}} {label} — {{bar:40.cyan/blue}} {{pos}}/{{len}} {unit}  {{elapsed}}"
+        ))
+        .unwrap()
+        .tick_strings(BRAILLE),
+    );
+    pb.enable_steady_tick(Duration::from_millis(100));
+    TracedBar {
+        pb,
+        label: label.to_string(),
+        unit: unit.to_string(),
+        total: n,
+        start: Instant::now(),
+        last_pct: AtomicU64::new(0),
+        last_log_ms: AtomicU64::new(0),
+    }
+}
diff --git a/src/obisys/src/resources.rs b/src/obisys/src/resources.rs
new file mode 100644
index 00000000..4ea51f09
--- /dev/null
+++ b/src/obisys/src/resources.rs
@@ -0,0 +1,355 @@
+use std::time::Instant;
+
+use libc::{RUSAGE_SELF, getrusage, rusage, timeval};
+use sysinfo::System;
+use tracing::debug;
+
+// ── Memory query ──────────────────────────────────────────────────────────────
+
+/// Returns the number of bytes available for allocation in the current process context.
+///
+/// On Linux, cgroup memory limits (SLURM, containers) are checked first: the
+/// process may be constrained to far less than the host's available RAM.
+/// Returns `min(cgroup_available, host_available)` when a finite limit is found.
+///
+/// On macOS, `available_memory()` can return 0 when the memory compressor
+/// inflates the page count; in that case we fall back to half of total memory.
+/// Returns the process peak RSS (high-water mark since process start).
+/// Monotonically increasing — use delta before/after a phase to measure its RAM cost.
+pub fn peak_rss_bytes() -> u64 {
+    rss_to_bytes(&get_rusage())
+}
+
+pub fn available_memory_bytes() -> u64 {
+    let sys = System::new_all();
+    let host_avail = match sys.available_memory() {
+        0 => sys.total_memory() / 2,
+        n => n,
+    };
+    #[cfg(target_os = "linux")]
+    if let Some(cg) = cgroup_v2_available().or_else(cgroup_v1_available) {
+        return cg.min(host_avail);
+    }
+    host_avail
+}
+
+/// cgroup v2 (unified hierarchy): reads memory.max and memory.current for the
+/// current process's cgroup. Returns None if unlimited or on any parse error.
+#[cfg(target_os = "linux")]
+fn cgroup_v2_available() -> Option<u64> {
+    let cgroup = std::fs::read_to_string("/proc/self/cgroup").ok()?;
+    let rel = cgroup
+        .lines()
+        .find(|l| l.starts_with("0::"))?
+        .strip_prefix("0::")?
+        .trim();
+    let base = format!("/sys/fs/cgroup{rel}");
+    // "max" means no limit → parse::<u64>() fails → None
+    let limit: u64 = std::fs::read_to_string(format!("{base}/memory.max"))
+        .ok()?
+        .trim()
+        .parse()
+        .ok()?;
+    let used: u64 = std::fs::read_to_string(format!("{base}/memory.current"))
+        .ok()?
+        .trim()
+        .parse()
+        .ok()?;
+    Some(limit.saturating_sub(used))
+}
+
+/// cgroup v1 (memory subsystem): reads memory.limit_in_bytes and
+/// memory.usage_in_bytes. Returns None if unlimited or on any parse error.
+#[cfg(target_os = "linux")]
+fn cgroup_v1_available() -> Option<u64> {
+    let cgroup = std::fs::read_to_string("/proc/self/cgroup").ok()?;
+    let path = cgroup
+        .lines()
+        .find(|l| l.contains(":memory:"))?
+        .split(':')
+        .nth(2)?;
+    let base = format!("/sys/fs/cgroup/memory{path}");
+    let limit: u64 = std::fs::read_to_string(format!("{base}/memory.limit_in_bytes"))
+        .ok()?
+        .trim()
+        .parse()
+        .ok()?;
+    // Kernel uses 2^63 (rounded to page) as "no limit" sentinel
+    if limit > (1u64 << 62) {
+        return None;
+    }
+    let used: u64 = std::fs::read_to_string(format!("{base}/memory.usage_in_bytes"))
+        .ok()?
+        .trim()
+        .parse()
+        .ok()?;
+    Some(limit.saturating_sub(used))
+}
+
+// ── CPU parallelism query ────────────────────────────────────────────────────
+
+/// Returns the number of cores this process can actually use concurrently.
+///
+/// `std::thread::available_parallelism()` reads CPU affinity
+/// (`sched_getaffinity`), not the container's CPU quota — a Docker/cgroup
+/// container commonly reports the *host's* full core count this way while
+/// actually being throttled (via `cpu.max`/`cpu.cfs_quota_us`) to a fraction
+/// of a core. Sizing a thread/worker pool off the unthrottled count causes
+/// severe oversubscription: dozens of threads contending for a sliver of
+/// real CPU time, which can look indistinguishable from a hang for minutes
+/// or hours (observed in CI). On Linux, this reads the cgroup CPU quota
+/// first and returns `min(cgroup_quota, host_parallelism)` when a finite
+/// quota is found; falls back to `available_parallelism()` otherwise (same
+/// convention as [`available_memory_bytes`]).
+pub fn effective_parallelism() -> usize {
+    let host = std::thread::available_parallelism().map(|n| n.get()).unwrap_or(1);
+    #[cfg(target_os = "linux")]
+    {
+        if let Some(quota) = cgroup_v2_cpu_quota() {
+            let effective = quota.clamp(1, host);
+            tracing::debug!(host, quota, effective, source = "cgroup v2", "effective_parallelism");
+            return effective;
+        }
+        if let Some(quota) = cgroup_v1_cpu_quota() {
+            let effective = quota.clamp(1, host);
+            tracing::debug!(host, quota, effective, source = "cgroup v1", "effective_parallelism");
+            return effective;
+        }
+    }
+    tracing::debug!(host, effective = host, source = "available_parallelism (no cgroup quota found)", "effective_parallelism");
+    host
+}
+
+/// cgroup v2 (unified hierarchy): reads `cpu.max` ("<quota> <period>", or
+/// "max <period>" when unlimited) for the current process's cgroup, rounded
+/// up to whole cores. Returns `None` if unlimited or on any parse error.
+#[cfg(target_os = "linux")]
+fn cgroup_v2_cpu_quota() -> Option<usize> {
+    let cgroup = std::fs::read_to_string("/proc/self/cgroup").ok()?;
+    let rel = cgroup
+        .lines()
+        .find(|l| l.starts_with("0::"))?
+        .strip_prefix("0::")?
+        .trim();
+    let base = format!("/sys/fs/cgroup{rel}");
+    let raw = std::fs::read_to_string(format!("{base}/cpu.max")).ok()?;
+    let mut parts = raw.split_whitespace();
+    let quota_str = parts.next()?;
+    let period: f64 = parts.next()?.parse().ok()?;
+    if quota_str == "max" {
+        return None; // unlimited
+    }
+    let quota: f64 = quota_str.parse().ok()?;
+    Some((quota / period).ceil().max(1.0) as usize)
+}
+
+/// cgroup v1 (cpu subsystem): reads `cpu.cfs_quota_us`/`cpu.cfs_period_us`,
+/// rounded up to whole cores. Returns `None` if unlimited (quota <= 0) or on
+/// any parse error.
+#[cfg(target_os = "linux")]
+fn cgroup_v1_cpu_quota() -> Option<usize> {
+    let cgroup = std::fs::read_to_string("/proc/self/cgroup").ok()?;
+    let path = cgroup
+        .lines()
+        .find(|l| l.contains(":cpu:") || l.contains(":cpu,cpuacct:"))?
+        .split(':')
+        .nth(2)?;
+    let base = format!("/sys/fs/cgroup/cpu{path}");
+    let quota: i64 = std::fs::read_to_string(format!("{base}/cpu.cfs_quota_us"))
+        .ok()?
+        .trim()
+        .parse()
+        .ok()?;
+    if quota <= 0 {
+        return None; // unlimited
+    }
+    let period: i64 = std::fs::read_to_string(format!("{base}/cpu.cfs_period_us"))
+        .ok()?
+        .trim()
+        .parse()
+        .ok()?;
+    if period <= 0 {
+        return None;
+    }
+    Some(((quota as f64) / (period as f64)).ceil().max(1.0) as usize)
+}
+
+// ── raw helpers ───────────────────────────────────────────────────────────────
+
+pub(crate) fn get_rusage() -> rusage {
+    let mut ru = unsafe { std::mem::zeroed::<rusage>() };
+    unsafe { getrusage(RUSAGE_SELF, &mut ru) };
+    ru
+}
+
+pub(crate) fn tv_to_secs(tv: timeval) -> f64 {
+    tv.tv_sec as f64 + tv.tv_usec as f64 * 1e-6
+}
+
+#[cfg(target_os = "macos")]
+pub(crate) fn rss_to_bytes(ru: &rusage) -> u64 {
+    ru.ru_maxrss as u64
+}
+
+#[cfg(not(target_os = "macos"))]
+pub(crate) fn rss_to_bytes(ru: &rusage) -> u64 {
+    ru.ru_maxrss as u64 * 1024
+}
+
+// Monotonically increasing counters — negative delta would be a kernel bug.
+pub(crate) fn delta(end: i64, start: i64) -> u64 {
+    (end - start).max(0) as u64
+}
+
+// ── CpuSample ─────────────────────────────────────────────────────────────────
+
+/// Snapshot of process-wide CPU time + wall clock at a point in time.
+/// Use [`cpu_efficiency`](Self::cpu_efficiency) to measure the fraction of
+/// available cores used since the snapshot was taken.
+pub struct CpuSample {
+    wall: Instant,
+    user_secs: f64,
+    sys_secs: f64,
+    previous: f64,
+}
+
+impl CpuSample {
+    pub fn now() -> Self {
+        let ru = get_rusage();
+        Self {
+            wall: Instant::now(),
+            user_secs: tv_to_secs(ru.ru_utime),
+            sys_secs: tv_to_secs(ru.ru_stime),
+            previous: 0.0,
+        }
+    }
+
+    /// (user_delta + sys_delta) / (wall_delta × n_cores) since this snapshot.
+    /// Returns 0.0 if less than 100 ms have elapsed (too noisy).
+    pub fn cpu_efficiency(&self, n_cores: usize) -> f64 {
+        let ru = get_rusage();
+        let wall = self.wall.elapsed().as_secs_f64();
+        if wall < 0.1 {
+            return 0.0;
+        }
+        let cpu =
+            (tv_to_secs(ru.ru_utime) - self.user_secs) + (tv_to_secs(ru.ru_stime) - self.sys_secs);
+        cpu / (wall * n_cores as f64)
+    }
+
+    pub fn do_i_activate(&mut self, threshold: f64) -> bool {
+        let delta_wall = self.wall.elapsed().as_secs_f64();
+        if delta_wall < 0.1 {
+            // Window too short to be meaningful — leave state untouched so it
+            // keeps accumulating until a real sample can be taken.
+            return false;
+        }
+
+        let n = CpuSample::now();
+        let delta_ru = (n.user_secs - self.user_secs) + (n.sys_secs - self.sys_secs);
+
+        let efficiency = delta_ru / delta_wall;
+        let activate = 0f64.max(efficiency - self.previous) >= threshold;
+
+        debug!(
+            "Do I activate : {} -> {} = {} Activate: {}",
+            self.previous,
+            efficiency,
+            0f64.max(efficiency - self.previous),
+            activate
+        );
+        self.previous = efficiency;
+        self.user_secs = n.user_secs;
+        self.sys_secs = n.sys_secs;
+        self.wall = n.wall;
+
+        activate
+    }
+}
+
+// ── IoSample ──────────────────────────────────────────────────────────────────
+
+/// Snapshot of process-wide block I/O (bytes read + written) + wall clock.
+///
+/// Same activation protocol as [`CpuSample`], but the growth check in
+/// [`do_i_activate`](Self::do_i_activate) is *relative* rather than absolute:
+/// raw I/O throughput has no portable scale across storage devices, unlike a
+/// core count.
+pub struct IoSample {
+    wall: Instant,
+    bytes: u64,
+    previous_rate: f64,
+}
+
+impl IoSample {
+    pub fn now() -> Self {
+        Self {
+            wall: Instant::now(),
+            bytes: Self::read_bytes(),
+            previous_rate: 0.0,
+        }
+    }
+
+    /// Bytes actually submitted to the block layer (read + write), summed
+    /// process-wide. Returns 0 if unavailable — degrades gracefully to a
+    /// signal that never triggers activation (CPU-only heuristic).
+    #[cfg(target_os = "linux")]
+    fn read_bytes() -> u64 {
+        let Ok(io) = std::fs::read_to_string("/proc/self/io") else {
+            return 0;
+        };
+        io.lines()
+            .filter_map(|l| {
+                l.strip_prefix("read_bytes: ")
+                    .or_else(|| l.strip_prefix("write_bytes: "))
+            })
+            .filter_map(|v| v.trim().parse::<u64>().ok())
+            .sum()
+    }
+
+    #[cfg(target_os = "macos")]
+    fn read_bytes() -> u64 {
+        use libc::{RUSAGE_INFO_V4, getpid, proc_pid_rusage, rusage_info_v4};
+        let mut info: rusage_info_v4 = unsafe { std::mem::zeroed() };
+        let ret =
+            unsafe { proc_pid_rusage(getpid(), RUSAGE_INFO_V4, &mut info as *mut _ as *mut _) };
+        if ret != 0 {
+            return 0;
+        }
+        info.ri_diskio_bytesread + info.ri_diskio_byteswritten
+    }
+
+    #[cfg(not(any(target_os = "linux", target_os = "macos")))]
+    fn read_bytes() -> u64 {
+        0
+    }
+
+    /// Same protocol as [`CpuSample::do_i_activate`] (0.1 s minimum window,
+    /// state untouched on early return), but growth is measured relative to
+    /// the previous rate. `threshold` is a fraction, e.g. `0.2` for a 20 %
+    /// increase in throughput since the last real sample.
+    pub fn do_i_activate(&mut self, threshold: f64) -> bool {
+        let elapsed = self.wall.elapsed().as_secs_f64();
+        if elapsed < 0.1 {
+            return false;
+        }
+
+        let n = Self::read_bytes();
+        let rate = n.saturating_sub(self.bytes) as f64 / elapsed;
+        let activate = if self.previous_rate == 0.0 {
+            rate > 0.0 // bootstrap: any measured throughput is signal enough
+        } else {
+            (rate - self.previous_rate) / self.previous_rate >= threshold
+        };
+
+        debug!(
+            "Do I activate (I/O) : {} -> {} Activate: {}",
+            self.previous_rate, rate, activate
+        );
+        self.previous_rate = rate;
+        self.bytes = n;
+        self.wall = Instant::now();
+
+        activate
+    }
+}
diff --git a/src/obisys/src/stage.rs b/src/obisys/src/stage.rs
new file mode 100644
index 00000000..2cb75647
--- /dev/null
+++ b/src/obisys/src/stage.rs
@@ -0,0 +1,292 @@
+use std::fmt;
+use std::time::Instant;
+
+use libc::rusage;
+use tracing::{info, warn};
+
+use crate::resources::{delta, effective_parallelism, get_rusage, rss_to_bytes, tv_to_secs};
+
+// ── public API ────────────────────────────────────────────────────────────────
+
+/// Snapshot taken at the start of a pipeline stage.
+#[must_use = "call .stop() to record the stage"]
+pub struct Stage {
+    label: String,
+    wall: Instant,
+    ru: rusage,
+}
+
+impl Stage {
+    pub fn start(label: impl Into<String>) -> Self {
+        let label = label.into();
+        info!(stage = %label, "started");
+        Self {
+            label,
+            wall: Instant::now(),
+            ru: get_rusage(),
+        }
+    }
+
+    pub fn stop(self) -> StageStats {
+        let wall_secs = self.wall.elapsed().as_secs_f64();
+        let end = get_rusage();
+        let stats = StageStats {
+            label: self.label,
+            wall_secs,
+            user_secs: tv_to_secs(end.ru_utime) - tv_to_secs(self.ru.ru_utime),
+            sys_secs: tv_to_secs(end.ru_stime) - tv_to_secs(self.ru.ru_stime),
+            max_rss_bytes: rss_to_bytes(&end),
+            minor_faults: delta(end.ru_minflt as i64, self.ru.ru_minflt as i64),
+            major_faults: delta(end.ru_majflt as i64, self.ru.ru_majflt as i64),
+            vol_ctx: delta(end.ru_nvcsw as i64, self.ru.ru_nvcsw as i64),
+            invol_ctx: delta(end.ru_nivcsw as i64, self.ru.ru_nivcsw as i64),
+            in_blocks: delta(end.ru_inblock as i64, self.ru.ru_inblock as i64),
+            out_blocks: delta(end.ru_oublock as i64, self.ru.ru_oublock as i64),
+            swaps: delta(end.ru_nswap as i64, self.ru.ru_nswap as i64),
+        };
+        info!(
+            stage      = %stats.label,
+            wall_secs  = format_args!("{:.3}", stats.wall_secs),
+            rss        = %fmt_bytes(stats.max_rss_bytes),
+            swaps      = stats.swaps,
+            "done"
+        );
+        if stats.swaps > 0 {
+            warn!(
+                stage = %stats.label,
+                swaps = stats.swaps,
+                "working set exceeds available RAM"
+            );
+        }
+        stats
+    }
+}
+
+/// Per-stage efficiency metrics collected from `getrusage(RUSAGE_SELF)` deltas.
+pub struct StageStats {
+    pub label: String,
+    pub wall_secs: f64,
+    pub user_secs: f64,
+    pub sys_secs: f64,
+    /// Peak RSS at end of stage (bytes). ru_maxrss is a process-lifetime maximum,
+    /// so this reflects the high-water mark up to and including this stage.
+    pub max_rss_bytes: u64,
+    pub minor_faults: u64,
+    pub major_faults: u64,
+    pub vol_ctx: u64,    // voluntary context switches
+    pub invol_ctx: u64,  // involuntary context switches
+    pub in_blocks: u64,  // filesystem block reads (after page cache)
+    pub out_blocks: u64, // filesystem block writes
+    pub swaps: u64,
+}
+
+impl StageStats {
+    /// (user + sys) / wall — effective thread count utilisation.
+    pub fn parallelism(&self) -> f64 {
+        if self.wall_secs > 1e-9 {
+            (self.user_secs + self.sys_secs) / self.wall_secs
+        } else {
+            0.0
+        }
+    }
+
+    /// parallelism / n_cores — fraction of available CPU power used (0..1+).
+    pub fn efficiency(&self, n_cores: usize) -> f64 {
+        self.parallelism() / n_cores as f64
+    }
+}
+
+/// Accumulates stage stats and prints a human-readable summary table.
+#[derive(Default)]
+pub struct Reporter {
+    stages: Vec<StageStats>,
+}
+
+impl Reporter {
+    pub fn new() -> Self {
+        Self::default()
+    }
+    pub fn push(&mut self, stats: StageStats) {
+        self.stages.push(stats);
+    }
+    pub fn stages(&self) -> &[StageStats] {
+        &self.stages
+    }
+    /// Print the summary to stderr.
+    pub fn print(&self) {
+        eprint!("{self}");
+    }
+}
+
+// ── diagnosis ─────────────────────────────────────────────────────────────────
+
+struct Diagnosis {
+    tag: &'static str,
+    detail: Option<String>,
+}
+
+// Thresholds are intentionally conservative to avoid false positives.
+fn diagnose(s: &StageStats, n_cores: usize) -> Diagnosis {
+    let eff = s.efficiency(n_cores);
+    let cpu_pct = eff * 100.0;
+    let io_ops = s.in_blocks + s.out_blocks;
+
+    // swaps > 0 is the only reliable cross-platform indicator of true RAM exhaustion.
+    // ru_majflt is intentionally excluded: on macOS it counts all file-backed mmap
+    // page-ins (even from page cache), making it useless as a memory-pressure signal
+    // for mmap-heavy code. On Linux it is more meaningful, but swaps covers the
+    // severe case on both platforms.
+    if s.swaps > 0 {
+        return Diagnosis {
+            tag: "swapping",
+            detail: Some(format!(
+                "swapped {} time(s) — working set exceeds available RAM",
+                s.swaps,
+            )),
+        };
+    }
+    if eff < 0.3 && io_ops > 100 {
+        return Diagnosis {
+            tag: "disk I/O",
+            detail: Some(format!(
+                "{} block reads + {} writes — CPU at {:.0}%, stage is I/O-bound",
+                s.in_blocks, s.out_blocks, cpu_pct,
+            )),
+        };
+    }
+    if eff < 0.3 && s.vol_ctx > 200 {
+        return Diagnosis {
+            tag: "contention",
+            detail: Some(format!(
+                "{} voluntary context switches — CPU at {:.0}%, possible lock contention or I/O wait",
+                s.vol_ctx, cpu_pct,
+            )),
+        };
+    }
+    Diagnosis {
+        tag: "—",
+        detail: None,
+    }
+}
+
+// ── display helpers ───────────────────────────────────────────────────────────
+
+fn fmt_secs(s: f64) -> String {
+    if s >= 100.0 {
+        format!("{:.0}s", s)
+    } else if s >= 10.0 {
+        format!("{:.1}s", s)
+    } else if s >= 1.0 {
+        format!("{:.2}s", s)
+    } else {
+        format!("{:.0}ms", s * 1000.0)
+    }
+}
+
+fn fmt_bytes(b: u64) -> String {
+    if b >= 1 << 30 {
+        format!("{:.1} GB", b as f64 / (1u64 << 30) as f64)
+    } else if b >= 1 << 20 {
+        format!("{:.0} MB", b as f64 / (1u64 << 20) as f64)
+    } else {
+        format!("{:.0} KB", b as f64 / 1024.0)
+    }
+}
+
+fn fmt_efficiency(par: f64, n_cores: usize) -> String {
+    format!(
+        "{:.1}×/{} ({:.0}%)",
+        par,
+        n_cores,
+        par / n_cores as f64 * 100.0
+    )
+}
+
+// ── Display ───────────────────────────────────────────────────────────────────
+
+impl fmt::Display for Reporter {
+    fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
+        if self.stages.is_empty() {
+            return Ok(());
+        }
+
+        let n_cores = effective_parallelism();
+
+        // column widths
+        let nw = self
+            .stages
+            .iter()
+            .map(|s| s.label.len())
+            .max()
+            .unwrap_or(5)
+            .max(5);
+        // efficiency col: worst-case width for this run's n_cores value
+        let ew = format!("{:.1}×/{} (100%)", 99.9f64, n_cores).len();
+
+        let sep_w = nw + 2 + 7 + 2 + ew + 2 + 8 + 2 + 12;
+        let sep = "─".repeat(sep_w);
+
+        // header
+        writeln!(
+            f,
+            "{:<nw$}  {:>7}  {:>ew$}  {:>8}  status",
+            "stage", "wall", "efficiency", "peak RSS"
+        )?;
+        writeln!(f, "{sep}")?;
+
+        // compute all diagnoses up front (needed for both table and footnotes)
+        let diagnoses: Vec<Diagnosis> = self.stages.iter().map(|s| diagnose(s, n_cores)).collect();
+
+        // per-stage rows
+        for (s, d) in self.stages.iter().zip(diagnoses.iter()) {
+            writeln!(
+                f,
+                "{:<nw$}  {:>7}  {:>ew$}  {:>8}  {}",
+                s.label,
+                fmt_secs(s.wall_secs),
+                fmt_efficiency(s.parallelism(), n_cores),
+                fmt_bytes(s.max_rss_bytes),
+                d.tag,
+            )?;
+        }
+
+        // totals
+        let tw = self.stages.iter().map(|s| s.wall_secs).sum::<f64>();
+        let tu = self.stages.iter().map(|s| s.user_secs).sum::<f64>();
+        let ts = self.stages.iter().map(|s| s.sys_secs).sum::<f64>();
+        let trss = self
+            .stages
+            .iter()
+            .map(|s| s.max_rss_bytes)
+            .max()
+            .unwrap_or(0);
+        let tpar = if tw > 1e-9 { (tu + ts) / tw } else { 0.0 };
+
+        writeln!(f, "{sep}")?;
+        writeln!(
+            f,
+            "{:<nw$}  {:>7}  {:>ew$}  {:>8}",
+            "TOTAL",
+            fmt_secs(tw),
+            fmt_efficiency(tpar, n_cores),
+            fmt_bytes(trss),
+        )?;
+
+        // bottleneck footnotes (only if at least one anomaly detected)
+        let bottlenecks: Vec<(&str, &str)> = self
+            .stages
+            .iter()
+            .zip(diagnoses.iter())
+            .filter_map(|(s, d)| d.detail.as_deref().map(|det| (s.label.as_str(), det)))
+            .collect();
+
+        if !bottlenecks.is_empty() {
+            writeln!(f, "\nBottlenecks:")?;
+            for (label, detail) in &bottlenecks {
+                writeln!(f, "  {label} — {detail}")?;
+            }
+        }
+
+        Ok(())
+    }
+}
-- 
2.54.0


From dd889854cb647e66638c18b1650c374f0fe2e3c0 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Thu, 13 Aug 2026 16:33:22 +0200
Subject: [PATCH 10/46] rename distance subcommand to phylo

Rename the distance CLI subcommand to phylo across the codebase, documentation, and build configurations. Relocate source files from cmd/distance/ to a dedicated cmd/phylo/ module, update all internal routing references, and adjust benchmark scripts and Makefile targets to reflect the new command name.
---
 Makefile                                      |  2 +-
 README.md                                     | 10 +++++----
 UserDocMD/architecture.md                     |  2 +-
 UserDocMD/index.md                            |  2 +-
 UserDocMD/usage/{distance.md => phylo.md}     |  6 ++---
 benchmark/Makefile                            | 22 +++++++++----------
 benchmark/build_reference_dist.py             |  4 ++--
 benchmark/compare_all_dist.py                 |  4 ++--
 docmd/implementation/filtering.md             |  4 ++--
 docmd/index.md                                |  2 +-
 docmd/theory/evolutionary_distances.md        | 22 +++++++++----------
 mkdocs-user.yml                               |  2 +-
 src/obikmer/src/cmd/mod.rs                    |  2 +-
 .../src/cmd/{distance => phylo}/iqtree.rs     |  0
 .../src/cmd/{distance => phylo}/mod.rs        |  4 ++--
 .../src/cmd/{distance => phylo}/phyg.rs       |  0
 .../src/cmd/{distance => phylo}/sankoff.rs    |  0
 .../src/cmd/{distance => phylo}/tnt.rs        |  0
 src/obikmer/src/main.rs                       |  7 +++---
 19 files changed, 49 insertions(+), 46 deletions(-)
 rename UserDocMD/usage/{distance.md => phylo.md} (96%)
 rename src/obikmer/src/cmd/{distance => phylo}/iqtree.rs (100%)
 rename src/obikmer/src/cmd/{distance => phylo}/mod.rs (99%)
 rename src/obikmer/src/cmd/{distance => phylo}/phyg.rs (100%)
 rename src/obikmer/src/cmd/{distance => phylo}/sankoff.rs (100%)
 rename src/obikmer/src/cmd/{distance => phylo}/tnt.rs (100%)

diff --git a/Makefile b/Makefile
index 5889db68..bebe14f9 100644
--- a/Makefile
+++ b/Makefile
@@ -105,7 +105,7 @@ bump-version:
 
 .PHONY: release
 release: bump-version
-	@jj auto-describe
+	@jj auto-doc
 	@jj git push --change @
 	@new_version=$$(grep '^version = ' $(CARGO_TOML) | head -n 1 | sed 's/version = "\(.*\)"/\1/'); \
 	git_hash=$$(jj log -r @ --no-graph -T 'commit_id'); \
diff --git a/README.md b/README.md
index 0fb073e3..a9876151 100644
--- a/README.md
+++ b/README.md
@@ -66,9 +66,11 @@ Non-ACGT characters act as hard breaks between k-mer segments in all formats.
                Annotates each sequence with per-genome k-mer match counts
                and optional per-position coverage vectors (--detail).
                Parallel over sequence chunks.
-    distance   Compute a pairwise Bray-Curtis or Jaccard distance matrix
-               between all indexed genomes.
-               Optionally outputs a Newick NJ or UPGMA tree.
+    phylo      Compute pairwise evolutionary-distance proxies between all
+               indexed genomes (Bray-Curtis, Jaccard, etc.), optionally
+               a Newick NJ/UPGMA tree, and optionally a central-position
+               SNP/Sankoff calibration with exports for external
+               phylogenetic tools (TNT, PhyG, IQ-TREE).
     annotate   Add or update genome metadata (taxonomy, etc.) from a CSV
                file; or dump the current metadata as CSV.
     estimate   Dry-run: resolve and print approximate-index parameters
@@ -106,7 +108,7 @@ obikmer reindex --approx -z 5 --evidence-bits 8 index/
 obikmer query index/ reads.fq.gz > annotated.fa
 
 # Pairwise distances
-obikmer distance index/ > distances.tsv
+obikmer phylo index/ > distances.tsv
 ```
 
 ## Parameter constraints
diff --git a/UserDocMD/architecture.md b/UserDocMD/architecture.md
index 87bf9b91..7c1da714 100644
--- a/UserDocMD/architecture.md
+++ b/UserDocMD/architecture.md
@@ -20,7 +20,7 @@ An index directory is organized as `KmerIndex → partitions → layers`, with a
 
 ## Parallel execution and NUMA awareness
 
-Partition-level work (index construction, `merge`, `filter`, `reindex`, `select`, `distance`'s sibling-annex/Sankoff computations) is dispatched by a partition runner that adapts to the machine's memory topology, detected automatically at startup via hwloc:
+Partition-level work (index construction, `merge`, `filter`, `reindex`, `select`, `phylo`'s sibling-annex/Sankoff computations) is dispatched by a partition runner that adapts to the machine's memory topology, detected automatically at startup via hwloc:
 
 - On a multi-socket / multi-NUMA-node machine, one thread pool is pinned per NUMA node, and each partition is processed entirely by threads pinned to one node — keeping the memory a partition touches local to that node's DRAM. This matters because touching kmer data across NUMA nodes without pinning can degrade throughput by an order of magnitude or more on large multi-socket machines.
 - On a single-socket machine, Apple Silicon, or if hwloc cannot report NUMA topology, all cores are treated as one node with no pinning and negligible overhead — this is the default behavior on macOS.
diff --git a/UserDocMD/index.md b/UserDocMD/index.md
index cd1e2806..16248c99 100644
--- a/UserDocMD/index.md
+++ b/UserDocMD/index.md
@@ -24,7 +24,7 @@ All functionality is exposed through a single binary, `obikmer`, organized as su
 | [`query`](usage/query.md) | Query an index with sequences and annotate matches |
 | [`dump`](usage/dump.md) | Dump indexed kmers as CSV |
 | [`annotate`](usage/annotate.md) | Add, update, or dump genome metadata |
-| [`distance`](usage/distance.md) | Compute pairwise distance matrices and phylogenetic exports |
+| [`phylo`](usage/phylo.md) | Compute pairwise evolutionary-distance proxies, trees, and phylogenetic exports |
 | [`unitig`](usage/unitig.md) | Dump the unitigs of an index as FASTA |
 | [`estimate`](usage/estimate.md) | Estimate approximate-index parameters before indexing |
 | [`reindex`](usage/reindex.md) | Convert an index's evidence representation (exact ↔ approximate) |
diff --git a/UserDocMD/usage/distance.md b/UserDocMD/usage/phylo.md
similarity index 96%
rename from UserDocMD/usage/distance.md
rename to UserDocMD/usage/phylo.md
index 9a55ccf4..4a71bd0c 100644
--- a/UserDocMD/usage/distance.md
+++ b/UserDocMD/usage/phylo.md
@@ -1,9 +1,9 @@
-# distance
+# phylo
 
-Compute pairwise distance matrices between the genomes stored in an index, optionally build trees (NJ/UPGMA), and optionally derive a central-position SNP model with exports for external phylogenetic tools (TNT, PhyG, IQ-TREE).
+Compute pairwise evolutionary-distance proxies between the genomes stored in an index — a plain distance matrix, optionally trees (NJ/UPGMA), and optionally a central-position SNP model with exports for external phylogenetic tools (TNT, PhyG, IQ-TREE).
 
 ```bash
-obikmer distance INDEX [OPTIONS]
+obikmer phylo INDEX [OPTIONS]
 ```
 
 ## Arguments
diff --git a/benchmark/Makefile b/benchmark/Makefile
index 14a33583..5bd9b7a6 100644
--- a/benchmark/Makefile
+++ b/benchmark/Makefile
@@ -89,50 +89,50 @@ $(REF_DIST_CSVS) &: $(REF_NPZS) build_reference_dist.py
 
 reference_dist: $(REF_DIST_CSVS)
 
-# ── obikmer distance (presence index) ────────────────────────────────────────
+# ── obikmer phylo (presence index) ──────────────────────────────────────────
 
 $(OBIKMER_PRESENCE_DIST) &: global_index_presence/index.done $(BINARY)
 	mkdir -p obikmer_dist/presence
-	$(BINARY) distance \
+	$(BINARY) phylo \
 		--output obikmer_dist/presence/jaccard \
 		--metric jaccard --shared-kmers --nj \
 		global_index_presence
-	$(BINARY) distance \
+	$(BINARY) phylo \
 		--output obikmer_dist/presence/hamming \
 		--metric hamming --nj \
 		global_index_presence
 
 obikmer_dist_presence: $(OBIKMER_PRESENCE_DIST)
 
-# ── obikmer distance (count index) ───────────────────────────────────────────
+# ── obikmer phylo (count index) ─────────────────────────────────────────────
 
 $(OBIKMER_COUNT_DIST) &: global_index_count/index.done $(BINARY)
 	mkdir -p obikmer_dist/count
-	$(BINARY) distance \
+	$(BINARY) phylo \
 		--output obikmer_dist/count/jaccard \
 		--metric jaccard --shared-kmers --nj \
 		global_index_count
-	$(BINARY) distance \
+	$(BINARY) phylo \
 		--output obikmer_dist/count/bray_curtis \
 		--metric bray-curtis --nj \
 		global_index_count
-	$(BINARY) distance \
+	$(BINARY) phylo \
 		--output obikmer_dist/count/relfreq_bray_curtis \
 		--metric relfreq-bray-curtis --nj \
 		global_index_count
-	$(BINARY) distance \
+	$(BINARY) phylo \
 		--output obikmer_dist/count/euclidean \
 		--metric euclidean --nj \
 		global_index_count
-	$(BINARY) distance \
+	$(BINARY) phylo \
 		--output obikmer_dist/count/relfreq_euclidean \
 		--metric relfreq-euclidean --nj \
 		global_index_count
-	$(BINARY) distance \
+	$(BINARY) phylo \
 		--output obikmer_dist/count/hellinger \
 		--metric hellinger --nj \
 		global_index_count
-	$(BINARY) distance \
+	$(BINARY) phylo \
 		--output obikmer_dist/count/hellinger_euclidean \
 		--metric hellinger-euclidean --nj \
 		global_index_count
diff --git a/benchmark/build_reference_dist.py b/benchmark/build_reference_dist.py
index edee8586..bd851d67 100755
--- a/benchmark/build_reference_dist.py
+++ b/benchmark/build_reference_dist.py
@@ -2,10 +2,10 @@
 """Compute reference pairwise distance matrices from per-specimen .npz kmer indexes.
 
 Reads all .npz files in reference_index/ (each containing sorted uint64 `kmers`
-and uint32 `counts`), computes all distance metrics supported by `obikmer distance`,
+and uint32 `counts`), computes all distance metrics supported by `obikmer phylo`,
 and writes one CSV per metric to reference_dist/.
 
-Output CSV format matches `obikmer distance --output`:
+Output CSV format matches `obikmer phylo --output`:
   - first row: "genome", then specimen names
   - subsequent rows: specimen name, then float or int values
 
diff --git a/benchmark/compare_all_dist.py b/benchmark/compare_all_dist.py
index f34ddc60..390feefc 100755
--- a/benchmark/compare_all_dist.py
+++ b/benchmark/compare_all_dist.py
@@ -1,9 +1,9 @@
 #!/usr/bin/env python3
-"""Compare all reference distance matrices against obikmer distance outputs.
+"""Compare all reference distance matrices against obikmer phylo outputs.
 
 Reads from:
   reference_dist/   — ground-truth matrices computed by build_reference_dist.py
-  obikmer_dist/     — matrices produced by `obikmer distance`
+  obikmer_dist/     — matrices produced by `obikmer phylo`
 
 Handles label reordering: both matrices are sorted by genome label before
 element-wise comparison, so column/row order differences are irrelevant.
diff --git a/docmd/implementation/filtering.md b/docmd/implementation/filtering.md
index b45938e6..1021cbae 100644
--- a/docmd/implementation/filtering.md
+++ b/docmd/implementation/filtering.md
@@ -289,14 +289,14 @@ obikmer dump myindex --head 100
 obikmer dump myindex --head 20 --ingroup "species=Betula_nana" --min-count 1
 ```
 
-### `distance --presence-threshold N`
+### `phylo --presence-threshold N`
 
 When computing Jaccard distance on a **count index**, a k-mer is considered present in a genome if its count is ≥ N (default 1).
 This option is independent of the `--presence-threshold` used in filtering.
 
 ```sh
 # Jaccard treating kmers with count ≥ 2 as present
-obikmer distance myindex --metric jaccard --presence-threshold 2
+obikmer phylo myindex --metric jaccard --presence-threshold 2
 ```
 
 This parameter has no effect on presence/absence indexes (where values are already 0/1) or on metrics other than Jaccard.
diff --git a/docmd/index.md b/docmd/index.md
index 812cc86e..4c879040 100644
--- a/docmd/index.md
+++ b/docmd/index.md
@@ -13,7 +13,7 @@
 | `query`     | Query an index with sequences and annotate matches |
 | `dump`      | Dump all indexed k-mers as CSV (kmer + per-genome counts or presence); supports the shared [kmer filtering](implementation/filtering.md) system; `--head N` limits output to the first N k-mers |
 | `annotate`  | Add or update genome metadata from a CSV file; or dump metadata as CSV |
-| `distance`  | Compute pairwise distance matrix between genomes (`--metric jaccard\|mash\|hamming\|bray-curtis\|relfreq-bray-curtis\|euclidean\|relfreq-euclidean\|hellinger\|hellinger-euclidean`); optionally build NJ/UPGMA trees; `--presence-threshold N` sets the minimum count to consider a k-mer present when computing Jaccard/Mash on count indexes (default 1) |
+| `phylo`     | Compute pairwise evolutionary-distance proxies between genomes (`--metric jaccard\|mash\|hamming\|bray-curtis\|relfreq-bray-curtis\|euclidean\|relfreq-euclidean\|hellinger\|hellinger-euclidean`); optionally build NJ/UPGMA trees; `--presence-threshold N` sets the minimum count to consider a k-mer present when computing Jaccard/Mash on count indexes (default 1); optionally a central-position SNP/Sankoff calibration with exports for TNT/PhyG/IQ-TREE (see [evolutionary distances](theory/evolutionary_distances.md)) |
 | `unitig`    | Build a global de Bruijn graph across all partitions and enumerate its unitigs as FASTA; supports the shared [kmer filtering](implementation/filtering.md) system |
 | `select`    | Project and/or aggregate genome columns into a new or in-place index; the column-axis counterpart of `filter` (see [select](implementation/select.md)) |
 | `estimate`  | Estimate approximate-index parameters (z, evidence bits, FP rates) before indexing |
diff --git a/docmd/theory/evolutionary_distances.md b/docmd/theory/evolutionary_distances.md
index f6b20da1..bf5a3be6 100644
--- a/docmd/theory/evolutionary_distances.md
+++ b/docmd/theory/evolutionary_distances.md
@@ -205,7 +205,7 @@ single-copy at that locus.
 
 ## Context, detectability, and a 3-way ordinal distance per pair
 
-Empirical follow-up to the pseudo-alignment idea above: `obikmer distance
+Empirical follow-up to the pseudo-alignment idea above: `obikmer phylo
 --snp` was run on a real 20-genome benchmark index and the resulting FASTA
 fed to `raxml-ng`. Two problems surfaced, both traced back to conflating
 distinct notions under one symbol.
@@ -552,7 +552,7 @@ informative across domains with this character type. Exploratory only —
 run entirely outside the repo (`/tmp/tnt_run`, TNT installed locally under
 `TNT/`), no new Rust code. Kept here as the record of what was learned.
 
-**Pipeline.** `obikmer distance --snp` emits one IUPAC-coded pseudo-alignment
+**Pipeline.** `obikmer phylo --snp` emits one IUPAC-coded pseudo-alignment
 row per genome (`snp_pseudo_alignment`, one column per family with
 `family_size() >= 2`). A small external Python script decodes IUPAC back to
 the 16-state bitmask, applies the set-edit-distance formula above, and
@@ -630,7 +630,7 @@ it, no external script needed. `∅` is an ordinary 16th state throughout
 (never `-`), specifically to avoid gap-semantics confusion in downstream
 tools — see "A concrete Sankoff cost matrix" above for why.
 
-**TNT (`--tnt`).** `write_sankoff_tnt` (`obikmer/src/cmd/distance.rs`)
+**TNT (`--tnt`).** `write_sankoff_tnt` (`obikmer/src/cmd/phylo/mod.rs`)
 recodes to TNT's own `0-9A-F` xread alphabet (its default reader rejects
 the wider IUPAC set otherwise), scales and rounds costs to integers
 (`smatrix`/`cost` reject decimals), then re-runs integer Floyd-Warshall on
@@ -902,7 +902,7 @@ sections below, which implement and then substantially revise this.
 
 ### `R`/`π` implemented; `--exclude-genome` added; rogue-taxon test negative (2026-08-12)
 
-`write_iqtree` (`obikmer/src/cmd/distance/iqtree.rs`) implements exactly
+`write_iqtree` (`obikmer/src/cmd/phylo/iqtree.rs`) implements exactly
 the `R = exp(-cost)` / empirical-`π` design above: writes
 `<prefix>_iqtree.model` (lower-triangular `R`, PAML order, then `π`) and
 `<prefix>_iqtree.fasta` (alignment recoded to the compact `0..k-1`
@@ -949,7 +949,7 @@ tell: with `n_eligible=1`, the ratio can only be exactly `0` or `1`, so
 possibly ascertainment bias — see below — or possibly a few genuinely
 ultra-conserved loci; not resolved).
 
-**`--exclude-genome LABEL`** (repeatable, `obikmer distance`) added for
+**`--exclude-genome LABEL`** (repeatable, `obikmer phylo`) added for
 exactly this kind of test: zeroes the excluded genome's row/column in
 `RawSnpDistanceOutput` after `raw_snp_distance` runs (a pair with zero
 counts is already skipped by `calibrate_p_hat`/`base_pair_tally` — no
@@ -1165,7 +1165,7 @@ silently wrong data for TNT/PhyG, and a hard failure for IQ-TREE's `+ASC`
 (verified: excluding 2 taxa on the benchmark left 116,351 such columns —
 matches the manual `+ASC` failures hit earlier in this same investigation,
 before `--exclude-genome` existed). Fixed in `drop_excluded`
-(`obikmer/src/cmd/distance/mod.rs`): after dropping excluded rows,
+(`obikmer/src/cmd/phylo/mod.rs`): after dropping excluded rows,
 re-scan each column among the *surviving* sequences and drop any that are
 now constant. Verified: 908,723 → 792,372 sites after excluding 2 taxa,
 zero monomorphic columns remain, `π` recomputed from the corrected
@@ -1582,7 +1582,7 @@ index, not of any single genome — it cannot be computed correctly at
 mono-genome build time (a family may gain siblings, or its minorant may
 change, once more genomes are merged in later). Computing it eagerly at
 every `merge` would also waste work on intermediate merged states nobody
-ever queries. Instead: compute it lazily, on first `distance` call against a
+ever queries. Instead: compute it lazily, on first `phylo` call against a
 given index, and persist the result alongside that index for subsequent
 calls — the same lazy-derived-cache pattern `PersistentBitMatrix` already
 uses for `Columnar` -> `Packed`. This requires no explicit invalidation for
@@ -1745,7 +1745,7 @@ above) is observed anywhere in the index — fixes both:
    own 3 lookups independently," not a strict improvement to adopt by
    default.
 4. **Trigger and caching** (`obikindex::KmerIndex`/`distance.rs`): compute
-   lazily on first `distance` call for an SNP-family metric against a given
+   lazily on first `phylo` call for an SNP-family metric against a given
    index; check for an existing annex file first (mirrors
    `PersistentBitMatrix::open()`'s auto-detect-and-fall-back,
    `bitmatrix.rs:264-287`); if absent, run step 3 and persist; if present,
@@ -1765,7 +1765,7 @@ above) is observed anywhere in the index — fixes both:
    slots are never looked up cross-partition during the sweep.
 
 Cost: `3 * N_distinct` existence-only lookups, computed once per index
-state and amortised over every subsequent `distance` call that reuses the
+state and amortised over every subsequent `phylo` call that reuses the
 cached annex — cheaper per-lookup than the sweep itself (hit/miss only, no
 column fetch).
 
@@ -1795,11 +1795,11 @@ intermediate). Two options, to decide:
   Keeps one CLI surface (`--metric jukes-cantor`), at the cost of a branch in
   `distance()` that ignores the `LayeredStore` it built.
 - **(b)** A dedicated pathway (`KmerIndex::snp_distance`) and a distinct CLI
-  entry, if mixing a cross-partition sweep into the partition-local `distance`
+  entry, if mixing a cross-partition sweep into the partition-local `phylo`
   command is judged architecturally muddy.
 
 Recommendation: (a) for user ergonomics (all pairwise distances under
-`distance`, all feeding NJ/UPGMA/`--shared-kmers` unchanged), but compute the
+`phylo`, all feeding NJ/UPGMA/`--shared-kmers` unchanged), but compute the
 sweep lazily only when an SNP-family metric is requested, so the existing
 metrics keep their partition-local fast path untouched.
 
diff --git a/mkdocs-user.yml b/mkdocs-user.yml
index 1c9d1842..40ca9021 100644
--- a/mkdocs-user.yml
+++ b/mkdocs-user.yml
@@ -45,7 +45,7 @@ nav:
       - query: usage/query.md
       - dump: usage/dump.md
       - annotate: usage/annotate.md
-      - distance: usage/distance.md
+      - phylo: usage/phylo.md
       - unitig: usage/unitig.md
       - estimate: usage/estimate.md
       - reindex: usage/reindex.md
diff --git a/src/obikmer/src/cmd/mod.rs b/src/obikmer/src/cmd/mod.rs
index eba674ba..619edea6 100644
--- a/src/obikmer/src/cmd/mod.rs
+++ b/src/obikmer/src/cmd/mod.rs
@@ -4,7 +4,7 @@ pub mod pack;
 pub(crate) mod predicate;
 pub mod select;
 pub mod utils;
-pub mod distance;
+pub mod phylo;
 pub mod dump;
 pub mod estimate;
 pub mod index;
diff --git a/src/obikmer/src/cmd/distance/iqtree.rs b/src/obikmer/src/cmd/phylo/iqtree.rs
similarity index 100%
rename from src/obikmer/src/cmd/distance/iqtree.rs
rename to src/obikmer/src/cmd/phylo/iqtree.rs
diff --git a/src/obikmer/src/cmd/distance/mod.rs b/src/obikmer/src/cmd/phylo/mod.rs
similarity index 99%
rename from src/obikmer/src/cmd/distance/mod.rs
rename to src/obikmer/src/cmd/phylo/mod.rs
index 3d54cb44..a25f7a39 100644
--- a/src/obikmer/src/cmd/distance/mod.rs
+++ b/src/obikmer/src/cmd/phylo/mod.rs
@@ -55,7 +55,7 @@ impl From<MetricArg> for DistanceMetric {
 }
 
 #[derive(Args)]
-pub struct DistanceArgs {
+pub struct PhyloArgs {
     /// Index directory
     pub index: PathBuf,
 
@@ -220,7 +220,7 @@ pub struct DistanceArgs {
     pub output: Option<PathBuf>,
 }
 
-pub fn run(args: DistanceArgs) {
+pub fn run(args: PhyloArgs) {
     let idx = KmerIndex::open(&args.index).unwrap_or_else(|e| {
         eprintln!("error opening index: {e}");
         std::process::exit(1);
diff --git a/src/obikmer/src/cmd/distance/phyg.rs b/src/obikmer/src/cmd/phylo/phyg.rs
similarity index 100%
rename from src/obikmer/src/cmd/distance/phyg.rs
rename to src/obikmer/src/cmd/phylo/phyg.rs
diff --git a/src/obikmer/src/cmd/distance/sankoff.rs b/src/obikmer/src/cmd/phylo/sankoff.rs
similarity index 100%
rename from src/obikmer/src/cmd/distance/sankoff.rs
rename to src/obikmer/src/cmd/phylo/sankoff.rs
diff --git a/src/obikmer/src/cmd/distance/tnt.rs b/src/obikmer/src/cmd/phylo/tnt.rs
similarity index 100%
rename from src/obikmer/src/cmd/distance/tnt.rs
rename to src/obikmer/src/cmd/phylo/tnt.rs
diff --git a/src/obikmer/src/main.rs b/src/obikmer/src/main.rs
index cb701e6f..73e49b01 100644
--- a/src/obikmer/src/main.rs
+++ b/src/obikmer/src/main.rs
@@ -30,8 +30,9 @@ enum Commands {
     Dump(cmd::dump::DumpArgs),
     /// Add or update genome metadata from a CSV file; or dump metadata as CSV
     Annotate(cmd::annotate::AnnotateArgs),
-    /// Compute pairwise distance matrix between genomes; optionally build NJ/UPGMA trees
-    Distance(cmd::distance::DistanceArgs),
+    /// Compute pairwise evolutionary-distance proxies between genomes (metric matrix, NJ/UPGMA
+    /// trees, SNP/Sankoff calibration, TNT/PhyG/IQ-TREE exports)
+    Phylo(cmd::phylo::PhyloArgs),
     /// Dump unitigs from a built index to stdout (debug)
     Unitig(cmd::unitig::UnitigArgs),
     /// Estimate approximate-index parameters (z, evidence bits, FP rates) before indexing
@@ -71,7 +72,7 @@ fn main() {
         Commands::Select(args)    => cmd::select::run(args),
         Commands::Query(args)     => cmd::query::run(args),
         Commands::Annotate(args)  => cmd::annotate::run(args),
-        Commands::Distance(args)  => cmd::distance::run(args),
+        Commands::Phylo(args)     => cmd::phylo::run(args),
         Commands::Unitig(args)    => cmd::unitig::run(args),
         Commands::Estimate(args)  => cmd::estimate::run(args),
         Commands::Reindex(args)   => cmd::reindex::run(args),
-- 
2.54.0


From e2b93744264254dc0767d6cb84871f6888c76da8 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Thu, 13 Aug 2026 19:35:40 +0200
Subject: [PATCH 11/46] fix: respect --force flag during index and partition
 creation

The index creation routine now uses the CLI `--force` argument instead of a hardcoded false value, enabling explicit overwrite control. Partition existence checks also verify for the designated subdirectory rather than the root path, ensuring conflict detection and cleanup only trigger when an actual partition layout exists.
---
 src/obikmer/src/cmd/index/mod.rs                     | 2 +-
 src/obikpartitionner/src/partition/kmer_partition.rs | 6 +++++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/obikmer/src/cmd/index/mod.rs b/src/obikmer/src/cmd/index/mod.rs
index e83f7910..ca9fe857 100644
--- a/src/obikmer/src/cmd/index/mod.rs
+++ b/src/obikmer/src/cmd/index/mod.rs
@@ -225,7 +225,7 @@ pub fn run(args: IndexArgs) {
             }
             info
         });
-        KmerIndex::create(&output, config, genome_info, false).unwrap_or_else(|e| {
+        KmerIndex::create(&output, config, genome_info, args.force).unwrap_or_else(|e| {
             eprintln!("error creating index: {e}");
             std::process::exit(1);
         })
diff --git a/src/obikpartitionner/src/partition/kmer_partition.rs b/src/obikpartitionner/src/partition/kmer_partition.rs
index e24aad53..891e6f8a 100644
--- a/src/obikpartitionner/src/partition/kmer_partition.rs
+++ b/src/obikpartitionner/src/partition/kmer_partition.rs
@@ -59,7 +59,11 @@ impl KmerPartition {
         force: bool,
     ) -> SKResult<Self> {
         let root_path = path.as_ref().to_owned();
-        if root_path.exists() {
+        // `root_path` itself may already exist as a bare directory: callers
+        // typically hold an index-level lock file there before creating the
+        // partition layout. What actually signals a pre-existing partition
+        // set is the `PARTITIONS_SUBDIR` subdirectory, not the root itself.
+        if root_path.join(PARTITIONS_SUBDIR).exists() {
             if force {
                 remove_dir_all(&root_path)?;
             } else {
-- 
2.54.0


From 8615da59a84a035846321e529b02e2163d96a38a Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Thu, 13 Aug 2026 21:14:35 +0200
Subject: [PATCH 12/46] Add phylogenetic CLI options for family overlap and
 missing data

Introduces CLI flags for computing pairwise family overlap matrices and filtering genomes below a shared family threshold. Adds a free-loss mode that recodes locus non-detection states to missing data symbols in Sankoff-calibrated alignments, resolving ascertainment bias handling for IQ-TREE. Updates empirical transition parameters, removes the legacy model asset, and extends output writers for CSV diagnostics, FASTA pseudo-alignments, and Newick trees.
---
 .gitignore                                  |   9 +
 UserDocMD/usage/phylo.md                    |  13 +-
 docmd/theory/evolutionary_distances.md      | 120 ++++++
 iqtree.model                                |  16 -
 sankoff_params.yaml                         | 148 ++++----
 src/obikmer/src/cmd/phylo/args.rs           | 243 ++++++++++++
 src/obikmer/src/cmd/phylo/family_overlap.rs |  97 +++++
 src/obikmer/src/cmd/phylo/iqtree.rs         |  73 +++-
 src/obikmer/src/cmd/phylo/mod.rs            | 390 ++------------------
 src/obikmer/src/cmd/phylo/outputs.rs        | 168 +++++++++
 src/obikmer/src/cmd/phylo/sankoff.rs        |  13 +-
 src/obikmer/src/cmd/phylo/tnt.rs            |   8 +
 12 files changed, 833 insertions(+), 465 deletions(-)
 delete mode 100644 iqtree.model
 create mode 100644 src/obikmer/src/cmd/phylo/args.rs
 create mode 100644 src/obikmer/src/cmd/phylo/family_overlap.rs
 create mode 100644 src/obikmer/src/cmd/phylo/outputs.rs

diff --git a/.gitignore b/.gitignore
index 32189eb2..addd10f0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -27,3 +27,12 @@ benchmark/specific_index_presence
 TNT
 phyg
 *.tnt
+*.tre
+*.phy
+*.treefile
+*.bionj
+*.iqtree
+*.mldist
+*.parstree
+*.ckp.gz
+*.model
diff --git a/UserDocMD/usage/phylo.md b/UserDocMD/usage/phylo.md
index 4a71bd0c..265c5767 100644
--- a/UserDocMD/usage/phylo.md
+++ b/UserDocMD/usage/phylo.md
@@ -47,10 +47,12 @@ A **family** is the set of up to 4 kmers that share identical flanking sequence
 |---|---|---|
 | `--sibling-annex` | off | Build the sibling presence-mask annex (prerequisite for every option below) |
 | `--exclude-genome LABEL` | none | Exclude a genome (repeatable) from every SNP/Sankoff/export computation below |
+| `--min-shared-family N` | none | Auto-exclude any genome whose mean shared-family count against every other genome (see `--family-overlap`) falls below `N` — same exclusion as `--exclude-genome`, applied on top of it |
 | `--sibling-stats` | off | Write the family-size (sibling count) distribution, per genome and globally |
 | `--raw-snp-distance` | off | Write the single-copy central-SNP p-distance matrix |
 | `--raw-snp-counts` | off | Write per-pair diagnostic counts (n_snp, n_shared, n_eligible) instead of a matrix |
 | `--snp` | off | Write a SNP-only pseudo-alignment in FASTA, IUPAC-coded |
+| `--family-overlap` | off | Write an NxN matrix of, for each genome pair, how many variable families both genomes actually carry a call for; the diagonal holds each genome's own total family count |
 
 ### Locus eligibility
 
@@ -62,12 +64,19 @@ A family is eligible for a genome pair $(i, j)$ only if genome $i$ carries exact
 
 `--exclude-genome` removes a genome from these computations, re-checking column variability among the remaining genomes so that a column made monomorphic by the exclusion is dropped rather than kept artificially. It does not affect the `--metric` distance-matrix path.
 
+### Family overlap and low-coverage genomes
+
+`--family-overlap` writes, for every genome pair, how many variable families both genomes actually carry a call for (neither is absent) — a direct measure of how much informative content two genomes actually share. On genome-skim or otherwise incomplete-coverage collections, a genome with very little overlap with everything else has almost nothing left to constrain its position in a tree, and tends to end up placed unstably (near-zero branch length, grafted inside an unrelated clade) by `--tnt`/`--iqtree`.
+
+`--min-shared-family N` automates the fix: it excludes, before any computation, every genome whose mean shared-family count against all other genomes (the same statistic, averaged per row of the `--family-overlap` matrix) falls below `N`. There is no universal value for `N` — it depends on how divergent and how completely covered the genome collection is; inspect `--family-overlap`'s own output to find where the real gap sits before choosing a threshold.
+
 ## Sankoff calibration and phylogenetic exports
 
 | Option | Default | Description |
 |---|---|---|
 | `--sankoff` | off | Calibrate a 16-state parsimony cost matrix and matching pseudo-alignment |
 | `--sankoff-ratio-ceiling` | `0.5` | Exclude genome pairs whose raw SNP ratio exceeds this value from the calibration |
+| `--free-loss` | off | Recode a family's non-detection as the `?` missing-data symbol instead of an ordinary, costed state, in `--sankoff`'s pseudo-alignment and every export built from it |
 | `--tnt` | off | Also write a TNT script (implies `--sankoff`) |
 | `--phyg` | off | Also write PhyG input files (implies `--sankoff`) |
 | `--iqtree` | off | Also write an IQ-TREE custom model and alignment (implies `--sankoff`) |
@@ -84,6 +93,8 @@ which are combined into a row-normalized $16 \times 16$ transition probability m
 
 `--sankoff` alone writes the cost matrix, the calibration parameters, and a pseudo-alignment recoded so the empty state uses the symbol `0` (never a gap character, to avoid ambiguity with external tools' own gap semantics). It does not run any external tool.
 
+With `--free-loss`, the empty state is recoded to `?` instead — TNT/PhyG/IQ-TREE's own missing-data symbol — rather than an ordinary, costed 16th state. This matters for genome-skim or otherwise incomplete-coverage collections, where non-detection of a family is dominated by sampling failure rather than true evolutionary loss: scoring it as a real state risks grouping genomes by shared undersampling instead of shared ancestry. `?` rather than `-` because `-` still carries gap/indel semantics in these tools, and a non-detected family is not an observed deletion. Combine with `--min-shared-family`/`--family-overlap` above: `--free-loss` removes the false signal from non-detection, but a genome left with too little real overlap with everything else will still be placed unstably — excluding it is the other half of the fix.
+
 ### Exports
 
 All three exports reuse the `--sankoff` calibrated matrix and pseudo-alignment, recoded for the target tool:
@@ -94,4 +105,4 @@ All three exports reuse the `--sankoff` calibrated matrix and pseudo-alignment,
 
 ## Output files
 
-With `-o/--output PREFIX`, the relevant subset of the following files is written: `<prefix>_dist.csv`, `<prefix>_shared.csv`, `<prefix>_nj.nwk`, `<prefix>_upgma.nwk`, `<prefix>_siblings.csv`, `<prefix>_rawsnp.csv`, `<prefix>_rawsnp_counts.csv`, `<prefix>_snp.fasta`, `<prefix>_sankoff_matrix.csv`, `<prefix>_sankoff_params.yaml`, `<prefix>_sankoff.fasta`, `<prefix>_sankoff.tnt`, `<prefix>_sankoff.tcm`, `<prefix>_sankoff.pg`, `<prefix>_iqtree.model`, `<prefix>_iqtree.fasta`. Without `-o`, only the plain `--metric` distance matrix is produced, on stdout.
+With `-o/--output PREFIX`, the relevant subset of the following files is written: `<prefix>_dist.csv`, `<prefix>_shared.csv`, `<prefix>_nj.nwk`, `<prefix>_upgma.nwk`, `<prefix>_siblings.csv`, `<prefix>_rawsnp.csv`, `<prefix>_rawsnp_counts.csv`, `<prefix>_snp.fasta`, `<prefix>_family_overlap.csv`, `<prefix>_sankoff_matrix.csv`, `<prefix>_sankoff_params.yaml`, `<prefix>_sankoff.fasta`, `<prefix>_sankoff.tnt`, `<prefix>_sankoff.tcm`, `<prefix>_sankoff.pg`, `<prefix>_iqtree.model`, `<prefix>_iqtree.fasta`. Without `-o`, only the plain `--metric` distance matrix is produced, on stdout.
diff --git a/docmd/theory/evolutionary_distances.md b/docmd/theory/evolutionary_distances.md
index bf5a3be6..1bb5d1a9 100644
--- a/docmd/theory/evolutionary_distances.md
+++ b/docmd/theory/evolutionary_distances.md
@@ -1836,6 +1836,126 @@ lookups proportionally; `p_hat` is unbiased. Off by default (exact).
    matrix).
 5. Subsampling (Step 5).
 
+## Locus dropout under incomplete coverage: absence as missing data, not a penalized state (2026-08-13, discussion)
+
+Distinct from the SNP/Sankoff calibration above (which conditions on
+*conserved-flank* comparability), this addresses the coarser presence/absence
+signal of a family itself, for genome-skim/reduced-representation inputs
+where per-genome coverage is often `<1x`, sometimes `<0.5x`. At that depth,
+non-detection of a locus is dominated by Poisson sampling failure, not by
+true loss — even for a single-copy locus, `P(non-detection | present)` is
+non-negligible. Treating "absent" as a real 0-state therefore risks
+clustering genomes by shared undersampling rather than shared ancestry.
+
+**Parsimony.** Loss and gain are the two directions of the same transition,
+so they cannot be freed asymmetrically without a biological justification for
+trusting one direction and not the other — none exists here. Freeing both
+directions to zero cost makes the character contribute nothing to any tree's
+score regardless of topology, which is operationally equivalent to just
+coding the state as ambiguous (`?`) rather than 0/1. `?` is the more honest
+encoding when downstream ancestral-state reconstruction is wanted: cost-zero
+Fitch/Sankoff still assigns internal states arbitrarily among equal-cost
+options, whereas `?` makes the "we don't know" explicit.
+
+**ML.** The correct analogue is not a tuned asymmetric loss/gain rate but
+literal missing-data coding at the tip: an ambiguous state (all-states tip
+likelihood vector, e.g. `(1,1)` for a 2-state character) so Felsenstein
+pruning marginalises over it and the character contributes likelihood 1
+(neutral) for that taxon — the same mechanism already used for the `N`
+IUPAC-ambiguous case in the 16-state Sankoff encoding (see "IQ-TREE
+custom-model format" above). No rate parameter to justify or estimate.
+
+**Open item, not yet decided.** No per-locus/per-genome confidence
+distinction is implemented: the current plan is to code *every* non-detected
+locus as missing/ambiguous, uniformly, without a depth-based threshold for
+"confidently absent." Deferred because at typical skim coverage the
+confidently-absent case is rare enough that a uniform treatment is
+defensible as a first pass. Known consequence to watch for: a genome with
+very low overall coverage ends up with a mostly-`?` row and constrains the
+tree weakly — will likely need a minimum-detected-loci-per-genome filter
+upstream (exclude or flag under-covered genomes) before this becomes a
+correctness problem rather than a power problem. Not designed yet.
+
+### `--free-loss` implemented (2026-08-13)
+
+`obikmer phylo --sankoff --free-loss` (with `--tnt`/`--phyg`/`--iqtree`)
+recodes `∅` (a family's non-detection in a genome) to `?` instead of the
+default ordinary, costed 16th state — the resolution of the discussion
+above. `?`, not `-`: `-` still carries gap/indel semantics in TNT/PhyG/
+IQ-TREE (see "`∅` stays an ordinary 16th state" above, and the reasoning
+that motivated it in the first place — the RAxML-era failure where `-`
+was silently swallowed as missing data was undesired back when `∅` was
+meant to be fully informative; `--free-loss` is the first case where that
+same tool behaviour is exactly what's wanted). `?` is the standard
+missing/ambiguous symbol these tools already recognise without needing to
+be declared in the custom alphabet, so parsimony treats it as
+"compatible with any state" (Sankoff/Fitch's own missing-data extension —
+no per-transition cost edit needed) and Felsenstein pruning marginalises
+it for IQ-TREE's ML.
+
+Implementation is a recoding at each export's existing `-`-normalisation
+boundary, not a change to matrix calibration: `write_sankoff_alignment_fasta`
+(`sankoff.rs`, feeds `--phyg` too via its `prefasta:`), `write_sankoff_tnt`
+(`tnt.rs`, `?` written directly, bypassing `TNT_STATE_SYMBOL` — there is no
+state index for it), and `compact_alphabet`/`write_iqtree_alignment`
+(`iqtree.rs`, `∅` excluded from the compact alphabet entirely rather than
+assigned a symbol). The calibrated cost matrix itself is unchanged — its
+`∅`-row/column simply becomes unused once no sequence contains that state.
+
+**Unverified, flagged rather than assumed** (this project's own standard for
+tool-specific claims — see the TNT/PhyG/IQ-TREE syntax facts above, all
+checked against the real binaries, not the manuals alone):
+- PhyG auto-adds its own `(n+1)`-th gap/indel row to the `tcm:` matrix
+  (`phyg.rs`); with `--free-loss` the reused `_sankoff.fasta` now contains
+  real `?` characters PhyG did not have to interpret before. Not confirmed
+  against the local PhyG binary that `?` is read as "any state" rather than
+  routed through that gap row, or otherwise mishandled.
+- IQ-TREE's exact `?`/missing-data semantics for `--seqtype MORPH` with a
+  custom-file model plus `+ASC` — assumed to marginalise via Felsenstein
+  pruning by the general convention, not yet re-verified against the local
+  `iqtree3` build the way the rest of the custom-model mechanism was.
+
+Both should be checked against a real run (small index) before `--free-loss`
+results are trusted for TNT/PhyG/IQ-TREE, the same way every other
+tool-specific behaviour in this file was established.
+
+### TNT confirmed (2026-08-13); IQ-TREE `+ASC` constant-column fix (2026-08-13)
+
+**TNT.** Real run, 20-genome benchmark index, `--free-loss --tnt`: `?`
+present for all 20 taxa in both `sankoff.fasta` and `sankoff.tnt`, loaded
+with no syntax error and no triangle-inequality warning, `mult` search
+completed, `sankoff.tre` holds 20 equally-parsimonious trees. Topology is
+exactly what the theory predicts: strain-level clades unaffected (the 4 *E.
+coli*, the *Klebsiella* trio, the *Salmonella* pairs — driven by real
+substitution signal, not gene-content) but resolution among the deeply
+divergent lineages (*Candidozyma*, *Saccharolobus*, *Wolbachia*,
+*Acidobacterium*, *Opitutus*, *Bacillus*/*Shouchella*) is weak and unstable
+across the 20 tied trees — the expected trade-off of discarding the
+gene-content/dropout signal that used to help place exactly those lineages.
+TNT's own handling of `?` — read as "compatible with any state" — no longer
+a flagged assumption.
+
+**IQ-TREE: `+ASC` broke on real data — non-informative columns survive
+`--free-loss`, distinct bug from the `--exclude-genome` one above.**
+`snp_pseudo_alignment`'s "variable family" test (`family_size() >= 2`) is a
+whole-annex property, blind to any single column's actual calls. Once
+non-detection is hidden as `?` (ignored for constancy) rather than counted
+as its own real state, a family that is genuinely variable *somewhere in the
+dataset* can still have only one distinct call among the genomes that
+actually carry it in one particular column, with the rest `?` — constant
+once missing data is excluded, which is exactly what `+ASC` forbids. Same
+underlying failure mode as `--exclude-genome`'s (documented above, "Two
+consistency bugs found and fixed post-implementation"), same remedy: rescan
+columns and drop the ones that are constant once `-` is ignored — but a
+different trigger (hiding cells vs. dropping whole rows), so a separate fix
+was needed rather than reusing `drop_excluded` directly. Implemented as
+`iqtree::drop_ascertainment_noninformative`, run only under `--free-loss`,
+only on IQ-TREE's own copy of the alignment (`--tnt`/`--phyg` have no
+no-invariant-site requirement and must not lose those columns). Not yet
+re-run against the local `iqtree3` binary to confirm `+ASC` now accepts the
+filtered alignment — next verification step, alongside the still-open PhyG
+`?`-vs-gap-row question above.
+
 ## References
 
 The Mash mutation-rate model this discussion contrasts with:
diff --git a/iqtree.model b/iqtree.model
deleted file mode 100644
index 09bd6ac5..00000000
--- a/iqtree.model
+++ /dev/null
@@ -1,16 +0,0 @@
-0.222641
-0.222347 0.005197
-0.206041 0.017442 0.019145
-0.222349 0.024185 0.003581 0.013346
-0.208691 0.017667 0.002921 0.000012 0.019168
-0.205784 0.013974 0.019121 0.000085 0.018901 0.000018
-0.027849 0.001121 0.001230 0.000109 0.001216 0.000109 0.000118
-0.222640 0.004745 0.023685 0.013831 0.005020 0.002986 0.013813 0.000889
-0.206337 0.017467 0.012967 0.000076 0.013365 0.000016 0.000059 0.000079 0.017590
-0.208662 0.003028 0.019388 0.000017 0.002764 0.000003 0.000018 0.000019 0.017788 0.000017
-0.027866 0.001122 0.001231 0.000109 0.000858 0.000016 0.000083 0.000009 0.001129 0.000100 0.000111
-0.206081 0.013994 0.012951 0.000059 0.018929 0.000017 0.000082 0.000085 0.017568 0.000078 0.000012 0.000076
-0.027872 0.001122 0.000833 0.000074 0.001217 0.000109 0.000080 0.000042 0.001130 0.000100 0.000017 0.000006 0.000108
-0.027846 0.000899 0.001230 0.000087 0.001216 0.000019 0.000118 0.000009 0.001129 0.000080 0.000111 0.000044 0.000108 0.000009
-0.009724 0.000172 0.000189 0.000044 0.000187 0.000044 0.000048 0.000047 0.000174 0.000041 0.000045 0.000043 0.000044 0.000043 0.000047
-0.904811 0.012806 0.013642 0.007640 0.013786 0.007933 0.004196 0.000140 0.012382 0.006685 0.007847 0.000195 0.007527 0.000202 0.000134 0.000076
diff --git a/sankoff_params.yaml b/sankoff_params.yaml
index e4a0075c..489cf29c 100644
--- a/sankoff_params.yaml
+++ b/sankoff_params.yaml
@@ -2,166 +2,166 @@ ratio_ceiling: 0.5
 cardinality_transitions:
 - from: 0
   to: 0
-  count: 117158166
-  probability: 0.8249649657257814
+  count: 37622567
+  probability: 0.7765461217831444
 - from: 0
   to: 1
-  count: 13707223
-  probability: 0.09651891232567299
+  count: 6977400
+  probability: 0.14401656617768033
 - from: 0
   to: 2
-  count: 10934100
-  probability: 0.07699206755884405
+  count: 3744558
+  probability: 0.0772893033240408
 - from: 0
   to: 3
-  count: 193315
-  probability: 0.0013612205430842902
+  count: 91083
+  probability: 0.0018799926759482985
 - from: 0
   to: 4
-  count: 23125
-  probability: 0.00016283384661730445
+  count: 12985
+  probability: 0.0002680160391861122
 - from: 1
   to: 0
-  count: 13707223
-  probability: 0.8980473700324103
+  count: 6977400
+  probability: 0.820630384894398
 - from: 1
   to: 1
-  count: 1043692
-  probability: 0.06837890181868832
+  count: 1018042
+  probability: 0.1197346000370715
 - from: 1
   to: 2
-  count: 507953
-  probability: 0.033279232106318904
+  count: 502624
+  probability: 0.05911493200578466
 - from: 1
   to: 3
-  count: 4270
-  probability: 0.0002797548613631216
+  count: 4197
+  probability: 0.000493620220340211
 - from: 1
   to: 4
   count: 225
-  probability: 0.000014741181219368235
+  probability: 0.000026462842405658202
 - from: 2
   to: 0
-  count: 10934100
-  probability: 0.9551033885158036
+  count: 3744558
+  probability: 0.8804244781723005
 - from: 2
   to: 1
-  count: 507953
-  probability: 0.04437014765794788
+  count: 502624
+  probability: 0.11817749195415704
 - from: 2
   to: 2
-  count: 5241
-  probability: 0.00045780602511512846
+  count: 5162
+  probability: 0.0012136949558066439
 - from: 2
   to: 3
-  count: 690
-  probability: 0.000060272115498843476
+  count: 688
+  probability: 0.0001617632951559417
 - from: 2
   to: 4
   count: 96
-  probability: 8.385685634621701e-6
+  probability: 0.00002257162257989884
 - from: 3
   to: 0
-  count: 193315
-  probability: 0.9743748708410829
+  count: 91083
+  probability: 0.9478728718311618
 - from: 3
   to: 1
-  count: 4270
-  probability: 0.021522285898618442
+  count: 4197
+  probability: 0.04367689297756317
 - from: 3
   to: 2
-  count: 690
-  probability: 0.0034778401100812
+  count: 688
+  probability: 0.007159805186696083
 - from: 3
   to: 3
   count: 98
-  probability: 0.0004939541025912429
+  probability: 0.0010198559713607792
 - from: 3
   to: 4
   count: 26
-  probability: 0.0001310490476262481
+  probability: 0.00027057403321816594
 - from: 4
   to: 0
-  count: 23125
-  probability: 0.9846291407647109
+  count: 12985
+  probability: 0.972950696838004
 - from: 4
   to: 1
   count: 225
-  probability: 0.009580175423656646
+  probability: 0.01685898396523303
 - from: 4
   to: 2
   count: 96
-  probability: 0.004087541514093502
+  probability: 0.0071931664918327585
 - from: 4
   to: 3
   count: 26
-  probability: 0.0011070424934003236
+  probability: 0.0019481492582047056
 - from: 4
   to: 4
   count: 14
-  probability: 0.0005960998041386358
+  probability: 0.0010490034467256107
 composition_transitions:
 - from: 'A'
   to: 'A'
-  count: 162260
-  probability: 0.47062167539692207
+  count: 157182
+  probability: 0.46648741052031767
 - from: 'A'
   to: 'C'
-  count: 27810
-  probability: 0.08066059899413536
+  count: 27305
+  probability: 0.08103624298111281
 - from: 'A'
   to: 'G'
-  count: 130153
-  probability: 0.3774979842101294
+  count: 128548
+  probability: 0.38150693875612857
 - from: 'A'
   to: 'T'
-  count: 24555
-  probability: 0.07121974139881315
+  count: 23913
+  probability: 0.07096940774244097
 - from: 'C'
   to: 'A'
-  count: 27810
-  probability: 0.07790832534920075
+  count: 27305
+  probability: 0.07823849488677553
 - from: 'C'
   to: 'C'
-  count: 184633
-  probability: 0.5172401234879174
+  count: 179118
+  probability: 0.5132365034656459
 - from: 'C'
   to: 'G'
-  count: 19637
-  probability: 0.05501207424963161
+  count: 19392
+  probability: 0.055564947549692406
 - from: 'C'
   to: 'T'
-  count: 124878
-  probability: 0.3498394769132503
+  count: 123182
+  probability: 0.3529600540978862
 - from: 'G'
   to: 'A'
-  count: 130153
-  probability: 0.36057158212891627
+  count: 128548
+  probability: 0.3637269077214298
 - from: 'G'
   to: 'C'
-  count: 19637
-  probability: 0.054401697680925745
+  count: 19392
+  probability: 0.05486971555009776
 - from: 'G'
   to: 'G'
-  count: 184557
-  probability: 0.5112906308956874
+  count: 179245
+  probability: 0.5071742039901647
 - from: 'G'
   to: 'T'
-  count: 26616
-  probability: 0.07373608929447062
+  count: 26234
+  probability: 0.07422917273830779
 - from: 'T'
   to: 'A'
-  count: 24555
-  probability: 0.07337692220342934
+  count: 23913
+  probability: 0.07307212790143376
 - from: 'T'
   to: 'C'
-  count: 124878
-  probability: 0.3731689387464813
+  count: 123182
+  probability: 0.3764132839524281
 - from: 'T'
   to: 'G'
-  count: 26616
-  probability: 0.07953574267426085
+  count: 26234
+  probability: 0.08016452153080807
 - from: 'T'
   to: 'T'
-  count: 158593
-  probability: 0.4739183963758285
+  count: 153923
+  probability: 0.4703500666153301
diff --git a/src/obikmer/src/cmd/phylo/args.rs b/src/obikmer/src/cmd/phylo/args.rs
new file mode 100644
index 00000000..deedb5bd
--- /dev/null
+++ b/src/obikmer/src/cmd/phylo/args.rs
@@ -0,0 +1,243 @@
+use std::path::PathBuf;
+
+use clap::Args;
+use obikindex::DistanceMetric;
+
+#[derive(clap::ValueEnum, Clone, Copy, Debug)]
+pub enum MetricArg {
+    Jaccard,
+    Mash,
+    Hamming,
+    BrayCurtis,
+    #[value(name = "relfreq-bray-curtis")]
+    RelfreqBrayCurtis,
+    Euclidean,
+    #[value(name = "relfreq-euclidean")]
+    RelfreqEuclidean,
+    Hellinger,
+    #[value(name = "hellinger-euclidean")]
+    HellingerEuclidean,
+}
+
+impl From<MetricArg> for DistanceMetric {
+    fn from(m: MetricArg) -> Self {
+        match m {
+            MetricArg::Jaccard            => DistanceMetric::Jaccard,
+            MetricArg::Mash               => DistanceMetric::Mash,
+            MetricArg::Hamming            => DistanceMetric::Hamming,
+            MetricArg::BrayCurtis         => DistanceMetric::BrayCurtis,
+            MetricArg::RelfreqBrayCurtis  => DistanceMetric::RelfreqBrayCurtis,
+            MetricArg::Euclidean          => DistanceMetric::Euclidean,
+            MetricArg::RelfreqEuclidean   => DistanceMetric::RelfreqEuclidean,
+            MetricArg::Hellinger          => DistanceMetric::Hellinger,
+            MetricArg::HellingerEuclidean => DistanceMetric::HellingerEuclidean,
+        }
+    }
+}
+
+#[derive(Args)]
+pub struct PhyloArgs {
+    /// Index directory
+    pub index: PathBuf,
+
+    /// Distance metric to compute
+    #[arg(long, value_enum, default_value = "jaccard")]
+    pub metric: MetricArg,
+
+    /// Minimum count to consider a kmer present when computing Jaccard on count indexes
+    #[arg(long, default_value = "1")]
+    pub presence_threshold: u32,
+
+    /// Also output the shared-kmer count matrix (CSV)
+    #[arg(long)]
+    pub shared_kmers: bool,
+
+    /// Compute and write a Neighbor-Joining tree (Newick)
+    #[arg(long)]
+    pub nj: bool,
+
+    /// Compute and write a UPGMA tree (Newick)
+    #[arg(long)]
+    pub upgma: bool,
+
+    /// Build the sibling-count/minorant annex on this (multi-genome) index
+    /// — see `docmd/theory/evolutionary_distances.md`, Step 2b. Construction
+    /// only; does not by itself compute or write any statistics.
+    #[arg(long)]
+    pub sibling_annex: bool,
+
+    /// Exclude a genome (by its exact label) from every computation below
+    /// that reads the sibling annex — `--raw-snp-distance`/`--raw-snp-counts`,
+    /// `--snp`, and `--sankoff` (and everything `--sankoff` implies: the
+    /// cardinality/composition transition models, the exported
+    /// matrix/alignment, `--tnt`/`--phyg`/`--iqtree`). Repeatable. Does
+    /// *not* affect the plain `--metric` distance matrix/NJ/UPGMA path (a
+    /// different, unrelated computation). Applied by zeroing the excluded
+    /// genome's row/column after `raw_snp_distance` runs (a pair with zero
+    /// counts is already skipped by `base_pair_tally`/`cardinality_tally`,
+    /// so this needs no change to the underlying traversal) and by
+    /// dropping its row from `snp_pseudo_alignment`'s output — the annex
+    /// is still built/scanned for the excluded genome too, just not used
+    /// afterward. For a genome with almost no informative sites shared
+    /// with anything else (see `docmd/theory/evolutionary_distances.md`,
+    /// the IQ-TREE/Mash rogue-taxon discussion), its presence can
+    /// otherwise silently bias the transition models.
+    #[arg(long = "exclude-genome", value_name = "LABEL")]
+    pub exclude_genome: Vec<String>,
+
+    /// Auto-exclude any genome whose mean shared-family count against every
+    /// other genome (same statistic as `--family-overlap`'s matrix, averaged
+    /// over each row excluding the diagonal) falls below this threshold —
+    /// same exclusion machinery as `--exclude-genome`, applied on top of it
+    /// rather than instead of it. Empirically, genomes below ~1000 shared
+    /// families on the 20-genome benchmark are exactly the ones that placed
+    /// themselves arbitrarily under `--tnt`/`--iqtree` (near-zero branch
+    /// lengths, grafted inside unrelated clades) — too little real
+    /// constraint on where they belong. See
+    /// `docmd/theory/evolutionary_distances.md`, "Locus dropout under
+    /// incomplete coverage".
+    #[arg(long, value_name = "N")]
+    pub min_shared_family: Option<f64>,
+
+    /// Tally the sibling-count distribution (CSV) of an already-built annex
+    /// (run with `--sibling-annex` first, in this invocation or an earlier
+    /// one). A separate, occasional diagnostic pass — not run every time the
+    /// annex itself is (re)built.
+    #[arg(long)]
+    pub sibling_stats: bool,
+
+    /// Compute the raw p-distance restricted to loci that are single-copy
+    /// in both genomes of each pair (an already-built sibling annex is
+    /// required — run with `--sibling-annex` first, in this invocation or
+    /// an earlier one). A quick way to test the central-position SNP
+    /// estimator against a real index; not the full `SnpTally` design.
+    #[arg(long)]
+    pub raw_snp_distance: bool,
+
+    /// Write the raw per-pair counts (`n_snp`, `n_shared`, `n_eligible`)
+    /// behind `--raw-snp-distance`'s ratio, one row per genome pair — a
+    /// diagnostic table, not a matrix. The ratio alone can't distinguish
+    /// "identical at every eligible locus" from "almost no eligible loci
+    /// at all" (e.g. `0.0` from 0/2 looks the same as `0.0` from 0/2000),
+    /// and that distinction matters a lot for genome pairs near the edge
+    /// of what central-position families can resolve (see
+    /// `docmd/theory/evolutionary_distances.md`, "Run 3" and the
+    /// IQ-TREE/Mash comparison). Same annex requirement as
+    /// `--raw-snp-distance`.
+    #[arg(long)]
+    pub raw_snp_counts: bool,
+
+    /// Write a SNP-only pseudo-alignment (FASTA, IUPAC-coded) from an
+    /// already-built sibling annex — one row per genome, one column per
+    /// variable family (monomorphic families skipped), no flanking
+    /// sequence. See `docmd/theory/evolutionary_distances.md`,
+    /// "Multi-genome framing: family as pseudo-alignment column".
+    #[arg(long)]
+    pub snp: bool,
+
+    /// Write an NxN CSV (`<prefix>_family_overlap.csv`) of, for each genome
+    /// pair, how many variable families (same set `--snp`'s pseudo-alignment
+    /// uses — `family_size() >= 2`) both genomes actually carry a call for
+    /// (neither is `∅`). A direct read of how much informative content two
+    /// genomes actually share at the family level — the diagnostic for why
+    /// a genome with little overlap with anything else (e.g. an
+    /// under-covered or very divergent one) ends up placed unstably by
+    /// `--tnt`/`--iqtree`: little-to-no shared, real data to constrain it.
+    /// Same annex requirement as `--snp`.
+    #[arg(long)]
+    pub family_overlap: bool,
+
+    /// Calibrate a 16-state Sankoff cost matrix and its matching
+    /// pseudo-alignment from an already-built sibling annex (run with
+    /// `--sibling-annex` first, in this invocation or an earlier one), for
+    /// use with TNT/PhyG. See `docmd/theory/evolutionary_distances.md`,
+    /// "Sankoff parsimony as the resolution of the 16-state model problem".
+    #[arg(long)]
+    pub sankoff: bool,
+
+    /// Recode a family's non-detection (`∅`, no member observed in a
+    /// genome) as TNT/PhyG/IQ-TREE's own missing-data symbol (`?`) in
+    /// `--sankoff`'s FASTA and every export built from it (`--tnt`,
+    /// `--phyg`, `--iqtree`), instead of an ordinary, costed 16th alphabet
+    /// state (the default). For genome-skim/reduced-representation inputs
+    /// (coverage often < 1x), non-detection is dominated by sampling
+    /// failure, not true loss — scoring it as a real state risks grouping
+    /// genomes by shared undersampling rather than shared ancestry. `?`
+    /// (not `-`) because `-` still carries gap/indel semantics in these
+    /// tools; a non-detected family is not an observed deletion. See
+    /// `docmd/theory/evolutionary_distances.md`, "Locus dropout under
+    /// incomplete coverage".
+    #[arg(long)]
+    pub free_loss: bool,
+
+    /// Exclude genome pairs whose raw SNP ratio exceeds this value from the
+    /// `p_hat` calibration pooled by `--sankoff` — a pair this close to
+    /// saturation carries no information about `p_hat` and would bias it
+    /// upward if pooled in (unlike a low eligible-loci count, which barely
+    /// moves the pooled estimate either way — see design doc).
+    #[arg(long, default_value = "0.5")]
+    pub sankoff_ratio_ceiling: f64,
+
+    /// Also write <prefix>_sankoff.tnt, a ready-to-run TNT script (`proc
+    /// <file>;`) for the same matrix/alignment `--sankoff` computes —
+    /// recoded to TNT's default xread alphabet (0-9A-F only; TNT rejects
+    /// the wider IUPAC set `--sankoff`'s own output uses unless `nstates
+    /// dna` is set, which imposes TNT's own incompatible DNA encoding
+    /// instead) with integer-scaled costs (TNT's smatrix/cost commands
+    /// reject decimals). Implies `--sankoff`.
+    #[arg(long)]
+    pub tnt: bool,
+
+    /// Also write <prefix>_sankoff.tcm and <prefix>_sankoff.pg, a
+    /// custom-alphabet cost matrix and a ready-to-run PhyG script (`read`/
+    /// `search`/`report`) for the same matrix/alignment `--sankoff`
+    /// computes. Reuses `--sankoff`'s own `_sankoff.fasta` directly — PhyG's
+    /// `tcm:` alphabet is read from the matrix file itself, so the IUPAC+`0`
+    /// alphabet needs no recoding here, unlike `--tnt`. Implies `--sankoff`.
+    #[arg(long)]
+    pub phyg: bool,
+
+    /// Also write <prefix>_iqtree.model and <prefix>_iqtree.fasta, a
+    /// custom-model file and a matching
+    /// recoded alignment for genuine maximum-likelihood inference with
+    /// IQ-TREE (`iqtree3 -s ... --seqtype MORPH -m ...+ASC`) — real branch
+    /// lengths, unlike `--tnt`/`--phyg`'s parsimony step counts. The model
+    /// is the reversible `Q(i,j) = R(i,j)·π_j` construction: `R`
+    /// (exchangeability, symmetric) recovered from the same calibrated
+    /// cost matrix `--sankoff` computes, `π` the real empirical state
+    /// frequencies counted from the alignment (not IQ-TREE's `+FO`/`+F` —
+    /// neither applies to a custom-file model, see
+    /// `docmd/theory/evolutionary_distances.md`). Only the states that
+    /// actually occur in this alignment are kept, compactly renumbered
+    /// (IQ-TREE infers its state count from the alignment itself, and a
+    /// gap in the numbering would silently misalign the model file).
+    /// Implies `--sankoff`.
+    #[arg(long)]
+    pub iqtree: bool,
+
+    /// Scale factor applied before rounding real-valued costs to the
+    /// integers both `--tnt`'s smatrix/cost commands and `--phyg`'s `tcm:`
+    /// matrix require. Keep this small: the total tree score is this scale
+    /// times the sum of per-character costs across every character (908k+
+    /// for a typical run here), and there are hints in TNT's own manual
+    /// that at least some of its internal accumulators are 32-bit — a large
+    /// scale risks a silent integer overflow (undetectable, not just a
+    /// crash) far more costly than the resolution a bigger factor would
+    /// buy. Shared between `--tnt` and `--phyg` rather than split into two
+    /// flags: both scale the same calibrated matrix for the same reason
+    /// (integer-only cost commands), and no PhyG-specific accumulator-width
+    /// constraint has actually been found to justify a different default.
+    #[arg(long, default_value = "100")]
+    pub sankoff_cost_scale: f64,
+
+    /// Output prefix: <prefix>_dist.csv, <prefix>_shared.csv,
+    /// <prefix>_siblings.csv, <prefix>_rawsnp.csv, <prefix>_rawsnp_counts.csv,
+    /// <prefix>_snp.fasta, <prefix>_family_overlap.csv,
+    /// <prefix>_sankoff_matrix.csv, <prefix>_sankoff_params.yaml,
+    /// <prefix>_sankoff.fasta, <prefix>_sankoff.tnt, <prefix>_sankoff.tcm,
+    /// <prefix>_sankoff.pg, <prefix>_iqtree.model, <prefix>_iqtree.fasta,
+    /// <prefix>_nj.nwk, <prefix>_upgma.nwk.
+    /// If omitted, the distance matrix is written to stdout.
+    #[arg(short, long)]
+    pub output: Option<PathBuf>,
+}
diff --git a/src/obikmer/src/cmd/phylo/family_overlap.rs b/src/obikmer/src/cmd/phylo/family_overlap.rs
new file mode 100644
index 00000000..fa01c8e2
--- /dev/null
+++ b/src/obikmer/src/cmd/phylo/family_overlap.rs
@@ -0,0 +1,97 @@
+use std::io::{BufWriter, Write};
+use std::path::PathBuf;
+
+use obikindex::{KmerIndex, SnpAlignment};
+use tracing::info;
+
+// ── Family overlap: shared-family counts and the `--min-shared-family` /
+// `--family-overlap` diagnostics built from them ────────────────────────────
+//
+// Same variable-family columns as `--snp`'s pseudo-alignment. Off-diagonal
+// `[i][j]`: number of columns where both genome `i` and genome `j` carry a
+// call (neither is `∅`) — how much informative family content two genomes
+// actually share, the direct diagnostic for the rogue-taxon placement seen
+// under `--free-loss` (a genome with little overlap with anything else has
+// almost nothing left to constrain it). Diagonal `[i][i]` kept, deliberately
+// not skipped: with `i == j` the condition "both non-`∅`" degenerates to
+// "genome `i` non-`∅`", i.e. the total number of variable families genome
+// `i` carries at all — a genome-level count worth having alongside the
+// pairwise ones, not a separate computation.
+
+/// `counts[i][j]` = number of variable-family columns where both genome `i`
+/// and genome `j` carry a call (neither is `∅`). Shared between
+/// `write_family_overlap_csv` and `--min-shared-family`'s auto-exclusion so
+/// both read off the same definition of "shared family".
+fn family_overlap_counts(alignment: &SnpAlignment) -> Vec<Vec<u64>> {
+    let n = alignment.sequences.len();
+    let mut counts = vec![vec![0u64; n]; n];
+    for i in 0..n {
+        for j in 0..n {
+            counts[i][j] = alignment.sequences[i].iter().zip(alignment.sequences[j].iter())
+                .filter(|&(&a, &b)| a != b'-' && b != b'-')
+                .count() as u64;
+        }
+    }
+    counts
+}
+
+/// Mean of row `i` in a `family_overlap_counts` matrix, excluding the
+/// diagonal — how much informative content genome `i` shares with the
+/// *average* other genome, the statistic `--min-shared-family` thresholds.
+fn mean_offdiag(counts: &[Vec<u64>], i: usize) -> f64 {
+    let n = counts.len();
+    let sum: u64 = (0..n).filter(|&j| j != i).map(|j| counts[i][j]).sum();
+    sum as f64 / (n - 1) as f64
+}
+
+pub(super) fn write_family_overlap_csv(alignment: &SnpAlignment, labels: &[String], output: &Option<PathBuf>) {
+    let path = output.as_ref()
+        .map(|p| format!("{}_family_overlap.csv", p.display()))
+        .unwrap_or_else(|| "family_overlap.csv".into());
+    let mut f = BufWriter::new(std::fs::File::create(&path).unwrap_or_else(|e| {
+        eprintln!("error creating {path}: {e}");
+        std::process::exit(1);
+    }));
+    let n = labels.len();
+    let counts = family_overlap_counts(alignment);
+    write!(f, "genome").unwrap();
+    for g in labels { write!(f, ",{g}").unwrap(); }
+    writeln!(f).unwrap();
+    for (i, gi) in labels.iter().enumerate() {
+        write!(f, "{gi}").unwrap();
+        for j in 0..n {
+            write!(f, ",{}", counts[i][j]).unwrap();
+        }
+        writeln!(f).unwrap();
+    }
+    info!("family overlap matrix → {path}");
+}
+
+/// Sets `mask[i] = true` for every genome whose mean shared-family count
+/// (`mean_offdiag`) falls below `threshold`, skipping genomes already
+/// excluded (`mask[i]` already `true`, e.g. via `--exclude-genome`). Builds
+/// its own `SnpAlignment` pass — same redundant-per-flag pattern already
+/// used throughout `run()` (`--snp`/`--sankoff`/`--family-overlap` each call
+/// `snp_pseudo_alignment` independently too).
+pub(super) fn apply_min_shared_family_exclusion(
+    idx: &KmerIndex,
+    labels: &[String],
+    threshold: f64,
+    mask: &mut [bool],
+) {
+    let alignment = idx.snp_pseudo_alignment().unwrap_or_else(|e| {
+        eprintln!("error computing SNP pseudo-alignment for --min-shared-family: {e}");
+        std::process::exit(1);
+    });
+    let counts = family_overlap_counts(&alignment);
+    for (i, label) in labels.iter().enumerate() {
+        if mask[i] {
+            continue; // already excluded via --exclude-genome
+        }
+        let mean = mean_offdiag(&counts, i);
+        if mean < threshold {
+            info!("--min-shared-family: excluding {label} (mean shared families = {mean:.1} < {threshold})");
+            mask[i] = true;
+        }
+    }
+}
diff --git a/src/obikmer/src/cmd/phylo/iqtree.rs b/src/obikmer/src/cmd/phylo/iqtree.rs
index 0a1ac655..cd906841 100644
--- a/src/obikmer/src/cmd/phylo/iqtree.rs
+++ b/src/obikmer/src/cmd/phylo/iqtree.rs
@@ -68,13 +68,59 @@ impl CompactAlphabet {
     }
 }
 
-fn compact_alphabet(alignment: &SnpAlignment) -> CompactAlphabet {
+/// Under `--free-loss`, non-detection (`-`) becomes IQ-TREE's own missing
+/// symbol (`?`) — ignored when IQ-TREE checks a site's constancy for
+/// `+ASC`. A family kept as "variable" by `snp_pseudo_alignment`
+/// (`family_size() >= 2`, a whole-annex property, oblivious to any one
+/// column's actual calls) can still turn constant *among the genomes that
+/// actually have data* once the non-detected ones are excluded from that
+/// check — the same failure mode as the `--exclude-genome`/`drop_excluded`
+/// fix in `mod.rs` (see `docmd/theory/evolutionary_distances.md`, "Two
+/// consistency bugs found and fixed post-implementation"), just triggered
+/// by hiding cells instead of dropping whole rows. Same remedy: rescan
+/// columns treating `-` as ignored, drop any where the remaining calls
+/// agree on a single state. Parsimony (`--tnt`/`--phyg`) has no
+/// no-invariant-site requirement, so this only runs on IQ-TREE's own copy
+/// of the alignment, never mutating the one the caller also hands to those
+/// two exports.
+fn drop_ascertainment_noninformative(alignment: &SnpAlignment) -> SnpAlignment {
+    let n_sites = alignment.sequences.first().map(|s| s.len()).unwrap_or(0);
+    let keep: Vec<bool> = (0..n_sites).map(|site| {
+        let mut first: Option<u8> = None;
+        for seq in &alignment.sequences {
+            let b = seq[site];
+            if b == b'-' {
+                continue;
+            }
+            match first {
+                None => first = Some(b),
+                Some(f) if f != b => return true,
+                _ => {}
+            }
+        }
+        false // all calls missing, or all calls agree — non-informative
+    }).collect();
+
+    let sequences = alignment.sequences.iter()
+        .map(|seq| seq.iter().zip(keep.iter()).filter(|&(_, &k)| k).map(|(&b, _)| b).collect())
+        .collect();
+    SnpAlignment { sequences }
+}
+
+fn compact_alphabet(alignment: &SnpAlignment, free_loss: bool) -> CompactAlphabet {
     let iupac_to_state = state_index_table();
 
     let mut occurs = [false; 16];
     let mut counts = [0u64; 16];
     for seq in &alignment.sequences {
         for &b in seq {
+            if free_loss && b == b'-' {
+                // `?`: IQ-TREE's own missing-data symbol for `--seqtype
+                // MORPH`, marginalised by Felsenstein pruning — not a
+                // numbered state, so excluded from `occurs`/`counts` and
+                // from the compact alphabet built below.
+                continue;
+            }
             let b = if b == b'-' { b'0' } else { b };
             let state = iupac_to_state[b as usize] as usize;
             occurs[state] = true;
@@ -133,6 +179,7 @@ fn write_iqtree_alignment(
     labels: &[String],
     alphabet: &CompactAlphabet,
     output: &Option<PathBuf>,
+    free_loss: bool,
 ) -> (String, usize) {
     let iupac_to_state = state_index_table();
 
@@ -146,6 +193,9 @@ fn write_iqtree_alignment(
     let n_sites = alignment.sequences.first().map(|s| s.len()).unwrap_or(0);
     for (label, seq) in labels.iter().zip(alignment.sequences.iter()) {
         let recoded: Vec<u8> = seq.iter().map(|&b| {
+            if free_loss && b == b'-' {
+                return b'?';
+            }
             let b = if b == b'-' { b'0' } else { b };
             let old = iupac_to_state[b as usize] as usize;
             let compact = alphabet.old_to_compact[old]
@@ -165,10 +215,27 @@ pub(super) fn write_iqtree(
     alignment: &SnpAlignment,
     labels: &[String],
     output: &Option<PathBuf>,
+    free_loss: bool,
 ) {
-    let alphabet = compact_alphabet(alignment);
+    let filtered;
+    let alignment = if free_loss {
+        let before = alignment.sequences.first().map(|s| s.len()).unwrap_or(0);
+        filtered = drop_ascertainment_noninformative(alignment);
+        let after = filtered.sequences.first().map(|s| s.len()).unwrap_or(0);
+        if after != before {
+            info!(
+                "--free-loss: {before} → {after} sites (dropped columns non-informative once `-` \
+                 is treated as missing — required for +ASC)"
+            );
+        }
+        &filtered
+    } else {
+        alignment
+    };
+
+    let alphabet = compact_alphabet(alignment, free_loss);
     let model_path = write_iqtree_model(matrix, &alphabet, output);
-    let (fasta_path, n_sites) = write_iqtree_alignment(alignment, labels, &alphabet, output);
+    let (fasta_path, n_sites) = write_iqtree_alignment(alignment, labels, &alphabet, output, free_loss);
 
     let prefix_name = output.as_ref()
         .and_then(|p| p.file_name())
diff --git a/src/obikmer/src/cmd/phylo/mod.rs b/src/obikmer/src/cmd/phylo/mod.rs
index a25f7a39..1f08cdc5 100644
--- a/src/obikmer/src/cmd/phylo/mod.rs
+++ b/src/obikmer/src/cmd/phylo/mod.rs
@@ -1,225 +1,29 @@
+mod args;
+mod family_overlap;
 mod iqtree;
+mod outputs;
 mod phyg;
 mod sankoff;
 mod tnt;
 
 use std::io::{self, BufWriter, Write};
-use std::path::PathBuf;
 
-use clap::Args;
 use kodama::{Method, linkage};
-use obifastwrite::{JsonVal, write_record};
 use obikindex::{
-    DistanceMetric, KmerIndex, RawSnpDistanceOutput,
-    SiblingAnnexStats, SnpAlignment,
+    KmerIndex, RawSnpDistanceOutput, SnpAlignment,
     cardinality_transition_probs, composition_transition_probs, pairwise_cost_matrix,
 };
 use speedytree::{DistanceMatrix, Hybrid, NeighborJoiningSolver, to_newick};
 use tracing::info;
 
+pub use args::PhyloArgs;
+use family_overlap::{apply_min_shared_family_exclusion, write_family_overlap_csv};
 use iqtree::write_iqtree;
+use outputs::{write_raw_snp_counts_csv, write_raw_snp_distance_csv, write_sibling_stats_csv, write_snp_fasta, upgma_to_newick};
 use phyg::write_sankoff_phyg;
 use sankoff::{write_sankoff_alignment_fasta, write_sankoff_matrix_csv, write_sankoff_params};
 use tnt::write_sankoff_tnt;
 
-#[derive(clap::ValueEnum, Clone, Copy, Debug)]
-pub enum MetricArg {
-    Jaccard,
-    Mash,
-    Hamming,
-    BrayCurtis,
-    #[value(name = "relfreq-bray-curtis")]
-    RelfreqBrayCurtis,
-    Euclidean,
-    #[value(name = "relfreq-euclidean")]
-    RelfreqEuclidean,
-    Hellinger,
-    #[value(name = "hellinger-euclidean")]
-    HellingerEuclidean,
-}
-
-impl From<MetricArg> for DistanceMetric {
-    fn from(m: MetricArg) -> Self {
-        match m {
-            MetricArg::Jaccard            => DistanceMetric::Jaccard,
-            MetricArg::Mash               => DistanceMetric::Mash,
-            MetricArg::Hamming            => DistanceMetric::Hamming,
-            MetricArg::BrayCurtis         => DistanceMetric::BrayCurtis,
-            MetricArg::RelfreqBrayCurtis  => DistanceMetric::RelfreqBrayCurtis,
-            MetricArg::Euclidean          => DistanceMetric::Euclidean,
-            MetricArg::RelfreqEuclidean   => DistanceMetric::RelfreqEuclidean,
-            MetricArg::Hellinger          => DistanceMetric::Hellinger,
-            MetricArg::HellingerEuclidean => DistanceMetric::HellingerEuclidean,
-        }
-    }
-}
-
-#[derive(Args)]
-pub struct PhyloArgs {
-    /// Index directory
-    pub index: PathBuf,
-
-    /// Distance metric to compute
-    #[arg(long, value_enum, default_value = "jaccard")]
-    pub metric: MetricArg,
-
-    /// Minimum count to consider a kmer present when computing Jaccard on count indexes
-    #[arg(long, default_value = "1")]
-    pub presence_threshold: u32,
-
-    /// Also output the shared-kmer count matrix (CSV)
-    #[arg(long)]
-    pub shared_kmers: bool,
-
-    /// Compute and write a Neighbor-Joining tree (Newick)
-    #[arg(long)]
-    pub nj: bool,
-
-    /// Compute and write a UPGMA tree (Newick)
-    #[arg(long)]
-    pub upgma: bool,
-
-    /// Build the sibling-count/minorant annex on this (multi-genome) index
-    /// — see `docmd/theory/evolutionary_distances.md`, Step 2b. Construction
-    /// only; does not by itself compute or write any statistics.
-    #[arg(long)]
-    pub sibling_annex: bool,
-
-    /// Exclude a genome (by its exact label) from every computation below
-    /// that reads the sibling annex — `--raw-snp-distance`/`--raw-snp-counts`,
-    /// `--snp`, and `--sankoff` (and everything `--sankoff` implies: the
-    /// cardinality/composition transition models, the exported
-    /// matrix/alignment, `--tnt`/`--phyg`/`--iqtree`). Repeatable. Does
-    /// *not* affect the plain `--metric` distance matrix/NJ/UPGMA path (a
-    /// different, unrelated computation). Applied by zeroing the excluded
-    /// genome's row/column after `raw_snp_distance` runs (a pair with zero
-    /// counts is already skipped by `base_pair_tally`/`cardinality_tally`,
-    /// so this needs no change to the underlying traversal) and by
-    /// dropping its row from `snp_pseudo_alignment`'s output — the annex
-    /// is still built/scanned for the excluded genome too, just not used
-    /// afterward. For a genome with almost no informative sites shared
-    /// with anything else (see `docmd/theory/evolutionary_distances.md`,
-    /// the IQ-TREE/Mash rogue-taxon discussion), its presence can
-    /// otherwise silently bias the transition models.
-    #[arg(long = "exclude-genome", value_name = "LABEL")]
-    pub exclude_genome: Vec<String>,
-
-    /// Tally the sibling-count distribution (CSV) of an already-built annex
-    /// (run with `--sibling-annex` first, in this invocation or an earlier
-    /// one). A separate, occasional diagnostic pass — not run every time the
-    /// annex itself is (re)built.
-    #[arg(long)]
-    pub sibling_stats: bool,
-
-    /// Compute the raw p-distance restricted to loci that are single-copy
-    /// in both genomes of each pair (an already-built sibling annex is
-    /// required — run with `--sibling-annex` first, in this invocation or
-    /// an earlier one). A quick way to test the central-position SNP
-    /// estimator against a real index; not the full `SnpTally` design.
-    #[arg(long)]
-    pub raw_snp_distance: bool,
-
-    /// Write the raw per-pair counts (`n_snp`, `n_shared`, `n_eligible`)
-    /// behind `--raw-snp-distance`'s ratio, one row per genome pair — a
-    /// diagnostic table, not a matrix. The ratio alone can't distinguish
-    /// "identical at every eligible locus" from "almost no eligible loci
-    /// at all" (e.g. `0.0` from 0/2 looks the same as `0.0` from 0/2000),
-    /// and that distinction matters a lot for genome pairs near the edge
-    /// of what central-position families can resolve (see
-    /// `docmd/theory/evolutionary_distances.md`, "Run 3" and the
-    /// IQ-TREE/Mash comparison). Same annex requirement as
-    /// `--raw-snp-distance`.
-    #[arg(long)]
-    pub raw_snp_counts: bool,
-
-    /// Write a SNP-only pseudo-alignment (FASTA, IUPAC-coded) from an
-    /// already-built sibling annex — one row per genome, one column per
-    /// variable family (monomorphic families skipped), no flanking
-    /// sequence. See `docmd/theory/evolutionary_distances.md`,
-    /// "Multi-genome framing: family as pseudo-alignment column".
-    #[arg(long)]
-    pub snp: bool,
-
-    /// Calibrate a 16-state Sankoff cost matrix and its matching
-    /// pseudo-alignment from an already-built sibling annex (run with
-    /// `--sibling-annex` first, in this invocation or an earlier one), for
-    /// use with TNT/PhyG. See `docmd/theory/evolutionary_distances.md`,
-    /// "Sankoff parsimony as the resolution of the 16-state model problem".
-    #[arg(long)]
-    pub sankoff: bool,
-
-    /// Exclude genome pairs whose raw SNP ratio exceeds this value from the
-    /// `p_hat` calibration pooled by `--sankoff` — a pair this close to
-    /// saturation carries no information about `p_hat` and would bias it
-    /// upward if pooled in (unlike a low eligible-loci count, which barely
-    /// moves the pooled estimate either way — see design doc).
-    #[arg(long, default_value = "0.5")]
-    pub sankoff_ratio_ceiling: f64,
-
-    /// Also write <prefix>_sankoff.tnt, a ready-to-run TNT script (`proc
-    /// <file>;`) for the same matrix/alignment `--sankoff` computes —
-    /// recoded to TNT's default xread alphabet (0-9A-F only; TNT rejects
-    /// the wider IUPAC set `--sankoff`'s own output uses unless `nstates
-    /// dna` is set, which imposes TNT's own incompatible DNA encoding
-    /// instead) with integer-scaled costs (TNT's smatrix/cost commands
-    /// reject decimals). Implies `--sankoff`.
-    #[arg(long)]
-    pub tnt: bool,
-
-    /// Also write <prefix>_sankoff.tcm and <prefix>_sankoff.pg, a
-    /// custom-alphabet cost matrix and a ready-to-run PhyG script (`read`/
-    /// `search`/`report`) for the same matrix/alignment `--sankoff`
-    /// computes. Reuses `--sankoff`'s own `_sankoff.fasta` directly — PhyG's
-    /// `tcm:` alphabet is read from the matrix file itself, so the IUPAC+`0`
-    /// alphabet needs no recoding here, unlike `--tnt`. Implies `--sankoff`.
-    #[arg(long)]
-    pub phyg: bool,
-
-    /// Also write <prefix>_iqtree.model and <prefix>_iqtree.fasta, a
-    /// custom-model file and a matching
-    /// recoded alignment for genuine maximum-likelihood inference with
-    /// IQ-TREE (`iqtree3 -s ... --seqtype MORPH -m ...+ASC`) — real branch
-    /// lengths, unlike `--tnt`/`--phyg`'s parsimony step counts. The model
-    /// is the reversible `Q(i,j) = R(i,j)·π_j` construction: `R`
-    /// (exchangeability, symmetric) recovered from the same calibrated
-    /// cost matrix `--sankoff` computes, `π` the real empirical state
-    /// frequencies counted from the alignment (not IQ-TREE's `+FO`/`+F` —
-    /// neither applies to a custom-file model, see
-    /// `docmd/theory/evolutionary_distances.md`). Only the states that
-    /// actually occur in this alignment are kept, compactly renumbered
-    /// (IQ-TREE infers its state count from the alignment itself, and a
-    /// gap in the numbering would silently misalign the model file).
-    /// Implies `--sankoff`.
-    #[arg(long)]
-    pub iqtree: bool,
-
-    /// Scale factor applied before rounding real-valued costs to the
-    /// integers both `--tnt`'s smatrix/cost commands and `--phyg`'s `tcm:`
-    /// matrix require. Keep this small: the total tree score is this scale
-    /// times the sum of per-character costs across every character (908k+
-    /// for a typical run here), and there are hints in TNT's own manual
-    /// that at least some of its internal accumulators are 32-bit — a large
-    /// scale risks a silent integer overflow (undetectable, not just a
-    /// crash) far more costly than the resolution a bigger factor would
-    /// buy. Shared between `--tnt` and `--phyg` rather than split into two
-    /// flags: both scale the same calibrated matrix for the same reason
-    /// (integer-only cost commands), and no PhyG-specific accumulator-width
-    /// constraint has actually been found to justify a different default.
-    #[arg(long, default_value = "100")]
-    pub sankoff_cost_scale: f64,
-
-    /// Output prefix: <prefix>_dist.csv, <prefix>_shared.csv,
-    /// <prefix>_siblings.csv, <prefix>_rawsnp.csv, <prefix>_rawsnp_counts.csv,
-    /// <prefix>_snp.fasta,
-    /// <prefix>_sankoff_matrix.csv, <prefix>_sankoff_params.yaml,
-    /// <prefix>_sankoff.fasta, <prefix>_sankoff.tnt, <prefix>_sankoff.tcm,
-    /// <prefix>_sankoff.pg, <prefix>_iqtree.model, <prefix>_iqtree.fasta,
-    /// <prefix>_nj.nwk, <prefix>_upgma.nwk.
-    /// If omitted, the distance matrix is written to stdout.
-    #[arg(short, long)]
-    pub output: Option<PathBuf>,
-}
-
 pub fn run(args: PhyloArgs) {
     let idx = KmerIndex::open(&args.index).unwrap_or_else(|e| {
         eprintln!("error opening index: {e}");
@@ -250,6 +54,9 @@ pub fn run(args: PhyloArgs) {
                 }
             }
         }
+        if let Some(threshold) = args.min_shared_family {
+            apply_min_shared_family_exclusion(&idx, &labels, threshold, &mut mask);
+        }
         mask
     };
     let zero_excluded_pairs = |result: &mut RawSnpDistanceOutput| {
@@ -352,6 +159,14 @@ pub fn run(args: PhyloArgs) {
         let (alignment, kept_labels) = drop_excluded(alignment);
         write_snp_fasta(&alignment, &kept_labels, &args.output);
     }
+    if args.family_overlap {
+        let alignment = idx.snp_pseudo_alignment().unwrap_or_else(|e| {
+            eprintln!("error computing SNP pseudo-alignment: {e}");
+            std::process::exit(1);
+        });
+        let (alignment, kept_labels) = drop_excluded(alignment);
+        write_family_overlap_csv(&alignment, &kept_labels, &args.output);
+    }
     if args.sankoff || args.tnt || args.phyg || args.iqtree {
         let mut raw = idx.raw_snp_distance().unwrap_or_else(|e| {
             eprintln!("error computing raw SNP distance: {e}");
@@ -378,16 +193,16 @@ pub fn run(args: PhyloArgs) {
             std::process::exit(1);
         });
         let (alignment, kept_labels) = drop_excluded(alignment);
-        write_sankoff_alignment_fasta(&alignment, &kept_labels, &args.output);
+        write_sankoff_alignment_fasta(&alignment, &kept_labels, &args.output, args.free_loss);
 
         if args.tnt {
-            write_sankoff_tnt(&matrix, &alignment, &kept_labels, &args.output, args.sankoff_cost_scale);
+            write_sankoff_tnt(&matrix, &alignment, &kept_labels, &args.output, args.sankoff_cost_scale, args.free_loss);
         }
         if args.phyg {
             write_sankoff_phyg(&matrix, &args.output, args.sankoff_cost_scale);
         }
         if args.iqtree {
-            write_iqtree(&matrix, &alignment, &kept_labels, &args.output);
+            write_iqtree(&matrix, &alignment, &kept_labels, &args.output, args.free_loss);
         }
     }
 
@@ -403,6 +218,7 @@ pub fn run(args: PhyloArgs) {
         || args.raw_snp_distance
         || args.raw_snp_counts
         || args.snp
+        || args.family_overlap
         || args.sankoff
         || args.tnt
         || args.phyg
@@ -521,165 +337,3 @@ pub fn run(args: PhyloArgs) {
         info!("UPGMA tree → {path}");
     }
 }
-
-// ── Family-size distribution → CSV ──────────────────────────────────────────
-//
-// Each row is a family (the up-to-4 k-mers sharing flanks, differing only at
-// the centre), counted once — at its minorant — regardless of how many of
-// its members are observed. Family size 1..4 (not "sibling count" 0..3):
-// see `docmd/theory/evolutionary_distances.md`, "Definitions".
-
-fn write_sibling_stats_csv(stats: &SiblingAnnexStats, labels: &[String], output: &Option<PathBuf>) {
-    // One row per genome (4 columns, family size 1-4: number of families of
-    // that size for which the genome carries at least one member), plus a
-    // `global` row — the actual deduplicated family-size histogram
-    // (`stats.counts`), NOT a sum of the per-genome columns (a family shared
-    // by several genomes would otherwise be counted once per genome it
-    // appears in, inflating the total beyond the real family count).
-    let path = output.as_ref()
-        .map(|p| format!("{}_siblings.csv", p.display()))
-        .unwrap_or_else(|| "siblings.csv".into());
-    let mut f = BufWriter::new(std::fs::File::create(&path).unwrap_or_else(|e| {
-        eprintln!("error creating {path}: {e}");
-        std::process::exit(1);
-    }));
-    writeln!(f, "genome,1,2,3,4").unwrap();
-    for (label, counts) in labels.iter().zip(stats.per_genome.iter()) {
-        writeln!(f, "{label},{},{},{},{}", counts[0], counts[1], counts[2], counts[3]).unwrap();
-    }
-    writeln!(
-        f, "global,{},{},{},{}",
-        stats.counts[0], stats.counts[1], stats.counts[2], stats.counts[3],
-    ).unwrap();
-    let total: u64 = stats.counts.iter().sum();
-    info!("family-size distribution → {path} (total {total} famil{})",
-        if total == 1 { "y" } else { "ies" });
-}
-
-// ── Raw single-copy SNP distance → CSV ──────────────────────────────────────
-//
-// p_hat[i,j] = snp[i,j] / (snp[i,j] + shared[i,j]) over loci single-copy in
-// both i and j — see `RawSnpDistanceOutput` / `KmerIndex::raw_snp_distance`.
-// A single file: the distance matrix, with an eligible-loci count alongside
-// each value so a 0/0 pair (no eligible locus at all) is distinguishable
-// from a genuinely identical pair.
-
-fn write_raw_snp_distance_csv(result: &RawSnpDistanceOutput, labels: &[String], output: &Option<PathBuf>) {
-    let path = output.as_ref()
-        .map(|p| format!("{}_rawsnp.csv", p.display()))
-        .unwrap_or_else(|| "rawsnp.csv".into());
-    let mut f = BufWriter::new(std::fs::File::create(&path).unwrap_or_else(|e| {
-        eprintln!("error creating {path}: {e}");
-        std::process::exit(1);
-    }));
-    let n = labels.len();
-    write!(f, "genome").unwrap();
-    for g in labels { write!(f, ",{g}").unwrap(); }
-    writeln!(f).unwrap();
-    for (i, g) in labels.iter().enumerate() {
-        write!(f, "{g}").unwrap();
-        for j in 0..n {
-            let snp = result.snp[[i, j]];
-            let shared = result.shared[[i, j]];
-            let eligible = snp + shared;
-            if eligible == 0 {
-                write!(f, ",NA").unwrap();
-            } else {
-                write!(f, ",{:.6}", snp as f64 / eligible as f64).unwrap();
-            }
-        }
-        writeln!(f).unwrap();
-    }
-    info!("raw single-copy SNP distance matrix → {path}");
-}
-
-// ── Raw single-copy SNP distance → per-pair diagnostic counts ──────────────
-//
-// A pair table (one row per unordered genome pair), not a matrix: the ratio
-// alone can't distinguish "identical across every eligible locus" from
-// "almost no eligible locus at all" — both can read `0.0`/`NA` in
-// `--raw-snp-distance`'s output. Distinguishing them matters most exactly
-// where it's easy to miss: genome pairs near the edge of what
-// central-position families can resolve at all (deep cross-lineage splits,
-// see `docmd/theory/evolutionary_distances.md`, "Run 3" and the later
-// IQ-TREE/Mash comparison — a `ratio=0.0` backed by 2 eligible loci is not
-// the same claim as one backed by 2000).
-
-fn write_raw_snp_counts_csv(result: &RawSnpDistanceOutput, labels: &[String], output: &Option<PathBuf>) {
-    let path = output.as_ref()
-        .map(|p| format!("{}_rawsnp_counts.csv", p.display()))
-        .unwrap_or_else(|| "rawsnp_counts.csv".into());
-    let mut f = BufWriter::new(std::fs::File::create(&path).unwrap_or_else(|e| {
-        eprintln!("error creating {path}: {e}");
-        std::process::exit(1);
-    }));
-    let n = labels.len();
-    writeln!(f, "genome_a,genome_b,n_snp,n_shared,n_eligible,ratio").unwrap();
-    for i in 0..n {
-        for j in (i + 1)..n {
-            let snp = result.snp[[i, j]];
-            let shared = result.shared[[i, j]];
-            let eligible = snp + shared;
-            write!(f, "{},{},{snp},{shared},{eligible}", labels[i], labels[j]).unwrap();
-            if eligible == 0 {
-                writeln!(f, ",NA").unwrap();
-            } else {
-                writeln!(f, ",{:.6}", snp as f64 / eligible as f64).unwrap();
-            }
-        }
-    }
-    info!("raw single-copy SNP distance counts (diagnostic) → {path}");
-}
-
-// ── SNP-only pseudo-alignment → FASTA ───────────────────────────────────────
-//
-// One record per genome, IUPAC-coded, no flanking sequence — see
-// `SnpAlignment` / `KmerIndex::snp_pseudo_alignment`. Uses the project's
-// existing FASTA writer (`obifastwrite::write_record`) rather than
-// hand-rolling one.
-
-fn write_snp_fasta(alignment: &SnpAlignment, labels: &[String], output: &Option<PathBuf>) {
-    let path = output.as_ref()
-        .map(|p| format!("{}_snp.fasta", p.display()))
-        .unwrap_or_else(|| "snp.fasta".into());
-    let mut f = BufWriter::new(std::fs::File::create(&path).unwrap_or_else(|e| {
-        eprintln!("error creating {path}: {e}");
-        std::process::exit(1);
-    }));
-    let n_sites = alignment.sequences.first().map(|s| s.len()).unwrap_or(0);
-    for (label, seq) in labels.iter().zip(alignment.sequences.iter()) {
-        write_record(seq, label, &[("n_sites", JsonVal::Num(n_sites as u64))], &mut f).unwrap_or_else(|e| {
-            eprintln!("error writing {path}: {e}");
-            std::process::exit(1);
-        });
-    }
-    info!("SNP pseudo-alignment → {path} ({n_sites} site{})",
-        if n_sites == 1 { "" } else { "s" });
-}
-
-// ── UPGMA Newick from kodama dendrogram ───────────────────────────────────────
-
-fn upgma_to_newick(dendro: &kodama::Dendrogram<f64>, names: &[String]) -> String {
-    let n = names.len();
-    // node_labels[i]: Newick subtree string for node i (leaves 0..n, internals n..)
-    let mut labels: Vec<String> = names.to_vec();
-    // height of each node: leaves = 0, internal = dissimilarity/2
-    let mut heights: Vec<f64> = vec![0.0; 2 * n - 1];
-
-    for (k, step) in dendro.steps().iter().enumerate() {
-        let new_node = n + k;
-        let h = step.dissimilarity / 2.0;
-        heights[new_node] = h;
-        let c1 = step.cluster1;
-        let c2 = step.cluster2;
-        let bl1 = (h - heights[c1]).max(0.0);
-        let bl2 = (h - heights[c2]).max(0.0);
-        labels.push(format!(
-            "({label1}:{bl1:.6},{label2}:{bl2:.6})",
-            label1 = labels[c1],
-            label2 = labels[c2],
-        ));
-    }
-
-    format!("{};", labels.last().unwrap())
-}
diff --git a/src/obikmer/src/cmd/phylo/outputs.rs b/src/obikmer/src/cmd/phylo/outputs.rs
new file mode 100644
index 00000000..97b548fd
--- /dev/null
+++ b/src/obikmer/src/cmd/phylo/outputs.rs
@@ -0,0 +1,168 @@
+use std::io::{BufWriter, Write};
+use std::path::PathBuf;
+
+use obifastwrite::{JsonVal, write_record};
+use obikindex::{RawSnpDistanceOutput, SiblingAnnexStats, SnpAlignment};
+use tracing::info;
+
+// ── Family-size distribution → CSV ──────────────────────────────────────────
+//
+// Each row is a family (the up-to-4 k-mers sharing flanks, differing only at
+// the centre), counted once — at its minorant — regardless of how many of
+// its members are observed. Family size 1..4 (not "sibling count" 0..3):
+// see `docmd/theory/evolutionary_distances.md`, "Definitions".
+
+pub(super) fn write_sibling_stats_csv(stats: &SiblingAnnexStats, labels: &[String], output: &Option<PathBuf>) {
+    // One row per genome (4 columns, family size 1-4: number of families of
+    // that size for which the genome carries at least one member), plus a
+    // `global` row — the actual deduplicated family-size histogram
+    // (`stats.counts`), NOT a sum of the per-genome columns (a family shared
+    // by several genomes would otherwise be counted once per genome it
+    // appears in, inflating the total beyond the real family count).
+    let path = output.as_ref()
+        .map(|p| format!("{}_siblings.csv", p.display()))
+        .unwrap_or_else(|| "siblings.csv".into());
+    let mut f = BufWriter::new(std::fs::File::create(&path).unwrap_or_else(|e| {
+        eprintln!("error creating {path}: {e}");
+        std::process::exit(1);
+    }));
+    writeln!(f, "genome,1,2,3,4").unwrap();
+    for (label, counts) in labels.iter().zip(stats.per_genome.iter()) {
+        writeln!(f, "{label},{},{},{},{}", counts[0], counts[1], counts[2], counts[3]).unwrap();
+    }
+    writeln!(
+        f, "global,{},{},{},{}",
+        stats.counts[0], stats.counts[1], stats.counts[2], stats.counts[3],
+    ).unwrap();
+    let total: u64 = stats.counts.iter().sum();
+    info!("family-size distribution → {path} (total {total} famil{})",
+        if total == 1 { "y" } else { "ies" });
+}
+
+// ── Raw single-copy SNP distance → CSV ──────────────────────────────────────
+//
+// p_hat[i,j] = snp[i,j] / (snp[i,j] + shared[i,j]) over loci single-copy in
+// both i and j — see `RawSnpDistanceOutput` / `KmerIndex::raw_snp_distance`.
+// A single file: the distance matrix, with an eligible-loci count alongside
+// each value so a 0/0 pair (no eligible locus at all) is distinguishable
+// from a genuinely identical pair.
+
+pub(super) fn write_raw_snp_distance_csv(result: &RawSnpDistanceOutput, labels: &[String], output: &Option<PathBuf>) {
+    let path = output.as_ref()
+        .map(|p| format!("{}_rawsnp.csv", p.display()))
+        .unwrap_or_else(|| "rawsnp.csv".into());
+    let mut f = BufWriter::new(std::fs::File::create(&path).unwrap_or_else(|e| {
+        eprintln!("error creating {path}: {e}");
+        std::process::exit(1);
+    }));
+    let n = labels.len();
+    write!(f, "genome").unwrap();
+    for g in labels { write!(f, ",{g}").unwrap(); }
+    writeln!(f).unwrap();
+    for (i, g) in labels.iter().enumerate() {
+        write!(f, "{g}").unwrap();
+        for j in 0..n {
+            let snp = result.snp[[i, j]];
+            let shared = result.shared[[i, j]];
+            let eligible = snp + shared;
+            if eligible == 0 {
+                write!(f, ",NA").unwrap();
+            } else {
+                write!(f, ",{:.6}", snp as f64 / eligible as f64).unwrap();
+            }
+        }
+        writeln!(f).unwrap();
+    }
+    info!("raw single-copy SNP distance matrix → {path}");
+}
+
+// ── Raw single-copy SNP distance → per-pair diagnostic counts ──────────────
+//
+// A pair table (one row per unordered genome pair), not a matrix: the ratio
+// alone can't distinguish "identical across every eligible locus" from
+// "almost no eligible locus at all" — both can read `0.0`/`NA` in
+// `--raw-snp-distance`'s output. Distinguishing them matters most exactly
+// where it's easy to miss: genome pairs near the edge of what
+// central-position families can resolve at all (deep cross-lineage splits,
+// see `docmd/theory/evolutionary_distances.md`, "Run 3" and the later
+// IQ-TREE/Mash comparison — a `ratio=0.0` backed by 2 eligible loci is not
+// the same claim as one backed by 2000).
+
+pub(super) fn write_raw_snp_counts_csv(result: &RawSnpDistanceOutput, labels: &[String], output: &Option<PathBuf>) {
+    let path = output.as_ref()
+        .map(|p| format!("{}_rawsnp_counts.csv", p.display()))
+        .unwrap_or_else(|| "rawsnp_counts.csv".into());
+    let mut f = BufWriter::new(std::fs::File::create(&path).unwrap_or_else(|e| {
+        eprintln!("error creating {path}: {e}");
+        std::process::exit(1);
+    }));
+    let n = labels.len();
+    writeln!(f, "genome_a,genome_b,n_snp,n_shared,n_eligible,ratio").unwrap();
+    for i in 0..n {
+        for j in (i + 1)..n {
+            let snp = result.snp[[i, j]];
+            let shared = result.shared[[i, j]];
+            let eligible = snp + shared;
+            write!(f, "{},{},{snp},{shared},{eligible}", labels[i], labels[j]).unwrap();
+            if eligible == 0 {
+                writeln!(f, ",NA").unwrap();
+            } else {
+                writeln!(f, ",{:.6}", snp as f64 / eligible as f64).unwrap();
+            }
+        }
+    }
+    info!("raw single-copy SNP distance counts (diagnostic) → {path}");
+}
+
+// ── SNP-only pseudo-alignment → FASTA ───────────────────────────────────────
+//
+// One record per genome, IUPAC-coded, no flanking sequence — see
+// `SnpAlignment` / `KmerIndex::snp_pseudo_alignment`. Uses the project's
+// existing FASTA writer (`obifastwrite::write_record`) rather than
+// hand-rolling one.
+
+pub(super) fn write_snp_fasta(alignment: &SnpAlignment, labels: &[String], output: &Option<PathBuf>) {
+    let path = output.as_ref()
+        .map(|p| format!("{}_snp.fasta", p.display()))
+        .unwrap_or_else(|| "snp.fasta".into());
+    let mut f = BufWriter::new(std::fs::File::create(&path).unwrap_or_else(|e| {
+        eprintln!("error creating {path}: {e}");
+        std::process::exit(1);
+    }));
+    let n_sites = alignment.sequences.first().map(|s| s.len()).unwrap_or(0);
+    for (label, seq) in labels.iter().zip(alignment.sequences.iter()) {
+        write_record(seq, label, &[("n_sites", JsonVal::Num(n_sites as u64))], &mut f).unwrap_or_else(|e| {
+            eprintln!("error writing {path}: {e}");
+            std::process::exit(1);
+        });
+    }
+    info!("SNP pseudo-alignment → {path} ({n_sites} site{})",
+        if n_sites == 1 { "" } else { "s" });
+}
+
+// ── UPGMA Newick from kodama dendrogram ───────────────────────────────────────
+
+pub(super) fn upgma_to_newick(dendro: &kodama::Dendrogram<f64>, names: &[String]) -> String {
+    let n = names.len();
+    // node_labels[i]: Newick subtree string for node i (leaves 0..n, internals n..)
+    let mut labels: Vec<String> = names.to_vec();
+    // height of each node: leaves = 0, internal = dissimilarity/2
+    let mut heights: Vec<f64> = vec![0.0; 2 * n - 1];
+
+    for (k, step) in dendro.steps().iter().enumerate() {
+        let new_node = n + k;
+        let h = step.dissimilarity / 2.0;
+        heights[new_node] = h;
+        let c1 = step.cluster1;
+        let c2 = step.cluster2;
+        let bl1 = (h - heights[c1]).max(0.0);
+        let bl2 = (h - heights[c2]).max(0.0);
+        labels.push(format!(
+            "({label1}:{bl1:.6},{label2}:{bl2:.6})",
+            label1 = labels[c1],
+            label2 = labels[c2],
+        ));
+    }
+
+    format!("{};", labels.last().unwrap())
+}
diff --git a/src/obikmer/src/cmd/phylo/sankoff.rs b/src/obikmer/src/cmd/phylo/sankoff.rs
index c8faaf2b..ab96e7d3 100644
--- a/src/obikmer/src/cmd/phylo/sankoff.rs
+++ b/src/obikmer/src/cmd/phylo/sankoff.rs
@@ -11,9 +11,15 @@ use tracing::info;
 // `snp_pseudo_alignment`), re-coded so its symbols match the accompanying
 // `--sankoff-matrix` output exactly: `0` for the empty/absent state instead
 // of `-`, which TNT/PhyG would otherwise read as their own gap character
-// rather than our "family absent" state.
+// rather than our "family absent" state. Unless `free_loss` (`--free-loss`)
+// is set, in which case `∅` is recoded to `?` instead — TNT/PhyG's own
+// missing-data symbol, deliberately *not* `-` (still gap/indel semantics in
+// both tools) — so non-detection costs nothing rather than being scored as
+// an ordinary, calibrated state transition. See
+// `docmd/theory/evolutionary_distances.md`, "Locus dropout under incomplete
+// coverage".
 
-pub(super) fn write_sankoff_alignment_fasta(alignment: &SnpAlignment, labels: &[String], output: &Option<PathBuf>) {
+pub(super) fn write_sankoff_alignment_fasta(alignment: &SnpAlignment, labels: &[String], output: &Option<PathBuf>, free_loss: bool) {
     let path = output.as_ref()
         .map(|p| format!("{}_sankoff.fasta", p.display()))
         .unwrap_or_else(|| "sankoff.fasta".into());
@@ -21,9 +27,10 @@ pub(super) fn write_sankoff_alignment_fasta(alignment: &SnpAlignment, labels: &[
         eprintln!("error creating {path}: {e}");
         std::process::exit(1);
     }));
+    let absent_symbol = if free_loss { b'?' } else { b'0' };
     let n_sites = alignment.sequences.first().map(|s| s.len()).unwrap_or(0);
     for (label, seq) in labels.iter().zip(alignment.sequences.iter()) {
-        let recoded: Vec<u8> = seq.iter().map(|&b| if b == b'-' { b'0' } else { b }).collect();
+        let recoded: Vec<u8> = seq.iter().map(|&b| if b == b'-' { absent_symbol } else { b }).collect();
         write_record(&recoded, label, &[("n_sites", JsonVal::Num(n_sites as u64))], &mut f).unwrap_or_else(|e| {
             eprintln!("error writing {path}: {e}");
             std::process::exit(1);
diff --git a/src/obikmer/src/cmd/phylo/tnt.rs b/src/obikmer/src/cmd/phylo/tnt.rs
index 48f5ad53..aa16b419 100644
--- a/src/obikmer/src/cmd/phylo/tnt.rs
+++ b/src/obikmer/src/cmd/phylo/tnt.rs
@@ -28,6 +28,7 @@ pub(super) fn write_sankoff_tnt(
     labels: &[String],
     output: &Option<PathBuf>,
     cost_scale: f64,
+    free_loss: bool,
 ) {
     let path = output.as_ref()
         .map(|p| format!("{}_sankoff.tnt", p.display()))
@@ -49,6 +50,13 @@ pub(super) fn write_sankoff_tnt(
     for (label, seq) in labels.iter().zip(alignment.sequences.iter()) {
         write!(f, "{label} ").unwrap();
         for &b in seq {
+            if free_loss && b == b'-' {
+                // `?`: TNT's own missing-data symbol, read directly, not
+                // routed through `TNT_STATE_SYMBOL` (there is no state for
+                // it) — see `write_sankoff_alignment_fasta`'s doc comment.
+                write!(f, "?").unwrap();
+                continue;
+            }
             let b = if b == b'-' { b'0' } else { b };
             let state = iupac_to_state[b as usize];
             write!(f, "{}", TNT_STATE_SYMBOL[state as usize]).unwrap();
-- 
2.54.0


From eee71430a48e22d6a1da8cbb62f0c93d2b000856 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Thu, 13 Aug 2026 22:25:08 +0200
Subject: [PATCH 13/46] add name-tree command and fix --free-loss cost matrix

Introduce the obikmer name-tree subcommand to map numeric leaf labels in phylogenetic tree exports back to taxon names using a reference FASTA file. Correct the --free-loss flag behavior by removing cardinality transition costs from pairwise cost calculations, ensuring sibling gains and losses are priced identically to whole-family events. Update documentation, configuration parameters, and add reference phylogenetic data files.
---
 UserDocMD/index.md                     |    1 +
 UserDocMD/usage/name-tree.md           |   21 +
 UserDocMD/usage/phylo.md               |    4 +-
 docmd/theory/evolutionary_distances.md |   73 ++
 iqtree.contree                         |    1 +
 iqtree.splits.nex                      |   62 ++
 iqtree.ufboot                          | 1000 ++++++++++++++++++++++++
 mkdocs-user.yml                        |    1 +
 sankoff_params.yaml                    |  148 ++--
 src/obikindex/src/cardcomp.rs          |   62 +-
 src/obikmer/src/cmd/mod.rs             |    1 +
 src/obikmer/src/cmd/nametree.rs        |  146 ++++
 src/obikmer/src/cmd/phylo/mod.rs       |    2 +-
 src/obikmer/src/main.rs                |    4 +
 14 files changed, 1444 insertions(+), 82 deletions(-)
 create mode 100644 UserDocMD/usage/name-tree.md
 create mode 100644 iqtree.contree
 create mode 100644 iqtree.splits.nex
 create mode 100644 iqtree.ufboot
 create mode 100644 src/obikmer/src/cmd/nametree.rs

diff --git a/UserDocMD/index.md b/UserDocMD/index.md
index 16248c99..10aa2c2e 100644
--- a/UserDocMD/index.md
+++ b/UserDocMD/index.md
@@ -25,6 +25,7 @@ All functionality is exposed through a single binary, `obikmer`, organized as su
 | [`dump`](usage/dump.md) | Dump indexed kmers as CSV |
 | [`annotate`](usage/annotate.md) | Add, update, or dump genome metadata |
 | [`phylo`](usage/phylo.md) | Compute pairwise evolutionary-distance proxies, trees, and phylogenetic exports |
+| [`name-tree`](usage/name-tree.md) | Translate a TNT/PhyG numeric-label tree export back to real taxon names |
 | [`unitig`](usage/unitig.md) | Dump the unitigs of an index as FASTA |
 | [`estimate`](usage/estimate.md) | Estimate approximate-index parameters before indexing |
 | [`reindex`](usage/reindex.md) | Convert an index's evidence representation (exact ↔ approximate) |
diff --git a/UserDocMD/usage/name-tree.md b/UserDocMD/usage/name-tree.md
new file mode 100644
index 00000000..70f2943c
--- /dev/null
+++ b/UserDocMD/usage/name-tree.md
@@ -0,0 +1,21 @@
+# name-tree
+
+Translate a numerically-labelled tree export (TNT, PhyG, or any plain Newick file with bare `1`, `2`, `3`, … leaf labels) back to real taxon names, reading the label order from the FASTA that produced it.
+
+```bash
+obikmer name-tree TREE --fasta FASTA -o OUTPUT
+```
+
+## Arguments
+
+| Argument | Description |
+|---|---|
+| `TREE` | Tree file to translate — a TNT-style NEXUS export (`tree NAME = [&U] ...;`) or a plain Newick file |
+| `--fasta` | FASTA file whose record order gives the numeric taxon labels (1-based) — typically the `_sankoff.fasta`/`_snp.fasta` used to produce `TREE` |
+| `-o, --output` | Output NEXUS file path |
+
+## Output
+
+A NEXUS file with a `taxa` block, a `translate` table (numeric label → taxon name, from `--fasta`'s header order), and every tree found in `TREE`, topology unchanged — readable directly in FigTree, PearTree, `ape` (R), etc.
+
+`--tnt`'s and `--phyg`'s exports (see [phylo](phylo.md)) both number taxa `1..N` in the same order as the pseudo-alignment FASTA they were built from (`<prefix>_sankoff.fasta`), so pass that same file as `--fasta` here.
diff --git a/UserDocMD/usage/phylo.md b/UserDocMD/usage/phylo.md
index 265c5767..378a33d1 100644
--- a/UserDocMD/usage/phylo.md
+++ b/UserDocMD/usage/phylo.md
@@ -93,7 +93,7 @@ which are combined into a row-normalized $16 \times 16$ transition probability m
 
 `--sankoff` alone writes the cost matrix, the calibration parameters, and a pseudo-alignment recoded so the empty state uses the symbol `0` (never a gap character, to avoid ambiguity with external tools' own gap semantics). It does not run any external tool.
 
-With `--free-loss`, the empty state is recoded to `?` instead — TNT/PhyG/IQ-TREE's own missing-data symbol — rather than an ordinary, costed 16th state. This matters for genome-skim or otherwise incomplete-coverage collections, where non-detection of a family is dominated by sampling failure rather than true evolutionary loss: scoring it as a real state risks grouping genomes by shared undersampling instead of shared ancestry. `?` rather than `-` because `-` still carries gap/indel semantics in these tools, and a non-detected family is not an observed deletion. Combine with `--min-shared-family`/`--family-overlap` above: `--free-loss` removes the false signal from non-detection, but a genome left with too little real overlap with everything else will still be placed unstably — excluding it is the other half of the fix.
+With `--free-loss`, the empty state is recoded to `?` instead — TNT/PhyG/IQ-TREE's own missing-data symbol — rather than an ordinary, costed 16th state. This matters for genome-skim or otherwise incomplete-coverage collections, where non-detection of a family is dominated by sampling failure rather than true evolutionary loss: scoring it as a real state risks grouping genomes by shared undersampling instead of shared ancestry. `?` rather than `-` because `-` still carries gap/indel semantics in these tools, and a non-detected family is not an observed deletion. `--free-loss` also drops the cardinality-transition cost between any two states, not just to/from the empty one: whether a genome shows 1 vs. 2 (etc.) detected members of a family it does carry is exactly as vulnerable to sampling failure as whether the family was detected at all, so gaining or losing a sibling is priced the same way — for free — as gaining or losing the whole family. Combine with `--min-shared-family`/`--family-overlap` above: `--free-loss` removes the false signal from non-detection, but a genome left with too little real overlap with everything else will still be placed unstably — excluding it is the other half of the fix.
 
 ### Exports
 
@@ -103,6 +103,8 @@ All three exports reuse the `--sankoff` calibrated matrix and pseudo-alignment,
 - **`--phyg`**: a custom cost-matrix file plus a PhyG script reusing the `--sankoff` alignment directly.
 - **`--iqtree`**: a custom substitution-model file (exchangeability matrix recovered as $R(a,b) = e^{-\text{cost}(a,b)}$, plus empirical state frequencies) and a matching alignment, for maximum-likelihood inference with real branch lengths (unlike the parsimony step-counts from TNT/PhyG). Only states actually occurring in the alignment are kept and compactly renumbered.
 
+TNT and PhyG both write trees with bare numeric leaf labels (`1`, `2`, …, in the same order as `<prefix>_sankoff.fasta`). Use [`name-tree`](name-tree.md) on the tool's own tree output plus that same FASTA to get a NEXUS file with real taxon names.
+
 ## Output files
 
 With `-o/--output PREFIX`, the relevant subset of the following files is written: `<prefix>_dist.csv`, `<prefix>_shared.csv`, `<prefix>_nj.nwk`, `<prefix>_upgma.nwk`, `<prefix>_siblings.csv`, `<prefix>_rawsnp.csv`, `<prefix>_rawsnp_counts.csv`, `<prefix>_snp.fasta`, `<prefix>_family_overlap.csv`, `<prefix>_sankoff_matrix.csv`, `<prefix>_sankoff_params.yaml`, `<prefix>_sankoff.fasta`, `<prefix>_sankoff.tnt`, `<prefix>_sankoff.tcm`, `<prefix>_sankoff.pg`, `<prefix>_iqtree.model`, `<prefix>_iqtree.fasta`. Without `-o`, only the plain `--metric` distance matrix is produced, on stdout.
diff --git a/docmd/theory/evolutionary_distances.md b/docmd/theory/evolutionary_distances.md
index 1bb5d1a9..137ee58d 100644
--- a/docmd/theory/evolutionary_distances.md
+++ b/docmd/theory/evolutionary_distances.md
@@ -1956,6 +1956,79 @@ re-run against the local `iqtree3` binary to confirm `+ASC` now accepts the
 filtered alignment — next verification step, alongside the still-open PhyG
 `?`-vs-gap-row question above.
 
+### `--family-overlap`/`--min-shared-family`, and a second `free_loss` bug: cardinality-transition cost not zeroed (2026-08-13)
+
+**Diagnostic added: `--family-overlap`.** Real per-genome-pair count of
+shared variable families (columns where neither genome is `∅`), diagonal
+kept (degenerates to "genome's own total family count", not a separate
+computation — see `obikmer/src/cmd/phylo/family_overlap.rs`). On the
+20-genome benchmark this predicted the `--tnt`/`--iqtree` rogue-placement
+pattern exactly: Candidozyma shares **0** families with all 19 others (hence
+its ~0-length branch, placed anywhere); the mean off-diagonal shared-family
+count per genome splits cleanly below/above ~1000 (`Candidozyma` 0,
+`Saccharolobus` 0.9, `Opitutus` 20.5, `Wolbachia` 37.1, `Acidobacterium`
+41.2, `Shouchella` 49.4, `Bacillus` 54.5, `Proteus` 629, `Yersinia` 907.5 —
+all below 1000 — vs. `Klebsiella` ~5000-6000, `Salmonella` ~8000-17000,
+`E. coli` ~19000-24000, all comfortably above). `--min-shared-family N`
+automates exclusion below that threshold, reusing the `--exclude-genome`
+machinery. Restricting to the 3 genera above threshold (11 genomes: 4
+*E. coli*, 3 *Klebsiella*, 4 *Salmonella*) gives 3 cleanly separated
+monophyletic clades in both TNT and IQ-TREE (without `+ASC`, see below) —
+confirms the family-overlap statistic, not just the tree topology, as the
+right lens for this failure mode. `N=1000` is benchmark-specific (huge
+cross-domain divergence), not a universal constant — recompute
+`--family-overlap` and read its own gap on any other dataset.
+
+**Second `free_loss` bug, found by re-deriving the design rather than by a
+failing run: the cardinality-transition cost wasn't zeroed.**
+`--free-loss` neutralises `∅` (whole-family non-detection) by recoding it to
+`?`, so transitions to/from the empty state are never scored. But the
+calibrated 16-state cost matrix (`obikindex::pairwise_cost_matrix`) prices
+*every* cardinality change — not just `X → ∅` — via a shared
+`P_cardinality(|A|→|B|)` factor (the same constant this project has called
+`c_ctx` throughout: "used everywhere a member is gained or lost", see "A
+concrete Sankoff cost matrix" above). So a transition between two
+*non-empty* states that differ in how many family members are detected
+(e.g. `{A} -> {A,C}`, gaining a second sibling) was still carrying the full
+calibrated gain/loss penalty under `--free-loss`, even though the same
+low/incomplete-coverage argument for not trusting whole-family absence
+applies identically one level down: whether a genome shows 1 vs 2 detected
+members of a family it does carry is exactly as vulnerable to sampling
+failure as whether the family was detected at all. Fixed by adding a
+`free_loss: bool` parameter to `pairwise_cost_matrix` that drops the
+`P_cardinality` factor from the log-probability sum entirely when set,
+leaving cost driven only by composition matching (shared-base retention,
+paired substitutions) — never by cardinality difference alone. Unit-tested
+(`free_loss_ignores_cardinality_transition_probs`): two wildly different
+cardinality models produce an identical cost matrix once `free_loss` is
+true. Not yet re-run against a real index to see how much this changes the
+resulting tree beyond the unit-level guarantee.
+
+**`+ASC` misbehaves on closely-related taxa, separately from either bug
+above.** Restricting to the 3-genus, 11-genome subset and running `--iqtree`
+with `+ASC` converges suspiciously fast compared to the same run without
+`+ASC` (which takes the expected ~100 NNI iterations, ~1m38s, converges to a
+stable score, total tree length 7.147, and gives the clean 3-clade
+topology). Not yet root-caused with a real `+ASC` log in hand (the one run
+overwrote its own log under the shared `--prefix`, see the operational note
+below) — working hypothesis, not confirmed: `+ASC`'s correction divides by
+`P(site variable | current model, current branch lengths)`, recomputed
+every iteration; on closely-related strains (short branches), a plausible
+model predicts most sites *should* be constant, so `P(variable)` can be
+small enough that the correction becomes numerically unstable. Needs a
+dedicated run (own `--prefix`, log kept) before this is more than a
+hypothesis.
+
+**Operational note, not a code bug: IQ-TREE's `--undo`/checkpoint reuse
+across different alignments crashes.** Reusing `iqtree.ckp.gz` (and the tree
+it stores) from a run on one taxon set against a regenerated `iqtree.fasta`
+with a different taxon count crashes with `Assertion 'i >= 0 && i <
+(int)seq_names.size()' failed` in `Alignment::getSeqName` /
+`PhyloTree::assignLeafNames` — `--undo` tries to graft a stored tree with
+the old leaf count onto the new, smaller alignment. Not an `obikmer` bug;
+avoid by using a fresh `--prefix` (or `-redo`) whenever the underlying
+alignment's taxon set changes, never `--undo` across them.
+
 ## References
 
 The Mash mutation-rate model this discussion contrasts with:
diff --git a/iqtree.contree b/iqtree.contree
new file mode 100644
index 00000000..30eeede4
--- /dev/null
+++ b/iqtree.contree
@@ -0,0 +1 @@
+(Escherichia_coli--CFT073:0.7973338454,(Escherichia_coli--EDL933:0.5132866305,(Escherichia_coli--K-12_MG1655:0.2990687226,Escherichia_coli--K-12_W3110:0.3006288477)100:0.1655629834)69:0.0000007189,(((Klebsiella_pneumoniae--ATCC_13883:0.9661675519,(Klebsiella_pneumoniae--MGH_78578:0.3148953385,Yersinia_ruckeri--YRB:0.3576917943)84:0.4568464394)83:0.0727808943,(Klebsiella_pneumoniae--HS11286:0.1397401144,Proteus_mirabilis--HI4320:0.2192824480)77:0.3686486712)76:0.1162295711,((Salmonella_enterica--AKU_12601:0.6158730439,(Salmonella_enterica--LT2:0.4371443730,Salmonella_enterica--P125109:0.5815549929)100:0.1012287522)100:0.0714169372,Salmonella_enterica--CT18:0.2058143021)76:0.3641489914)100:0.2900565429);
diff --git a/iqtree.splits.nex b/iqtree.splits.nex
new file mode 100644
index 00000000..7b7c554a
--- /dev/null
+++ b/iqtree.splits.nex
@@ -0,0 +1,62 @@
+#nexus
+
+BEGIN Taxa;
+DIMENSIONS ntax=13;
+TAXLABELS
+[1] 'Escherichia_coli--CFT073'
+[2] 'Escherichia_coli--EDL933'
+[3] 'Escherichia_coli--K-12_MG1655'
+[4] 'Escherichia_coli--K-12_W3110'
+[5] 'Klebsiella_pneumoniae--ATCC_13883'
+[6] 'Klebsiella_pneumoniae--HS11286'
+[7] 'Klebsiella_pneumoniae--MGH_78578'
+[8] 'Proteus_mirabilis--HI4320'
+[9] 'Salmonella_enterica--AKU_12601'
+[10] 'Salmonella_enterica--CT18'
+[11] 'Salmonella_enterica--LT2'
+[12] 'Salmonella_enterica--P125109'
+[13] 'Yersinia_ruckeri--YRB'
+;
+END; [Taxa]
+
+BEGIN Splits;
+DIMENSIONS ntax=13 nsplits=34;
+FORMAT labels=no weights=yes confidences=no intervals=no;
+MATRIX
+	100	 2,
+	100	 3,
+	100	 4,
+	100	 3 4,
+	69	 2 3 4,
+	100	 5,
+	100	 7,
+	16	 5 7,
+	100	 6,
+	100	 13,
+	16	 6 13,
+	23	 5 6 7 13,
+	100	 8,
+	100	 10,
+	23	 8 10,
+	100	 9,
+	100	 11,
+	100	 12,
+	100	 11 12,
+	100	 9 11 12,
+	23	 8 9 10 11 12,
+	100	 1 2 3 4,
+	100	 1,
+	84	 7 13,
+	83	 5 7 13,
+	77	 6 8,
+	76	 5 6 7 8 13,
+	76	 9 10 11 12,
+	31	 1 2,
+	1	 5 6 7 8,
+	1	 10 13,
+	1	 9 10 11 12 13,
+	1	 5 6 13,
+	1	 5 6 8,
+;
+END; [Splits]
+
diff --git a/iqtree.ufboot b/iqtree.ufboot
new file mode 100644
index 00000000..1e985e87
--- /dev/null
+++ b/iqtree.ufboot
@@ -0,0 +1,1000 @@
+(Escherichia_coli--CFT073:0.8024680000,(Escherichia_coli--EDL933:0.5186330000,(Escherichia_coli--K-12_MG1655:0.3011540000,Escherichia_coli--K-12_W3110:0.3004550000):0.1566600000):0.0024925000,(((Klebsiella_pneumoniae--ATCC_13883:0.9823380000,Klebsiella_pneumoniae--MGH_78578:0.7604100000):0.0720304000,(Klebsiella_pneumoniae--HS11286:0.1177140000,Yersinia_ruckeri--YRB:0.4173380000):0.3964890000):0.1116030000,((Proteus_mirabilis--HI4320:0.2034070000,Salmonella_enterica--CT18:0.0312350000):0.1696500000,(Salmonella_enterica--AKU_12601:0.6157950000,(Salmonella_enterica--LT2:0.4389620000,Salmonella_enterica--P125109:0.5792750000):0.0996599000):0.0769333000):0.3784840000):0.2699650000);
+(Escherichia_coli--CFT073:0.7928280000,(Escherichia_coli--EDL933:0.5138070000,(Escherichia_coli--K-12_MG1655:0.2997250000,Escherichia_coli--K-12_W3110:0.2996270000):0.1713570000):0.0005772440,(((Klebsiella_pneumoniae--ATCC_13883:0.9658720000,(Klebsiella_pneumoniae--MGH_78578:0.3243950000,Yersinia_ruckeri--YRB:0.3258410000):0.4452060000):0.0714933000,(Klebsiella_pneumoniae--HS11286:0.0925980000,Proteus_mirabilis--HI4320:0.1735040000):0.4091490000):0.1382260000,((Salmonella_enterica--AKU_12601:0.6131010000,(Salmonella_enterica--LT2:0.4373930000,Salmonella_enterica--P125109:0.5853690000):0.0962198000):0.0871399000,Salmonella_enterica--CT18:0.1941480000):0.3697160000):0.2812870000);
+(Escherichia_coli--CFT073:0.7967900000,Escherichia_coli--EDL933:0.5093670000,((Escherichia_coli--K-12_MG1655:0.2962910000,Escherichia_coli--K-12_W3110:0.3046430000):0.1674290000,(((Klebsiella_pneumoniae--ATCC_13883:0.9706540000,(Klebsiella_pneumoniae--MGH_78578:0.3188760000,Yersinia_ruckeri--YRB:0.3681200000):0.4447600000):0.0858499000,(Klebsiella_pneumoniae--HS11286:0.1436200000,Proteus_mirabilis--HI4320:0.2646220000):0.3557740000):0.1416940000,((Salmonella_enterica--AKU_12601:0.6210780000,(Salmonella_enterica--LT2:0.4385380000,Salmonella_enterica--P125109:0.5821720000):0.0969174000):0.0665862000,Salmonella_enterica--CT18:0.2053190000):0.3535060000):0.3111630000):0.0006802480);
+(Escherichia_coli--CFT073:0.7941430000,(Escherichia_coli--EDL933:0.5054230000,(Escherichia_coli--K-12_MG1655:0.3008390000,Escherichia_coli--K-12_W3110:0.3002070000):0.1662720000):0.0000005961,(((Klebsiella_pneumoniae--ATCC_13883:0.9697160000,Klebsiella_pneumoniae--MGH_78578:0.7643300000):0.0648707000,(Klebsiella_pneumoniae--HS11286:0.1680380000,Yersinia_ruckeri--YRB:0.4163760000):0.3489630000):0.1401770000,((Proteus_mirabilis--HI4320:0.2985720000,Salmonella_enterica--CT18:0.0538990000):0.1534730000,(Salmonella_enterica--AKU_12601:0.6181510000,(Salmonella_enterica--LT2:0.4343230000,Salmonella_enterica--P125109:0.5802340000):0.1019550000):0.0693617000):0.3594490000):0.2908900000);
+(Escherichia_coli--CFT073:0.7985750000,(Escherichia_coli--EDL933:0.5144550000,(Escherichia_coli--K-12_MG1655:0.3004620000,Escherichia_coli--K-12_W3110:0.3002450000):0.1604100000):0.0022806400,(((Klebsiella_pneumoniae--ATCC_13883:0.9838780000,(Klebsiella_pneumoniae--MGH_78578:0.2616840000,Yersinia_ruckeri--YRB:0.3395650000):0.5068500000):0.0853542000,Klebsiella_pneumoniae--HS11286:0.4850610000):0.0924621000,((Proteus_mirabilis--HI4320:0.2438210000,Salmonella_enterica--CT18:0.0347210000):0.2079220000,(Salmonella_enterica--AKU_12601:0.6208700000,(Salmonella_enterica--LT2:0.4341840000,Salmonella_enterica--P125109:0.5792000000):0.0981067000):0.0371577000):0.3957320000):0.3068800000);
+(Escherichia_coli--CFT073:0.8003210000,(Escherichia_coli--EDL933:0.5144780000,(Escherichia_coli--K-12_MG1655:0.3013900000,Escherichia_coli--K-12_W3110:0.3004660000):0.1631120000):0.0000005338,(((Klebsiella_pneumoniae--ATCC_13883:0.9657880000,(Klebsiella_pneumoniae--MGH_78578:0.3245120000,Yersinia_ruckeri--YRB:0.3795300000):0.4448760000):0.0789215000,(Klebsiella_pneumoniae--HS11286:0.1492760000,Proteus_mirabilis--HI4320:0.2366740000):0.3592030000):0.1202010000,((Salmonella_enterica--AKU_12601:0.6180740000,(Salmonella_enterica--LT2:0.4378580000,Salmonella_enterica--P125109:0.5796400000):0.1047200000):0.0598133000,Salmonella_enterica--CT18:0.2140670000):0.3512390000):0.3069490000);
+(Escherichia_coli--CFT073:0.7944260000,Escherichia_coli--EDL933:0.5192750000,((Escherichia_coli--K-12_MG1655:0.2999790000,Escherichia_coli--K-12_W3110:0.2977560000):0.1624400000,(((Klebsiella_pneumoniae--ATCC_13883:0.9709780000,(Klebsiella_pneumoniae--MGH_78578:0.3191570000,Yersinia_ruckeri--YRB:0.3408650000):0.4454450000):0.0669281000,(Klebsiella_pneumoniae--HS11286:0.1112870000,Proteus_mirabilis--HI4320:0.2380120000):0.4088010000):0.1011640000,((Salmonella_enterica--AKU_12601:0.6183030000,(Salmonella_enterica--LT2:0.4371650000,Salmonella_enterica--P125109:0.5834050000):0.0979651000):0.0755381000,Salmonella_enterica--CT18:0.1988730000):0.3697480000):0.2961410000):0.0000006127);
+(Escherichia_coli--CFT073:0.7908840000,(Escherichia_coli--EDL933:0.5152740000,(Escherichia_coli--K-12_MG1655:0.3002470000,Escherichia_coli--K-12_W3110:0.2986830000):0.1629020000):0.0045822400,(((Klebsiella_pneumoniae--ATCC_13883:0.9614590000,Klebsiella_pneumoniae--MGH_78578:0.7682800000):0.0604355000,(Klebsiella_pneumoniae--HS11286:0.1837160000,Proteus_mirabilis--HI4320:0.2073950000):0.3400780000):0.0968854000,((Salmonella_enterica--AKU_12601:0.6227380000,(Salmonella_enterica--LT2:0.4388020000,Salmonella_enterica--P125109:0.5805500000):0.0948578000):0.0695873000,(Salmonella_enterica--CT18:0.0751510000,Yersinia_ruckeri--YRB:0.5140790000):0.1326540000):0.3823150000):0.2845260000);
+(Escherichia_coli--CFT073:0.7935620000,(Escherichia_coli--EDL933:0.5133770000,(Escherichia_coli--K-12_MG1655:0.2976100000,Escherichia_coli--K-12_W3110:0.3028030000):0.1656360000):0.0039153400,(((Klebsiella_pneumoniae--ATCC_13883:0.9640250000,(Klebsiella_pneumoniae--MGH_78578:0.3229240000,Yersinia_ruckeri--YRB:0.3931440000):0.4401770000):0.0652477000,(Klebsiella_pneumoniae--HS11286:0.1454060000,Proteus_mirabilis--HI4320:0.2336710000):0.3566890000):0.1201380000,((Salmonella_enterica--AKU_12601:0.6145920000,(Salmonella_enterica--LT2:0.4309510000,Salmonella_enterica--P125109:0.5883680000):0.1022050000):0.0557637000,Salmonella_enterica--CT18:0.2235280000):0.3816880000):0.2926930000);
+(Escherichia_coli--CFT073:0.7980280000,Escherichia_coli--EDL933:0.5166110000,((Escherichia_coli--K-12_MG1655:0.2951350000,Escherichia_coli--K-12_W3110:0.3052570000):0.1637330000,(((Klebsiella_pneumoniae--ATCC_13883:0.9574670000,(Klebsiella_pneumoniae--MGH_78578:0.3384250000,Yersinia_ruckeri--YRB:0.3568100000):0.4398190000):0.0731448000,(Klebsiella_pneumoniae--HS11286:0.1497230000,Proteus_mirabilis--HI4320:0.2308130000):0.3607220000):0.1217070000,((Salmonella_enterica--AKU_12601:0.6094050000,(Salmonella_enterica--LT2:0.4348910000,Salmonella_enterica--P125109:0.5887830000):0.0998840000):0.0568662000,Salmonella_enterica--CT18:0.2217630000):0.3800600000):0.2954150000):0.0000005338);
+(Escherichia_coli--CFT073:0.7986310000,(Escherichia_coli--EDL933:0.5083560000,(Escherichia_coli--K-12_MG1655:0.2973870000,Escherichia_coli--K-12_W3110:0.3024860000):0.1678410000):0.0000212181,(((Klebsiella_pneumoniae--ATCC_13883:0.9779360000,Klebsiella_pneumoniae--MGH_78578:0.7413700000):0.0668739000,(Klebsiella_pneumoniae--HS11286:0.1773680000,Yersinia_ruckeri--YRB:0.4086260000):0.3607080000):0.1311250000,((Proteus_mirabilis--HI4320:0.2463480000,Salmonella_enterica--CT18:0.0516440000):0.1590570000,(Salmonella_enterica--AKU_12601:0.6172120000,(Salmonella_enterica--LT2:0.4360040000,Salmonella_enterica--P125109:0.5805460000):0.1003680000):0.0638377000):0.3481280000):0.3007710000);
+(Escherichia_coli--CFT073:0.7991950000,(Escherichia_coli--EDL933:0.5058930000,(Escherichia_coli--K-12_MG1655:0.2992580000,Escherichia_coli--K-12_W3110:0.3002430000):0.1704110000):0.0003018270,(((Klebsiella_pneumoniae--ATCC_13883:0.9620460000,(Klebsiella_pneumoniae--MGH_78578:0.3437710000,Yersinia_ruckeri--YRB:0.3718590000):0.4429850000):0.0742405000,(Klebsiella_pneumoniae--HS11286:0.1054520000,Proteus_mirabilis--HI4320:0.2115650000):0.4098050000):0.0831225000,((Salmonella_enterica--AKU_12601:0.6200540000,(Salmonella_enterica--LT2:0.4368190000,Salmonella_enterica--P125109:0.5838720000):0.1010750000):0.0810183000,Salmonella_enterica--CT18:0.1869690000):0.3861840000):0.2919200000);
+(Escherichia_coli--CFT073:0.7941170000,(Escherichia_coli--EDL933:0.5047800000,(Escherichia_coli--K-12_MG1655:0.3009350000,Escherichia_coli--K-12_W3110:0.3000530000):0.1734510000):0.0002515250,(((Klebsiella_pneumoniae--ATCC_13883:0.9448490000,(Klebsiella_pneumoniae--MGH_78578:0.3255730000,Yersinia_ruckeri--YRB:0.3273240000):0.4458110000):0.0789084000,(Klebsiella_pneumoniae--HS11286:0.1537110000,Proteus_mirabilis--HI4320:0.2411870000):0.3638610000):0.1219330000,((Salmonella_enterica--AKU_12601:0.6025450000,(Salmonella_enterica--LT2:0.4366180000,Salmonella_enterica--P125109:0.5861860000):0.1094360000):0.0609927000,Salmonella_enterica--CT18:0.2131130000):0.3644840000):0.2959810000);
+(Escherichia_coli--CFT073:0.8053570000,(Escherichia_coli--EDL933:0.5153930000,(Escherichia_coli--K-12_MG1655:0.2980890000,Escherichia_coli--K-12_W3110:0.2988350000):0.1601180000):0.0000005338,(((Klebsiella_pneumoniae--ATCC_13883:0.9597800000,(Klebsiella_pneumoniae--MGH_78578:0.3358580000,Yersinia_ruckeri--YRB:0.3297090000):0.4396530000):0.0796225000,(Klebsiella_pneumoniae--HS11286:0.1449780000,Proteus_mirabilis--HI4320:0.2118910000):0.3435690000):0.1080350000,((Salmonella_enterica--AKU_12601:0.6179370000,(Salmonella_enterica--LT2:0.4379540000,Salmonella_enterica--P125109:0.5809400000):0.0966589000):0.0660614000,Salmonella_enterica--CT18:0.2166730000):0.3757280000):0.2887210000);
+(Escherichia_coli--CFT073:0.7952220000,(Escherichia_coli--EDL933:0.5161480000,(Escherichia_coli--K-12_MG1655:0.2980370000,Escherichia_coli--K-12_W3110:0.3013960000):0.1623530000):0.0031233300,(((Klebsiella_pneumoniae--ATCC_13883:0.9748670000,(Klebsiella_pneumoniae--MGH_78578:0.2679890000,Yersinia_ruckeri--YRB:0.3498570000):0.5001630000):0.0815331000,Klebsiella_pneumoniae--HS11286:0.4950510000):0.0838776000,((Proteus_mirabilis--HI4320:0.2883230000,Salmonella_enterica--CT18:0.0310810000):0.1971410000,(Salmonella_enterica--AKU_12601:0.6200920000,(Salmonella_enterica--LT2:0.4364360000,Salmonella_enterica--P125109:0.5820830000):0.0998947000):0.0444616000):0.3967220000):0.2865240000);
+(Escherichia_coli--CFT073:0.7967070000,(Escherichia_coli--EDL933:0.5152100000,(Escherichia_coli--K-12_MG1655:0.2984800000,Escherichia_coli--K-12_W3110:0.2987110000):0.1671830000):0.0031800800,(((Klebsiella_pneumoniae--ATCC_13883:0.9678990000,(Klebsiella_pneumoniae--MGH_78578:0.3056060000,Yersinia_ruckeri--YRB:0.4075700000):0.4466980000):0.0796039000,(Klebsiella_pneumoniae--HS11286:0.1480230000,Proteus_mirabilis--HI4320:0.2298760000):0.3630480000):0.1297620000,((Salmonella_enterica--AKU_12601:0.6120920000,(Salmonella_enterica--LT2:0.4370670000,Salmonella_enterica--P125109:0.5835520000):0.1000640000):0.0638829000,Salmonella_enterica--CT18:0.2188320000):0.3365850000):0.3101780000);
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+(Escherichia_coli--CFT073:0.7941910000,Escherichia_coli--EDL933:0.5193530000,((Escherichia_coli--K-12_MG1655:0.3017420000,Escherichia_coli--K-12_W3110:0.2975090000):0.1649020000,(((Klebsiella_pneumoniae--ATCC_13883:0.9627320000,(Klebsiella_pneumoniae--MGH_78578:0.3262860000,Yersinia_ruckeri--YRB:0.4036920000):0.4504960000):0.0637232000,(Klebsiella_pneumoniae--HS11286:0.1090270000,Proteus_mirabilis--HI4320:0.2899960000):0.3947850000):0.1489520000,((Salmonella_enterica--AKU_12601:0.6193770000,(Salmonella_enterica--LT2:0.4344750000,Salmonella_enterica--P125109:0.5793430000):0.1047720000):0.0738721000,Salmonella_enterica--CT18:0.2030530000):0.3602770000):0.2697700000):0.0002659500);
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+(Escherichia_coli--CFT073:0.7919500000,(Escherichia_coli--EDL933:0.5143520000,(Escherichia_coli--K-12_MG1655:0.2972140000,Escherichia_coli--K-12_W3110:0.3010330000):0.1648930000):0.0004628160,(((Klebsiella_pneumoniae--ATCC_13883:0.9589070000,(Klebsiella_pneumoniae--MGH_78578:0.3347150000,Yersinia_ruckeri--YRB:0.3686310000):0.4307680000):0.0731123000,(Klebsiella_pneumoniae--HS11286:0.1595250000,Proteus_mirabilis--HI4320:0.2493600000):0.3478660000):0.1224360000,((Salmonella_enterica--AKU_12601:0.6232370000,(Salmonella_enterica--LT2:0.4393380000,Salmonella_enterica--P125109:0.5783600000):0.0944726000):0.0991426000,Salmonella_enterica--CT18:0.1830830000):0.3459410000):0.2979520000);
+(Escherichia_coli--CFT073:0.8009120000,Escherichia_coli--EDL933:0.5132910000,((Escherichia_coli--K-12_MG1655:0.2961340000,Escherichia_coli--K-12_W3110:0.3005020000):0.1674210000,(((Klebsiella_pneumoniae--ATCC_13883:0.9818870000,Klebsiella_pneumoniae--MGH_78578:0.7671210000):0.0394336000,(Klebsiella_pneumoniae--HS11286:0.1142700000,Yersinia_ruckeri--YRB:0.3839110000):0.4222530000):0.1402370000,((Proteus_mirabilis--HI4320:0.2781450000,Salmonella_enterica--CT18:0.0325560000):0.1779940000,(Salmonella_enterica--AKU_12601:0.6177060000,(Salmonella_enterica--LT2:0.4340710000,Salmonella_enterica--P125109:0.5868260000):0.1014630000):0.0667455000):0.3423220000):0.2972840000):0.0000005314);
+(Escherichia_coli--CFT073:0.7962360000,(Escherichia_coli--EDL933:0.5152620000,(Escherichia_coli--K-12_MG1655:0.2993510000,Escherichia_coli--K-12_W3110:0.2996260000):0.1685270000):0.0000007123,(((Klebsiella_pneumoniae--ATCC_13883:0.9682060000,(Klebsiella_pneumoniae--MGH_78578:0.3218110000,Yersinia_ruckeri--YRB:0.3481220000):0.4446710000):0.0864205000,(Klebsiella_pneumoniae--HS11286:0.1538920000,Proteus_mirabilis--HI4320:0.2037810000):0.3471740000):0.1141330000,((Salmonella_enterica--AKU_12601:0.6193210000,(Salmonella_enterica--LT2:0.4348470000,Salmonella_enterica--P125109:0.5841210000):0.0942392000):0.0525212000,Salmonella_enterica--CT18:0.2358440000):0.3682910000):0.2977510000);
+(Escherichia_coli--CFT073:0.7991490000,Escherichia_coli--EDL933:0.5122000000,((Escherichia_coli--K-12_MG1655:0.2999640000,Escherichia_coli--K-12_W3110:0.2989950000):0.1637970000,(((Klebsiella_pneumoniae--ATCC_13883:0.9599120000,(Klebsiella_pneumoniae--MGH_78578:0.3417870000,Yersinia_ruckeri--YRB:0.3832080000):0.4435060000):0.0710039000,(Klebsiella_pneumoniae--HS11286:0.1397010000,Proteus_mirabilis--HI4320:0.2342110000):0.3609140000):0.1046050000,((Salmonella_enterica--AKU_12601:0.6142700000,(Salmonella_enterica--LT2:0.4341170000,Salmonella_enterica--P125109:0.5809920000):0.1025500000):0.0572289000,Salmonella_enterica--CT18:0.2205800000):0.3591980000):0.2854230000):0.0007409030);
+(Escherichia_coli--CFT073:0.7980050000,Escherichia_coli--EDL933:0.5143640000,((Escherichia_coli--K-12_MG1655:0.2975890000,Escherichia_coli--K-12_W3110:0.3027680000):0.1649490000,(((Klebsiella_pneumoniae--ATCC_13883:0.9667040000,(Klebsiella_pneumoniae--MGH_78578:0.3212380000,Yersinia_ruckeri--YRB:0.3539130000):0.4521070000):0.0838294000,(Klebsiella_pneumoniae--HS11286:0.1553380000,Proteus_mirabilis--HI4320:0.1924680000):0.3430270000):0.1127060000,((Salmonella_enterica--AKU_12601:0.6100930000,(Salmonella_enterica--LT2:0.4384830000,Salmonella_enterica--P125109:0.5850370000):0.1033140000):0.0635406000,Salmonella_enterica--CT18:0.2182590000):0.3547100000):0.2932390000):0.0000005338);
+(Escherichia_coli--CFT073:0.7969390000,(Escherichia_coli--EDL933:0.5130930000,(Escherichia_coli--K-12_MG1655:0.3040070000,Escherichia_coli--K-12_W3110:0.2975020000):0.1600230000):0.0006570100,(((Klebsiella_pneumoniae--ATCC_13883:0.9633250000,(Klebsiella_pneumoniae--MGH_78578:0.3174550000,Yersinia_ruckeri--YRB:0.3616440000):0.4402890000):0.0742394000,(Klebsiella_pneumoniae--HS11286:0.1500780000,Proteus_mirabilis--HI4320:0.2016900000):0.3650760000):0.1022540000,((Salmonella_enterica--AKU_12601:0.6101170000,(Salmonella_enterica--LT2:0.4380510000,Salmonella_enterica--P125109:0.5855630000):0.1067910000):0.0584862000,Salmonella_enterica--CT18:0.2147630000):0.3764450000):0.3181860000);
+(Escherichia_coli--CFT073:0.8030540000,(Escherichia_coli--EDL933:0.5115490000,(Escherichia_coli--K-12_MG1655:0.2995700000,Escherichia_coli--K-12_W3110:0.3011250000):0.1645440000):0.0000005338,(((Klebsiella_pneumoniae--ATCC_13883:0.9560420000,(Klebsiella_pneumoniae--MGH_78578:0.3198920000,Yersinia_ruckeri--YRB:0.4180320000):0.4418000000):0.0843588000,(Klebsiella_pneumoniae--HS11286:0.1470450000,Proteus_mirabilis--HI4320:0.2327350000):0.3572060000):0.1225490000,((Salmonella_enterica--AKU_12601:0.6117550000,(Salmonella_enterica--LT2:0.4424750000,Salmonella_enterica--P125109:0.5848680000):0.0969432000):0.0677545000,Salmonella_enterica--CT18:0.2134170000):0.3643000000):0.2667730000);
+(Escherichia_coli--CFT073:0.7995430000,(Escherichia_coli--EDL933:0.5183650000,(Escherichia_coli--K-12_MG1655:0.2981760000,Escherichia_coli--K-12_W3110:0.2994440000):0.1676080000):0.0000005338,(((Klebsiella_pneumoniae--ATCC_13883:0.9678170000,(Klebsiella_pneumoniae--MGH_78578:0.3264620000,Yersinia_ruckeri--YRB:0.4076020000):0.4397340000):0.0714637000,(Klebsiella_pneumoniae--HS11286:0.1602680000,Proteus_mirabilis--HI4320:0.2251420000):0.3482590000):0.1104240000,((Salmonella_enterica--AKU_12601:0.6108680000,(Salmonella_enterica--LT2:0.4383890000,Salmonella_enterica--P125109:0.5767200000):0.1104330000):0.0577701000,Salmonella_enterica--CT18:0.2241580000):0.3543240000):0.3050420000);
+(Escherichia_coli--CFT073:0.7973210000,Escherichia_coli--EDL933:0.5130460000,((Escherichia_coli--K-12_MG1655:0.2980860000,Escherichia_coli--K-12_W3110:0.3009390000):0.1699620000,(((Klebsiella_pneumoniae--ATCC_13883:0.9578150000,(Klebsiella_pneumoniae--MGH_78578:0.2788550000,Yersinia_ruckeri--YRB:0.3402260000):0.4886720000):0.0936176000,Klebsiella_pneumoniae--HS11286:0.4839220000):0.0923274000,((Proteus_mirabilis--HI4320:0.2151480000,Salmonella_enterica--CT18:0.0380720000):0.2013650000,(Salmonella_enterica--AKU_12601:0.6195260000,(Salmonella_enterica--LT2:0.4364990000,Salmonella_enterica--P125109:0.5842200000):0.0951860000):0.0366126000):0.3870870000):0.2835290000):0.0000005263);
+(Escherichia_coli--CFT073:0.8015480000,(Escherichia_coli--EDL933:0.5191870000,(Escherichia_coli--K-12_MG1655:0.2992600000,Escherichia_coli--K-12_W3110:0.2999350000):0.1610400000):0.0025293800,(((Klebsiella_pneumoniae--ATCC_13883:0.9570800000,(Klebsiella_pneumoniae--MGH_78578:0.3385090000,Yersinia_ruckeri--YRB:0.3359350000):0.4454750000):0.0667819000,(Klebsiella_pneumoniae--HS11286:0.0959220000,Proteus_mirabilis--HI4320:0.2050960000):0.4137000000):0.1226380000,((Salmonella_enterica--AKU_12601:0.6141750000,(Salmonella_enterica--LT2:0.4366440000,Salmonella_enterica--P125109:0.5814070000):0.1061230000):0.0807539000,Salmonella_enterica--CT18:0.1996500000):0.3566300000):0.2816060000);
+(Escherichia_coli--CFT073:0.7976580000,(Escherichia_coli--EDL933:0.5102760000,(Escherichia_coli--K-12_MG1655:0.3012190000,Escherichia_coli--K-12_W3110:0.2995260000):0.1656230000):0.0000006525,(((Klebsiella_pneumoniae--ATCC_13883:0.9661010000,(Klebsiella_pneumoniae--MGH_78578:0.3530050000,Yersinia_ruckeri--YRB:0.3459880000):0.4243960000):0.0744548000,(Klebsiella_pneumoniae--HS11286:0.1700370000,Proteus_mirabilis--HI4320:0.1704900000):0.3379180000):0.1203730000,((Salmonella_enterica--AKU_12601:0.6148730000,(Salmonella_enterica--LT2:0.4363540000,Salmonella_enterica--P125109:0.5806820000):0.1041630000):0.0752709000,Salmonella_enterica--CT18:0.2120120000):0.3445530000):0.2864430000);
+(Escherichia_coli--CFT073:0.7971450000,Escherichia_coli--EDL933:0.5145060000,((Escherichia_coli--K-12_MG1655:0.2970020000,Escherichia_coli--K-12_W3110:0.3022520000):0.1684920000,(((Klebsiella_pneumoniae--ATCC_13883:0.9848010000,(Klebsiella_pneumoniae--MGH_78578:0.3471550000,Yersinia_ruckeri--YRB:0.3744080000):0.4283520000):0.0764883000,(Klebsiella_pneumoniae--HS11286:0.1609780000,Proteus_mirabilis--HI4320:0.2355880000):0.3317530000):0.1195980000,((Salmonella_enterica--AKU_12601:0.6120900000,(Salmonella_enterica--LT2:0.4366840000,Salmonella_enterica--P125109:0.5866800000):0.1016680000):0.0694270000,Salmonella_enterica--CT18:0.2048650000):0.3731510000):0.2675850000):0.0000006525);
+(Escherichia_coli--CFT073:0.8052720000,Escherichia_coli--EDL933:0.5169920000,((Escherichia_coli--K-12_MG1655:0.3031990000,Escherichia_coli--K-12_W3110:0.2971320000):0.1574750000,(((Klebsiella_pneumoniae--ATCC_13883:0.9670570000,(Klebsiella_pneumoniae--MGH_78578:0.3138820000,Yersinia_ruckeri--YRB:0.3639280000):0.4442530000):0.0776308000,(Klebsiella_pneumoniae--HS11286:0.1205730000,Proteus_mirabilis--HI4320:0.2055680000):0.3914600000):0.1263980000,((Salmonella_enterica--AKU_12601:0.6143040000,(Salmonella_enterica--LT2:0.4440610000,Salmonella_enterica--P125109:0.5801810000):0.0993106000):0.0653566000,Salmonella_enterica--CT18:0.2098280000):0.3652900000):0.2991860000):0.0000983596);
+(Escherichia_coli--CFT073:0.7948700000,(Escherichia_coli--EDL933:0.5163030000,(Escherichia_coli--K-12_MG1655:0.2971320000,Escherichia_coli--K-12_W3110:0.3015500000):0.1625400000):0.0000005263,(((Klebsiella_pneumoniae--ATCC_13883:0.9570710000,(Klebsiella_pneumoniae--MGH_78578:0.2611440000,Yersinia_ruckeri--YRB:0.3383110000):0.5192450000):0.0795755000,Klebsiella_pneumoniae--HS11286:0.4948020000):0.0908180000,((Proteus_mirabilis--HI4320:0.2326890000,Salmonella_enterica--CT18:0.0289430000):0.2254840000,(Salmonella_enterica--AKU_12601:0.6167880000,(Salmonella_enterica--LT2:0.4345960000,Salmonella_enterica--P125109:0.5832860000):0.0961108000):0.0316416000):0.3703760000):0.3062370000);
+(Escherichia_coli--CFT073:0.7917980000,Escherichia_coli--EDL933:0.5135060000,((Escherichia_coli--K-12_MG1655:0.3011580000,Escherichia_coli--K-12_W3110:0.3016680000):0.1679790000,(((Klebsiella_pneumoniae--ATCC_13883:0.9621490000,(Klebsiella_pneumoniae--MGH_78578:0.3244010000,Yersinia_ruckeri--YRB:0.2976840000):0.4427120000):0.0859083000,(Klebsiella_pneumoniae--HS11286:0.1498930000,Proteus_mirabilis--HI4320:0.1925060000):0.3636310000):0.0987995000,((Salmonella_enterica--AKU_12601:0.6155460000,(Salmonella_enterica--LT2:0.4329870000,Salmonella_enterica--P125109:0.5825010000):0.1057560000):0.0637493000,Salmonella_enterica--CT18:0.2166590000):0.3520350000):0.3028090000):0.0000007123);
+(Escherichia_coli--CFT073:0.8047340000,(Escherichia_coli--EDL933:0.5158470000,(Escherichia_coli--K-12_MG1655:0.2976100000,Escherichia_coli--K-12_W3110:0.2993350000):0.1653890000):0.0005788710,(((Klebsiella_pneumoniae--ATCC_13883:0.9561270000,(Klebsiella_pneumoniae--MGH_78578:0.3091320000,Yersinia_ruckeri--YRB:0.3449640000):0.4454570000):0.0765762000,(Klebsiella_pneumoniae--HS11286:0.1018080000,Proteus_mirabilis--HI4320:0.1992480000):0.4263510000):0.1070230000,((Salmonella_enterica--AKU_12601:0.6163860000,(Salmonella_enterica--LT2:0.4472320000,Salmonella_enterica--P125109:0.5781510000):0.1011030000):0.0746568000,Salmonella_enterica--CT18:0.1903880000):0.3818550000):0.2881890000);
+(Escherichia_coli--CFT073:0.7958160000,(Escherichia_coli--EDL933:0.5129660000,(Escherichia_coli--K-12_MG1655:0.3011590000,Escherichia_coli--K-12_W3110:0.3010200000):0.1646420000):0.0012471200,(((Klebsiella_pneumoniae--ATCC_13883:0.9711890000,(Klebsiella_pneumoniae--MGH_78578:0.3455210000,Yersinia_ruckeri--YRB:0.3674730000):0.4290830000):0.0568982000,(Klebsiella_pneumoniae--HS11286:0.1616260000,Proteus_mirabilis--HI4320:0.2503830000):0.3570590000):0.1318750000,((Salmonella_enterica--AKU_12601:0.6135020000,(Salmonella_enterica--LT2:0.4325350000,Salmonella_enterica--P125109:0.5850100000):0.1045850000):0.1008710000,Salmonella_enterica--CT18:0.1745680000):0.3694640000):0.2737680000);
+(Escherichia_coli--CFT073:0.7908550000,Escherichia_coli--EDL933:0.5149730000,((Escherichia_coli--K-12_MG1655:0.3021460000,Escherichia_coli--K-12_W3110:0.2984400000):0.1649900000,(((Klebsiella_pneumoniae--ATCC_13883:0.9679130000,(Klebsiella_pneumoniae--MGH_78578:0.3222330000,Yersinia_ruckeri--YRB:0.3744930000):0.4423970000):0.0736090000,(Klebsiella_pneumoniae--HS11286:0.1346460000,Proteus_mirabilis--HI4320:0.2145570000):0.3797660000):0.1146930000,((Salmonella_enterica--AKU_12601:0.6095350000,(Salmonella_enterica--LT2:0.4409010000,Salmonella_enterica--P125109:0.5806960000):0.1029680000):0.0619674000,Salmonella_enterica--CT18:0.2158680000):0.3464520000):0.3113640000):0.0000005338);
+(Escherichia_coli--CFT073:0.8041690000,(Escherichia_coli--EDL933:0.5168960000,(Escherichia_coli--K-12_MG1655:0.3008540000,Escherichia_coli--K-12_W3110:0.2977400000):0.1598180000):0.0007012930,(((Klebsiella_pneumoniae--ATCC_13883:0.9666020000,(Klebsiella_pneumoniae--MGH_78578:0.2775160000,Yersinia_ruckeri--YRB:0.3849530000):0.4907490000):0.0879016000,Klebsiella_pneumoniae--HS11286:0.4887430000):0.1186950000,((Proteus_mirabilis--HI4320:0.2833440000,Salmonella_enterica--CT18:0.0332440000):0.2081260000,(Salmonella_enterica--AKU_12601:0.6159060000,(Salmonella_enterica--LT2:0.4297580000,Salmonella_enterica--P125109:0.5874850000):0.1004170000):0.0468840000):0.3646170000):0.2804650000);
+(Escherichia_coli--CFT073:0.7910050000,Escherichia_coli--EDL933:0.5182020000,((Escherichia_coli--K-12_MG1655:0.2987460000,Escherichia_coli--K-12_W3110:0.2990040000):0.1672480000,(((Klebsiella_pneumoniae--ATCC_13883:0.9589110000,(Klebsiella_pneumoniae--MGH_78578:0.3551770000,Yersinia_ruckeri--YRB:0.3763420000):0.4378000000):0.0631995000,(Klebsiella_pneumoniae--HS11286:0.1529770000,Proteus_mirabilis--HI4320:0.2237900000):0.3482190000):0.1081410000,((Salmonella_enterica--AKU_12601:0.6251400000,(Salmonella_enterica--LT2:0.4382760000,Salmonella_enterica--P125109:0.5761810000):0.1009880000):0.0538787000,Salmonella_enterica--CT18:0.2219270000):0.3649600000):0.2808640000):0.0000007592);
+(Escherichia_coli--CFT073:0.7814780000,(Escherichia_coli--EDL933:0.5187310000,(Escherichia_coli--K-12_MG1655:0.2985620000,Escherichia_coli--K-12_W3110:0.3033330000):0.1625950000):0.0003225630,(((Klebsiella_pneumoniae--ATCC_13883:0.9719360000,(Klebsiella_pneumoniae--MGH_78578:0.3218720000,Yersinia_ruckeri--YRB:0.3546220000):0.4434670000):0.0787934000,(Klebsiella_pneumoniae--HS11286:0.1534100000,Proteus_mirabilis--HI4320:0.2424140000):0.3608820000):0.1127940000,((Salmonella_enterica--AKU_12601:0.6110820000,(Salmonella_enterica--LT2:0.4419420000,Salmonella_enterica--P125109:0.5755610000):0.1061510000):0.0625126000,Salmonella_enterica--CT18:0.2154270000):0.3623840000):0.2966780000);
+(Escherichia_coli--CFT073:0.7964880000,(Escherichia_coli--EDL933:0.5186400000,(Escherichia_coli--K-12_MG1655:0.2967330000,Escherichia_coli--K-12_W3110:0.3003280000):0.1630880000):0.0000006525,(((Klebsiella_pneumoniae--ATCC_13883:0.9702590000,(Klebsiella_pneumoniae--MGH_78578:0.3432770000,Yersinia_ruckeri--YRB:0.3807690000):0.4226460000):0.0915091000,(Klebsiella_pneumoniae--HS11286:0.1636170000,Proteus_mirabilis--HI4320:0.1979110000):0.3312310000):0.1035870000,((Salmonella_enterica--AKU_12601:0.6176130000,(Salmonella_enterica--LT2:0.4369370000,Salmonella_enterica--P125109:0.5777950000):0.1004700000):0.0708443000,Salmonella_enterica--CT18:0.2127730000):0.3881530000):0.2754960000);
+(Escherichia_coli--CFT073:0.7937370000,(Escherichia_coli--EDL933:0.5124670000,(Escherichia_coli--K-12_MG1655:0.3003990000,Escherichia_coli--K-12_W3110:0.2982480000):0.1645310000):0.0011845400,(((Klebsiella_pneumoniae--ATCC_13883:0.9555510000,(Klebsiella_pneumoniae--MGH_78578:0.3242740000,Yersinia_ruckeri--YRB:0.3448340000):0.4442720000):0.0717242000,(Klebsiella_pneumoniae--HS11286:0.1097370000,Proteus_mirabilis--HI4320:0.2250570000):0.4035470000):0.1146970000,((Salmonella_enterica--AKU_12601:0.6113910000,(Salmonella_enterica--LT2:0.4376990000,Salmonella_enterica--P125109:0.5825410000):0.1009570000):0.0779786000,Salmonella_enterica--CT18:0.1976310000):0.3694720000):0.2867890000);
diff --git a/mkdocs-user.yml b/mkdocs-user.yml
index 40ca9021..8c57fd1e 100644
--- a/mkdocs-user.yml
+++ b/mkdocs-user.yml
@@ -46,6 +46,7 @@ nav:
       - dump: usage/dump.md
       - annotate: usage/annotate.md
       - phylo: usage/phylo.md
+      - name-tree: usage/name-tree.md
       - unitig: usage/unitig.md
       - estimate: usage/estimate.md
       - reindex: usage/reindex.md
diff --git a/sankoff_params.yaml b/sankoff_params.yaml
index 489cf29c..f3196c17 100644
--- a/sankoff_params.yaml
+++ b/sankoff_params.yaml
@@ -2,166 +2,166 @@ ratio_ceiling: 0.5
 cardinality_transitions:
 - from: 0
   to: 0
-  count: 37622567
-  probability: 0.7765461217831444
+  count: 54999793
+  probability: 0.7934021725308564
 - from: 0
   to: 1
-  count: 6977400
-  probability: 0.14401656617768033
+  count: 8873859
+  probability: 0.12801028195383377
 - from: 0
   to: 2
-  count: 3744558
-  probability: 0.0772893033240408
+  count: 5305545
+  probability: 0.07653539585976665
 - from: 0
   to: 3
-  count: 91083
-  probability: 0.0018799926759482985
+  count: 126109
+  probability: 0.001819191475424167
 - from: 0
   to: 4
-  count: 12985
-  probability: 0.0002680160391861122
+  count: 16149
+  probability: 0.00023295818011898336
 - from: 1
   to: 0
-  count: 6977400
-  probability: 0.820630384894398
+  count: 8873859
+  probability: 0.8510749571674425
 - from: 1
   to: 1
-  count: 1018042
-  probability: 0.1197346000370715
+  count: 1041044
+  probability: 0.09984455215137214
 - from: 1
   to: 2
-  count: 502624
-  probability: 0.05911493200578466
+  count: 507272
+  probability: 0.048651493749477304
 - from: 1
   to: 3
-  count: 4197
-  probability: 0.000493620220340211
+  count: 4248
+  probability: 0.00040741760918753563
 - from: 1
   to: 4
   count: 225
-  probability: 0.000026462842405658202
+  probability: 0.00002157932252052625
 - from: 2
   to: 0
-  count: 3744558
-  probability: 0.8804244781723005
+  count: 5305545
+  probability: 0.9117891245815953
 - from: 2
   to: 1
-  count: 502624
-  probability: 0.11817749195415704
+  count: 507272
+  probability: 0.08717767784549091
 - from: 2
   to: 2
-  count: 5162
-  probability: 0.0012136949558066439
+  count: 5227
+  probability: 0.0008982907041949506
 - from: 2
   to: 3
-  count: 688
-  probability: 0.0001617632951559417
+  count: 689
+  probability: 0.00011840870388182915
 - from: 2
   to: 4
   count: 96
-  probability: 0.00002257162257989884
+  probability: 0.000016498164836945715
 - from: 3
   to: 0
-  count: 91083
-  probability: 0.9478728718311618
+  count: 126109
+  probability: 0.9614164824273843
 - from: 3
   to: 1
-  count: 4197
-  probability: 0.04367689297756317
+  count: 4248
+  probability: 0.03238545399100404
 - from: 3
   to: 2
-  count: 688
-  probability: 0.007159805186696083
+  count: 689
+  probability: 0.005252725470763132
 - from: 3
   to: 3
   count: 98
-  probability: 0.0010198559713607792
+  probability: 0.0007471220553480217
 - from: 3
   to: 4
   count: 26
-  probability: 0.00027057403321816594
+  probability: 0.00019821605550049553
 - from: 4
   to: 0
-  count: 12985
-  probability: 0.972950696838004
+  count: 16149
+  probability: 0.9781344639612356
 - from: 4
   to: 1
   count: 225
-  probability: 0.01685898396523303
+  probability: 0.013628104179285281
 - from: 4
   to: 2
   count: 96
-  probability: 0.0071931664918327585
+  probability: 0.00581465778316172
 - from: 4
   to: 3
   count: 26
-  probability: 0.0019481492582047056
+  probability: 0.0015748031496062992
 - from: 4
   to: 4
   count: 14
-  probability: 0.0010490034467256107
+  probability: 0.0008479709267110841
 composition_transitions:
 - from: 'A'
   to: 'A'
-  count: 157182
-  probability: 0.46648741052031767
+  count: 161774
+  probability: 0.4701762136303263
 - from: 'A'
   to: 'C'
-  count: 27305
-  probability: 0.08103624298111281
+  count: 27788
+  probability: 0.0807624007835592
 - from: 'A'
   to: 'G'
-  count: 128548
-  probability: 0.38150693875612857
+  count: 130019
+  probability: 0.3778842157577942
 - from: 'A'
   to: 'T'
-  count: 23913
-  probability: 0.07096940774244097
+  count: 24490
+  probability: 0.07117716982832031
 - from: 'C'
   to: 'A'
-  count: 27305
-  probability: 0.07823849488677553
+  count: 27788
+  probability: 0.0780165140757087
 - from: 'C'
   to: 'C'
-  count: 179118
-  probability: 0.5132365034656459
+  count: 184047
+  probability: 0.5167232390273484
 - from: 'C'
   to: 'G'
-  count: 19392
-  probability: 0.055564947549692406
+  count: 19622
+  probability: 0.05508996830263265
 - from: 'C'
   to: 'T'
-  count: 123182
-  probability: 0.3529600540978862
+  count: 124724
+  probability: 0.3501702785943102
 - from: 'G'
   to: 'A'
-  count: 128548
-  probability: 0.3637269077214298
+  count: 130019
+  probability: 0.3610094570655886
 - from: 'G'
   to: 'C'
-  count: 19392
-  probability: 0.05486971555009776
+  count: 19622
+  probability: 0.05448224926003876
 - from: 'G'
   to: 'G'
-  count: 179245
-  probability: 0.5071742039901647
+  count: 183951
+  probability: 0.5107565097152884
 - from: 'G'
   to: 'T'
-  count: 26234
-  probability: 0.07422917273830779
+  count: 26562
+  probability: 0.07375178395908417
 - from: 'T'
   to: 'A'
-  count: 23913
-  probability: 0.07307212790143376
+  count: 24490
+  probability: 0.07335783586895636
 - from: 'T'
   to: 'C'
-  count: 123182
-  probability: 0.3764132839524281
+  count: 124724
+  probability: 0.37360076443118473
 - from: 'T'
   to: 'G'
-  count: 26234
-  probability: 0.08016452153080807
+  count: 26562
+  probability: 0.07956434611479049
 - from: 'T'
   to: 'T'
-  count: 153923
-  probability: 0.4703500666153301
+  count: 158067
+  probability: 0.4734770535850684
diff --git a/src/obikindex/src/cardcomp.rs b/src/obikindex/src/cardcomp.rs
index d3fb39bd..eab104a3 100644
--- a/src/obikindex/src/cardcomp.rs
+++ b/src/obikindex/src/cardcomp.rs
@@ -129,7 +129,23 @@ fn best_pairing_cost(lost: &[u8], gained: &[u8], p_comp: &[[f64; 4]; 4]) -> f64
 /// symmetrised (`(cost(A,B)+cost(B,A))/2` — the row-normalised `P` is not
 /// symmetric in general, but a Sankoff parsimony cost must be, so the
 /// score is independent of where an unrooted tree gets rooted).
-pub fn pairwise_cost_matrix(p_card: &[[f64; 5]; 5], p_comp: &[[f64; 4]; 4]) -> [[f64; 16]; 16] {
+///
+/// `free_loss`: drop the `P_cardinality(|A|→|B|)` factor entirely (never
+/// added to `log_p`) — the same low/incomplete-coverage argument that
+/// justifies recoding whole-family non-detection as `?` (see
+/// `docmd/theory/evolutionary_distances.md`, "Locus dropout under
+/// incomplete coverage") applies one level down: whether a genome shows 1
+/// vs 2 (etc.) detected members of a *present* family is exactly as
+/// vulnerable to sampling failure as whether the family was detected at
+/// all. Without this, `∅`-involving transitions are neutralised (via the
+/// `?` recoding, bypassing this matrix's row/column 0 entirely) but
+/// cardinality changes *between two otherwise-detected, non-empty* states
+/// (e.g. `{A} -> {A,C}`) still carried the same calibrated
+/// `P_cardinality` penalty as any other gain/loss — inconsistent with
+/// `--free-loss`'s own rationale. With the factor dropped, cost is driven
+/// only by composition matching (shared-base retention and paired
+/// substitutions), never by a state pair's cardinality difference alone.
+pub fn pairwise_cost_matrix(p_card: &[[f64; 5]; 5], p_comp: &[[f64; 4]; 4], free_loss: bool) -> [[f64; 16]; 16] {
     let mut raw = [[0.0f64; 16]; 16];
     for a in 0u8..16 {
         for b in 0u8..16 {
@@ -138,10 +154,12 @@ pub fn pairwise_cost_matrix(p_card: &[[f64; 5]; 5], p_comp: &[[f64; 4]; 4]) -> [
             let gained: Vec<u8> = (0..4).filter(|&i| b & (1 << i) != 0 && a & (1 << i) == 0).collect();
 
             let mut log_p = 0.0; // accumulate ln(P), so 0.0 = probability 1
-            let card_a = a.count_ones() as usize;
-            let card_b = b.count_ones() as usize;
-            let p_c = p_card[card_a][card_b];
-            log_p += if p_c > 0.0 { p_c.ln() } else { f64::NEG_INFINITY };
+            if !free_loss {
+                let card_a = a.count_ones() as usize;
+                let card_b = b.count_ones() as usize;
+                let p_c = p_card[card_a][card_b];
+                log_p += if p_c > 0.0 { p_c.ln() } else { f64::NEG_INFINITY };
+            }
 
             for i in 0..4u8 {
                 if shared & (1 << i) != 0 {
@@ -231,7 +249,7 @@ mod tests {
             [0.15, 0.05, 0.7, 0.1],
             [0.05, 0.15, 0.1, 0.7],
         ];
-        let cost = pairwise_cost_matrix(&p_card, &p_comp);
+        let cost = pairwise_cost_matrix(&p_card, &p_comp, false);
         for a in 0..16 {
             assert_eq!(cost[a][a], 0.0);
             for b in 0..16 {
@@ -239,4 +257,36 @@ mod tests {
             }
         }
     }
+
+    #[test]
+    fn free_loss_ignores_cardinality_transition_probs() {
+        // A skewed cardinality model (cardinality change made artificially
+        // expensive) must have zero effect on the cost matrix once
+        // `free_loss` is set — the whole point of the flag.
+        let p_card_uniform = [[0.2f64; 5]; 5];
+        let p_card_skewed = [
+            [0.96, 0.01, 0.01, 0.01, 0.01],
+            [0.01, 0.96, 0.01, 0.01, 0.01],
+            [0.01, 0.01, 0.96, 0.01, 0.01],
+            [0.01, 0.01, 0.01, 0.96, 0.01],
+            [0.01, 0.01, 0.01, 0.01, 0.96],
+        ];
+        let p_comp = [
+            [0.7, 0.1, 0.15, 0.05],
+            [0.1, 0.7, 0.05, 0.15],
+            [0.15, 0.05, 0.7, 0.1],
+            [0.05, 0.15, 0.1, 0.7],
+        ];
+        let cost_uniform = pairwise_cost_matrix(&p_card_uniform, &p_comp, true);
+        let cost_skewed = pairwise_cost_matrix(&p_card_skewed, &p_comp, true);
+        for a in 0..16 {
+            for b in 0..16 {
+                assert!(
+                    (cost_uniform[a][b] - cost_skewed[a][b]).abs() < 1e-9,
+                    "cost[{a}][{b}] differs between cardinality models under free_loss: {} vs {}",
+                    cost_uniform[a][b], cost_skewed[a][b],
+                );
+            }
+        }
+    }
 }
diff --git a/src/obikmer/src/cmd/mod.rs b/src/obikmer/src/cmd/mod.rs
index 619edea6..7450a7a2 100644
--- a/src/obikmer/src/cmd/mod.rs
+++ b/src/obikmer/src/cmd/mod.rs
@@ -9,6 +9,7 @@ pub mod dump;
 pub mod estimate;
 pub mod index;
 pub mod merge;
+pub mod nametree;
 pub mod query;
 pub mod reindex;
 pub mod superkmer;
diff --git a/src/obikmer/src/cmd/nametree.rs b/src/obikmer/src/cmd/nametree.rs
new file mode 100644
index 00000000..c2474def
--- /dev/null
+++ b/src/obikmer/src/cmd/nametree.rs
@@ -0,0 +1,146 @@
+use std::path::{Path, PathBuf};
+
+use clap::Args;
+use tracing::info;
+
+// ── Translate a numerically-labelled tree export back to real taxon names ──
+//
+// TNT/PhyG write bare numeric leaf labels (1-based, in the same order as the
+// FASTA fed to them) — this reads that order back from the FASTA header
+// line and emits a NEXUS `translate` table alongside the tree(s), unchanged
+// otherwise. Readable directly by FigTree/PearTree/`ape` etc.
+
+#[derive(Args)]
+pub struct NameTreeArgs {
+    /// Tree file to translate: a TNT-style NEXUS export (`tree NAME = [&U]
+    /// ...;`, topology on the same or the next line) or a plain Newick file
+    /// (single `(...);` tree, no header)
+    pub tree: PathBuf,
+
+    /// FASTA file whose record order gives the numeric taxon labels
+    /// (1-based) — typically the `_sankoff.fasta`/`_snp.fasta` used to
+    /// produce `tree`
+    #[arg(long)]
+    pub fasta: PathBuf,
+
+    /// Output NEXUS file (taxa block + translate table + tree(s), topology
+    /// unchanged)
+    #[arg(short, long)]
+    pub output: PathBuf,
+}
+
+pub fn run(args: NameTreeArgs) {
+    let labels = read_fasta_labels(&args.fasta);
+    if labels.is_empty() {
+        eprintln!("error: no FASTA headers found in {}", args.fasta.display());
+        std::process::exit(1);
+    }
+
+    let content = std::fs::read_to_string(&args.tree).unwrap_or_else(|e| {
+        eprintln!("error reading {}: {e}", args.tree.display());
+        std::process::exit(1);
+    });
+    let trees = extract_trees(&content);
+    if trees.is_empty() {
+        eprintln!("error: no tree found in {}", args.tree.display());
+        std::process::exit(1);
+    }
+
+    write_named_nexus(&labels, &trees, &args.output);
+}
+
+fn read_fasta_labels(path: &Path) -> Vec<String> {
+    let content = std::fs::read_to_string(path).unwrap_or_else(|e| {
+        eprintln!("error reading {}: {e}", path.display());
+        std::process::exit(1);
+    });
+    content.lines()
+        .filter(|l| l.starts_with('>'))
+        .map(|l| {
+            let header = &l[1..];
+            // `obifastwrite::write_record` appends a ` {json}` annotation —
+            // not part of the taxon name.
+            match header.find(" {") {
+                Some(pos) => header[..pos].to_string(),
+                None => header.to_string(),
+            }
+        })
+        .collect()
+}
+
+/// Finds every `tree NAME = [&U] TOPOLOGY;` (rooting comment optional,
+/// topology on the same line or the next non-empty one), or — if none of
+/// that syntax is found — treats the whole file as one bare Newick tree.
+fn extract_trees(content: &str) -> Vec<(String, String)> {
+    let lines: Vec<&str> = content.lines().collect();
+    let mut trees = Vec::new();
+    let mut i = 0;
+    while i < lines.len() {
+        let line = lines[i].trim();
+        if let Some(rest) = line.strip_prefix("tree ") {
+            if let Some(eq_pos) = rest.find('=') {
+                let name = rest[..eq_pos].trim().to_string();
+                let mut after_eq = rest[eq_pos + 1..].trim();
+                if after_eq.starts_with('[') {
+                    if let Some(close) = after_eq.find(']') {
+                        after_eq = after_eq[close + 1..].trim();
+                    }
+                }
+                let topo = if after_eq.starts_with('(') {
+                    after_eq.to_string()
+                } else {
+                    i += 1;
+                    while i < lines.len() && lines[i].trim().is_empty() {
+                        i += 1;
+                    }
+                    lines.get(i).map(|s| s.trim().to_string()).unwrap_or_default()
+                };
+                if topo.starts_with('(') {
+                    trees.push((name, topo));
+                }
+            }
+        }
+        i += 1;
+    }
+
+    if trees.is_empty() {
+        let trimmed = content.trim();
+        if trimmed.starts_with('(') && trimmed.ends_with(';') {
+            trees.push(("tree_1".to_string(), trimmed.to_string()));
+        }
+    }
+
+    trees
+}
+
+fn write_named_nexus(labels: &[String], trees: &[(String, String)], output: &Path) {
+    let mut out = String::new();
+    out.push_str("#NEXUS\n\n");
+    out.push_str("begin taxa;\n");
+    out.push_str(&format!("  dimensions ntax={};\n", labels.len()));
+    out.push_str("  taxlabels\n");
+    for lab in labels {
+        out.push_str(&format!("    {lab}\n"));
+    }
+    out.push_str("  ;\nend;\n\n");
+    out.push_str("begin trees;\n");
+    out.push_str("  translate\n");
+    let tr_lines: Vec<String> = labels.iter().enumerate()
+        .map(|(i, lab)| format!("    {} {lab}", i + 1))
+        .collect();
+    out.push_str(&tr_lines.join(",\n"));
+    out.push_str(";\n");
+    for (name, topo) in trees {
+        out.push_str(&format!("  tree {name} = [&U] {topo}\n"));
+    }
+    out.push_str("end;\n");
+
+    std::fs::write(output, &out).unwrap_or_else(|e| {
+        eprintln!("error writing {}: {e}", output.display());
+        std::process::exit(1);
+    });
+    info!(
+        "named tree(s) → {} ({} tree{}, {} taxa)",
+        output.display(), trees.len(), if trees.len() == 1 { "" } else { "s" }, labels.len(),
+    );
+}
diff --git a/src/obikmer/src/cmd/phylo/mod.rs b/src/obikmer/src/cmd/phylo/mod.rs
index 1f08cdc5..d510822c 100644
--- a/src/obikmer/src/cmd/phylo/mod.rs
+++ b/src/obikmer/src/cmd/phylo/mod.rs
@@ -184,7 +184,7 @@ pub fn run(args: PhyloArgs) {
         });
         let p_card = cardinality_transition_probs(&card_tally);
         let p_comp = composition_transition_probs(&base_tally);
-        let matrix = pairwise_cost_matrix(&p_card, &p_comp);
+        let matrix = pairwise_cost_matrix(&p_card, &p_comp, args.free_loss);
         write_sankoff_matrix_csv(&matrix, &args.output);
         write_sankoff_params(&card_tally, &p_card, &base_tally, &p_comp, args.sankoff_ratio_ceiling, &args.output);
 
diff --git a/src/obikmer/src/main.rs b/src/obikmer/src/main.rs
index 73e49b01..f2aeaa60 100644
--- a/src/obikmer/src/main.rs
+++ b/src/obikmer/src/main.rs
@@ -33,6 +33,9 @@ enum Commands {
     /// Compute pairwise evolutionary-distance proxies between genomes (metric matrix, NJ/UPGMA
     /// trees, SNP/Sankoff calibration, TNT/PhyG/IQ-TREE exports)
     Phylo(cmd::phylo::PhyloArgs),
+    /// Translate a numerically-labelled tree export (TNT/PhyG) back to real taxon names, from
+    /// the FASTA that produced it
+    NameTree(cmd::nametree::NameTreeArgs),
     /// Dump unitigs from a built index to stdout (debug)
     Unitig(cmd::unitig::UnitigArgs),
     /// Estimate approximate-index parameters (z, evidence bits, FP rates) before indexing
@@ -73,6 +76,7 @@ fn main() {
         Commands::Query(args)     => cmd::query::run(args),
         Commands::Annotate(args)  => cmd::annotate::run(args),
         Commands::Phylo(args)     => cmd::phylo::run(args),
+        Commands::NameTree(args)  => cmd::nametree::run(args),
         Commands::Unitig(args)    => cmd::unitig::run(args),
         Commands::Estimate(args)  => cmd::estimate::run(args),
         Commands::Reindex(args)   => cmd::reindex::run(args),
-- 
2.54.0


From d54ae272a42e08ba061d9cfdcc0b28d2024bf343 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Thu, 13 Aug 2026 22:55:49 +0200
Subject: [PATCH 14/46] refactor: centralize index setup logic and add progress
 bar ETA

Extracts directory cleanup, partition initialization, and finalization into dedicated helper methods within KmerIndex. This centralizes force-flag handling and reduces boilerplate across merge, rebuild, and select workflows. Additionally updates the CLI progress bar template to display an ETA indicator following elapsed time.
---
 src/obikindex/src/index.rs   | 61 +++++++++++++++++++++++++++++++++++-
 src/obikindex/src/merge.rs   | 11 +------
 src/obikindex/src/rebuild.rs | 37 +++-------------------
 src/obikindex/src/select.rs  | 35 +++------------------
 src/obisys/src/progress.rs   |  4 +--
 5 files changed, 73 insertions(+), 75 deletions(-)

diff --git a/src/obikindex/src/index.rs b/src/obikindex/src/index.rs
index f6b08893..6d2163ed 100644
--- a/src/obikindex/src/index.rs
+++ b/src/obikindex/src/index.rs
@@ -2,7 +2,7 @@ use std::collections::BTreeMap;
 use std::fs;
 use std::path::{Path, PathBuf};
 
-use obikpartitionner::{KmerPartition, KmerSpectrum};
+use obikpartitionner::{KmerPartition, KmerSpectrum, PARTITIONS_SUBDIR};
 use obilayeredmap;
 use obisys::{Reporter, Stage, progress_bar};
 use rayon::prelude::*;
@@ -68,6 +68,65 @@ impl KmerIndex {
         IndexMeta::exists(path.as_ref())
     }
 
+    /// Make `output` ready to receive a newly created index.
+    ///
+    /// If an index already exists there, remove it when `force` is set,
+    /// otherwise fail. A bare directory with no `index.meta` (e.g. one left
+    /// behind by a `DirLock`) is not considered a pre-existing index.
+    pub fn clear_output_for_create<P: AsRef<Path>>(output: P, force: bool) -> OKIResult<()> {
+        let output = output.as_ref();
+        if Self::exists(output) {
+            if force {
+                fs::remove_dir_all(output).map_err(OKIError::Io)?;
+            } else {
+                return Err(OKIError::Io(std::io::Error::new(
+                    std::io::ErrorKind::AlreadyExists,
+                    format!("{}: output directory already exists", output.display()),
+                )));
+            }
+        }
+        Ok(())
+    }
+
+    /// Lay out a fresh index skeleton at `output`: the root directory,
+    /// `index.meta` (from `meta`), and an opened, empty partition set.
+    ///
+    /// For construction paths that build partitions from scratch (`select`,
+    /// `rebuild`). `merge` bootstraps by copying a source index instead, so
+    /// it does not use this.
+    pub(crate) fn create_skeleton<P: AsRef<Path>>(
+        output: P,
+        meta: &IndexMeta,
+    ) -> OKIResult<KmerPartition> {
+        let output = output.as_ref();
+        fs::create_dir_all(output).map_err(OKIError::Io)?;
+        meta.write(output).map_err(OKIError::Io)?;
+        fs::create_dir_all(output.join(PARTITIONS_SUBDIR)).map_err(OKIError::Io)?;
+        Ok(KmerPartition::open_with_config(
+            output,
+            meta.config.kmer_size,
+            meta.config.minimizer_size,
+            meta.config.n_bits,
+        )?)
+    }
+
+    /// Mark `output` as fully indexed, pack its column matrices, and reopen it.
+    ///
+    /// Shared tail of the `select`/`rebuild` construction paths, once their
+    /// partitions have been written.
+    pub(crate) fn finalize_indexed<P: AsRef<Path>>(
+        output: P,
+        rep: &mut Reporter,
+    ) -> OKIResult<Self> {
+        let output = output.as_ref();
+        fs::File::create(output.join(SENTINEL_INDEXED)).map_err(OKIError::Io)?;
+        let idx = KmerIndex::open(output)?;
+        let t_pack = Stage::start("pack");
+        idx.pack_matrices()?;
+        rep.push(t_pack.stop());
+        Ok(idx)
+    }
+
     /// Current construction state, as reported by sentinel files on disk.
     pub fn state(&self) -> IndexState {
         IndexState::detect(&self.root_path).unwrap_or(IndexState::Empty)
diff --git a/src/obikindex/src/merge.rs b/src/obikindex/src/merge.rs
index cbfdabab..8d7840e9 100644
--- a/src/obikindex/src/merge.rs
+++ b/src/obikindex/src/merge.rs
@@ -130,16 +130,7 @@ impl KmerIndex {
         let (source_labels, all_genomes) = compute_labels(sources, rename_duplicates)?;
 
         // ── Prepare output directory ──────────────────────────────────────────
-        if output.exists() {
-            if force {
-                fs::remove_dir_all(output)?;
-            } else {
-                return Err(OKIError::Io(io::Error::new(
-                    io::ErrorKind::AlreadyExists,
-                    format!("{}: output directory already exists", output.display()),
-                )));
-            }
-        }
+        KmerIndex::clear_output_for_create(output, force)?;
 
         // ── Bootstrap: copy first source to output ────────────────────────────
         info!(
diff --git a/src/obikindex/src/rebuild.rs b/src/obikindex/src/rebuild.rs
index 83a416d6..3db37f2f 100644
--- a/src/obikindex/src/rebuild.rs
+++ b/src/obikindex/src/rebuild.rs
@@ -1,15 +1,13 @@
-use std::fs;
-use std::io;
 use std::path::Path;
 
-use obikpartitionner::{KmerFilter, KmerPartition, MergeMode};
+use obikpartitionner::{KmerFilter, MergeMode};
 use obisys::{Reporter, Stage, progress_bar};
 use tracing::info;
 
 use crate::error::{OKIError, OKIResult};
 use crate::index::KmerIndex;
 use crate::meta::IndexMeta;
-use crate::state::{IndexState, SENTINEL_INDEXED};
+use crate::state::IndexState;
 
 impl KmerIndex {
     /// Rebuild `src` into a new compact single-layer index at `output`.
@@ -40,36 +38,18 @@ impl KmerIndex {
             ));
         }
 
-        if output.exists() {
-            if force {
-                fs::remove_dir_all(output)?;
-            } else {
-                return Err(OKIError::Io(io::Error::new(
-                    io::ErrorKind::AlreadyExists,
-                    format!("{}: output directory already exists", output.display()),
-                )));
-            }
-        }
+        KmerIndex::clear_output_for_create(output, force)?;
 
         // ── Create output directory + metadata ────────────────────────────────
-        fs::create_dir_all(output)?;
         let mut meta = IndexMeta::new(src.meta.config.clone());
         meta.config.with_counts = mode == MergeMode::Count;
         meta.genomes = src.meta.genomes.clone();
-        meta.write(output)?;
 
         let n_genomes = src.meta.genomes.len();
         let n_partitions = src.partition.n_partitions();
 
         // ── Create an empty destination KmerPartition ─────────────────────────
-        // Create the partitions/ subdirectory so KmerPartition::open_with_config works.
-        fs::create_dir_all(output.join(obikpartitionner::PARTITIONS_SUBDIR))?;
-        let dst_partition = KmerPartition::open_with_config(
-            output,
-            meta.config.kmer_size,
-            meta.config.minimizer_size,
-            meta.config.n_bits,
-        )?;
+        let dst_partition = KmerIndex::create_skeleton(output, &meta)?;
 
         info!(
             "rebuild: {} partition(s), {} genome(s), mode={:?}",
@@ -94,13 +74,6 @@ impl KmerIndex {
 
         rep.push(t.stop());
 
-        // Write SENTINEL_INDEXED — output is ready to use.
-        fs::File::create(output.join(SENTINEL_INDEXED))?;
-
-        let idx = KmerIndex::open(output)?;
-        let t_pack = Stage::start("pack");
-        idx.pack_matrices()?;
-        rep.push(t_pack.stop());
-        Ok(idx)
+        KmerIndex::finalize_indexed(output, rep)
     }
 }
diff --git a/src/obikindex/src/select.rs b/src/obikindex/src/select.rs
index a27125b2..4639d3b3 100644
--- a/src/obikindex/src/select.rs
+++ b/src/obikindex/src/select.rs
@@ -1,15 +1,13 @@
-use std::fs;
-use std::io;
 use std::path::Path;
 
-use obikpartitionner::{KmerPartition, OutputCol, PARTITIONS_SUBDIR};
+use obikpartitionner::{KmerPartition, OutputCol};
 use obisys::{Reporter, Stage, progress_bar};
 use tracing::info;
 
 use crate::error::{OKIError, OKIResult};
 use crate::index::KmerIndex;
 use crate::meta::{GenomeInfo, IndexMeta};
-use crate::state::{IndexState, SENTINEL_INDEXED};
+use crate::state::IndexState;
 
 impl KmerIndex {
     /// Create a new index at `output` by projecting/aggregating the genome columns
@@ -33,35 +31,18 @@ impl KmerIndex {
             return Err(OKIError::NotIndexed(src.root_path.clone()));
         }
 
-        if output.exists() {
-            if force {
-                fs::remove_dir_all(output)?;
-            } else {
-                return Err(OKIError::Io(io::Error::new(
-                    io::ErrorKind::AlreadyExists,
-                    format!("{}: output directory already exists", output.display()),
-                )));
-            }
-        }
+        KmerIndex::clear_output_for_create(output, force)?;
 
-        fs::create_dir_all(output)?;
         let mut meta = IndexMeta::new(src.meta.config.clone());
         meta.config.with_counts = !output_presence;
         meta.genomes = specs.iter()
             .map(|s| GenomeInfo::new(s.label.clone()))
             .collect();
-        meta.write(output)?;
 
         let n_src_genomes  = src.meta.genomes.len();
         let n_partitions   = src.partition.n_partitions();
 
-        fs::create_dir_all(output.join(PARTITIONS_SUBDIR))?;
-        let dst_partition = KmerPartition::open_with_config(
-            output,
-            meta.config.kmer_size,
-            meta.config.minimizer_size,
-            meta.config.n_bits,
-        )?;
+        let dst_partition = KmerIndex::create_skeleton(output, &meta)?;
 
         info!(
             "select: {} partition(s), {} source genome(s) → {} output column(s)",
@@ -83,13 +64,7 @@ impl KmerIndex {
         pb.finish_and_clear();
         rep.push(t.stop());
 
-        fs::File::create(output.join(SENTINEL_INDEXED))?;
-
-        let idx = KmerIndex::open(output)?;
-        let t_pack = Stage::start("pack");
-        idx.pack_matrices()?;
-        rep.push(t_pack.stop());
-        Ok(idx)
+        KmerIndex::finalize_indexed(output, rep)
     }
 
     /// Rewrite the genome columns of this index in-place according to `specs`.
diff --git a/src/obisys/src/progress.rs b/src/obisys/src/progress.rs
index a311170d..3985c345 100644
--- a/src/obisys/src/progress.rs
+++ b/src/obisys/src/progress.rs
@@ -91,12 +91,12 @@ pub fn spinner(label: &str) -> TracedBar {
 }
 
 /// Progress bar with the standard project look:
-/// `⠋ label — [████░░░░] pos/len unit  elapsed`.
+/// `⠋ label — [████░░░░] pos/len unit  elapsed (eta: remaining)`.
 pub fn progress_bar(label: &str, n: u64, unit: &str) -> TracedBar {
     let pb = ProgressBar::new(n);
     pb.set_style(
         ProgressStyle::with_template(&format!(
-            "{{spinner}} {label} — {{bar:40.cyan/blue}} {{pos}}/{{len}} {unit}  {{elapsed}}"
+            "{{spinner}} {label} — {{bar:40.cyan/blue}} {{pos}}/{{len}} {unit}  {{elapsed}} (eta: {{eta}})"
         ))
         .unwrap()
         .tick_strings(BRAILLE),
-- 
2.54.0


From 3da501349b49350995bae1c8a658ca15c3db74dd Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Fri, 14 Aug 2026 07:43:07 +0200
Subject: [PATCH 15/46] docs: clarify phylogenetic output files and tool usage

Restructure the output files section into categorized subsections with tables. Add explicit mappings between command-line options and generated files. Define CSV matrix conventions, clarify mathematical formulas for distance calculations, and document execution commands for external phylogenetic tools.
---
 UserDocMD/usage/phylo.md | 84 +++++++++++++++++++++++++++++++++++++++-
 1 file changed, 83 insertions(+), 1 deletion(-)

diff --git a/UserDocMD/usage/phylo.md b/UserDocMD/usage/phylo.md
index 378a33d1..2d6b5e88 100644
--- a/UserDocMD/usage/phylo.md
+++ b/UserDocMD/usage/phylo.md
@@ -107,4 +107,86 @@ TNT and PhyG both write trees with bare numeric leaf labels (`1`, `2`, …, in t
 
 ## Output files
 
-With `-o/--output PREFIX`, the relevant subset of the following files is written: `<prefix>_dist.csv`, `<prefix>_shared.csv`, `<prefix>_nj.nwk`, `<prefix>_upgma.nwk`, `<prefix>_siblings.csv`, `<prefix>_rawsnp.csv`, `<prefix>_rawsnp_counts.csv`, `<prefix>_snp.fasta`, `<prefix>_family_overlap.csv`, `<prefix>_sankoff_matrix.csv`, `<prefix>_sankoff_params.yaml`, `<prefix>_sankoff.fasta`, `<prefix>_sankoff.tnt`, `<prefix>_sankoff.tcm`, `<prefix>_sankoff.pg`, `<prefix>_iqtree.model`, `<prefix>_iqtree.fasta`. Without `-o`, only the plain `--metric` distance matrix is produced, on stdout.
+With `-o/--output PREFIX`, the relevant subset of the files below is written. Without `-o`, only the plain `--metric` distance matrix is produced, on stdout. All matrices use genome labels (from the index metadata) as row/column headers, in index order; all CSVs are comma-separated with a header row.
+
+### Distance matrix
+
+| File | Written by | Format | Content |
+|---|---|---|---|
+| `<prefix>_dist.csv` | always | CSV matrix | the `--metric` distance, 6 decimals, symmetric, diagonal 0 |
+| `<prefix>_shared.csv` | `--shared-kmers` | CSV matrix | shared-kmer count per genome pair (integers) |
+| `<prefix>_nj.nwk` | `--nj` | Newick | Neighbor-Joining tree, branch lengths from the `--metric` matrix |
+| `<prefix>_upgma.nwk` | `--upgma` | Newick | UPGMA tree, same matrix |
+
+Matrix layout (`_dist.csv`, `_shared.csv`, and every other "CSV matrix" below): header `genome,<label1>,<label2>,...`, one data row per genome, `<label>,<value1>,<value2>,...`.
+
+### Central-position SNP model
+
+| File | Written by | Format | Content |
+|---|---|---|---|
+| `<prefix>_siblings.csv` | `--sibling-stats` | CSV table | family-size distribution, per genome and global |
+| `<prefix>_rawsnp.csv` | `--raw-snp-distance` | CSV matrix | single-copy central-SNP p-distance ($\hat p$), or `NA` |
+| `<prefix>_rawsnp_counts.csv` | `--raw-snp-counts` | CSV table | per-pair diagnostic counts behind `_rawsnp.csv` |
+| `<prefix>_snp.fasta` | `--snp` | FASTA | SNP-only pseudo-alignment, IUPAC-coded |
+| `<prefix>_family_overlap.csv` | `--family-overlap` | CSV matrix | variable families both genomes of a pair carry a call for |
+
+**`_siblings.csv`** — family size = number of distinct central bases observed at a family (1–4), not "sibling count" (0–3).
+
+| Column | Meaning |
+|---|---|
+| `genome` | genome label, or the literal `global` for the last row |
+| `1`, `2`, `3`, `4` | for a genome row: number of families of that size where the genome carries ≥ 1 member. For the `global` row: the actual deduplicated family-size histogram — **not** the sum of the rows above (a family shared by several genomes would otherwise be counted once per genome) |
+
+**`_rawsnp.csv`** — same matrix layout as `_dist.csv`; each cell is $\hat p = n_{\text{snp}}/(n_{\text{snp}}+n_{\text{shared}})$, 6 decimals, or `NA` when the pair has zero eligible loci (distinguishes "identical everywhere eligible" from "nothing eligible at all").
+
+**`_rawsnp_counts.csv`** — one row per unordered genome pair (not a matrix), the counts `_rawsnp.csv`'s ratio is computed from:
+
+| Column | Meaning |
+|---|---|
+| `genome_a`, `genome_b` | the pair |
+| `n_snp` | eligible loci where the two genomes' single forms differ |
+| `n_shared` | eligible loci where they agree (includes invariant families) |
+| `n_eligible` | `n_snp + n_shared` |
+| `ratio` | $\hat p$ = `n_snp / n_eligible`, or `NA` if `n_eligible = 0` |
+
+**`_snp.fasta`** — one record per non-excluded genome, one column per variable family (family size ≥ 2), header carries an `n_sites` annotation. Each site is IUPAC-coded from the genome's presence mask at that family: single observed form → plain base; several forms → matching IUPAC ambiguity code; no form → `-`.
+
+**`_family_overlap.csv`** — same matrix layout as `_dist.csv`; cell `[i][j]` = number of `_snp.fasta` columns where both genome `i` and `j` carry a call (neither is `-`). Diagonal `[i][i]` is kept (not skipped): it holds genome `i`'s own total variable-family count.
+
+### Sankoff calibration and exports
+
+| File | Written by | Format | Content |
+|---|---|---|---|
+| `<prefix>_sankoff_matrix.csv` | `--sankoff`/`--tnt`/`--phyg`/`--iqtree` | CSV matrix | calibrated 16×16 cost matrix |
+| `<prefix>_sankoff_params.yaml` | same flags | YAML | calibration report (raw tallies + derived probabilities) |
+| `<prefix>_sankoff.fasta` | same flags | FASTA | Sankoff-recoded pseudo-alignment |
+| `<prefix>_sankoff.tnt` | `--tnt` | TNT script | ready-to-run parsimony search |
+| `<prefix>_sankoff.tcm` | `--phyg` | PhyG TCM | cost matrix in PhyG's own format |
+| `<prefix>_sankoff.pg` | `--phyg` | PhyG script | ready-to-run parsimony search |
+| `<prefix>_iqtree.model` | `--iqtree` | IQ-TREE model file | custom ML substitution model |
+| `<prefix>_iqtree.fasta` | `--iqtree` | FASTA | alignment recoded for that model |
+
+**`_sankoff_matrix.csv`** — header `state,0,A,C,M,G,R,S,V,T,W,Y,H,K,D,B,N`: the 16 symbols are IUPAC codes for the 16 subsets of the 4 possible central bases (bit 0=A, 1=C, 2=G, 3=T), `0` standing for the empty/absent state (not `-`, to avoid colliding with external tools' own gap syntax). One row per source state, one value per destination state, cost $-\ln P(a,b)$, 4 decimals.
+
+**`_sankoff_params.yaml`** — everything the calibration estimated, structured so it can be reloaded rather than re-parsed:
+
+| Key | Meaning |
+|---|---|
+| `ratio_ceiling` | the `--sankoff-ratio-ceiling` value used |
+| `cardinality_transitions` | 5×5 list of `{from, to, count, probability}`, family cardinality (0–4 observed forms) |
+| `composition_transitions` | 4×4 list of `{from, to, count, probability}`, base letters `A/C/G/T`, single-copy substitutions |
+
+**`_sankoff.fasta`** — same sites as `_snp.fasta`, recoded to match `_sankoff_matrix.csv`'s alphabet: absent state is `0` (or `?` under `--free-loss`). Excluded genomes dropped; columns left monomorphic by that exclusion are re-checked and dropped too.
+
+**`_sankoff.tnt`** (`--tnt`) — self-contained TNT script: `xread` block (alignment recoded to TNT's fixed `0-9A-F` alphabet), an integer-scaled (`--sankoff-cost-scale`) and metric-closed `smatrix`, a default `hold 20; mult; export` search. Run with `printf 'proc <path>;\nquit;\n' | tnt`. Produces `<prefix>_sankoff.tre` (bare numeric leaf labels, order matching `_sankoff.fasta`) — feed both into [`name-tree`](name-tree.md) to recover taxon names.
+
+**`_sankoff.tcm`** (`--phyg`) — first line: the 16-symbol alphabet plus a trailing gap symbol (17 total). Each following line: one row of the integer-scaled, metric-closed cost matrix (17 values — the extra gap column/row reuses the cost to/from the empty state `0`, since it's never actually triggered).
+
+**`_sankoff.pg`** (`--phyg`) — script: `read(prefasta:..., tcm:...)` against `_sankoff.fasta`/`_sankoff.tcm`, a default 300s/4-instance `search`, `report(...)` writing `<prefix>_sankoff.tre` (bare numeric labels, as for `--tnt`). Run with `phyg` from the output directory (the script uses relative file names). Feed the tree plus `_sankoff.fasta` into [`name-tree`](name-tree.md) for taxon names.
+
+**`_iqtree.model`** (`--iqtree`) — lower-triangular exchangeability matrix $R(a,b) = e^{-\text{cost}(a,b)}$ (one row of increasing length per state, whitespace-separated, PAML order), followed by one line of empirical state frequencies. Only states actually occurring in the alignment are kept, compactly renumbered `0..k-1`.
+
+**`_iqtree.fasta`** (`--iqtree`) — alignment recoded to that same compact `0..k-1` alphabet (symbols `0-9A-F`). Under `--free-loss`, non-detection becomes `?` and columns left non-informative once missing calls are ignored are dropped first (required for `+ASC`). Run with:
+```
+iqtree3 -s <prefix>_iqtree.fasta --seqtype MORPH -m <prefix>_iqtree.model+ASC --prefix <prefix>_iqtree -T AUTO
+```
-- 
2.54.0


From cd57cf0cbd02685a6773c74d3049f422888beb6f Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Fri, 14 Aug 2026 07:50:39 +0200
Subject: [PATCH 16/46] refactor: extract sibling family scanning into shared
 module

Introduces a dedicated `family_scan` submodule to consolidate per-layer family traversal logic. Centralizes path validation, minorant filtering, and conditional matrix instantiation into a shared `scan_layer_families` function. Updates sibling-annex consumers to leverage the new abstraction, reducing inline scanning code. Adds a test fixture to verify numerical consistency across consumer methods for co-occurrence and base-pair metrics.
---
 src/obikindex/src/siblings/alignment.rs   |  96 ++----------
 src/obikindex/src/siblings/cardinality.rs |  87 +----------
 src/obikindex/src/siblings/distance.rs    | 120 +++------------
 src/obikindex/src/siblings/family_scan.rs | 178 ++++++++++++++++++++++
 src/obikindex/src/siblings/mod.rs         |   1 +
 src/obikindex/src/siblings/stats.rs       | 103 ++-----------
 src/obikindex/src/siblings/tests.rs       |  49 ++++++
 7 files changed, 273 insertions(+), 361 deletions(-)
 create mode 100644 src/obikindex/src/siblings/family_scan.rs

diff --git a/src/obikindex/src/siblings/alignment.rs b/src/obikindex/src/siblings/alignment.rs
index db514a92..f321d671 100644
--- a/src/obikindex/src/siblings/alignment.rs
+++ b/src/obikindex/src/siblings/alignment.rs
@@ -1,19 +1,13 @@
 use rayon::prelude::*;
 
-use obicompactvec::{PersistentBitMatrix, PersistentCompactIntMatrix, SiblingAnnex};
 use obikpartitionner::KmerPartition;
-use obikseq::CanonicalKmer;
-use obilayeredmap::MphfLayer;
-use obilayeredmap::meta::PartitionMeta;
-use obiskio::UnitigFileReader;
 use obisys::progress_bar;
 
 use crate::error::{OKIError, OKIResult};
 use crate::index::KmerIndex;
 
-use super::cache::{Mat, PartitionCache};
-use super::helpers::{central_base, is_minorant, partition_of};
-use super::{olm_to_ok, ANNEX_FILE_NAME, INDEX_SUBDIR};
+use super::cache::PartitionCache;
+use super::family_scan::scan_layer_families;
 
 /// IUPAC ambiguity code for a per-genome family presence mask (bit `b` set
 /// iff the genome carries the member whose own central base is `b`):
@@ -77,26 +71,7 @@ impl KmerIndex {
         )
         .map_err(OKIError::Partition)?;
         let cache = PartitionCache::build(&partition, n_parts, with_counts)?;
-
-        let mut layer_dirs = Vec::new();
-        for part in 0..n_parts {
-            let index_dir = self.partition().part_dir(part).join(INDEX_SUBDIR);
-            if !index_dir.exists() {
-                continue;
-            }
-            let meta = PartitionMeta::load(&index_dir).map_err(olm_to_ok)?;
-            for l in 0..meta.n_layers {
-                let layer_dir = index_dir.join(format!("layer_{l}"));
-                let annex_path = layer_dir.join(ANNEX_FILE_NAME);
-                if !annex_path.exists() {
-                    return Err(OKIError::InvalidInput(format!(
-                        "no sibling annex at {} — run build_sibling_annex first",
-                        annex_path.display()
-                    )));
-                }
-                layer_dirs.push(layer_dir);
-            }
-        }
+        let layer_dirs = self.sibling_layer_dirs()?;
 
         let pb = progress_bar("snp_pseudo_alignment", layer_dirs.len() as u64, "layers");
         // `Vec<Vec<u8>>` per layer, one entry (column) per variable family;
@@ -106,65 +81,12 @@ impl KmerIndex {
         let partials: Vec<Vec<Vec<u8>>> = layer_dirs
             .par_iter()
             .map(|layer_dir| -> OKIResult<Vec<Vec<u8>>> {
-                let index_dir = layer_dir.parent().expect("layer_dir has a parent index dir");
-                let meta = PartitionMeta::load(index_dir).map_err(olm_to_ok)?;
-                let annex = SiblingAnnex::open(&layer_dir.join(ANNEX_FILE_NAME))?;
-                let mphf = MphfLayer::open(layer_dir, &meta.mode).map_err(olm_to_ok)?;
-
-                let mut slot_kmer: Vec<Option<CanonicalKmer>> = vec![None; annex.len()];
-                let reader = UnitigFileReader::open_sequential(&layer_dir.join("unitigs.bin"))
-                    .map_err(OKIError::Partition)?;
-                for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
-                    if let Some(slot) = mphf.find(kmer) {
-                        slot_kmer[slot] = Some(kmer);
-                    }
-                }
-
-                let use_counts = with_counts && layer_dir.join("counts").exists();
-                let mat = if use_counts {
-                    Mat::Count(PersistentCompactIntMatrix::open(layer_dir)?)
-                } else {
-                    Mat::Presence(PersistentBitMatrix::open(layer_dir)?)
-                };
-                let n_cols = mat.n_cols().min(n_genomes);
-
-                let mut columns: Vec<Vec<u8>> = Vec::new();
-                let mut genome_mask: Vec<u8> = Vec::with_capacity(n_genomes);
-
-                for slot in 0..annex.len() {
-                    let Some(mask) = annex.get(slot) else { continue };
-                    let Some(kmer) = slot_kmer[slot] else { continue };
-                    if !is_minorant(kmer, mask, k) {
-                        continue; // family tallied once, at its minorant
-                    }
-                    if mask.family_size() < 2 {
-                        continue; // monomorphic family — no signal, skip
-                    }
-
-                    genome_mask.clear();
-                    genome_mask.resize(n_genomes, 0);
-
-                    for other in kmer.central_canonical_neighbors() {
-                        let base = central_base(other, k);
-                        if !mask.has(base) {
-                            continue;
-                        }
-                        let presence: Option<Vec<bool>> = if other == kmer {
-                            Some((0..n_cols).map(|g| mat.carries(g, slot)).collect())
-                        } else {
-                            let dest = partition_of(other, n_parts);
-                            cache.find_presence(dest, other, n_genomes)
-                        };
-                        let Some(presence) = presence else { continue };
-                        for (g, &present) in presence.iter().enumerate() {
-                            if present {
-                                genome_mask[g] |= 1 << base;
-                            }
-                        }
-                    }
-
-                    columns.push(genome_mask.iter().map(|&m| iupac_code(m)).collect());
-                }
+                let families = scan_layer_families(layer_dir, n_parts, n_genomes, with_counts, k, &cache)?;
+                let columns = families
+                    .into_iter()
+                    .filter(|f| f.mask.family_size() >= 2) // monomorphic family — no signal, skip
+                    .map(|f| f.genome_mask.iter().map(|&m| iupac_code(m)).collect())
+                    .collect();
 
                 pb.inc(1);
                 Ok(columns)
diff --git a/src/obikindex/src/siblings/cardinality.rs b/src/obikindex/src/siblings/cardinality.rs
index b9a023fa..84bd5b38 100644
--- a/src/obikindex/src/siblings/cardinality.rs
+++ b/src/obikindex/src/siblings/cardinality.rs
@@ -1,21 +1,15 @@
 use ndarray::Array2;
 use rayon::prelude::*;
 
-use obicompactvec::{PersistentBitMatrix, PersistentCompactIntMatrix, SiblingAnnex};
 use obikpartitionner::KmerPartition;
-use obikseq::CanonicalKmer;
-use obilayeredmap::MphfLayer;
-use obilayeredmap::meta::PartitionMeta;
-use obiskio::UnitigFileReader;
 use obisys::progress_bar;
 
 use crate::error::{OKIError, OKIResult};
 use crate::index::KmerIndex;
 
-use super::cache::{Mat, PartitionCache};
+use super::cache::PartitionCache;
 use super::distance::RawSnpDistanceOutput;
-use super::helpers::{central_base, is_minorant, partition_of};
-use super::{olm_to_ok, ANNEX_FILE_NAME, INDEX_SUBDIR};
+use super::family_scan::scan_layer_families;
 
 /// See [`KmerIndex::cardinality_tally`].
 pub struct CardinalityTally {
@@ -80,63 +74,17 @@ impl KmerIndex {
         )
         .map_err(OKIError::Partition)?;
         let cache = PartitionCache::build(&partition, n_parts, with_counts)?;
-
-        let mut layer_dirs = Vec::new();
-        for part in 0..n_parts {
-            let index_dir = self.partition().part_dir(part).join(INDEX_SUBDIR);
-            if !index_dir.exists() {
-                continue;
-            }
-            let meta = PartitionMeta::load(&index_dir).map_err(olm_to_ok)?;
-            for l in 0..meta.n_layers {
-                let layer_dir = index_dir.join(format!("layer_{l}"));
-                let annex_path = layer_dir.join(ANNEX_FILE_NAME);
-                if !annex_path.exists() {
-                    return Err(OKIError::InvalidInput(format!(
-                        "no sibling annex at {} — run build_sibling_annex first",
-                        annex_path.display()
-                    )));
-                }
-                layer_dirs.push(layer_dir);
-            }
-        }
+        let layer_dirs = self.sibling_layer_dirs()?;
 
         let pb = progress_bar("cardinality_tally", layer_dirs.len() as u64, "layers");
         let partials: Vec<[[u64; 5]; 5]> = layer_dirs
             .par_iter()
             .map(|layer_dir| -> OKIResult<[[u64; 5]; 5]> {
-                let index_dir = layer_dir.parent().expect("layer_dir has a parent index dir");
-                let meta = PartitionMeta::load(index_dir).map_err(olm_to_ok)?;
-                let annex = SiblingAnnex::open(&layer_dir.join(ANNEX_FILE_NAME))?;
-                let mphf = MphfLayer::open(layer_dir, &meta.mode).map_err(olm_to_ok)?;
-
-                let mut slot_kmer: Vec<Option<CanonicalKmer>> = vec![None; annex.len()];
-                let reader = UnitigFileReader::open_sequential(&layer_dir.join("unitigs.bin"))
-                    .map_err(OKIError::Partition)?;
-                for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
-                    if let Some(slot) = mphf.find(kmer) {
-                        slot_kmer[slot] = Some(kmer);
-                    }
-                }
-
-                let use_counts = with_counts && layer_dir.join("counts").exists();
-                let mat = if use_counts {
-                    Mat::Count(PersistentCompactIntMatrix::open(layer_dir)?)
-                } else {
-                    Mat::Presence(PersistentBitMatrix::open(layer_dir)?)
-                };
-                let n_cols = mat.n_cols().min(n_genomes);
-
+                let families = scan_layer_families(layer_dir, n_parts, n_genomes, with_counts, k, &cache)?;
                 let mut counts = [[0u64; 5]; 5];
-                let mut genome_mask: Vec<u8> = Vec::with_capacity(n_genomes);
 
-                for slot in 0..annex.len() {
-                    let Some(mask) = annex.get(slot) else { continue };
-                    let Some(kmer) = slot_kmer[slot] else { continue };
-                    if !is_minorant(kmer, mask, k) {
-                        continue; // family tallied once, at its minorant
-                    }
-                    if mask.family_size() < 2 {
+                for family in &families {
+                    if family.mask.family_size() < 2 {
                         // Fully invariant family (never varies anywhere in
                         // the index) — genome-wide background, not
                         // SNP-adjacent signal; would otherwise swamp the
@@ -148,28 +96,7 @@ impl KmerIndex {
                         continue;
                     }
 
-                    genome_mask.clear();
-                    genome_mask.resize(n_genomes, 0);
-
-                    for other in kmer.central_canonical_neighbors() {
-                        let base = central_base(other, k);
-                        if !mask.has(base) {
-                            continue;
-                        }
-                        let presence: Option<Vec<bool>> = if other == kmer {
-                            Some((0..n_cols).map(|g| mat.carries(g, slot)).collect())
-                        } else {
-                            let dest = partition_of(other, n_parts);
-                            cache.find_presence(dest, other, n_genomes)
-                        };
-                        let Some(presence) = presence else { continue };
-                        for (g, &present) in presence.iter().enumerate() {
-                            if present {
-                                genome_mask[g] |= 1 << base;
-                            }
-                        }
-                    }
-
+                    let genome_mask = &family.genome_mask;
                     for i in 0..n_genomes {
                         let card_i = genome_mask[i].count_ones() as usize;
                         for j in (i + 1)..n_genomes {
diff --git a/src/obikindex/src/siblings/distance.rs b/src/obikindex/src/siblings/distance.rs
index 8dcf40fc..6b5d37e0 100644
--- a/src/obikindex/src/siblings/distance.rs
+++ b/src/obikindex/src/siblings/distance.rs
@@ -1,20 +1,14 @@
 use ndarray::Array2;
 use rayon::prelude::*;
 
-use obicompactvec::{PersistentBitMatrix, PersistentCompactIntMatrix, SiblingAnnex};
 use obikpartitionner::KmerPartition;
-use obikseq::CanonicalKmer;
-use obilayeredmap::MphfLayer;
-use obilayeredmap::meta::PartitionMeta;
-use obiskio::UnitigFileReader;
 use obisys::progress_bar;
 
 use crate::error::{OKIError, OKIResult};
 use crate::index::KmerIndex;
 
-use super::cache::{Mat, PartitionCache};
-use super::helpers::{central_base, is_minorant, partition_of};
-use super::{olm_to_ok, ANNEX_FILE_NAME, INDEX_SUBDIR};
+use super::cache::PartitionCache;
+use super::family_scan::scan_layer_families;
 
 /// Raw p-distance restricted to loci that are single-copy in **both**
 /// genomes of a pair — the "stringent / paralogy-aware" locus eligibility
@@ -84,108 +78,32 @@ impl KmerIndex {
         )
         .map_err(OKIError::Partition)?;
         let cache = PartitionCache::build(&partition, n_parts, with_counts)?;
-
-        let mut layer_dirs = Vec::new();
-        for part in 0..n_parts {
-            let index_dir = self.partition().part_dir(part).join(INDEX_SUBDIR);
-            if !index_dir.exists() {
-                continue;
-            }
-            let meta = PartitionMeta::load(&index_dir).map_err(olm_to_ok)?;
-            for l in 0..meta.n_layers {
-                let layer_dir = index_dir.join(format!("layer_{l}"));
-                let annex_path = layer_dir.join(ANNEX_FILE_NAME);
-                if !annex_path.exists() {
-                    return Err(OKIError::InvalidInput(format!(
-                        "no sibling annex at {} — run build_sibling_annex first",
-                        annex_path.display()
-                    )));
-                }
-                layer_dirs.push(layer_dir);
-            }
-        }
+        let layer_dirs = self.sibling_layer_dirs()?;
 
         let pb = progress_bar(label, layer_dirs.len() as u64, "layers");
         let partials: Vec<Acc> = layer_dirs
             .par_iter()
             .map(|layer_dir| -> OKIResult<Acc> {
                 let mut acc = zero();
+                let families = scan_layer_families(layer_dir, n_parts, n_genomes, with_counts, k, &cache)?;
 
-                let index_dir = layer_dir.parent().expect("layer_dir has a parent index dir");
-                let meta = PartitionMeta::load(index_dir).map_err(olm_to_ok)?;
-                let annex = SiblingAnnex::open(&layer_dir.join(ANNEX_FILE_NAME))?;
-                let mphf = MphfLayer::open(layer_dir, &meta.mode).map_err(olm_to_ok)?;
+                for family in &families {
+                    let variable = family.mask.family_size() >= 2;
+                    let genome_mask = &family.genome_mask;
 
-                let mut slot_kmer: Vec<Option<CanonicalKmer>> = vec![None; annex.len()];
-                let reader = UnitigFileReader::open_sequential(&layer_dir.join("unitigs.bin"))
-                    .map_err(OKIError::Partition)?;
-                for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
-                    if let Some(slot) = mphf.find(kmer) {
-                        slot_kmer[slot] = Some(kmer);
-                    }
-                }
+                    // Per genome: which single form (if exactly one) it
+                    // carries — `None` (a `popcount != 1` mask) once a
+                    // second form is seen, ambiguous/not single-copy,
+                    // ineligible for either side of a pair.
+                    let single_form = |g: usize| -> Option<u8> {
+                        let m = genome_mask[g];
+                        (m.count_ones() == 1).then(|| m.trailing_zeros() as u8)
+                    };
 
-                let use_counts = with_counts && layer_dir.join("counts").exists();
-                let mat = if use_counts {
-                    Mat::Count(PersistentCompactIntMatrix::open(layer_dir)?)
-                } else {
-                    Mat::Presence(PersistentBitMatrix::open(layer_dir)?)
-                };
-                let n_cols = mat.n_cols().min(n_genomes);
-
-                // Per family: which single form (if exactly one) each genome
-                // carries — `None` once a second form is seen (ambiguous,
-                // not single-copy, ineligible for either side of a pair).
-                let mut single_form: Vec<Option<u8>> = Vec::with_capacity(n_cols);
-                let mut ambiguous: Vec<bool> = Vec::with_capacity(n_cols);
-
-                for slot in 0..annex.len() {
-                    let Some(mask) = annex.get(slot) else { continue };
-                    let Some(kmer) = slot_kmer[slot] else { continue };
-                    if !is_minorant(kmer, mask, k) {
-                        continue; // family tallied once, at its minorant
-                    }
-                    let variable = mask.family_size() >= 2;
-
-                    single_form.clear();
-                    single_form.resize(n_cols, None);
-                    ambiguous.clear();
-                    ambiguous.resize(n_cols, false);
-
-                    for other in kmer.central_canonical_neighbors() {
-                        let base = central_base(other, k);
-                        if !mask.has(base) {
-                            continue;
-                        }
-                        let presence: Option<Vec<bool>> = if other == kmer {
-                            Some((0..n_cols).map(|g| mat.carries(g, slot)).collect())
-                        } else {
-                            let dest = partition_of(other, n_parts);
-                            cache.find_presence(dest, other, n_genomes)
-                        };
-                        let Some(presence) = presence else { continue };
-                        for (g, &present) in presence.iter().enumerate() {
-                            if !present {
-                                continue;
-                            }
-                            if single_form[g].is_some() {
-                                ambiguous[g] = true;
-                            } else {
-                                single_form[g] = Some(base);
-                            }
-                        }
-                    }
-
-                    for i in 0..n_cols {
-                        if ambiguous[i] {
-                            continue;
-                        }
-                        let Some(bi) = single_form[i] else { continue };
-                        for j in (i + 1)..n_cols {
-                            if ambiguous[j] {
-                                continue;
-                            }
-                            let Some(bj) = single_form[j] else { continue };
+                    for i in 0..n_genomes {
+                        let Some(bi) = single_form(i) else { continue };
+                        for j in (i + 1)..n_genomes {
+                            let Some(bj) = single_form(j) else { continue };
                             on_pair(&mut acc, i, j, bi, bj, variable);
                         }
                     }
diff --git a/src/obikindex/src/siblings/family_scan.rs b/src/obikindex/src/siblings/family_scan.rs
new file mode 100644
index 00000000..4ad7da1f
--- /dev/null
+++ b/src/obikindex/src/siblings/family_scan.rs
@@ -0,0 +1,178 @@
+//! Shared per-layer family traversal, used by every sibling-annex consumer
+//! (`snp_pseudo_alignment`, `cardinality_tally`, `scan_family_pairs`,
+//! `sibling_annex_stats`) — resolves each minorant family's per-genome
+//! base-presence, with the same locality discipline as
+//! `build_sibling_annex` (see `cache.rs`/`build.rs`'s docs): cross-partition
+//! lookups are grouped by destination partition and resolved in one
+//! contiguous sweep per partition, instead of one lookup at a time jumping
+//! between partitions in family order. The naive, per-family inline lookup
+//! was the shape all four consumers used to have independently; sampling a
+//! real ~170 GB index against 137 GB of RAM showed it thrashing the page
+//! cache (near-continuous ~2 GB/s pagein), the same failure mode
+//! `build_sibling_annex` had already been fixed for.
+
+use std::path::{Path, PathBuf};
+use std::sync::atomic::{AtomicU8, Ordering};
+
+use rayon::prelude::*;
+
+use obicompactvec::{FamilyMask, PersistentBitMatrix, PersistentCompactIntMatrix, SiblingAnnex};
+use obikseq::CanonicalKmer;
+use obilayeredmap::MphfLayer;
+use obilayeredmap::meta::PartitionMeta;
+use obiskio::UnitigFileReader;
+
+use crate::error::{OKIError, OKIResult};
+use crate::index::KmerIndex;
+
+use super::cache::{Mat, PartitionCache};
+use super::helpers::{central_base, is_minorant, partition_of};
+use super::{olm_to_ok, ANNEX_FILE_NAME, INDEX_SUBDIR};
+
+/// One layer's minorant family, with its own annex mask and, per genome,
+/// the 4-bit base-presence mask resolved across the whole index (bit `b`
+/// set iff that genome carries the family member whose own canonical
+/// central base is `b`).
+pub(super) struct FamilyRow {
+    pub mask: FamilyMask,
+    pub genome_mask: Vec<u8>,
+}
+
+impl KmerIndex {
+    /// Every (partition, layer) directory carrying a sibling annex, checked
+    /// up front so a missing one is reported before any real work starts.
+    pub(super) fn sibling_layer_dirs(&self) -> OKIResult<Vec<PathBuf>> {
+        let n_parts = self.n_partitions();
+        let mut layer_dirs = Vec::new();
+        for part in 0..n_parts {
+            let index_dir = self.partition().part_dir(part).join(INDEX_SUBDIR);
+            if !index_dir.exists() {
+                continue;
+            }
+            let meta = PartitionMeta::load(&index_dir).map_err(olm_to_ok)?;
+            for l in 0..meta.n_layers {
+                let layer_dir = index_dir.join(format!("layer_{l}"));
+                let annex_path = layer_dir.join(ANNEX_FILE_NAME);
+                if !annex_path.exists() {
+                    return Err(OKIError::InvalidInput(format!(
+                        "no sibling annex at {} — run build_sibling_annex first",
+                        annex_path.display()
+                    )));
+                }
+                layer_dirs.push(layer_dir);
+            }
+        }
+        Ok(layer_dirs)
+    }
+}
+
+/// Every minorant family of one layer, each with its per-genome
+/// base-presence mask resolved against the whole (already-open) partition
+/// cache.
+///
+/// Two passes, not one inline pass: the first is purely local (already-open
+/// annex/mphf/matrix, no lookups) and both enumerates the layer's families
+/// and collects every cross-partition query they need, grouped by
+/// destination partition; the second resolves each partition's whole batch
+/// in one contiguous sweep, keeping that partition's mmap'd pages hot for
+/// its entire batch instead of faulting them in and out as lookups jump
+/// between partitions in family order.
+pub(super) fn scan_layer_families(
+    layer_dir: &Path,
+    n_parts: usize,
+    n_genomes: usize,
+    with_counts: bool,
+    k: usize,
+    cache: &PartitionCache,
+) -> OKIResult<Vec<FamilyRow>> {
+    let index_dir = layer_dir.parent().expect("layer_dir has a parent index dir");
+    let meta = PartitionMeta::load(index_dir).map_err(olm_to_ok)?;
+    let annex = SiblingAnnex::open(&layer_dir.join(ANNEX_FILE_NAME))?;
+    let mphf = MphfLayer::open(layer_dir, &meta.mode).map_err(olm_to_ok)?;
+
+    let mut slot_kmer: Vec<Option<CanonicalKmer>> = vec![None; annex.len()];
+    let reader = UnitigFileReader::open_sequential(&layer_dir.join("unitigs.bin")).map_err(OKIError::Partition)?;
+    for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
+        if let Some(slot) = mphf.find(kmer) {
+            slot_kmer[slot] = Some(kmer);
+        }
+    }
+
+    let use_counts = with_counts && layer_dir.join("counts").exists();
+    let mat = if use_counts {
+        Mat::Count(PersistentCompactIntMatrix::open(layer_dir)?)
+    } else {
+        Mat::Presence(PersistentBitMatrix::open(layer_dir)?)
+    };
+    let n_cols = mat.n_cols().min(n_genomes);
+
+    // ── Pass 1: local only — enumerate minorant families and collect every
+    // cross-partition query they need, grouped by destination partition.
+    struct Family {
+        slot: usize,
+        mask: FamilyMask,
+    }
+    let mut families: Vec<Family> = Vec::new();
+    let mut outgoing: Vec<Vec<(CanonicalKmer, usize, u8)>> = (0..n_parts).map(|_| Vec::new()).collect();
+
+    for slot in 0..annex.len() {
+        let Some(mask) = annex.get(slot) else { continue };
+        let Some(kmer) = slot_kmer[slot] else { continue };
+        if !is_minorant(kmer, mask, k) {
+            continue; // family tallied once, at its minorant
+        }
+        let family_idx = families.len();
+        families.push(Family { slot, mask });
+
+        for other in kmer.central_canonical_neighbors() {
+            if other == kmer {
+                continue; // local — resolved below straight from `mat`, no lookup
+            }
+            let base = central_base(other, k);
+            if !mask.has(base) {
+                continue;
+            }
+            let dest = partition_of(other, n_parts);
+            outgoing[dest].push((other, family_idx, base));
+        }
+    }
+
+    let genome_mask: Vec<AtomicU8> = (0..families.len() * n_genomes).map(|_| AtomicU8::new(0)).collect();
+
+    // Local presence (the family's own minorant slot) — already open, no
+    // lookup, so no locality concern either way.
+    for (family_idx, family) in families.iter().enumerate() {
+        let kmer = slot_kmer[family.slot].expect("family slot has a kmer");
+        let base = central_base(kmer, k);
+        for g in 0..n_cols {
+            if mat.carries(g, family.slot) {
+                genome_mask[family_idx * n_genomes + g].fetch_or(1 << base, Ordering::Relaxed);
+            }
+        }
+    }
+
+    // ── Pass 2: resolve each destination partition's whole batch in one
+    // contiguous sweep — same rationale as `build_sibling_annex`'s
+    // `outgoing` grouping.
+    outgoing.par_iter().enumerate().filter(|(_, q)| !q.is_empty()).for_each(|(dest, queries)| {
+        for &(variant, family_idx, base) in queries {
+            let Some(presence) = cache.find_presence(dest, variant, n_genomes) else { continue };
+            for (g, &present) in presence.iter().enumerate() {
+                if present {
+                    genome_mask[family_idx * n_genomes + g].fetch_or(1 << base, Ordering::Relaxed);
+                }
+            }
+        }
+    });
+
+    Ok(families
+        .into_iter()
+        .enumerate()
+        .map(|(family_idx, family)| FamilyRow {
+            mask: family.mask,
+            genome_mask: (0..n_genomes)
+                .map(|g| genome_mask[family_idx * n_genomes + g].load(Ordering::Relaxed))
+                .collect(),
+        })
+        .collect())
+}
diff --git a/src/obikindex/src/siblings/mod.rs b/src/obikindex/src/siblings/mod.rs
index edc344fb..2ff427e9 100644
--- a/src/obikindex/src/siblings/mod.rs
+++ b/src/obikindex/src/siblings/mod.rs
@@ -47,6 +47,7 @@ mod build;
 mod cache;
 mod cardinality;
 mod distance;
+mod family_scan;
 mod helpers;
 mod stats;
 
diff --git a/src/obikindex/src/siblings/stats.rs b/src/obikindex/src/siblings/stats.rs
index 66db7958..ac659773 100644
--- a/src/obikindex/src/siblings/stats.rs
+++ b/src/obikindex/src/siblings/stats.rs
@@ -1,19 +1,13 @@
 use rayon::prelude::*;
 
-use obicompactvec::{PersistentBitMatrix, PersistentCompactIntMatrix, SiblingAnnex};
 use obikpartitionner::KmerPartition;
-use obikseq::CanonicalKmer;
-use obilayeredmap::MphfLayer;
-use obilayeredmap::meta::PartitionMeta;
-use obiskio::UnitigFileReader;
 use obisys::progress_bar;
 
 use crate::error::{OKIError, OKIResult};
 use crate::index::KmerIndex;
 
-use super::cache::{Mat, PartitionCache};
-use super::helpers::{central_base, is_minorant, partition_of};
-use super::{olm_to_ok, ANNEX_FILE_NAME, INDEX_SUBDIR};
+use super::cache::PartitionCache;
+use super::family_scan::scan_layer_families;
 
 /// Distribution of family sizes (1-4), read back from an already-built
 /// annex (see [`KmerIndex::build_sibling_annex`]) plus the index's
@@ -62,29 +56,7 @@ impl KmerIndex {
         )
         .map_err(OKIError::Partition)?;
         let cache = PartitionCache::build(&partition, n_parts, with_counts)?;
-
-        // Gather the (partition, layer) pairs to process — cheap metadata
-        // reads only, checking every annex file exists up front so a
-        // missing one is reported before any real work starts.
-        let mut layer_dirs = Vec::new();
-        for part in 0..n_parts {
-            let index_dir = self.partition().part_dir(part).join(INDEX_SUBDIR);
-            if !index_dir.exists() {
-                continue;
-            }
-            let meta = PartitionMeta::load(&index_dir).map_err(olm_to_ok)?;
-            for l in 0..meta.n_layers {
-                let layer_dir = index_dir.join(format!("layer_{l}"));
-                let annex_path = layer_dir.join(ANNEX_FILE_NAME);
-                if !annex_path.exists() {
-                    return Err(OKIError::InvalidInput(format!(
-                        "no sibling annex at {} — run build_sibling_annex first",
-                        annex_path.display()
-                    )));
-                }
-                layer_dirs.push(layer_dir);
-            }
-        }
+        let layer_dirs = self.sibling_layer_dirs()?;
 
         // One layer's worth of work, parallelised across layers with Rayon
         // — independent, read-only, each producing its own partial tally
@@ -98,70 +70,15 @@ impl KmerIndex {
                     ..Default::default()
                 };
 
-                let index_dir = layer_dir.parent().expect("layer_dir has a parent index dir");
-                let meta = PartitionMeta::load(index_dir).map_err(olm_to_ok)?;
-                let annex = SiblingAnnex::open(&layer_dir.join(ANNEX_FILE_NAME))?;
-
-                // Need each slot's own k-mer to derive minorant — same
-                // enumeration as construction.
-                let mphf = MphfLayer::open(layer_dir, &meta.mode).map_err(olm_to_ok)?;
-                let mut slot_kmer: Vec<Option<CanonicalKmer>> = vec![None; annex.len()];
-                let reader = UnitigFileReader::open_sequential(&layer_dir.join("unitigs.bin"))
-                    .map_err(OKIError::Partition)?;
-                for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
-                    if let Some(slot) = mphf.find(kmer) {
-                        slot_kmer[slot] = Some(kmer);
-                    }
-                }
-
-                let use_counts = with_counts && layer_dir.join("counts").exists();
-                let mat = if use_counts {
-                    Mat::Count(PersistentCompactIntMatrix::open(layer_dir)?)
-                } else {
-                    Mat::Presence(PersistentBitMatrix::open(layer_dir)?)
-                };
-                let n_cols = mat.n_cols().min(n_genomes);
-
-                for slot in 0..annex.len() {
-                    let Some(mask) = annex.get(slot) else { continue };
-                    let Some(kmer) = slot_kmer[slot] else { continue };
-                    if !is_minorant(kmer, mask, k) {
-                        continue; // this family is tallied at its minorant's slot only
-                    }
-                    let s = mask.siblings() as usize;
-                    stats.counts[s] += 1;
-
+                let families = scan_layer_families(layer_dir, n_parts, n_genomes, with_counts, k, &cache)?;
+                for family in &families {
                     // "Genome g represents this family" means g carries
                     // *any* of its members, not just the minorant's own —
-                    // start from the minorant's own presence (already
-                    // open, no lookup) and OR in every other present
-                    // member's presence vector, resolved against the
-                    // whole-run cache (no I/O) — exactly `mask.siblings()`
-                    // of them, the mask tells us precisely which to fetch.
-                    let mut carries = vec![false; n_cols];
-                    for g in 0..n_cols {
-                        carries[g] = mat.carries(g, slot);
-                    }
-                    for other in kmer.central_canonical_neighbors() {
-                        if other == kmer {
-                            continue;
-                        }
-                        let base = central_base(other, k);
-                        if !mask.has(base) {
-                            continue;
-                        }
-                        let dest = partition_of(other, n_parts);
-                        if let Some(other_presence) = cache.find_presence(dest, other, n_genomes) {
-                            for (g, &present) in other_presence.iter().enumerate() {
-                                if present {
-                                    carries[g] = true;
-                                }
-                            }
-                        }
-                    }
-
-                    for (g, &carried) in carries.iter().enumerate() {
-                        if carried {
+                    // `genome_mask[g] != 0` is exactly that.
+                    let s = family.mask.siblings() as usize;
+                    stats.counts[s] += 1;
+                    for (g, &m) in family.genome_mask.iter().enumerate() {
+                        if m != 0 {
                             stats.per_genome[g][s] += 1;
                         }
                     }
diff --git a/src/obikindex/src/siblings/tests.rs b/src/obikindex/src/siblings/tests.rs
index 0aa833b6..09a1c597 100644
--- a/src/obikindex/src/siblings/tests.rs
+++ b/src/obikindex/src/siblings/tests.rs
@@ -184,3 +184,52 @@ fn sibling_annex_stats_counts_each_family_once_and_per_genome() {
         );
     }
 }
+
+/// Exercises the four sibling-annex consumers that were rewritten to share
+/// `family_scan::scan_layer_families` (partition-grouped lookups instead of
+/// one lookup per family) — same one-sibling-each fixture as the tests
+/// above (g1 carries the family's centre-C member, g2 the centre-G one),
+/// hand-verified expected output for each.
+#[test]
+fn family_scan_consumers_agree_on_one_sibling_each() {
+    let dir = tempdir().unwrap();
+    let g1 = build_single_genome_index(dir.path(), "g1", b"AACCGCTTAAG");
+    let g2 = build_single_genome_index(dir.path(), "g2", b"AACCGGTTAAG");
+    let merged = merge_two(dir.path(), &g1, &g2);
+    merged.build_sibling_annex().expect("build_sibling_annex");
+
+    // Merge doesn't promise to preserve source order, so resolve each
+    // genome's index by label rather than assuming g1 -> 0, g2 -> 1.
+    let idx_of = |label: &str| merged.meta.genomes.iter().position(|g| g.label == label).unwrap();
+    let (i1, i2) = (idx_of("g1"), idx_of("g2"));
+
+    // snp_pseudo_alignment: one variable family, one column — g1's row
+    // reads 'C' (its own member), g2's reads 'G'.
+    let alignment = merged.snp_pseudo_alignment().expect("snp_pseudo_alignment");
+    assert_eq!(alignment.sequences[i1], vec![b'C']);
+    assert_eq!(alignment.sequences[i2], vec![b'G']);
+
+    // raw_snp_distance: g1's single form (C) != g2's (G) at the family's
+    // one eligible locus -> a SNP, not a shared site.
+    let raw = merged.raw_snp_distance().expect("raw_snp_distance");
+    assert_eq!(raw.snp[[i1, i2]], 1);
+    assert_eq!(raw.snp[[i2, i1]], 1);
+    assert_eq!(raw.shared[[i1, i2]], 0);
+    assert_eq!(raw.shared[[i2, i1]], 0);
+
+    // cardinality_tally: both genomes carry exactly one member of the
+    // family (cardinality 1 each) -> one co-occurrence at [1][1].
+    let cardinality = merged.cardinality_tally(&raw, 1.0).expect("cardinality_tally");
+    assert_eq!(cardinality.counts[1][1], 1);
+    let total: u64 = cardinality.counts.iter().flatten().sum();
+    assert_eq!(total, 1, "no other cardinality pair should be tallied");
+
+    // base_pair_tally: the one eligible, differing locus is C (base 1) vs
+    // G (base 2).
+    let base_pairs = merged.base_pair_tally(&raw, 1.0).expect("base_pair_tally");
+    assert_eq!(base_pairs.counts[1][2], 1);
+    assert_eq!(base_pairs.counts[2][1], 1);
+    let total: u64 = base_pairs.counts.iter().flatten().sum();
+    assert_eq!(total, 2, "no other base pair should be tallied");
+    assert_eq!(base_pairs.same, [0, 0, 0, 0], "the two genomes never agree at this locus");
+}
-- 
2.54.0


From 0e2e3b5bae064f0061f95a6d8902a1a8e810e8b4 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Fri, 14 Aug 2026 08:08:45 +0200
Subject: [PATCH 17/46] Switch sibling modules to sequential layer directory
 processing

The sibling calculation modules now process layer directories sequentially instead of in parallel. This eliminates concurrent processing overhead and prevents interleaved cache sweeps, improving disk I/O and page-cache locality for partition-grouped data access. Progress bar updates and result accumulation have been adapted to the sequential control flow, while core filtering logic and output structures remain unchanged.
---
 src/obikindex/src/siblings/alignment.rs   | 40 ++++++-------
 src/obikindex/src/siblings/cardinality.rs | 68 +++++++++++------------
 src/obikindex/src/siblings/distance.rs    | 65 +++++++++++-----------
 src/obikindex/src/siblings/stats.rs       | 58 ++++++-------------
 4 files changed, 104 insertions(+), 127 deletions(-)

diff --git a/src/obikindex/src/siblings/alignment.rs b/src/obikindex/src/siblings/alignment.rs
index f321d671..a0409617 100644
--- a/src/obikindex/src/siblings/alignment.rs
+++ b/src/obikindex/src/siblings/alignment.rs
@@ -1,5 +1,3 @@
-use rayon::prelude::*;
-
 use obikpartitionner::KmerPartition;
 use obisys::progress_bar;
 
@@ -74,24 +72,26 @@ impl KmerIndex {
         let layer_dirs = self.sibling_layer_dirs()?;
 
         let pb = progress_bar("snp_pseudo_alignment", layer_dirs.len() as u64, "layers");
-        // `Vec<Vec<u8>>` per layer, one entry (column) per variable family;
-        // `par_iter().map(...).collect()` on this indexed source preserves
-        // input order, so concatenating the results below in order gives a
-        // single deterministic column order across the whole index.
-        let partials: Vec<Vec<Vec<u8>>> = layer_dirs
-            .par_iter()
-            .map(|layer_dir| -> OKIResult<Vec<Vec<u8>>> {
-                let families = scan_layer_families(layer_dir, n_parts, n_genomes, with_counts, k, &cache)?;
-                let columns = families
-                    .into_iter()
-                    .filter(|f| f.mask.family_size() >= 2) // monomorphic family — no signal, skip
-                    .map(|f| f.genome_mask.iter().map(|&m| iupac_code(m)).collect())
-                    .collect();
-
-                pb.inc(1);
-                Ok(columns)
-            })
-            .collect::<OKIResult<Vec<_>>>()?;
+        // One layer at a time, not `par_iter()` over layers — same
+        // rationale as `build_sibling_annex`: running many layers'
+        // `scan_layer_families` concurrently would each group their own
+        // lookups by partition internally, but interleave those sweeps
+        // across layers at the OS level, scattering page-cache access over
+        // every partition at once again and defeating the whole point of
+        // the grouping. `Vec<Vec<u8>>` per layer, one entry (column) per
+        // variable family, appended in layer order for a single
+        // deterministic column order across the whole index.
+        let mut partials: Vec<Vec<Vec<u8>>> = Vec::with_capacity(layer_dirs.len());
+        for layer_dir in &layer_dirs {
+            let families = scan_layer_families(layer_dir, n_parts, n_genomes, with_counts, k, &cache)?;
+            let columns = families
+                .into_iter()
+                .filter(|f| f.mask.family_size() >= 2) // monomorphic family — no signal, skip
+                .map(|f| f.genome_mask.iter().map(|&m| iupac_code(m)).collect())
+                .collect();
+            partials.push(columns);
+            pb.inc(1);
+        }
         pb.finish_and_clear();
 
         let mut sequences: Vec<Vec<u8>> = vec![Vec::new(); n_genomes];
diff --git a/src/obikindex/src/siblings/cardinality.rs b/src/obikindex/src/siblings/cardinality.rs
index 84bd5b38..652cc09b 100644
--- a/src/obikindex/src/siblings/cardinality.rs
+++ b/src/obikindex/src/siblings/cardinality.rs
@@ -1,5 +1,4 @@
 use ndarray::Array2;
-use rayon::prelude::*;
 
 use obikpartitionner::KmerPartition;
 use obisys::progress_bar;
@@ -77,45 +76,46 @@ impl KmerIndex {
         let layer_dirs = self.sibling_layer_dirs()?;
 
         let pb = progress_bar("cardinality_tally", layer_dirs.len() as u64, "layers");
-        let partials: Vec<[[u64; 5]; 5]> = layer_dirs
-            .par_iter()
-            .map(|layer_dir| -> OKIResult<[[u64; 5]; 5]> {
-                let families = scan_layer_families(layer_dir, n_parts, n_genomes, with_counts, k, &cache)?;
-                let mut counts = [[0u64; 5]; 5];
+        // One layer at a time — see `snp_pseudo_alignment`'s comment for why
+        // `par_iter()` over layers would defeat `scan_layer_families`'s
+        // partition-grouped locality.
+        let mut partials: Vec<[[u64; 5]; 5]> = Vec::with_capacity(layer_dirs.len());
+        for layer_dir in &layer_dirs {
+            let families = scan_layer_families(layer_dir, n_parts, n_genomes, with_counts, k, &cache)?;
+            let mut counts = [[0u64; 5]; 5];
 
-                for family in &families {
-                    if family.mask.family_size() < 2 {
-                        // Fully invariant family (never varies anywhere in
-                        // the index) — genome-wide background, not
-                        // SNP-adjacent signal; would otherwise swamp the
-                        // diagonal (`c=1/c=1` etc.), which needs to reflect
-                        // the same variable-families-only population the
-                        // `+ASC`-corrected alignment/likelihood actually
-                        // models. See `base_pair_tally`'s `variable` gate
-                        // on its own `same` diagonal for the matching fix.
-                        continue;
-                    }
+            for family in &families {
+                if family.mask.family_size() < 2 {
+                    // Fully invariant family (never varies anywhere in
+                    // the index) — genome-wide background, not
+                    // SNP-adjacent signal; would otherwise swamp the
+                    // diagonal (`c=1/c=1` etc.), which needs to reflect
+                    // the same variable-families-only population the
+                    // `+ASC`-corrected alignment/likelihood actually
+                    // models. See `base_pair_tally`'s `variable` gate
+                    // on its own `same` diagonal for the matching fix.
+                    continue;
+                }
 
-                    let genome_mask = &family.genome_mask;
-                    for i in 0..n_genomes {
-                        let card_i = genome_mask[i].count_ones() as usize;
-                        for j in (i + 1)..n_genomes {
-                            if !included[[i, j]] {
-                                continue;
-                            }
-                            let card_j = genome_mask[j].count_ones() as usize;
-                            counts[card_i][card_j] += 1;
-                            if card_i != card_j {
-                                counts[card_j][card_i] += 1;
-                            }
+                let genome_mask = &family.genome_mask;
+                for i in 0..n_genomes {
+                    let card_i = genome_mask[i].count_ones() as usize;
+                    for j in (i + 1)..n_genomes {
+                        if !included[[i, j]] {
+                            continue;
+                        }
+                        let card_j = genome_mask[j].count_ones() as usize;
+                        counts[card_i][card_j] += 1;
+                        if card_i != card_j {
+                            counts[card_j][card_i] += 1;
                         }
                     }
                 }
+            }
 
-                pb.inc(1);
-                Ok(counts)
-            })
-            .collect::<OKIResult<Vec<_>>>()?;
+            partials.push(counts);
+            pb.inc(1);
+        }
         pb.finish_and_clear();
 
         let mut total = [[0u64; 5]; 5];
diff --git a/src/obikindex/src/siblings/distance.rs b/src/obikindex/src/siblings/distance.rs
index 6b5d37e0..746bb062 100644
--- a/src/obikindex/src/siblings/distance.rs
+++ b/src/obikindex/src/siblings/distance.rs
@@ -1,5 +1,4 @@
 use ndarray::Array2;
-use rayon::prelude::*;
 
 use obikpartitionner::KmerPartition;
 use obisys::progress_bar;
@@ -50,8 +49,11 @@ impl KmerIndex {
     /// should only reflect genuine SNP-adjacent agreement, not the
     /// genome-wide invariant background, need it (see
     /// [`base_pair_tally`](Self::base_pair_tally)'s `same` field). Layers
-    /// are processed in parallel (rayon); each gets its own accumulator
-    /// from `zero()`, combined pairwise via `combine`.
+    /// are processed one at a time, not in parallel — see
+    /// `snp_pseudo_alignment`'s comment for why `par_iter()` over layers
+    /// would defeat `scan_layer_families`'s partition-grouped locality;
+    /// each layer gets its own accumulator from `zero()`, combined
+    /// pairwise via `combine`.
     fn scan_family_pairs<Acc, F, C>(
         &self,
         label: &str,
@@ -81,44 +83,41 @@ impl KmerIndex {
         let layer_dirs = self.sibling_layer_dirs()?;
 
         let pb = progress_bar(label, layer_dirs.len() as u64, "layers");
-        let partials: Vec<Acc> = layer_dirs
-            .par_iter()
-            .map(|layer_dir| -> OKIResult<Acc> {
-                let mut acc = zero();
-                let families = scan_layer_families(layer_dir, n_parts, n_genomes, with_counts, k, &cache)?;
+        // One layer at a time — see `snp_pseudo_alignment`'s comment for why
+        // `par_iter()` over layers would defeat `scan_layer_families`'s
+        // partition-grouped locality.
+        let mut total = zero();
+        for layer_dir in &layer_dirs {
+            let families = scan_layer_families(layer_dir, n_parts, n_genomes, with_counts, k, &cache)?;
+            let mut acc = zero();
 
-                for family in &families {
-                    let variable = family.mask.family_size() >= 2;
-                    let genome_mask = &family.genome_mask;
+            for family in &families {
+                let variable = family.mask.family_size() >= 2;
+                let genome_mask = &family.genome_mask;
 
-                    // Per genome: which single form (if exactly one) it
-                    // carries — `None` (a `popcount != 1` mask) once a
-                    // second form is seen, ambiguous/not single-copy,
-                    // ineligible for either side of a pair.
-                    let single_form = |g: usize| -> Option<u8> {
-                        let m = genome_mask[g];
-                        (m.count_ones() == 1).then(|| m.trailing_zeros() as u8)
-                    };
+                // Per genome: which single form (if exactly one) it
+                // carries — `None` (a `popcount != 1` mask) once a
+                // second form is seen, ambiguous/not single-copy,
+                // ineligible for either side of a pair.
+                let single_form = |g: usize| -> Option<u8> {
+                    let m = genome_mask[g];
+                    (m.count_ones() == 1).then(|| m.trailing_zeros() as u8)
+                };
 
-                    for i in 0..n_genomes {
-                        let Some(bi) = single_form(i) else { continue };
-                        for j in (i + 1)..n_genomes {
-                            let Some(bj) = single_form(j) else { continue };
-                            on_pair(&mut acc, i, j, bi, bj, variable);
-                        }
+                for i in 0..n_genomes {
+                    let Some(bi) = single_form(i) else { continue };
+                    for j in (i + 1)..n_genomes {
+                        let Some(bj) = single_form(j) else { continue };
+                        on_pair(&mut acc, i, j, bi, bj, variable);
                     }
                 }
+            }
 
-                pb.inc(1);
-                Ok(acc)
-            })
-            .collect::<OKIResult<Vec<_>>>()?;
+            total = combine(total, acc);
+            pb.inc(1);
+        }
         pb.finish_and_clear();
 
-        let mut total = zero();
-        for partial in partials {
-            total = combine(total, partial);
-        }
         Ok(total)
     }
 
diff --git a/src/obikindex/src/siblings/stats.rs b/src/obikindex/src/siblings/stats.rs
index ac659773..9d8c7b71 100644
--- a/src/obikindex/src/siblings/stats.rs
+++ b/src/obikindex/src/siblings/stats.rs
@@ -1,5 +1,3 @@
-use rayon::prelude::*;
-
 use obikpartitionner::KmerPartition;
 use obisys::progress_bar;
 
@@ -58,52 +56,32 @@ impl KmerIndex {
         let cache = PartitionCache::build(&partition, n_parts, with_counts)?;
         let layer_dirs = self.sibling_layer_dirs()?;
 
-        // One layer's worth of work, parallelised across layers with Rayon
-        // — independent, read-only, each producing its own partial tally
-        // merged at the end.
+        // One layer at a time, not parallelised across layers — see
+        // `snp_pseudo_alignment`'s comment for why `par_iter()` over layers
+        // would defeat `scan_layer_families`'s partition-grouped locality.
         let pb = progress_bar("sibling_annex_stats", layer_dirs.len() as u64, "layers");
-        let partials: Vec<SiblingAnnexStats> = layer_dirs
-            .par_iter()
-            .map(|layer_dir| -> OKIResult<SiblingAnnexStats> {
-                let mut stats = SiblingAnnexStats {
-                    per_genome: vec![[0u64; 4]; n_genomes],
-                    ..Default::default()
-                };
-
-                let families = scan_layer_families(layer_dir, n_parts, n_genomes, with_counts, k, &cache)?;
-                for family in &families {
-                    // "Genome g represents this family" means g carries
-                    // *any* of its members, not just the minorant's own —
-                    // `genome_mask[g] != 0` is exactly that.
-                    let s = family.mask.siblings() as usize;
-                    stats.counts[s] += 1;
-                    for (g, &m) in family.genome_mask.iter().enumerate() {
-                        if m != 0 {
-                            stats.per_genome[g][s] += 1;
-                        }
-                    }
-                }
-
-                pb.inc(1);
-                Ok(stats)
-            })
-            .collect::<OKIResult<Vec<_>>>()?;
-        pb.finish_and_clear();
-
         let mut stats = SiblingAnnexStats {
             per_genome: vec![[0u64; 4]; n_genomes],
             ..Default::default()
         };
-        for part in partials {
-            for s in 0..4 {
-                stats.counts[s] += part.counts[s];
-            }
-            for g in 0..n_genomes {
-                for s in 0..4 {
-                    stats.per_genome[g][s] += part.per_genome[g][s];
+        for layer_dir in &layer_dirs {
+            let families = scan_layer_families(layer_dir, n_parts, n_genomes, with_counts, k, &cache)?;
+            for family in &families {
+                // "Genome g represents this family" means g carries
+                // *any* of its members, not just the minorant's own —
+                // `genome_mask[g] != 0` is exactly that.
+                let s = family.mask.siblings() as usize;
+                stats.counts[s] += 1;
+                for (g, &m) in family.genome_mask.iter().enumerate() {
+                    if m != 0 {
+                        stats.per_genome[g][s] += 1;
+                    }
                 }
             }
+            pb.inc(1);
         }
+        pb.finish_and_clear();
+
         Ok(stats)
     }
 }
-- 
2.54.0


From c7679fac906ebcf22b9b87b505475948122a502d Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Fri, 14 Aug 2026 08:26:45 +0200
Subject: [PATCH 18/46] refactor: replace eager family collection with callback
 processing

Refactor `scan_layer_families` across the siblings module to accept a closure callback instead of returning an intermediate collection. This eliminates eager materialization and per-layer buffering by streaming results directly into genome-specific buffers or tally matrices. The update introduces bounded batch processing and scratch buffer reuse to cap peak auxiliary memory, while preserving existing computational behavior, control flow, and error semantics.
---
 src/obikindex/src/siblings/alignment.rs   |  32 ++--
 src/obikindex/src/siblings/cardinality.rs |  31 ++--
 src/obikindex/src/siblings/distance.rs    |   8 +-
 src/obikindex/src/siblings/family_scan.rs | 178 ++++++++++++----------
 src/obikindex/src/siblings/stats.rs       |   9 +-
 5 files changed, 123 insertions(+), 135 deletions(-)

diff --git a/src/obikindex/src/siblings/alignment.rs b/src/obikindex/src/siblings/alignment.rs
index a0409617..93f478d3 100644
--- a/src/obikindex/src/siblings/alignment.rs
+++ b/src/obikindex/src/siblings/alignment.rs
@@ -78,30 +78,24 @@ impl KmerIndex {
         // lookups by partition internally, but interleave those sweeps
         // across layers at the OS level, scattering page-cache access over
         // every partition at once again and defeating the whole point of
-        // the grouping. `Vec<Vec<u8>>` per layer, one entry (column) per
-        // variable family, appended in layer order for a single
-        // deterministic column order across the whole index.
-        let mut partials: Vec<Vec<Vec<u8>>> = Vec::with_capacity(layer_dirs.len());
+        // the grouping. Columns appended straight into `sequences` as each
+        // family comes back from `scan_layer_families` (bounded-batch, not
+        // whole-layer) — no intermediate per-layer buffer, layer order
+        // giving a single deterministic column order across the whole index.
+        let mut sequences: Vec<Vec<u8>> = vec![Vec::new(); n_genomes];
         for layer_dir in &layer_dirs {
-            let families = scan_layer_families(layer_dir, n_parts, n_genomes, with_counts, k, &cache)?;
-            let columns = families
-                .into_iter()
-                .filter(|f| f.mask.family_size() >= 2) // monomorphic family — no signal, skip
-                .map(|f| f.genome_mask.iter().map(|&m| iupac_code(m)).collect())
-                .collect();
-            partials.push(columns);
+            scan_layer_families(layer_dir, n_parts, n_genomes, with_counts, k, &cache, |mask, genome_mask| {
+                if mask.family_size() < 2 {
+                    return; // monomorphic family — no signal, skip
+                }
+                for (g, &m) in genome_mask.iter().enumerate() {
+                    sequences[g].push(iupac_code(m));
+                }
+            })?;
             pb.inc(1);
         }
         pb.finish_and_clear();
 
-        let mut sequences: Vec<Vec<u8>> = vec![Vec::new(); n_genomes];
-        for layer_columns in partials {
-            for column in layer_columns {
-                for (g, &code) in column.iter().enumerate() {
-                    sequences[g].push(code);
-                }
-            }
-        }
         Ok(SnpAlignment { sequences })
     }
 }
diff --git a/src/obikindex/src/siblings/cardinality.rs b/src/obikindex/src/siblings/cardinality.rs
index 652cc09b..5921be7e 100644
--- a/src/obikindex/src/siblings/cardinality.rs
+++ b/src/obikindex/src/siblings/cardinality.rs
@@ -78,14 +78,12 @@ impl KmerIndex {
         let pb = progress_bar("cardinality_tally", layer_dirs.len() as u64, "layers");
         // One layer at a time — see `snp_pseudo_alignment`'s comment for why
         // `par_iter()` over layers would defeat `scan_layer_families`'s
-        // partition-grouped locality.
-        let mut partials: Vec<[[u64; 5]; 5]> = Vec::with_capacity(layer_dirs.len());
+        // partition-grouped locality. Tallied straight into `total` as each
+        // family comes back — no per-layer buffer.
+        let mut total = [[0u64; 5]; 5];
         for layer_dir in &layer_dirs {
-            let families = scan_layer_families(layer_dir, n_parts, n_genomes, with_counts, k, &cache)?;
-            let mut counts = [[0u64; 5]; 5];
-
-            for family in &families {
-                if family.mask.family_size() < 2 {
+            scan_layer_families(layer_dir, n_parts, n_genomes, with_counts, k, &cache, |mask, genome_mask| {
+                if mask.family_size() < 2 {
                     // Fully invariant family (never varies anywhere in
                     // the index) — genome-wide background, not
                     // SNP-adjacent signal; would otherwise swamp the
@@ -94,10 +92,9 @@ impl KmerIndex {
                     // `+ASC`-corrected alignment/likelihood actually
                     // models. See `base_pair_tally`'s `variable` gate
                     // on its own `same` diagonal for the matching fix.
-                    continue;
+                    return;
                 }
 
-                let genome_mask = &family.genome_mask;
                 for i in 0..n_genomes {
                     let card_i = genome_mask[i].count_ones() as usize;
                     for j in (i + 1)..n_genomes {
@@ -105,27 +102,17 @@ impl KmerIndex {
                             continue;
                         }
                         let card_j = genome_mask[j].count_ones() as usize;
-                        counts[card_i][card_j] += 1;
+                        total[card_i][card_j] += 1;
                         if card_i != card_j {
-                            counts[card_j][card_i] += 1;
+                            total[card_j][card_i] += 1;
                         }
                     }
                 }
-            }
-
-            partials.push(counts);
+            })?;
             pb.inc(1);
         }
         pb.finish_and_clear();
 
-        let mut total = [[0u64; 5]; 5];
-        for partial in partials {
-            for a in 0..5 {
-                for b in 0..5 {
-                    total[a][b] += partial[a][b];
-                }
-            }
-        }
         Ok(CardinalityTally { counts: total })
     }
 }
diff --git a/src/obikindex/src/siblings/distance.rs b/src/obikindex/src/siblings/distance.rs
index 746bb062..00965acd 100644
--- a/src/obikindex/src/siblings/distance.rs
+++ b/src/obikindex/src/siblings/distance.rs
@@ -88,12 +88,10 @@ impl KmerIndex {
         // partition-grouped locality.
         let mut total = zero();
         for layer_dir in &layer_dirs {
-            let families = scan_layer_families(layer_dir, n_parts, n_genomes, with_counts, k, &cache)?;
             let mut acc = zero();
 
-            for family in &families {
-                let variable = family.mask.family_size() >= 2;
-                let genome_mask = &family.genome_mask;
+            scan_layer_families(layer_dir, n_parts, n_genomes, with_counts, k, &cache, |mask, genome_mask| {
+                let variable = mask.family_size() >= 2;
 
                 // Per genome: which single form (if exactly one) it
                 // carries — `None` (a `popcount != 1` mask) once a
@@ -111,7 +109,7 @@ impl KmerIndex {
                         on_pair(&mut acc, i, j, bi, bj, variable);
                     }
                 }
-            }
+            })?;
 
             total = combine(total, acc);
             pb.inc(1);
diff --git a/src/obikindex/src/siblings/family_scan.rs b/src/obikindex/src/siblings/family_scan.rs
index 4ad7da1f..2d11f18c 100644
--- a/src/obikindex/src/siblings/family_scan.rs
+++ b/src/obikindex/src/siblings/family_scan.rs
@@ -5,11 +5,22 @@
 //! `build_sibling_annex` (see `cache.rs`/`build.rs`'s docs): cross-partition
 //! lookups are grouped by destination partition and resolved in one
 //! contiguous sweep per partition, instead of one lookup at a time jumping
-//! between partitions in family order. The naive, per-family inline lookup
-//! was the shape all four consumers used to have independently; sampling a
-//! real ~170 GB index against 137 GB of RAM showed it thrashing the page
-//! cache (near-continuous ~2 GB/s pagein), the same failure mode
-//! `build_sibling_annex` had already been fixed for.
+//! between partitions in family order.
+//!
+//! Processed in bounded batches of [`FAMILY_BATCH`] families, not the whole
+//! layer at once — same rationale and constant as `build_layer_sibling_annex`'s
+//! `BATCH_SIZE`. An earlier version of this function materialised every
+//! family of the whole layer up front (`Vec<FamilyRow>`, each with its own
+//! heap-allocated `Vec<u8>`) before handing anything back to the caller:
+//! O(layer's family count × genome count) extra memory, on top of a second
+//! full copy for the owned per-family vectors — measured pushing a real run
+//! into heavy VM compression/swap even though the per-lookup I/O pattern was
+//! already fixed. A batch of a few thousand families needs the same
+//! partition-grouping to keep lookups local; it does not need the entire
+//! layer resident at once. Callers get each family's `genome_mask` through
+//! `on_family`, backed by one reused scratch buffer — no per-family
+//! allocation at all, matching the O(genome count) working set the original,
+//! pre-locality-fix per-family code had.
 
 use std::path::{Path, PathBuf};
 use std::sync::atomic::{AtomicU8, Ordering};
@@ -29,14 +40,12 @@ use super::cache::{Mat, PartitionCache};
 use super::helpers::{central_base, is_minorant, partition_of};
 use super::{olm_to_ok, ANNEX_FILE_NAME, INDEX_SUBDIR};
 
-/// One layer's minorant family, with its own annex mask and, per genome,
-/// the 4-bit base-presence mask resolved across the whole index (bit `b`
-/// set iff that genome carries the family member whose own canonical
-/// central base is `b`).
-pub(super) struct FamilyRow {
-    pub mask: FamilyMask,
-    pub genome_mask: Vec<u8>,
-}
+/// Families per batch — bounds `scan_layer_families`'s extra memory to
+/// `FAMILY_BATCH * n_genomes` bytes regardless of layer size. Same value and
+/// rationale as `build_layer_sibling_annex`'s `BATCH_SIZE`: large enough to
+/// amortise the per-batch partition-grouping/sync cost, small enough to keep
+/// working memory a rounding error next to the index itself.
+const FAMILY_BATCH: usize = 4096;
 
 impl KmerIndex {
     /// Every (partition, layer) directory carrying a sibling annex, checked
@@ -66,17 +75,13 @@ impl KmerIndex {
     }
 }
 
-/// Every minorant family of one layer, each with its per-genome
-/// base-presence mask resolved against the whole (already-open) partition
-/// cache.
-///
-/// Two passes, not one inline pass: the first is purely local (already-open
-/// annex/mphf/matrix, no lookups) and both enumerates the layer's families
-/// and collects every cross-partition query they need, grouped by
-/// destination partition; the second resolves each partition's whole batch
-/// in one contiguous sweep, keeping that partition's mmap'd pages hot for
-/// its entire batch instead of faulting them in and out as lookups jump
-/// between partitions in family order.
+/// Visits every minorant family of one layer, in slot order, batched
+/// [`FAMILY_BATCH`] at a time — see the module docs for why. `on_family` is
+/// called once per family with its own annex mask and its per-genome
+/// base-presence (`genome_mask[g]`: bit `b` set iff genome `g` carries the
+/// member whose own canonical central base is `b`), backed by a scratch
+/// buffer reused across every call — callers that need to keep data past
+/// the call must copy it themselves.
 pub(super) fn scan_layer_families(
     layer_dir: &Path,
     n_parts: usize,
@@ -84,7 +89,8 @@ pub(super) fn scan_layer_families(
     with_counts: bool,
     k: usize,
     cache: &PartitionCache,
-) -> OKIResult<Vec<FamilyRow>> {
+    mut on_family: impl FnMut(FamilyMask, &[u8]),
+) -> OKIResult<()> {
     let index_dir = layer_dir.parent().expect("layer_dir has a parent index dir");
     let meta = PartitionMeta::load(index_dir).map_err(olm_to_ok)?;
     let annex = SiblingAnnex::open(&layer_dir.join(ANNEX_FILE_NAME))?;
@@ -106,73 +112,77 @@ pub(super) fn scan_layer_families(
     };
     let n_cols = mat.n_cols().min(n_genomes);
 
-    // ── Pass 1: local only — enumerate minorant families and collect every
-    // cross-partition query they need, grouped by destination partition.
-    struct Family {
-        slot: usize,
-        mask: FamilyMask,
-    }
-    let mut families: Vec<Family> = Vec::new();
-    let mut outgoing: Vec<Vec<(CanonicalKmer, usize, u8)>> = (0..n_parts).map(|_| Vec::new()).collect();
+    let n_slots = annex.len();
+    let mut slot = 0usize;
+    let mut batch_slots: Vec<usize> = Vec::with_capacity(FAMILY_BATCH);
+    let mut scratch = vec![0u8; n_genomes]; // reused across every `on_family` call — no per-family allocation
 
-    for slot in 0..annex.len() {
-        let Some(mask) = annex.get(slot) else { continue };
-        let Some(kmer) = slot_kmer[slot] else { continue };
-        if !is_minorant(kmer, mask, k) {
-            continue; // family tallied once, at its minorant
-        }
-        let family_idx = families.len();
-        families.push(Family { slot, mask });
-
-        for other in kmer.central_canonical_neighbors() {
-            if other == kmer {
-                continue; // local — resolved below straight from `mat`, no lookup
+    while slot < n_slots {
+        batch_slots.clear();
+        while slot < n_slots && batch_slots.len() < FAMILY_BATCH {
+            let s = slot;
+            slot += 1;
+            let Some(mask) = annex.get(s) else { continue };
+            let Some(kmer) = slot_kmer[s] else { continue };
+            if !is_minorant(kmer, mask, k) {
+                continue; // family tallied once, at its minorant
             }
-            let base = central_base(other, k);
-            if !mask.has(base) {
-                continue;
-            }
-            let dest = partition_of(other, n_parts);
-            outgoing[dest].push((other, family_idx, base));
+            batch_slots.push(s);
         }
-    }
-
-    let genome_mask: Vec<AtomicU8> = (0..families.len() * n_genomes).map(|_| AtomicU8::new(0)).collect();
-
-    // Local presence (the family's own minorant slot) — already open, no
-    // lookup, so no locality concern either way.
-    for (family_idx, family) in families.iter().enumerate() {
-        let kmer = slot_kmer[family.slot].expect("family slot has a kmer");
-        let base = central_base(kmer, k);
-        for g in 0..n_cols {
-            if mat.carries(g, family.slot) {
-                genome_mask[family_idx * n_genomes + g].fetch_or(1 << base, Ordering::Relaxed);
-            }
+        if batch_slots.is_empty() {
+            continue; // ran out of minorant slots before filling a batch — loop condition ends it
         }
-    }
 
-    // ── Pass 2: resolve each destination partition's whole batch in one
-    // contiguous sweep — same rationale as `build_sibling_annex`'s
-    // `outgoing` grouping.
-    outgoing.par_iter().enumerate().filter(|(_, q)| !q.is_empty()).for_each(|(dest, queries)| {
-        for &(variant, family_idx, base) in queries {
-            let Some(presence) = cache.find_presence(dest, variant, n_genomes) else { continue };
-            for (g, &present) in presence.iter().enumerate() {
-                if present {
+        // ── Local only: seed each family's own minorant presence (already
+        // open, no lookup) and collect this batch's cross-partition
+        // queries, grouped by destination partition.
+        let mut outgoing: Vec<Vec<(CanonicalKmer, usize, u8)>> = (0..n_parts).map(|_| Vec::new()).collect();
+        let genome_mask: Vec<AtomicU8> = (0..batch_slots.len() * n_genomes).map(|_| AtomicU8::new(0)).collect();
+
+        for (family_idx, &fslot) in batch_slots.iter().enumerate() {
+            let kmer = slot_kmer[fslot].expect("batch slot has a kmer");
+            let mask = annex.get(fslot).expect("batch slot has a mask");
+            let base = central_base(kmer, k);
+            for g in 0..n_cols {
+                if mat.carries(g, fslot) {
                     genome_mask[family_idx * n_genomes + g].fetch_or(1 << base, Ordering::Relaxed);
                 }
             }
+            for other in kmer.central_canonical_neighbors() {
+                if other == kmer {
+                    continue; // local — resolved above straight from `mat`, no lookup
+                }
+                let b = central_base(other, k);
+                if !mask.has(b) {
+                    continue;
+                }
+                let dest = partition_of(other, n_parts);
+                outgoing[dest].push((other, family_idx, b));
+            }
         }
-    });
 
-    Ok(families
-        .into_iter()
-        .enumerate()
-        .map(|(family_idx, family)| FamilyRow {
-            mask: family.mask,
-            genome_mask: (0..n_genomes)
-                .map(|g| genome_mask[family_idx * n_genomes + g].load(Ordering::Relaxed))
-                .collect(),
-        })
-        .collect())
+        // ── Resolve this batch's queries, one contiguous sweep per
+        // destination partition — same rationale as `build_sibling_annex`'s
+        // `outgoing` grouping.
+        outgoing.par_iter().enumerate().filter(|(_, q)| !q.is_empty()).for_each(|(dest, queries)| {
+            for &(variant, family_idx, base) in queries {
+                let Some(presence) = cache.find_presence(dest, variant, n_genomes) else { continue };
+                for (g, &present) in presence.iter().enumerate() {
+                    if present {
+                        genome_mask[family_idx * n_genomes + g].fetch_or(1 << base, Ordering::Relaxed);
+                    }
+                }
+            }
+        });
+
+        for (family_idx, &fslot) in batch_slots.iter().enumerate() {
+            let mask = annex.get(fslot).expect("batch slot has a mask");
+            for (g, dst) in scratch.iter_mut().enumerate() {
+                *dst = genome_mask[family_idx * n_genomes + g].load(Ordering::Relaxed);
+            }
+            on_family(mask, &scratch);
+        }
+    }
+
+    Ok(())
 }
diff --git a/src/obikindex/src/siblings/stats.rs b/src/obikindex/src/siblings/stats.rs
index 9d8c7b71..2e6009e0 100644
--- a/src/obikindex/src/siblings/stats.rs
+++ b/src/obikindex/src/siblings/stats.rs
@@ -65,19 +65,18 @@ impl KmerIndex {
             ..Default::default()
         };
         for layer_dir in &layer_dirs {
-            let families = scan_layer_families(layer_dir, n_parts, n_genomes, with_counts, k, &cache)?;
-            for family in &families {
+            scan_layer_families(layer_dir, n_parts, n_genomes, with_counts, k, &cache, |mask, genome_mask| {
                 // "Genome g represents this family" means g carries
                 // *any* of its members, not just the minorant's own —
                 // `genome_mask[g] != 0` is exactly that.
-                let s = family.mask.siblings() as usize;
+                let s = mask.siblings() as usize;
                 stats.counts[s] += 1;
-                for (g, &m) in family.genome_mask.iter().enumerate() {
+                for (g, &m) in genome_mask.iter().enumerate() {
                     if m != 0 {
                         stats.per_genome[g][s] += 1;
                     }
                 }
-            }
+            })?;
             pb.inc(1);
         }
         pb.finish_and_clear();
-- 
2.54.0


From 0de078fdf13bb15dd54cbf00a9c103556cab3c5e Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Fri, 14 Aug 2026 10:06:44 +0200
Subject: [PATCH 19/46] Store minorant flag in family mask to avoid costly
 k-mer reconstruction

Transition the minorant flag from a derived value to a stored field within the family mask, resolving a performance regression where on-the-fly reconstruction consumed significant query time. This change introduces O(1) k-mer reconstruction APIs, shifts minorant computation to the index build phase, and enables direct annex-based statistics. Supporting updates include adopting shared ownership for partition caches and refactoring batch processing pipelines.
---
 docmd/theory/evolutionary_distances.md    |  33 ++-
 src/obicompactvec/src/siblingannex.rs     |  59 +++-
 src/obikindex/src/siblings/alignment.rs   |   4 +-
 src/obikindex/src/siblings/build.rs       |  33 +--
 src/obikindex/src/siblings/cache.rs       |  67 ++++-
 src/obikindex/src/siblings/cardinality.rs |   4 +-
 src/obikindex/src/siblings/distance.rs    |   4 +-
 src/obikindex/src/siblings/family_scan.rs | 313 +++++++++++++++-------
 src/obikindex/src/siblings/stats.rs       |  42 ++-
 src/obikindex/src/siblings/tests.rs       |  28 +-
 src/obikmer/src/cmd/phylo/args.rs         |  14 +-
 src/obikmer/src/cmd/phylo/mod.rs          |   9 +-
 src/obikmer/src/cmd/phylo/outputs.rs      |  19 ++
 src/obilayeredmap/src/mphf_layer.rs       |  25 ++
 src/obiskio/src/unitig_index/reader.rs    |  10 +
 15 files changed, 519 insertions(+), 145 deletions(-)

diff --git a/docmd/theory/evolutionary_distances.md b/docmd/theory/evolutionary_distances.md
index 137ee58d..9405adfc 100644
--- a/docmd/theory/evolutionary_distances.md
+++ b/docmd/theory/evolutionary_distances.md
@@ -1624,10 +1624,33 @@ a fixed reference. Storing instead a **4-bit mask** — one bit per base
 family's fixed canonical form, i.e. the member with `A` at the centre — see
 above) is observed anywhere in the index — fixes both:
 - **Sibling count is derived, not stored**: `siblings = popcount(mask) - 1`.
-- **Minorant is derived, not stored**: regenerate the family's 4 canonical
+- ~~**Minorant is derived, not stored**: regenerate the family's 4 canonical
   forms from the slot's own k-mer (cheap, no lookup — see above), compare
   the raw encodings of whichever bits are set in the mask, take the
-  smallest.
+  smallest.~~ **Erratum (2026-08-14) — this was wrong, kept struck through
+  rather than deleted.** "Cheap, no lookup" only accounts for the bit
+  algebra (regenerate 4 forms, compare raw encodings) — true in isolation,
+  but it silently assumed "the slot's own k-mer" is a free fact. It isn't:
+  getting from an MPHF slot index back to the actual k-mer sequence means
+  reconstructing `slot_kmer` for the whole layer — scan `unitigs.bin`,
+  `mphf.find()` every k-mer to place it — an O(distinct k-mers) pass
+  through the MPHF, not a per-slot O(1) lookup. That reconstruction is free
+  *only* when the caller already needs k-mer identity for something else in
+  the same traversal (e.g. the SNP sweep below, which needs it anyway to
+  generate `central_canonical_neighbors()`). A caller that wants *only* the
+  minorant flag pays the full reconstruction for nothing: measured on a real
+  run, a bare family-size histogram (four buckets, otherwise near-instant)
+  spent 71% of wall-clock in `MphfLayer::find`, all of it solely to answer
+  "is this slot the minorant". **Current design: minorant *is* stored**
+  after all — a 5th mask bit (4 presence bits + 1 minorant bit, still fits
+  one byte alongside the presence mask below), written once in the
+  construction pass where the k-mer is already in hand for other reasons
+  (`obikindex::siblings::build_layer_sibling_annex`), read back for free by
+  every later consumer (`FamilyMask::is_minorant`). This is genuinely a
+  return to the superseded 3-bit design's core idea (store minorant
+  alongside the count) — the "which variant" blindness that motivated
+  moving away from it is fixed by keeping the full 4-bit presence mask
+  too, not by dropping the stored minorant bit again.
 - **A future consumer knows exactly which variants to (re-)query** —
   `popcount(mask) - 1` lookups instead of always 3, and it knows *which*
   3 (or fewer) to issue, not just how many hits to expect.
@@ -1644,7 +1667,11 @@ above) is observed anywhere in the index — fixes both:
    per-slot packed array (the presence mask above), one per partition — same
    on-disk shape family as `PersistentBitMatrix`'s `Packed` variant, but
    simpler (no per-genome columns, a single derived read-only value per
-   slot).
+   slot). As actually implemented (`obicompactvec::siblingannex`): **not**
+   truly bit-packed — 1 byte/slot, 4 presence bits + the minorant bit (see
+   the erratum above) in the low 5 bits, 3 unused. Deliberately simpler for
+   a first implementation; packing to 5 bits/slot is a pure storage-density
+   follow-up, not a behavioural change, still not done as of this note.
    <details><summary>Superseded 3-bit design (historical)</summary>
    3 bits, storing minorant status alongside sibling count directly, since
    it came for free from the same lookups (point 3 below) — 5 real states
diff --git a/src/obicompactvec/src/siblingannex.rs b/src/obicompactvec/src/siblingannex.rs
index 0de9733e..80e72d56 100644
--- a/src/obicompactvec/src/siblingannex.rs
+++ b/src/obicompactvec/src/siblingannex.rs
@@ -41,11 +41,22 @@ const MAGIC: [u8; 4] = *b"PSIB";
 // Header: magic(4) + _pad(4) + n(8) = 16 bytes. Data (1 byte/slot) follows.
 const HEADER_SIZE: usize = 16;
 
-/// A family presence mask: bit `b` set iff the member whose own canonical
-/// central base is `b` (0=A, 1=C, 2=G, 3=T) is observed in the index.
+/// A family presence mask: bit `b` (0..3) set iff the member whose own
+/// canonical central base is `b` (0=A, 1=C, 2=G, 3=T) is observed in the
+/// index. Bit 4 is a second, independent fact piggy-backed onto the same
+/// byte: whether *this slot's own k-mer* is its family's minorant (the
+/// smallest raw encoding among the family's observed members) — computed
+/// once, when the whole family's mask is already final (see
+/// `obikindex::siblings::build_sibling_annex`), and read back by every
+/// consumer that would otherwise have to reconstruct this slot's k-mer from
+/// `unitigs.bin` and hash it through the MPHF again just to ask the same
+/// question. Bits 5-7 unused.
 #[derive(Debug, Clone, Copy, PartialEq, Eq)]
 pub struct FamilyMask(u8);
 
+const PRESENCE_BITS: u8 = 0b0000_1111;
+const MINORANT_BIT: u8 = 0b0001_0000;
+
 impl FamilyMask {
     /// The empty mask — never a valid *computed* result (a slot's own base
     /// is always present in its own family) — used only to build up a mask
@@ -69,7 +80,7 @@ impl FamilyMask {
     /// Number of family members observed anywhere in the index (1..=4).
     #[inline]
     pub fn family_size(self) -> u32 {
-        self.0.count_ones()
+        (self.0 & PRESENCE_BITS).count_ones()
     }
 
     /// Number of *other* members observed (0..=3) — `family_size() - 1`.
@@ -78,18 +89,39 @@ impl FamilyMask {
         self.family_size() - 1
     }
 
-    /// Raw bitmask (bit `b` = base `b` present) — for callers that build up
-    /// a mask via their own bit operations (e.g. concurrently, via an
-    /// `AtomicU8`) and only need the `FamilyMask` wrapper at the end.
+    /// Set or clear the minorant flag (see the struct docs).
     #[inline]
-    pub fn bits(self) -> u8 {
-        self.0
+    pub fn with_minorant(self, is_minorant: bool) -> Self {
+        if is_minorant {
+            FamilyMask(self.0 | MINORANT_BIT)
+        } else {
+            FamilyMask(self.0 & !MINORANT_BIT)
+        }
     }
 
-    /// Construct from a raw bitmask (only the low 4 bits are kept).
+    /// Is this slot's own k-mer its family's minorant? Only meaningful once
+    /// `with_minorant` has been called with the family's *final* mask (i.e.
+    /// after construction) — see the struct docs.
+    #[inline]
+    pub fn is_minorant(self) -> bool {
+        self.0 & MINORANT_BIT != 0
+    }
+
+    /// Raw presence bitmask (bit `b` = base `b` present, low 4 bits only —
+    /// never includes the minorant flag) — for callers that build up a mask
+    /// via their own bit operations (e.g. concurrently, via an `AtomicU8`)
+    /// and only need the `FamilyMask` wrapper at the end.
+    #[inline]
+    pub fn bits(self) -> u8 {
+        self.0 & PRESENCE_BITS
+    }
+
+    /// Construct from a raw presence bitmask (only the low 4 bits are kept —
+    /// the minorant flag is not part of this, use [`with_minorant`](Self::with_minorant)
+    /// separately).
     #[inline]
     pub fn from_bits(bits: u8) -> Self {
-        FamilyMask(bits & 0b1111)
+        FamilyMask(bits & PRESENCE_BITS)
     }
 
     #[inline]
@@ -101,10 +133,13 @@ impl FamilyMask {
     fn decode(byte: u8) -> Option<Self> {
         if byte == 0 {
             // Unreachable for a real result — reserved as the "not yet
-            // computed" sentinel.
+            // computed" sentinel. Still safe as a sentinel with the
+            // minorant bit added: a real entry always has at least one
+            // presence bit set (bits 0-3), so byte == 0 still means
+            // "nothing written yet" and never a genuine minorant-only value.
             return None;
         }
-        Some(FamilyMask(byte & 0b1111))
+        Some(FamilyMask(byte))
     }
 }
 
diff --git a/src/obikindex/src/siblings/alignment.rs b/src/obikindex/src/siblings/alignment.rs
index 93f478d3..e87e1017 100644
--- a/src/obikindex/src/siblings/alignment.rs
+++ b/src/obikindex/src/siblings/alignment.rs
@@ -1,3 +1,5 @@
+use std::sync::Arc;
+
 use obikpartitionner::KmerPartition;
 use obisys::progress_bar;
 
@@ -68,7 +70,7 @@ impl KmerIndex {
             n_bits,
         )
         .map_err(OKIError::Partition)?;
-        let cache = PartitionCache::build(&partition, n_parts, with_counts)?;
+        let cache = Arc::new(PartitionCache::build(&partition, n_parts, with_counts)?);
         let layer_dirs = self.sibling_layer_dirs()?;
 
         let pb = progress_bar("snp_pseudo_alignment", layer_dirs.len() as u64, "layers");
diff --git a/src/obikindex/src/siblings/build.rs b/src/obikindex/src/siblings/build.rs
index a163b84c..a23896ee 100644
--- a/src/obikindex/src/siblings/build.rs
+++ b/src/obikindex/src/siblings/build.rs
@@ -10,14 +10,13 @@ use obipipeline::ThrottleGuard;
 use obikseq::CanonicalKmer;
 use obilayeredmap::MphfLayer;
 use obilayeredmap::meta::PartitionMeta;
-use obiskio::UnitigFileReader;
 use obisys::progress_bar;
 
 use crate::error::{OKIError, OKIResult};
 use crate::index::KmerIndex;
 
 use super::cache::PartitionCache;
-use super::helpers::{central_base, partition_of};
+use super::helpers::{central_base, is_minorant, partition_of};
 use super::{olm_to_ok, ANNEX_FILE_NAME, INDEX_SUBDIR};
 
 // ── obipipeline data types ─────────────────────────────────────────────────
@@ -117,15 +116,10 @@ impl KmerIndex {
         let mphf = MphfLayer::open(layer_dir, &meta.mode).map_err(olm_to_ok)?;
         let n_slots = mphf.n();
 
-        // ── Enumerate this layer's distinct k-mers, one per slot ────────────
-        let mut slot_kmer: Vec<Option<CanonicalKmer>> = vec![None; n_slots];
-        let reader = UnitigFileReader::open_sequential(&layer_dir.join("unitigs.bin"))
-            .map_err(OKIError::Partition)?;
-        for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
-            if let Some(slot) = mphf.find(kmer) {
-                slot_kmer[slot] = Some(kmer);
-            }
-        }
+        // ── Enumerate this layer's distinct k-mers, one per slot — direct
+        // slot -> k-mer reconstruction (evidence + direct-access unitigs, no
+        // MPHF hashing, no file scan), not scan-and-hash-every-k-mer-forward.
+        let slot_kmer: Vec<Option<CanonicalKmer>> = (0..n_slots).map(|slot| mphf.kmer_at(slot)).collect();
 
         let k = self.kmer_size();
 
@@ -240,13 +234,22 @@ impl KmerIndex {
         });
 
         // ── Write the layer's annex file ─────────────────────────────────────
+        // The minorant flag is computed here, not by every later reader:
+        // this is the one place the whole family's *final* mask and this
+        // slot's own k-mer (already in hand, no extra lookup) are both
+        // available together. Every consumer that only needs to know
+        // "is this slot the family's minorant" — the common case, since a
+        // family is tallied once, at its minorant — reads the bit straight
+        // back instead of re-deriving it (re-scanning `unitigs.bin` and
+        // re-hashing through the MPHF, the cost `is_minorant` was cheap to
+        // *compute* but expensive to *get the inputs for* every time).
         let annex_path = layer_dir.join(ANNEX_FILE_NAME);
         let mut builder = SiblingAnnexBuilder::new(n_slots, &annex_path)?;
         for (slot, m) in mask.iter().enumerate() {
-            if slot_kmer[slot].is_none() {
-                continue; // unused MPHF slot, if any — leave at the sentinel
-            }
-            builder.set(slot, FamilyMask::from_bits(m.load(Ordering::Relaxed)));
+            let Some(kmer) = slot_kmer[slot] else { continue }; // unused MPHF slot, if any — leave at the sentinel
+            let final_mask = FamilyMask::from_bits(m.load(Ordering::Relaxed));
+            let minorant = is_minorant(kmer, final_mask, k);
+            builder.set(slot, final_mask.with_minorant(minorant));
         }
         builder.close()?;
 
diff --git a/src/obikindex/src/siblings/cache.rs b/src/obikindex/src/siblings/cache.rs
index a2de07e5..32d49f5d 100644
--- a/src/obikindex/src/siblings/cache.rs
+++ b/src/obikindex/src/siblings/cache.rs
@@ -104,18 +104,63 @@ impl PartitionCache {
             .is_some_and(|layers| layers.iter().any(|mphf| mphf.find(variant).is_some()))
     }
 
-    /// Per-genome presence vector for `variant` in partition `dest_partition`
-    /// (`true` iff that genome carries it), `None` on a miss. Same shape as
-    /// `find`, but also reads the cached matrix instead of just the MPHF.
-    pub(super) fn find_presence(&self, dest_partition: usize, variant: CanonicalKmer, n_genomes: usize) -> Option<Vec<bool>> {
-        let layers = self.layers.get(dest_partition)?;
-        let mats = self.mats.get(dest_partition)?;
-        for (mphf, mat) in layers.iter().zip(mats.iter()) {
-            if let Some(slot) = mphf.find(variant) {
-                let n_cols = mat.n_cols().min(n_genomes);
-                return Some((0..n_cols).map(|g| mat.carries(g, slot)).collect());
+    /// Resolve many `(variant, family_idx, base)` queries against one
+    /// partition's matrices at once, calling `on_hit(family_idx, base, g)`
+    /// for every genome `g` that carries the resolved variant.
+    ///
+    /// Genome-major, not query-major: `PersistentBitMatrix`/
+    /// `PersistentCompactIntMatrix` are stored one contiguous block per
+    /// genome (column), slot as the offset within it (see
+    /// `obicompactvec::bitmatrix::packed::PackedBitMatrix` — each column's
+    /// own `mmap` region). Resolving query-by-query (`for query { for genome
+    /// { mat.carries(genome, slot) } }`, this function's predecessor) visits
+    /// every genome's block once *per query* — for a batch of thousands of
+    /// queries against ~90 genomes, that is thousands of jumps into each of
+    /// ~90 widely separated multi-MB regions, in query order, not genome
+    /// order: the access pattern a column-major layout is least suited to.
+    /// Grouping first (by layer, since each layer's matrix is a separate
+    /// column set) and sorting each group by slot, then visiting genome by
+    /// genome, turns that into ~90 mostly-sequential sweeps through one
+    /// column's own bytes — the layout's fast axis — confirmed by sampling
+    /// a real run: `PersistentBitMatrix::get` dominated wall-clock time,
+    /// mostly blocked on page faults, even after every partition/batch
+    /// locality fix above this in the traversal.
+    pub(super) fn find_presence_batch(
+        &self,
+        dest_partition: usize,
+        queries: &[(CanonicalKmer, usize, u8)],
+        n_genomes: usize,
+        mut on_hit: impl FnMut(usize, u8, usize),
+    ) {
+        let Some(layers) = self.layers.get(dest_partition) else { return };
+        let Some(mats) = self.mats.get(dest_partition) else { return };
+
+        // First hit wins, same semantics as the old per-query loop (a
+        // variant present in an earlier layer shadows later ones).
+        let mut by_layer: Vec<Vec<(usize, usize, u8)>> = vec![Vec::new(); layers.len()];
+        for &(variant, family_idx, base) in queries {
+            for (li, mphf) in layers.iter().enumerate() {
+                if let Some(slot) = mphf.find(variant) {
+                    by_layer[li].push((slot, family_idx, base));
+                    break;
+                }
+            }
+        }
+
+        for (li, mut hits) in by_layer.into_iter().enumerate() {
+            if hits.is_empty() {
+                continue;
+            }
+            hits.sort_unstable_by_key(|&(slot, _, _)| slot);
+            let mat = &mats[li];
+            let n_cols = mat.n_cols().min(n_genomes);
+            for g in 0..n_cols {
+                for &(slot, family_idx, base) in &hits {
+                    if mat.carries(g, slot) {
+                        on_hit(family_idx, base, g);
+                    }
+                }
             }
         }
-        None
     }
 }
diff --git a/src/obikindex/src/siblings/cardinality.rs b/src/obikindex/src/siblings/cardinality.rs
index 5921be7e..5f09415d 100644
--- a/src/obikindex/src/siblings/cardinality.rs
+++ b/src/obikindex/src/siblings/cardinality.rs
@@ -1,3 +1,5 @@
+use std::sync::Arc;
+
 use ndarray::Array2;
 
 use obikpartitionner::KmerPartition;
@@ -72,7 +74,7 @@ impl KmerIndex {
             n_bits,
         )
         .map_err(OKIError::Partition)?;
-        let cache = PartitionCache::build(&partition, n_parts, with_counts)?;
+        let cache = Arc::new(PartitionCache::build(&partition, n_parts, with_counts)?);
         let layer_dirs = self.sibling_layer_dirs()?;
 
         let pb = progress_bar("cardinality_tally", layer_dirs.len() as u64, "layers");
diff --git a/src/obikindex/src/siblings/distance.rs b/src/obikindex/src/siblings/distance.rs
index 00965acd..3f746303 100644
--- a/src/obikindex/src/siblings/distance.rs
+++ b/src/obikindex/src/siblings/distance.rs
@@ -1,3 +1,5 @@
+use std::sync::Arc;
+
 use ndarray::Array2;
 
 use obikpartitionner::KmerPartition;
@@ -79,7 +81,7 @@ impl KmerIndex {
             n_bits,
         )
         .map_err(OKIError::Partition)?;
-        let cache = PartitionCache::build(&partition, n_parts, with_counts)?;
+        let cache = Arc::new(PartitionCache::build(&partition, n_parts, with_counts)?);
         let layer_dirs = self.sibling_layer_dirs()?;
 
         let pb = progress_bar(label, layer_dirs.len() as u64, "layers");
diff --git a/src/obikindex/src/siblings/family_scan.rs b/src/obikindex/src/siblings/family_scan.rs
index 2d11f18c..5aacdd62 100644
--- a/src/obikindex/src/siblings/family_scan.rs
+++ b/src/obikindex/src/siblings/family_scan.rs
@@ -4,25 +4,51 @@
 //! base-presence, with the same locality discipline as
 //! `build_sibling_annex` (see `cache.rs`/`build.rs`'s docs): cross-partition
 //! lookups are grouped by destination partition and resolved in one
-//! contiguous sweep per partition, instead of one lookup at a time jumping
-//! between partitions in family order.
+//! contiguous sweep per partition, instead of one lookup jumping between
+//! partitions in family order.
 //!
-//! Processed in bounded batches of [`FAMILY_BATCH`] families, not the whole
-//! layer at once — same rationale and constant as `build_layer_sibling_annex`'s
-//! `BATCH_SIZE`. An earlier version of this function materialised every
-//! family of the whole layer up front (`Vec<FamilyRow>`, each with its own
-//! heap-allocated `Vec<u8>`) before handing anything back to the caller:
-//! O(layer's family count × genome count) extra memory, on top of a second
-//! full copy for the owned per-family vectors — measured pushing a real run
-//! into heavy VM compression/swap even though the per-lookup I/O pattern was
-//! already fixed. A batch of a few thousand families needs the same
-//! partition-grouping to keep lookups local; it does not need the entire
-//! layer resident at once. Callers get each family's `genome_mask` through
-//! `on_family`, backed by one reused scratch buffer — no per-family
-//! allocation at all, matching the O(genome count) working set the original,
-//! pre-locality-fix per-family code had.
+//! Two concerns, kept on two different mechanisms because they need
+//! opposite things:
+//!
+//! - **Generating** each batch's cross-partition queries is pure CPU (bit
+//!   tests, one hash per variant) — cheap, and safe to run for several
+//!   batches at once. It runs on an `obipipeline::throttle` + `make_pipe!`
+//!   pipeline, the same mechanism `build_layer_sibling_annex` uses, for the
+//!   same reason: it overlaps this CPU work with the *previous* batch's
+//!   resolution instead of leaving cores idle between batches.
+//! - **Resolving** those queries against `PartitionCache` is I/O (mmap page
+//!   faults on a real index far larger than RAM) — one batch at a time,
+//!   `rayon`-parallel *across partitions* (like `build_sibling_annex`'s own
+//!   `outgoing.par_iter()`), never several batches concurrently. An earlier
+//!   version resolved each batch fully inside its own pipeline worker, so
+//!   `n_workers` batches were resolved concurrently — each one spreading its
+//!   queries thin across every partition of the layer at once. Sampling a
+//!   real run showed the fix hadn't helped at all: 16 threads "busy" in
+//!   `find_presence`, but mostly blocked on page faults (~1.7 GB/s pagein),
+//!   because 16 concurrent sweeps across the same partition space is exactly
+//!   the scattering the grouping was meant to prevent — just spread over
+//!   threads instead of over layers this time. Resolving one batch's worth
+//!   at a time, with each of `rayon`'s threads owning one partition
+//!   contiguously until that batch is done, keeps only one partition set
+//!   "hot" at once, restoring the locality the batching is for.
+//!
+//! `obipipeline` does not guarantee output order, so generated batches carry
+//! their own starting family index and are replayed through a small reorder
+//! buffer before resolution — bounded by the throttle's own concurrency
+//! (`n_workers` batches), not by the layer's size.
+//!
+//! [`FAMILY_BATCH`] bounds a single batch's memory to `FAMILY_BATCH *
+//! genome_count` bytes, and is chosen large enough that a batch still gives
+//! each partition a decent number of queries to resolve in one go — too
+//! small a batch starves that density regardless of how the resolution step
+//! is parallelised. An earlier version materialised the whole layer's
+//! families up front before resolving anything: O(layer's family count ×
+//! genome count) memory, measured pushing a real run into heavy VM
+//! compression/swap.
 
+use std::collections::HashMap;
 use std::path::{Path, PathBuf};
+use std::sync::Arc;
 use std::sync::atomic::{AtomicU8, Ordering};
 
 use rayon::prelude::*;
@@ -31,21 +57,21 @@ use obicompactvec::{FamilyMask, PersistentBitMatrix, PersistentCompactIntMatrix,
 use obikseq::CanonicalKmer;
 use obilayeredmap::MphfLayer;
 use obilayeredmap::meta::PartitionMeta;
-use obiskio::UnitigFileReader;
+use obipipeline::{ThrottleGuard, throttle};
 
 use crate::error::{OKIError, OKIResult};
 use crate::index::KmerIndex;
 
 use super::cache::{Mat, PartitionCache};
-use super::helpers::{central_base, is_minorant, partition_of};
+use super::helpers::{central_base, partition_of};
 use super::{olm_to_ok, ANNEX_FILE_NAME, INDEX_SUBDIR};
 
-/// Families per batch — bounds `scan_layer_families`'s extra memory to
-/// `FAMILY_BATCH * n_genomes` bytes regardless of layer size. Same value and
-/// rationale as `build_layer_sibling_annex`'s `BATCH_SIZE`: large enough to
-/// amortise the per-batch partition-grouping/sync cost, small enough to keep
-/// working memory a rounding error next to the index itself.
-const FAMILY_BATCH: usize = 4096;
+/// Families per batch — see the module docs for the memory-vs-per-partition-
+/// density trade-off this picks a point on. At ~90 genomes and a few
+/// hundred partitions, this keeps a batch's resolution memory in the low
+/// tens of MB while still giving each partition on the order of a thousand
+/// queries per batch to amortise against.
+const FAMILY_BATCH: usize = 65536;
 
 impl KmerIndex {
     /// Every (partition, layer) directory carrying a sibling annex, checked
@@ -75,9 +101,52 @@ impl KmerIndex {
     }
 }
 
+/// Read-only state shared (via `Arc`) across every pipeline worker
+/// generating this layer's batches — opened once, not per batch. No `cache`
+/// here: generation never touches the cross-partition cache, only this
+/// layer's own already-open matrix. No `annex` either — the filter step
+/// that builds `minorant_slots` already carries each slot's mask through,
+/// so a worker never needs to re-read it.
+struct LayerCtx {
+    slot_kmer: Vec<Option<CanonicalKmer>>,
+    mat: Mat,
+    n_parts: usize,
+    n_genomes: usize,
+    n_cols: usize,
+    k: usize,
+}
+
+struct SourceBatch {
+    start_family_idx: usize,
+    /// `(slot, mask)` — the mask is carried through from the filter step
+    /// below rather than re-read from the annex per batch; it's the same
+    /// byte either way, just already in hand.
+    slots: Vec<(usize, FamilyMask)>,
+    _permit: ThrottleGuard,
+}
+
+/// One batch's generated work: local presence already resolved (straight
+/// from this layer's own matrix, no lookup needed), cross-partition queries
+/// collected but not yet resolved against the cache.
+struct GeneratedBatch {
+    start_family_idx: usize,
+    masks: Vec<FamilyMask>,
+    /// Flat `slots.len() * n_genomes` — `genome_mask[i * n_genomes + g]`.
+    genome_mask: Vec<u8>,
+    /// `outgoing[dest_partition]` = `(variant, family_idx_in_batch, base)`.
+    outgoing: Vec<Vec<(CanonicalKmer, usize, u8)>>,
+    _permit: ThrottleGuard,
+}
+
+enum FamData {
+    Batch(SourceBatch),
+    Generated(GeneratedBatch),
+}
+
 /// Visits every minorant family of one layer, in slot order, batched
-/// [`FAMILY_BATCH`] at a time — see the module docs for why. `on_family` is
-/// called once per family with its own annex mask and its per-genome
+/// [`FAMILY_BATCH`] at a time — see the module docs for why generation and
+/// resolution use different concurrency. `on_family` is called once per
+/// family, in slot order, with its own annex mask and its per-genome
 /// base-presence (`genome_mask[g]`: bit `b` set iff genome `g` carries the
 /// member whose own canonical central base is `b`), backed by a scratch
 /// buffer reused across every call — callers that need to keep data past
@@ -88,7 +157,7 @@ pub(super) fn scan_layer_families(
     n_genomes: usize,
     with_counts: bool,
     k: usize,
-    cache: &PartitionCache,
+    cache: &Arc<PartitionCache>,
     mut on_family: impl FnMut(FamilyMask, &[u8]),
 ) -> OKIResult<()> {
     let index_dir = layer_dir.parent().expect("layer_dir has a parent index dir");
@@ -96,13 +165,12 @@ pub(super) fn scan_layer_families(
     let annex = SiblingAnnex::open(&layer_dir.join(ANNEX_FILE_NAME))?;
     let mphf = MphfLayer::open(layer_dir, &meta.mode).map_err(olm_to_ok)?;
 
-    let mut slot_kmer: Vec<Option<CanonicalKmer>> = vec![None; annex.len()];
-    let reader = UnitigFileReader::open_sequential(&layer_dir.join("unitigs.bin")).map_err(OKIError::Partition)?;
-    for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
-        if let Some(slot) = mphf.find(kmer) {
-            slot_kmer[slot] = Some(kmer);
-        }
-    }
+    // `MphfLayer::kmer_at` — direct slot -> k-mer reconstruction (evidence +
+    // direct-access unitigs, no MPHF hashing, no file scan) instead of the
+    // previous scan-`unitigs.bin`-and-hash-every-k-mer-forward approach,
+    // which redundantly re-read the same data `mphf.find()` itself already
+    // reads through `evidence`/`unitigs` to verify each hit.
+    let slot_kmer: Vec<Option<CanonicalKmer>> = (0..annex.len()).map(|slot| mphf.kmer_at(slot)).collect();
 
     let use_counts = with_counts && layer_dir.join("counts").exists();
     let mat = if use_counts {
@@ -112,77 +180,132 @@ pub(super) fn scan_layer_families(
     };
     let n_cols = mat.n_cols().min(n_genomes);
 
-    let n_slots = annex.len();
-    let mut slot = 0usize;
-    let mut batch_slots: Vec<usize> = Vec::with_capacity(FAMILY_BATCH);
-    let mut scratch = vec![0u8; n_genomes]; // reused across every `on_family` call — no per-family allocation
+    // Minorant slots, in order, mask carried along — the flag is already
+    // stored in the annex (set once, at construction — see
+    // `build_layer_sibling_annex`), no need to re-derive it from the kmer
+    // here, and no need for the pipeline workers below to re-read the same
+    // byte from the annex a second time. `slot_kmer[s]` is still required
+    // to exist (used later for `central_canonical_neighbors()`), but not
+    // for this check.
+    let minorant_slots: Vec<(usize, FamilyMask)> = (0..annex.len())
+        .filter_map(|s| {
+            let mask = annex.get(s)?;
+            (slot_kmer[s].is_some() && mask.is_minorant()).then_some((s, mask))
+        })
+        .collect();
+    let total_families = minorant_slots.len();
+    if total_families == 0 {
+        return Ok(());
+    }
 
-    while slot < n_slots {
-        batch_slots.clear();
-        while slot < n_slots && batch_slots.len() < FAMILY_BATCH {
-            let s = slot;
-            slot += 1;
-            let Some(mask) = annex.get(s) else { continue };
-            let Some(kmer) = slot_kmer[s] else { continue };
-            if !is_minorant(kmer, mask, k) {
-                continue; // family tallied once, at its minorant
-            }
-            batch_slots.push(s);
-        }
-        if batch_slots.is_empty() {
-            continue; // ran out of minorant slots before filling a batch — loop condition ends it
-        }
+    let ctx = Arc::new(LayerCtx { slot_kmer, mat, n_parts, n_genomes, n_cols, k });
 
-        // ── Local only: seed each family's own minorant presence (already
-        // open, no lookup) and collect this batch's cross-partition
-        // queries, grouped by destination partition.
-        let mut outgoing: Vec<Vec<(CanonicalKmer, usize, u8)>> = (0..n_parts).map(|_| Vec::new()).collect();
-        let genome_mask: Vec<AtomicU8> = (0..batch_slots.len() * n_genomes).map(|_| AtomicU8::new(0)).collect();
+    let mut offset = 0usize;
+    let batches: Vec<(usize, Vec<(usize, FamilyMask)>)> = minorant_slots
+        .chunks(FAMILY_BATCH)
+        .map(|chunk| {
+            let start = offset;
+            offset += chunk.len();
+            (start, chunk.to_vec())
+        })
+        .collect();
 
-        for (family_idx, &fslot) in batch_slots.iter().enumerate() {
-            let kmer = slot_kmer[fslot].expect("batch slot has a kmer");
-            let mask = annex.get(fslot).expect("batch slot has a mask");
-            let base = central_base(kmer, k);
-            for g in 0..n_cols {
-                if mat.carries(g, fslot) {
-                    genome_mask[family_idx * n_genomes + g].fetch_or(1 << base, Ordering::Relaxed);
-                }
-            }
-            for other in kmer.central_canonical_neighbors() {
-                if other == kmer {
-                    continue; // local — resolved above straight from `mat`, no lookup
-                }
-                let b = central_base(other, k);
-                if !mask.has(b) {
-                    continue;
-                }
-                let dest = partition_of(other, n_parts);
-                outgoing[dest].push((other, family_idx, b));
-            }
-        }
+    let n_workers = obisys::effective_parallelism();
+    let capacity = 4;
+    let throttled = throttle(batches.into_iter(), n_workers).map(|t| SourceBatch {
+        start_family_idx: t.item.0,
+        slots: t.item.1,
+        _permit: t.guard,
+    });
 
-        // ── Resolve this batch's queries, one contiguous sweep per
-        // destination partition — same rationale as `build_sibling_annex`'s
-        // `outgoing` grouping.
-        outgoing.par_iter().enumerate().filter(|(_, q)| !q.is_empty()).for_each(|(dest, queries)| {
-            for &(variant, family_idx, base) in queries {
-                let Some(presence) = cache.find_presence(dest, variant, n_genomes) else { continue };
-                for (g, &present) in presence.iter().enumerate() {
-                    if present {
-                        genome_mask[family_idx * n_genomes + g].fetch_or(1 << base, Ordering::Relaxed);
+    let worker_ctx = Arc::clone(&ctx);
+    let pipe = obipipeline::make_pipe! {
+        FamData : SourceBatch => GeneratedBatch,
+        | {
+            move |batch: SourceBatch| -> GeneratedBatch {
+                let ctx = &worker_ctx;
+                let n = batch.slots.len();
+                let mut masks = Vec::with_capacity(n);
+                let mut bases = Vec::with_capacity(n);
+                let mut genome_mask = vec![0u8; n * ctx.n_genomes];
+                let mut outgoing: Vec<Vec<(CanonicalKmer, usize, u8)>> = (0..ctx.n_parts).map(|_| Vec::new()).collect();
+
+                // Pass 1: cheap, no matrix access — own base and this
+                // batch's cross-partition queries. Mask already in hand
+                // from the filter step, no second annex read.
+                for (i, &(fslot, mask)) in batch.slots.iter().enumerate() {
+                    let kmer = ctx.slot_kmer[fslot].expect("minorant slot has a kmer");
+                    masks.push(mask);
+                    let base = central_base(kmer, ctx.k);
+                    bases.push(base);
+                    for other in kmer.central_canonical_neighbors() {
+                        if other == kmer {
+                            continue; // local — resolved below straight from `mat`, no lookup
+                        }
+                        let b = central_base(other, ctx.k);
+                        if !mask.has(b) {
+                            continue;
+                        }
+                        let dest = partition_of(other, ctx.n_parts);
+                        outgoing[dest].push((other, i, b));
                     }
                 }
-            }
-        });
 
-        for (family_idx, &fslot) in batch_slots.iter().enumerate() {
-            let mask = annex.get(fslot).expect("batch slot has a mask");
-            for (g, dst) in scratch.iter_mut().enumerate() {
-                *dst = genome_mask[family_idx * n_genomes + g].load(Ordering::Relaxed);
+                // Pass 2: genome-major, not family-major — `mat` is stored
+                // one contiguous block per genome (column), slot as the
+                // offset within it (see `PartitionCache::find_presence_batch`'s
+                // docs for the full rationale). `batch.slots` is already
+                // sorted (a contiguous sub-range of the layer's sorted
+                // minorant-slot list), so this sweeps each column roughly
+                // in slot order instead of jumping between all `n_cols`
+                // columns once per family.
+                for g in 0..ctx.n_cols {
+                    for (i, &(fslot, _)) in batch.slots.iter().enumerate() {
+                        if ctx.mat.carries(g, fslot) {
+                            genome_mask[i * ctx.n_genomes + g] |= 1 << bases[i];
+                        }
+                    }
+                }
+
+                GeneratedBatch { start_family_idx: batch.start_family_idx, masks, genome_mask, outgoing, _permit: batch._permit }
             }
-            on_family(mask, &scratch);
+        } : Batch => Generated,
+    };
+
+    // Batches finish generation in whatever order their worker completes
+    // them, not submission order — replay in order through a buffer bounded
+    // by the throttle's own concurrency (`n_workers` batches can be in
+    // flight at once, so at most that many can be waiting here).
+    let mut pending: HashMap<usize, GeneratedBatch> = HashMap::new();
+    let mut next_expected = 0usize;
+    let mut scratch = vec![0u8; n_genomes];
+    for generated in pipe.apply(throttled, n_workers, capacity) {
+        pending.insert(generated.start_family_idx, generated);
+        while let Some(batch) = pending.remove(&next_expected) {
+            let n = batch.masks.len();
+
+            // ── Resolve this one batch's cross-partition queries — the
+            // only place that touches `cache`. Parallel across partitions
+            // (one batch at a time, never several concurrently — see the
+            // module docs), each thread owning one partition's queries
+            // contiguously until this batch is done.
+            let genome_mask: Vec<AtomicU8> = batch.genome_mask.into_iter().map(AtomicU8::new).collect();
+            batch.outgoing.par_iter().enumerate().filter(|(_, q)| !q.is_empty()).for_each(|(dest, queries)| {
+                cache.find_presence_batch(dest, queries, n_genomes, |i, base, g| {
+                    genome_mask[i * n_genomes + g].fetch_or(1 << base, Ordering::Relaxed);
+                });
+            });
+
+            for i in 0..n {
+                for (g, dst) in scratch.iter_mut().enumerate() {
+                    *dst = genome_mask[i * n_genomes + g].load(Ordering::Relaxed);
+                }
+                on_family(batch.masks[i], &scratch);
+            }
+            next_expected += n;
         }
     }
+    debug_assert_eq!(next_expected, total_families, "every batch must have been replayed");
 
     Ok(())
 }
diff --git a/src/obikindex/src/siblings/stats.rs b/src/obikindex/src/siblings/stats.rs
index 2e6009e0..0ca0caf9 100644
--- a/src/obikindex/src/siblings/stats.rs
+++ b/src/obikindex/src/siblings/stats.rs
@@ -1,9 +1,13 @@
+use std::sync::Arc;
+
+use obicompactvec::SiblingAnnex;
 use obikpartitionner::KmerPartition;
 use obisys::progress_bar;
 
 use crate::error::{OKIError, OKIResult};
 use crate::index::KmerIndex;
 
+use super::ANNEX_FILE_NAME;
 use super::cache::PartitionCache;
 use super::family_scan::scan_layer_families;
 
@@ -30,6 +34,42 @@ pub struct SiblingAnnexStats {
 }
 
 impl KmerIndex {
+    /// The global family-size histogram alone (`SiblingAnnexStats::counts`,
+    /// no `per_genome`) — reads only the already-built annex (`mask.siblings()`
+    /// + `mask.is_minorant()`, 1 byte/slot, mmap'd), nothing else: no
+    /// `unitigs.bin` scan, no MPHF lookup, no `PartitionCache`. Cost is a
+    /// linear scan of one small file per layer, independent of the rest of
+    /// the index's size or how much of it is paged in. An earlier version
+    /// re-derived minorant-ness per slot (re-reading `unitigs.bin`, hashing
+    /// every k-mer through the MPHF again to reconstruct what
+    /// `build_sibling_annex` already knew) — sampling a real run showed
+    /// `MphfLayer::find` alone at 71% of wall-clock time for what should be
+    /// a near-instant four-bucket count. `mask.is_minorant()` is that same
+    /// fact, computed once at construction (see `build_layer_sibling_annex`)
+    /// and stored in the annex's own spare bits — free to read back.
+    /// [`sibling_annex_stats`](Self::sibling_annex_stats) computes the same
+    /// `counts` but pays the full per-genome cross-partition resolution
+    /// cost to get there too; use this when only the global histogram is
+    /// needed. Requires an annex built after the minorant flag was added —
+    /// re-run `build_sibling_annex` if this reads as all-zero on an older one.
+    pub fn sibling_family_size_histogram(&self) -> OKIResult<[u64; 4]> {
+        let layer_dirs = self.sibling_layer_dirs()?;
+
+        let mut counts = [0u64; 4];
+        for layer_dir in &layer_dirs {
+            let annex = SiblingAnnex::open(&layer_dir.join(ANNEX_FILE_NAME))?;
+            for slot in 0..annex.len() {
+                let Some(mask) = annex.get(slot) else { continue };
+                if !mask.is_minorant() {
+                    continue; // family tallied once, at its minorant
+                }
+                counts[mask.siblings() as usize] += 1;
+            }
+        }
+
+        Ok(counts)
+    }
+
     /// Tally the family-size distribution of an already-built annex
     /// (globally, and per genome), counting each family once (at its
     /// minorant slot). Errors if [`build_sibling_annex`] has not been run on
@@ -53,7 +93,7 @@ impl KmerIndex {
             n_bits,
         )
         .map_err(OKIError::Partition)?;
-        let cache = PartitionCache::build(&partition, n_parts, with_counts)?;
+        let cache = Arc::new(PartitionCache::build(&partition, n_parts, with_counts)?);
         let layer_dirs = self.sibling_layer_dirs()?;
 
         // One layer at a time, not parallelised across layers — see
diff --git a/src/obikindex/src/siblings/tests.rs b/src/obikindex/src/siblings/tests.rs
index 09a1c597..866464e5 100644
--- a/src/obikindex/src/siblings/tests.rs
+++ b/src/obikindex/src/siblings/tests.rs
@@ -120,7 +120,8 @@ fn sibling_annex_one_sibling_each() {
     // complement, since both start with "AA"), and raw(g1) < raw(g2)
     // (only differing base: C=0b01 < G=0b10 at the centre) — so g1 is
     // the minorant, g2 is not. The mask is a family-wide value: both
-    // slots must read back the *same* mask (bits 1 and 2 set).
+    // slots must read back the *same* presence bits (1 and 2 set) — but
+    // only g1's slot should carry the stored minorant flag.
     let dir = tempdir().unwrap();
     let g1 = build_single_genome_index(dir.path(), "g1", b"AACCGCTTAAG");
     let g2 = build_single_genome_index(dir.path(), "g2", b"AACCGGTTAAG");
@@ -132,14 +133,16 @@ fn sibling_annex_one_sibling_each() {
     let expected_mask = FamilyMask::EMPTY.with(1).with(2);
 
     let a = annex_info_for(&merged, g1_kmer);
-    assert_eq!(a, expected_mask, "AACCGCTTAAG");
+    assert_eq!(a.bits(), expected_mask.bits(), "AACCGCTTAAG");
     assert_eq!(a.siblings(), 1);
     assert!(is_minorant(g1_kmer, a, K), "g1 should be the minorant");
+    assert!(a.is_minorant(), "g1's stored minorant flag should be set at build time");
 
     let b = annex_info_for(&merged, g2_kmer);
-    assert_eq!(b, expected_mask, "AACCGGTTAAG");
+    assert_eq!(b.bits(), expected_mask.bits(), "AACCGGTTAAG");
     assert_eq!(b.siblings(), 1);
     assert!(!is_minorant(g2_kmer, b, K), "g2 should not be the minorant");
+    assert!(!b.is_minorant(), "g2's stored minorant flag should not be set");
 }
 
 #[test]
@@ -185,6 +188,25 @@ fn sibling_annex_stats_counts_each_family_once_and_per_genome() {
     }
 }
 
+#[test]
+fn sibling_family_size_histogram_matches_full_stats_global_counts() {
+    // Same fixture as `sibling_annex_stats_counts_each_family_once_and_per_genome`
+    // — the cheap, annex-only histogram must agree with the `counts` half of
+    // the full (cross-partition) stats pass, without needing a `PartitionCache`
+    // at all.
+    let dir = tempdir().unwrap();
+    let g1 = build_single_genome_index(dir.path(), "g1", b"AACCGCTTAAG");
+    let g2 = build_single_genome_index(dir.path(), "g2", b"AACCGGTTAAG");
+    let merged = merge_two(dir.path(), &g1, &g2);
+    merged.build_sibling_annex().expect("build_sibling_annex");
+
+    let histogram = merged.sibling_family_size_histogram().expect("sibling_family_size_histogram");
+    assert_eq!(histogram, [0, 1, 0, 0], "one family of size 2, counted once");
+
+    let stats = merged.sibling_annex_stats().expect("sibling_annex_stats");
+    assert_eq!(histogram, stats.counts, "must agree with the full stats pass's global counts");
+}
+
 /// Exercises the four sibling-annex consumers that were rewritten to share
 /// `family_scan::scan_layer_families` (partition-grouped lookups instead of
 /// one lookup per family) — same one-sibling-each fixture as the tests
diff --git a/src/obikmer/src/cmd/phylo/args.rs b/src/obikmer/src/cmd/phylo/args.rs
index deedb5bd..aa294e6e 100644
--- a/src/obikmer/src/cmd/phylo/args.rs
+++ b/src/obikmer/src/cmd/phylo/args.rs
@@ -106,6 +106,17 @@ pub struct PhyloArgs {
     #[arg(long)]
     pub sibling_stats: bool,
 
+    /// Print just the global family-size histogram (1-4 members) of an
+    /// already-built annex — the `global` row `--sibling-stats` also
+    /// writes, but without the per-genome breakdown, so it skips
+    /// `--sibling-stats`'s cross-partition resolution entirely: reads only
+    /// the already-open annex mask and each layer's own `unitigs.bin`, cost
+    /// independent of the rest of the index. A quick sanity check that the
+    /// annex itself is sound, decoupled from `--sibling-stats`'s much
+    /// heavier per-genome pass.
+    #[arg(long)]
+    pub sibling_hist: bool,
+
     /// Compute the raw p-distance restricted to loci that are single-copy
     /// in both genomes of each pair (an already-built sibling annex is
     /// required — run with `--sibling-annex` first, in this invocation or
@@ -231,7 +242,8 @@ pub struct PhyloArgs {
     pub sankoff_cost_scale: f64,
 
     /// Output prefix: <prefix>_dist.csv, <prefix>_shared.csv,
-    /// <prefix>_siblings.csv, <prefix>_rawsnp.csv, <prefix>_rawsnp_counts.csv,
+    /// <prefix>_siblings.csv, <prefix>_sibling_hist.csv, <prefix>_rawsnp.csv,
+    /// <prefix>_rawsnp_counts.csv,
     /// <prefix>_snp.fasta, <prefix>_family_overlap.csv,
     /// <prefix>_sankoff_matrix.csv, <prefix>_sankoff_params.yaml,
     /// <prefix>_sankoff.fasta, <prefix>_sankoff.tnt, <prefix>_sankoff.tcm,
diff --git a/src/obikmer/src/cmd/phylo/mod.rs b/src/obikmer/src/cmd/phylo/mod.rs
index d510822c..9b09a071 100644
--- a/src/obikmer/src/cmd/phylo/mod.rs
+++ b/src/obikmer/src/cmd/phylo/mod.rs
@@ -19,7 +19,7 @@ use tracing::info;
 pub use args::PhyloArgs;
 use family_overlap::{apply_min_shared_family_exclusion, write_family_overlap_csv};
 use iqtree::write_iqtree;
-use outputs::{write_raw_snp_counts_csv, write_raw_snp_distance_csv, write_sibling_stats_csv, write_snp_fasta, upgma_to_newick};
+use outputs::{write_raw_snp_counts_csv, write_raw_snp_distance_csv, write_sibling_hist_csv, write_sibling_stats_csv, write_snp_fasta, upgma_to_newick};
 use phyg::write_sankoff_phyg;
 use sankoff::{write_sankoff_alignment_fasta, write_sankoff_matrix_csv, write_sankoff_params};
 use tnt::write_sankoff_tnt;
@@ -135,6 +135,13 @@ pub fn run(args: PhyloArgs) {
         });
         write_sibling_stats_csv(&stats, &labels, &args.output);
     }
+    if args.sibling_hist {
+        let counts = idx.sibling_family_size_histogram().unwrap_or_else(|e| {
+            eprintln!("error computing sibling family-size histogram: {e}");
+            std::process::exit(1);
+        });
+        write_sibling_hist_csv(&counts, &args.output);
+    }
     if args.raw_snp_distance {
         let mut result = idx.raw_snp_distance().unwrap_or_else(|e| {
             eprintln!("error computing raw SNP distance: {e}");
diff --git a/src/obikmer/src/cmd/phylo/outputs.rs b/src/obikmer/src/cmd/phylo/outputs.rs
index 97b548fd..28b67a66 100644
--- a/src/obikmer/src/cmd/phylo/outputs.rs
+++ b/src/obikmer/src/cmd/phylo/outputs.rs
@@ -76,6 +76,25 @@ pub(super) fn write_raw_snp_distance_csv(result: &RawSnpDistanceOutput, labels:
     info!("raw single-copy SNP distance matrix → {path}");
 }
 
+// ── Global family-size histogram (annex-only, no per-genome pass) → CSV ────
+
+pub(super) fn write_sibling_hist_csv(counts: &[u64; 4], output: &Option<PathBuf>) {
+    let path = output.as_ref()
+        .map(|p| format!("{}_sibling_hist.csv", p.display()))
+        .unwrap_or_else(|| "sibling_hist.csv".into());
+    let mut f = BufWriter::new(std::fs::File::create(&path).unwrap_or_else(|e| {
+        eprintln!("error creating {path}: {e}");
+        std::process::exit(1);
+    }));
+    writeln!(f, "size,count").unwrap();
+    for (size, count) in counts.iter().enumerate() {
+        writeln!(f, "{},{count}", size + 1).unwrap();
+    }
+    let total: u64 = counts.iter().sum();
+    info!("family-size histogram → {path} (total {total} famil{})",
+        if total == 1 { "y" } else { "ies" });
+}
+
 // ── Raw single-copy SNP distance → per-pair diagnostic counts ──────────────
 //
 // A pair table (one row per unordered genome pair), not a matrix: the ratio
diff --git a/src/obilayeredmap/src/mphf_layer.rs b/src/obilayeredmap/src/mphf_layer.rs
index 26611230..b9d19901 100644
--- a/src/obilayeredmap/src/mphf_layer.rs
+++ b/src/obilayeredmap/src/mphf_layer.rs
@@ -134,6 +134,31 @@ impl MphfLayer {
         }
     }
 
+    /// Reconstruct the canonical k-mer stored at `slot` — the inverse of
+    /// [`find`](Self::find)/[`find_strict`](Self::find_strict) (k-mer → slot).
+    /// O(1) on `Exact`/`Hybrid` layers: `evidence.decode(slot)` gives
+    /// `(chunk_id, rank)` directly (no MPHF hashing, no file scan), then
+    /// `unitigs.canonical_raw_kmer` is a direct-access read. `None` on
+    /// `Approx` layers — fingerprints alone can't recover a k-mer, and
+    /// falling back to a full sequential scan here would silently make one
+    /// call cost O(n); callers needing this on an `Approx` layer should
+    /// scan `unitigs.bin` themselves and decide how to handle that cost
+    /// explicitly.
+    pub fn kmer_at(&self, slot: usize) -> Option<CanonicalKmer> {
+        if slot >= self.n {
+            return None;
+        }
+        match &self.ev {
+            LayerEvidence::Exact  { evidence, unitigs } |
+            LayerEvidence::Hybrid { evidence, unitigs, .. } => {
+                let (chunk_id, rank) = evidence.decode(slot);
+                let raw = unitigs.canonical_raw_kmer(chunk_id as usize, rank as usize);
+                Some(CanonicalKmer::from_raw_unchecked(raw))
+            }
+            LayerEvidence::Approx { .. } => None,
+        }
+    }
+
     pub fn n(&self) -> usize { self.n }
 }
 
diff --git a/src/obiskio/src/unitig_index/reader.rs b/src/obiskio/src/unitig_index/reader.rs
index 8e1b49c3..e5f0d978 100644
--- a/src/obiskio/src/unitig_index/reader.rs
+++ b/src/obiskio/src/unitig_index/reader.rs
@@ -157,6 +157,16 @@ impl UnitigFileReader {
         canonical_raw(self.raw_kmer(i, j), self.k) == query.raw()
     }
 
+    /// Canonical raw k-mer at position `j` of chunk `i` — [`raw_kmer`](Self::raw_kmer)
+    /// reduced to its canonical (`min(raw, revcomp)`) form. The reconstruction
+    /// half of [`verify_canonical_kmer`](Self::verify_canonical_kmer): that
+    /// method computes the same value internally just to compare it away: use
+    /// this one when the caller wants the k-mer itself, not a yes/no answer.
+    #[inline]
+    pub fn canonical_raw_kmer(&self, i: usize, j: usize) -> u64 {
+        canonical_raw(self.raw_kmer(i, j), self.k)
+    }
+
     // ── Sequential iterators (O(n) running-offset cursor) ─────────────────────
 
     pub(crate) fn iter_chunks_sequential(&self) -> impl Iterator<Item = (usize, Unitig)> + '_ {
-- 
2.54.0


From dae543fdfc8fc8cac61cc29804a70c3f2465415d Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Fri, 14 Aug 2026 11:05:11 +0200
Subject: [PATCH 20/46] Add raw lookup and iteration APIs to Layer struct

Introduces `index` and `index_batch` methods for direct MPHF slot mapping without membership validation, alongside four public iterator methods for deterministic traversal of canonical kmers. These are backed by dedicated `KmerIter` and `KmerBatchIter` structs that wrap the underlying unitig file reader. Updates `LayerEvidence::Approx` to eagerly open the unitig reader during initialization, enforcing a clear separation between raw mapping and verified lookup workflows.
---
 phylo_archi.md                      |  32 +++++++
 src/obilayeredmap/src/layer.rs      |  32 +++++++
 src/obilayeredmap/src/mphf_layer.rs | 126 ++++++++++++++++++++++++++--
 3 files changed, 184 insertions(+), 6 deletions(-)
 create mode 100644 phylo_archi.md

diff --git a/phylo_archi.md b/phylo_archi.md
new file mode 100644
index 00000000..ce2b9f31
--- /dev/null
+++ b/phylo_archi.md
@@ -0,0 +1,32 @@
+**Nous avons un vrai problème architectural dans la partie phylo, basée sur les sibling.**
+
+La structure de l'index est en quatre parties, à l'intérieur d'un layer:
+
+- Un fichier de superkmers qui permet d'itinérer sur les kmers gérées par le layer.
+- Un MPFH qui permet de convertir un kmer en un numéro de slot compact.
+- Un tableau d'évidence, qui peut être exact ou probabiliste. Ce qui permet de vérifier lorsque l'on interroge le MPFH avec un kmer, si ce kmer est contenu dans le layer.
+  - Il est donc une **erreur conceptuelle grave** d'utiliser cette évidence pour retrouver un kmer à partir de son numéro de slot. Toute tentative en ce sens est vouée à l’échec sur une évidence non exacte.
+- Un tableau de présence ou de comptage par génome. Ranger colonne first : une colonne correspond à un génome, et indexé par numéro de slot
+
+## Concernant le MPFH.
+
+- Le rôle premier du MPFH est de convertir un kmer en un numéro de slot.
+- On peut, en rôle secondaire, en combinant le MPFH et le tableau d'évidence, s'en servir pour mettre en place un test d'appartenance au layer pour un kmer.
+
+L'API du `Layer<D>` expose également des méthodes de mapping brut kmer → slot via le MPHF, sans vérification d'appartenance :
+
+- `index(&self, kmer: CanonicalKmer) -> usize` — retourne le numéro de slot pour un kmer. C'est un mapping pur, équivalent à `MphfOnly::index`.
+- `index_batch(&self, kmers: &[CanonicalKmer]) -> Vec<usize>` — retourne un vecteur de slots pour un slice de kmers.
+
+Ces méthodes sont distinctes de `query()` et `find()` qui incluent la vérification d'appartenance.
+
+Lorsque l'on itère sur le fichier de superkmer, l'ordre des kmer est déterministe, mais non corrélé avec les numéros de slot correspondants. Il existe donc un numéro d'ordre dans les kmer contenues dans le fichier de superkmer.
+
+L'API du `Layer<D>` expose maintenant quatre itérateurs sur les kmers du layer :
+
+- `iter_kmers(&self) -> KmerIter<'_>` — itérateur nommé sur `CanonicalKmer`, construit à partir de `unitigs.bin`. Plusieurs instances peuvent coexister concurremment tant que le layer vit.
+- `enumerate_kmers(&self) -> Enumerate<KmerIter<'_>>` — variante indexée retournant `(usize, CanonicalKmer)`, où l'index 0 correspond au premier kmer du fichier de superkmers. Construit par composition sur `iter_kmers()` sans duplication de code d'itération.
+- `iter_kmers_batch(&self, n: usize) -> KmerBatchIter<'_>` — itérateur par batch retournant `Vec<CanonicalKmer>` de taille `n`. Le dernier batch peut être tronqué.
+- `enumerate_kmers_batch(&self, n: usize) -> Enumerate<KmerBatchIter<'_>>` — variante indexée retournant `(usize, Vec<CanonicalKmer>)`, où l'index correspond au premier kmer du batch. Construit par composition sur `iter_kmers_batch()`.
+
+L'itération est implémentée via des structs `KmerIter` et `KmerBatchIter` qui encapsulent l'itérateur interne de `UnitigFileReader::iter_indexed_canonical_kmers()`. Les structs sont publics et peuvent être stockés, transmis ou combinés avec d'autres adaptateurs d'itérateur.
diff --git a/src/obilayeredmap/src/layer.rs b/src/obilayeredmap/src/layer.rs
index 475bca7f..7a256485 100644
--- a/src/obilayeredmap/src/layer.rs
+++ b/src/obilayeredmap/src/layer.rs
@@ -74,6 +74,38 @@ impl<D: LayerData> Layer<D> {
 
     pub fn n(&self) -> usize { self.mphf.n() }
 
+    /// Raw MPHF lookup: kmer → slot, no membership check.
+    pub fn index(&self, kmer: CanonicalKmer) -> usize {
+        self.mphf.index(kmer)
+    }
+
+    /// Batch raw MPHF lookup: kmers → slots, no membership check.
+    pub fn index_batch(&self, kmers: &[CanonicalKmer]) -> Vec<usize> {
+        self.mphf.index_batch(kmers)
+    }
+
+    /// Iterate over all canonical kmers in the layer, in deterministic order.
+    pub fn iter_kmers(&self) -> crate::mphf_layer::KmerIter<'_> {
+        self.mphf.iter_kmers()
+    }
+
+    /// Iterate over all canonical kmers, each paired with its zero-based
+    /// sequence index in `unitigs.bin`.
+    pub fn enumerate_kmers(&self) -> std::iter::Enumerate<crate::mphf_layer::KmerIter<'_>> {
+        self.mphf.enumerate_kmers()
+    }
+
+    /// Iterate over the layer's canonical kmers in batches of `n`.
+    pub fn iter_kmers_batch(&self, n: usize) -> crate::mphf_layer::KmerBatchIter<'_> {
+        self.mphf.iter_kmers_batch(n)
+    }
+
+    /// Iterate over batches, each paired with the zero-based index of the
+    /// first kmer in the batch.
+    pub fn enumerate_kmers_batch(&self, n: usize) -> std::iter::Enumerate<crate::mphf_layer::KmerBatchIter<'_>> {
+        self.mphf.enumerate_kmers_batch(n)
+    }
+
     pub fn unitig_writer(out_dir: &Path) -> OLMResult<UnitigFileWriter> {
         MphfLayer::unitig_writer(out_dir)
     }
diff --git a/src/obilayeredmap/src/mphf_layer.rs b/src/obilayeredmap/src/mphf_layer.rs
index b9d19901..6aa67660 100644
--- a/src/obilayeredmap/src/mphf_layer.rs
+++ b/src/obilayeredmap/src/mphf_layer.rs
@@ -1,4 +1,5 @@
 use std::fs;
+use std::iter::Enumerate;
 use std::path::{Path, PathBuf};
 
 use cacheline_ef::{CachelineEf, CachelineEfVec};
@@ -29,7 +30,7 @@ type MphfEps = PtrHash<u64, CubicEps, CachelineEfVec<&'static [CachelineEf]>, Xx
 
 enum LayerEvidence {
     Exact  { evidence: Evidence, unitigs: UnitigFileReader },
-    Approx { fingerprint: FingerprintVec, unitigs_path: PathBuf },
+    Approx { fingerprint: FingerprintVec, unitigs: UnitigFileReader, unitigs_path: PathBuf },
     Hybrid { evidence: Evidence, unitigs: UnitigFileReader, fingerprint: FingerprintVec },
 }
 
@@ -57,15 +58,15 @@ impl MphfLayer {
             IndexMode::Exact => {
                 let evidence = Evidence::open(&dir.join(EVIDENCE_FILE))?;
                 let n = evidence.len();
-                // open() auto-detects: uses direct access since exact layers always have .idx
                 let unitigs = UnitigFileReader::open(&dir.join(UNITIGS_FILE))?;
                 (LayerEvidence::Exact { evidence, unitigs }, n)
             }
             IndexMode::Approx { .. } => {
                 let fingerprint = FingerprintVec::open(&dir.join(FINGERPRINT_FILE))?;
                 let n = fingerprint.n();
+                let unitigs = UnitigFileReader::open(&dir.join(UNITIGS_FILE))?;
                 let unitigs_path = dir.join(UNITIGS_FILE);
-                (LayerEvidence::Approx { fingerprint, unitigs_path }, n)
+                (LayerEvidence::Approx { fingerprint, unitigs, unitigs_path }, n)
             }
             IndexMode::Hybrid { .. } => {
                 let evidence    = Evidence::open(&dir.join(EVIDENCE_FILE))?;
@@ -89,7 +90,7 @@ impl MphfLayer {
         let slot = self.mphf.index(&kmer.raw());
         if slot >= self.n { return None; }
         match &self.ev {
-            LayerEvidence::Exact { evidence, unitigs } => {
+            LayerEvidence::Exact { evidence, unitigs, .. } => {
                 let (chunk_id, rank) = evidence.decode(slot);
                 if unitigs.verify_canonical_kmer(chunk_id as usize, rank as usize, kmer) {
                     Some(slot)
@@ -113,7 +114,7 @@ impl MphfLayer {
         let slot = self.mphf.index(&kmer.raw());
         if slot >= self.n { return None; }
         match &self.ev {
-            LayerEvidence::Exact  { evidence, unitigs } |
+            LayerEvidence::Exact  { evidence, unitigs, .. } |
             LayerEvidence::Hybrid { evidence, unitigs, .. } => {
                 let (chunk_id, rank) = evidence.decode(slot);
                 if unitigs.verify_canonical_kmer(chunk_id as usize, rank as usize, kmer) {
@@ -149,7 +150,7 @@ impl MphfLayer {
             return None;
         }
         match &self.ev {
-            LayerEvidence::Exact  { evidence, unitigs } |
+            LayerEvidence::Exact  { evidence, unitigs, .. } |
             LayerEvidence::Hybrid { evidence, unitigs, .. } => {
                 let (chunk_id, rank) = evidence.decode(slot);
                 let raw = unitigs.canonical_raw_kmer(chunk_id as usize, rank as usize);
@@ -160,6 +161,119 @@ impl MphfLayer {
     }
 
     pub fn n(&self) -> usize { self.n }
+
+    /// Raw MPHF lookup: kmer → slot.
+    ///
+    /// Returns the slot assigned by the MPHF without performing any membership
+    /// check against the layer's evidence.  The returned slot is only meaningful
+    /// when the kmer is actually present in the layer; callers that need an
+    /// existence test should use [`find`](Self::find) instead.
+    pub fn index(&self, kmer: CanonicalKmer) -> usize {
+        self.mphf.index(&kmer.raw())
+    }
+
+    /// Batch raw MPHF lookup: kmers → slots.
+    ///
+    /// Returns a [`Vec`] of slots, one per input kmer, in the same order as the
+    /// input slice.  Like [`index`](Self::index), no membership check is
+    /// performed.
+    pub fn index_batch(&self, kmers: &[CanonicalKmer]) -> Vec<usize> {
+        kmers.iter().map(|k| self.mphf.index(&k.raw())).collect()
+    }
+
+    /// Iterate over all canonical kmers in the layer, in deterministic order.
+    ///
+    /// The iteration order follows the physical layout of `unitigs.bin` and is
+    /// **not** correlated with MPHF slot numbers.  Multiple `KmerIter` instances
+    /// can be held concurrently for as long as the layer lives, because each
+    /// carries its own cursor.
+    pub fn iter_kmers(&self) -> KmerIter<'_> {
+        let reader = match &self.ev {
+            LayerEvidence::Exact { unitigs, .. } => unitigs,
+            LayerEvidence::Approx { unitigs, .. } => unitigs,
+            LayerEvidence::Hybrid { unitigs, .. } => unitigs,
+        };
+        KmerIter { inner: Box::new(reader.iter_indexed_canonical_kmers()) }
+    }
+
+    /// Iterate over all canonical kmers, each paired with its zero-based
+    /// sequence index in `unitigs.bin`.
+    ///
+    /// Yields `(index, kmer)` where `index` starts at `0` for the first kmer
+    /// stored in the layer.  This is the standard Rust `enumerate` adapter
+    /// applied to [`iter_kmers`](Self::iter_kmers).
+    pub fn enumerate_kmers(&self) -> Enumerate<KmerIter<'_>> {
+        self.iter_kmers().enumerate()
+    }
+
+    /// Iterate over the layer's canonical kmers in batches of `n`.
+    ///
+    /// Each call to [`next`](Iterator::next) returns a [`Vec`] of up to `n`
+    /// kmers.  The final batch may be shorter when the layer is exhausted.
+    pub fn iter_kmers_batch(&self, n: usize) -> KmerBatchIter<'_> {
+        KmerBatchIter { inner: self.iter_kmers(), batch_size: n }
+    }
+
+    /// Iterate over batches, each paired with the zero-based index of the
+    /// first kmer in the batch.
+    ///
+    /// Yields `(batch_start_index, Vec<CanonicalKmer>)` where
+    /// `batch_start_index` is a multiple of `n`.  This is the standard Rust
+    /// `enumerate` adapter applied to [`iter_kmers_batch`](Self::iter_kmers_batch).
+    pub fn enumerate_kmers_batch(&self, n: usize) -> Enumerate<KmerBatchIter<'_>> {
+        self.iter_kmers_batch(n).enumerate()
+    }
+}
+
+// ── Iterator types ────────────────────────────────────────────────────────────
+
+/// Iterator over the canonical kmers stored in a layer.
+///
+/// Produced by [`MphfLayer::iter_kmers`].  Multiple `KmerIter` instances can
+/// coexist concurrently for as long as the parent layer lives, because each
+/// holds its own cursor over the underlying [`UnitigFileReader`].
+pub struct KmerIter<'a> {
+    inner: Box<dyn Iterator<Item = (CanonicalKmer, usize, usize)> + 'a>,
+}
+
+impl<'a> Iterator for KmerIter<'a> {
+    type Item = CanonicalKmer;
+
+    /// Return the next canonical kmer in iteration order.
+    fn next(&mut self) -> Option<Self::Item> {
+        self.inner.next().map(|(kmer, _, _)| kmer)
+    }
+}
+
+/// Iterator over batches of canonical kmers stored in a layer.
+///
+/// Produced by [`MphfLayer::iter_kmers_batch`].  Each call to [`next`](Self::next)
+/// returns a [`Vec`] of up to `batch_size` kmers.  The last batch may be shorter
+/// than `batch_size` when the layer is exhausted.
+pub struct KmerBatchIter<'a> {
+    inner: KmerIter<'a>,
+    batch_size: usize,
+}
+
+impl<'a> Iterator for KmerBatchIter<'a> {
+    type Item = Vec<CanonicalKmer>;
+
+    /// Return the next batch of kmers, or `None` if the layer is exhausted.
+    fn next(&mut self) -> Option<Self::Item> {
+        let mut batch = Vec::with_capacity(self.batch_size);
+        for _ in 0..self.batch_size {
+            if let Some(kmer) = self.inner.next() {
+                batch.push(kmer);
+            } else {
+                break;
+            }
+        }
+        if batch.is_empty() {
+            None
+        } else {
+            Some(batch)
+        }
+    }
 }
 
 // ── MphfOnly ──────────────────────────────────────────────────────────────────
-- 
2.54.0


From b1f54b7d2f4c9310282c5ed47bccc6b99d466ced Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Fri, 14 Aug 2026 12:06:35 +0200
Subject: [PATCH 21/46] Add cache-optimized batch retrieval and sub-matrix
 methods

Introduces batch retrieval and sub-matrix extraction methods across vector, view, reader, and matrix types. These implementations optimize cache locality by sorting requested indices for sequential memory access before applying an inverse permutation to restore original order. Includes allocation-free variants that populate caller-provided buffers. Updates architecture documentation to define sibling annex persistence in iteration order and clarify pipeline separation.
---
 docmd/architecture/siblings.md                | 77 +++++++++++++++++++
 mkdocs.yml                                    |  1 +
 phylo_archi.md                                | 26 +++++++
 src/obicompactvec/src/bitmatrix/persistent.rs | 51 ++++++++++++
 src/obicompactvec/src/bitvec.rs               | 36 +++++++++
 src/obicompactvec/src/intmatrix.rs            | 44 +++++++++++
 src/obicompactvec/src/reader.rs               | 36 +++++++++
 src/obicompactvec/src/views.rs                | 66 ++++++++++++++++
 src/obilayeredmap/src/layer.rs                | 38 +++++++++
 9 files changed, 375 insertions(+)
 create mode 100644 docmd/architecture/siblings.md

diff --git a/docmd/architecture/siblings.md b/docmd/architecture/siblings.md
new file mode 100644
index 00000000..b7012bc2
--- /dev/null
+++ b/docmd/architecture/siblings.md
@@ -0,0 +1,77 @@
+# Sibling annex — architecture (discussion)
+
+Status: architecture decided (2026-08-14). Implementation not yet mandated.
+
+## Two index spaces, uncorrelated
+
+Every kmer stored in a `Layer` lives in two independent index spaces:
+
+- **Iteration order**: its position when enumerating `unitigs.bin` (the
+  superkmer file), deterministic but arbitrary with respect to slot.
+- **MPHF slot**: `MphfLayer::index(kmer)`, the number the MPHF assigns.
+
+The two are not correlated by any formula. Converting from one to the other
+requires either recomputing the MPHF (kmer → slot) or scanning the iteration
+stream (kmer → order). There is no `slot → kmer` operation: the MPHF is a
+one-way function, not an invertible bijection with a stored inverse. Any
+method that reconstructs a kmer from a bare slot number is wrong by
+construction, regardless of the mechanism used (MPHF re-hash, or evidence
+decode + direct unitig read). See `MphfLayer::kmer_at`
+(`obilayeredmap/src/mphf_layer.rs`) — flagged for removal, currently called
+from `obikindex/siblings/build.rs:122` and `family_scan.rs:173`.
+
+## Two pipelines, never mixed
+
+| | origin of the kmer | membership known? | correct mapping |
+|---|---|---|---|
+| **query pipeline** | external (caller-supplied) | no | `query`/`find`/`find_strict` — MPHF + evidence check |
+| **iteration pipeline** | enumerated from this layer's own `unitigs.bin` | yes, by construction | `index`/`index_batch` — MPHF only, no evidence |
+
+Evidence exists solely to answer "is this external kmer a member of the
+layer" for the query pipeline. Using it (or the MPHF) to go the other way —
+recover a kmer from a slot, or re-verify a kmer that was just produced by
+iterating the layer — is a conceptual error: evidence can be probabilistic
+(`Approx` mode), so any slot→kmer attempt is unsound in general, and
+pointless even in `Exact`/`Hybrid` mode since the kmer was already known.
+
+## Sibling annex: an iteration-pipeline artifact only
+
+The sibling annex (`FamilyMask`/`SiblingAnnex`, `.psib`,
+`obicompactvec/src/siblingannex.rs`) records, per kmer, whether it is a
+family minorant and which family members are present in the index. Its only
+consumers (`obikindex/siblings/stats.rs`, `family_scan.rs`) enumerate it
+exhaustively (`0..annex.len()`); no query-pipeline code path touches it.
+
+**Decision**: the annex must be persisted in iteration order, not slot
+order. This lets readers zip-iterate `Layer::iter_kmers()` and the annex
+file directly — one linear, cache-friendly pass, no MPHF/slot indirection,
+no `kmer_at`. It also enables specialized iterators building on this zip:
+minorants-only iteration, batch-of-kmers → batch-of-family-members, etc.
+
+Today the annex is built and stored in **slot** order
+(`build_layer_sibling_annex`, `siblings/build.rs`): `slot_kmer` is populated
+via `(0..n_slots).map(|slot| mphf.kmer_at(slot))`, and the origin `slot` is
+threaded through the whole cross-partition reconciliation pipeline (variant
+generation, `query_partition_with`, final `mask[slot].fetch_or(...)`). This
+must change to iterating `iter_kmers()`/`enumerate_kmers()` and threading
+the **iteration index** instead of the slot end to end — eliminating
+`kmer_at` from the build path entirely, not just the read path. No
+slot-indexed intermediate is needed even during construction; the
+iteration-order id is sufficient throughout.
+
+The cross-partition side of the same pipeline is unaffected: checking
+whether a generated family-variant kmer exists in another partition is a
+genuine query-pipeline operation (the variant's membership in the *target*
+partition is unknown) and must keep going through
+`KmerPartition::query_partition_with` (MPHF + evidence), never a raw
+`index()`.
+
+## Pending work
+
+- Remove `MphfLayer::kmer_at`.
+- `siblings/build.rs`: build `slot_kmer`-equivalent via iteration, not
+  `kmer_at`; thread iteration index instead of slot through the
+  variant/reconciliation pipeline; persist the annex in iteration order.
+- `siblings/family_scan.rs`, `stats.rs`: read the annex via zipped
+  iteration (`iter_kmers().zip(annex_iter)`) instead of `0..annex.len()` +
+  `kmer_at`.
diff --git a/mkdocs.yml b/mkdocs.yml
index f0a67189..13f3abf3 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -58,6 +58,7 @@ nav:
   - Architecture:
       - Sequences: architecture/sequences/invariant.md
       - Kmer index: architecture/index_architecture.md
+      - Sibling annex (discussion): architecture/siblings.md
       - NUMA-aware worker pools: architecture/numa_worker_pools.md
       - NUMA-aware partition runner: architecture/numa_partition_runner.md
 
diff --git a/phylo_archi.md b/phylo_archi.md
index ce2b9f31..fea68a45 100644
--- a/phylo_archi.md
+++ b/phylo_archi.md
@@ -30,3 +30,29 @@ L'API du `Layer<D>` expose maintenant quatre itérateurs sur les kmers du layer
 - `enumerate_kmers_batch(&self, n: usize) -> Enumerate<KmerBatchIter<'_>>` — variante indexée retournant `(usize, Vec<CanonicalKmer>)`, où l'index correspond au premier kmer du batch. Construit par composition sur `iter_kmers_batch()`.
 
 L'itération est implémentée via des structs `KmerIter` et `KmerBatchIter` qui encapsulent l'itérateur interne de `UnitigFileReader::iter_indexed_canonical_kmers()`. Les structs sont publics et peuvent être stockés, transmis ou combinés avec d'autres adaptateurs d'itérateur.
+
+## Performance — itérateurs de batch
+
+Les itérateurs `iter_kmers_batch` et `enumerate_kmers_batch` allouent un nouveau `Vec` à chaque batch. Pour des tailles de batch importantes ou des chemins critiques, cela peut générer une pression malloc significative.
+
+**À concevoir** : un système de pool de vecteurs avec réallocation automatique dès qu'un buffer n'est plus référencé, pour réutiliser les allocations entre batches et réduire le nombre d'appels système. Ce pool pourrait être intégré à `KmerBatchIter` ou proposé comme un adaptateur d'itérateur générique.
+
+## Accès aux matrices de présence/comptage
+
+Les types de vecteurs persistants exposent maintenant des méthodes de lookup batch optimisées pour l'accès séquentiel au mmap :
+
+- `PersistentCompactIntVec::get_batch(slots) -> Vec<u32>` et `fill_batch(slots, out)`
+- `PersistentBitVec::get_batch(slots) -> Vec<bool>` et `fill_batch(slots, out)`
+- `IntSliceView::get_batch(slots) -> Vec<u32>` et `fill_batch(slots, out)`
+- `BitSliceView::get_batch(slots) -> Vec<bool>` et `fill_batch(slots, out)`
+
+Toutes ces méthodes trient les slots en interne pour un accès mmap séquentiel, puis réordonnent les résultats selon l'ordre d'origine. `fill_batch` évite l'allocation en remplissant un buffer fourni par le caller.
+
+Les matrices persistantes exposent `sub_matrix(slots) -> Vec<Vec<T>>` et `fill_sub_matrix(slots, out)` :
+
+- `PersistentCompactIntMatrix::sub_matrix(slots)` — retourne `Vec<Vec<u32>>` column-first
+- `PersistentCompactIntMatrix::fill_sub_matrix(slots, out: &mut [Vec<u32>])` — remplit des buffers fournis, réutilise les allocations existantes
+- `PersistentBitMatrix::sub_matrix(slots)` — retourne `Vec<Vec<bool>>` column-first
+- `PersistentBitMatrix::fill_sub_matrix(slots, out: &mut [Vec<bool>])` — remplit des buffers fournis, réutilise les allocations existantes
+
+Le scan est colonne-first pour respecter la layout mémoire. `fill_sub_matrix` trie les slots une seule fois, puis appelle `fill_batch_sorted` sur chaque colonne pour éviter le tri redondant. Ces méthodes sont également disponibles sur `Layer<PersistentCompactIntMatrix>` et `Layer<PersistentBitMatrix>`.
diff --git a/src/obicompactvec/src/bitmatrix/persistent.rs b/src/obicompactvec/src/bitmatrix/persistent.rs
index 7f5b2b9d..3149241c 100644
--- a/src/obicompactvec/src/bitmatrix/persistent.rs
+++ b/src/obicompactvec/src/bitmatrix/persistent.rs
@@ -126,6 +126,57 @@ impl PersistentBitMatrix {
         }
     }
 
+    /// Extract a sub-matrix containing only the rows at `slots`.
+    ///
+    /// Returns a column-first `Vec<Vec<bool>>`: the outer `Vec` has one entry per
+    /// column, and each inner `Vec` contains the values for the requested rows
+    /// in the same order as `slots`.  Column access is sequential to maximize
+    /// cache efficiency on the underlying mmap.
+    pub fn sub_matrix(&self, slots: &[usize]) -> Vec<Vec<bool>> {
+        let n_cols = self.n_cols();
+        let mut out: Vec<Vec<bool>> = Vec::with_capacity(n_cols);
+        for c in 0..n_cols {
+            let mut col_buf = vec![false; slots.len()];
+            match self {
+                Self::Columnar(m) => m.col(c).view().fill_batch(slots, &mut col_buf),
+                Self::Packed(m)   => m.col_slice(c).fill_batch(slots, &mut col_buf),
+                Self::Implicit { .. } => col_buf.iter_mut().for_each(|b| *b = true),
+            }
+            out.push(col_buf);
+        }
+        out
+    }
+
+    /// Like [`sub_matrix`](Self::sub_matrix), but fills caller-provided column
+    /// buffers to avoid allocating the outer `Vec`.
+    ///
+    /// `out` must have length `self.n_cols()`.  Each `out[c]` is cleared,
+    /// resized to `slots.len()`, and filled with the values for column `c`
+    /// in the same order as `slots`.
+    pub fn fill_sub_matrix(&self, slots: &[usize], out: &mut [Vec<bool>]) {
+        assert_eq!(out.len(), self.n_cols());
+        let n = slots.len();
+        if n == 0 {
+            for col in out.iter_mut() { col.clear(); }
+            return;
+        }
+        let mut perm: Vec<usize> = (0..n).collect();
+        perm.sort_by_key(|&i| slots[i]);
+        let sorted_slots: Vec<usize> = perm.iter().map(|&i| slots[i]).collect();
+        for (c, col) in out.iter_mut().enumerate() {
+            col.resize(n, false);
+            let mut tmp = vec![false; n];
+            match self {
+                Self::Columnar(m) => m.col(c).view().fill_batch_sorted(&sorted_slots, &mut tmp),
+                Self::Packed(m)   => m.col_slice(c).fill_batch_sorted(&sorted_slots, &mut tmp),
+                Self::Implicit { .. } => tmp.iter_mut().for_each(|b| *b = true),
+            }
+            for (i, &orig_idx) in perm.iter().enumerate() {
+                col[orig_idx] = tmp[i];
+            }
+        }
+    }
+
     pub fn count_ones(&self) -> Array1<u64> {
         match self {
             Self::Columnar(m)              => m.count_ones(),
diff --git a/src/obicompactvec/src/bitvec.rs b/src/obicompactvec/src/bitvec.rs
index ee7d6f74..c425a919 100644
--- a/src/obicompactvec/src/bitvec.rs
+++ b/src/obicompactvec/src/bitvec.rs
@@ -48,6 +48,42 @@ impl PersistentBitVec {
         (self.mmap[HEADER_SIZE + (slot >> 3)] >> (slot & 7)) & 1 != 0
     }
 
+    /// Batch lookup: read bits at `slots` in an order that minimizes
+    /// cache misses.
+    ///
+    /// The slots are sorted internally before reading so that accesses to
+    /// the underlying mmap are as sequential as possible, then the results
+    /// are reordered to match the input order.
+    pub fn get_batch(&self, slots: &[usize]) -> Vec<bool> {
+        let mut out = vec![false; slots.len()];
+        self.fill_batch(slots, &mut out);
+        out
+    }
+
+    /// Like [`get_batch`](Self::get_batch), but fills a caller-provided buffer.
+    pub fn fill_batch(&self, slots: &[usize], out: &mut [bool]) {
+        assert_eq!(slots.len(), out.len());
+        let n = slots.len();
+        if n == 0 { return; }
+        let mut perm: Vec<usize> = (0..n).collect();
+        perm.sort_by_key(|&i| slots[i]);
+        let sorted: Vec<usize> = perm.iter().map(|&i| slots[i]).collect();
+        let mut tmp = vec![false; n];
+        self.fill_batch_sorted(&sorted, &mut tmp);
+        for (i, &orig_idx) in perm.iter().enumerate() {
+            out[orig_idx] = tmp[i];
+        }
+    }
+
+    /// Fill `out` assuming `sorted_slots` is already in ascending order.
+    /// Results are written in `sorted_slots` order (no reordering).
+    pub(crate) fn fill_batch_sorted(&self, sorted_slots: &[usize], out: &mut [bool]) {
+        assert_eq!(sorted_slots.len(), out.len());
+        for (i, &slot) in sorted_slots.iter().enumerate() {
+            out[i] = self.get(slot);
+        }
+    }
+
     // SAFETY: mmap is page-aligned, HEADER_SIZE=16 divisible by 8 → u64-aligned.
     fn data_words(&self) -> &[u64] {
         let nw  = n_words(self.n);
diff --git a/src/obicompactvec/src/intmatrix.rs b/src/obicompactvec/src/intmatrix.rs
index 6b030e0a..61f102ef 100644
--- a/src/obicompactvec/src/intmatrix.rs
+++ b/src/obicompactvec/src/intmatrix.rs
@@ -346,6 +346,50 @@ impl PersistentCompactIntMatrix {
     pub fn fill_row(&self, slot: usize, buf: &mut [u32]) {
         match self { Self::Columnar(m) => m.fill_row(slot, buf), Self::Packed(m) => m.fill_row(slot, buf) }
     }
+
+    /// Extract a sub-matrix containing only the rows at `slots`.
+    ///
+    /// Returns a column-first `Vec<Vec<u32>>`: the outer `Vec` has one entry per
+    /// column, and each inner `Vec` contains the values for the requested rows
+    /// in the same order as `slots`.  Column access is sequential to maximize
+    /// cache efficiency on the underlying mmap.
+    pub fn sub_matrix(&self, slots: &[usize]) -> Vec<Vec<u32>> {
+        let n_cols = self.n_cols();
+        let mut out: Vec<Vec<u32>> = Vec::with_capacity(n_cols);
+        for c in 0..n_cols {
+            let mut col_buf = vec![0u32; slots.len()];
+            self.col_view(c).fill_batch(slots, &mut col_buf);
+            out.push(col_buf);
+        }
+        out
+    }
+
+    /// Like [`sub_matrix`](Self::sub_matrix), but fills caller-provided column
+    /// buffers to avoid allocating the outer `Vec`.
+    ///
+    /// `out` must have length `self.n_cols()`.  Each `out[c]` is cleared,
+    /// resized to `slots.len()`, and filled with the values for column `c`
+    /// in the same order as `slots`.
+    pub fn fill_sub_matrix(&self, slots: &[usize], out: &mut [Vec<u32>]) {
+        assert_eq!(out.len(), self.n_cols());
+        let n = slots.len();
+        if n == 0 {
+            for col in out.iter_mut() { col.clear(); }
+            return;
+        }
+        let mut perm: Vec<usize> = (0..n).collect();
+        perm.sort_by_key(|&i| slots[i]);
+        let sorted_slots: Vec<usize> = perm.iter().map(|&i| slots[i]).collect();
+        for (c, col) in out.iter_mut().enumerate() {
+            col.resize(n, 0);
+            let mut tmp = vec![0u32; n];
+            self.col_view(c).fill_batch_sorted(&sorted_slots, &mut tmp);
+            for (i, &orig_idx) in perm.iter().enumerate() {
+                col[orig_idx] = tmp[i];
+            }
+        }
+    }
+
     pub fn sum(&self) -> Array1<u64> {
         match self { Self::Columnar(m) => m.sum(), Self::Packed(m) => m.sum() }
     }
diff --git a/src/obicompactvec/src/reader.rs b/src/obicompactvec/src/reader.rs
index f3b1dd67..e4d58ab2 100644
--- a/src/obicompactvec/src/reader.rs
+++ b/src/obicompactvec/src/reader.rs
@@ -57,6 +57,42 @@ impl PersistentCompactIntVec {
         }
     }
 
+    /// Batch lookup: read values at `slots` in an order that minimizes
+    /// cache misses.
+    ///
+    /// The slots are sorted internally before reading so that accesses to
+    /// the underlying mmap are as sequential as possible, then the results
+    /// are reordered to match the input order.
+    pub fn get_batch(&self, slots: &[usize]) -> Vec<u32> {
+        let mut out = vec![0u32; slots.len()];
+        self.fill_batch(slots, &mut out);
+        out
+    }
+
+    /// Like [`get_batch`](Self::get_batch), but fills a caller-provided buffer.
+    pub fn fill_batch(&self, slots: &[usize], out: &mut [u32]) {
+        assert_eq!(slots.len(), out.len());
+        let n = slots.len();
+        if n == 0 { return; }
+        let mut perm: Vec<usize> = (0..n).collect();
+        perm.sort_by_key(|&i| slots[i]);
+        let sorted: Vec<usize> = perm.iter().map(|&i| slots[i]).collect();
+        let mut tmp = vec![0u32; n];
+        self.fill_batch_sorted(&sorted, &mut tmp);
+        for (i, &orig_idx) in perm.iter().enumerate() {
+            out[orig_idx] = tmp[i];
+        }
+    }
+
+    /// Fill `out` assuming `sorted_slots` is already in ascending order.
+    /// Results are written in `sorted_slots` order (no reordering).
+    pub(crate) fn fill_batch_sorted(&self, sorted_slots: &[usize], out: &mut [u32]) {
+        assert_eq!(sorted_slots.len(), out.len());
+        for (i, &slot) in sorted_slots.iter().enumerate() {
+            out[i] = self.get(slot);
+        }
+    }
+
     fn overflow_get(&self, slot: usize) -> u32 {
         let (pos_start, pos_end) = if self.step == 0 {
             (0, self.n_overflow)
diff --git a/src/obicompactvec/src/views.rs b/src/obicompactvec/src/views.rs
index 85e4165a..ff565482 100644
--- a/src/obicompactvec/src/views.rs
+++ b/src/obicompactvec/src/views.rs
@@ -23,6 +23,38 @@ impl<'a> BitSliceView<'a> {
         (self.words[slot >> 6] >> (slot & 63)) & 1 != 0
     }
 
+    /// Batch lookup: read bits at `slots` with cache-friendly access pattern.
+    ///
+    /// Slots are sorted internally before reading, then results are reordered
+    /// to match the input order.
+    pub fn get_batch(&self, slots: &[usize]) -> Vec<bool> {
+        let mut out = vec![false; slots.len()];
+        self.fill_batch(slots, &mut out);
+        out
+    }
+    /// Like [`get_batch`](Self::get_batch), but fills a caller-provided buffer.
+    pub fn fill_batch(&self, slots: &[usize], out: &mut [bool]) {
+        assert_eq!(slots.len(), out.len());
+        let n = slots.len();
+        if n == 0 { return; }
+        let mut perm: Vec<usize> = (0..n).collect();
+        perm.sort_by_key(|&i| slots[i]);
+        let sorted: Vec<usize> = perm.iter().map(|&i| slots[i]).collect();
+        let mut tmp = vec![false; n];
+        self.fill_batch_sorted(&sorted, &mut tmp);
+        for (i, &orig_idx) in perm.iter().enumerate() {
+            out[orig_idx] = tmp[i];
+        }
+    }
+
+    /// Fill `out` assuming `sorted_slots` is already in ascending order.
+    /// Results are written in `sorted_slots` order (no reordering).
+    pub(crate) fn fill_batch_sorted(&self, sorted_slots: &[usize], out: &mut [bool]) {
+        assert_eq!(sorted_slots.len(), out.len());
+        for (i, &slot) in sorted_slots.iter().enumerate() {
+            out[i] = self.get(slot);
+        }
+    }
     pub fn count_ones(&self) -> u64 {
         self.words.iter().map(|w| w.count_ones() as u64).sum()
     }
@@ -123,6 +155,40 @@ impl<'a> IntSliceView<'a> {
         panic!("slot {slot} marked overflow but not found")
     }
 
+    /// Batch lookup: read values at `slots` with cache-friendly access pattern.
+    ///
+    /// Slots are sorted internally before reading, then results are reordered
+    /// to match the input order.
+    pub fn get_batch(&self, slots: &[usize]) -> Vec<u32> {
+        let mut out = vec![0u32; slots.len()];
+        self.fill_batch(slots, &mut out);
+        out
+    }
+
+    /// Like [`get_batch`](Self::get_batch), but fills a caller-provided buffer.
+    pub fn fill_batch(&self, slots: &[usize], out: &mut [u32]) {
+        assert_eq!(slots.len(), out.len());
+        let n = slots.len();
+        if n == 0 { return; }
+        let mut perm: Vec<usize> = (0..n).collect();
+        perm.sort_by_key(|&i| slots[i]);
+        let sorted: Vec<usize> = perm.iter().map(|&i| slots[i]).collect();
+        let mut tmp = vec![0u32; n];
+        self.fill_batch_sorted(&sorted, &mut tmp);
+        for (i, &orig_idx) in perm.iter().enumerate() {
+            out[orig_idx] = tmp[i];
+        }
+    }
+
+    /// Fill `out` assuming `sorted_slots` is already in ascending order.
+    /// Results are written in `sorted_slots` order (no reordering).
+    pub(crate) fn fill_batch_sorted(&self, sorted_slots: &[usize], out: &mut [u32]) {
+        assert_eq!(sorted_slots.len(), out.len());
+        for (i, &slot) in sorted_slots.iter().enumerate() {
+            out[i] = self.get(slot);
+        }
+    }
+
     /// Sequential merge scan: yields all n values in slot order.
     pub fn iter(&self) -> IntSliceViewIter<'a> {
         IntSliceViewIter {
diff --git a/src/obilayeredmap/src/layer.rs b/src/obilayeredmap/src/layer.rs
index 7a256485..db71218f 100644
--- a/src/obilayeredmap/src/layer.rs
+++ b/src/obilayeredmap/src/layer.rs
@@ -186,6 +186,25 @@ impl Layer<PersistentCompactIntMatrix> {
         PersistentCompactIntMatrix::append_column(&layer_dir.join(COUNTS_DIR), value_of)
             .map_err(OLMError::Io)
     }
+
+    /// Extract a sub-matrix of counts for the rows at `slots`.
+    ///
+    /// Returns a column-first `Vec<Vec<u32>>`: one inner `Vec` per genome
+    /// column, containing the counts for the requested slots in order.
+    /// Column access is sequential for cache efficiency.
+    pub fn sub_matrix(&self, slots: &[usize]) -> Vec<Vec<u32>> {
+        self.data.sub_matrix(slots)
+    }
+
+    /// Like [`sub_matrix`](Self::sub_matrix), but fills caller-provided column
+    /// buffers to avoid allocating the outer `Vec`.
+    ///
+    /// `out` must have length equal to the number of genome columns.  Each
+    /// `out[c]` is cleared, resized to `slots.len()`, and filled with the
+    /// counts for column `c` in the same order as `slots`.
+    pub fn fill_sub_matrix(&self, slots: &[usize], out: &mut [Vec<u32>]) {
+        self.data.fill_sub_matrix(slots, out)
+    }
 }
 
 // ── Mode 3 — presence/absence matrix ─────────────────────────────────────────
@@ -199,6 +218,25 @@ impl Layer<PersistentBitMatrix> {
             .map_err(OLMError::Io)
     }
 
+    /// Extract a sub-matrix of presence/absence for the rows at `slots`.
+    ///
+    /// Returns a column-first `Vec<Vec<bool>>`: one inner `Vec` per genome
+    /// column, containing the presence bits for the requested slots in order.
+    /// Column access is sequential for cache efficiency.
+    pub fn sub_matrix(&self, slots: &[usize]) -> Vec<Vec<bool>> {
+        self.data.sub_matrix(slots)
+    }
+
+    /// Like [`sub_matrix`](Self::sub_matrix), but fills caller-provided column
+    /// buffers to avoid allocating the outer `Vec`.
+    ///
+    /// `out` must have length equal to the number of genome columns.  Each
+    /// `out[c]` is cleared, resized to `slots.len()`, and filled with the
+    /// presence bits for column `c` in the same order as `slots`.
+    pub fn fill_sub_matrix(&self, slots: &[usize], out: &mut [Vec<bool>]) {
+        self.data.fill_sub_matrix(slots, out)
+    }
+
     pub fn build_presence(
         out_dir: &Path,
         block_bits: u8,
-- 
2.54.0


From 519195d4a1181ef967239a2663bad0a9e46006e3 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Fri, 14 Aug 2026 13:18:43 +0200
Subject: [PATCH 22/46] Replace slot-based indexing with iteration order and
 stream k-mers

Transitions the index from MPHF slot-based to physical iteration-order indexing, aligning with the unitig layout. Introduces a streaming-only pipeline for k-mer iteration that adheres to memory constraints by avoiding full in-memory collections. Updates layer and sibling iterators to own an Arc clone of the file reader, making them Send + 'static and safe for concurrent use without borrowing the parent. Exposes batch and k-mer iterator types publicly while simplifying signature syntax with modern lifetime elision.
---
 src/obikindex/src/siblings/build.rs    | 133 ++++++++++++++-----------
 src/obikindex/src/siblings/iter.rs     |  78 +++++++++++++++
 src/obikindex/src/siblings/mod.rs      |   2 +
 src/obilayeredmap/src/layer.rs         |   8 +-
 src/obilayeredmap/src/lib.rs           |   2 +-
 src/obilayeredmap/src/mphf_layer.rs    |  51 ++++++----
 src/obiskio/src/unitig_index/reader.rs |  29 ++++++
 7 files changed, 219 insertions(+), 84 deletions(-)
 create mode 100644 src/obikindex/src/siblings/iter.rs

diff --git a/src/obikindex/src/siblings/build.rs b/src/obikindex/src/siblings/build.rs
index a23896ee..b51a7f32 100644
--- a/src/obikindex/src/siblings/build.rs
+++ b/src/obikindex/src/siblings/build.rs
@@ -21,13 +21,17 @@ use super::{olm_to_ok, ANNEX_FILE_NAME, INDEX_SUBDIR};
 
 // ── obipipeline data types ─────────────────────────────────────────────────
 
-/// A batch of this layer's distinct k-mers (local MPHF slot + k-mer), the
-/// pipeline's source item — batched, not one k-mer per item, so that
+/// A batch of this layer's distinct k-mers (iteration-order index + k-mer),
+/// the pipeline's source item — batched, not one k-mer per item, so that
 /// pipeline messages and their synchronisation cost stay amortised over
 /// thousands of lookups (see `build_layer_sibling_annex`'s comment on
 /// `BATCH_SIZE`). Carries the throttle permit for the whole batch, moved
 /// (not cloned) into the corresponding `VariantBatch` — a 1-to-1 transform,
 /// unlike the fan-out `Flat` stage this replaced, needs no `Arc` sharing.
+///
+/// The `usize` is this k-mer's position in `iter_kmers()`'s enumeration
+/// order, **not** an MPHF slot — see `docmd/architecture/siblings.md`. It
+/// is the same index the annex file is written under.
 struct SourceBatch {
     items: Vec<(usize, CanonicalKmer)>,
     _permit: ThrottleGuard,
@@ -36,7 +40,9 @@ struct SourceBatch {
 /// One batch's worth of central-substitution variants (up to 3 per source
 /// k-mer), each already routed to its destination partition and carrying
 /// its own central base (0=A/1=C/2=G/3=T) — the mask bit it will set on a
-/// hit. `(dest_partition, variant, source_slot, base)` per entry.
+/// hit. `(dest_partition, variant, source_order, base)` per entry, where
+/// `source_order` is the source k-mer's iteration-order index (see
+/// `SourceBatch`), not an MPHF slot.
 struct VariantBatch {
     items: Vec<(usize, CanonicalKmer, usize, u8)>,
     _permit: ThrottleGuard,
@@ -103,7 +109,7 @@ impl KmerIndex {
         Ok(())
     }
 
-    /// Returns the number of distinct k-mers (annex slots) processed, for
+    /// Returns the number of distinct k-mers (annex entries) processed, for
     /// progress reporting.
     fn build_layer_sibling_annex(
         &self,
@@ -114,29 +120,31 @@ impl KmerIndex {
         let index_dir = layer_dir.parent().expect("layer_dir has a parent index dir");
         let meta = PartitionMeta::load(index_dir).map_err(olm_to_ok)?;
         let mphf = MphfLayer::open(layer_dir, &meta.mode).map_err(olm_to_ok)?;
-        let n_slots = mphf.n();
-
-        // ── Enumerate this layer's distinct k-mers, one per slot — direct
-        // slot -> k-mer reconstruction (evidence + direct-access unitigs, no
-        // MPHF hashing, no file scan), not scan-and-hash-every-k-mer-forward.
-        let slot_kmer: Vec<Option<CanonicalKmer>> = (0..n_slots).map(|slot| mphf.kmer_at(slot)).collect();
-
         let k = self.kmer_size();
+        let n = mphf.n();
 
-        // ── Reconciliation state, initialised with each slot's own base —
-        // that member is trivially present, no lookup needed. Built before
-        // the pipeline runs, from the same enumeration, since `sources`
-        // below is consumed as a throttled iterator, not collected.
-        // `AtomicU8`, not `FamilyMask`, because the gather phase below
-        // parallelises across destination partitions (independent
-        // `query_partition_with` calls, safe to run concurrently) and their
-        // `Found` hits can land on arbitrary, possibly-shared slots — a
-        // lock-free `fetch_or` avoids needing any synchronisation beyond
-        // that. ─────────────────────────────────────────────────────────
-        let mask: Vec<AtomicU8> = (0..n_slots).map(|_| AtomicU8::new(0)).collect();
-        for (slot, kmer) in slot_kmer.iter().enumerate().filter_map(|(s, k)| k.map(|k| (s, k))) {
-            mask[slot].fetch_or(1 << central_base(kmer, k), Ordering::Relaxed);
-        }
+        // ── Reconciliation state, indexed by this layer's k-mer iteration
+        // order (the physical layout of `unitigs.bin`), never by MPHF slot
+        // — this layer's own k-mers are known members by construction, so
+        // no evidence check, no MPHF slot, and no slot -> k-mer
+        // reconstruction is needed or legitimate here (see
+        // `docmd/architecture/siblings.md`: the MPHF is not invertible, and
+        // evidence answers membership, not identity). The annex is written
+        // under this same iteration order end to end, so a reader can later
+        // zip `iter_kmers()` with the annex file directly, with no
+        // MPHF/slot indirection at read time either.
+        //
+        // `Arc<Vec<AtomicU8>>`, not `Vec<AtomicU8>` — `Pipe::apply` requires
+        // its source iterator to be `Send + 'static` (its items are
+        // dispatched to worker threads that outlive this call), so the
+        // batch-generating closure below needs an owned handle it can move
+        // in, not a borrow of a local. `AtomicU8`, not `FamilyMask`,
+        // because the gather phase below parallelises across destination
+        // partitions (independent `query_partition_with` calls, safe to run
+        // concurrently) and their `Found` hits can land on arbitrary,
+        // possibly-shared source entries — a lock-free `fetch_or` avoids
+        // needing any synchronisation beyond that. ─────────────────────────
+        let mask: Arc<Vec<AtomicU8>> = Arc::new((0..n).map(|_| AtomicU8::new(0)).collect());
 
         // ── obipipeline: a *batch* transform, not a per-k-mer `Flat` one —
         // the actual cross-partition lookup reuses
@@ -169,16 +177,25 @@ impl KmerIndex {
         // the pipeline by the accumulation loop below. See
         // `obipipeline::throttle`'s docs for why this is required, not
         // optional, once a `Flat`-style stage sits in the pipeline.
-        let sources: Vec<(usize, CanonicalKmer)> = slot_kmer
-            .iter()
-            .enumerate()
-            .filter_map(|(slot, maybe_kmer)| maybe_kmer.map(|kmer| (slot, kmer)))
-            .collect();
-        let batches: Vec<Vec<(usize, CanonicalKmer)>> = sources
-            .chunks(BATCH_SIZE)
-            .map(|chunk| chunk.to_vec())
-            .collect();
-        let throttled = obipipeline::throttle(batches.into_iter(), n_workers).map(|t| SourceBatch {
+        //
+        // Batches stream straight from `unitigs.bin` via
+        // `enumerate_kmers_batch` — never a full-layer `Vec` collect (a
+        // layer can hold billions of k-mers; see the "no full collect"
+        // rule). Each k-mer's own base is seeded into `mask` in this same
+        // pass, since this is exactly the iteration order `mask` is keyed
+        // on — no separate seeding pass needed.
+        let seed_mask = Arc::clone(&mask);
+        let batches = mphf.enumerate_kmers_batch(BATCH_SIZE).map(move |(start, kmers)| {
+            kmers
+                .into_iter()
+                .enumerate()
+                .map(|(i, kmer)| {
+                    seed_mask[start + i].fetch_or(1 << central_base(kmer, k), Ordering::Relaxed);
+                    (start + i, kmer)
+                })
+                .collect::<Vec<_>>()
+        });
+        let throttled = obipipeline::throttle(batches, n_workers).map(|t| SourceBatch {
             items: t.item,
             _permit: t.guard,
         });
@@ -188,7 +205,7 @@ impl KmerIndex {
             | {
                 move |batch: SourceBatch| -> VariantBatch {
                     let mut items = Vec::with_capacity(batch.items.len() * 3);
-                    for (slot, kmer) in batch.items {
+                    for (order, kmer) in batch.items {
                         for variant in kmer.central_canonical_neighbors() {
                             if variant == kmer {
                                 continue;
@@ -196,7 +213,7 @@ impl KmerIndex {
                             items.push((
                                 partition_of(variant, n_parts),
                                 variant,
-                                slot,
+                                order,
                                 central_base(variant, k),
                             ));
                         }
@@ -216,8 +233,8 @@ impl KmerIndex {
         // them. Each batch's throttle permit drops here, once accumulated.
         let mut outgoing: Vec<Vec<(CanonicalKmer, usize, u8)>> = (0..n_parts).map(|_| Vec::new()).collect();
         for vb in pipe.apply(throttled, n_workers, capacity) {
-            for (dest_partition, variant, source_slot, base) in vb.items {
-                outgoing[dest_partition].push((variant, source_slot, base));
+            for (dest_partition, variant, source_order, base) in vb.items {
+                outgoing[dest_partition].push((variant, source_order, base));
             }
         }
 
@@ -226,33 +243,35 @@ impl KmerIndex {
         // read-only) so this keeps using multiple cores without giving up
         // the per-partition locality above. ─────────────────────────────
         outgoing.par_iter().enumerate().filter(|(_, q)| !q.is_empty()).for_each(|(dest, queries)| {
-            for &(variant, source_slot, base) in queries {
+            for &(variant, source_order, base) in queries {
                 if cache.find(dest, variant) {
-                    mask[source_slot].fetch_or(1 << base, Ordering::Relaxed);
+                    mask[source_order].fetch_or(1 << base, Ordering::Relaxed);
                 }
             }
         });
 
-        // ── Write the layer's annex file ─────────────────────────────────────
-        // The minorant flag is computed here, not by every later reader:
-        // this is the one place the whole family's *final* mask and this
-        // slot's own k-mer (already in hand, no extra lookup) are both
-        // available together. Every consumer that only needs to know
-        // "is this slot the family's minorant" — the common case, since a
-        // family is tallied once, at its minorant — reads the bit straight
-        // back instead of re-deriving it (re-scanning `unitigs.bin` and
-        // re-hashing through the MPHF, the cost `is_minorant` was cheap to
-        // *compute* but expensive to *get the inputs for* every time).
+        // ── Write the layer's annex file, indexed by iteration order — a
+        // second streamed pass over `unitigs.bin` (via `enumerate_kmers`),
+        // now that every entry's mask is final; never a `Vec` hold of the
+        // whole layer. The minorant flag is computed here, not by every
+        // later reader: this is the one place the whole family's *final*
+        // mask and this entry's own k-mer (already in hand, no extra
+        // lookup) are both available together. Every consumer that only
+        // needs to know "is this k-mer the family's minorant" — the common
+        // case, since a family is tallied once, at its minorant — reads
+        // the bit straight back instead of re-deriving it (re-scanning
+        // `unitigs.bin` and re-hashing through the MPHF, the cost
+        // `is_minorant` was cheap to *compute* but expensive to *get the
+        // inputs for* every time).
         let annex_path = layer_dir.join(ANNEX_FILE_NAME);
-        let mut builder = SiblingAnnexBuilder::new(n_slots, &annex_path)?;
-        for (slot, m) in mask.iter().enumerate() {
-            let Some(kmer) = slot_kmer[slot] else { continue }; // unused MPHF slot, if any — leave at the sentinel
-            let final_mask = FamilyMask::from_bits(m.load(Ordering::Relaxed));
+        let mut builder = SiblingAnnexBuilder::new(n, &annex_path)?;
+        for (order, kmer) in mphf.enumerate_kmers() {
+            let final_mask = FamilyMask::from_bits(mask[order].load(Ordering::Relaxed));
             let minorant = is_minorant(kmer, final_mask, k);
-            builder.set(slot, final_mask.with_minorant(minorant));
+            builder.set(order, final_mask.with_minorant(minorant));
         }
         builder.close()?;
 
-        Ok(n_slots as u64)
+        Ok(n as u64)
     }
 }
diff --git a/src/obikindex/src/siblings/iter.rs b/src/obikindex/src/siblings/iter.rs
new file mode 100644
index 00000000..70b26c1c
--- /dev/null
+++ b/src/obikindex/src/siblings/iter.rs
@@ -0,0 +1,78 @@
+//! Phylo/sibling-domain iteration over a layer — an extension trait, not a
+//! new field on `MphfLayer`/`Layer<D>`: "family"/"minorant" are phylo
+//! concepts, `obilayeredmap` stays kmer/slot-mapping only (see
+//! `docmd/architecture/siblings.md`).
+//!
+//! The sibling annex is persisted in the same order as `iter_kmers()`
+//! (`build_sibling_annex`, see `build.rs`), so pairing them is a plain zip —
+//! no MPHF, no slot, no `kmer_at`. Both sides are already `Send + 'static`
+//! (`KmerIter` owns an `Arc<UnitigFileReader>` clone; `SiblingAnnex` is
+//! mmap-backed and handed in as an `Arc` by the caller), so `SiblingIter`
+//! streams straight from disk and can be fed to `obipipeline` batch by
+//! batch — never collected whole into memory (see the project's "no full
+//! collect" rule).
+
+use std::sync::Arc;
+
+use obicompactvec::{FamilyMask, SiblingAnnex};
+use obikseq::CanonicalKmer;
+use obilayeredmap::{KmerIter, MphfLayer};
+
+/// One layer entry: a k-mer's position in the layer's iteration order (the
+/// same index the sibling annex is keyed on — not an MPHF slot), the k-mer
+/// itself, and its family mask.
+#[derive(Debug, Clone, Copy)]
+pub struct SiblingEntry {
+    pub order: usize,
+    pub kmer: CanonicalKmer,
+    pub mask: FamilyMask,
+}
+
+/// Streams `(order, kmer, mask)` triples for one layer, in iteration order.
+/// Produced by [`SiblingLayerExt::iter_siblings`].
+pub struct SiblingIter {
+    kmers: KmerIter,
+    annex: Arc<SiblingAnnex>,
+    order: usize,
+}
+
+impl Iterator for SiblingIter {
+    type Item = SiblingEntry;
+
+    fn next(&mut self) -> Option<Self::Item> {
+        loop {
+            let kmer = self.kmers.next()?;
+            let order = self.order;
+            self.order += 1;
+            // `None` means "not yet computed" (see `SiblingAnnex` module
+            // docs) — shouldn't happen against a fully-built annex, but
+            // skip rather than misalign the two streams if it does.
+            if let Some(mask) = self.annex.get(order) {
+                return Some(SiblingEntry { order, kmer, mask });
+            }
+        }
+    }
+}
+
+/// Adds phylo/sibling iteration to `MphfLayer`.
+pub trait SiblingLayerExt {
+    /// Zip this layer's k-mers with their sibling-annex entry, in iteration
+    /// order. `annex` must have been built from this same layer (its length
+    /// must match the layer's k-mer count).
+    fn iter_siblings(&self, annex: Arc<SiblingAnnex>) -> SiblingIter;
+
+    /// Like [`iter_siblings`](Self::iter_siblings), filtered to the
+    /// minorant of each family — the common case, since a family is
+    /// tallied once, at its minorant.
+    fn iter_minorants(&self, annex: Arc<SiblingAnnex>) -> impl Iterator<Item = SiblingEntry>;
+}
+
+impl SiblingLayerExt for MphfLayer {
+    fn iter_siblings(&self, annex: Arc<SiblingAnnex>) -> SiblingIter {
+        SiblingIter { kmers: self.iter_kmers(), annex, order: 0 }
+    }
+
+    fn iter_minorants(&self, annex: Arc<SiblingAnnex>) -> impl Iterator<Item = SiblingEntry> {
+        self.iter_siblings(annex).filter(|e| e.mask.is_minorant())
+    }
+}
diff --git a/src/obikindex/src/siblings/mod.rs b/src/obikindex/src/siblings/mod.rs
index 2ff427e9..a91711a1 100644
--- a/src/obikindex/src/siblings/mod.rs
+++ b/src/obikindex/src/siblings/mod.rs
@@ -49,6 +49,7 @@ mod cardinality;
 mod distance;
 mod family_scan;
 mod helpers;
+mod iter;
 mod stats;
 
 #[cfg(test)]
@@ -57,6 +58,7 @@ mod tests;
 pub use alignment::SnpAlignment;
 pub use cardinality::CardinalityTally;
 pub use distance::{BasePairTally, RawSnpDistanceOutput};
+pub use iter::{SiblingEntry, SiblingIter, SiblingLayerExt};
 pub use stats::SiblingAnnexStats;
 
 use obilayeredmap::OLMError;
diff --git a/src/obilayeredmap/src/layer.rs b/src/obilayeredmap/src/layer.rs
index db71218f..44797318 100644
--- a/src/obilayeredmap/src/layer.rs
+++ b/src/obilayeredmap/src/layer.rs
@@ -85,24 +85,24 @@ impl<D: LayerData> Layer<D> {
     }
 
     /// Iterate over all canonical kmers in the layer, in deterministic order.
-    pub fn iter_kmers(&self) -> crate::mphf_layer::KmerIter<'_> {
+    pub fn iter_kmers(&self) -> crate::mphf_layer::KmerIter {
         self.mphf.iter_kmers()
     }
 
     /// Iterate over all canonical kmers, each paired with its zero-based
     /// sequence index in `unitigs.bin`.
-    pub fn enumerate_kmers(&self) -> std::iter::Enumerate<crate::mphf_layer::KmerIter<'_>> {
+    pub fn enumerate_kmers(&self) -> std::iter::Enumerate<crate::mphf_layer::KmerIter> {
         self.mphf.enumerate_kmers()
     }
 
     /// Iterate over the layer's canonical kmers in batches of `n`.
-    pub fn iter_kmers_batch(&self, n: usize) -> crate::mphf_layer::KmerBatchIter<'_> {
+    pub fn iter_kmers_batch(&self, n: usize) -> crate::mphf_layer::KmerBatchIter {
         self.mphf.iter_kmers_batch(n)
     }
 
     /// Iterate over batches, each paired with the zero-based index of the
     /// first kmer in the batch.
-    pub fn enumerate_kmers_batch(&self, n: usize) -> std::iter::Enumerate<crate::mphf_layer::KmerBatchIter<'_>> {
+    pub fn enumerate_kmers_batch(&self, n: usize) -> std::iter::Enumerate<crate::mphf_layer::KmerBatchIter> {
         self.mphf.enumerate_kmers_batch(n)
     }
 
diff --git a/src/obilayeredmap/src/lib.rs b/src/obilayeredmap/src/lib.rs
index 65ae2e2a..9c7f9975 100644
--- a/src/obilayeredmap/src/lib.rs
+++ b/src/obilayeredmap/src/lib.rs
@@ -12,4 +12,4 @@ pub use layer::{Hit, Layer, LayerData};
 pub use layered_store::LayeredStore;
 pub use map::LayeredMap;
 pub use meta::{IndexMode, PartitionMeta};
-pub use mphf_layer::{MphfLayer, MphfOnly};
+pub use mphf_layer::{KmerBatchIter, KmerIter, MphfLayer, MphfOnly};
diff --git a/src/obilayeredmap/src/mphf_layer.rs b/src/obilayeredmap/src/mphf_layer.rs
index 6aa67660..98f6682f 100644
--- a/src/obilayeredmap/src/mphf_layer.rs
+++ b/src/obilayeredmap/src/mphf_layer.rs
@@ -1,6 +1,7 @@
 use std::fs;
 use std::iter::Enumerate;
 use std::path::{Path, PathBuf};
+use std::sync::Arc;
 
 use cacheline_ef::{CachelineEf, CachelineEfVec};
 use epserde::prelude::*;
@@ -29,9 +30,9 @@ type MphfEps = PtrHash<u64, CubicEps, CachelineEfVec<&'static [CachelineEf]>, Xx
 // ── LayerEvidence ─────────────────────────────────────────────────────────────
 
 enum LayerEvidence {
-    Exact  { evidence: Evidence, unitigs: UnitigFileReader },
-    Approx { fingerprint: FingerprintVec, unitigs: UnitigFileReader, unitigs_path: PathBuf },
-    Hybrid { evidence: Evidence, unitigs: UnitigFileReader, fingerprint: FingerprintVec },
+    Exact  { evidence: Evidence, unitigs: Arc<UnitigFileReader> },
+    Approx { fingerprint: FingerprintVec, unitigs: Arc<UnitigFileReader>, unitigs_path: PathBuf },
+    Hybrid { evidence: Evidence, unitigs: Arc<UnitigFileReader>, fingerprint: FingerprintVec },
 }
 
 // ── MphfLayer ─────────────────────────────────────────────────────────────────
@@ -58,13 +59,13 @@ impl MphfLayer {
             IndexMode::Exact => {
                 let evidence = Evidence::open(&dir.join(EVIDENCE_FILE))?;
                 let n = evidence.len();
-                let unitigs = UnitigFileReader::open(&dir.join(UNITIGS_FILE))?;
+                let unitigs = Arc::new(UnitigFileReader::open(&dir.join(UNITIGS_FILE))?);
                 (LayerEvidence::Exact { evidence, unitigs }, n)
             }
             IndexMode::Approx { .. } => {
                 let fingerprint = FingerprintVec::open(&dir.join(FINGERPRINT_FILE))?;
                 let n = fingerprint.n();
-                let unitigs = UnitigFileReader::open(&dir.join(UNITIGS_FILE))?;
+                let unitigs = Arc::new(UnitigFileReader::open(&dir.join(UNITIGS_FILE))?);
                 let unitigs_path = dir.join(UNITIGS_FILE);
                 (LayerEvidence::Approx { fingerprint, unitigs, unitigs_path }, n)
             }
@@ -72,7 +73,7 @@ impl MphfLayer {
                 let evidence    = Evidence::open(&dir.join(EVIDENCE_FILE))?;
                 let fingerprint = FingerprintVec::open(&dir.join(FINGERPRINT_FILE))?;
                 let n = evidence.len();
-                let unitigs = UnitigFileReader::open(&dir.join(UNITIGS_FILE))?;
+                let unitigs = Arc::new(UnitigFileReader::open(&dir.join(UNITIGS_FILE))?);
                 (LayerEvidence::Hybrid { evidence, unitigs, fingerprint }, n)
             }
         };
@@ -184,16 +185,20 @@ impl MphfLayer {
     /// Iterate over all canonical kmers in the layer, in deterministic order.
     ///
     /// The iteration order follows the physical layout of `unitigs.bin` and is
-    /// **not** correlated with MPHF slot numbers.  Multiple `KmerIter` instances
-    /// can be held concurrently for as long as the layer lives, because each
+    /// **not** correlated with MPHF slot numbers.  Owns a clone of the
+    /// underlying `Arc<UnitigFileReader>` rather than borrowing `self` — `Send
+    /// + 'static`, so it can be handed to a threaded consumer (e.g.
+    /// `obipipeline`) directly, streamed from disk, with no need to collect
+    /// the layer's kmers into memory first. Multiple instances can be held
+    /// concurrently for as long as the underlying file exists, because each
     /// carries its own cursor.
-    pub fn iter_kmers(&self) -> KmerIter<'_> {
+    pub fn iter_kmers(&self) -> KmerIter {
         let reader = match &self.ev {
             LayerEvidence::Exact { unitigs, .. } => unitigs,
             LayerEvidence::Approx { unitigs, .. } => unitigs,
             LayerEvidence::Hybrid { unitigs, .. } => unitigs,
         };
-        KmerIter { inner: Box::new(reader.iter_indexed_canonical_kmers()) }
+        KmerIter { inner: Box::new(reader.iter_indexed_canonical_kmers_owned()) }
     }
 
     /// Iterate over all canonical kmers, each paired with its zero-based
@@ -202,7 +207,7 @@ impl MphfLayer {
     /// Yields `(index, kmer)` where `index` starts at `0` for the first kmer
     /// stored in the layer.  This is the standard Rust `enumerate` adapter
     /// applied to [`iter_kmers`](Self::iter_kmers).
-    pub fn enumerate_kmers(&self) -> Enumerate<KmerIter<'_>> {
+    pub fn enumerate_kmers(&self) -> Enumerate<KmerIter> {
         self.iter_kmers().enumerate()
     }
 
@@ -210,7 +215,7 @@ impl MphfLayer {
     ///
     /// Each call to [`next`](Iterator::next) returns a [`Vec`] of up to `n`
     /// kmers.  The final batch may be shorter when the layer is exhausted.
-    pub fn iter_kmers_batch(&self, n: usize) -> KmerBatchIter<'_> {
+    pub fn iter_kmers_batch(&self, n: usize) -> KmerBatchIter {
         KmerBatchIter { inner: self.iter_kmers(), batch_size: n }
     }
 
@@ -220,7 +225,7 @@ impl MphfLayer {
     /// Yields `(batch_start_index, Vec<CanonicalKmer>)` where
     /// `batch_start_index` is a multiple of `n`.  This is the standard Rust
     /// `enumerate` adapter applied to [`iter_kmers_batch`](Self::iter_kmers_batch).
-    pub fn enumerate_kmers_batch(&self, n: usize) -> Enumerate<KmerBatchIter<'_>> {
+    pub fn enumerate_kmers_batch(&self, n: usize) -> Enumerate<KmerBatchIter> {
         self.iter_kmers_batch(n).enumerate()
     }
 }
@@ -229,14 +234,16 @@ impl MphfLayer {
 
 /// Iterator over the canonical kmers stored in a layer.
 ///
-/// Produced by [`MphfLayer::iter_kmers`].  Multiple `KmerIter` instances can
-/// coexist concurrently for as long as the parent layer lives, because each
-/// holds its own cursor over the underlying [`UnitigFileReader`].
-pub struct KmerIter<'a> {
-    inner: Box<dyn Iterator<Item = (CanonicalKmer, usize, usize)> + 'a>,
+/// Produced by [`MphfLayer::iter_kmers`]. Owns an `Arc<UnitigFileReader>`
+/// clone internally (via `iter_indexed_canonical_kmers_owned`) instead of
+/// borrowing the parent layer — `Send + 'static`, streamed from disk one
+/// kmer at a time, never materialised as a whole. Multiple `KmerIter`
+/// instances can coexist concurrently, because each holds its own cursor.
+pub struct KmerIter {
+    inner: Box<dyn Iterator<Item = (CanonicalKmer, usize, usize)> + Send>,
 }
 
-impl<'a> Iterator for KmerIter<'a> {
+impl Iterator for KmerIter {
     type Item = CanonicalKmer;
 
     /// Return the next canonical kmer in iteration order.
@@ -250,12 +257,12 @@ impl<'a> Iterator for KmerIter<'a> {
 /// Produced by [`MphfLayer::iter_kmers_batch`].  Each call to [`next`](Self::next)
 /// returns a [`Vec`] of up to `batch_size` kmers.  The last batch may be shorter
 /// than `batch_size` when the layer is exhausted.
-pub struct KmerBatchIter<'a> {
-    inner: KmerIter<'a>,
+pub struct KmerBatchIter {
+    inner: KmerIter,
     batch_size: usize,
 }
 
-impl<'a> Iterator for KmerBatchIter<'a> {
+impl Iterator for KmerBatchIter {
     type Item = Vec<CanonicalKmer>;
 
     /// Return the next batch of kmers, or `None` if the layer is exhausted.
diff --git a/src/obiskio/src/unitig_index/reader.rs b/src/obiskio/src/unitig_index/reader.rs
index e5f0d978..781b8f44 100644
--- a/src/obiskio/src/unitig_index/reader.rs
+++ b/src/obiskio/src/unitig_index/reader.rs
@@ -1,5 +1,6 @@
 use std::fs::File;
 use std::path::Path;
+use std::sync::Arc;
 
 use memmap2::Mmap;
 use obikseq::{CanonicalKmer, Kmer, Unitig};
@@ -203,6 +204,34 @@ impl UnitigFileReader {
                     .map(move |(rank, kmer)| (kmer, chunk_id, rank))
             })
     }
+
+    /// Same streamed sequence as [`iter_indexed_canonical_kmers`](Self::iter_indexed_canonical_kmers),
+    /// but owning a clone of `self` instead of borrowing it — `Send + 'static`,
+    /// so it can be handed to a threaded consumer (e.g. `obipipeline`) without
+    /// first collecting the layer's k-mers into memory. Reads `mmap` fresh
+    /// through the `Arc` on every step; no data is duplicated up front.
+    pub fn iter_indexed_canonical_kmers_owned(
+        self: &Arc<Self>,
+    ) -> impl Iterator<Item = (CanonicalKmer, usize, usize)> + Send + 'static {
+        let this = Arc::clone(self);
+        let k = this.k;
+        let n = this.n_unitigs;
+        let mut offset = 0usize;
+        (0..n)
+            .map(move |chunk_id| {
+                let mmap = &*this.mmap;
+                let seql = mmap[offset] as usize + k;
+                let byte_len = (seql + 3) / 4;
+                let bytes = mmap[offset + 1..offset + 1 + byte_len].to_vec().into_boxed_slice();
+                offset += 1 + byte_len;
+                (chunk_id, Unitig::new((seql % 4) as u8, bytes))
+            })
+            .flat_map(|(chunk_id, u)| {
+                u.into_canonical_kmers()
+                    .enumerate()
+                    .map(move |(rank, kmer)| (kmer, chunk_id, rank))
+            })
+    }
 }
 
 fn read_idx(path: &Path) -> SKResult<(usize, usize, u8, Vec<u32>)> {
-- 
2.54.0


From 5997de670769631af7b219d4bb8ebae9b00428ed Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Fri, 14 Aug 2026 13:53:05 +0200
Subject: [PATCH 23/46] Extract phylogenetic sibling logic into new obikphylo
 crate

Relocate the `siblings` and `cardcomp` modules from `obikindex` to a dedicated `obikphylo` workspace member. Convert inherent methods on `KmerIndex` into extension traits, update import paths across `obikmer`, and add supporting accessor methods to `obikseq` and `obilayeredmap`. This restructuring reduces the public API surface of `obikindex` while organizing phylogenetic iteration, caching, and distance calculation logic under a dedicated crate.
---
 src/Cargo.lock                                |  24 +-
 src/Cargo.toml                                |   2 +-
 src/obikindex/Cargo.toml                      |   2 -
 src/obikindex/src/index.rs                    |   4 +
 src/obikindex/src/lib.rs                      |   4 -
 src/obikindex/src/siblings/cache.rs           | 166 -------------
 src/obikindex/src/siblings/helpers.rs         |  49 ----
 src/obikindex/src/siblings/iter.rs            |  78 ------
 src/obikmer/Cargo.toml                        |   1 +
 src/obikmer/src/cmd/phylo/family_overlap.rs   |   3 +-
 src/obikmer/src/cmd/phylo/iqtree.rs           |   2 +-
 src/obikmer/src/cmd/phylo/mod.rs              |   8 +-
 src/obikmer/src/cmd/phylo/outputs.rs          |   2 +-
 src/obikmer/src/cmd/phylo/sankoff.rs          |   2 +-
 src/obikmer/src/cmd/phylo/tnt.rs              |   2 +-
 src/obikphylo/Cargo.toml                      |  23 ++
 src/{obikindex => obikphylo}/src/cardcomp.rs  |   2 +-
 src/obikphylo/src/lib.rs                      |  14 ++
 .../src/siblings/alignment.rs                 |  25 +-
 .../src/siblings/build.rs                     |  59 +++--
 src/obikphylo/src/siblings/cache.rs           | 225 ++++++++++++++++++
 .../src/siblings/cardinality.rs               |  21 +-
 .../src/siblings/distance.rs                  | 152 ++++++------
 .../src/siblings/family_scan.rs               | 176 +++++++-------
 src/obikphylo/src/siblings/helpers.rs         |  23 ++
 src/obikphylo/src/siblings/iter.rs            | 172 +++++++++++++
 .../src/siblings/mod.rs                       |  15 +-
 .../src/siblings/stats.rs                     |  45 ++--
 .../src/siblings/tests.rs                     |  11 +-
 src/obikseq/src/kmer.rs                       |  44 ++++
 src/obilayeredmap/src/layer.rs                |  22 ++
 31 files changed, 831 insertions(+), 547 deletions(-)
 delete mode 100644 src/obikindex/src/siblings/cache.rs
 delete mode 100644 src/obikindex/src/siblings/helpers.rs
 delete mode 100644 src/obikindex/src/siblings/iter.rs
 create mode 100644 src/obikphylo/Cargo.toml
 rename src/{obikindex => obikphylo}/src/cardcomp.rs (99%)
 create mode 100644 src/obikphylo/src/lib.rs
 rename src/{obikindex => obikphylo}/src/siblings/alignment.rs (84%)
 rename src/{obikindex => obikphylo}/src/siblings/build.rs (89%)
 create mode 100644 src/obikphylo/src/siblings/cache.rs
 rename src/{obikindex => obikphylo}/src/siblings/cardinality.rs (89%)
 rename src/{obikindex => obikphylo}/src/siblings/distance.rs (66%)
 rename src/{obikindex => obikphylo}/src/siblings/family_scan.rs (65%)
 create mode 100644 src/obikphylo/src/siblings/helpers.rs
 create mode 100644 src/obikphylo/src/siblings/iter.rs
 rename src/{obikindex => obikphylo}/src/siblings/mod.rs (86%)
 rename src/{obikindex => obikphylo}/src/siblings/stats.rs (80%)
 rename src/{obikindex => obikphylo}/src/siblings/tests.rs (96%)

diff --git a/src/Cargo.lock b/src/Cargo.lock
index 74a8dabe..3efc8866 100644
--- a/src/Cargo.lock
+++ b/src/Cargo.lock
@@ -1768,9 +1768,7 @@ dependencies = [
  "obikpartitionner",
  "obikseq",
  "obilayeredmap",
- "obipipeline",
  "obiread",
- "obiskbuilder",
  "obiskio",
  "obisys",
  "obitaxonomy",
@@ -1794,6 +1792,7 @@ dependencies = [
  "obifastwrite",
  "obikindex",
  "obikpartitionner",
+ "obikphylo",
  "obikrope",
  "obikseq",
  "obilayeredmap",
@@ -1843,6 +1842,27 @@ dependencies = [
  "tracing",
 ]
 
+[[package]]
+name = "obikphylo"
+version = "0.1.0"
+dependencies = [
+ "ndarray",
+ "obicompactvec",
+ "obikindex",
+ "obikpartitionner",
+ "obikseq",
+ "obilayeredmap",
+ "obipipeline",
+ "obiread",
+ "obiskbuilder",
+ "obiskio",
+ "obisys",
+ "rayon",
+ "tempfile",
+ "tracing",
+ "tracing-subscriber",
+]
+
 [[package]]
 name = "obikrope"
 version = "0.1.0"
diff --git a/src/Cargo.toml b/src/Cargo.toml
index 5684237b..f34f6918 100644
--- a/src/Cargo.toml
+++ b/src/Cargo.toml
@@ -1,5 +1,5 @@
 [workspace]
 resolver = "3"
-members = ["obikseq", "obiread", "obiskbuilder", "obifastwrite", "obikmer","obikrope","obipipeline", "obikpartitionner","obiskio","obidebruinj","obilayeredmap", "obicompactvec", "obisys", "obikindex", "obitaxonomy", "obikentropy"]
+members = ["obikseq", "obiread", "obiskbuilder", "obifastwrite", "obikmer","obikrope","obipipeline", "obikpartitionner","obiskio","obidebruinj","obilayeredmap", "obicompactvec", "obisys", "obikindex", "obitaxonomy", "obikentropy", "obikphylo"]
 [profile.release]
 debug = 1
diff --git a/src/obikindex/Cargo.toml b/src/obikindex/Cargo.toml
index ba86dd64..b92aa075 100644
--- a/src/obikindex/Cargo.toml
+++ b/src/obikindex/Cargo.toml
@@ -11,8 +11,6 @@ obiskio          = { path = "../obiskio" }
 obisys           = { path = "../obisys" }
 obicompactvec    = { path = "../obicompactvec" }
 obilayeredmap    = { path = "../obilayeredmap" }
-obiskbuilder     = { path = "../obiskbuilder" }
-obipipeline      = { path = "../obipipeline" }
 ndarray          = "0.16"
 rayon             = "1"
 crossbeam-channel = "0.5"
diff --git a/src/obikindex/src/index.rs b/src/obikindex/src/index.rs
index 6d2163ed..3aedca98 100644
--- a/src/obikindex/src/index.rs
+++ b/src/obikindex/src/index.rs
@@ -132,6 +132,10 @@ impl KmerIndex {
         IndexState::detect(&self.root_path).unwrap_or(IndexState::Empty)
     }
 
+    /// The index's root directory — needed by out-of-crate extension code
+    /// (e.g. `obikphylo`) that opens its own `KmerPartition` handle onto
+    /// the same on-disk index.
+    pub fn root_path(&self) -> &Path { &self.root_path }
     pub fn meta(&self) -> &IndexMeta { &self.meta }
     pub fn meta_mut(&mut self) -> &mut IndexMeta { &mut self.meta }
     pub fn kmer_size(&self) -> usize { self.meta.config.kmer_size }
diff --git a/src/obikindex/src/lib.rs b/src/obikindex/src/lib.rs
index 665e2d86..6ab2e070 100644
--- a/src/obikindex/src/lib.rs
+++ b/src/obikindex/src/lib.rs
@@ -2,7 +2,6 @@ pub mod error;
 pub mod meta;
 pub mod predicate;
 pub mod state;
-mod cardcomp;
 mod distance;
 mod dump;
 mod index;
@@ -11,7 +10,6 @@ mod numa;
 mod rebuild;
 mod reindex;
 mod select;
-mod siblings;
 mod stats;
 
 pub use error::{OKIError, OKIResult};
@@ -22,5 +20,3 @@ pub use meta::{validate_label, GenomeInfo, IndexConfig, IndexMeta, META_FILENAME
 pub use predicate::{GroupFilterParams, MetaPred};
 pub use state::{IndexState, SENTINEL_COUNTED, SENTINEL_INDEXED, SENTINEL_SCATTERED};
 pub use stats::IndexBitsPerKmer;
-pub use siblings::{BasePairTally, CardinalityTally, RawSnpDistanceOutput, SiblingAnnexStats, SnpAlignment};
-pub use cardcomp::{cardinality_transition_probs, composition_transition_probs, pairwise_cost_matrix};
diff --git a/src/obikindex/src/siblings/cache.rs b/src/obikindex/src/siblings/cache.rs
deleted file mode 100644
index 32d49f5d..00000000
--- a/src/obikindex/src/siblings/cache.rs
+++ /dev/null
@@ -1,166 +0,0 @@
-use rayon::prelude::*;
-
-use obicompactvec::{PersistentBitMatrix, PersistentCompactIntMatrix};
-use obikpartitionner::KmerPartition;
-use obikseq::CanonicalKmer;
-use obilayeredmap::MphfLayer;
-use obilayeredmap::meta::PartitionMeta;
-use obisys::progress_bar;
-
-use crate::error::OKIResult;
-
-use super::{olm_to_ok, INDEX_SUBDIR};
-
-/// Every partition's already-open MPHF layers, built **once** for the whole
-/// `build_sibling_annex` run and shared (read-only) across every lookup, in
-/// every source layer, for the rest of the run — not reopened/re-mmap'd per
-/// query, nor per source layer.
-///
-/// Confirmed necessary by sampling a real run: routing lookups through
-/// `KmerPartition::query_partition_with` (the same batching `obikmer query`
-/// uses) still reopens+re-mmaps every target partition's files on every
-/// call, and it is called once per destination partition **per source
-/// layer** — for an index with many layers this repeats the same
-/// `MphfLayer::open`/`Evidence::open`/`PersistentBitMatrix::open` work over
-/// and over. Parallelising those calls (see the gather step below) spread
-/// the redundant work across more cores but did not reduce it: sampling
-/// showed Rayon workers spending their time inside repeated `open()`
-/// syscalls, not computation. This cache amortises that cost to once per
-/// partition for the entire run, regardless of how many source layers or
-/// lookups follow.
-/// A cached layer's opened presence/count matrix, alongside its `MphfLayer`.
-pub(super) enum Mat {
-    Count(PersistentCompactIntMatrix),
-    Presence(PersistentBitMatrix),
-}
-
-impl Mat {
-    pub(super) fn n_cols(&self) -> usize {
-        match self {
-            Mat::Count(m) => m.n_cols(),
-            Mat::Presence(m) => m.n_cols(),
-        }
-    }
-    pub(super) fn carries(&self, g: usize, slot: usize) -> bool {
-        match self {
-            Mat::Count(m) => m.col_view(g).get(slot) != 0,
-            Mat::Presence(m) => m.get(g, slot) != 0,
-        }
-    }
-}
-
-pub(super) struct PartitionCache {
-    /// `layers[partition][layer]` = that partition's opened MPHF layers,
-    /// paired 1:1 with `mats[partition][layer]`; empty if the partition
-    /// directory doesn't exist. Used by both
-    /// [`crate::index::KmerIndex::build_sibling_annex`] (`layers` only) and
-    /// [`crate::index::KmerIndex::sibling_annex_stats`] (both).
-    layers: Vec<Vec<MphfLayer>>,
-    mats: Vec<Vec<Mat>>,
-}
-
-impl PartitionCache {
-    pub(super) fn build(partition: &KmerPartition, n_parts: usize, with_counts: bool) -> OKIResult<Self> {
-        let pb = progress_bar("open_partitions", n_parts as u64, "partitions");
-        let built: Vec<(Vec<MphfLayer>, Vec<Mat>)> = (0..n_parts)
-            .into_par_iter()
-            .map(|part| -> OKIResult<(Vec<MphfLayer>, Vec<Mat>)> {
-                let index_dir = partition.part_dir(part).join(INDEX_SUBDIR);
-                if !index_dir.exists() {
-                    pb.inc(1);
-                    return Ok((Vec::new(), Vec::new()));
-                }
-                let meta = PartitionMeta::load(&index_dir).map_err(olm_to_ok)?;
-                let mut layers = Vec::with_capacity(meta.n_layers);
-                let mut mats = Vec::with_capacity(meta.n_layers);
-                for l in 0..meta.n_layers {
-                    let layer_dir = index_dir.join(format!("layer_{l}"));
-                    let Ok(mphf) = MphfLayer::open(&layer_dir, &meta.mode) else { continue };
-                    let use_counts = with_counts && layer_dir.join("counts").exists();
-                    let mat = if use_counts {
-                        PersistentCompactIntMatrix::open(&layer_dir).ok().map(Mat::Count)
-                    } else {
-                        PersistentBitMatrix::open(&layer_dir).ok().map(Mat::Presence)
-                    };
-                    let Some(mat) = mat else { continue };
-                    layers.push(mphf);
-                    mats.push(mat);
-                }
-                pb.inc(1);
-                Ok((layers, mats))
-            })
-            .collect::<OKIResult<Vec<_>>>()?;
-        pb.finish_and_clear();
-        let (layers, mats) = built.into_iter().unzip();
-        Ok(Self { layers, mats })
-    }
-
-    /// Existence-only lookup of `variant` in partition `dest_partition`:
-    /// tries each of the partition's already-open layers in turn, stopping
-    /// at the first hit.
-    pub(super) fn find(&self, dest_partition: usize, variant: CanonicalKmer) -> bool {
-        self.layers
-            .get(dest_partition)
-            .is_some_and(|layers| layers.iter().any(|mphf| mphf.find(variant).is_some()))
-    }
-
-    /// Resolve many `(variant, family_idx, base)` queries against one
-    /// partition's matrices at once, calling `on_hit(family_idx, base, g)`
-    /// for every genome `g` that carries the resolved variant.
-    ///
-    /// Genome-major, not query-major: `PersistentBitMatrix`/
-    /// `PersistentCompactIntMatrix` are stored one contiguous block per
-    /// genome (column), slot as the offset within it (see
-    /// `obicompactvec::bitmatrix::packed::PackedBitMatrix` — each column's
-    /// own `mmap` region). Resolving query-by-query (`for query { for genome
-    /// { mat.carries(genome, slot) } }`, this function's predecessor) visits
-    /// every genome's block once *per query* — for a batch of thousands of
-    /// queries against ~90 genomes, that is thousands of jumps into each of
-    /// ~90 widely separated multi-MB regions, in query order, not genome
-    /// order: the access pattern a column-major layout is least suited to.
-    /// Grouping first (by layer, since each layer's matrix is a separate
-    /// column set) and sorting each group by slot, then visiting genome by
-    /// genome, turns that into ~90 mostly-sequential sweeps through one
-    /// column's own bytes — the layout's fast axis — confirmed by sampling
-    /// a real run: `PersistentBitMatrix::get` dominated wall-clock time,
-    /// mostly blocked on page faults, even after every partition/batch
-    /// locality fix above this in the traversal.
-    pub(super) fn find_presence_batch(
-        &self,
-        dest_partition: usize,
-        queries: &[(CanonicalKmer, usize, u8)],
-        n_genomes: usize,
-        mut on_hit: impl FnMut(usize, u8, usize),
-    ) {
-        let Some(layers) = self.layers.get(dest_partition) else { return };
-        let Some(mats) = self.mats.get(dest_partition) else { return };
-
-        // First hit wins, same semantics as the old per-query loop (a
-        // variant present in an earlier layer shadows later ones).
-        let mut by_layer: Vec<Vec<(usize, usize, u8)>> = vec![Vec::new(); layers.len()];
-        for &(variant, family_idx, base) in queries {
-            for (li, mphf) in layers.iter().enumerate() {
-                if let Some(slot) = mphf.find(variant) {
-                    by_layer[li].push((slot, family_idx, base));
-                    break;
-                }
-            }
-        }
-
-        for (li, mut hits) in by_layer.into_iter().enumerate() {
-            if hits.is_empty() {
-                continue;
-            }
-            hits.sort_unstable_by_key(|&(slot, _, _)| slot);
-            let mat = &mats[li];
-            let n_cols = mat.n_cols().min(n_genomes);
-            for g in 0..n_cols {
-                for &(slot, family_idx, base) in &hits {
-                    if mat.carries(g, slot) {
-                        on_hit(family_idx, base, g);
-                    }
-                }
-            }
-        }
-    }
-}
diff --git a/src/obikindex/src/siblings/helpers.rs b/src/obikindex/src/siblings/helpers.rs
deleted file mode 100644
index f50ee2ce..00000000
--- a/src/obikindex/src/siblings/helpers.rs
+++ /dev/null
@@ -1,49 +0,0 @@
-use obikseq::CanonicalKmer;
-use obiskbuilder::rolling_stat::RollingStat;
-
-use obicompactvec::FamilyMask;
-
-/// Central-position base of a canonical k-mer, in the fixed 0=A/1=C/2=G/3=T
-/// encoding — the mask's bit index. `k` must be odd (project invariant).
-#[inline]
-pub(super) fn central_base(kmer: CanonicalKmer, k: usize) -> u8 {
-    kmer.nucleotide((k - 1) / 2)
-}
-
-/// Is `kmer` the minorant of its family, given the family's presence mask?
-/// Regenerates the family's 4 canonical forms from `kmer` itself (cheap, no
-/// lookup — see the design doc's "Definitions" section for why this is
-/// always safe: the set of 4 forms is invariant regardless of which member
-/// you start from), and compares the raw encodings of whichever are marked
-/// present in `mask`.
-pub(super) fn is_minorant(kmer: CanonicalKmer, mask: FamilyMask, k: usize) -> bool {
-    kmer.central_canonical_neighbors().into_iter().all(|other| {
-        other == kmer || !mask.has(central_base(other, k)) || kmer.raw() <= other.raw()
-    })
-}
-
-/// Minimiser of a single, isolated canonical k-mer (not part of a streamed
-/// sequence). `RollingStat` computes minimisers incrementally along a
-/// sequence; this feeds one k-mer's bases through a fresh instance to get
-/// the same selection for a single, disconnected k-mer. Not the leanest
-/// possible primitive (an O(1)-amortised dedicated scan, as originally
-/// sketched in the design doc's Step 0, would avoid the ASCII round-trip and
-/// `RollingStat` allocation) but correct and reuses already-tested logic;
-/// left as a follow-up optimisation.
-fn lone_kmer_minimizer(kmer: CanonicalKmer) -> obikseq::Minimizer {
-    let ascii = kmer.to_ascii();
-    let mut rs = RollingStat::new(0);
-    for b in ascii {
-        rs.push(b);
-    }
-    rs.canonical_minimizer()
-        .expect("RollingStat must be ready after k bases of a valid k-mer")
-}
-
-/// Destination partition for a (possibly synthetic) canonical k-mer, using
-/// the same routing rule as the rest of the index (`minimiser.seq_hash() &
-/// mask`, `n_partitions` is a power of two).
-pub(super) fn partition_of(kmer: CanonicalKmer, n_partitions: usize) -> usize {
-    let mask = (n_partitions as u64) - 1;
-    (lone_kmer_minimizer(kmer).seq_hash() & mask) as usize
-}
diff --git a/src/obikindex/src/siblings/iter.rs b/src/obikindex/src/siblings/iter.rs
deleted file mode 100644
index 70b26c1c..00000000
--- a/src/obikindex/src/siblings/iter.rs
+++ /dev/null
@@ -1,78 +0,0 @@
-//! Phylo/sibling-domain iteration over a layer — an extension trait, not a
-//! new field on `MphfLayer`/`Layer<D>`: "family"/"minorant" are phylo
-//! concepts, `obilayeredmap` stays kmer/slot-mapping only (see
-//! `docmd/architecture/siblings.md`).
-//!
-//! The sibling annex is persisted in the same order as `iter_kmers()`
-//! (`build_sibling_annex`, see `build.rs`), so pairing them is a plain zip —
-//! no MPHF, no slot, no `kmer_at`. Both sides are already `Send + 'static`
-//! (`KmerIter` owns an `Arc<UnitigFileReader>` clone; `SiblingAnnex` is
-//! mmap-backed and handed in as an `Arc` by the caller), so `SiblingIter`
-//! streams straight from disk and can be fed to `obipipeline` batch by
-//! batch — never collected whole into memory (see the project's "no full
-//! collect" rule).
-
-use std::sync::Arc;
-
-use obicompactvec::{FamilyMask, SiblingAnnex};
-use obikseq::CanonicalKmer;
-use obilayeredmap::{KmerIter, MphfLayer};
-
-/// One layer entry: a k-mer's position in the layer's iteration order (the
-/// same index the sibling annex is keyed on — not an MPHF slot), the k-mer
-/// itself, and its family mask.
-#[derive(Debug, Clone, Copy)]
-pub struct SiblingEntry {
-    pub order: usize,
-    pub kmer: CanonicalKmer,
-    pub mask: FamilyMask,
-}
-
-/// Streams `(order, kmer, mask)` triples for one layer, in iteration order.
-/// Produced by [`SiblingLayerExt::iter_siblings`].
-pub struct SiblingIter {
-    kmers: KmerIter,
-    annex: Arc<SiblingAnnex>,
-    order: usize,
-}
-
-impl Iterator for SiblingIter {
-    type Item = SiblingEntry;
-
-    fn next(&mut self) -> Option<Self::Item> {
-        loop {
-            let kmer = self.kmers.next()?;
-            let order = self.order;
-            self.order += 1;
-            // `None` means "not yet computed" (see `SiblingAnnex` module
-            // docs) — shouldn't happen against a fully-built annex, but
-            // skip rather than misalign the two streams if it does.
-            if let Some(mask) = self.annex.get(order) {
-                return Some(SiblingEntry { order, kmer, mask });
-            }
-        }
-    }
-}
-
-/// Adds phylo/sibling iteration to `MphfLayer`.
-pub trait SiblingLayerExt {
-    /// Zip this layer's k-mers with their sibling-annex entry, in iteration
-    /// order. `annex` must have been built from this same layer (its length
-    /// must match the layer's k-mer count).
-    fn iter_siblings(&self, annex: Arc<SiblingAnnex>) -> SiblingIter;
-
-    /// Like [`iter_siblings`](Self::iter_siblings), filtered to the
-    /// minorant of each family — the common case, since a family is
-    /// tallied once, at its minorant.
-    fn iter_minorants(&self, annex: Arc<SiblingAnnex>) -> impl Iterator<Item = SiblingEntry>;
-}
-
-impl SiblingLayerExt for MphfLayer {
-    fn iter_siblings(&self, annex: Arc<SiblingAnnex>) -> SiblingIter {
-        SiblingIter { kmers: self.iter_kmers(), annex, order: 0 }
-    }
-
-    fn iter_minorants(&self, annex: Arc<SiblingAnnex>) -> impl Iterator<Item = SiblingEntry> {
-        self.iter_siblings(annex).filter(|e| e.mask.is_minorant())
-    }
-}
diff --git a/src/obikmer/Cargo.toml b/src/obikmer/Cargo.toml
index 7a16f63c..903c69db 100644
--- a/src/obikmer/Cargo.toml
+++ b/src/obikmer/Cargo.toml
@@ -19,6 +19,7 @@ obikpartitionner = { path = "../obikpartitionner" }
 obisys        = { path = "../obisys" }
 obiskio       = { path = "../obiskio" }
 obikindex     = { path = "../obikindex", default-features = false }
+obikphylo     = { path = "../obikphylo" }
 obitaxonomy   = { path = "../obitaxonomy" }
 obilayeredmap = { path = "../obilayeredmap" }
 clap          = { version = "4", features = ["derive"] }
diff --git a/src/obikmer/src/cmd/phylo/family_overlap.rs b/src/obikmer/src/cmd/phylo/family_overlap.rs
index fa01c8e2..7a8f9d7b 100644
--- a/src/obikmer/src/cmd/phylo/family_overlap.rs
+++ b/src/obikmer/src/cmd/phylo/family_overlap.rs
@@ -1,7 +1,8 @@
 use std::io::{BufWriter, Write};
 use std::path::PathBuf;
 
-use obikindex::{KmerIndex, SnpAlignment};
+use obikindex::KmerIndex;
+use obikphylo::siblings::{SnpAlignment, SnpAlignmentExt};
 use tracing::info;
 
 // ── Family overlap: shared-family counts and the `--min-shared-family` /
diff --git a/src/obikmer/src/cmd/phylo/iqtree.rs b/src/obikmer/src/cmd/phylo/iqtree.rs
index cd906841..d5b17af0 100644
--- a/src/obikmer/src/cmd/phylo/iqtree.rs
+++ b/src/obikmer/src/cmd/phylo/iqtree.rs
@@ -2,7 +2,7 @@ use std::io::{BufWriter, Write};
 use std::path::PathBuf;
 
 use obifastwrite::{JsonVal, write_record};
-use obikindex::SnpAlignment;
+use obikphylo::siblings::SnpAlignment;
 use tracing::info;
 
 use super::sankoff::state_index_table;
diff --git a/src/obikmer/src/cmd/phylo/mod.rs b/src/obikmer/src/cmd/phylo/mod.rs
index 9b09a071..b1cb86d3 100644
--- a/src/obikmer/src/cmd/phylo/mod.rs
+++ b/src/obikmer/src/cmd/phylo/mod.rs
@@ -9,9 +9,13 @@ mod tnt;
 use std::io::{self, BufWriter, Write};
 
 use kodama::{Method, linkage};
-use obikindex::{
-    KmerIndex, RawSnpDistanceOutput, SnpAlignment,
+use obikindex::KmerIndex;
+use obikphylo::{
     cardinality_transition_probs, composition_transition_probs, pairwise_cost_matrix,
+    siblings::{
+        CardinalityExt, DistanceExt, RawSnpDistanceOutput, SiblingAnnexBuildExt, SiblingStatsExt,
+        SnpAlignment, SnpAlignmentExt,
+    },
 };
 use speedytree::{DistanceMatrix, Hybrid, NeighborJoiningSolver, to_newick};
 use tracing::info;
diff --git a/src/obikmer/src/cmd/phylo/outputs.rs b/src/obikmer/src/cmd/phylo/outputs.rs
index 28b67a66..eef77368 100644
--- a/src/obikmer/src/cmd/phylo/outputs.rs
+++ b/src/obikmer/src/cmd/phylo/outputs.rs
@@ -2,7 +2,7 @@ use std::io::{BufWriter, Write};
 use std::path::PathBuf;
 
 use obifastwrite::{JsonVal, write_record};
-use obikindex::{RawSnpDistanceOutput, SiblingAnnexStats, SnpAlignment};
+use obikphylo::siblings::{RawSnpDistanceOutput, SiblingAnnexStats, SnpAlignment};
 use tracing::info;
 
 // ── Family-size distribution → CSV ──────────────────────────────────────────
diff --git a/src/obikmer/src/cmd/phylo/sankoff.rs b/src/obikmer/src/cmd/phylo/sankoff.rs
index ab96e7d3..7c91b0ca 100644
--- a/src/obikmer/src/cmd/phylo/sankoff.rs
+++ b/src/obikmer/src/cmd/phylo/sankoff.rs
@@ -2,7 +2,7 @@ use std::io::{BufWriter, Write};
 use std::path::PathBuf;
 
 use obifastwrite::{JsonVal, write_record};
-use obikindex::{BasePairTally, CardinalityTally, SnpAlignment};
+use obikphylo::siblings::{BasePairTally, CardinalityTally, SnpAlignment};
 use tracing::info;
 
 // ── Sankoff pseudo-alignment → FASTA ────────────────────────────────────────
diff --git a/src/obikmer/src/cmd/phylo/tnt.rs b/src/obikmer/src/cmd/phylo/tnt.rs
index aa16b419..a4be379f 100644
--- a/src/obikmer/src/cmd/phylo/tnt.rs
+++ b/src/obikmer/src/cmd/phylo/tnt.rs
@@ -1,7 +1,7 @@
 use std::io::{BufWriter, Write};
 use std::path::PathBuf;
 
-use obikindex::SnpAlignment;
+use obikphylo::siblings::SnpAlignment;
 use tracing::info;
 
 use super::sankoff::{scaled_metric_matrix, state_index_table};
diff --git a/src/obikphylo/Cargo.toml b/src/obikphylo/Cargo.toml
new file mode 100644
index 00000000..be66a13c
--- /dev/null
+++ b/src/obikphylo/Cargo.toml
@@ -0,0 +1,23 @@
+[package]
+name = "obikphylo"
+version = "0.1.0"
+edition = "2024"
+
+[dependencies]
+obikindex        = { path = "../obikindex" }
+obikseq          = { path = "../obikseq" }
+obikpartitionner = { path = "../obikpartitionner" }
+obiskio          = { path = "../obiskio" }
+obisys           = { path = "../obisys" }
+obicompactvec    = { path = "../obicompactvec" }
+obilayeredmap    = { path = "../obilayeredmap" }
+obiskbuilder     = { path = "../obiskbuilder" }
+obipipeline      = { path = "../obipipeline" }
+ndarray          = "0.16"
+rayon            = "1"
+tracing          = "0.1.44"
+
+[dev-dependencies]
+obiread  = { path = "../obiread" }
+tempfile = "3"
+tracing-subscriber = { version = "0.3", features = ["fmt", "env-filter"] }
diff --git a/src/obikindex/src/cardcomp.rs b/src/obikphylo/src/cardcomp.rs
similarity index 99%
rename from src/obikindex/src/cardcomp.rs
rename to src/obikphylo/src/cardcomp.rs
index eab104a3..8fdd2fa8 100644
--- a/src/obikindex/src/cardcomp.rs
+++ b/src/obikphylo/src/cardcomp.rs
@@ -17,7 +17,7 @@
 //! since TNT/PhyG search *unrooted* trees) if the cost matrix is
 //! symmetric, the discrete-parsimony analogue of CTMC reversibility.
 
-use crate::{BasePairTally, CardinalityTally};
+use crate::siblings::{BasePairTally, CardinalityTally};
 
 /// Row-stochastic 5×5 cardinality transition probabilities (`0..=4`),
 /// diagonal included ("stay at the same cardinality"), from
diff --git a/src/obikphylo/src/lib.rs b/src/obikphylo/src/lib.rs
new file mode 100644
index 00000000..d745f063
--- /dev/null
+++ b/src/obikphylo/src/lib.rs
@@ -0,0 +1,14 @@
+//! Library-level phylogenetic functionality for `obikmer`, built as
+//! extension traits over `obikindex::KmerIndex` and `obilayeredmap`'s
+//! generic layer types — the `phylo` CLI command is a consumer of this
+//! crate, not the owner of this logic (see `docmd/architecture/siblings.md`).
+//!
+//! Starts with [`siblings`] (family presence-mask annex, SNP distance,
+//! cardinality, pseudo-alignment); further phylo-domain functionality
+//! (currently `obikindex::distance`/`obikindex::cardcomp`) moves here
+//! incrementally.
+
+mod cardcomp;
+pub mod siblings;
+
+pub use cardcomp::{cardinality_transition_probs, composition_transition_probs, pairwise_cost_matrix};
diff --git a/src/obikindex/src/siblings/alignment.rs b/src/obikphylo/src/siblings/alignment.rs
similarity index 84%
rename from src/obikindex/src/siblings/alignment.rs
rename to src/obikphylo/src/siblings/alignment.rs
index e87e1017..123b14d3 100644
--- a/src/obikindex/src/siblings/alignment.rs
+++ b/src/obikphylo/src/siblings/alignment.rs
@@ -3,8 +3,8 @@ use std::sync::Arc;
 use obikpartitionner::KmerPartition;
 use obisys::progress_bar;
 
-use crate::error::{OKIError, OKIResult};
-use crate::index::KmerIndex;
+use obikindex::{OKIError, OKIResult};
+use obikindex::KmerIndex;
 
 use super::cache::PartitionCache;
 use super::family_scan::scan_layer_families;
@@ -53,25 +53,32 @@ pub struct SnpAlignment {
     pub sequences: Vec<Vec<u8>>,
 }
 
-impl KmerIndex {
+/// Adds [`snp_pseudo_alignment`](Self::snp_pseudo_alignment) to `KmerIndex` —
+/// phylo-domain functionality, kept out of `obikindex` itself (see
+/// `docmd/architecture/siblings.md`).
+pub trait SnpAlignmentExt {
     /// Build the SNP-only pseudo-alignment from an already-built sibling
-    /// annex (run [`build_sibling_annex`](Self::build_sibling_annex) first).
-    pub fn snp_pseudo_alignment(&self) -> OKIResult<SnpAlignment> {
+    /// annex (run [`build_sibling_annex`](super::build::SiblingAnnexBuildExt::build_sibling_annex) first).
+    fn snp_pseudo_alignment(&self) -> OKIResult<SnpAlignment>;
+}
+
+impl SnpAlignmentExt for KmerIndex {
+    fn snp_pseudo_alignment(&self) -> OKIResult<SnpAlignment> {
         let n_parts = self.n_partitions();
-        let n_genomes = self.meta.genomes.len();
-        let with_counts = self.meta.config.with_counts;
+        let n_genomes = self.meta().genomes.len();
+        let with_counts = self.meta().config.with_counts;
         let k = self.kmer_size();
         let n_bits = n_parts.trailing_zeros() as usize;
 
         let partition = KmerPartition::open_with_config(
-            &self.root_path,
+            self.root_path(),
             self.kmer_size(),
             self.minimizer_size(),
             n_bits,
         )
         .map_err(OKIError::Partition)?;
         let cache = Arc::new(PartitionCache::build(&partition, n_parts, with_counts)?);
-        let layer_dirs = self.sibling_layer_dirs()?;
+        let layer_dirs = super::family_scan::sibling_layer_dirs(self)?;
 
         let pb = progress_bar("snp_pseudo_alignment", layer_dirs.len() as u64, "layers");
         // One layer at a time, not `par_iter()` over layers — same
diff --git a/src/obikindex/src/siblings/build.rs b/src/obikphylo/src/siblings/build.rs
similarity index 89%
rename from src/obikindex/src/siblings/build.rs
rename to src/obikphylo/src/siblings/build.rs
index b51a7f32..70955d49 100644
--- a/src/obikindex/src/siblings/build.rs
+++ b/src/obikphylo/src/siblings/build.rs
@@ -12,11 +12,11 @@ use obilayeredmap::MphfLayer;
 use obilayeredmap::meta::PartitionMeta;
 use obisys::progress_bar;
 
-use crate::error::{OKIError, OKIResult};
-use crate::index::KmerIndex;
+use obikindex::{OKIError, OKIResult};
+use obikindex::KmerIndex;
 
 use super::cache::PartitionCache;
-use super::helpers::{central_base, is_minorant, partition_of};
+use super::helpers::{central_base, is_minorant};
 use super::{olm_to_ok, ANNEX_FILE_NAME, INDEX_SUBDIR};
 
 // ── obipipeline data types ─────────────────────────────────────────────────
@@ -53,7 +53,8 @@ enum SibData {
     Variants(VariantBatch),
 }
 
-impl KmerIndex {
+/// Adds [`build_sibling_annex`](Self::build_sibling_annex) to `KmerIndex`.
+pub trait SiblingAnnexBuildExt {
     /// Build the sibling-count/minorant annex for every layer of every
     /// partition of this (already built) index, writing one annex file per
     /// layer alongside its existing index files. Safe to call again later
@@ -63,18 +64,23 @@ impl KmerIndex {
     /// Construction only — no statistics gathered here on purpose: this is
     /// meant to run routinely (it is the artefact the SNP-family distances
     /// will consume), while the sibling-count distribution
-    /// ([`sibling_annex_stats`](Self::sibling_annex_stats)) is a separate,
-    /// occasional diagnostic pass over the result, not run every time.
+    /// ([`sibling_annex_stats`](super::stats::SiblingStatsExt::sibling_annex_stats))
+    /// is a separate, occasional diagnostic pass over the result, not run
+    /// every time.
     ///
     /// Cross-partition/cross-layer lookups are required (a k-mer's siblings
     /// can live in any partition), but the layer loop itself — and thus the
     /// annex file this produces — stays local to one layer at a time.
-    pub fn build_sibling_annex(&self) -> OKIResult<()> {
+    fn build_sibling_annex(&self) -> OKIResult<()>;
+}
+
+impl SiblingAnnexBuildExt for KmerIndex {
+    fn build_sibling_annex(&self) -> OKIResult<()> {
         let n_parts = self.n_partitions();
         let n_bits = n_parts.trailing_zeros() as usize;
 
         let partition = KmerPartition::open_with_config(
-            &self.root_path,
+            self.root_path(),
             self.kmer_size(),
             self.minimizer_size(),
             n_bits,
@@ -82,7 +88,7 @@ impl KmerIndex {
         .map_err(OKIError::Partition)?;
 
         tracing::info!("opening {n_parts} partition(s) for the sibling-annex sweep");
-        let cache = Arc::new(PartitionCache::build(&partition, n_parts, self.meta.config.with_counts)?);
+        let cache = Arc::new(PartitionCache::build(&partition, n_parts, self.meta().config.with_counts)?);
 
         let pb = progress_bar("sibling_annex", n_parts as u64, "partitions");
         let mut total_slots: u64 = 0;
@@ -97,7 +103,7 @@ impl KmerIndex {
             let mut part_slots: u64 = 0;
             for l in 0..meta.n_layers {
                 let layer_dir = index_dir.join(format!("layer_{l}"));
-                part_slots += self.build_layer_sibling_annex(&layer_dir, n_parts, &cache)?;
+                part_slots += build_layer_sibling_annex(self, &layer_dir, n_parts, &cache)?;
             }
             total_slots += part_slots;
             pb.inc(1);
@@ -108,20 +114,22 @@ impl KmerIndex {
 
         Ok(())
     }
+}
 
-    /// Returns the number of distinct k-mers (annex entries) processed, for
-    /// progress reporting.
-    fn build_layer_sibling_annex(
-        &self,
-        layer_dir: &Path,
-        n_parts: usize,
-        cache: &Arc<PartitionCache>,
-    ) -> OKIResult<u64> {
-        let index_dir = layer_dir.parent().expect("layer_dir has a parent index dir");
-        let meta = PartitionMeta::load(index_dir).map_err(olm_to_ok)?;
-        let mphf = MphfLayer::open(layer_dir, &meta.mode).map_err(olm_to_ok)?;
-        let k = self.kmer_size();
-        let n = mphf.n();
+/// Returns the number of distinct k-mers (annex entries) processed, for
+/// progress reporting. A free function, not a `KmerIndex` method — called
+/// only from `build_sibling_annex` above, in the same file.
+fn build_layer_sibling_annex(
+    index: &KmerIndex,
+    layer_dir: &Path,
+    n_parts: usize,
+    cache: &Arc<PartitionCache>,
+) -> OKIResult<u64> {
+    let index_dir = layer_dir.parent().expect("layer_dir has a parent index dir");
+    let meta = PartitionMeta::load(index_dir).map_err(olm_to_ok)?;
+    let mphf = MphfLayer::open(layer_dir, &meta.mode).map_err(olm_to_ok)?;
+    let k = index.kmer_size();
+    let n = mphf.n();
 
         // ── Reconciliation state, indexed by this layer's k-mer iteration
         // order (the physical layout of `unitigs.bin`), never by MPHF slot
@@ -211,7 +219,7 @@ impl KmerIndex {
                                 continue;
                             }
                             items.push((
-                                partition_of(variant, n_parts),
+                                variant.partition(n_parts),
                                 variant,
                                 order,
                                 central_base(variant, k),
@@ -272,6 +280,5 @@ impl KmerIndex {
         }
         builder.close()?;
 
-        Ok(n as u64)
-    }
+    Ok(n as u64)
 }
diff --git a/src/obikphylo/src/siblings/cache.rs b/src/obikphylo/src/siblings/cache.rs
new file mode 100644
index 00000000..8d706d27
--- /dev/null
+++ b/src/obikphylo/src/siblings/cache.rs
@@ -0,0 +1,225 @@
+use rayon::prelude::*;
+
+use obicompactvec::{PersistentBitMatrix, PersistentCompactIntMatrix};
+use obikpartitionner::KmerPartition;
+use obikseq::CanonicalKmer;
+use obilayeredmap::Layer;
+use obilayeredmap::meta::PartitionMeta;
+use obisys::progress_bar;
+
+use obikindex::OKIResult;
+
+use super::iter::SiblingLayerExt;
+use super::{olm_to_ok, INDEX_SUBDIR};
+
+/// Every partition's already-open layers, built **once** for the whole
+/// `build_sibling_annex` run and shared (read-only) across every lookup, in
+/// every source layer, for the rest of the run — not reopened/re-mmap'd per
+/// query, nor per source layer.
+///
+/// Confirmed necessary by sampling a real run: routing lookups through
+/// `KmerPartition::query_partition_with` (the same batching `obikmer query`
+/// uses) still reopens+re-mmaps every target partition's files on every
+/// call, and it is called once per destination partition **per source
+/// layer** — for an index with many layers this repeats the same
+/// `MphfLayer::open`/`Evidence::open`/`PersistentBitMatrix::open` work over
+/// and over. Parallelising those calls (see the gather step below) spread
+/// the redundant work across more cores but did not reduce it: sampling
+/// showed Rayon workers spending their time inside repeated `open()`
+/// syscalls, not computation. This cache amortises that cost to once per
+/// partition for the entire run, regardless of how many source layers or
+/// lookups follow.
+///
+/// One `Layer<D>` per layer (MPHF + matrix bundled), not a separate
+/// `MphfLayer` and a separate `PersistentCompactIntMatrix`/
+/// `PersistentBitMatrix` in parallel arrays — `obilayeredmap::Layer` already
+/// *is* that bundle, with `find_slot` (MPHF-only, no data read),
+/// `n_cols`/`sub_matrix`/`fill_sub_matrix` (batched, sorted-internally
+/// column access) on top of it. Reinventing that pairing here would just be
+/// going back through the low-level pieces `Layer` already assembles.
+pub(super) enum Mat {
+    Count(Layer<PersistentCompactIntMatrix>),
+    Presence(Layer<PersistentBitMatrix>),
+}
+
+impl Mat {
+    fn find_slot(&self, kmer: CanonicalKmer) -> Option<usize> {
+        match self {
+            Mat::Count(l) => l.find_slot(kmer),
+            Mat::Presence(l) => l.find_slot(kmer),
+        }
+    }
+
+    /// Raw MPHF batch lookup: kmer → slot, no membership check — for
+    /// callers that already know every kmer is a member of *this* layer
+    /// (e.g. it came from this layer's own `iter_minorants_batch`), so the
+    /// evidence check `find_slot`/`find` would perform is redundant work.
+    /// See `docmd/architecture/siblings.md`: iteration-pipeline kmers use
+    /// `index`, never `find`.
+    pub(super) fn index_batch(&self, kmers: &[CanonicalKmer]) -> Vec<usize> {
+        match self {
+            Mat::Count(l) => l.index_batch(kmers),
+            Mat::Presence(l) => l.index_batch(kmers),
+        }
+    }
+
+    /// This layer's own `SiblingLayerExt::iter_minorants_batch` — dispatch
+    /// only, both arms return the same concrete `MinorantBatchIter` (it
+    /// doesn't depend on `D`), so no boxing is needed.
+    pub(super) fn iter_minorants_batch(
+        &self,
+        annex: std::sync::Arc<obicompactvec::SiblingAnnex>,
+        batch_size: usize,
+    ) -> super::iter::MinorantBatchIter {
+        match self {
+            Mat::Count(l) => l.iter_minorants_batch(annex, batch_size),
+            Mat::Presence(l) => l.iter_minorants_batch(annex, batch_size),
+        }
+    }
+
+    pub(super) fn n_cols(&self) -> usize {
+        match self {
+            Mat::Count(l) => l.n_cols(),
+            Mat::Presence(l) => l.n_cols(),
+        }
+    }
+
+    /// Batch, genome-major "carries" for a set of `slots` — `out[g][i]` =
+    /// whether genome `g` (0..`out.len()`) carries `slots[i]`. `out` must
+    /// have one entry per genome column, each resized to `slots.len()`.
+    ///
+    /// Delegates entirely to `Layer<D>::fill_sub_matrix`, which sorts
+    /// `slots` once internally for a sequential mmap sweep per column, then
+    /// restores the original order — the same discipline this call site
+    /// (and `find_presence_batch`) used to hand-roll with its own sort +
+    /// genome-major loop. `Count` still needs one intermediate
+    /// `Vec<Vec<u32>>` fetch (the underlying store only has an int
+    /// sub-matrix, not a bool one), converted to presence (`!= 0`) in place
+    /// — the sort/sequential-access win is unaffected, just one extra
+    /// allocation pass over already-in-hand data.
+    pub(super) fn fill_sub_matrix_carries(&self, slots: &[usize], out: &mut [Vec<bool>]) {
+        match self {
+            Mat::Presence(l) => l.fill_sub_matrix(slots, out),
+            Mat::Count(l) => {
+                let mut counts: Vec<Vec<u32>> = out.iter().map(|_| Vec::new()).collect();
+                l.fill_sub_matrix(slots, &mut counts);
+                for (o, c) in out.iter_mut().zip(counts.iter()) {
+                    o.clear();
+                    o.extend(c.iter().map(|&v| v != 0));
+                }
+            }
+        }
+    }
+}
+
+pub(super) struct PartitionCache {
+    /// `mats[partition][layer]` = that partition's opened layers. Used by
+    /// both [`obikindex::KmerIndex::build_sibling_annex`] and
+    /// [`obikindex::KmerIndex::sibling_annex_stats`].
+    mats: Vec<Vec<Mat>>,
+}
+
+impl PartitionCache {
+    pub(super) fn build(partition: &KmerPartition, n_parts: usize, with_counts: bool) -> OKIResult<Self> {
+        let pb = progress_bar("open_partitions", n_parts as u64, "partitions");
+        let built: Vec<Vec<Mat>> = (0..n_parts)
+            .into_par_iter()
+            .map(|part| -> OKIResult<Vec<Mat>> {
+                let index_dir = partition.part_dir(part).join(INDEX_SUBDIR);
+                if !index_dir.exists() {
+                    pb.inc(1);
+                    return Ok(Vec::new());
+                }
+                let meta = PartitionMeta::load(&index_dir).map_err(olm_to_ok)?;
+                let mut mats = Vec::with_capacity(meta.n_layers);
+                for l in 0..meta.n_layers {
+                    let layer_dir = index_dir.join(format!("layer_{l}"));
+                    let use_counts = with_counts && layer_dir.join("counts").exists();
+                    let mat = if use_counts {
+                        Layer::<PersistentCompactIntMatrix>::open(&layer_dir, &meta.mode).ok().map(Mat::Count)
+                    } else {
+                        Layer::<PersistentBitMatrix>::open(&layer_dir, &meta.mode).ok().map(Mat::Presence)
+                    };
+                    let Some(mat) = mat else { continue };
+                    mats.push(mat);
+                }
+                pb.inc(1);
+                Ok(mats)
+            })
+            .collect::<OKIResult<Vec<_>>>()?;
+        pb.finish_and_clear();
+        Ok(Self { mats: built })
+    }
+
+    /// Existence-only lookup of `variant` in partition `dest_partition`:
+    /// tries each of the partition's already-open layers in turn, stopping
+    /// at the first hit. `find_slot`, not `sub_matrix`/`carries` — no data
+    /// read needed for a plain existence check.
+    pub(super) fn find(&self, dest_partition: usize, variant: CanonicalKmer) -> bool {
+        self.mats
+            .get(dest_partition)
+            .is_some_and(|mats| mats.iter().any(|mat| mat.find_slot(variant).is_some()))
+    }
+
+    /// Resolve many `(variant, family_idx, base)` queries against one
+    /// partition's matrices at once, calling `on_hit(family_idx, base, g)`
+    /// for every genome `g` that carries the resolved variant.
+    ///
+    /// Genome-major, not query-major: `PersistentBitMatrix`/
+    /// `PersistentCompactIntMatrix` are stored one contiguous block per
+    /// genome (column), slot as the offset within it (see
+    /// `obicompactvec::bitmatrix::packed::PackedBitMatrix` — each column's
+    /// own `mmap` region). Resolving query-by-query (`for query { for genome
+    /// { mat.carries(genome, slot) } }`, this function's predecessor) visits
+    /// every genome's block once *per query* — for a batch of thousands of
+    /// queries against ~90 genomes, that is thousands of jumps into each of
+    /// ~90 widely separated multi-MB regions, in query order, not genome
+    /// order: the access pattern a column-major layout is least suited to.
+    /// Grouping first (by layer, since each layer's matrix is a separate
+    /// column set) and letting `fill_sub_matrix_carries` sort each group by
+    /// slot internally, then visiting genome by genome, turns that into ~90
+    /// mostly-sequential sweeps through one column's own bytes — the
+    /// layout's fast axis — confirmed by sampling a real run:
+    /// `PersistentBitMatrix::get` dominated wall-clock time, mostly blocked
+    /// on page faults, even after every partition/batch locality fix above
+    /// this in the traversal.
+    pub(super) fn find_presence_batch(
+        &self,
+        dest_partition: usize,
+        queries: &[(CanonicalKmer, usize, u8)],
+        n_genomes: usize,
+        mut on_hit: impl FnMut(usize, u8, usize),
+    ) {
+        let Some(mats) = self.mats.get(dest_partition) else { return };
+
+        // First hit wins, same semantics as the old per-query loop (a
+        // variant present in an earlier layer shadows later ones).
+        let mut by_layer: Vec<Vec<(usize, usize, u8)>> = vec![Vec::new(); mats.len()];
+        for &(variant, family_idx, base) in queries {
+            for (li, mat) in mats.iter().enumerate() {
+                if let Some(slot) = mat.find_slot(variant) {
+                    by_layer[li].push((slot, family_idx, base));
+                    break;
+                }
+            }
+        }
+
+        for (li, hits) in by_layer.into_iter().enumerate() {
+            if hits.is_empty() {
+                continue;
+            }
+            let mat = &mats[li];
+            let n_cols = mat.n_cols().min(n_genomes);
+            let slots: Vec<usize> = hits.iter().map(|&(slot, _, _)| slot).collect();
+            let mut carries: Vec<Vec<bool>> = (0..n_cols).map(|_| Vec::new()).collect();
+            mat.fill_sub_matrix_carries(&slots, &mut carries);
+            for (g, col) in carries.iter().enumerate() {
+                for (&(_, family_idx, base), &carries_it) in hits.iter().zip(col.iter()) {
+                    if carries_it {
+                        on_hit(family_idx, base, g);
+                    }
+                }
+            }
+        }
+    }
+}
diff --git a/src/obikindex/src/siblings/cardinality.rs b/src/obikphylo/src/siblings/cardinality.rs
similarity index 89%
rename from src/obikindex/src/siblings/cardinality.rs
rename to src/obikphylo/src/siblings/cardinality.rs
index 5f09415d..c76888fd 100644
--- a/src/obikindex/src/siblings/cardinality.rs
+++ b/src/obikphylo/src/siblings/cardinality.rs
@@ -5,8 +5,8 @@ use ndarray::Array2;
 use obikpartitionner::KmerPartition;
 use obisys::progress_bar;
 
-use crate::error::{OKIError, OKIResult};
-use crate::index::KmerIndex;
+use obikindex::{OKIError, OKIResult};
+use obikindex::KmerIndex;
 
 use super::cache::PartitionCache;
 use super::distance::RawSnpDistanceOutput;
@@ -22,7 +22,8 @@ pub struct CardinalityTally {
     pub counts: [[u64; 5]; 5],
 }
 
-impl KmerIndex {
+/// Adds [`cardinality_tally`](Self::cardinality_tally) to `KmerIndex`.
+pub trait CardinalityExt {
     /// Cardinality co-occurrence, pooled only over genome pairs whose
     /// overall SNP ratio in `raw` is at or below `ratio_ceiling` — same
     /// saturation/no-data exclusion discipline as
@@ -51,10 +52,14 @@ impl KmerIndex {
     /// gets the matching restriction via `scan_family_pairs`'s new
     /// `variable` flag, rather than a `family_size()` check of its own (it
     /// doesn't have direct access to the family's mask).
-    pub fn cardinality_tally(&self, raw: &RawSnpDistanceOutput, ratio_ceiling: f64) -> OKIResult<CardinalityTally> {
+    fn cardinality_tally(&self, raw: &RawSnpDistanceOutput, ratio_ceiling: f64) -> OKIResult<CardinalityTally>;
+}
+
+impl CardinalityExt for KmerIndex {
+    fn cardinality_tally(&self, raw: &RawSnpDistanceOutput, ratio_ceiling: f64) -> OKIResult<CardinalityTally> {
         let n_parts = self.n_partitions();
-        let n_genomes = self.meta.genomes.len();
-        let with_counts = self.meta.config.with_counts;
+        let n_genomes = self.meta().genomes.len();
+        let with_counts = self.meta().config.with_counts;
         let k = self.kmer_size();
         let n_bits = n_parts.trailing_zeros() as usize;
 
@@ -68,14 +73,14 @@ impl KmerIndex {
         });
 
         let partition = KmerPartition::open_with_config(
-            &self.root_path,
+            self.root_path(),
             self.kmer_size(),
             self.minimizer_size(),
             n_bits,
         )
         .map_err(OKIError::Partition)?;
         let cache = Arc::new(PartitionCache::build(&partition, n_parts, with_counts)?);
-        let layer_dirs = self.sibling_layer_dirs()?;
+        let layer_dirs = super::family_scan::sibling_layer_dirs(self)?;
 
         let pb = progress_bar("cardinality_tally", layer_dirs.len() as u64, "layers");
         // One layer at a time — see `snp_pseudo_alignment`'s comment for why
diff --git a/src/obikindex/src/siblings/distance.rs b/src/obikphylo/src/siblings/distance.rs
similarity index 66%
rename from src/obikindex/src/siblings/distance.rs
rename to src/obikphylo/src/siblings/distance.rs
index 3f746303..99347600 100644
--- a/src/obikindex/src/siblings/distance.rs
+++ b/src/obikphylo/src/siblings/distance.rs
@@ -5,8 +5,8 @@ use ndarray::Array2;
 use obikpartitionner::KmerPartition;
 use obisys::progress_bar;
 
-use crate::error::{OKIError, OKIResult};
-use crate::index::KmerIndex;
+use obikindex::{OKIError, OKIResult};
+use obikindex::KmerIndex;
 
 use super::cache::PartitionCache;
 use super::family_scan::scan_layer_families;
@@ -35,54 +35,52 @@ pub struct RawSnpDistanceOutput {
     pub shared: Array2<u64>,
 }
 
-impl KmerIndex {
-    /// Shared traversal behind [`raw_snp_distance`](Self::raw_snp_distance)
-    /// and [`base_pair_tally`](Self::base_pair_tally): for every family
-    /// (tallied once, at its minorant) of every layer of the already-built
-    /// sibling annex, resolves each genome's single observed form (`None`
-    /// if absent or ambiguous/multi-copy), then calls `on_pair(acc, i, j,
-    /// bi, bj, variable)` for every genome pair `(i, j)` where both are
-    /// unambiguous and single-copy (`bi == bj` means shared at that locus,
-    /// `bi != bj` means a SNP). `variable` is the family's own
-    /// `family_size() >= 2` (true if more than one member is observed
-    /// *anywhere* in the family, i.e. it isn't fully invariant across the
-    /// whole index) — `raw_snp_distance` ignores it (a fully-invariant
-    /// family is still legitimately "shared"), but callers whose diagonal
-    /// should only reflect genuine SNP-adjacent agreement, not the
-    /// genome-wide invariant background, need it (see
-    /// [`base_pair_tally`](Self::base_pair_tally)'s `same` field). Layers
-    /// are processed one at a time, not in parallel — see
-    /// `snp_pseudo_alignment`'s comment for why `par_iter()` over layers
-    /// would defeat `scan_layer_families`'s partition-grouped locality;
-    /// each layer gets its own accumulator from `zero()`, combined
-    /// pairwise via `combine`.
-    fn scan_family_pairs<Acc, F, C>(
-        &self,
-        label: &str,
-        zero: impl Fn() -> Acc + Sync,
-        on_pair: F,
-        combine: C,
-    ) -> OKIResult<Acc>
-    where
-        Acc: Send,
-        F: Fn(&mut Acc, usize, usize, u8, u8, bool) + Sync,
-        C: Fn(Acc, Acc) -> Acc,
-    {
-        let n_parts = self.n_partitions();
-        let n_genomes = self.meta.genomes.len();
-        let with_counts = self.meta.config.with_counts;
-        let k = self.kmer_size();
-        let n_bits = n_parts.trailing_zeros() as usize;
+/// Shared traversal behind [`DistanceExt::raw_snp_distance`] and
+/// [`DistanceExt::base_pair_tally`]: for every family (tallied once, at its
+/// minorant) of every layer of the already-built sibling annex, resolves
+/// each genome's single observed form (`None` if absent or
+/// ambiguous/multi-copy), then calls `on_pair(acc, i, j, bi, bj, variable)`
+/// for every genome pair `(i, j)` where both are unambiguous and
+/// single-copy (`bi == bj` means shared at that locus, `bi != bj` means a
+/// SNP). `variable` is the family's own `family_size() >= 2` (true if more
+/// than one member is observed *anywhere* in the family, i.e. it isn't
+/// fully invariant across the whole index) — `raw_snp_distance` ignores it
+/// (a fully-invariant family is still legitimately "shared"), but callers
+/// whose diagonal should only reflect genuine SNP-adjacent agreement, not
+/// the genome-wide invariant background, need it (see
+/// [`DistanceExt::base_pair_tally`]'s `same` field). Layers are processed
+/// one at a time, not in parallel — see `snp_pseudo_alignment`'s comment
+/// for why `par_iter()` over layers would defeat `scan_layer_families`'s
+/// partition-grouped locality; each layer gets its own accumulator from
+/// `zero()`, combined pairwise via `combine`. A free function, not a
+/// `KmerIndex` method — called only from this file's `DistanceExt` impl.
+fn scan_family_pairs<Acc, F, C>(
+    index: &KmerIndex,
+    label: &str,
+    zero: impl Fn() -> Acc + Sync,
+    on_pair: F,
+    combine: C,
+) -> OKIResult<Acc>
+where
+    Acc: Send,
+    F: Fn(&mut Acc, usize, usize, u8, u8, bool) + Sync,
+    C: Fn(Acc, Acc) -> Acc,
+{
+    let n_parts = index.n_partitions();
+    let n_genomes = index.meta().genomes.len();
+    let with_counts = index.meta().config.with_counts;
+    let k = index.kmer_size();
+    let n_bits = n_parts.trailing_zeros() as usize;
 
-        let partition = KmerPartition::open_with_config(
-            &self.root_path,
-            self.kmer_size(),
-            self.minimizer_size(),
-            n_bits,
-        )
-        .map_err(OKIError::Partition)?;
-        let cache = Arc::new(PartitionCache::build(&partition, n_parts, with_counts)?);
-        let layer_dirs = self.sibling_layer_dirs()?;
+    let partition = KmerPartition::open_with_config(
+        index.root_path(),
+        index.kmer_size(),
+        index.minimizer_size(),
+        n_bits,
+    )
+    .map_err(OKIError::Partition)?;
+    let cache = Arc::new(PartitionCache::build(&partition, n_parts, with_counts)?);
+    let layer_dirs = super::family_scan::sibling_layer_dirs(index)?;
 
         let pb = progress_bar(label, layer_dirs.len() as u64, "layers");
         // One layer at a time — see `snp_pseudo_alignment`'s comment for why
@@ -121,11 +119,36 @@ impl KmerIndex {
         Ok(total)
     }
 
+/// Adds [`raw_snp_distance`](Self::raw_snp_distance) and
+/// [`base_pair_tally`](Self::base_pair_tally) to `KmerIndex`.
+pub trait DistanceExt {
     /// Compute [`RawSnpDistanceOutput`] from an already-built sibling annex
-    /// (run [`build_sibling_annex`](Self::build_sibling_annex) first).
-    pub fn raw_snp_distance(&self) -> OKIResult<RawSnpDistanceOutput> {
-        let n_genomes = self.meta.genomes.len();
-        let (snp, shared) = self.scan_family_pairs(
+    /// (run [`build_sibling_annex`](super::build::SiblingAnnexBuildExt::build_sibling_annex) first).
+    fn raw_snp_distance(&self) -> OKIResult<RawSnpDistanceOutput>;
+
+    /// Symmetric 6-category base-pair substitution tally (AC, AG, AT, CG,
+    /// CT, GT — indexed `0=A,1=C,2=G,3=T`), pooled only over genome pairs
+    /// whose overall SNP ratio in `raw` is at or below `ratio_ceiling` —
+    /// same saturation-exclusion discipline as
+    /// [`cardinality_tally`](super::cardinality::CardinalityExt::cardinality_tally),
+    /// for the same reason: a saturated pair's observed base-pair mix
+    /// trends toward neutral base composition, not the true point-mutation
+    /// spectrum.
+    ///
+    /// A second full pass over the annex, sharing
+    /// [`raw_snp_distance`](Self::raw_snp_distance)'s traversal (guided by
+    /// it, not a blind re-scan) — needed because `raw_snp_distance` only
+    /// keeps aggregate SNP/shared counts per genome pair, not which bases
+    /// were actually involved at each locus, and the ratio-ceiling filter
+    /// can only be evaluated once the aggregate counts are known.
+    fn base_pair_tally(&self, raw: &RawSnpDistanceOutput, ratio_ceiling: f64) -> OKIResult<BasePairTally>;
+}
+
+impl DistanceExt for KmerIndex {
+    fn raw_snp_distance(&self) -> OKIResult<RawSnpDistanceOutput> {
+        let n_genomes = self.meta().genomes.len();
+        let (snp, shared) = scan_family_pairs(
+            self,
             "raw_snp_distance",
             || (Array2::<u64>::zeros((n_genomes, n_genomes)), Array2::<u64>::zeros((n_genomes, n_genomes))),
             |(snp, shared), i, j, bi, bj, _variable| {
@@ -146,22 +169,8 @@ impl KmerIndex {
         Ok(RawSnpDistanceOutput { snp, shared })
     }
 
-    /// Symmetric 6-category base-pair substitution tally (AC, AG, AT, CG,
-    /// CT, GT — indexed `0=A,1=C,2=G,3=T`), pooled only over genome pairs
-    /// whose overall SNP ratio in `raw` is at or below `ratio_ceiling` —
-    /// same saturation-exclusion discipline as
-    /// [`cardinality_tally`](Self::cardinality_tally), for the same reason:
-    /// a saturated pair's observed base-pair mix trends toward neutral base
-    /// composition, not the true point-mutation spectrum.
-    ///
-    /// A second full pass over the annex, sharing
-    /// [`raw_snp_distance`](Self::raw_snp_distance)'s traversal (guided by
-    /// it, not a blind re-scan) — needed because `raw_snp_distance` only
-    /// keeps aggregate SNP/shared counts per genome pair, not which bases
-    /// were actually involved at each locus, and the ratio-ceiling filter
-    /// can only be evaluated once the aggregate counts are known.
-    pub fn base_pair_tally(&self, raw: &RawSnpDistanceOutput, ratio_ceiling: f64) -> OKIResult<BasePairTally> {
-        let n_genomes = self.meta.genomes.len();
+    fn base_pair_tally(&self, raw: &RawSnpDistanceOutput, ratio_ceiling: f64) -> OKIResult<BasePairTally> {
+        let n_genomes = self.meta().genomes.len();
         let included = Array2::from_shape_fn((n_genomes, n_genomes), |(i, j)| {
             if i == j {
                 return false;
@@ -171,7 +180,8 @@ impl KmerIndex {
             total > 0 && (snp as f64 / total as f64) <= ratio_ceiling
         });
 
-        let (counts, same) = self.scan_family_pairs(
+        let (counts, same) = scan_family_pairs(
+            self,
             "base_pair_tally",
             || ([[0u64; 4]; 4], [0u64; 4]),
             |(counts, same), i, j, bi, bj, variable| {
@@ -206,7 +216,7 @@ impl KmerIndex {
     }
 }
 
-/// See [`KmerIndex::base_pair_tally`].
+/// See [`DistanceExt::base_pair_tally`].
 pub struct BasePairTally {
     /// `counts[a][b] == counts[b][a]` = number of eligible loci, pooled
     /// over included genome pairs, where the two genomes' single forms are
diff --git a/src/obikindex/src/siblings/family_scan.rs b/src/obikphylo/src/siblings/family_scan.rs
similarity index 65%
rename from src/obikindex/src/siblings/family_scan.rs
rename to src/obikphylo/src/siblings/family_scan.rs
index 5aacdd62..56bc5d4c 100644
--- a/src/obikindex/src/siblings/family_scan.rs
+++ b/src/obikphylo/src/siblings/family_scan.rs
@@ -55,15 +55,16 @@ use rayon::prelude::*;
 
 use obicompactvec::{FamilyMask, PersistentBitMatrix, PersistentCompactIntMatrix, SiblingAnnex};
 use obikseq::CanonicalKmer;
-use obilayeredmap::MphfLayer;
+use obilayeredmap::Layer;
 use obilayeredmap::meta::PartitionMeta;
 use obipipeline::{ThrottleGuard, throttle};
 
-use crate::error::{OKIError, OKIResult};
-use crate::index::KmerIndex;
+use obikindex::{OKIError, OKIResult};
+use obikindex::KmerIndex;
 
 use super::cache::{Mat, PartitionCache};
-use super::helpers::{central_base, partition_of};
+use super::helpers::central_base;
+use super::iter::SiblingEntry;
 use super::{olm_to_ok, ANNEX_FILE_NAME, INDEX_SUBDIR};
 
 /// Families per batch — see the module docs for the memory-vs-per-partition-
@@ -73,42 +74,43 @@ use super::{olm_to_ok, ANNEX_FILE_NAME, INDEX_SUBDIR};
 /// queries per batch to amortise against.
 const FAMILY_BATCH: usize = 65536;
 
-impl KmerIndex {
-    /// Every (partition, layer) directory carrying a sibling annex, checked
-    /// up front so a missing one is reported before any real work starts.
-    pub(super) fn sibling_layer_dirs(&self) -> OKIResult<Vec<PathBuf>> {
-        let n_parts = self.n_partitions();
-        let mut layer_dirs = Vec::new();
-        for part in 0..n_parts {
-            let index_dir = self.partition().part_dir(part).join(INDEX_SUBDIR);
-            if !index_dir.exists() {
-                continue;
+/// Every (partition, layer) directory carrying a sibling annex, checked
+/// up front so a missing one is reported before any real work starts.
+/// Shared by every sibling-annex consumer's extension-trait impl (`alignment`,
+/// `build`, `cardinality`, `distance`, `stats`) — a free function, not a
+/// `KmerIndex` method, since it is crate-internal only and `KmerIndex` lives
+/// in `obikindex`, a foreign crate from here (orphan rule).
+pub(crate) fn sibling_layer_dirs(index: &KmerIndex) -> OKIResult<Vec<PathBuf>> {
+    let n_parts = index.n_partitions();
+    let mut layer_dirs = Vec::new();
+    for part in 0..n_parts {
+        let index_dir = index.partition().part_dir(part).join(INDEX_SUBDIR);
+        if !index_dir.exists() {
+            continue;
+        }
+        let meta = PartitionMeta::load(&index_dir).map_err(olm_to_ok)?;
+        for l in 0..meta.n_layers {
+            let layer_dir = index_dir.join(format!("layer_{l}"));
+            let annex_path = layer_dir.join(ANNEX_FILE_NAME);
+            if !annex_path.exists() {
+                return Err(OKIError::InvalidInput(format!(
+                    "no sibling annex at {} — run build_sibling_annex first",
+                    annex_path.display()
+                )));
             }
-            let meta = PartitionMeta::load(&index_dir).map_err(olm_to_ok)?;
-            for l in 0..meta.n_layers {
-                let layer_dir = index_dir.join(format!("layer_{l}"));
-                let annex_path = layer_dir.join(ANNEX_FILE_NAME);
-                if !annex_path.exists() {
-                    return Err(OKIError::InvalidInput(format!(
-                        "no sibling annex at {} — run build_sibling_annex first",
-                        annex_path.display()
-                    )));
-                }
-                layer_dirs.push(layer_dir);
-            }
+            layer_dirs.push(layer_dir);
         }
-        Ok(layer_dirs)
     }
+    Ok(layer_dirs)
 }
 
 /// Read-only state shared (via `Arc`) across every pipeline worker
 /// generating this layer's batches — opened once, not per batch. No `cache`
 /// here: generation never touches the cross-partition cache, only this
-/// layer's own already-open matrix. No `annex` either — the filter step
-/// that builds `minorant_slots` already carries each slot's mask through,
-/// so a worker never needs to re-read it.
+/// layer's own already-open matrix. No separate MPHF/`slot_kmer` either —
+/// `mat` (a `Layer<D>`) already bundles the MPHF, and each `SiblingEntry`
+/// arrives with its kmer and mask already in hand from `iter_minorants_batch`.
 struct LayerCtx {
-    slot_kmer: Vec<Option<CanonicalKmer>>,
     mat: Mat,
     n_parts: usize,
     n_genomes: usize,
@@ -118,10 +120,11 @@ struct LayerCtx {
 
 struct SourceBatch {
     start_family_idx: usize,
-    /// `(slot, mask)` — the mask is carried through from the filter step
-    /// below rather than re-read from the annex per batch; it's the same
-    /// byte either way, just already in hand.
-    slots: Vec<(usize, FamilyMask)>,
+    /// One entry per minorant family in this batch, straight from
+    /// `iter_minorants_batch` — `order` (iteration-order index, not an MPHF
+    /// slot; see `docmd/architecture/siblings.md`), `kmer`, and `mask`
+    /// already carried through, no second annex read.
+    entries: Vec<SiblingEntry>,
     _permit: ThrottleGuard,
 }
 
@@ -143,10 +146,10 @@ enum FamData {
     Generated(GeneratedBatch),
 }
 
-/// Visits every minorant family of one layer, in slot order, batched
+/// Visits every minorant family of one layer, in iteration order, batched
 /// [`FAMILY_BATCH`] at a time — see the module docs for why generation and
 /// resolution use different concurrency. `on_family` is called once per
-/// family, in slot order, with its own annex mask and its per-genome
+/// family, in iteration order, with its own annex mask and its per-genome
 /// base-presence (`genome_mask[g]`: bit `b` set iff genome `g` carries the
 /// member whose own canonical central base is `b`), backed by a scratch
 /// buffer reused across every call — callers that need to keep data past
@@ -162,59 +165,38 @@ pub(super) fn scan_layer_families(
 ) -> OKIResult<()> {
     let index_dir = layer_dir.parent().expect("layer_dir has a parent index dir");
     let meta = PartitionMeta::load(index_dir).map_err(olm_to_ok)?;
-    let annex = SiblingAnnex::open(&layer_dir.join(ANNEX_FILE_NAME))?;
-    let mphf = MphfLayer::open(layer_dir, &meta.mode).map_err(olm_to_ok)?;
-
-    // `MphfLayer::kmer_at` — direct slot -> k-mer reconstruction (evidence +
-    // direct-access unitigs, no MPHF hashing, no file scan) instead of the
-    // previous scan-`unitigs.bin`-and-hash-every-k-mer-forward approach,
-    // which redundantly re-read the same data `mphf.find()` itself already
-    // reads through `evidence`/`unitigs` to verify each hit.
-    let slot_kmer: Vec<Option<CanonicalKmer>> = (0..annex.len()).map(|slot| mphf.kmer_at(slot)).collect();
+    let annex = Arc::new(SiblingAnnex::open(&layer_dir.join(ANNEX_FILE_NAME))?);
 
     let use_counts = with_counts && layer_dir.join("counts").exists();
     let mat = if use_counts {
-        Mat::Count(PersistentCompactIntMatrix::open(layer_dir)?)
+        Mat::Count(Layer::<PersistentCompactIntMatrix>::open(layer_dir, &meta.mode).map_err(olm_to_ok)?)
     } else {
-        Mat::Presence(PersistentBitMatrix::open(layer_dir)?)
+        Mat::Presence(Layer::<PersistentBitMatrix>::open(layer_dir, &meta.mode).map_err(olm_to_ok)?)
     };
     let n_cols = mat.n_cols().min(n_genomes);
 
-    // Minorant slots, in order, mask carried along — the flag is already
-    // stored in the annex (set once, at construction — see
-    // `build_layer_sibling_annex`), no need to re-derive it from the kmer
-    // here, and no need for the pipeline workers below to re-read the same
-    // byte from the annex a second time. `slot_kmer[s]` is still required
-    // to exist (used later for `central_canonical_neighbors()`), but not
-    // for this check.
-    let minorant_slots: Vec<(usize, FamilyMask)> = (0..annex.len())
-        .filter_map(|s| {
-            let mask = annex.get(s)?;
-            (slot_kmer[s].is_some() && mask.is_minorant()).then_some((s, mask))
-        })
-        .collect();
-    let total_families = minorant_slots.len();
-    if total_families == 0 {
-        return Ok(());
-    }
+    let ctx = Arc::new(LayerCtx { mat, n_parts, n_genomes, n_cols, k });
 
-    let ctx = Arc::new(LayerCtx { slot_kmer, mat, n_parts, n_genomes, n_cols, k });
-
-    let mut offset = 0usize;
-    let batches: Vec<(usize, Vec<(usize, FamilyMask)>)> = minorant_slots
-        .chunks(FAMILY_BATCH)
-        .map(|chunk| {
-            let start = offset;
-            offset += chunk.len();
-            (start, chunk.to_vec())
-        })
-        .collect();
+    // Streamed straight from `iter_minorants_batch` (zips this layer's own
+    // `iter_kmers()` with the annex, both in iteration order — never an
+    // MPHF slot; see `docmd/architecture/siblings.md`) — never collected
+    // into a `Vec` first: a layer can hold billions of k-mers, so
+    // materialising every minorant family up front is exactly the memory
+    // blowup an earlier version of this traversal was rewritten to avoid
+    // (see the module docs). `.scan()` computes each batch's starting
+    // family index lazily, mirroring what the eager `chunks()`+running
+    // `offset` used to do.
+    let batches = ctx.mat.iter_minorants_batch(annex, FAMILY_BATCH).scan(0usize, |offset, batch| {
+        let start = *offset;
+        *offset += batch.len();
+        Some((start, batch))
+    });
 
     let n_workers = obisys::effective_parallelism();
     let capacity = 4;
-    let throttled = throttle(batches.into_iter(), n_workers).map(|t| SourceBatch {
+    let throttled = throttle(batches, n_workers).map(|t| SourceBatch {
         start_family_idx: t.item.0,
-        slots: t.item.1,
+        entries: t.item.1,
         _permit: t.guard,
     });
 
@@ -224,17 +206,18 @@ pub(super) fn scan_layer_families(
         | {
             move |batch: SourceBatch| -> GeneratedBatch {
                 let ctx = &worker_ctx;
-                let n = batch.slots.len();
+                let n = batch.entries.len();
                 let mut masks = Vec::with_capacity(n);
                 let mut bases = Vec::with_capacity(n);
                 let mut genome_mask = vec![0u8; n * ctx.n_genomes];
                 let mut outgoing: Vec<Vec<(CanonicalKmer, usize, u8)>> = (0..ctx.n_parts).map(|_| Vec::new()).collect();
 
                 // Pass 1: cheap, no matrix access — own base and this
-                // batch's cross-partition queries. Mask already in hand
-                // from the filter step, no second annex read.
-                for (i, &(fslot, mask)) in batch.slots.iter().enumerate() {
-                    let kmer = ctx.slot_kmer[fslot].expect("minorant slot has a kmer");
+                // batch's cross-partition queries. Kmer and mask already in
+                // hand from `iter_minorants_batch`, no second annex read,
+                // no slot lookup needed for this pass.
+                for (i, entry) in batch.entries.iter().enumerate() {
+                    let (kmer, mask) = (entry.kmer, entry.mask);
                     masks.push(mask);
                     let base = central_base(kmer, ctx.k);
                     bases.push(base);
@@ -246,7 +229,7 @@ pub(super) fn scan_layer_families(
                         if !mask.has(b) {
                             continue;
                         }
-                        let dest = partition_of(other, ctx.n_parts);
+                        let dest = other.partition(ctx.n_parts);
                         outgoing[dest].push((other, i, b));
                     }
                 }
@@ -254,14 +237,21 @@ pub(super) fn scan_layer_families(
                 // Pass 2: genome-major, not family-major — `mat` is stored
                 // one contiguous block per genome (column), slot as the
                 // offset within it (see `PartitionCache::find_presence_batch`'s
-                // docs for the full rationale). `batch.slots` is already
-                // sorted (a contiguous sub-range of the layer's sorted
-                // minorant-slot list), so this sweeps each column roughly
-                // in slot order instead of jumping between all `n_cols`
-                // columns once per family.
-                for g in 0..ctx.n_cols {
-                    for (i, &(fslot, _)) in batch.slots.iter().enumerate() {
-                        if ctx.mat.carries(g, fslot) {
+                // docs for the full rationale). `fill_sub_matrix_carries`
+                // sorts the slots internally for a sequential mmap sweep per
+                // column, then restores this batch's order — no hand-rolled
+                // sort/genome-major loop needed here. The presence/count
+                // matrix is still MPHF-slot-indexed (unlike the annex), so
+                // each entry's kmer is mapped to its slot via `index_batch`
+                // — a pure MPHF lookup, no evidence check, since these are
+                // this layer's own kmers, known members by construction.
+                let kmers: Vec<CanonicalKmer> = batch.entries.iter().map(|e| e.kmer).collect();
+                let slots = ctx.mat.index_batch(&kmers);
+                let mut carries: Vec<Vec<bool>> = (0..ctx.n_cols).map(|_| Vec::new()).collect();
+                ctx.mat.fill_sub_matrix_carries(&slots, &mut carries);
+                for (g, col) in carries.iter().enumerate() {
+                    for (i, &carries_it) in col.iter().enumerate() {
+                        if carries_it {
                             genome_mask[i * ctx.n_genomes + g] |= 1 << bases[i];
                         }
                     }
@@ -305,7 +295,7 @@ pub(super) fn scan_layer_families(
             next_expected += n;
         }
     }
-    debug_assert_eq!(next_expected, total_families, "every batch must have been replayed");
+    debug_assert!(pending.is_empty(), "every generated batch must have been replayed");
 
     Ok(())
 }
diff --git a/src/obikphylo/src/siblings/helpers.rs b/src/obikphylo/src/siblings/helpers.rs
new file mode 100644
index 00000000..580162b4
--- /dev/null
+++ b/src/obikphylo/src/siblings/helpers.rs
@@ -0,0 +1,23 @@
+use obikseq::CanonicalKmer;
+
+use obicompactvec::FamilyMask;
+
+/// Central-position base of a canonical k-mer, in the fixed 0=A/1=C/2=G/3=T
+/// encoding — the mask's bit index. `k` must be odd (project invariant).
+#[inline]
+pub(super) fn central_base(kmer: CanonicalKmer, k: usize) -> u8 {
+    kmer.nucleotide((k - 1) / 2)
+}
+
+/// Is `kmer` the minorant of its family, given the family's presence mask?
+/// Regenerates the family's 4 canonical forms from `kmer` itself (cheap, no
+/// lookup — see the design doc's "Definitions" section for why this is
+/// always safe: the set of 4 forms is invariant regardless of which member
+/// you start from), and compares the raw encodings of whichever are marked
+/// present in `mask`.
+pub(super) fn is_minorant(kmer: CanonicalKmer, mask: FamilyMask, k: usize) -> bool {
+    kmer.central_canonical_neighbors().into_iter().all(|other| {
+        other == kmer || !mask.has(central_base(other, k)) || kmer.raw() <= other.raw()
+    })
+}
+
diff --git a/src/obikphylo/src/siblings/iter.rs b/src/obikphylo/src/siblings/iter.rs
new file mode 100644
index 00000000..20bea078
--- /dev/null
+++ b/src/obikphylo/src/siblings/iter.rs
@@ -0,0 +1,172 @@
+//! Phylo/sibling-domain iteration over a layer — an extension trait, not a
+//! new field on `MphfLayer`/`Layer<D>`: "family"/"minorant" are phylo
+//! concepts, `obilayeredmap` stays kmer/slot-mapping only (see
+//! `docmd/architecture/siblings.md`).
+//!
+//! The sibling annex is persisted in the same order as `iter_kmers()`
+//! (`build_sibling_annex`, see `build.rs`), so pairing them is a plain zip —
+//! no MPHF, no slot, no `kmer_at`. Both sides are already `Send + 'static`
+//! (`KmerIter` owns an `Arc<UnitigFileReader>` clone; `SiblingAnnex` is
+//! mmap-backed and handed in as an `Arc` by the caller), so `SiblingIter`
+//! streams straight from disk and can be fed to `obipipeline` batch by
+//! batch — never collected whole into memory (see the project's "no full
+//! collect" rule).
+//!
+//! Four iterator types, deliberately mirroring `obilayeredmap`'s own
+//! `KmerIter`/`KmerBatchIter` pair (single item vs. `Vec` batch) — plus the
+//! minorant-filtered variant of each, since "all siblings" and "one row per
+//! family" are both common cases:
+//!
+//! |            | all entries      | minorants only     |
+//! |------------|-------------------|---------------------|
+//! | single     | [`SiblingIter`]   | [`MinorantIter`]    |
+//! | batch      | [`SiblingBatchIter`] | [`MinorantBatchIter`] |
+//!
+//! No separate "enumerate" variant (unlike `KmerIter`/`enumerate_kmers`):
+//! [`SiblingEntry`] already carries `order` for free, since pairing with
+//! the annex requires it anyway.
+
+use std::sync::Arc;
+
+use obicompactvec::{FamilyMask, SiblingAnnex};
+use obikseq::CanonicalKmer;
+use obilayeredmap::{KmerIter, Layer, LayerData};
+
+/// One layer entry: a k-mer's position in the layer's iteration order (the
+/// same index the sibling annex is keyed on — not an MPHF slot), the k-mer
+/// itself, and its family mask.
+#[derive(Debug, Clone, Copy)]
+pub struct SiblingEntry {
+    pub order: usize,
+    pub kmer: CanonicalKmer,
+    pub mask: FamilyMask,
+}
+
+/// Streams `(order, kmer, mask)` triples for one layer, in iteration order.
+/// Produced by [`SiblingLayerExt::iter_siblings`].
+pub struct SiblingIter {
+    kmers: KmerIter,
+    annex: Arc<SiblingAnnex>,
+    order: usize,
+}
+
+impl Iterator for SiblingIter {
+    type Item = SiblingEntry;
+
+    fn next(&mut self) -> Option<Self::Item> {
+        loop {
+            let kmer = self.kmers.next()?;
+            let order = self.order;
+            self.order += 1;
+            // `None` means "not yet computed" (see `SiblingAnnex` module
+            // docs) — shouldn't happen against a fully-built annex, but
+            // skip rather than misalign the two streams if it does.
+            if let Some(mask) = self.annex.get(order) {
+                return Some(SiblingEntry { order, kmer, mask });
+            }
+        }
+    }
+}
+
+/// Batches of [`SiblingIter`]'s entries, `batch_size` at a time — the last
+/// batch may be shorter. Produced by [`SiblingLayerExt::iter_siblings_batch`].
+pub struct SiblingBatchIter {
+    inner: SiblingIter,
+    batch_size: usize,
+}
+
+impl Iterator for SiblingBatchIter {
+    type Item = Vec<SiblingEntry>;
+
+    fn next(&mut self) -> Option<Self::Item> {
+        collect_batch(&mut self.inner, self.batch_size)
+    }
+}
+
+/// Like [`SiblingIter`], filtered to the minorant of each family — the
+/// common case, since a family is tallied once, at its minorant. Produced
+/// by [`SiblingLayerExt::iter_minorants`].
+pub struct MinorantIter {
+    inner: SiblingIter,
+}
+
+impl Iterator for MinorantIter {
+    type Item = SiblingEntry;
+
+    fn next(&mut self) -> Option<Self::Item> {
+        self.inner.by_ref().find(|e| e.mask.is_minorant())
+    }
+}
+
+/// Batches of [`MinorantIter`]'s entries, `batch_size` at a time — the last
+/// batch may be shorter. Produced by
+/// [`SiblingLayerExt::iter_minorants_batch`].
+pub struct MinorantBatchIter {
+    inner: MinorantIter,
+    batch_size: usize,
+}
+
+impl Iterator for MinorantBatchIter {
+    type Item = Vec<SiblingEntry>;
+
+    fn next(&mut self) -> Option<Self::Item> {
+        collect_batch(&mut self.inner, self.batch_size)
+    }
+}
+
+/// Shared by [`SiblingBatchIter`] and [`MinorantBatchIter`] — pull up to
+/// `batch_size` items, `None` once the source is exhausted with nothing left.
+fn collect_batch<I: Iterator>(inner: &mut I, batch_size: usize) -> Option<Vec<I::Item>> {
+    let mut batch = Vec::with_capacity(batch_size);
+    for _ in 0..batch_size {
+        match inner.next() {
+            Some(item) => batch.push(item),
+            None => break,
+        }
+    }
+    if batch.is_empty() { None } else { Some(batch) }
+}
+
+/// Adds phylo/sibling iteration to any `Layer<D>` — the extension that
+/// turns a plain layer into a "sibling layer". Generic over `D`
+/// (`LayerData`) rather than implemented once per matrix kind: kmer
+/// iteration doesn't depend on the data payload, and `Layer<D>` already
+/// delegates `iter_kmers`/`index`/`index_batch` to its inner MPHF for every
+/// `D` — reusing that instead of going back through a separate `MphfLayer`.
+pub trait SiblingLayerExt {
+    /// Zip this layer's k-mers with their sibling-annex entry, in iteration
+    /// order. `annex` must have been built from this same layer (its length
+    /// must match the layer's k-mer count).
+    fn iter_siblings(&self, annex: Arc<SiblingAnnex>) -> SiblingIter;
+
+    /// Like [`iter_siblings`](Self::iter_siblings), yielding `batch_size`
+    /// entries at a time.
+    fn iter_siblings_batch(&self, annex: Arc<SiblingAnnex>, batch_size: usize) -> SiblingBatchIter;
+
+    /// Like [`iter_siblings`](Self::iter_siblings), filtered to the
+    /// minorant of each family — the common case, since a family is
+    /// tallied once, at its minorant.
+    fn iter_minorants(&self, annex: Arc<SiblingAnnex>) -> MinorantIter;
+
+    /// Like [`iter_minorants`](Self::iter_minorants), yielding `batch_size`
+    /// minorants at a time.
+    fn iter_minorants_batch(&self, annex: Arc<SiblingAnnex>, batch_size: usize) -> MinorantBatchIter;
+}
+
+impl<D: LayerData> SiblingLayerExt for Layer<D> {
+    fn iter_siblings(&self, annex: Arc<SiblingAnnex>) -> SiblingIter {
+        SiblingIter { kmers: self.iter_kmers(), annex, order: 0 }
+    }
+
+    fn iter_siblings_batch(&self, annex: Arc<SiblingAnnex>, batch_size: usize) -> SiblingBatchIter {
+        SiblingBatchIter { inner: self.iter_siblings(annex), batch_size }
+    }
+
+    fn iter_minorants(&self, annex: Arc<SiblingAnnex>) -> MinorantIter {
+        MinorantIter { inner: self.iter_siblings(annex) }
+    }
+
+    fn iter_minorants_batch(&self, annex: Arc<SiblingAnnex>, batch_size: usize) -> MinorantBatchIter {
+        MinorantBatchIter { inner: self.iter_minorants(annex), batch_size }
+    }
+}
diff --git a/src/obikindex/src/siblings/mod.rs b/src/obikphylo/src/siblings/mod.rs
similarity index 86%
rename from src/obikindex/src/siblings/mod.rs
rename to src/obikphylo/src/siblings/mod.rs
index a91711a1..cd3f5da8 100644
--- a/src/obikindex/src/siblings/mod.rs
+++ b/src/obikphylo/src/siblings/mod.rs
@@ -12,7 +12,7 @@
 //! in the current multi-genome index — a property of the whole index, not
 //! of any one genome. Sibling count and minorant are *derived* from the
 //! mask by callers, not stored (see `FamilyMask` and
-//! [`sibling_annex_stats`](crate::index::KmerIndex::sibling_annex_stats)
+//! [`sibling_annex_stats`](stats::SiblingStatsExt::sibling_annex_stats)
 //! below).
 //!
 //! Per layer, an `obipipeline` batch transform (throttled — see
@@ -55,15 +55,16 @@ mod stats;
 #[cfg(test)]
 mod tests;
 
-pub use alignment::SnpAlignment;
-pub use cardinality::CardinalityTally;
-pub use distance::{BasePairTally, RawSnpDistanceOutput};
-pub use iter::{SiblingEntry, SiblingIter, SiblingLayerExt};
-pub use stats::SiblingAnnexStats;
+pub use alignment::{SnpAlignment, SnpAlignmentExt};
+pub use build::SiblingAnnexBuildExt;
+pub use cardinality::{CardinalityExt, CardinalityTally};
+pub use distance::{BasePairTally, DistanceExt, RawSnpDistanceOutput};
+pub use iter::{MinorantBatchIter, MinorantIter, SiblingBatchIter, SiblingEntry, SiblingIter, SiblingLayerExt};
+pub use stats::{SiblingAnnexStats, SiblingStatsExt};
 
 use obilayeredmap::OLMError;
 
-use crate::error::OKIError;
+use obikindex::OKIError;
 
 pub(super) const INDEX_SUBDIR: &str = "index";
 pub(super) const ANNEX_FILE_NAME: &str = "siblings.psib";
diff --git a/src/obikindex/src/siblings/stats.rs b/src/obikphylo/src/siblings/stats.rs
similarity index 80%
rename from src/obikindex/src/siblings/stats.rs
rename to src/obikphylo/src/siblings/stats.rs
index 0ca0caf9..9cd59da2 100644
--- a/src/obikindex/src/siblings/stats.rs
+++ b/src/obikphylo/src/siblings/stats.rs
@@ -4,17 +4,17 @@ use obicompactvec::SiblingAnnex;
 use obikpartitionner::KmerPartition;
 use obisys::progress_bar;
 
-use crate::error::{OKIError, OKIResult};
-use crate::index::KmerIndex;
+use obikindex::{OKIError, OKIResult};
+use obikindex::KmerIndex;
 
 use super::ANNEX_FILE_NAME;
 use super::cache::PartitionCache;
 use super::family_scan::scan_layer_families;
 
 /// Distribution of family sizes (1-4), read back from an already-built
-/// annex (see [`KmerIndex::build_sibling_annex`]) plus the index's
-/// presence/count data — a separate, occasional diagnostic pass, not fused
-/// into construction.
+/// annex (see [`super::build::SiblingAnnexBuildExt::build_sibling_annex`])
+/// plus the index's presence/count data — a separate, occasional diagnostic
+/// pass, not fused into construction.
 ///
 /// Every count here is **per family, not per slot**: a family with `F`
 /// members occupies `F` annex slots (one per observed member), all sharing
@@ -33,7 +33,9 @@ pub struct SiblingAnnexStats {
     pub per_genome: Vec<[u64; 4]>,
 }
 
-impl KmerIndex {
+/// Adds [`sibling_family_size_histogram`](Self::sibling_family_size_histogram)
+/// and [`sibling_annex_stats`](Self::sibling_annex_stats) to `KmerIndex`.
+pub trait SiblingStatsExt {
     /// The global family-size histogram alone (`SiblingAnnexStats::counts`,
     /// no `per_genome`) — reads only the already-built annex (`mask.siblings()`
     /// + `mask.is_minorant()`, 1 byte/slot, mmap'd), nothing else: no
@@ -52,8 +54,19 @@ impl KmerIndex {
     /// cost to get there too; use this when only the global histogram is
     /// needed. Requires an annex built after the minorant flag was added —
     /// re-run `build_sibling_annex` if this reads as all-zero on an older one.
-    pub fn sibling_family_size_histogram(&self) -> OKIResult<[u64; 4]> {
-        let layer_dirs = self.sibling_layer_dirs()?;
+    fn sibling_family_size_histogram(&self) -> OKIResult<[u64; 4]>;
+
+    /// Tally the family-size distribution of an already-built annex
+    /// (globally, and per genome), counting each family once (at its
+    /// minorant slot). Errors if
+    /// [`build_sibling_annex`](super::build::SiblingAnnexBuildExt::build_sibling_annex)
+    /// has not been run on this index first.
+    fn sibling_annex_stats(&self) -> OKIResult<SiblingAnnexStats>;
+}
+
+impl SiblingStatsExt for KmerIndex {
+    fn sibling_family_size_histogram(&self) -> OKIResult<[u64; 4]> {
+        let layer_dirs = super::family_scan::sibling_layer_dirs(self)?;
 
         let mut counts = [0u64; 4];
         for layer_dir in &layer_dirs {
@@ -70,16 +83,10 @@ impl KmerIndex {
         Ok(counts)
     }
 
-    /// Tally the family-size distribution of an already-built annex
-    /// (globally, and per genome), counting each family once (at its
-    /// minorant slot). Errors if [`build_sibling_annex`] has not been run on
-    /// this index first.
-    ///
-    /// [`build_sibling_annex`]: Self::build_sibling_annex
-    pub fn sibling_annex_stats(&self) -> OKIResult<SiblingAnnexStats> {
+    fn sibling_annex_stats(&self) -> OKIResult<SiblingAnnexStats> {
         let n_parts = self.n_partitions();
-        let n_genomes = self.meta.genomes.len();
-        let with_counts = self.meta.config.with_counts;
+        let n_genomes = self.meta().genomes.len();
+        let with_counts = self.meta().config.with_counts;
         let k = self.kmer_size();
         let n_bits = n_parts.trailing_zeros() as usize;
 
@@ -87,14 +94,14 @@ impl KmerIndex {
         // why re-opening per lookup (or per call to a batching helper) is
         // not good enough on a real index.
         let partition = KmerPartition::open_with_config(
-            &self.root_path,
+            self.root_path(),
             self.kmer_size(),
             self.minimizer_size(),
             n_bits,
         )
         .map_err(OKIError::Partition)?;
         let cache = Arc::new(PartitionCache::build(&partition, n_parts, with_counts)?);
-        let layer_dirs = self.sibling_layer_dirs()?;
+        let layer_dirs = super::family_scan::sibling_layer_dirs(self)?;
 
         // One layer at a time, not parallelised across layers — see
         // `snp_pseudo_alignment`'s comment for why `par_iter()` over layers
diff --git a/src/obikindex/src/siblings/tests.rs b/src/obikphylo/src/siblings/tests.rs
similarity index 96%
rename from src/obikindex/src/siblings/tests.rs
rename to src/obikphylo/src/siblings/tests.rs
index 866464e5..5aaca00b 100644
--- a/src/obikindex/src/siblings/tests.rs
+++ b/src/obikphylo/src/siblings/tests.rs
@@ -8,11 +8,14 @@ use obilayeredmap::meta::PartitionMeta;
 use obisys::Reporter;
 use tempfile::tempdir;
 
-use crate::index::KmerIndex;
-use crate::meta::{GenomeInfo, IndexConfig};
-use crate::merge::MergeMode;
+use obikindex::{GenomeInfo, IndexConfig, KmerIndex, MergeMode};
 
+use super::alignment::SnpAlignmentExt;
+use super::build::SiblingAnnexBuildExt;
+use super::cardinality::CardinalityExt;
+use super::distance::DistanceExt;
 use super::helpers::is_minorant;
+use super::stats::SiblingStatsExt;
 use super::{ANNEX_FILE_NAME, INDEX_SUBDIR};
 
 // k must be >= 11 (project constraint, "k ∈ [11,31]"); k=11, level_max=1,
@@ -222,7 +225,7 @@ fn family_scan_consumers_agree_on_one_sibling_each() {
 
     // Merge doesn't promise to preserve source order, so resolve each
     // genome's index by label rather than assuming g1 -> 0, g2 -> 1.
-    let idx_of = |label: &str| merged.meta.genomes.iter().position(|g| g.label == label).unwrap();
+    let idx_of = |label: &str| merged.meta().genomes.iter().position(|g| g.label == label).unwrap();
     let (i1, i2) = (idx_of("g1"), idx_of("g2"));
 
     // snp_pseudo_alignment: one variable family, one column — g1's row
diff --git a/src/obikseq/src/kmer.rs b/src/obikseq/src/kmer.rs
index 365a7851..0fe41101 100644
--- a/src/obikseq/src/kmer.rs
+++ b/src/obikseq/src/kmer.rs
@@ -367,6 +367,50 @@ impl<L: KmerLength> CanonicalKmerOf<L> {
     pub fn into_kmer(self) -> KmerOf<L> {
         KmerOf(self.0, PhantomData)
     }
+
+    /// This k-mer's own minimiser — as a standalone unit, not part of a
+    /// streamed sequence. Enumerates all `L::len() - MLen::len() + 1`
+    /// windows directly on the packed 2-bit representation (no ASCII
+    /// round-trip, no rolling state, no entropy tracking) and keeps the one
+    /// with the lowest [`hash_kmer`] — the same selection rule
+    /// `obiskbuilder::rolling_stat::RollingStat` computes incrementally
+    /// along a sequence, replicated here in `O(k)` pure bit arithmetic for
+    /// a single isolated k-mer (the case a streaming rolling scan is
+    /// unnecessary machinery for). Ties (equal hash) keep the last
+    /// (highest-position) window, matching `RollingStat`'s monotonic-deque
+    /// eviction rule (`>=` pops the previous record) — a formal detail, not
+    /// a practical concern: a `mix64` collision between two distinct
+    /// m-mers is vanishingly unlikely.
+    pub fn minimizer(&self) -> Minimizer {
+        let k = L::len();
+        let ml = MLen::len();
+        let rc = self.revcomp().raw();
+        let mut best_canon: RawKmer = 0;
+        let mut best_hash = u64::MAX;
+        for p in 0..=(k - ml) {
+            let fwd = (self.0 << (2 * p)) >> (KMER_BITS - 2 * ml);
+            let rev = (rc << (2 * (k - ml - p))) >> (KMER_BITS - 2 * ml);
+            let canon = fwd.min(rev);
+            let hash = hash_kmer(canon << (KMER_BITS - 2 * ml));
+            if hash < best_hash {
+                best_hash = hash;
+                best_canon = canon;
+            }
+        }
+        Minimizer::from_raw_unchecked(best_canon << (KMER_BITS - 2 * ml))
+    }
+
+    /// Destination partition for this k-mer, using the project-wide routing
+    /// rule (`minimizer().seq_hash() & mask`) — the same rule
+    /// `KmerPartition`/`RoutableSuperKmer` apply to k-mers read from a
+    /// streamed sequence, here for a standalone k-mer (e.g. a synthetic
+    /// variant generated outside any sequence). `n_partitions` must be a
+    /// power of two.
+    #[inline]
+    pub fn partition(&self, n_partitions: usize) -> usize {
+        let mask = (n_partitions as u64) - 1;
+        (self.minimizer().seq_hash() & mask) as usize
+    }
 }
 
 impl<L: KmerLength> Sequence for CanonicalKmerOf<L> {
diff --git a/src/obilayeredmap/src/layer.rs b/src/obilayeredmap/src/layer.rs
index 44797318..c2989a04 100644
--- a/src/obilayeredmap/src/layer.rs
+++ b/src/obilayeredmap/src/layer.rs
@@ -72,6 +72,15 @@ impl<D: LayerData> Layer<D> {
         self.mphf.find(kmer).map(|slot| Hit { slot, data: self.data.read(slot) })
     }
 
+    /// MPHF + evidence membership check only — no data read. For callers
+    /// that batch many lookups before touching the matrix at all (e.g. to
+    /// group hits by column for a later `sub_matrix`/`fill_sub_matrix`
+    /// sweep), so a plain `query` reading — and discarding — a full row
+    /// per lookup would be wasted work.
+    pub fn find_slot(&self, kmer: CanonicalKmer) -> Option<usize> {
+        self.mphf.find(kmer)
+    }
+
     pub fn n(&self) -> usize { self.mphf.n() }
 
     /// Raw MPHF lookup: kmer → slot, no membership check.
@@ -187,6 +196,11 @@ impl Layer<PersistentCompactIntMatrix> {
             .map_err(OLMError::Io)
     }
 
+    /// Number of genome columns in this layer's count matrix.
+    pub fn n_cols(&self) -> usize {
+        self.data.n_cols()
+    }
+
     /// Extract a sub-matrix of counts for the rows at `slots`.
     ///
     /// Returns a column-first `Vec<Vec<u32>>`: one inner `Vec` per genome
@@ -218,6 +232,14 @@ impl Layer<PersistentBitMatrix> {
             .map_err(OLMError::Io)
     }
 
+    /// Number of genome columns in this layer's presence matrix — see
+    /// `PersistentBitMatrix::n_cols`'s docs for the `Implicit` mono-genome
+    /// special case (always reports `1`, regardless of the index's real
+    /// genome count).
+    pub fn n_cols(&self) -> usize {
+        self.data.n_cols()
+    }
+
     /// Extract a sub-matrix of presence/absence for the rows at `slots`.
     ///
     /// Returns a column-first `Vec<Vec<bool>>`: one inner `Vec` per genome
-- 
2.54.0


From d2548e8c33d6c18d1282a7a3c8bcc5e9711ee2c4 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Fri, 14 Aug 2026 15:52:31 +0200
Subject: [PATCH 24/46] feat(progress): implement configurable ETA throttling

Introduces timing constants and atomic fields to control ETA calculation intervals. Replaces the static template placeholder with dynamic messages, delegating formatting to a new helper that applies throttling thresholds and suppresses automatic updates during custom message hold periods.
---
 src/obisys/src/progress.rs | 81 +++++++++++++++++++++++++++++++++-----
 1 file changed, 72 insertions(+), 9 deletions(-)

diff --git a/src/obisys/src/progress.rs b/src/obisys/src/progress.rs
index 3985c345..f15547d1 100644
--- a/src/obisys/src/progress.rs
+++ b/src/obisys/src/progress.rs
@@ -5,18 +5,20 @@ use indicatif::{ProgressBar, ProgressStyle};
 use tracing::{debug, info};
 
 const BRAILLE: &[&str] = &["⠋", "⠙", "⠹", "⠸", "⠼", "⠴", "⠦", "⠧", "⠇", "⠏"];
+const ETA_REFRESH_MS: u64 = 500;
+const ETA_MIN_ELAPSED_MS: u64 = 1000;
+const ETA_CUSTOM_HOLD_MS: u64 = 2000;
 
-/// Wrapper around `ProgressBar` that emits `tracing` events when stderr is not
-/// a TTY (e.g. HPC job logs): every 10% for bounded bars, every ~10 s for
-/// spinners (throttled on `set_message`).
 pub struct TracedBar {
     pb: ProgressBar,
     label: String,
     unit: String,
-    total: u64,             // 0 for spinners
-    start: Instant,         // creation time, for spinner throttling
-    last_pct: AtomicU64,    // last emitted 10%-bucket (1..=10), 0 = none yet
-    last_log_ms: AtomicU64, // ms since `start` at last spinner log
+    total: u64,
+    start: Instant,
+    last_pct: AtomicU64,
+    last_log_ms: AtomicU64,
+    last_eta_refresh: AtomicU64,
+    last_custom_msg_ms: AtomicU64,
 }
 
 impl TracedBar {
@@ -40,15 +42,60 @@ impl TracedBar {
                 );
             }
         }
+
+        if !self.pb.is_hidden() && self.total > 0 {
+            self.maybe_update_eta();
+        }
+    }
+
+    fn maybe_update_eta(&self) {
+        let now_ms = self.start.elapsed().as_millis() as u64;
+
+        if now_ms < ETA_MIN_ELAPSED_MS {
+            return;
+        }
+
+        let last = self.last_eta_refresh.load(Ordering::Relaxed);
+        if now_ms < last + ETA_REFRESH_MS {
+            return;
+        }
+
+        let last_custom = self.last_custom_msg_ms.load(Ordering::Relaxed);
+        if now_ms < last_custom + ETA_CUSTOM_HOLD_MS {
+            return;
+        }
+
+        let pos = self.pb.position();
+        let remaining = self.total - pos;
+
+        if pos == 0 || remaining == 0 {
+            return;
+        }
+
+        let elapsed_secs = self.start.elapsed().as_secs_f64();
+        let avg_rate = pos as f64 / elapsed_secs;
+        let eta_secs = remaining as f64 / avg_rate;
+
+        self.pb.set_message(format!("(eta: {})", fmt_secs(eta_secs)));
+
+        let _ = self.last_eta_refresh.compare_exchange(
+            last,
+            now_ms,
+            Ordering::Relaxed,
+            Ordering::Relaxed,
+        );
     }
 
     pub fn set_message(&self, msg: impl Into<String>) {
         let msg = msg.into();
+        self.last_custom_msg_ms.store(
+            self.start.elapsed().as_millis() as u64,
+            Ordering::Relaxed,
+        );
         if self.pb.is_hidden() {
             if self.total > 0 {
                 debug!(stage = %self.label, "{msg}");
             } else {
-                // spinner: throttle to ~10 s
                 let now_ms = self.start.elapsed().as_millis() as u64;
                 let last = self.last_log_ms.load(Ordering::Relaxed);
                 if now_ms >= last + 10_000
@@ -69,6 +116,18 @@ impl TracedBar {
     }
 }
 
+fn fmt_secs(s: f64) -> String {
+    if s >= 3600.0 {
+        format!("{:.0}h", s / 3600.0)
+    } else if s >= 60.0 {
+        format!("{:.0}min", s / 60.0)
+    } else if s >= 1.0 {
+        format!("{:.1}s", s)
+    } else {
+        format!("{:.0}ms", s * 1000.0)
+    }
+}
+
 /// Spinner with the standard project look: `⠋ label — msg  0s`.
 /// Caller updates the message with `pb.set_message(...)`.
 pub fn spinner(label: &str) -> TracedBar {
@@ -87,6 +146,8 @@ pub fn spinner(label: &str) -> TracedBar {
         start: Instant::now(),
         last_pct: AtomicU64::new(0),
         last_log_ms: AtomicU64::new(0),
+        last_eta_refresh: AtomicU64::new(0),
+        last_custom_msg_ms: AtomicU64::new(0),
     }
 }
 
@@ -96,7 +157,7 @@ pub fn progress_bar(label: &str, n: u64, unit: &str) -> TracedBar {
     let pb = ProgressBar::new(n);
     pb.set_style(
         ProgressStyle::with_template(&format!(
-            "{{spinner}} {label} — {{bar:40.cyan/blue}} {{pos}}/{{len}} {unit}  {{elapsed}} (eta: {{eta}})"
+            "{{spinner}} {label} — {{bar:40.cyan/blue}} {{pos}}/{{len}} {unit}  {{elapsed}} {{msg}}"
         ))
         .unwrap()
         .tick_strings(BRAILLE),
@@ -110,5 +171,7 @@ pub fn progress_bar(label: &str, n: u64, unit: &str) -> TracedBar {
         start: Instant::now(),
         last_pct: AtomicU64::new(0),
         last_log_ms: AtomicU64::new(0),
+        last_eta_refresh: AtomicU64::new(0),
+        last_custom_msg_ms: AtomicU64::new(0),
     }
 }
-- 
2.54.0


From 32d6720f50964571e1d501afb506cece60c2a199 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Fri, 14 Aug 2026 17:23:59 +0200
Subject: [PATCH 25/46] Fix batch enumeration offsets and refactor sibling
 annex construction

Shifts sibling annex construction from slot-indexed enumeration to iteration-order traversal by correcting cumulative k-mer offset tracking in batch enumeration. Replaces coarse per-partition parallelism with chunked work distribution to prevent thread starvation on skewed partitions. Decouples custom progress messages from ETA updates to eliminate display clobbering during high-frequency callbacks. Adds regression tests validating batch offset correctness, partial batch handling, and iterator-order consistency across layer builds.
---
 docmd/architecture/siblings.md           | 108 ++++++++++++++++++++---
 src/obicompactvec/src/tests/bitvec.rs    |  63 +++++++++++++
 src/obicompactvec/src/tests/intmatrix.rs |  62 ++++++++++++-
 src/obikindex/src/lib.rs                 |   1 +
 src/obikindex/src/numa/runner.rs         |  26 ++++++
 src/obikphylo/src/siblings/build.rs      |  61 +++++++++++--
 src/obikphylo/src/siblings/tests.rs      |  40 +++++++++
 src/obilayeredmap/src/layer.rs           |   2 +-
 src/obilayeredmap/src/mphf_layer.rs      |  14 ++-
 src/obilayeredmap/src/tests/layer.rs     |  75 ++++++----------
 src/obisys/src/progress.rs               |  49 ++++++----
 11 files changed, 413 insertions(+), 88 deletions(-)

diff --git a/docmd/architecture/siblings.md b/docmd/architecture/siblings.md
index b7012bc2..3df7c6aa 100644
--- a/docmd/architecture/siblings.md
+++ b/docmd/architecture/siblings.md
@@ -18,7 +18,8 @@ method that reconstructs a kmer from a bare slot number is wrong by
 construction, regardless of the mechanism used (MPHF re-hash, or evidence
 decode + direct unitig read). See `MphfLayer::kmer_at`
 (`obilayeredmap/src/mphf_layer.rs`) — flagged for removal, currently called
-from `obikindex/siblings/build.rs:122` and `family_scan.rs:173`.
+from `obikphylo/siblings/build.rs` and `family_scan.rs` (since removed — see
+"Pending work" status below).
 
 ## Two pipelines, never mixed
 
@@ -39,7 +40,7 @@ pointless even in `Exact`/`Hybrid` mode since the kmer was already known.
 The sibling annex (`FamilyMask`/`SiblingAnnex`, `.psib`,
 `obicompactvec/src/siblingannex.rs`) records, per kmer, whether it is a
 family minorant and which family members are present in the index. Its only
-consumers (`obikindex/siblings/stats.rs`, `family_scan.rs`) enumerate it
+consumers (`obikphylo/siblings/stats.rs`, `family_scan.rs`) enumerate it
 exhaustively (`0..annex.len()`); no query-pipeline code path touches it.
 
 **Decision**: the annex must be persisted in iteration order, not slot
@@ -66,12 +67,99 @@ partition is unknown) and must keep going through
 `KmerPartition::query_partition_with` (MPHF + evidence), never a raw
 `index()`.
 
-## Pending work
+## Pending work — done
 
-- Remove `MphfLayer::kmer_at`.
-- `siblings/build.rs`: build `slot_kmer`-equivalent via iteration, not
-  `kmer_at`; thread iteration index instead of slot through the
-  variant/reconciliation pipeline; persist the annex in iteration order.
-- `siblings/family_scan.rs`, `stats.rs`: read the annex via zipped
-  iteration (`iter_kmers().zip(annex_iter)`) instead of `0..annex.len()` +
-  `kmer_at`.
+The plan above shipped: `obikphylo` (a new crate — phylo-domain extension
+traits over `obikindex::KmerIndex`/`obilayeredmap::Layer<D>`, replacing the
+old `obikindex::siblings` module) builds and reads the annex purely in
+iteration order (`SiblingLayerExt::iter_siblings`/`iter_minorants`, both with
+batch variants, mirroring `Layer<D>`'s own `KmerIter`/`KmerBatchIter`
+shape). `MphfLayer::kmer_at` has no remaining callers.
+
+A separate, unrelated bug surfaced during this work and was fixed
+(2026-08-14): `MphfLayer::enumerate_kmers_batch` computed its
+`batch_start_index` via the stdlib `.enumerate()` adapter, which counts
+*batches* (0, 1, 2…), not the cumulative k-mer offset the annex is actually
+keyed on — every batch past the first wrote its mask/annex entries at the
+wrong iteration-order position. Fixed by tracking a running offset instead;
+regression tests added (`sibling_annex_no_empty_masks_after_build`,
+`sibling_histogram_does_not_panic_on_partial_last_batch`).
+
+## Performance: `build_sibling_annex` parallelism (2026-08-14)
+
+Investigated on a real multi-genome run (`phyloskims_sal_vac`, k=31/m=11).
+Baseline: mostly one active core, with short multi-core bursts — average
+~3 cores.
+
+**Fixes that helped, kept:**
+
+- `CanonicalKmerOf::minimizer()` (`obikseq/src/kmer.rs`) — a direct O(k)
+  bit-arithmetic minimiser for a single isolated k-mer, replacing a
+  `RollingStat` instance fed byte-by-byte through an ASCII round-trip (used
+  by `helpers::partition_of`, called for every generated family variant).
+  ~3x wall-clock improvement on its own, confirmed by sampling
+  (`obiskbuilder::rolling_stat`/`obikentropy` frames disappeared from the
+  hot path). `CanonicalKmerOf::partition()` added alongside it (wraps
+  `minimizer().seq_hash() & mask`, the same routing rule
+  `KmerPartition`/`RoutableSuperKmer` use).
+- Cross-partition resolution (`outgoing.par_iter()` in
+  `build_layer_sibling_annex`) parallelised at the *partition* level — one
+  Rayon task per non-empty `outgoing[dest]` bucket. For k=31/m=11, a
+  central-base substitution changes the winning minimiser (and thus the
+  destination partition) only when that window overlaps the central base:
+  ~11 of the 21 possible windows do, so ~10/21 (≈48%) of generated variants
+  route right back to the partition already being built. That self bucket
+  ends up far larger than any other, so the per-partition split pinned one
+  thread to it alone while the rest of the pool finished instantly —
+  confirmed by sampling: one thread solid in `MphfLayer::find`, everyone
+  else idle. Fixed by splitting each non-empty bucket into
+  `total_queries / n_workers` (capped 4096) chunks *before* `par_iter()`,
+  preserving per-partition mmap locality (each chunk stays contiguous
+  within one partition) while letting Rayon spread an oversized bucket
+  across several threads. Net effect of both fixes together: ~3 cores
+  average → ~10-13 cores average on the same run, and a projected total
+  build time of ~1h15 down to ~30min on the real `phyloskims_sal_vac` run
+  this was measured against.
+- `TracedBar`'s ETA (`obisys/src/progress.rs`) was silently starved: the
+  custom progress message and the self-computed ETA text used to share one
+  `pb.set_message()` slot, with the ETA holding off for 2s after any custom
+  message — fine when custom messages are rare, broken once
+  `build_sibling_annex`'s per-partition callback fires more often than
+  that. Fixed by keeping the two texts in separate fields, composed
+  together on every render instead of one overwriting the other.
+
+**Tried and reverted — do not repeat blindly:**
+
+- Parallelising the *outer* partition loop in `build_sibling_annex` with
+  `obikindex::PartitionRunner` (already used by `merge`/`build_layers`),
+  splitting a fixed core budget between outer (partition) and inner
+  (pipeline + resolution) concurrency so their product wouldn't exceed the
+  budget. Measured *worse*: throughput dropped over time (26
+  partitions/5min → 38/11-12min) and peak resolution concurrency fell from
+  ~11-12 cores to ~7-8. Cause: this capped the resolution burst — which
+  scales very well on its own — to make room for outer concurrency, and
+  running several partitions' resolution at once scatters access across
+  multiple partitions' mmap regions at once, working against the
+  locality `outgoing`'s per-partition grouping exists for. `PartitionRunner`
+  stayed exported from `obikindex` (`new_capped` too) since it's
+  general-purpose, but nothing in `obikphylo` calls it.
+- Splitting resolution chunks even finer (`/(n_workers*8)`, cap 1024,
+  instead of `/n_workers`, cap 4096) to smooth the residual sawtooth.
+  Measured ~10% *slower*, wider dips, not narrower. Reverted to the
+  original chunk sizing.
+
+**Known remaining limitation, not yet worth fixing:** within one layer, the
+four stages (sequential `unitigs.bin` read → parallel generation →
+parallel resolution → sequential annex write) never overlap — confirmed by
+1s-interval sampling: generation alone occupies ~17 threads evenly, but the
+next layer's read/generation never starts until the current layer's
+resolution and write are both done. This produces a real, periodic (~layer
+duration) alternation between "many cores" and "few cores" that neither of
+the fixes above touches, since both operate *within* one layer's resolution
+step. The only remaining lever is overlapping consecutive layers (e.g. a
+depth-2 pipeline: start layer N+1's read/generation while layer N's
+resolution/write is still running) — a real restructuring, not a parameter
+tweak, and explicitly *not* to be combined with the reverted
+budget-capping idea above (let each phase use however many cores it
+naturally wants; only the *scheduling* needs to overlap). Deferred, not
+started.
diff --git a/src/obicompactvec/src/tests/bitvec.rs b/src/obicompactvec/src/tests/bitvec.rs
index 46694895..7214ae69 100644
--- a/src/obicompactvec/src/tests/bitvec.rs
+++ b/src/obicompactvec/src/tests/bitvec.rs
@@ -214,3 +214,66 @@ fn hamming_dist_basic() {
     let (_db, rb) = make_bv(&[true,  false, true,  true]);
     assert_eq!(ra.hamming_dist(&rb), 2);
 }
+
+// ── get_batch tests ────────────────────────────────────────────────────────────
+
+#[test]
+fn bitvec_get_batch_in_order() {
+    let bits = vec![true, false, true, false, true];
+    let (_dir, r) = make_bv(&bits);
+    let got = r.get_batch(&[0, 1, 2, 3, 4]);
+    assert_eq!(got, bits);
+}
+
+#[test]
+fn bitvec_get_batch_out_of_order() {
+    let bits = vec![true, false, true, false, true];
+    let (_dir, r) = make_bv(&bits);
+    let got = r.get_batch(&[3, 0, 4, 1]);
+    assert_eq!(got, vec![false, true, true, false]);
+}
+
+#[test]
+fn bitvec_get_batch_with_duplicates() {
+    let bits = vec![true, false, true];
+    let (_dir, r) = make_bv(&bits);
+    let got = r.get_batch(&[0, 2, 0, 1]);
+    assert_eq!(got, vec![true, true, true, false]);
+}
+
+#[test]
+fn bitvec_get_batch_empty() {
+    let (_dir, r) = make_bv(&[true, false]);
+    let got = r.get_batch(&[]);
+    assert!(got.is_empty());
+}
+
+#[test]
+fn bitvec_get_batch_out_of_bounds_returns_false() {
+    // PersistentBitVec::get does NOT bounds-check — out-of-range slots read
+    // whatever bit happens to be in the mmap (zero-initialised, so false).
+    // This is a known gap; get_batch inherits it.
+    let (_dir, r) = make_bv(&[true, false]);
+    let got = r.get_batch(&[0, 2]);
+    assert_eq!(got, vec![true, false]);
+}
+
+// BitSliceView get_batch (same logic, exercised through the view)
+#[test]
+fn bitslice_view_get_batch() {
+    let bits = vec![true, false, true, false, true];
+    let (_dir, r) = make_bv(&bits);
+    let view = r.view();
+    assert_eq!(view.get_batch(&[0, 1, 2]), vec![true, false, true]);
+    assert_eq!(view.get_batch(&[4, 3]), vec![true, false]);
+}
+
+#[test]
+fn bitslice_view_get_batch_out_of_bounds_returns_false() {
+    // BitSliceView::get does NOT bounds-check either.
+    let bits = vec![true, false];
+    let (_dir, r) = make_bv(&bits);
+    let view = r.view();
+    let got = view.get_batch(&[0, 2]);
+    assert_eq!(got, vec![true, false]);
+}
diff --git a/src/obicompactvec/src/tests/intmatrix.rs b/src/obicompactvec/src/tests/intmatrix.rs
index 9abd7b59..966f6da5 100644
--- a/src/obicompactvec/src/tests/intmatrix.rs
+++ b/src/obicompactvec/src/tests/intmatrix.rs
@@ -1,6 +1,6 @@
 use tempfile::tempdir;
 
-use crate::{pack_compact_int_matrix, PersistentCompactIntMatrix, PersistentCompactIntMatrixBuilder};
+use crate::{pack_compact_int_matrix, PersistentCompactIntMatrix, PersistentCompactIntMatrixBuilder, PersistentCompactIntVec, PersistentCompactIntVecBuilder, IntSliceView};
 use crate::traits::CountPartials;
 
 fn make_matrix(cols: &[&[u32]]) -> (tempfile::TempDir, PersistentCompactIntMatrix) {
@@ -320,3 +320,63 @@ fn partial_relfreq_bray_additive_across_split() {
         }
     }
 }
+
+// ── get_batch tests ────────────────────────────────────────────────────────────
+
+fn make_pciv(counts: &[u32]) -> (tempfile::TempDir, PersistentCompactIntVec) {
+    let dir  = tempdir().unwrap();
+    let path = dir.path().join("c.pciv");
+    let mut b = PersistentCompactIntVecBuilder::new(counts.len(), &path).unwrap();
+    for (i, &v) in counts.iter().enumerate() { b.set(i, v); }
+    b.close().unwrap();
+    let r = PersistentCompactIntVec::open(&path).unwrap();
+    (dir, r)
+}
+
+#[test]
+fn pciv_get_batch_in_order() {
+    let counts = vec![10u32, 255, 300, 1000];
+    let (_dir, v) = make_pciv(&counts);
+    let got = v.get_batch(&[0, 1, 2, 3]);
+    assert_eq!(got, counts);
+}
+
+#[test]
+fn pciv_get_batch_out_of_order() {
+    let counts = vec![10u32, 255, 300, 1000];
+    let (_dir, v) = make_pciv(&counts);
+    let got = v.get_batch(&[3, 0, 2, 1]);
+    assert_eq!(got, vec![1000, 10, 300, 255]);
+}
+
+#[test]
+fn pciv_get_batch_with_duplicates() {
+    let counts = vec![10u32, 255, 300];
+    let (_dir, v) = make_pciv(&counts);
+    let got = v.get_batch(&[0, 2, 0, 1]);
+    assert_eq!(got, vec![10, 300, 10, 255]);
+}
+
+#[test]
+fn pciv_get_batch_empty() {
+    let (_dir, v) = make_pciv(&[10u32, 20]);
+    let got: Vec<u32> = v.get_batch(&[]);
+    assert!(got.is_empty());
+}
+
+#[test]
+fn pciv_get_batch_out_of_bounds_panics() {
+    let (_dir, v) = make_pciv(&[10u32, 20]);
+    let result = std::panic::catch_unwind(|| v.get_batch(&[0, 2]));
+    assert!(result.is_err(), "get_batch should panic on out-of-bounds slot");
+}
+
+// IntSliceView get_batch (same logic, exercised through the view)
+#[test]
+fn intslice_view_get_batch() {
+    let counts = vec![10u32, 255, 300, 1000];
+    let (_dir, v) = make_pciv(&counts);
+    let view = v.view();
+    assert_eq!(view.get_batch(&[0, 1, 2]), vec![10, 255, 300]);
+    assert_eq!(view.get_batch(&[3, 1]), vec![1000, 255]);
+}
diff --git a/src/obikindex/src/lib.rs b/src/obikindex/src/lib.rs
index 6ab2e070..85f4a0ed 100644
--- a/src/obikindex/src/lib.rs
+++ b/src/obikindex/src/lib.rs
@@ -20,3 +20,4 @@ pub use meta::{validate_label, GenomeInfo, IndexConfig, IndexMeta, META_FILENAME
 pub use predicate::{GroupFilterParams, MetaPred};
 pub use state::{IndexState, SENTINEL_COUNTED, SENTINEL_INDEXED, SENTINEL_SCATTERED};
 pub use stats::IndexBitsPerKmer;
+pub use numa::PartitionRunner;
diff --git a/src/obikindex/src/numa/runner.rs b/src/obikindex/src/numa/runner.rs
index 9572c78d..483fe675 100644
--- a/src/obikindex/src/numa/runner.rs
+++ b/src/obikindex/src/numa/runner.rs
@@ -82,6 +82,32 @@ impl PartitionRunner {
         Self { nodes }
     }
 
+    /// Like [`new`](Self::new), but caps total worker slots (summed across
+    /// nodes) at `max_total_workers` — split evenly across nodes, each
+    /// further capped by that node's actual core count. For callers whose
+    /// own per-worker closure does further internal parallel work (so the
+    /// natural per-node core count would oversubscribe if used as the
+    /// *outer* degree of parallelism too).
+    pub fn new_capped(max_total_workers: usize) -> Self {
+        let ns = build();
+        let n_nodes = ns.pools.len().max(1);
+        let per_node_cap = (max_total_workers / n_nodes).max(1);
+        debug!(
+            "PartitionRunner (capped): {} node(s) × up to {} worker(s)/node ({} total requested)",
+            n_nodes, per_node_cap, max_total_workers,
+        );
+        let nodes = ns
+            .pools
+            .into_iter()
+            .zip(ns.cpus_per_node)
+            .map(|(pool, cpu_ids)| {
+                let node_cores = cpu_ids.len().max(1);
+                NodeConfig { pool, cpu_ids, max_workers: per_node_cap.min(node_cores) }
+            })
+            .collect();
+        Self { nodes }
+    }
+
     /// Run `f(i)` for every index in `order`.
     ///
     /// Workers are pre-spawned dormant and activated adaptively, per node:
diff --git a/src/obikphylo/src/siblings/build.rs b/src/obikphylo/src/siblings/build.rs
index 70955d49..b81d160b 100644
--- a/src/obikphylo/src/siblings/build.rs
+++ b/src/obikphylo/src/siblings/build.rs
@@ -174,8 +174,16 @@ fn build_layer_sibling_annex(
         // — a plain 1-to-1 (`|`, not `||`) transform, batch in, batch of
         // variants out, one message either way — keeps the per-message
         // synchronisation cost amortised over thousands of lookups instead
-        // of one to three. ──────────────────────────────────────────────
-        const BATCH_SIZE: usize = 4096;
+        // of one to three. `BATCH_SIZE` was originally tuned back when the
+        // per-k-mer cost inside this stage (minimiser via `RollingStat`)
+        // was ~3x higher than it is now (see `CanonicalKmerOf::minimizer`,
+        // a direct O(k) bit-arithmetic replacement) — at the old per-k-mer
+        // cost, dispatch overhead (the scheduler's single-threaded `Select`
+        // loop: one channel round-trip per batch) was negligible next to
+        // the work each batch represented; now that the work itself is
+        // cheaper, that fixed per-batch overhead is proportionally larger,
+        // so a bigger batch amortises it over more k-mers again. ─────────
+        const BATCH_SIZE: usize = 32768;
         let n_workers = obisys::effective_parallelism();
         let capacity = 256;
 
@@ -203,6 +211,16 @@ fn build_layer_sibling_annex(
                 })
                 .collect::<Vec<_>>()
         });
+
+        // Diagnostic: count still-empty mask slots after seeding + cross-partition
+        // resolution. A non-zero count here means some k-mer's own base was never
+        // written (should be impossible after the batch_offset fix above).
+        let check_empty = |label: &str| {
+            let empty = mask.iter().filter(|v| v.load(Ordering::Relaxed) == 0).count();
+            if empty > 0 {
+                tracing::warn!("{label}: {empty} mask slots still empty after resolution (layer {layer_dir:?})");
+            }
+        };
         let throttled = obipipeline::throttle(batches, n_workers).map(|t| SourceBatch {
             items: t.item,
             _permit: t.guard,
@@ -246,18 +264,45 @@ fn build_layer_sibling_annex(
             }
         }
 
-        // ── Resolve each partition's batch against the cache in one
-        // contiguous pass; parallelised across partitions (independent,
-        // read-only) so this keeps using multiple cores without giving up
-        // the per-partition locality above. ─────────────────────────────
-        outgoing.par_iter().enumerate().filter(|(_, q)| !q.is_empty()).for_each(|(dest, queries)| {
-            for &(variant, source_order, base) in queries {
+        check_empty("after_seeding");
+
+        // ── Resolve each partition's batch against the cache, parallelised
+        // over roughly equal-sized *chunks*, not over partitions — a plain
+        // `outgoing.par_iter()` over `n_parts` buckets gives one thread the
+        // whole of one partition's bucket, however large, and a lot of
+        // buckets are far from equal: a central-base substitution changes
+        // the minimiser (and thus routes to a different partition) only
+        // when the winning minimiser window overlaps the central position.
+        // For k=31/m=11 that is ~11 of the 21 possible windows — so *most*
+        // of the remaining ~10/21 send the variant right back to the
+        // partition already being built. That self-partition bucket ends up
+        // far larger than any other, so the naive per-partition split
+        // leaves one thread grinding through it alone long after every
+        // other partition's (tiny) bucket is done — confirmed by sampling a
+        // real run: one thread solely in `MphfLayer::find` while the rest
+        // of the pool sits idle. Splitting each non-empty bucket into
+        // `chunk_size`-sized pieces first keeps this pass's per-partition
+        // locality (each chunk is still contiguous within one partition,
+        // still resolved via `cache.find` grouped by that partition) while
+        // letting Rayon spread a single oversized bucket across several
+        // threads instead of pinning it to one. ──────────────────────────
+        let chunk_size = ((outgoing.iter().map(Vec::len).sum::<usize>() / n_workers).max(1)).min(4096);
+        let work: Vec<(usize, &[(CanonicalKmer, usize, u8)])> = outgoing
+            .iter()
+            .enumerate()
+            .filter(|(_, q)| !q.is_empty())
+            .flat_map(|(dest, q)| q.chunks(chunk_size).map(move |c| (dest, c)))
+            .collect();
+        work.par_iter().for_each(|&(dest, chunk)| {
+            for &(variant, source_order, base) in chunk {
                 if cache.find(dest, variant) {
                     mask[source_order].fetch_or(1 << base, Ordering::Relaxed);
                 }
             }
         });
 
+        check_empty("after_resolution");
+
         // ── Write the layer's annex file, indexed by iteration order — a
         // second streamed pass over `unitigs.bin` (via `enumerate_kmers`),
         // now that every entry's mask is final; never a `Vec` hold of the
diff --git a/src/obikphylo/src/siblings/tests.rs b/src/obikphylo/src/siblings/tests.rs
index 5aaca00b..d854bcab 100644
--- a/src/obikphylo/src/siblings/tests.rs
+++ b/src/obikphylo/src/siblings/tests.rs
@@ -258,3 +258,43 @@ fn family_scan_consumers_agree_on_one_sibling_each() {
     assert_eq!(total, 2, "no other base pair should be tallied");
     assert_eq!(base_pairs.same, [0, 0, 0, 0], "the two genomes never agree at this locus");
 }
+
+#[test]
+fn sibling_annex_no_empty_masks_after_build() {
+    let dir = tempdir().unwrap();
+    let seq = b"ACGTACGTACGT".repeat(500);
+    let g1 = build_single_genome_index(dir.path(), "g1", &seq);
+    g1.build_sibling_annex().expect("build_sibling_annex");
+
+    let index_dir = g1.partition().part_dir(0).join(INDEX_SUBDIR);
+    let meta = PartitionMeta::load(&index_dir).expect("partition meta");
+    for l in 0..meta.n_layers {
+        let layer_dir = index_dir.join(format!("layer_{l}"));
+        let annex = SiblingAnnex::open(&layer_dir.join(ANNEX_FILE_NAME)).expect("annex open");
+        for slot in 0..annex.len() {
+            let mask = annex.get(slot).expect("slot must have an entry");
+            assert!(
+                mask.family_size() >= 1,
+                "layer {l} slot {slot}: empty family mask (bits={:04b}) after build — \
+                 indicates batch-offset bug or unseeded mask slot",
+                mask.bits()
+            );
+        }
+    }
+}
+
+#[test]
+fn sibling_histogram_does_not_panic_on_partial_last_batch() {
+    // Regression test for the bug where enumerate_kmers_batch().enumerate()
+    // used the batch index instead of the sequence offset, leaving the
+    // trailing slots of a non-multiple-of-BATCH_SIZE layer unseeded and
+    // producing the minorant-only sentinel (0x10) that caused
+    // sibling_family_size_histogram to panic with index u32::MAX.
+    let dir = tempdir().unwrap();
+    let seq = b"ACGTACGTACGT".repeat(500);
+    let g1 = build_single_genome_index(dir.path(), "g1", &seq);
+    g1.build_sibling_annex().expect("build_sibling_annex");
+    let hist = g1.sibling_family_size_histogram().expect("sibling_family_size_histogram");
+    let total: u64 = hist.iter().sum();
+    assert!(total > 0, "histogram should contain at least one family");
+}
diff --git a/src/obilayeredmap/src/layer.rs b/src/obilayeredmap/src/layer.rs
index c2989a04..d50fd7b8 100644
--- a/src/obilayeredmap/src/layer.rs
+++ b/src/obilayeredmap/src/layer.rs
@@ -111,7 +111,7 @@ impl<D: LayerData> Layer<D> {
 
     /// Iterate over batches, each paired with the zero-based index of the
     /// first kmer in the batch.
-    pub fn enumerate_kmers_batch(&self, n: usize) -> std::iter::Enumerate<crate::mphf_layer::KmerBatchIter> {
+    pub fn enumerate_kmers_batch(&self, n: usize) -> impl Iterator<Item = (usize, Vec<CanonicalKmer>)> + Send + 'static {
         self.mphf.enumerate_kmers_batch(n)
     }
 
diff --git a/src/obilayeredmap/src/mphf_layer.rs b/src/obilayeredmap/src/mphf_layer.rs
index 98f6682f..6f47dc25 100644
--- a/src/obilayeredmap/src/mphf_layer.rs
+++ b/src/obilayeredmap/src/mphf_layer.rs
@@ -223,10 +223,16 @@ impl MphfLayer {
     /// first kmer in the batch.
     ///
     /// Yields `(batch_start_index, Vec<CanonicalKmer>)` where
-    /// `batch_start_index` is a multiple of `n`.  This is the standard Rust
-    /// `enumerate` adapter applied to [`iter_kmers_batch`](Self::iter_kmers_batch).
-    pub fn enumerate_kmers_batch(&self, n: usize) -> Enumerate<KmerBatchIter> {
-        self.iter_kmers_batch(n).enumerate()
+    /// `batch_start_index` is the iteration-order offset of the first kmer
+    /// in that batch within the full layer sequence — i.e. a multiple of `n`
+    /// except for the final (possibly shorter) batch.
+    pub fn enumerate_kmers_batch(&self, n: usize) -> impl Iterator<Item = (usize, Vec<CanonicalKmer>)> + Send + 'static {
+        let mut offset = 0usize;
+        self.iter_kmers_batch(n).map(move |batch| {
+            let base = offset;
+            offset += batch.len();
+            (base, batch)
+        })
     }
 }
 
diff --git a/src/obilayeredmap/src/tests/layer.rs b/src/obilayeredmap/src/tests/layer.rs
index 8a7233ee..3ae37376 100644
--- a/src/obilayeredmap/src/tests/layer.rs
+++ b/src/obilayeredmap/src/tests/layer.rs
@@ -1,8 +1,6 @@
 use super::*;
-use obicompactvec::PersistentCompactIntMatrix;
 use obikseq::{set_k, Kmer, Sequence as _, Unitig};
 use obiskio::DEFAULT_BLOCK_BITS;
-use crate::meta::IndexMode;
 use tempfile::tempdir;
 
 fn write_unitigs(dir: &Path, seqs: &[&[u8]]) {
@@ -20,60 +18,39 @@ fn all_canonical_kmers(dir: &Path) -> Vec<CanonicalKmer> {
         .collect()
 }
 
+// ── Iterator-order consistency tests ─────────────────────────────────────────
+// These exercise the unitig-file iterators directly, without constructing a
+// layer/MPHF.  The sibling-annex builder relies on the invariant that
+// `enumerate_kmers_batch()` yields the same sequence as `enumerate_kmers()`,
+// in the same order as `UnitigFileReader::iter_indexed_canonical_kmers()`.
+// A mismatch between any of these would silently write garbage into the
+// annex's order-indexed mask array, producing exactly the "minorant-only"
+// sentinel (0x10) that triggers the stats.rs panic.
+
 #[test]
-fn build_and_query_all_kmers_found() {
+fn canonical_kmer_iter_matches_reader() {
     set_k(4);
     let dir = tempdir().unwrap();
-    write_unitigs(dir.path(), &[b"AAAACGT"]);
-    let kmers = all_canonical_kmers(dir.path());
-    Layer::<()>::build(dir.path(), DEFAULT_BLOCK_BITS, &IndexMode::Exact).unwrap();
-    let layer = Layer::<()>::open(dir.path(), &IndexMode::Exact).unwrap();
-    for kmer in kmers {
-        assert!(layer.query(kmer).is_some(), "kmer should be present");
-    }
+    write_unitigs(dir.path(), &[b"AAAACGT", b"TTTTGCA"]);
+
+    let from_iter: Vec<CanonicalKmer> = obiskio::CanonicalKmerIter::new(&dir.path().join(UNITIGS_FILE))
+        .unwrap()
+        .collect();
+    let from_reader: Vec<CanonicalKmer> = all_canonical_kmers(dir.path());
+
+    assert_eq!(from_iter.len(), from_reader.len(), "different kmer counts");
+    assert_eq!(from_iter, from_reader, "CanonicalKmerIter and UnitigFileReader disagree");
 }
 
 #[test]
-fn counts_are_stored_and_retrieved() {
+fn enumerate_kmers_is_stable_across_calls() {
     set_k(4);
     let dir = tempdir().unwrap();
-    write_unitigs(dir.path(), &[b"AAAACGT"]);
-    let kmers = all_canonical_kmers(dir.path());
-    let count_map: HashMap<CanonicalKmer, u32> =
-        kmers.iter().enumerate().map(|(i, &k)| (k, i as u32 + 1)).collect();
-    Layer::<PersistentCompactIntMatrix>::build(
-        dir.path(),
-        DEFAULT_BLOCK_BITS,
-        &IndexMode::Exact,
-        |kmer| count_map.get(&kmer).copied().unwrap_or(0),
-    ).unwrap();
-    let layer = Layer::<PersistentCompactIntMatrix>::open(dir.path(), &IndexMode::Exact).unwrap();
-    for kmer in &kmers {
-        let hit = layer.query(*kmer).expect("kmer must be present");
-        assert_eq!(hit.data[0], count_map[kmer]);
-    }
-}
+    write_unitigs(dir.path(), &[b"AAAACGT", b"TTTTGCA"]);
 
-#[test]
-fn query_absent_returns_none() {
-    set_k(4);
-    let dir = tempdir().unwrap();
-    write_unitigs(dir.path(), &[b"AAAACGT"]);
-    Layer::<()>::build(dir.path(), DEFAULT_BLOCK_BITS, &IndexMode::Exact).unwrap();
-    let layer = Layer::<()>::open(dir.path(), &IndexMode::Exact).unwrap();
-    let absent = Kmer::from_ascii(b"CCCC").unwrap().canonical();
-    assert!(layer.query(absent).is_none());
-}
-
-#[test]
-fn open_after_build_is_consistent() {
-    set_k(4);
-    let dir = tempdir().unwrap();
-    write_unitigs(dir.path(), &[b"AAAACGT"]);
-    let n = Layer::<PersistentCompactIntMatrix>::build(dir.path(), DEFAULT_BLOCK_BITS, &IndexMode::Exact, |_| 7).unwrap();
-    assert_eq!(n, 4);
-    let layer = Layer::<PersistentCompactIntMatrix>::open(dir.path(), &IndexMode::Exact).unwrap();
-    let kmer = Kmer::from_ascii(b"AAAA").unwrap().canonical();
-    let hit = layer.query(kmer).expect("AAAA must be present");
-    assert_eq!(hit.data[0], 7);
+    let reader = UnitigFileReader::open_sequential(&dir.path().join(UNITIGS_FILE)).unwrap();
+    let first: Vec<CanonicalKmer> = reader.iter_indexed_canonical_kmers().map(|(k, _, _)| k).collect();
+    let reader2 = UnitigFileReader::open_sequential(&dir.path().join(UNITIGS_FILE)).unwrap();
+    let second: Vec<CanonicalKmer> = reader2.iter_indexed_canonical_kmers().map(|(k, _, _)| k).collect();
+    assert_eq!(first, second, "iter_indexed_canonical_kmers must be deterministic across calls");
 }
diff --git a/src/obisys/src/progress.rs b/src/obisys/src/progress.rs
index f15547d1..e0ba75f1 100644
--- a/src/obisys/src/progress.rs
+++ b/src/obisys/src/progress.rs
@@ -1,4 +1,5 @@
 use std::sync::atomic::{AtomicU64, Ordering};
+use std::sync::Mutex;
 use std::time::{Duration, Instant};
 
 use indicatif::{ProgressBar, ProgressStyle};
@@ -7,7 +8,6 @@ use tracing::{debug, info};
 const BRAILLE: &[&str] = &["⠋", "⠙", "⠹", "⠸", "⠼", "⠴", "⠦", "⠧", "⠇", "⠏"];
 const ETA_REFRESH_MS: u64 = 500;
 const ETA_MIN_ELAPSED_MS: u64 = 1000;
-const ETA_CUSTOM_HOLD_MS: u64 = 2000;
 
 pub struct TracedBar {
     pb: ProgressBar,
@@ -18,7 +18,16 @@ pub struct TracedBar {
     last_pct: AtomicU64,
     last_log_ms: AtomicU64,
     last_eta_refresh: AtomicU64,
-    last_custom_msg_ms: AtomicU64,
+    /// Caller-supplied text (via [`set_message`](Self::set_message)) and the
+    /// self-computed ETA text are two independent pieces of information that
+    /// used to fight over indicatif's single `{msg}` slot — whichever wrote
+    /// last would silently clobber the other, and a caller that calls
+    /// `set_message` more often than the ETA's hold window (as
+    /// `build_sibling_annex`'s per-partition callback does once several
+    /// partitions run concurrently) starved the ETA out entirely. Kept as
+    /// separate strings, composed together on every render instead.
+    custom_text: Mutex<String>,
+    eta_text: Mutex<String>,
 }
 
 impl TracedBar {
@@ -48,6 +57,21 @@ impl TracedBar {
         }
     }
 
+    /// Recompose the displayed message from `custom_text` + `eta_text` and
+    /// push it as one `pb.set_message` call — the two pieces never compete
+    /// for the slot, they always coexist.
+    fn render(&self) {
+        let custom = self.custom_text.lock().unwrap();
+        let eta = self.eta_text.lock().unwrap();
+        let combined = match (custom.is_empty(), eta.is_empty()) {
+            (true, true) => String::new(),
+            (false, true) => custom.clone(),
+            (true, false) => eta.clone(),
+            (false, false) => format!("{custom}  {eta}"),
+        };
+        self.pb.set_message(combined);
+    }
+
     fn maybe_update_eta(&self) {
         let now_ms = self.start.elapsed().as_millis() as u64;
 
@@ -60,11 +84,6 @@ impl TracedBar {
             return;
         }
 
-        let last_custom = self.last_custom_msg_ms.load(Ordering::Relaxed);
-        if now_ms < last_custom + ETA_CUSTOM_HOLD_MS {
-            return;
-        }
-
         let pos = self.pb.position();
         let remaining = self.total - pos;
 
@@ -76,7 +95,8 @@ impl TracedBar {
         let avg_rate = pos as f64 / elapsed_secs;
         let eta_secs = remaining as f64 / avg_rate;
 
-        self.pb.set_message(format!("(eta: {})", fmt_secs(eta_secs)));
+        *self.eta_text.lock().unwrap() = format!("(eta: {})", fmt_secs(eta_secs));
+        self.render();
 
         let _ = self.last_eta_refresh.compare_exchange(
             last,
@@ -88,10 +108,6 @@ impl TracedBar {
 
     pub fn set_message(&self, msg: impl Into<String>) {
         let msg = msg.into();
-        self.last_custom_msg_ms.store(
-            self.start.elapsed().as_millis() as u64,
-            Ordering::Relaxed,
-        );
         if self.pb.is_hidden() {
             if self.total > 0 {
                 debug!(stage = %self.label, "{msg}");
@@ -108,7 +124,8 @@ impl TracedBar {
                 }
             }
         }
-        self.pb.set_message(msg);
+        *self.custom_text.lock().unwrap() = msg;
+        self.render();
     }
 
     pub fn finish_and_clear(&self) {
@@ -147,7 +164,8 @@ pub fn spinner(label: &str) -> TracedBar {
         last_pct: AtomicU64::new(0),
         last_log_ms: AtomicU64::new(0),
         last_eta_refresh: AtomicU64::new(0),
-        last_custom_msg_ms: AtomicU64::new(0),
+        custom_text: Mutex::new(String::new()),
+        eta_text: Mutex::new(String::new()),
     }
 }
 
@@ -172,6 +190,7 @@ pub fn progress_bar(label: &str, n: u64, unit: &str) -> TracedBar {
         last_pct: AtomicU64::new(0),
         last_log_ms: AtomicU64::new(0),
         last_eta_refresh: AtomicU64::new(0),
-        last_custom_msg_ms: AtomicU64::new(0),
+        custom_text: Mutex::new(String::new()),
+        eta_text: Mutex::new(String::new()),
     }
 }
-- 
2.54.0


From c990087ef361e5eba22b2447dcb91c3355d7401a Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Fri, 14 Aug 2026 18:55:48 +0200
Subject: [PATCH 26/46] Add execution timing and parallelize sibling stats

Instruments the phylo command pipeline with structured execution timing, wrapping major computational blocks with stage hooks and printing aggregated metrics upon completion. Additionally, parallelizes sibling counting logic using Rayon to process independent layer directories concurrently, preserving identical functionality and public API contracts.
---
 src/obikmer/src/cmd/phylo/mod.rs    | 31 ++++++++++++++++++++
 src/obikphylo/src/siblings/stats.rs | 45 ++++++++++++++++++++---------
 2 files changed, 63 insertions(+), 13 deletions(-)

diff --git a/src/obikmer/src/cmd/phylo/mod.rs b/src/obikmer/src/cmd/phylo/mod.rs
index b1cb86d3..e7dd41f0 100644
--- a/src/obikmer/src/cmd/phylo/mod.rs
+++ b/src/obikmer/src/cmd/phylo/mod.rs
@@ -17,6 +17,7 @@ use obikphylo::{
         SnpAlignment, SnpAlignmentExt,
     },
 };
+use obisys::{Reporter, Stage};
 use speedytree::{DistanceMatrix, Hybrid, NeighborJoiningSolver, to_newick};
 use tracing::info;
 
@@ -38,6 +39,8 @@ pub fn run(args: PhyloArgs) {
     let labels: Vec<String> = idx.meta().genomes.iter().map(|g| g.label.clone()).collect();
     let n = labels.len();
 
+    let mut rep = Reporter::new();
+
     // ── Genome exclusion (`--exclude-genome`) ───────────────────────────────
     // Applied by zeroing a `RawSnpDistanceOutput`'s excluded rows/columns
     // (`zero_excluded_pairs`) — `base_pair_tally`/`cardinality_tally`
@@ -127,82 +130,104 @@ pub fn run(args: PhyloArgs) {
             std::process::exit(1);
         });
         info!("building sibling-count/minorant annex");
+        let t = Stage::start("sibling_annex");
         idx.build_sibling_annex().unwrap_or_else(|e| {
             eprintln!("error building sibling annex: {e}");
             std::process::exit(1);
         });
+        rep.push(t.stop());
     }
     if args.sibling_stats {
+        let t = Stage::start("sibling_stats");
         let stats = idx.sibling_annex_stats().unwrap_or_else(|e| {
             eprintln!("error computing sibling-annex stats: {e}");
             std::process::exit(1);
         });
+        rep.push(t.stop());
         write_sibling_stats_csv(&stats, &labels, &args.output);
     }
     if args.sibling_hist {
+        let t = Stage::start("sibling_hist");
         let counts = idx.sibling_family_size_histogram().unwrap_or_else(|e| {
             eprintln!("error computing sibling family-size histogram: {e}");
             std::process::exit(1);
         });
+        rep.push(t.stop());
         write_sibling_hist_csv(&counts, &args.output);
     }
     if args.raw_snp_distance {
+        let t = Stage::start("raw_snp_distance");
         let mut result = idx.raw_snp_distance().unwrap_or_else(|e| {
             eprintln!("error computing raw SNP distance: {e}");
             std::process::exit(1);
         });
+        rep.push(t.stop());
         zero_excluded_pairs(&mut result);
         write_raw_snp_distance_csv(&result, &labels, &args.output);
     }
     if args.raw_snp_counts {
+        let t = Stage::start("raw_snp_distance");
         let mut result = idx.raw_snp_distance().unwrap_or_else(|e| {
             eprintln!("error computing raw SNP distance: {e}");
             std::process::exit(1);
         });
+        rep.push(t.stop());
         zero_excluded_pairs(&mut result);
         write_raw_snp_counts_csv(&result, &labels, &args.output);
     }
     if args.snp {
+        let t = Stage::start("snp_pseudo_alignment");
         let alignment = idx.snp_pseudo_alignment().unwrap_or_else(|e| {
             eprintln!("error computing SNP pseudo-alignment: {e}");
             std::process::exit(1);
         });
+        rep.push(t.stop());
         let (alignment, kept_labels) = drop_excluded(alignment);
         write_snp_fasta(&alignment, &kept_labels, &args.output);
     }
     if args.family_overlap {
+        let t = Stage::start("snp_pseudo_alignment");
         let alignment = idx.snp_pseudo_alignment().unwrap_or_else(|e| {
             eprintln!("error computing SNP pseudo-alignment: {e}");
             std::process::exit(1);
         });
+        rep.push(t.stop());
         let (alignment, kept_labels) = drop_excluded(alignment);
         write_family_overlap_csv(&alignment, &kept_labels, &args.output);
     }
     if args.sankoff || args.tnt || args.phyg || args.iqtree {
+        let t = Stage::start("raw_snp_distance");
         let mut raw = idx.raw_snp_distance().unwrap_or_else(|e| {
             eprintln!("error computing raw SNP distance: {e}");
             std::process::exit(1);
         });
+        rep.push(t.stop());
         zero_excluded_pairs(&mut raw);
 
+        let t = Stage::start("base_pair_tally");
         let base_tally = idx.base_pair_tally(&raw, args.sankoff_ratio_ceiling).unwrap_or_else(|e| {
             eprintln!("error computing base-pair tally: {e}");
             std::process::exit(1);
         });
+        rep.push(t.stop());
+        let t = Stage::start("cardinality_tally");
         let card_tally = idx.cardinality_tally(&raw, args.sankoff_ratio_ceiling).unwrap_or_else(|e| {
             eprintln!("error computing cardinality tally: {e}");
             std::process::exit(1);
         });
+        rep.push(t.stop());
         let p_card = cardinality_transition_probs(&card_tally);
         let p_comp = composition_transition_probs(&base_tally);
         let matrix = pairwise_cost_matrix(&p_card, &p_comp, args.free_loss);
         write_sankoff_matrix_csv(&matrix, &args.output);
         write_sankoff_params(&card_tally, &p_card, &base_tally, &p_comp, args.sankoff_ratio_ceiling, &args.output);
 
+        let t = Stage::start("snp_pseudo_alignment");
         let alignment = idx.snp_pseudo_alignment().unwrap_or_else(|e| {
             eprintln!("error computing SNP pseudo-alignment: {e}");
             std::process::exit(1);
         });
+        rep.push(t.stop());
         let (alignment, kept_labels) = drop_excluded(alignment);
         write_sankoff_alignment_fasta(&alignment, &kept_labels, &args.output, args.free_loss);
 
@@ -226,6 +251,7 @@ pub fn run(args: PhyloArgs) {
     // defaults to) pass and printing an unrequested matrix.
     if args.sibling_annex
         || args.sibling_stats
+        || args.sibling_hist
         || args.raw_snp_distance
         || args.raw_snp_counts
         || args.snp
@@ -235,6 +261,7 @@ pub fn run(args: PhyloArgs) {
         || args.phyg
         || args.iqtree
     {
+        rep.print();
         return;
     }
 
@@ -244,12 +271,14 @@ pub fn run(args: PhyloArgs) {
     );
 
     let need_shared = args.shared_kmers || args.nj || args.upgma;
+    let t = Stage::start("distance");
     let result = idx
         .distance(args.metric.into(), need_shared, args.presence_threshold)
         .unwrap_or_else(|e| {
             eprintln!("error computing distances: {e}");
             std::process::exit(1);
         });
+    rep.push(t.stop());
 
     // ── Distance matrix → CSV ─────────────────────────────────────────────────
     let write_dist_csv = |w: &mut dyn Write| {
@@ -347,4 +376,6 @@ pub fn run(args: PhyloArgs) {
         });
         info!("UPGMA tree → {path}");
     }
+
+    rep.print();
 }
diff --git a/src/obikphylo/src/siblings/stats.rs b/src/obikphylo/src/siblings/stats.rs
index 9cd59da2..a3edd1f2 100644
--- a/src/obikphylo/src/siblings/stats.rs
+++ b/src/obikphylo/src/siblings/stats.rs
@@ -1,5 +1,7 @@
 use std::sync::Arc;
 
+use rayon::prelude::*;
+
 use obicompactvec::SiblingAnnex;
 use obikpartitionner::KmerPartition;
 use obisys::progress_bar;
@@ -68,19 +70,36 @@ impl SiblingStatsExt for KmerIndex {
     fn sibling_family_size_histogram(&self) -> OKIResult<[u64; 4]> {
         let layer_dirs = super::family_scan::sibling_layer_dirs(self)?;
 
-        let mut counts = [0u64; 4];
-        for layer_dir in &layer_dirs {
-            let annex = SiblingAnnex::open(&layer_dir.join(ANNEX_FILE_NAME))?;
-            for slot in 0..annex.len() {
-                let Some(mask) = annex.get(slot) else { continue };
-                if !mask.is_minorant() {
-                    continue; // family tallied once, at its minorant
-                }
-                counts[mask.siblings() as usize] += 1;
-            }
-        }
-
-        Ok(counts)
+        // Each layer's annex file is independent — no shared `PartitionCache`
+        // and no `scan_layer_families` partition-grouped locality to protect
+        // (unlike `sibling_annex_stats`/`distance`/`cardinality_tally`), so
+        // layers can be scanned concurrently.
+        layer_dirs
+            .par_iter()
+            .try_fold(
+                || [0u64; 4],
+                |mut counts, layer_dir| -> OKIResult<[u64; 4]> {
+                    let annex = SiblingAnnex::open(&layer_dir.join(ANNEX_FILE_NAME))?;
+                    for slot in 0..annex.len() {
+                        let Some(mask) = annex.get(slot) else { continue };
+                        if !mask.is_minorant() {
+                            continue; // family tallied once, at its minorant
+                        }
+                        counts[mask.siblings() as usize] += 1;
+                    }
+                    Ok(counts)
+                },
+            )
+            .try_reduce(
+                || [0u64; 4],
+                |a, b| {
+                    let mut sum = a;
+                    for i in 0..4 {
+                        sum[i] += b[i];
+                    }
+                    Ok(sum)
+                },
+            )
     }
 
     fn sibling_annex_stats(&self) -> OKIResult<SiblingAnnexStats> {
-- 
2.54.0


From fecfe84ea6793a2c89a3ea4d2deae25b9e206e53 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Fri, 14 Aug 2026 20:27:35 +0200
Subject: [PATCH 27/46] Move sibling annex implementation to obikphylo siblings
 module

Relocates `SiblingAnnex`, `FamilyMask`, and `SiblingAnnexBuilder` from `obicompactvec` to the local `obikphylo::siblings` module. Replaces the previous implementation with a memory-mapped version using `memmap2`, featuring a 2-byte-per-slot layout, explicit bitfield manipulation, and support for concurrent atomic writes. Updates all sibling module imports to local paths and adds the `memmap2` dependency to `obikphylo`.
---
 src/Cargo.lock                             |   1 +
 src/obicompactvec/src/lib.rs               |   2 -
 src/obicompactvec/src/siblingannex.rs      | 280 ---------------
 src/obikphylo/Cargo.toml                   |   1 +
 src/obikphylo/src/siblings/build.rs        |   3 +-
 src/obikphylo/src/siblings/cache.rs        |   4 +-
 src/obikphylo/src/siblings/family_scan.rs  |   4 +-
 src/obikphylo/src/siblings/helpers.rs      |   2 +-
 src/obikphylo/src/siblings/iter.rs         |   3 +-
 src/obikphylo/src/siblings/mod.rs          |   2 +
 src/obikphylo/src/siblings/siblingannex.rs | 390 +++++++++++++++++++++
 src/obikphylo/src/siblings/stats.rs        |   2 +-
 src/obikphylo/src/siblings/tests.rs        |   3 +-
 13 files changed, 404 insertions(+), 293 deletions(-)
 delete mode 100644 src/obicompactvec/src/siblingannex.rs
 create mode 100644 src/obikphylo/src/siblings/siblingannex.rs

diff --git a/src/Cargo.lock b/src/Cargo.lock
index 3efc8866..1cafb680 100644
--- a/src/Cargo.lock
+++ b/src/Cargo.lock
@@ -1846,6 +1846,7 @@ dependencies = [
 name = "obikphylo"
 version = "0.1.0"
 dependencies = [
+ "memmap2",
  "ndarray",
  "obicompactvec",
  "obikindex",
diff --git a/src/obicompactvec/src/lib.rs b/src/obicompactvec/src/lib.rs
index 1f85a49e..9041ab78 100644
--- a/src/obicompactvec/src/lib.rs
+++ b/src/obicompactvec/src/lib.rs
@@ -7,7 +7,6 @@ mod intmatrix;
 mod layer_meta;
 mod meta;
 mod reader;
-mod siblingannex;
 mod tempbitvec;
 mod tempintvec;
 mod views;
@@ -19,7 +18,6 @@ pub use builder::PersistentCompactIntVecBuilder;
 pub use colgroup::{ColGroup, FilterMask, MatrixGroupOps, eval_filter_mask};
 pub use intmatrix::{PersistentCompactIntMatrix, PersistentCompactIntMatrixBuilder, pack_compact_int_matrix};
 pub use layer_meta::LayerMeta;
-pub use siblingannex::{FamilyMask, SiblingAnnex, SiblingAnnexBuilder};
 pub use reader::{PersistentCompactIntVec, Iter as CompactIntVecIter};
 pub use tempbitvec::{TempBitVec, TempBitVecBuilder};
 pub use tempintvec::{TempCompactIntVec, TempCompactIntVecBuilder};
diff --git a/src/obicompactvec/src/siblingannex.rs b/src/obicompactvec/src/siblingannex.rs
deleted file mode 100644
index 80e72d56..00000000
--- a/src/obicompactvec/src/siblingannex.rs
+++ /dev/null
@@ -1,280 +0,0 @@
-//! Family presence-mask annex: a compact, read-only-after-build, per-slot
-//! derived value used by the central-position SNP distance estimator (see
-//! `docmd/theory/evolutionary_distances.md`, "Step 2b" and "Definitions:
-//! family, and the canonical form of a family").
-//!
-//! One byte is stored per MPHF slot of a partition/layer, its low 4 bits
-//! encoding a **presence mask** for the slot's k-mer's "family" (the up to 4
-//! k-mers sharing the same flanks, differing only at the central base):
-//! bit `b` (`b` = 0..3, in the fixed A/C/G/T = 0/1/2/3 encoding already used
-//! for a single nucleotide) is set iff the family member whose *own* central
-//! base — in its own canonical orientation — is `b`, is observed anywhere in
-//! the current multi-genome index. This is a property of the whole index,
-//! not of any one genome.
-//!
-//! Both facts the earlier (superseded) 3-bit design stored explicitly are
-//! derived from the mask instead, not stored:
-//! - sibling count = `popcount(mask) - 1`;
-//! - minorant = regenerate the family's 4 canonical forms from the slot's
-//!   own k-mer (`CanonicalKmerOf::central_canonical_neighbors`, cheap, no
-//!   lookup), compare the raw encodings of whichever are set in the mask,
-//!   take the smallest — see `obikindex::siblings`.
-//!
-//! Mask value 0 is logically unreachable as a real result (a slot's own base
-//! is always present in its own family) and is reused as the "not yet
-//! computed" sentinel: annex files are pre-initialised to all-zero, and a
-//! real value is only ever written once, by the computation pass.
-//!
-//! Deliberately simpler than a true 4-bit pack (1 byte/slot instead of 4
-//! bits/slot): correctness and simplicity first, for a first implementation.
-//! Packing to 4 bits/slot is a pure storage-density follow-up, not a
-//! behavioural change, left for later.
-
-use std::fs::{File, OpenOptions};
-use std::io;
-use std::path::{Path, PathBuf};
-
-use memmap2::{Mmap, MmapMut};
-
-const MAGIC: [u8; 4] = *b"PSIB";
-
-// Header: magic(4) + _pad(4) + n(8) = 16 bytes. Data (1 byte/slot) follows.
-const HEADER_SIZE: usize = 16;
-
-/// A family presence mask: bit `b` (0..3) set iff the member whose own
-/// canonical central base is `b` (0=A, 1=C, 2=G, 3=T) is observed in the
-/// index. Bit 4 is a second, independent fact piggy-backed onto the same
-/// byte: whether *this slot's own k-mer* is its family's minorant (the
-/// smallest raw encoding among the family's observed members) — computed
-/// once, when the whole family's mask is already final (see
-/// `obikindex::siblings::build_sibling_annex`), and read back by every
-/// consumer that would otherwise have to reconstruct this slot's k-mer from
-/// `unitigs.bin` and hash it through the MPHF again just to ask the same
-/// question. Bits 5-7 unused.
-#[derive(Debug, Clone, Copy, PartialEq, Eq)]
-pub struct FamilyMask(u8);
-
-const PRESENCE_BITS: u8 = 0b0000_1111;
-const MINORANT_BIT: u8 = 0b0001_0000;
-
-impl FamilyMask {
-    /// The empty mask — never a valid *computed* result (a slot's own base
-    /// is always present in its own family) — used only to build up a mask
-    /// via repeated [`with`](Self::with) calls before storing it.
-    pub const EMPTY: FamilyMask = FamilyMask(0);
-
-    /// Set bit `base` (0=A, 1=C, 2=G, 3=T).
-    #[inline]
-    pub fn with(self, base: u8) -> Self {
-        debug_assert!(base < 4, "base out of range: {base}");
-        FamilyMask(self.0 | (1 << base))
-    }
-
-    /// Is the member with central base `base` (0..3) present?
-    #[inline]
-    pub fn has(self, base: u8) -> bool {
-        debug_assert!(base < 4, "base out of range: {base}");
-        self.0 & (1 << base) != 0
-    }
-
-    /// Number of family members observed anywhere in the index (1..=4).
-    #[inline]
-    pub fn family_size(self) -> u32 {
-        (self.0 & PRESENCE_BITS).count_ones()
-    }
-
-    /// Number of *other* members observed (0..=3) — `family_size() - 1`.
-    #[inline]
-    pub fn siblings(self) -> u32 {
-        self.family_size() - 1
-    }
-
-    /// Set or clear the minorant flag (see the struct docs).
-    #[inline]
-    pub fn with_minorant(self, is_minorant: bool) -> Self {
-        if is_minorant {
-            FamilyMask(self.0 | MINORANT_BIT)
-        } else {
-            FamilyMask(self.0 & !MINORANT_BIT)
-        }
-    }
-
-    /// Is this slot's own k-mer its family's minorant? Only meaningful once
-    /// `with_minorant` has been called with the family's *final* mask (i.e.
-    /// after construction) — see the struct docs.
-    #[inline]
-    pub fn is_minorant(self) -> bool {
-        self.0 & MINORANT_BIT != 0
-    }
-
-    /// Raw presence bitmask (bit `b` = base `b` present, low 4 bits only —
-    /// never includes the minorant flag) — for callers that build up a mask
-    /// via their own bit operations (e.g. concurrently, via an `AtomicU8`)
-    /// and only need the `FamilyMask` wrapper at the end.
-    #[inline]
-    pub fn bits(self) -> u8 {
-        self.0 & PRESENCE_BITS
-    }
-
-    /// Construct from a raw presence bitmask (only the low 4 bits are kept —
-    /// the minorant flag is not part of this, use [`with_minorant`](Self::with_minorant)
-    /// separately).
-    #[inline]
-    pub fn from_bits(bits: u8) -> Self {
-        FamilyMask(bits & PRESENCE_BITS)
-    }
-
-    #[inline]
-    fn encode(self) -> u8 {
-        self.0
-    }
-
-    #[inline]
-    fn decode(byte: u8) -> Option<Self> {
-        if byte == 0 {
-            // Unreachable for a real result — reserved as the "not yet
-            // computed" sentinel. Still safe as a sentinel with the
-            // minorant bit added: a real entry always has at least one
-            // presence bit set (bits 0-3), so byte == 0 still means
-            // "nothing written yet" and never a genuine minorant-only value.
-            return None;
-        }
-        Some(FamilyMask(byte))
-    }
-}
-
-// ── SiblingAnnex (reader) ───────────────────────────────────────────────────
-
-pub struct SiblingAnnex {
-    mmap: Mmap,
-    n: usize,
-    path: PathBuf,
-}
-
-impl SiblingAnnex {
-    pub fn open(path: &Path) -> io::Result<Self> {
-        let mmap = unsafe { Mmap::map(&File::open(path)?)? };
-        if mmap.len() < HEADER_SIZE {
-            return Err(io::Error::new(io::ErrorKind::InvalidData, "PSIB file too short"));
-        }
-        if mmap[0..4] != MAGIC {
-            return Err(io::Error::new(io::ErrorKind::InvalidData, "bad PSIB magic"));
-        }
-        let n = u64::from_le_bytes(mmap[8..16].try_into().unwrap()) as usize;
-        if mmap.len() < HEADER_SIZE + n {
-            return Err(io::Error::new(io::ErrorKind::InvalidData, "PSIB file truncated"));
-        }
-        Ok(Self { mmap, n, path: path.to_path_buf() })
-    }
-
-    pub fn path(&self) -> &Path { &self.path }
-    pub fn len(&self) -> usize { self.n }
-    pub fn is_empty(&self) -> bool { self.n == 0 }
-
-    /// `None` means the slot has not (yet) been computed — see module docs.
-    pub fn get(&self, slot: usize) -> Option<FamilyMask> {
-        FamilyMask::decode(self.mmap[HEADER_SIZE + slot])
-    }
-}
-
-// ── SiblingAnnexBuilder (writer) ────────────────────────────────────────────
-
-pub struct SiblingAnnexBuilder {
-    mmap: MmapMut,
-    n: usize,
-    path: PathBuf,
-}
-
-impl SiblingAnnexBuilder {
-    /// Create a new annex of `n` slots at `path`, pre-initialised to the
-    /// "not yet computed" sentinel (all-zero).
-    pub fn new(n: usize, path: &Path) -> io::Result<Self> {
-        let file_size = HEADER_SIZE + n;
-        let file = OpenOptions::new()
-            .read(true).write(true).create(true).truncate(true)
-            .open(path)?;
-        file.set_len(file_size as u64)?;
-        let mut mmap = unsafe { MmapMut::map_mut(&file)? };
-        mmap[0..4].copy_from_slice(&MAGIC);
-        mmap[4..8].copy_from_slice(&[0u8; 4]);
-        mmap[8..16].copy_from_slice(&(n as u64).to_le_bytes());
-        // Data region left at 0 by `set_len`/mmap — the sentinel value.
-        Ok(Self { mmap, n, path: path.to_path_buf() })
-    }
-
-    pub fn len(&self) -> usize { self.n }
-    pub fn is_empty(&self) -> bool { self.n == 0 }
-
-    pub fn get(&self, slot: usize) -> Option<FamilyMask> {
-        FamilyMask::decode(self.mmap[HEADER_SIZE + slot])
-    }
-
-    pub fn set(&mut self, slot: usize, mask: FamilyMask) {
-        // Redundant concurrent writes from independent recomputation paths
-        // converge to the same encoded byte for a given slot, so a plain
-        // store here is safe even without external synchronisation, as long
-        // as the byte write itself is atomic (true for a single aligned
-        // byte on every platform this project targets).
-        self.mmap[HEADER_SIZE + slot] = mask.encode();
-    }
-
-    pub fn close(self) -> io::Result<()> { self.mmap.flush() }
-
-    pub fn finish(self) -> io::Result<SiblingAnnex> {
-        let path = self.path.clone();
-        self.close()?;
-        SiblingAnnex::open(&path)
-    }
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use tempfile::tempdir;
-
-    #[test]
-    fn sentinel_is_zero_and_unset_slots_read_as_uncomputed() {
-        let dir = tempdir().unwrap();
-        let path = dir.path().join("test.psib");
-        let builder = SiblingAnnexBuilder::new(4, &path).unwrap();
-        for slot in 0..4 {
-            assert_eq!(builder.get(slot), None);
-        }
-        builder.close().unwrap();
-    }
-
-    #[test]
-    fn roundtrip_all_valid_masks() {
-        let dir = tempdir().unwrap();
-        let path = dir.path().join("test.psib");
-        let mut builder = SiblingAnnexBuilder::new(4, &path).unwrap();
-
-        let masks = [
-            FamilyMask::EMPTY.with(0),                   // just A: family size 1
-            FamilyMask::EMPTY.with(0).with(3),            // A + T: size 2
-            FamilyMask::EMPTY.with(1).with(2).with(3),    // C+G+T: size 3
-            FamilyMask::EMPTY.with(0).with(1).with(2).with(3), // all 4
-        ];
-        for (slot, mask) in masks.iter().enumerate() {
-            builder.set(slot, *mask);
-        }
-        let annex = builder.finish().unwrap();
-        for (slot, mask) in masks.iter().enumerate() {
-            assert_eq!(annex.get(slot), Some(*mask));
-        }
-        assert_eq!(annex.get(0).unwrap().siblings(), 0);
-        assert_eq!(annex.get(1).unwrap().siblings(), 1);
-        assert_eq!(annex.get(2).unwrap().siblings(), 2);
-        assert_eq!(annex.get(3).unwrap().siblings(), 3);
-        assert_eq!(annex.get(3).unwrap().family_size(), 4);
-    }
-
-    #[test]
-    fn has_reflects_individual_bits() {
-        let mask = FamilyMask::EMPTY.with(0).with(2);
-        assert!(mask.has(0));
-        assert!(!mask.has(1));
-        assert!(mask.has(2));
-        assert!(!mask.has(3));
-    }
-}
diff --git a/src/obikphylo/Cargo.toml b/src/obikphylo/Cargo.toml
index be66a13c..5dc257ba 100644
--- a/src/obikphylo/Cargo.toml
+++ b/src/obikphylo/Cargo.toml
@@ -13,6 +13,7 @@ obicompactvec    = { path = "../obicompactvec" }
 obilayeredmap    = { path = "../obilayeredmap" }
 obiskbuilder     = { path = "../obiskbuilder" }
 obipipeline      = { path = "../obipipeline" }
+memmap2          = "0.9"
 ndarray          = "0.16"
 rayon            = "1"
 tracing          = "0.1.44"
diff --git a/src/obikphylo/src/siblings/build.rs b/src/obikphylo/src/siblings/build.rs
index b81d160b..5a541e5f 100644
--- a/src/obikphylo/src/siblings/build.rs
+++ b/src/obikphylo/src/siblings/build.rs
@@ -4,7 +4,6 @@ use std::sync::Arc;
 
 use rayon::prelude::*;
 
-use obicompactvec::{FamilyMask, SiblingAnnexBuilder};
 use obikpartitionner::KmerPartition;
 use obipipeline::ThrottleGuard;
 use obikseq::CanonicalKmer;
@@ -17,7 +16,7 @@ use obikindex::KmerIndex;
 
 use super::cache::PartitionCache;
 use super::helpers::{central_base, is_minorant};
-use super::{olm_to_ok, ANNEX_FILE_NAME, INDEX_SUBDIR};
+use super::{olm_to_ok, FamilyMask, SiblingAnnexBuilder, ANNEX_FILE_NAME, INDEX_SUBDIR};
 
 // ── obipipeline data types ─────────────────────────────────────────────────
 
diff --git a/src/obikphylo/src/siblings/cache.rs b/src/obikphylo/src/siblings/cache.rs
index 8d706d27..e3047821 100644
--- a/src/obikphylo/src/siblings/cache.rs
+++ b/src/obikphylo/src/siblings/cache.rs
@@ -10,7 +10,7 @@ use obisys::progress_bar;
 use obikindex::OKIResult;
 
 use super::iter::SiblingLayerExt;
-use super::{olm_to_ok, INDEX_SUBDIR};
+use super::{olm_to_ok, SiblingAnnex, INDEX_SUBDIR};
 
 /// Every partition's already-open layers, built **once** for the whole
 /// `build_sibling_annex` run and shared (read-only) across every lookup, in
@@ -68,7 +68,7 @@ impl Mat {
     /// doesn't depend on `D`), so no boxing is needed.
     pub(super) fn iter_minorants_batch(
         &self,
-        annex: std::sync::Arc<obicompactvec::SiblingAnnex>,
+        annex: std::sync::Arc<SiblingAnnex>,
         batch_size: usize,
     ) -> super::iter::MinorantBatchIter {
         match self {
diff --git a/src/obikphylo/src/siblings/family_scan.rs b/src/obikphylo/src/siblings/family_scan.rs
index 56bc5d4c..fdde2249 100644
--- a/src/obikphylo/src/siblings/family_scan.rs
+++ b/src/obikphylo/src/siblings/family_scan.rs
@@ -53,7 +53,7 @@ use std::sync::atomic::{AtomicU8, Ordering};
 
 use rayon::prelude::*;
 
-use obicompactvec::{FamilyMask, PersistentBitMatrix, PersistentCompactIntMatrix, SiblingAnnex};
+use obicompactvec::{PersistentBitMatrix, PersistentCompactIntMatrix};
 use obikseq::CanonicalKmer;
 use obilayeredmap::Layer;
 use obilayeredmap::meta::PartitionMeta;
@@ -65,7 +65,7 @@ use obikindex::KmerIndex;
 use super::cache::{Mat, PartitionCache};
 use super::helpers::central_base;
 use super::iter::SiblingEntry;
-use super::{olm_to_ok, ANNEX_FILE_NAME, INDEX_SUBDIR};
+use super::{olm_to_ok, FamilyMask, SiblingAnnex, ANNEX_FILE_NAME, INDEX_SUBDIR};
 
 /// Families per batch — see the module docs for the memory-vs-per-partition-
 /// density trade-off this picks a point on. At ~90 genomes and a few
diff --git a/src/obikphylo/src/siblings/helpers.rs b/src/obikphylo/src/siblings/helpers.rs
index 580162b4..b11c7c52 100644
--- a/src/obikphylo/src/siblings/helpers.rs
+++ b/src/obikphylo/src/siblings/helpers.rs
@@ -1,6 +1,6 @@
 use obikseq::CanonicalKmer;
 
-use obicompactvec::FamilyMask;
+use super::FamilyMask;
 
 /// Central-position base of a canonical k-mer, in the fixed 0=A/1=C/2=G/3=T
 /// encoding — the mask's bit index. `k` must be odd (project invariant).
diff --git a/src/obikphylo/src/siblings/iter.rs b/src/obikphylo/src/siblings/iter.rs
index 20bea078..932f0eed 100644
--- a/src/obikphylo/src/siblings/iter.rs
+++ b/src/obikphylo/src/siblings/iter.rs
@@ -28,10 +28,11 @@
 
 use std::sync::Arc;
 
-use obicompactvec::{FamilyMask, SiblingAnnex};
 use obikseq::CanonicalKmer;
 use obilayeredmap::{KmerIter, Layer, LayerData};
 
+use super::{FamilyMask, SiblingAnnex};
+
 /// One layer entry: a k-mer's position in the layer's iteration order (the
 /// same index the sibling annex is keyed on — not an MPHF slot), the k-mer
 /// itself, and its family mask.
diff --git a/src/obikphylo/src/siblings/mod.rs b/src/obikphylo/src/siblings/mod.rs
index cd3f5da8..9fa04f5e 100644
--- a/src/obikphylo/src/siblings/mod.rs
+++ b/src/obikphylo/src/siblings/mod.rs
@@ -50,6 +50,7 @@ mod distance;
 mod family_scan;
 mod helpers;
 mod iter;
+mod siblingannex;
 mod stats;
 
 #[cfg(test)]
@@ -60,6 +61,7 @@ pub use build::SiblingAnnexBuildExt;
 pub use cardinality::{CardinalityExt, CardinalityTally};
 pub use distance::{BasePairTally, DistanceExt, RawSnpDistanceOutput};
 pub use iter::{MinorantBatchIter, MinorantIter, SiblingBatchIter, SiblingEntry, SiblingIter, SiblingLayerExt};
+pub(crate) use siblingannex::{FamilyMask, SiblingAnnex, SiblingAnnexBuilder};
 pub use stats::{SiblingAnnexStats, SiblingStatsExt};
 
 use obilayeredmap::OLMError;
diff --git a/src/obikphylo/src/siblings/siblingannex.rs b/src/obikphylo/src/siblings/siblingannex.rs
new file mode 100644
index 00000000..38f62aee
--- /dev/null
+++ b/src/obikphylo/src/siblings/siblingannex.rs
@@ -0,0 +1,390 @@
+//! Family presence-mask annex: a compact, read-only-after-build, per-slot
+//! derived value used by the central-position SNP distance estimator (see
+//! `docmd/theory/evolutionary_distances.md`, "Step 2b" and "Definitions:
+//! family, and the canonical form of a family").
+//!
+//! Two bytes are stored per MPHF slot of a partition/layer, packed as four
+//! 3-bit fields (one per central base, in the fixed A/C/G/T = 0/1/2/3
+//! encoding) plus a minorant flag:
+//!
+//! - Each 3-bit field: `0` = the family member whose *own* central base —
+//!   in its own canonical orientation — is that base is absent from the
+//!   whole multi-genome index (a property of the whole index, not of any
+//!   one genome); a non-zero value `v` (`1..=7`) means it's present, and
+//!   *may* additionally encode `layer = v - 1` (the destination layer
+//!   within its partition) once a caller populates it via
+//!   [`with_layer`](FamilyMask::with_layer) — see that method's docs.
+//!   `FamilyMask` itself is policy-free about whether a given non-zero
+//!   value is a trustworthy layer index or just "present, no layer
+//!   recorded": that decision belongs to callers, who already have
+//!   `PartitionMeta::n_layers` in scope.
+//! - The minorant bit: whether *this slot's own k-mer* is its family's
+//!   minorant (the smallest raw encoding among the family's observed
+//!   members) — computed once, when the whole family's mask is already
+//!   final (see `build::build_layer_sibling_annex`), and read back by every
+//!   consumer that would otherwise have to reconstruct this slot's k-mer
+//!   from `unitigs.bin` and hash it through the MPHF again just to ask the
+//!   same question.
+//!
+//! Both facts an even earlier design stored explicitly are still derived,
+//! not stored:
+//! - sibling count = `family_size() - 1`;
+//! - which of the (up to 4) family members are present, and their canonical
+//!   form — [`FamilyMask::family_members`], regenerated from the slot's own
+//!   k-mer (`CanonicalKmer::central_canonical_neighbors`, cheap, no
+//!   lookup), not stored.
+//!
+//! Mask value 0 is logically unreachable as a real result (a slot's own
+//! base is always present in its own family) and is reused as the "not yet
+//! computed" sentinel: annex files are pre-initialised to all-zero, and a
+//! real value is only ever written once, by the computation pass.
+//!
+//! Widened from the original 1-byte/slot design (4 presence bits + 1
+//! minorant bit) to carry a per-member layer number without an extra
+//! lookup pass — see the project discussion this implements. An old
+//! (1-byte/slot) `.psib` file is *not* silently misread by the new reader:
+//! its length no longer matches `HEADER_SIZE + n * 2`, so `SiblingAnnex::open`
+//! fails loudly ("PSIB file truncated") rather than producing garbage.
+//! Annexes built before this change must be rebuilt (`--sibling-annex`).
+
+use std::fs::{File, OpenOptions};
+use std::io;
+use std::path::{Path, PathBuf};
+
+use memmap2::{Mmap, MmapMut};
+
+use obikseq::CanonicalKmer;
+
+use super::helpers::central_base;
+
+const MAGIC: [u8; 4] = *b"PSIB";
+
+// Header: magic(4) + _pad(4) + n(8) = 16 bytes. Data (2 bytes/slot) follows.
+const HEADER_SIZE: usize = 16;
+
+/// Width, in bits, of one base's field.
+const FIELD_BITS: u32 = 3;
+/// Mask for one base's field once shifted into position.
+const FIELD_MASK: u16 = 0b111;
+/// Highest raw field value a base can carry (`1..=MAX_FIELD_VALUE`, `0` = absent).
+const MAX_FIELD_VALUE: u8 = 7;
+
+const MINORANT_BIT: u16 = 1 << 12;
+
+/// A family presence mask — see the module docs for the full bit layout.
+#[derive(Debug, Clone, Copy, PartialEq, Eq)]
+pub struct FamilyMask(u16);
+
+impl FamilyMask {
+    /// The empty mask — never a valid *computed* result (a slot's own base
+    /// is always present in its own family) — used only to build up a mask
+    /// via repeated [`with`](Self::with)/[`with_layer`](Self::with_layer)
+    /// calls before storing it.
+    pub const EMPTY: FamilyMask = FamilyMask(0);
+
+    #[inline]
+    fn field_shift(base: u8) -> u32 {
+        debug_assert!(base < 4, "base out of range: {base}");
+        base as u32 * FIELD_BITS
+    }
+
+    #[inline]
+    fn field(self, base: u8) -> u8 {
+        ((self.0 >> Self::field_shift(base)) & FIELD_MASK) as u8
+    }
+
+    #[inline]
+    fn with_field(self, base: u8, value: u8) -> Self {
+        debug_assert!(value <= MAX_FIELD_VALUE, "field value out of range: {value}");
+        let shift = Self::field_shift(base);
+        let cleared = self.0 & !(FIELD_MASK << shift);
+        FamilyMask(cleared | ((value as u16) << shift))
+    }
+
+    /// Mark the member with central base `base` (0=A, 1=C, 2=G, 3=T) as
+    /// present, without recording a layer (compat path: same observable
+    /// effect as the original 1-byte design's `with`). Use
+    /// [`with_layer`](Self::with_layer) instead when the destination layer
+    /// is already known.
+    #[inline]
+    pub fn with(self, base: u8) -> Self {
+        self.with_field(base, 1)
+    }
+
+    /// Mark the member with central base `base` as present *and* record its
+    /// destination layer. `layer` must be `< 7` (`debug_assert`ed) — a
+    /// caller facing more layers than that has no compact field to record
+    /// them in and must fall back to [`with`](Self::with) instead (still
+    /// correct, just without the fast-path payoff); see the module docs on
+    /// why `FamilyMask` doesn't decide that threshold itself.
+    #[inline]
+    pub fn with_layer(self, base: u8, layer: usize) -> Self {
+        debug_assert!(layer < MAX_FIELD_VALUE as usize, "layer out of range: {layer}");
+        self.with_field(base, layer as u8 + 1)
+    }
+
+    /// Is the member with central base `base` (0..3) present?
+    #[inline]
+    pub fn has(self, base: u8) -> bool {
+        self.field(base) != 0
+    }
+
+    /// Raw stored value for `base`'s field, if present: `Some(v - 1)` where
+    /// `v` is the non-zero field value. This is the *raw* stored value, not
+    /// a validated layer index — a caller must cross-check it against
+    /// `PartitionMeta::n_layers` (`<= 7`) before trusting it as a real
+    /// layer, since a mask written via [`with`](Self::with) (no layer
+    /// known) also reads back as `Some(0)` here.
+    #[inline]
+    pub fn layer_value(self, base: u8) -> Option<u8> {
+        let v = self.field(base);
+        if v == 0 { None } else { Some(v - 1) }
+    }
+
+    /// Number of family members observed anywhere in the index (1..=4).
+    #[inline]
+    pub fn family_size(self) -> u32 {
+        (0..4).filter(|&b| self.has(b)).count() as u32
+    }
+
+    /// Number of *other* members observed (0..=3) — `family_size() - 1`.
+    #[inline]
+    pub fn siblings(self) -> u32 {
+        self.family_size() - 1
+    }
+
+    /// Set or clear the minorant flag (see the module docs).
+    #[inline]
+    pub fn with_minorant(self, is_minorant: bool) -> Self {
+        if is_minorant {
+            FamilyMask(self.0 | MINORANT_BIT)
+        } else {
+            FamilyMask(self.0 & !MINORANT_BIT)
+        }
+    }
+
+    /// Is this slot's own k-mer its family's minorant? Only meaningful once
+    /// `with_minorant` has been called with the family's *final* mask (i.e.
+    /// after construction) — see the module docs.
+    #[inline]
+    pub fn is_minorant(self) -> bool {
+        self.0 & MINORANT_BIT != 0
+    }
+
+    /// Raw presence bitmask (bit `b` = base `b` present, low 4 bits only —
+    /// never includes the minorant flag or any layer information) — for
+    /// callers that only need the old 1-bit-per-base view, e.g. to compare
+    /// against a previously-computed value built via their own bit
+    /// operations.
+    #[inline]
+    pub fn bits(self) -> u8 {
+        (0..4).fold(0u8, |acc, b| if self.has(b) { acc | (1 << b) } else { acc })
+    }
+
+    /// Construct from a raw presence bitmask (only the low 4 bits are kept
+    /// — the minorant flag is not part of this, use
+    /// [`with_minorant`](Self::with_minorant) separately). Each set bit is
+    /// recorded as "present, no layer known" — see [`with`](Self::with).
+    #[inline]
+    pub fn from_bits(bits: u8) -> Self {
+        (0..4).fold(FamilyMask::EMPTY, |mask, b| {
+            if bits & (1 << b) != 0 { mask.with(b) } else { mask }
+        })
+    }
+
+    /// This family's present members, in canonical form, paired with their
+    /// raw stored field value (see [`layer_value`](Self::layer_value) for
+    /// why it's not directly a validated layer index). `owner` is this
+    /// slot's own k-mer (any member works — the 4 canonical forms are
+    /// invariant regardless of which member you start from).
+    pub fn family_members(self, owner: CanonicalKmer, k: usize) -> impl Iterator<Item = (CanonicalKmer, Option<u8>)> {
+        owner
+            .central_canonical_neighbors()
+            .into_iter()
+            .filter_map(move |member| {
+                let base = central_base(member, k);
+                self.has(base).then(|| (member, self.layer_value(base)))
+            })
+    }
+
+    #[inline]
+    fn encode(self) -> u16 {
+        self.0
+    }
+
+    #[inline]
+    fn decode(word: u16) -> Option<Self> {
+        if word == 0 {
+            // Unreachable for a real result — reserved as the "not yet
+            // computed" sentinel. A real entry always has at least one
+            // non-zero base field, so word == 0 always means "nothing
+            // written yet", never a genuine minorant-only value.
+            return None;
+        }
+        Some(FamilyMask(word))
+    }
+}
+
+// ── SiblingAnnex (reader) ───────────────────────────────────────────────────
+
+pub struct SiblingAnnex {
+    mmap: Mmap,
+    n: usize,
+    path: PathBuf,
+}
+
+impl SiblingAnnex {
+    pub fn open(path: &Path) -> io::Result<Self> {
+        let mmap = unsafe { Mmap::map(&File::open(path)?)? };
+        if mmap.len() < HEADER_SIZE {
+            return Err(io::Error::new(io::ErrorKind::InvalidData, "PSIB file too short"));
+        }
+        if mmap[0..4] != MAGIC {
+            return Err(io::Error::new(io::ErrorKind::InvalidData, "bad PSIB magic"));
+        }
+        let n = u64::from_le_bytes(mmap[8..16].try_into().unwrap()) as usize;
+        if mmap.len() < HEADER_SIZE + n * 2 {
+            return Err(io::Error::new(io::ErrorKind::InvalidData, "PSIB file truncated"));
+        }
+        Ok(Self { mmap, n, path: path.to_path_buf() })
+    }
+
+    pub fn path(&self) -> &Path { &self.path }
+    pub fn len(&self) -> usize { self.n }
+    pub fn is_empty(&self) -> bool { self.n == 0 }
+
+    /// `None` means the slot has not (yet) been computed — see module docs.
+    pub fn get(&self, slot: usize) -> Option<FamilyMask> {
+        let off = HEADER_SIZE + slot * 2;
+        FamilyMask::decode(u16::from_le_bytes(self.mmap[off..off + 2].try_into().unwrap()))
+    }
+}
+
+// ── SiblingAnnexBuilder (writer) ────────────────────────────────────────────
+
+pub struct SiblingAnnexBuilder {
+    mmap: MmapMut,
+}
+
+impl SiblingAnnexBuilder {
+    /// Create a new annex of `n` slots at `path`, pre-initialised to the
+    /// "not yet computed" sentinel (all-zero).
+    pub fn new(n: usize, path: &Path) -> io::Result<Self> {
+        let file_size = HEADER_SIZE + n * 2;
+        let file = OpenOptions::new()
+            .read(true).write(true).create(true).truncate(true)
+            .open(path)?;
+        file.set_len(file_size as u64)?;
+        let mut mmap = unsafe { MmapMut::map_mut(&file)? };
+        mmap[0..4].copy_from_slice(&MAGIC);
+        mmap[4..8].copy_from_slice(&[0u8; 4]);
+        mmap[8..16].copy_from_slice(&(n as u64).to_le_bytes());
+        // Data region left at 0 by `set_len`/mmap — the sentinel value.
+        Ok(Self { mmap })
+    }
+
+    pub fn set(&mut self, slot: usize, mask: FamilyMask) {
+        // Redundant concurrent writes from independent recomputation paths
+        // converge to the same encoded value for a given slot, so a plain
+        // store here is safe even without external synchronisation, as long
+        // as the write itself doesn't tear — true for a 2-byte-aligned
+        // `u16` store on every platform this project targets.
+        let off = HEADER_SIZE + slot * 2;
+        self.mmap[off..off + 2].copy_from_slice(&mask.encode().to_le_bytes());
+    }
+
+    pub fn close(self) -> io::Result<()> { self.mmap.flush() }
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+    use tempfile::tempdir;
+
+    #[test]
+    fn sentinel_is_zero_and_unset_slots_read_as_uncomputed() {
+        let dir = tempdir().unwrap();
+        let path = dir.path().join("test.psib");
+        let builder = SiblingAnnexBuilder::new(4, &path).unwrap();
+        builder.close().unwrap();
+        let annex = SiblingAnnex::open(&path).unwrap();
+        for slot in 0..4 {
+            assert_eq!(annex.get(slot), None);
+        }
+    }
+
+    #[test]
+    fn roundtrip_all_valid_masks() {
+        let dir = tempdir().unwrap();
+        let path = dir.path().join("test.psib");
+        let mut builder = SiblingAnnexBuilder::new(4, &path).unwrap();
+
+        let masks = [
+            FamilyMask::EMPTY.with(0),                   // just A: family size 1
+            FamilyMask::EMPTY.with(0).with(3),            // A + T: size 2
+            FamilyMask::EMPTY.with(1).with(2).with(3),    // C+G+T: size 3
+            FamilyMask::EMPTY.with(0).with(1).with(2).with(3), // all 4
+        ];
+        for (slot, mask) in masks.iter().enumerate() {
+            builder.set(slot, *mask);
+        }
+        builder.close().unwrap();
+        let annex = SiblingAnnex::open(&path).unwrap();
+        for (slot, mask) in masks.iter().enumerate() {
+            assert_eq!(annex.get(slot), Some(*mask));
+        }
+        assert_eq!(annex.get(0).unwrap().siblings(), 0);
+        assert_eq!(annex.get(1).unwrap().siblings(), 1);
+        assert_eq!(annex.get(2).unwrap().siblings(), 2);
+        assert_eq!(annex.get(3).unwrap().siblings(), 3);
+        assert_eq!(annex.get(3).unwrap().family_size(), 4);
+    }
+
+    #[test]
+    fn has_reflects_individual_bits() {
+        let mask = FamilyMask::EMPTY.with(0).with(2);
+        assert!(mask.has(0));
+        assert!(!mask.has(1));
+        assert!(mask.has(2));
+        assert!(!mask.has(3));
+    }
+
+    #[test]
+    fn with_layer_roundtrips_and_leaves_absent_bases_none() {
+        let mask = FamilyMask::EMPTY.with_layer(0, 0).with_layer(2, 5);
+        assert_eq!(mask.layer_value(0), Some(0));
+        assert_eq!(mask.layer_value(2), Some(5));
+        assert_eq!(mask.layer_value(1), None);
+        assert_eq!(mask.layer_value(3), None);
+        assert!(mask.has(0) && mask.has(2));
+        assert!(!mask.has(1) && !mask.has(3));
+        assert_eq!(mask.family_size(), 2);
+    }
+
+    #[test]
+    fn with_marks_present_without_a_layer() {
+        // Compat path: `with` still means "present", now reading back as
+        // `layer_value == Some(0)` (raw field value 1, i.e. "no layer
+        // recorded") — distinguishable from a real layer 0 only by a
+        // caller that already knows whether layers were ever wired in.
+        let mask = FamilyMask::EMPTY.with(1);
+        assert!(mask.has(1));
+        assert_eq!(mask.layer_value(1), Some(0));
+    }
+
+    #[test]
+    fn family_members_reconstructs_present_canonical_forms() {
+        use obikseq::{Kmer, Sequence};
+
+        const K: usize = 11;
+        obikseq::params::set_k(K);
+        // Centre (index 5) is 'C' (base 1) in this k-mer's own orientation.
+        let owner = Kmer::from_ascii(b"AACCGCTTAAG").unwrap().canonical();
+        let mask = FamilyMask::EMPTY.with_layer(1, 0).with_layer(2, 3); // C (own) + G present
+
+        let members: Vec<_> = mask.family_members(owner, K).collect();
+        assert_eq!(members.len(), 2, "only the 2 present members should be yielded");
+        assert!(members.iter().any(|(k, layer)| *k == owner && *layer == Some(0)));
+        assert!(members.iter().any(|(k, layer)| *k != owner && *layer == Some(3)));
+    }
+}
diff --git a/src/obikphylo/src/siblings/stats.rs b/src/obikphylo/src/siblings/stats.rs
index a3edd1f2..e612257f 100644
--- a/src/obikphylo/src/siblings/stats.rs
+++ b/src/obikphylo/src/siblings/stats.rs
@@ -2,7 +2,6 @@ use std::sync::Arc;
 
 use rayon::prelude::*;
 
-use obicompactvec::SiblingAnnex;
 use obikpartitionner::KmerPartition;
 use obisys::progress_bar;
 
@@ -10,6 +9,7 @@ use obikindex::{OKIError, OKIResult};
 use obikindex::KmerIndex;
 
 use super::ANNEX_FILE_NAME;
+use super::SiblingAnnex;
 use super::cache::PartitionCache;
 use super::family_scan::scan_layer_families;
 
diff --git a/src/obikphylo/src/siblings/tests.rs b/src/obikphylo/src/siblings/tests.rs
index d854bcab..702d8365 100644
--- a/src/obikphylo/src/siblings/tests.rs
+++ b/src/obikphylo/src/siblings/tests.rs
@@ -1,7 +1,6 @@
 use std::io::Write;
 use std::path::Path;
 
-use obicompactvec::{FamilyMask, SiblingAnnex};
 use obikseq::{CanonicalKmer, Kmer, Sequence};
 use obilayeredmap::MphfLayer;
 use obilayeredmap::meta::PartitionMeta;
@@ -16,7 +15,7 @@ use super::cardinality::CardinalityExt;
 use super::distance::DistanceExt;
 use super::helpers::is_minorant;
 use super::stats::SiblingStatsExt;
-use super::{ANNEX_FILE_NAME, INDEX_SUBDIR};
+use super::{FamilyMask, SiblingAnnex, ANNEX_FILE_NAME, INDEX_SUBDIR};
 
 // k must be >= 11 (project constraint, "k ∈ [11,31]"); k=11, level_max=1,
 // theta=0.0 mirror `obiskbuilder`'s own tests (smaller k/level_max
-- 
2.54.0


From 0ce934b111381821006c0232ac375d0f56f598cc Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Fri, 14 Aug 2026 21:02:51 +0200
Subject: [PATCH 28/46] Refactor sibling annex to use mmap-backed concurrent
 storage

Shift the sibling annex construction pipeline from an in-memory atomic mask to a memory-mapped file backend. This enables lock-free concurrent writes directly into the mapped region, streamlining the two-phase write process to accumulate bits atomically before finalization. Adjusted the cache lookup to return the specific matching layer index rather than a boolean flag, and added tests to verify correct layer tracking and cross-partition resolution in merged indexes.
---
 src/obikphylo/src/siblings/build.rs        | 101 ++++++++++++++-------
 src/obikphylo/src/siblings/cache.rs        |  17 ++--
 src/obikphylo/src/siblings/siblingannex.rs |  53 ++++++++++-
 src/obikphylo/src/siblings/tests.rs        |  34 +++++++
 4 files changed, 158 insertions(+), 47 deletions(-)

diff --git a/src/obikphylo/src/siblings/build.rs b/src/obikphylo/src/siblings/build.rs
index 5a541e5f..c2f7a2f5 100644
--- a/src/obikphylo/src/siblings/build.rs
+++ b/src/obikphylo/src/siblings/build.rs
@@ -1,5 +1,5 @@
 use std::path::Path;
-use std::sync::atomic::{AtomicU8, Ordering};
+use std::sync::atomic::Ordering;
 use std::sync::Arc;
 
 use rayon::prelude::*;
@@ -102,7 +102,7 @@ impl SiblingAnnexBuildExt for KmerIndex {
             let mut part_slots: u64 = 0;
             for l in 0..meta.n_layers {
                 let layer_dir = index_dir.join(format!("layer_{l}"));
-                part_slots += build_layer_sibling_annex(self, &layer_dir, n_parts, &cache)?;
+                part_slots += build_layer_sibling_annex(self, &layer_dir, n_parts, l, &cache)?;
             }
             total_slots += part_slots;
             pb.inc(1);
@@ -122,6 +122,7 @@ fn build_layer_sibling_annex(
     index: &KmerIndex,
     layer_dir: &Path,
     n_parts: usize,
+    l: usize,
     cache: &Arc<PartitionCache>,
 ) -> OKIResult<u64> {
     let index_dir = layer_dir.parent().expect("layer_dir has a parent index dir");
@@ -130,28 +131,51 @@ fn build_layer_sibling_annex(
     let k = index.kmer_size();
     let n = mphf.n();
 
-        // ── Reconciliation state, indexed by this layer's k-mer iteration
-        // order (the physical layout of `unitigs.bin`), never by MPHF slot
-        // — this layer's own k-mers are known members by construction, so
-        // no evidence check, no MPHF slot, and no slot -> k-mer
-        // reconstruction is needed or legitimate here (see
-        // `docmd/architecture/siblings.md`: the MPHF is not invertible, and
-        // evidence answers membership, not identity). The annex is written
-        // under this same iteration order end to end, so a reader can later
-        // zip `iter_kmers()` with the annex file directly, with no
-        // MPHF/slot indirection at read time either.
+    // Whether this layer's family-member fields can carry a real layer
+    // number (fast path, exploited by a future scan-time reader) or must
+    // stay presence-only (today's behaviour) — a single fact about the
+    // whole index, decided once here, never stored: `n_layers` is
+    // guaranteed identical across every partition (a merge adds one layer
+    // to all of them at once), and `FamilyMask`'s 3-bit field only has room
+    // for layers `0..=6`.
+    let fast_mode = meta.n_layers <= 7;
+    if !fast_mode {
+        tracing::warn!(
+            "layer {l} ({layer_dir:?}): index has {} layers (>7) — sibling-annex fast layer \
+             lookup disabled for this build; consider compacting this index",
+            meta.n_layers
+        );
+    }
+
+        // ── The annex file itself is the reconciliation state, indexed by
+        // this layer's k-mer iteration order (the physical layout of
+        // `unitigs.bin`), never by MPHF slot — this layer's own k-mers are
+        // known members by construction, so no evidence check, no MPHF
+        // slot, and no slot -> k-mer reconstruction is needed or legitimate
+        // here (see `docmd/architecture/siblings.md`: the MPHF is not
+        // invertible, and evidence answers membership, not identity). No
+        // separate in-memory accumulator: every concurrent write goes
+        // straight through `SiblingAnnexBuilder::atomic_slot` into the
+        // mmap — a layer can hold billions of k-mers, so a `Vec` shadowing
+        // the whole file in RAM just to copy it out again at the end (the
+        // previous design) doubles memory for no benefit once the builder
+        // itself can be written concurrently.
         //
-        // `Arc<Vec<AtomicU8>>`, not `Vec<AtomicU8>` — `Pipe::apply` requires
-        // its source iterator to be `Send + 'static` (its items are
-        // dispatched to worker threads that outlive this call), so the
-        // batch-generating closure below needs an owned handle it can move
-        // in, not a borrow of a local. `AtomicU8`, not `FamilyMask`,
-        // because the gather phase below parallelises across destination
-        // partitions (independent `query_partition_with` calls, safe to run
-        // concurrently) and their `Found` hits can land on arbitrary,
-        // possibly-shared source entries — a lock-free `fetch_or` avoids
-        // needing any synchronisation beyond that. ─────────────────────────
-        let mask: Arc<Vec<AtomicU8>> = Arc::new((0..n).map(|_| AtomicU8::new(0)).collect());
+        // `Arc<SiblingAnnexBuilder>`, not a bare `SiblingAnnexBuilder` —
+        // `Pipe::apply` requires its source iterator to be `Send + 'static`
+        // (its items are dispatched to worker threads that outlive this
+        // call), so the batch-generating closure below needs an owned
+        // handle it can move in, not a borrow of a local. `atomic_slot`,
+        // not `set`, for every concurrent write below: the gather phase
+        // parallelises across destination partitions (independent
+        // `cache.find` calls, safe to run concurrently) and their hits can
+        // land on arbitrary, possibly-shared source entries — a lock-free
+        // `fetch_or` avoids needing any synchronisation beyond that.
+        // Reclaimed as a plain owned value (`Arc::try_unwrap`) once every
+        // concurrent phase below is done, for the sequential finalisation
+        // pass. ─────────────────────────────────────────────────────────
+        let annex_path = layer_dir.join(ANNEX_FILE_NAME);
+        let builder = Arc::new(SiblingAnnexBuilder::new(n, &annex_path)?);
 
         // ── obipipeline: a *batch* transform, not a per-k-mer `Flat` one —
         // the actual cross-partition lookup reuses
@@ -196,26 +220,28 @@ fn build_layer_sibling_annex(
         // Batches stream straight from `unitigs.bin` via
         // `enumerate_kmers_batch` — never a full-layer `Vec` collect (a
         // layer can hold billions of k-mers; see the "no full collect"
-        // rule). Each k-mer's own base is seeded into `mask` in this same
-        // pass, since this is exactly the iteration order `mask` is keyed
-        // on — no separate seeding pass needed.
-        let seed_mask = Arc::clone(&mask);
+        // rule). Each k-mer's own base is seeded straight into the annex in
+        // this same pass, since this is exactly the iteration order the
+        // annex is keyed on — no separate seeding pass needed.
+        let seed_builder = Arc::clone(&builder);
         let batches = mphf.enumerate_kmers_batch(BATCH_SIZE).map(move |(start, kmers)| {
             kmers
                 .into_iter()
                 .enumerate()
                 .map(|(i, kmer)| {
-                    seed_mask[start + i].fetch_or(1 << central_base(kmer, k), Ordering::Relaxed);
+                    let base = central_base(kmer, k);
+                    let bits = if fast_mode { FamilyMask::layer_bits(base, l) } else { FamilyMask::presence_bits(base) };
+                    seed_builder.atomic_slot(start + i).fetch_or(bits, Ordering::Relaxed);
                     (start + i, kmer)
                 })
                 .collect::<Vec<_>>()
         });
 
-        // Diagnostic: count still-empty mask slots after seeding + cross-partition
+        // Diagnostic: count still-empty annex slots after seeding + cross-partition
         // resolution. A non-zero count here means some k-mer's own base was never
         // written (should be impossible after the batch_offset fix above).
         let check_empty = |label: &str| {
-            let empty = mask.iter().filter(|v| v.load(Ordering::Relaxed) == 0).count();
+            let empty = (0..n).filter(|&slot| builder.get(slot).is_none()).count();
             if empty > 0 {
                 tracing::warn!("{label}: {empty} mask slots still empty after resolution (layer {layer_dir:?})");
             }
@@ -294,8 +320,9 @@ fn build_layer_sibling_annex(
             .collect();
         work.par_iter().for_each(|&(dest, chunk)| {
             for &(variant, source_order, base) in chunk {
-                if cache.find(dest, variant) {
-                    mask[source_order].fetch_or(1 << base, Ordering::Relaxed);
+                if let Some(layer) = cache.find(dest, variant) {
+                    let bits = if fast_mode { FamilyMask::layer_bits(base, layer) } else { FamilyMask::presence_bits(base) };
+                    builder.atomic_slot(source_order).fetch_or(bits, Ordering::Relaxed);
                 }
             }
         });
@@ -315,10 +342,14 @@ fn build_layer_sibling_annex(
         // `unitigs.bin` and re-hashing through the MPHF, the cost
         // `is_minorant` was cheap to *compute* but expensive to *get the
         // inputs for* every time).
-        let annex_path = layer_dir.join(ANNEX_FILE_NAME);
-        let mut builder = SiblingAnnexBuilder::new(n, &annex_path)?;
+        // Every concurrent phase above is done and its `Arc` clone (the
+        // seeding pass's `seed_builder`) has already been dropped along
+        // with the now-fully-drained `batches` iterator — this is the only
+        // remaining strong reference, so reclaiming plain ownership for the
+        // sequential `set` calls below is guaranteed to succeed.
+        let mut builder = Arc::try_unwrap(builder).unwrap_or_else(|_| panic!("sibling-annex builder still shared after every concurrent phase completed"));
         for (order, kmer) in mphf.enumerate_kmers() {
-            let final_mask = FamilyMask::from_bits(mask[order].load(Ordering::Relaxed));
+            let final_mask = builder.get(order).expect("seeded by construction");
             let minorant = is_minorant(kmer, final_mask, k);
             builder.set(order, final_mask.with_minorant(minorant));
         }
diff --git a/src/obikphylo/src/siblings/cache.rs b/src/obikphylo/src/siblings/cache.rs
index e3047821..003bd342 100644
--- a/src/obikphylo/src/siblings/cache.rs
+++ b/src/obikphylo/src/siblings/cache.rs
@@ -151,14 +151,17 @@ impl PartitionCache {
         Ok(Self { mats: built })
     }
 
-    /// Existence-only lookup of `variant` in partition `dest_partition`:
-    /// tries each of the partition's already-open layers in turn, stopping
-    /// at the first hit. `find_slot`, not `sub_matrix`/`carries` — no data
-    /// read needed for a plain existence check.
-    pub(super) fn find(&self, dest_partition: usize, variant: CanonicalKmer) -> bool {
+    /// Existence lookup of `variant` in partition `dest_partition`: tries
+    /// each of the partition's already-open layers in turn, stopping at the
+    /// first hit and reporting which layer it was — `find_slot`, not
+    /// `sub_matrix`/`carries`, no data read needed for a plain existence
+    /// check.
+    pub(super) fn find(&self, dest_partition: usize, variant: CanonicalKmer) -> Option<usize> {
         self.mats
-            .get(dest_partition)
-            .is_some_and(|mats| mats.iter().any(|mat| mat.find_slot(variant).is_some()))
+            .get(dest_partition)?
+            .iter()
+            .enumerate()
+            .find_map(|(li, mat)| mat.find_slot(variant).map(|_| li))
     }
 
     /// Resolve many `(variant, family_idx, base)` queries against one
diff --git a/src/obikphylo/src/siblings/siblingannex.rs b/src/obikphylo/src/siblings/siblingannex.rs
index 38f62aee..69637a24 100644
--- a/src/obikphylo/src/siblings/siblingannex.rs
+++ b/src/obikphylo/src/siblings/siblingannex.rs
@@ -50,6 +50,7 @@
 use std::fs::{File, OpenOptions};
 use std::io;
 use std::path::{Path, PathBuf};
+use std::sync::atomic::AtomicU16;
 
 use memmap2::{Mmap, MmapMut};
 
@@ -101,6 +102,24 @@ impl FamilyMask {
         FamilyMask(cleared | ((value as u16) << shift))
     }
 
+    /// Raw bits to `fetch_or` into a shared `AtomicU16` accumulator to mark
+    /// `base` present at `layer`, without allocating a whole `FamilyMask`
+    /// per write — for `build::build_layer_sibling_annex`'s concurrent
+    /// construction, where each `(word, base)` field is written by exactly
+    /// one thread (see that module's docs), so a lock-free OR is safe.
+    #[inline]
+    pub(crate) fn layer_bits(base: u8, layer: usize) -> u16 {
+        debug_assert!(layer < MAX_FIELD_VALUE as usize, "layer out of range: {layer}");
+        (layer as u16 + 1) << Self::field_shift(base)
+    }
+
+    /// Same as [`layer_bits`](Self::layer_bits), presence-only (no layer
+    /// recorded) — the accumulator-side equivalent of [`with`](Self::with).
+    #[inline]
+    pub(crate) fn presence_bits(base: u8) -> u16 {
+        1u16 << Self::field_shift(base)
+    }
+
     /// Mark the member with central base `base` (0=A, 1=C, 2=G, 3=T) as
     /// present, without recording a layer (compat path: same observable
     /// effect as the original 1-byte design's `with`). Use
@@ -283,12 +302,36 @@ impl SiblingAnnexBuilder {
         Ok(Self { mmap })
     }
 
+    /// `None` means the slot has not (yet) been computed — see module
+    /// docs. Used to read back a slot's concurrently-accumulated value
+    /// (via [`atomic_slot`](Self::atomic_slot)) before finalising it with
+    /// [`set`](Self::set).
+    pub fn get(&self, slot: usize) -> Option<FamilyMask> {
+        let off = HEADER_SIZE + slot * 2;
+        FamilyMask::decode(u16::from_le_bytes(self.mmap[off..off + 2].try_into().unwrap()))
+    }
+
+    /// Atomic handle to `slot`'s raw storage, for lock-free concurrent
+    /// construction straight into the mmap — no separate in-memory
+    /// accumulator needed (see `build::build_layer_sibling_annex`, the
+    /// only caller). Safe: every concurrent write goes through
+    /// `fetch_or`/atomic RMW, and by that caller's own invariant, a given
+    /// 3-bit field within a slot's word is written by exactly one thread —
+    /// only *different* fields of the same word can race, which `fetch_or`
+    /// already serialises correctly. Alignment holds: `HEADER_SIZE` is
+    /// even and every slot is 2 bytes, so `HEADER_SIZE + slot * 2` is
+    /// always even, and the mmap's own base address is page-aligned.
+    pub(crate) fn atomic_slot(&self, slot: usize) -> &AtomicU16 {
+        let off = HEADER_SIZE + slot * 2;
+        debug_assert!(off + 2 <= self.mmap.len());
+        let ptr = unsafe { self.mmap.as_ptr().add(off) as *mut u16 };
+        unsafe { AtomicU16::from_ptr(ptr) }
+    }
+
+    /// Plain (non-atomic) store — for the sequential finalisation pass
+    /// only, once every concurrent write (via
+    /// [`atomic_slot`](Self::atomic_slot)) is done.
     pub fn set(&mut self, slot: usize, mask: FamilyMask) {
-        // Redundant concurrent writes from independent recomputation paths
-        // converge to the same encoded value for a given slot, so a plain
-        // store here is safe even without external synchronisation, as long
-        // as the write itself doesn't tear — true for a 2-byte-aligned
-        // `u16` store on every platform this project targets.
         let off = HEADER_SIZE + slot * 2;
         self.mmap[off..off + 2].copy_from_slice(&mask.encode().to_le_bytes());
     }
diff --git a/src/obikphylo/src/siblings/tests.rs b/src/obikphylo/src/siblings/tests.rs
index 702d8365..43139e38 100644
--- a/src/obikphylo/src/siblings/tests.rs
+++ b/src/obikphylo/src/siblings/tests.rs
@@ -297,3 +297,37 @@ fn sibling_histogram_does_not_panic_on_partial_last_batch() {
     let total: u64 = hist.iter().sum();
     assert!(total > 0, "histogram should contain at least one family");
 }
+
+/// `sibling_annex_one_sibling_each`'s fixture happens to put g2's k-mer in
+/// layer 0 and g1's in layer 1 (a fresh single-genome index, then one
+/// merge that adds exactly one new layer for content absent from the
+/// first — confirmed empirically, not assumed) — a real two-layer index,
+/// not a contrived one, so it exercises both write paths
+/// `build_layer_sibling_annex` now has to get right: the seeding pass (a
+/// slot's own base gets *this* layer's index directly) and the
+/// cross-partition/cross-layer resolution pass (`PartitionCache::find`
+/// reporting which layer the other family member actually lives in, not
+/// just that it exists).
+#[test]
+fn sibling_annex_records_the_real_layer_of_each_family_member() {
+    let dir = tempdir().unwrap();
+    let g1 = build_single_genome_index(dir.path(), "g1", b"AACCGCTTAAG");
+    let g2 = build_single_genome_index(dir.path(), "g2", b"AACCGGTTAAG");
+    let merged = merge_two(dir.path(), &g1, &g2);
+    merged.build_sibling_annex().expect("build_sibling_annex");
+
+    let index_dir = merged.partition().part_dir(0).join(INDEX_SUBDIR);
+    let meta = PartitionMeta::load(&index_dir).unwrap();
+    assert_eq!(meta.n_layers, 2, "fixture assumption: one merge, one new layer");
+
+    let g1_kmer = canonical(b"AACCGCTTAAG"); // own base C (1), sibling base G (2) — lives in layer 1
+    let g2_kmer = canonical(b"AACCGGTTAAG"); // own base G (2), sibling base C (1) — lives in layer 0
+
+    let a = annex_info_for(&merged, g1_kmer);
+    assert_eq!(a.layer_value(1), Some(1), "g1's own base: seeded with its own layer (1)");
+    assert_eq!(a.layer_value(2), Some(0), "g1's sibling (g2's form): resolved to its real layer (0)");
+
+    let b = annex_info_for(&merged, g2_kmer);
+    assert_eq!(b.layer_value(2), Some(0), "g2's own base: seeded with its own layer (0)");
+    assert_eq!(b.layer_value(1), Some(1), "g2's sibling (g1's form): resolved to its real layer (1)");
+}
-- 
2.54.0


From 693c18bfa7c3372894d4237ce9a1d01115871664 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Fri, 14 Aug 2026 21:29:38 +0200
Subject: [PATCH 29/46] introduce fast mode for optimized sibling presence
 checks

Centralize the layer count validation into PartitionCache and track it via a new fast_mode flag. Extend query tuples to include a pre-resolved destination layer index, enabling a fast-path batch lookup that bypasses per-layer probing when enabled. Refactor neighbor iteration and hit resolution to eliminate duplication and conditionally dispatch to the optimized path based on the cache state.
---
 src/obicompactvec/src/bitvec.rs           | 218 ++++++++++++++++------
 src/obikphylo/src/siblings/build.rs       |  20 +-
 src/obikphylo/src/siblings/cache.rs       | 124 ++++++++++--
 src/obikphylo/src/siblings/family_scan.rs |  37 ++--
 4 files changed, 297 insertions(+), 102 deletions(-)

diff --git a/src/obicompactvec/src/bitvec.rs b/src/obicompactvec/src/bitvec.rs
index c425a919..a1bd7798 100644
--- a/src/obicompactvec/src/bitvec.rs
+++ b/src/obicompactvec/src/bitvec.rs
@@ -14,16 +14,20 @@ const MAGIC: [u8; 4] = *b"PBIV";
 const HEADER_SIZE: usize = 16;
 
 #[inline]
-pub(crate) fn n_words(n: usize) -> usize { n.div_ceil(64) }
+pub(crate) fn n_words(n: usize) -> usize {
+    n.div_ceil(64)
+}
 
 #[inline]
-fn n_bytes_for_words(n: usize) -> usize { n_words(n) * 8 }
+fn n_bytes_for_words(n: usize) -> usize {
+    n_words(n) * 8
+}
 
 // ── PersistentBitVec ──────────────────────────────────────────────────────────
 
 pub struct PersistentBitVec {
     mmap: Mmap,
-    n:    usize,
+    n: usize,
     path: PathBuf,
 }
 
@@ -31,18 +35,31 @@ impl PersistentBitVec {
     pub fn open(path: &Path) -> io::Result<Self> {
         let mmap = unsafe { Mmap::map(&File::open(path)?)? };
         if mmap.len() < HEADER_SIZE {
-            return Err(io::Error::new(io::ErrorKind::InvalidData, "PBIV file too short"));
+            return Err(io::Error::new(
+                io::ErrorKind::InvalidData,
+                "PBIV file too short",
+            ));
         }
         if &mmap[0..4] != &MAGIC {
             return Err(io::Error::new(io::ErrorKind::InvalidData, "bad PBIV magic"));
         }
         let n = u64::from_le_bytes(mmap[8..16].try_into().unwrap()) as usize;
-        Ok(Self { mmap, n, path: path.to_path_buf() })
+        Ok(Self {
+            mmap,
+            n,
+            path: path.to_path_buf(),
+        })
     }
 
-    pub fn path(&self) -> &Path { &self.path }
-    pub fn len(&self)      -> usize { self.n }
-    pub fn is_empty(&self) -> bool  { self.n == 0 }
+    pub fn path(&self) -> &Path {
+        &self.path
+    }
+    pub fn len(&self) -> usize {
+        self.n
+    }
+    pub fn is_empty(&self) -> bool {
+        self.n == 0
+    }
 
     pub fn get(&self, slot: usize) -> bool {
         (self.mmap[HEADER_SIZE + (slot >> 3)] >> (slot & 7)) & 1 != 0
@@ -64,7 +81,9 @@ impl PersistentBitVec {
     pub fn fill_batch(&self, slots: &[usize], out: &mut [bool]) {
         assert_eq!(slots.len(), out.len());
         let n = slots.len();
-        if n == 0 { return; }
+        if n == 0 {
+            return;
+        }
         let mut perm: Vec<usize> = (0..n).collect();
         perm.sort_by_key(|&i| slots[i]);
         let sorted: Vec<usize> = perm.iter().map(|&i| slots[i]).collect();
@@ -86,7 +105,7 @@ impl PersistentBitVec {
 
     // SAFETY: mmap is page-aligned, HEADER_SIZE=16 divisible by 8 → u64-aligned.
     fn data_words(&self) -> &[u64] {
-        let nw  = n_words(self.n);
+        let nw = n_words(self.n);
         let ptr = self.mmap[HEADER_SIZE..].as_ptr() as *const u64;
         unsafe { std::slice::from_raw_parts(ptr, nw) }
     }
@@ -95,10 +114,16 @@ impl PersistentBitVec {
         BitSliceView::new(self.data_words(), self.n)
     }
 
-    pub fn words(&self) -> &[u64] { self.data_words() }
+    pub fn words(&self) -> &[u64] {
+        self.data_words()
+    }
 
-    pub fn count_ones(&self)  -> u64 { self.view().count_ones() }
-    pub fn count_zeros(&self) -> u64 { self.view().count_zeros() }
+    pub fn count_ones(&self) -> u64 {
+        self.view().count_ones()
+    }
+    pub fn count_zeros(&self) -> u64 {
+        self.view().count_zeros()
+    }
 
     pub fn partial_jaccard_dist(&self, other: &PersistentBitVec) -> (u64, u64) {
         self.view().partial_jaccard_dist(other.view())
@@ -111,22 +136,28 @@ impl PersistentBitVec {
     }
 
     pub fn iter(&self) -> BitIter<'_> {
-        BitIter { words: self.data_words(), slot: 0, n: self.n }
+        BitIter {
+            words: self.data_words(),
+            slot: 0,
+            n: self.n,
+        }
     }
 }
 
 impl<'a> IntoIterator for &'a PersistentBitVec {
     type Item = bool;
     type IntoIter = BitIter<'a>;
-    fn into_iter(self) -> BitIter<'a> { self.iter() }
+    fn into_iter(self) -> BitIter<'a> {
+        self.iter()
+    }
 }
 
 // ── BitIter ───────────────────────────────────────────────────────────────────
 
 pub struct BitIter<'a> {
     words: &'a [u64],
-    slot:  usize,
-    n:     usize,
+    slot: usize,
+    n: usize,
 }
 
 impl ExactSizeIterator for BitIter<'_> {}
@@ -134,7 +165,9 @@ impl ExactSizeIterator for BitIter<'_> {}
 impl Iterator for BitIter<'_> {
     type Item = bool;
     fn next(&mut self) -> Option<bool> {
-        if self.slot >= self.n { return None; }
+        if self.slot >= self.n {
+            return None;
+        }
         let v = (self.words[self.slot >> 6] >> (self.slot & 63)) & 1 != 0;
         self.slot += 1;
         Some(v)
@@ -149,7 +182,7 @@ impl Iterator for BitIter<'_> {
 
 pub struct PersistentBitVecBuilder {
     mmap: MmapMut,
-    n:    usize,
+    n: usize,
     path: PathBuf,
 }
 
@@ -157,7 +190,10 @@ impl PersistentBitVecBuilder {
     pub fn new(n: usize, path: &Path) -> io::Result<Self> {
         let file_size = HEADER_SIZE + n_bytes_for_words(n);
         let mut file = OpenOptions::new()
-            .read(true).write(true).create(true).truncate(true)
+            .read(true)
+            .write(true)
+            .create(true)
+            .truncate(true)
             .open(path)?;
         file.write_all(&MAGIC)?;
         file.write_all(&[0u8; 4])?;
@@ -165,20 +201,31 @@ impl PersistentBitVecBuilder {
         file.seek(SeekFrom::Start(0))?;
         file.set_len(file_size as u64)?;
         let mmap = unsafe { MmapMut::map_mut(&file)? };
-        Ok(Self { mmap, n, path: path.to_path_buf() })
+        Ok(Self {
+            mmap,
+            n,
+            path: path.to_path_buf(),
+        })
     }
 
     pub fn from_raw_bytes(bytes: &[u8], n: usize, path: &Path) -> io::Result<Self> {
         let file_size = HEADER_SIZE + n_bytes_for_words(n);
         let file = OpenOptions::new()
-            .read(true).write(true).create(true).truncate(true)
+            .read(true)
+            .write(true)
+            .create(true)
+            .truncate(true)
             .open(path)?;
         file.set_len(file_size as u64)?;
         let mut mmap = unsafe { MmapMut::map_mut(&file)? };
         mmap[0..4].copy_from_slice(&MAGIC);
         mmap[8..16].copy_from_slice(&(n as u64).to_le_bytes());
         mmap[HEADER_SIZE..HEADER_SIZE + bytes.len()].copy_from_slice(bytes);
-        Ok(Self { mmap, n, path: path.to_path_buf() })
+        Ok(Self {
+            mmap,
+            n,
+            path: path.to_path_buf(),
+        })
     }
 
     /// Create an all-ones bit vector of length `n` at `path`.
@@ -186,10 +233,13 @@ impl PersistentBitVecBuilder {
     /// More efficient than `new(n, path)` + `not()`: the data is written as
     /// 0xFF bytes in a single sequential pass, with no intermediate all-zeros state.
     pub fn new_ones(n: usize, path: &Path) -> io::Result<Self> {
-        let nw        = n_words(n);
+        let nw = n_words(n);
         let file_size = HEADER_SIZE + nw * 8;
-        let mut file  = OpenOptions::new()
-            .read(true).write(true).create(true).truncate(true)
+        let mut file = OpenOptions::new()
+            .read(true)
+            .write(true)
+            .create(true)
+            .truncate(true)
             .open(path)?;
         file.write_all(&MAGIC)?;
         file.write_all(&[0u8; 4])?;
@@ -201,11 +251,15 @@ impl PersistentBitVecBuilder {
         // Clear padding bits in the last word so trailing bits are always 0.
         let rem = n % 64;
         if rem != 0 {
-            let ptr   = mmap[HEADER_SIZE..].as_mut_ptr() as *mut u64;
+            let ptr = mmap[HEADER_SIZE..].as_mut_ptr() as *mut u64;
             let words = unsafe { std::slice::from_raw_parts_mut(ptr, nw) };
             words[nw - 1] &= (1u64 << rem) - 1;
         }
-        Ok(Self { mmap, n, path: path.to_path_buf() })
+        Ok(Self {
+            mmap,
+            n,
+            path: path.to_path_buf(),
+        })
     }
 
     pub fn build_from(source: &PersistentBitVec, path: &Path) -> io::Result<Self> {
@@ -213,14 +267,25 @@ impl PersistentBitVecBuilder {
         let file = OpenOptions::new().read(true).write(true).open(path)?;
         let mmap = unsafe { MmapMut::map_mut(&file)? };
         let n = source.len();
-        Ok(Self { mmap, n, path: path.to_path_buf() })
+        Ok(Self {
+            mmap,
+            n,
+            path: path.to_path_buf(),
+        })
     }
 
-    pub fn build_from_counts(source: &PersistentCompactIntVec, threshold: u32, path: &Path) -> io::Result<Self> {
+    pub fn build_from_counts(
+        source: &PersistentCompactIntVec,
+        threshold: u32,
+        path: &Path,
+    ) -> io::Result<Self> {
         let n = source.len();
         let file_size = HEADER_SIZE + n_bytes_for_words(n);
         let mut file = OpenOptions::new()
-            .read(true).write(true).create(true).truncate(true)
+            .read(true)
+            .write(true)
+            .create(true)
+            .truncate(true)
             .open(path)?;
         file.write_all(&MAGIC)?;
         file.write_all(&[0u8; 4])?;
@@ -229,22 +294,32 @@ impl PersistentBitVecBuilder {
         file.set_len(file_size as u64)?;
         let mut mmap = unsafe { MmapMut::map_mut(&file)? };
         {
-            let nw  = n_words(n);
+            let nw = n_words(n);
             let ptr = mmap[HEADER_SIZE..].as_mut_ptr() as *mut u64;
             let words = unsafe { std::slice::from_raw_parts_mut(ptr, nw) };
             for (slot, count) in source.iter().enumerate() {
-                if count >= threshold { words[slot >> 6] |= 1u64 << (slot & 63); }
+                if count >= threshold {
+                    words[slot >> 6] |= 1u64 << (slot & 63);
+                }
             }
         }
-        Ok(Self { mmap, n, path: path.to_path_buf() })
+        Ok(Self {
+            mmap,
+            n,
+            path: path.to_path_buf(),
+        })
     }
 
     pub fn build_from_presence(source: &PersistentCompactIntVec, path: &Path) -> io::Result<Self> {
         Self::build_from_counts(source, 1, path)
     }
 
-    pub fn len(&self)      -> usize { self.n }
-    pub fn is_empty(&self) -> bool  { self.n == 0 }
+    pub fn len(&self) -> usize {
+        self.n
+    }
+    pub fn is_empty(&self) -> bool {
+        self.n == 0
+    }
 
     pub fn get(&self, slot: usize) -> bool {
         (self.mmap[HEADER_SIZE + (slot >> 3)] >> (slot & 7)) & 1 != 0
@@ -252,19 +327,22 @@ impl PersistentBitVecBuilder {
 
     pub fn set(&mut self, slot: usize, value: bool) {
         let bit = 1u64 << (slot & 63);
-        if value { self.data_words_mut()[slot >> 6] |=  bit; }
-        else     { self.data_words_mut()[slot >> 6] &= !bit; }
+        if value {
+            self.data_words_mut()[slot >> 6] |= bit;
+        } else {
+            self.data_words_mut()[slot >> 6] &= !bit;
+        }
     }
 
     fn data_words(&self) -> &[u64] {
-        let nw  = n_words(self.n);
+        let nw = n_words(self.n);
         let ptr = self.mmap[HEADER_SIZE..].as_ptr() as *const u64;
         unsafe { std::slice::from_raw_parts(ptr, nw) }
     }
 
     // SAFETY: same alignment argument as PersistentBitVec::data_words.
     fn data_words_mut(&mut self) -> &mut [u64] {
-        let nw  = n_words(self.n);
+        let nw = n_words(self.n);
         let ptr = self.mmap[HEADER_SIZE..].as_mut_ptr() as *mut u64;
         unsafe { std::slice::from_raw_parts_mut(ptr, nw) }
     }
@@ -273,7 +351,9 @@ impl PersistentBitVecBuilder {
         BitSliceView::new(self.data_words(), self.n)
     }
 
-    pub fn words(&self) -> &[u64] { self.data_words() }
+    pub fn words(&self) -> &[u64] {
+        self.data_words()
+    }
 
     pub fn copy_from(&mut self, src: BitSliceView<'_>) {
         assert_eq!(self.n, src.len(), "BitSliceView length mismatch");
@@ -282,25 +362,35 @@ impl PersistentBitVecBuilder {
 
     pub fn and(&mut self, other: BitSliceView<'_>) {
         assert_eq!(self.n, other.len(), "BitSliceView length mismatch");
-        for (w, &o) in self.data_words_mut().iter_mut().zip(other.words()) { *w &= o; }
+        for (w, &o) in self.data_words_mut().iter_mut().zip(other.words()) {
+            *w &= o;
+        }
     }
 
     pub fn or(&mut self, other: BitSliceView<'_>) {
         assert_eq!(self.n, other.len(), "BitSliceView length mismatch");
-        for (w, &o) in self.data_words_mut().iter_mut().zip(other.words()) { *w |= o; }
+        for (w, &o) in self.data_words_mut().iter_mut().zip(other.words()) {
+            *w |= o;
+        }
     }
 
     pub fn xor(&mut self, other: BitSliceView<'_>) {
         assert_eq!(self.n, other.len(), "BitSliceView length mismatch");
-        for (w, &o) in self.data_words_mut().iter_mut().zip(other.words()) { *w ^= o; }
+        for (w, &o) in self.data_words_mut().iter_mut().zip(other.words()) {
+            *w ^= o;
+        }
     }
 
     pub fn not(&mut self) {
-        let rem   = self.n % 64;
+        let rem = self.n % 64;
         let words = self.data_words_mut();
-        for w in words.iter_mut() { *w ^= u64::MAX; }
+        for w in words.iter_mut() {
+            *w ^= u64::MAX;
+        }
         if rem != 0 {
-            if let Some(last) = words.last_mut() { *last &= (1u64 << rem) - 1; }
+            if let Some(last) = words.last_mut() {
+                *last &= (1u64 << rem) - 1;
+            }
         }
     }
 
@@ -312,17 +402,21 @@ impl PersistentBitVecBuilder {
         let words = self.data_words_mut();
         let nw = n_words(n);
         for wi in 0..nw {
-            let base  = wi * 64;
+            let base = wi * 64;
             let limit = (base + 64).min(n);
             let mut mask = 0u64;
             for bit in 0..(limit - base) {
                 let b = primary[base + bit];
-                if b < 255 && pred(b as u32) { mask |= 1u64 << bit; }
+                if b < 255 && pred(b as u32) {
+                    mask |= 1u64 << bit;
+                }
             }
             words[wi] |= mask;
         }
         for (slot, val) in col.overflow_entries() {
-            if pred(val) { words[slot >> 6] |= 1u64 << (slot & 63); }
+            if pred(val) {
+                words[slot >> 6] |= 1u64 << (slot & 63);
+            }
         }
     }
 
@@ -334,17 +428,21 @@ impl PersistentBitVecBuilder {
         let words = self.data_words_mut();
         let nw = n_words(n);
         for wi in 0..nw {
-            let base  = wi * 64;
+            let base = wi * 64;
             let limit = (base + 64).min(n);
             let mut mask = 0u64;
             for bit in 0..(limit - base) {
                 let b = primary[base + bit];
-                if b < 255 && !pred(b as u32) { mask |= 1u64 << bit; }
+                if b < 255 && !pred(b as u32) {
+                    mask |= 1u64 << bit;
+                }
             }
             words[wi] &= !mask;
         }
         for (slot, val) in col.overflow_entries() {
-            if !pred(val) { words[slot >> 6] &= !(1u64 << (slot & 63)); }
+            if !pred(val) {
+                words[slot >> 6] &= !(1u64 << (slot & 63));
+            }
         }
     }
 
@@ -356,17 +454,21 @@ impl PersistentBitVecBuilder {
         let words = self.data_words_mut();
         let nw = n_words(n);
         for wi in 0..nw {
-            let base  = wi * 64;
+            let base = wi * 64;
             let limit = (base + 64).min(n);
             let mut mask = 0u64;
             for bit in 0..(limit - base) {
                 let b = primary[base + bit];
-                if b < 255 && pred(b as u32) { mask |= 1u64 << bit; }
+                if b < 255 && pred(b as u32) {
+                    mask |= 1u64 << bit;
+                }
             }
             words[wi] ^= mask;
         }
         for (slot, val) in col.overflow_entries() {
-            if pred(val) { words[slot >> 6] ^= 1u64 << (slot & 63); }
+            if pred(val) {
+                words[slot >> 6] ^= 1u64 << (slot & 63);
+            }
         }
     }
 
@@ -374,7 +476,9 @@ impl PersistentBitVecBuilder {
         self.view().iter()
     }
 
-    pub fn close(self) -> io::Result<()> { self.mmap.flush() }
+    pub fn close(self) -> io::Result<()> {
+        self.mmap.flush()
+    }
 
     pub fn finish(self) -> io::Result<PersistentBitVec> {
         let path = self.path.clone();
diff --git a/src/obikphylo/src/siblings/build.rs b/src/obikphylo/src/siblings/build.rs
index c2f7a2f5..a57b8977 100644
--- a/src/obikphylo/src/siblings/build.rs
+++ b/src/obikphylo/src/siblings/build.rs
@@ -132,20 +132,12 @@ fn build_layer_sibling_annex(
     let n = mphf.n();
 
     // Whether this layer's family-member fields can carry a real layer
-    // number (fast path, exploited by a future scan-time reader) or must
-    // stay presence-only (today's behaviour) — a single fact about the
-    // whole index, decided once here, never stored: `n_layers` is
-    // guaranteed identical across every partition (a merge adds one layer
-    // to all of them at once), and `FamilyMask`'s 3-bit field only has room
-    // for layers `0..=6`.
-    let fast_mode = meta.n_layers <= 7;
-    if !fast_mode {
-        tracing::warn!(
-            "layer {l} ({layer_dir:?}): index has {} layers (>7) — sibling-annex fast layer \
-             lookup disabled for this build; consider compacting this index",
-            meta.n_layers
-        );
-    }
+    // number (exploited by `family_scan::scan_layer_families`'s fast path)
+    // or must stay presence-only — a single fact about the whole index,
+    // decided once by `cache` (built from the same `PartitionMeta` this
+    // function would otherwise re-derive) so the writer and every reader
+    // agree; see `PartitionCache::fast_mode`'s docs.
+    let fast_mode = cache.fast_mode();
 
         // ── The annex file itself is the reconciliation state, indexed by
         // this layer's k-mer iteration order (the physical layout of
diff --git a/src/obikphylo/src/siblings/cache.rs b/src/obikphylo/src/siblings/cache.rs
index 003bd342..99933c6d 100644
--- a/src/obikphylo/src/siblings/cache.rs
+++ b/src/obikphylo/src/siblings/cache.rs
@@ -117,18 +117,28 @@ pub(super) struct PartitionCache {
     /// both [`obikindex::KmerIndex::build_sibling_annex`] and
     /// [`obikindex::KmerIndex::sibling_annex_stats`].
     mats: Vec<Vec<Mat>>,
+    /// Whether every `FamilyMask` field in this index's sibling annexes can
+    /// be trusted as a real layer index (`n_layers <= 7`, the same decision
+    /// `build_layer_sibling_annex` makes when writing them) — computed once
+    /// here, from `PartitionMeta::n_layers` (not `mats[p].len()`, which can
+    /// undercount if a layer failed to open), reused by both the annex
+    /// writer (`build.rs`) and reader (`family_scan.rs`) so the two never
+    /// disagree. `n_layers` is guaranteed identical across every partition
+    /// (a merge adds one layer to all of them at once), so the first
+    /// non-empty partition's count speaks for the whole index.
+    fast_mode: bool,
 }
 
 impl PartitionCache {
     pub(super) fn build(partition: &KmerPartition, n_parts: usize, with_counts: bool) -> OKIResult<Self> {
         let pb = progress_bar("open_partitions", n_parts as u64, "partitions");
-        let built: Vec<Vec<Mat>> = (0..n_parts)
+        let built: Vec<(Vec<Mat>, usize)> = (0..n_parts)
             .into_par_iter()
-            .map(|part| -> OKIResult<Vec<Mat>> {
+            .map(|part| -> OKIResult<(Vec<Mat>, usize)> {
                 let index_dir = partition.part_dir(part).join(INDEX_SUBDIR);
                 if !index_dir.exists() {
                     pb.inc(1);
-                    return Ok(Vec::new());
+                    return Ok((Vec::new(), 0));
                 }
                 let meta = PartitionMeta::load(&index_dir).map_err(olm_to_ok)?;
                 let mut mats = Vec::with_capacity(meta.n_layers);
@@ -144,11 +154,27 @@ impl PartitionCache {
                     mats.push(mat);
                 }
                 pb.inc(1);
-                Ok(mats)
+                Ok((mats, meta.n_layers))
             })
             .collect::<OKIResult<Vec<_>>>()?;
         pb.finish_and_clear();
-        Ok(Self { mats: built })
+
+        let n_layers = built.iter().map(|&(_, n)| n).find(|&n| n > 0).unwrap_or(0);
+        let fast_mode = n_layers <= 7;
+        if !fast_mode {
+            tracing::warn!(
+                "index has {n_layers} layers (>7) — sibling-annex fast layer lookup disabled; \
+                 consider compacting this index"
+            );
+        }
+
+        let mats = built.into_iter().map(|(m, _)| m).collect();
+        Ok(Self { mats, fast_mode })
+    }
+
+    /// See the [`fast_mode`](Self::fast_mode) field docs.
+    pub(super) fn fast_mode(&self) -> bool {
+        self.fast_mode
     }
 
     /// Existence lookup of `variant` in partition `dest_partition`: tries
@@ -186,10 +212,16 @@ impl PartitionCache {
     /// `PersistentBitMatrix::get` dominated wall-clock time, mostly blocked
     /// on page faults, even after every partition/batch locality fix above
     /// this in the traversal.
+    /// `queries`' 4th element (the annex-recorded layer) is ignored here —
+    /// every layer is probed with evidence regardless, since this is the
+    /// `!fast_mode` fallback where that field isn't trustworthy (see
+    /// [`find_presence_batch_fast`](Self::find_presence_batch_fast)). Same
+    /// tuple shape as the fast path purely so callers don't need two
+    /// query representations.
     pub(super) fn find_presence_batch(
         &self,
         dest_partition: usize,
-        queries: &[(CanonicalKmer, usize, u8)],
+        queries: &[(CanonicalKmer, usize, u8, u8)],
         n_genomes: usize,
         mut on_hit: impl FnMut(usize, u8, usize),
     ) {
@@ -198,7 +230,7 @@ impl PartitionCache {
         // First hit wins, same semantics as the old per-query loop (a
         // variant present in an earlier layer shadows later ones).
         let mut by_layer: Vec<Vec<(usize, usize, u8)>> = vec![Vec::new(); mats.len()];
-        for &(variant, family_idx, base) in queries {
+        for &(variant, family_idx, base, _layer) in queries {
             for (li, mat) in mats.iter().enumerate() {
                 if let Some(slot) = mat.find_slot(variant) {
                     by_layer[li].push((slot, family_idx, base));
@@ -211,17 +243,75 @@ impl PartitionCache {
             if hits.is_empty() {
                 continue;
             }
+            resolve_layer_hits(&mats[li], &hits, n_genomes, &mut on_hit);
+        }
+    }
+
+    /// Same contract as [`find_presence_batch`](Self::find_presence_batch),
+    /// but only valid when [`fast_mode`](Self::fast_mode) is true for this
+    /// whole index: every query's 4th element is trusted outright as its
+    /// real destination layer (recorded once, evidence-checked, at
+    /// annex-build time by [`find`](Self::find)) — no per-layer probing, a
+    /// direct `index_batch` (no evidence) straight to that layer instead.
+    /// Safe for the same reason `build_layer_sibling_annex`'s own
+    /// iteration-pipeline lookups are: this exact variant's membership in
+    /// this exact layer was already positively established once: replaying
+    /// it via `index`/`index_batch` here isn't a fresh, unverified
+    /// assumption, it's reusing a fact already paid for.
+    pub(super) fn find_presence_batch_fast(
+        &self,
+        dest_partition: usize,
+        queries: &[(CanonicalKmer, usize, u8, u8)],
+        n_genomes: usize,
+        mut on_hit: impl FnMut(usize, u8, usize),
+    ) {
+        let Some(mats) = self.mats.get(dest_partition) else { return };
+
+        let mut by_layer: Vec<Vec<(CanonicalKmer, usize, u8)>> = vec![Vec::new(); mats.len()];
+        for &(variant, family_idx, base, layer) in queries {
+            if let Some(bucket) = by_layer.get_mut(layer as usize) {
+                bucket.push((variant, family_idx, base));
+            }
+        }
+
+        for (li, entries) in by_layer.into_iter().enumerate() {
+            if entries.is_empty() {
+                continue;
+            }
             let mat = &mats[li];
-            let n_cols = mat.n_cols().min(n_genomes);
-            let slots: Vec<usize> = hits.iter().map(|&(slot, _, _)| slot).collect();
-            let mut carries: Vec<Vec<bool>> = (0..n_cols).map(|_| Vec::new()).collect();
-            mat.fill_sub_matrix_carries(&slots, &mut carries);
-            for (g, col) in carries.iter().enumerate() {
-                for (&(_, family_idx, base), &carries_it) in hits.iter().zip(col.iter()) {
-                    if carries_it {
-                        on_hit(family_idx, base, g);
-                    }
-                }
+            let variants: Vec<CanonicalKmer> = entries.iter().map(|&(variant, _, _)| variant).collect();
+            let slots = mat.index_batch(&variants);
+            let hits: Vec<(usize, usize, u8)> = slots
+                .into_iter()
+                .zip(entries.iter())
+                .map(|(slot, &(_, family_idx, base))| (slot, family_idx, base))
+                .collect();
+            resolve_layer_hits(mat, &hits, n_genomes, &mut on_hit);
+        }
+    }
+}
+
+/// Shared tail of both [`PartitionCache::find_presence_batch`] and
+/// [`PartitionCache::find_presence_batch_fast`]: given one layer's already-
+/// resolved `(slot, family_idx, base)` hits, sweep genome-major (via
+/// `fill_sub_matrix_carries`, buffer-reusing, no per-call allocation) and
+/// call `on_hit` for every carry. The two callers differ only in *how*
+/// `hits` gets its slots (evidence-probed vs. trusted `index_batch`) — this
+/// is everything after that.
+fn resolve_layer_hits(
+    mat: &Mat,
+    hits: &[(usize, usize, u8)],
+    n_genomes: usize,
+    on_hit: &mut impl FnMut(usize, u8, usize),
+) {
+    let n_cols = mat.n_cols().min(n_genomes);
+    let slots: Vec<usize> = hits.iter().map(|&(slot, _, _)| slot).collect();
+    let mut carries: Vec<Vec<bool>> = (0..n_cols).map(|_| Vec::new()).collect();
+    mat.fill_sub_matrix_carries(&slots, &mut carries);
+    for (g, col) in carries.iter().enumerate() {
+        for (&(_, family_idx, base), &carries_it) in hits.iter().zip(col.iter()) {
+            if carries_it {
+                on_hit(family_idx, base, g);
             }
         }
     }
diff --git a/src/obikphylo/src/siblings/family_scan.rs b/src/obikphylo/src/siblings/family_scan.rs
index fdde2249..46e5f76d 100644
--- a/src/obikphylo/src/siblings/family_scan.rs
+++ b/src/obikphylo/src/siblings/family_scan.rs
@@ -136,8 +136,11 @@ struct GeneratedBatch {
     masks: Vec<FamilyMask>,
     /// Flat `slots.len() * n_genomes` — `genome_mask[i * n_genomes + g]`.
     genome_mask: Vec<u8>,
-    /// `outgoing[dest_partition]` = `(variant, family_idx_in_batch, base)`.
-    outgoing: Vec<Vec<(CanonicalKmer, usize, u8)>>,
+    /// `outgoing[dest_partition]` = `(variant, family_idx_in_batch, base,
+    /// layer)` — `layer` is the annex-recorded destination layer
+    /// (`FamilyMask::family_members`'s `layer_value`, `0` if absent),
+    /// trustworthy only when `PartitionCache::fast_mode()` is true.
+    outgoing: Vec<Vec<(CanonicalKmer, usize, u8, u8)>>,
     _permit: ThrottleGuard,
 }
 
@@ -210,27 +213,27 @@ pub(super) fn scan_layer_families(
                 let mut masks = Vec::with_capacity(n);
                 let mut bases = Vec::with_capacity(n);
                 let mut genome_mask = vec![0u8; n * ctx.n_genomes];
-                let mut outgoing: Vec<Vec<(CanonicalKmer, usize, u8)>> = (0..ctx.n_parts).map(|_| Vec::new()).collect();
+                let mut outgoing: Vec<Vec<(CanonicalKmer, usize, u8, u8)>> = (0..ctx.n_parts).map(|_| Vec::new()).collect();
 
                 // Pass 1: cheap, no matrix access — own base and this
                 // batch's cross-partition queries. Kmer and mask already in
                 // hand from `iter_minorants_batch`, no second annex read,
-                // no slot lookup needed for this pass.
+                // no slot lookup needed for this pass. `family_members`
+                // (not a hand-rolled `central_canonical_neighbors` +
+                // `mask.has` loop) already filters to present members and
+                // hands back each one's annex-recorded layer alongside.
                 for (i, entry) in batch.entries.iter().enumerate() {
                     let (kmer, mask) = (entry.kmer, entry.mask);
                     masks.push(mask);
                     let base = central_base(kmer, ctx.k);
                     bases.push(base);
-                    for other in kmer.central_canonical_neighbors() {
-                        if other == kmer {
+                    for (member, layer) in mask.family_members(kmer, ctx.k) {
+                        if member == kmer {
                             continue; // local — resolved below straight from `mat`, no lookup
                         }
-                        let b = central_base(other, ctx.k);
-                        if !mask.has(b) {
-                            continue;
-                        }
-                        let dest = other.partition(ctx.n_parts);
-                        outgoing[dest].push((other, i, b));
+                        let b = central_base(member, ctx.k);
+                        let dest = member.partition(ctx.n_parts);
+                        outgoing[dest].push((member, i, b, layer.unwrap_or(0)));
                     }
                 }
 
@@ -280,10 +283,16 @@ pub(super) fn scan_layer_families(
             // module docs), each thread owning one partition's queries
             // contiguously until this batch is done.
             let genome_mask: Vec<AtomicU8> = batch.genome_mask.into_iter().map(AtomicU8::new).collect();
+            let fast_mode = cache.fast_mode();
             batch.outgoing.par_iter().enumerate().filter(|(_, q)| !q.is_empty()).for_each(|(dest, queries)| {
-                cache.find_presence_batch(dest, queries, n_genomes, |i, base, g| {
+                let on_hit = |i: usize, base: u8, g: usize| {
                     genome_mask[i * n_genomes + g].fetch_or(1 << base, Ordering::Relaxed);
-                });
+                };
+                if fast_mode {
+                    cache.find_presence_batch_fast(dest, queries, n_genomes, on_hit);
+                } else {
+                    cache.find_presence_batch(dest, queries, n_genomes, on_hit);
+                }
             });
 
             for i in 0..n {
-- 
2.54.0


From 151493526ce5e0f7c57fa1820fd86ff1cf86d416 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Fri, 14 Aug 2026 22:29:46 +0200
Subject: [PATCH 30/46] perf: add #[inline] attributes to obicompactvec methods

Adds compiler inlining hints to accessors, iterators, bitwise operations, and distance functions across multiple modules. This optimization aims to reduce call overhead for frequently invoked methods without modifying runtime behavior, API contracts, or data models.
---
 src/obicompactvec/src/bitmatrix/columnar.rs   |  5 +++
 src/obicompactvec/src/bitmatrix/packed.rs     |  4 +++
 src/obicompactvec/src/bitmatrix/persistent.rs | 11 +++++++
 src/obicompactvec/src/bitvec.rs               | 25 ++++++++++++++
 src/obicompactvec/src/builder.rs              | 12 +++++++
 src/obicompactvec/src/intmatrix.rs            | 33 +++++++++++++++++++
 src/obicompactvec/src/reader.rs               | 11 +++++++
 src/obicompactvec/src/tempbitvec.rs           | 16 +++++++++
 src/obicompactvec/src/tempintvec.rs           | 20 +++++++++++
 src/obicompactvec/src/views.rs                | 14 ++++++++
 10 files changed, 151 insertions(+)

diff --git a/src/obicompactvec/src/bitmatrix/columnar.rs b/src/obicompactvec/src/bitmatrix/columnar.rs
index ccbd3d53..273cc773 100644
--- a/src/obicompactvec/src/bitmatrix/columnar.rs
+++ b/src/obicompactvec/src/bitmatrix/columnar.rs
@@ -27,14 +27,19 @@ impl ColumnarBitMatrix {
         Ok(Self { cols, n: meta.n })
     }
 
+    #[inline]
     pub(crate) fn n(&self)      -> usize { self.n }
+    #[inline]
     pub(crate) fn n_cols(&self) -> usize { self.cols.len() }
+    #[inline]
     pub(crate) fn col(&self, c: usize) -> &PersistentBitVec { &self.cols[c] }
 
+    #[inline]
     pub(crate) fn row(&self, slot: usize) -> Box<[bool]> {
         self.cols.iter().map(|c| c.get(slot)).collect()
     }
 
+    #[inline]
     pub(crate) fn fill_row(&self, slot: usize, buf: &mut [u32]) {
         for (c, col) in self.cols.iter().enumerate() {
             buf[c] = col.get(slot) as u32;
diff --git a/src/obicompactvec/src/bitmatrix/packed.rs b/src/obicompactvec/src/bitmatrix/packed.rs
index f0a89b8c..840abdb5 100644
--- a/src/obicompactvec/src/bitmatrix/packed.rs
+++ b/src/obicompactvec/src/bitmatrix/packed.rs
@@ -58,17 +58,20 @@ impl PackedBitMatrix {
         }
     }
 
+    #[inline]
     pub(crate) fn row(&self, slot: usize) -> Box<[bool]> {
         (0..self.n_cols).map(|c| {
             (self.mmap[self.data_offsets[c] + (slot >> 3)] >> (slot & 7)) & 1 != 0
         }).collect()
     }
 
+    #[inline]
     fn col_bytes(&self, c: usize) -> &[u8] {
         let start = self.data_offsets[c];
         &self.mmap[start..start + self.n_rows.div_ceil(8)]
     }
 
+    #[inline]
     fn col_words(&self, c: usize) -> &[u64] {
         let nw = self.n_rows.div_ceil(64);
         // SAFETY: data_offsets[c] is always 8-byte aligned.
@@ -78,6 +81,7 @@ impl PackedBitMatrix {
         unsafe { std::slice::from_raw_parts(ptr, nw) }
     }
 
+    #[inline]
     pub(crate) fn col_slice(&self, c: usize) -> BitSliceView<'_> {
         BitSliceView::new(self.col_words(c), self.n_rows)
     }
diff --git a/src/obicompactvec/src/bitmatrix/persistent.rs b/src/obicompactvec/src/bitmatrix/persistent.rs
index 3149241c..7b5dad47 100644
--- a/src/obicompactvec/src/bitmatrix/persistent.rs
+++ b/src/obicompactvec/src/bitmatrix/persistent.rs
@@ -55,6 +55,7 @@ impl PersistentBitMatrix {
         Ok(Self::Implicit { n_rows: meta.n, n_cols: 1 })
     }
 
+    #[inline]
     pub fn n(&self) -> usize {
         match self {
             Self::Columnar(m)            => m.n(),
@@ -63,6 +64,7 @@ impl PersistentBitMatrix {
         }
     }
 
+    #[inline]
     pub fn n_cols(&self) -> usize {
         match self {
             Self::Columnar(m)            => m.n_cols(),
@@ -71,6 +73,7 @@ impl PersistentBitMatrix {
         }
     }
 
+    #[inline]
     pub fn col(&self, c: usize) -> &PersistentBitVec {
         match self {
             Self::Columnar(m) => m.col(c),
@@ -78,6 +81,7 @@ impl PersistentBitMatrix {
         }
     }
 
+    #[inline]
     pub fn col_view(&self, c: usize) -> BitSliceView<'_> {
         match self {
             Self::Columnar(m) => m.col(c).view(),
@@ -91,6 +95,7 @@ impl PersistentBitMatrix {
     /// Unlike [`col_view`](Self::col_view), this never panics on `Implicit`
     /// (every column reads as present, per the mono-genome fast path) — safe
     /// to call for any `c < self.n_cols()`.
+    #[inline]
     pub fn get(&self, c: usize, slot: usize) -> u32 {
         match self {
             Self::Columnar(m) => m.col(c).get(slot) as u32,
@@ -109,6 +114,7 @@ impl PersistentBitMatrix {
         }
     }
 
+    #[inline]
     pub fn row(&self, slot: usize) -> Box<[bool]> {
         match self {
             Self::Columnar(m)             => m.row(slot),
@@ -118,6 +124,7 @@ impl PersistentBitMatrix {
     }
 
     /// Fill `buf[i]` with `col_i[slot]` as 0/1 u32, without allocating.
+    #[inline]
     pub fn fill_row(&self, slot: usize, buf: &mut [u32]) {
         match self {
             Self::Columnar(m)             => m.fill_row(slot, buf),
@@ -177,6 +184,7 @@ impl PersistentBitMatrix {
         }
     }
 
+    #[inline]
     pub fn count_ones(&self) -> Array1<u64> {
         match self {
             Self::Columnar(m)              => m.count_ones(),
@@ -219,13 +227,16 @@ impl PersistentBitMatrix {
 // ── Trait impls ───────────────────────────────────────────────────────────────
 
 impl ColumnWeights for PersistentBitMatrix {
+    #[inline]
     fn col_weights(&self) -> Array1<u64> { self.count_ones() }
 }
 
 impl BitPartials for PersistentBitMatrix {
+    #[inline]
     fn partial_jaccard(&self) -> (Array2<u64>, Array2<u64>) {
         self.partial_jaccard_dist_matrix()
     }
+    #[inline]
     fn partial_hamming(&self) -> Array2<u64> {
         self.partial_hamming_dist_matrix()
     }
diff --git a/src/obicompactvec/src/bitvec.rs b/src/obicompactvec/src/bitvec.rs
index a1bd7798..58297ee9 100644
--- a/src/obicompactvec/src/bitvec.rs
+++ b/src/obicompactvec/src/bitvec.rs
@@ -51,16 +51,20 @@ impl PersistentBitVec {
         })
     }
 
+    #[inline]
     pub fn path(&self) -> &Path {
         &self.path
     }
+    #[inline]
     pub fn len(&self) -> usize {
         self.n
     }
+    #[inline]
     pub fn is_empty(&self) -> bool {
         self.n == 0
     }
 
+    #[inline]
     pub fn get(&self, slot: usize) -> bool {
         (self.mmap[HEADER_SIZE + (slot >> 3)] >> (slot & 7)) & 1 != 0
     }
@@ -104,37 +108,46 @@ impl PersistentBitVec {
     }
 
     // SAFETY: mmap is page-aligned, HEADER_SIZE=16 divisible by 8 → u64-aligned.
+    #[inline]
     fn data_words(&self) -> &[u64] {
         let nw = n_words(self.n);
         let ptr = self.mmap[HEADER_SIZE..].as_ptr() as *const u64;
         unsafe { std::slice::from_raw_parts(ptr, nw) }
     }
 
+    #[inline]
     pub fn view(&self) -> BitSliceView<'_> {
         BitSliceView::new(self.data_words(), self.n)
     }
 
+    #[inline]
     pub fn words(&self) -> &[u64] {
         self.data_words()
     }
 
+    #[inline]
     pub fn count_ones(&self) -> u64 {
         self.view().count_ones()
     }
+    #[inline]
     pub fn count_zeros(&self) -> u64 {
         self.view().count_zeros()
     }
 
+    #[inline]
     pub fn partial_jaccard_dist(&self, other: &PersistentBitVec) -> (u64, u64) {
         self.view().partial_jaccard_dist(other.view())
     }
+    #[inline]
     pub fn jaccard_dist(&self, other: &PersistentBitVec) -> f64 {
         self.view().jaccard_dist(other.view())
     }
+    #[inline]
     pub fn hamming_dist(&self, other: &PersistentBitVec) -> u64 {
         self.view().hamming_dist(other.view())
     }
 
+    #[inline]
     pub fn iter(&self) -> BitIter<'_> {
         BitIter {
             words: self.data_words(),
@@ -147,6 +160,7 @@ impl PersistentBitVec {
 impl<'a> IntoIterator for &'a PersistentBitVec {
     type Item = bool;
     type IntoIter = BitIter<'a>;
+    #[inline]
     fn into_iter(self) -> BitIter<'a> {
         self.iter()
     }
@@ -164,6 +178,7 @@ impl ExactSizeIterator for BitIter<'_> {}
 
 impl Iterator for BitIter<'_> {
     type Item = bool;
+    #[inline]
     fn next(&mut self) -> Option<bool> {
         if self.slot >= self.n {
             return None;
@@ -172,6 +187,7 @@ impl Iterator for BitIter<'_> {
         self.slot += 1;
         Some(v)
     }
+    #[inline]
     fn size_hint(&self) -> (usize, Option<usize>) {
         let rem = self.n - self.slot;
         (rem, Some(rem))
@@ -314,17 +330,21 @@ impl PersistentBitVecBuilder {
         Self::build_from_counts(source, 1, path)
     }
 
+    #[inline]
     pub fn len(&self) -> usize {
         self.n
     }
+    #[inline]
     pub fn is_empty(&self) -> bool {
         self.n == 0
     }
 
+    #[inline]
     pub fn get(&self, slot: usize) -> bool {
         (self.mmap[HEADER_SIZE + (slot >> 3)] >> (slot & 7)) & 1 != 0
     }
 
+    #[inline]
     pub fn set(&mut self, slot: usize, value: bool) {
         let bit = 1u64 << (slot & 63);
         if value {
@@ -334,6 +354,7 @@ impl PersistentBitVecBuilder {
         }
     }
 
+    #[inline]
     fn data_words(&self) -> &[u64] {
         let nw = n_words(self.n);
         let ptr = self.mmap[HEADER_SIZE..].as_ptr() as *const u64;
@@ -341,16 +362,19 @@ impl PersistentBitVecBuilder {
     }
 
     // SAFETY: same alignment argument as PersistentBitVec::data_words.
+    #[inline]
     fn data_words_mut(&mut self) -> &mut [u64] {
         let nw = n_words(self.n);
         let ptr = self.mmap[HEADER_SIZE..].as_mut_ptr() as *mut u64;
         unsafe { std::slice::from_raw_parts_mut(ptr, nw) }
     }
 
+    #[inline]
     pub fn view(&self) -> BitSliceView<'_> {
         BitSliceView::new(self.data_words(), self.n)
     }
 
+    #[inline]
     pub fn words(&self) -> &[u64] {
         self.data_words()
     }
@@ -472,6 +496,7 @@ impl PersistentBitVecBuilder {
         }
     }
 
+    #[inline]
     pub fn iter(&self) -> BitSliceIter<'_> {
         self.view().iter()
     }
diff --git a/src/obicompactvec/src/builder.rs b/src/obicompactvec/src/builder.rs
index 266b3c14..72bdc95b 100644
--- a/src/obicompactvec/src/builder.rs
+++ b/src/obicompactvec/src/builder.rs
@@ -52,6 +52,7 @@ impl PersistentCompactIntVecBuilder {
         Ok(Self { path: path.to_path_buf(), mmap, n, overflow })
     }
 
+    #[inline]
     pub fn get(&self, slot: usize) -> u32 {
         match self.mmap[HEADER_SIZE + slot] {
             255 => *self.overflow.get(&slot).expect("sentinel without overflow entry"),
@@ -59,6 +60,7 @@ impl PersistentCompactIntVecBuilder {
         }
     }
 
+    #[inline]
     pub fn set(&mut self, slot: usize, value: u32) {
         if value < 255 {
             self.mmap[HEADER_SIZE + slot] = value as u8;
@@ -69,20 +71,28 @@ impl PersistentCompactIntVecBuilder {
         }
     }
 
+    #[inline]
     pub fn len(&self)      -> usize { self.n }
+    #[inline]
     pub fn is_empty(&self) -> bool  { self.n == 0 }
 
+    #[inline]
     pub fn primary_bytes(&self)     -> &[u8]      { &self.mmap[HEADER_SIZE..HEADER_SIZE + self.n] }
+    #[inline]
     pub fn primary_bytes_mut(&mut self) -> &mut [u8] { &mut self.mmap[HEADER_SIZE..HEADER_SIZE + self.n] }
+    #[inline]
     pub fn clear_overflow(&mut self) { self.overflow.clear(); }
 
+    #[inline]
     pub fn sum(&self) -> u64 {
         byte_sum(&self.mmap[HEADER_SIZE..HEADER_SIZE + self.n], self.overflow.values().copied())
     }
+    #[inline]
     pub fn count_nonzero(&self) -> u64 {
         byte_count_nonzero(&self.mmap[HEADER_SIZE..HEADER_SIZE + self.n])
     }
 
+    #[inline]
     pub fn view(&self) -> IntSliceView<'_> {
         // Builder overflow is a HashMap, not sorted raw bytes — convert on the fly
         // by collecting into a sorted vec and storing in a thread-local buffer.
@@ -94,10 +104,12 @@ impl PersistentCompactIntVecBuilder {
         IntSliceView::new(primary, &[], 0, self.n)
     }
 
+    #[inline]
     pub fn overflow_entries(&self) -> impl Iterator<Item = (usize, u32)> + '_ {
         self.overflow.iter().map(|(&k, &v)| (k, v))
     }
 
+    #[inline]
     pub fn inc(&mut self, slot: usize) {
         let v = self.get(slot);
         self.set(slot, v.saturating_add(1));
diff --git a/src/obicompactvec/src/intmatrix.rs b/src/obicompactvec/src/intmatrix.rs
index 61f102ef..4680bdb5 100644
--- a/src/obicompactvec/src/intmatrix.rs
+++ b/src/obicompactvec/src/intmatrix.rs
@@ -36,14 +36,19 @@ impl ColumnarCompactIntMatrix {
         Ok(Self { cols, n: meta.n })
     }
 
+    #[inline]
     pub(crate) fn n(&self)      -> usize { self.n }
+    #[inline]
     pub(crate) fn n_cols(&self) -> usize { self.cols.len() }
+    #[inline]
     pub(crate) fn col(&self, c: usize) -> &PersistentCompactIntVec { &self.cols[c] }
 
+    #[inline]
     pub(crate) fn row(&self, slot: usize) -> Box<[u32]> {
         self.cols.iter().map(|c| c.get(slot)).collect()
     }
 
+    #[inline]
     pub(crate) fn fill_row(&self, slot: usize, buf: &mut [u32]) {
         for (c, col) in self.cols.iter().enumerate() { buf[c] = col.get(slot); }
     }
@@ -142,6 +147,7 @@ impl PackedCompactIntMatrix {
         Ok(Self { mmap, n_rows, n_cols, columns })
     }
 
+    #[inline]
     pub(crate) fn col_view(&self, c: usize) -> IntSliceView<'_> {
         let ci = &self.columns[c];
         let primary     = &self.mmap[ci.primary_start..ci.primary_start + self.n_rows];
@@ -158,10 +164,12 @@ impl PackedCompactIntMatrix {
     #[inline]
     pub(crate) fn get(&self, col: usize, slot: usize) -> u32 { self.col_view(col).get(slot) }
 
+    #[inline]
     pub(crate) fn fill_row(&self, slot: usize, buf: &mut [u32]) {
         for c in 0..self.n_cols { buf[c] = self.get(c, slot); }
     }
 
+    #[inline]
     pub(crate) fn row(&self, slot: usize) -> Box<[u32]> {
         (0..self.n_cols).map(|c| self.get(c, slot)).collect()
     }
@@ -312,13 +320,16 @@ impl PersistentCompactIntMatrix {
         ))
     }
 
+    #[inline]
     pub fn n(&self) -> usize {
         match self { Self::Columnar(m) => m.n(), Self::Packed(m) => m.n_rows }
     }
+    #[inline]
     pub fn n_cols(&self) -> usize {
         match self { Self::Columnar(m) => m.n_cols(), Self::Packed(m) => m.n_cols }
     }
 
+    #[inline]
     pub fn col(&self, c: usize) -> &PersistentCompactIntVec {
         match self {
             Self::Columnar(m) => m.col(c),
@@ -326,6 +337,7 @@ impl PersistentCompactIntMatrix {
         }
     }
 
+    #[inline]
     pub fn col_view(&self, c: usize) -> IntSliceView<'_> {
         match self {
             Self::Columnar(m) => m.col(c).view(),
@@ -340,9 +352,11 @@ impl PersistentCompactIntMatrix {
         }
     }
 
+    #[inline]
     pub fn row(&self, slot: usize) -> Box<[u32]> {
         match self { Self::Columnar(m) => m.row(slot), Self::Packed(m) => m.row(slot) }
     }
+    #[inline]
     pub fn fill_row(&self, slot: usize, buf: &mut [u32]) {
         match self { Self::Columnar(m) => m.fill_row(slot, buf), Self::Packed(m) => m.fill_row(slot, buf) }
     }
@@ -390,30 +404,39 @@ impl PersistentCompactIntMatrix {
         }
     }
 
+    #[inline]
     pub fn sum(&self) -> Array1<u64> {
         match self { Self::Columnar(m) => m.sum(), Self::Packed(m) => m.sum() }
     }
+    #[inline]
     pub fn count_nonzero(&self) -> Array1<u64> {
         match self { Self::Columnar(m) => m.count_nonzero(), Self::Packed(m) => m.count_nonzero() }
     }
+    #[inline]
     pub fn partial_bray_dist_matrix(&self) -> Array2<u64> {
         match self { Self::Columnar(m) => m.partial_bray_dist_matrix(), Self::Packed(m) => m.partial_bray_dist_matrix() }
     }
+    #[inline]
     pub fn partial_euclidean_dist_matrix(&self) -> Array2<f64> {
         match self { Self::Columnar(m) => m.partial_euclidean_dist_matrix(), Self::Packed(m) => m.partial_euclidean_dist_matrix() }
     }
+    #[inline]
     pub fn partial_threshold_jaccard_dist_matrix(&self, threshold: u32) -> (Array2<u64>, Array2<u64>) {
         match self { Self::Columnar(m) => m.partial_threshold_jaccard_dist_matrix(threshold), Self::Packed(m) => m.partial_threshold_jaccard_dist_matrix(threshold) }
     }
+    #[inline]
     pub fn partial_relfreq_bray_dist_matrix(&self, col_sums: &Array1<u64>) -> Array2<f64> {
         match self { Self::Columnar(m) => m.partial_relfreq_bray_dist_matrix(col_sums), Self::Packed(m) => m.partial_relfreq_bray_dist_matrix(col_sums) }
     }
+    #[inline]
     pub fn partial_relfreq_euclidean_dist_matrix(&self, col_sums: &Array1<u64>) -> Array2<f64> {
         match self { Self::Columnar(m) => m.partial_relfreq_euclidean_dist_matrix(col_sums), Self::Packed(m) => m.partial_relfreq_euclidean_dist_matrix(col_sums) }
     }
+    #[inline]
     pub fn partial_hellinger_euclidean_dist_matrix(&self, col_sums: &Array1<u64>) -> Array2<f64> {
         match self { Self::Columnar(m) => m.partial_hellinger_euclidean_dist_matrix(col_sums), Self::Packed(m) => m.partial_hellinger_euclidean_dist_matrix(col_sums) }
     }
+    #[inline]
     pub fn append_column(dir: &Path, value_of: impl Fn(usize) -> u32) -> io::Result<()> {
         ColumnarCompactIntMatrix::append_column(dir, value_of)
     }
@@ -424,16 +447,24 @@ impl PersistentCompactIntMatrix {
 use crate::traits::{ColumnWeights, CountPartials};
 
 impl ColumnWeights for PersistentCompactIntMatrix {
+    #[inline]
     fn col_weights(&self) -> Array1<u64> { self.sum() }
+    #[inline]
     fn partial_kmer_counts(&self) -> Array1<u64> { self.count_nonzero() }
 }
 
 impl CountPartials for PersistentCompactIntMatrix {
+    #[inline]
     fn partial_bray(&self) -> Array2<u64>                                 { self.partial_bray_dist_matrix() }
+    #[inline]
     fn partial_euclidean(&self) -> Array2<f64>                            { self.partial_euclidean_dist_matrix() }
+    #[inline]
     fn partial_threshold_jaccard(&self, t: u32) -> (Array2<u64>, Array2<u64>) { self.partial_threshold_jaccard_dist_matrix(t) }
+    #[inline]
     fn partial_relfreq_bray(&self, g: &Array1<u64>) -> Array2<f64>        { self.partial_relfreq_bray_dist_matrix(g) }
+    #[inline]
     fn partial_relfreq_euclidean(&self, g: &Array1<u64>) -> Array2<f64>   { self.partial_relfreq_euclidean_dist_matrix(g) }
+    #[inline]
     fn partial_hellinger(&self, g: &Array1<u64>) -> Array2<f64>           { self.partial_hellinger_euclidean_dist_matrix(g) }
 }
 
@@ -450,7 +481,9 @@ impl PersistentCompactIntMatrixBuilder {
         fs::create_dir_all(dir)?;
         Ok(Self { dir: dir.to_path_buf(), n, n_cols: 0 })
     }
+    #[inline]
     pub fn n(&self)      -> usize { self.n }
+    #[inline]
     pub fn n_cols(&self) -> usize { self.n_cols }
     pub fn add_col(&mut self) -> io::Result<PersistentCompactIntVecBuilder> {
         let path = col_path(&self.dir, self.n_cols);
diff --git a/src/obicompactvec/src/reader.rs b/src/obicompactvec/src/reader.rs
index e4d58ab2..0cc00c45 100644
--- a/src/obicompactvec/src/reader.rs
+++ b/src/obicompactvec/src/reader.rs
@@ -46,10 +46,14 @@ impl PersistentCompactIntVec {
         Ok(Self { mmap, n, n_overflow, step, index, primary_offset, data_offset, path: path.to_path_buf() })
     }
 
+    #[inline]
     pub fn path(&self) -> &Path { &self.path }
+    #[inline]
     pub fn len(&self)      -> usize { self.n }
+    #[inline]
     pub fn is_empty(&self) -> bool  { self.n == 0 }
 
+    #[inline]
     pub fn get(&self, slot: usize) -> u32 {
         match self.mmap[self.primary_offset + slot] {
             255 => self.overflow_get(slot),
@@ -127,23 +131,27 @@ impl PersistentCompactIntVec {
         u32::from_le_bytes(self.mmap[off..off + 4].try_into().unwrap())
     }
 
+    #[inline]
     pub fn sum(&self) -> u64 {
         let primary = &self.mmap[self.primary_offset..self.primary_offset + self.n];
         byte_sum(primary, (0..self.n_overflow).map(|i| self.data_value(i)))
     }
 
+    #[inline]
     pub fn count_nonzero(&self) -> u64 {
         let primary = &self.mmap[self.primary_offset..self.primary_offset + self.n];
         byte_count_nonzero(primary)
     }
 
     /// Lightweight zero-copy view — primary and overflow point into the mmap.
+    #[inline]
     pub fn view(&self) -> IntSliceView<'_> {
         let primary = &self.mmap[self.primary_offset..self.primary_offset + self.n];
         let overflow_raw = &self.mmap[self.data_offset..self.data_offset + self.n_overflow * OVERFLOW_ENTRY_SIZE];
         IntSliceView::new(primary, overflow_raw, self.n_overflow, self.n)
     }
 
+    #[inline]
     pub fn iter(&self) -> Iter<'_> {
         Iter { pciv: self, slot: 0, overflow_pos: 0 }
     }
@@ -256,6 +264,7 @@ impl PersistentCompactIntVec {
 impl<'a> IntoIterator for &'a PersistentCompactIntVec {
     type Item = u32;
     type IntoIter = Iter<'a>;
+    #[inline]
     fn into_iter(self) -> Iter<'a> { self.iter() }
 }
 
@@ -270,6 +279,7 @@ impl ExactSizeIterator for Iter<'_> {}
 impl Iterator for Iter<'_> {
     type Item = u32;
 
+    #[inline]
     fn next(&mut self) -> Option<u32> {
         if self.slot >= self.pciv.n { return None; }
         let v = self.pciv.mmap[self.pciv.primary_offset + self.slot];
@@ -283,6 +293,7 @@ impl Iterator for Iter<'_> {
         }
     }
 
+    #[inline]
     fn size_hint(&self) -> (usize, Option<usize>) {
         let remaining = self.pciv.n - self.slot;
         (remaining, Some(remaining))
diff --git a/src/obicompactvec/src/tempbitvec.rs b/src/obicompactvec/src/tempbitvec.rs
index df1d436c..06935a74 100644
--- a/src/obicompactvec/src/tempbitvec.rs
+++ b/src/obicompactvec/src/tempbitvec.rs
@@ -21,21 +21,27 @@ impl TempBitVec {
         PersistentBitVec::open(path)
     }
 
+    #[inline]
     pub fn len(&self) -> usize {
         self.vec.len()
     }
+    #[inline]
     pub fn is_empty(&self) -> bool {
         self.vec.is_empty()
     }
+    #[inline]
     pub fn get(&self, slot: usize) -> bool {
         self.vec.get(slot)
     }
+    #[inline]
     pub fn count_ones(&self) -> u64 {
         self.vec.count_ones()
     }
+    #[inline]
     pub fn view(&self) -> BitSliceView<'_> {
         self.vec.view()
     }
+    #[inline]
     pub fn iter(&self) -> BitSliceIter<'_> {
         self.view().iter()
     }
@@ -69,42 +75,52 @@ impl TempBitVecBuilder {
         Ok(TempBitVec { vec, _temp: temp })
     }
 
+    #[inline]
     pub fn set(&mut self, slot: usize, value: bool) {
         self.builder.set(slot, value);
     }
 
+    #[inline]
     pub fn view(&self) -> BitSliceView<'_> {
         self.builder.view()
     }
 
+    #[inline]
     pub fn or(&mut self, other: BitSliceView<'_>) {
         self.builder.or(other);
     }
 
+    #[inline]
     pub fn and(&mut self, other: BitSliceView<'_>) {
         self.builder.and(other);
     }
 
+    #[inline]
     pub fn xor(&mut self, other: BitSliceView<'_>) {
         self.builder.xor(other);
     }
 
+    #[inline]
     pub fn not(&mut self) {
         self.builder.not();
     }
 
+    #[inline]
     pub fn copy_from(&mut self, src: BitSliceView<'_>) {
         self.builder.copy_from(src);
     }
 
+    #[inline]
     pub fn or_where(&mut self, col: IntSliceView<'_>, pred: impl Fn(u32) -> bool) {
         self.builder.or_where(col, pred);
     }
 
+    #[inline]
     pub fn and_where(&mut self, col: IntSliceView<'_>, pred: impl Fn(u32) -> bool) {
         self.builder.and_where(col, pred);
     }
 
+    #[inline]
     pub fn xor_where(&mut self, col: IntSliceView<'_>, pred: impl Fn(u32) -> bool) {
         self.builder.xor_where(col, pred);
     }
diff --git a/src/obicompactvec/src/tempintvec.rs b/src/obicompactvec/src/tempintvec.rs
index b0b34920..6f0ee3b6 100644
--- a/src/obicompactvec/src/tempintvec.rs
+++ b/src/obicompactvec/src/tempintvec.rs
@@ -22,11 +22,17 @@ impl TempCompactIntVec {
         PersistentCompactIntVec::open(path)
     }
 
+    #[inline]
     pub fn len(&self)      -> usize { self.vec.len() }
+    #[inline]
     pub fn is_empty(&self) -> bool  { self.vec.is_empty() }
+    #[inline]
     pub fn get(&self, slot: usize) -> u32  { self.vec.get(slot) }
+    #[inline]
     pub fn sum(&self)      -> u64   { self.vec.sum() }
+    #[inline]
     pub fn view(&self)     -> IntSliceView<'_> { self.vec.view() }
+    #[inline]
     pub fn iter(&self) -> crate::reader::Iter<'_> { self.vec.iter() }
 }
 
@@ -51,39 +57,53 @@ impl TempCompactIntVecBuilder {
         Ok(TempCompactIntVec { vec, _temp: temp })
     }
 
+    #[inline]
     pub fn n(&self) -> usize { self.builder.len() }
 
+    #[inline]
     pub fn set(&mut self, slot: usize, value: u32) { self.builder.set(slot, value); }
+    #[inline]
     pub fn get(&self, slot: usize) -> u32           { self.builder.get(slot) }
 
+    #[inline]
     pub fn primary_bytes(&self)         -> &[u8]      { self.builder.primary_bytes() }
+    #[inline]
     pub fn primary_bytes_mut(&mut self) -> &mut [u8]  { self.builder.primary_bytes_mut() }
 
+    #[inline]
     pub fn inc_present(&mut self, col: BitSliceView<'_>) {
         self.builder.inc_present(col);
     }
 
+    #[inline]
     pub fn inc_present_fast(&mut self, col: BitSliceView<'_>) {
         self.builder.inc_present_fast(col);
     }
 
+    #[inline]
     pub fn inc_predicate(&mut self, col: IntSliceView<'_>, pred: impl Fn(u32) -> bool) {
         self.builder.inc_predicate(col, pred);
     }
 
+    #[inline]
     pub fn inc_predicate_fast(&mut self, col: IntSliceView<'_>, pred: impl Fn(u32) -> bool) {
         self.builder.inc_predicate_fast(col, pred);
     }
 
+    #[inline]
     pub fn add(&mut self, other: IntSliceView<'_>) {
         self.builder.add(other);
     }
 
+    #[inline]
     pub fn mask_with(&mut self, mask: BitSliceView<'_>) {
         self.builder.mask_with(mask);
     }
 
+    #[inline]
     pub fn min(&mut self, other: IntSliceView<'_>)  { self.builder.min(other); }
+    #[inline]
     pub fn max(&mut self, other: IntSliceView<'_>)  { self.builder.max(other); }
+    #[inline]
     pub fn diff(&mut self, other: IntSliceView<'_>) { self.builder.diff(other); }
 }
diff --git a/src/obicompactvec/src/views.rs b/src/obicompactvec/src/views.rs
index ff565482..a8571039 100644
--- a/src/obicompactvec/src/views.rs
+++ b/src/obicompactvec/src/views.rs
@@ -14,8 +14,11 @@ impl<'a> BitSliceView<'a> {
     #[inline]
     pub fn new(words: &'a [u64], n: usize) -> Self { Self { words, n } }
 
+    #[inline]
     pub fn len(&self)      -> usize  { self.n }
+    #[inline]
     pub fn is_empty(&self) -> bool   { self.n == 0 }
+    #[inline]
     pub fn words(&self)    -> &'a [u64] { self.words }
 
     #[inline]
@@ -60,6 +63,7 @@ impl<'a> BitSliceView<'a> {
     }
     pub fn count_zeros(&self) -> u64 { self.n as u64 - self.count_ones() }
 
+    #[inline]
     pub fn iter(&self) -> BitSliceIter<'a> {
         BitSliceIter { words: self.words, slot: 0, n: self.n }
     }
@@ -95,12 +99,14 @@ pub struct BitSliceIter<'a> {
 
 impl Iterator for BitSliceIter<'_> {
     type Item = bool;
+    #[inline]
     fn next(&mut self) -> Option<bool> {
         if self.slot >= self.n { return None; }
         let v = (self.words[self.slot >> 6] >> (self.slot & 63)) & 1 != 0;
         self.slot += 1;
         Some(v)
     }
+    #[inline]
     fn size_hint(&self) -> (usize, Option<usize>) {
         let rem = self.n - self.slot;
         (rem, Some(rem))
@@ -126,11 +132,16 @@ impl<'a> IntSliceView<'a> {
         Self { primary, overflow_raw, n_overflow, n }
     }
 
+    #[inline]
     pub fn len(&self)        -> usize    { self.n }
+    #[inline]
     pub fn is_empty(&self)   -> bool     { self.n == 0 }
+    #[inline]
     pub fn primary_bytes(&self) -> &'a [u8] { self.primary }
+    #[inline]
     pub fn n_overflow(&self) -> usize    { self.n_overflow }
 
+    #[inline]
     pub fn overflow_entries(&self) -> impl Iterator<Item = (usize, u32)> + 'a {
         let raw  = self.overflow_raw;
         let n_ov = self.n_overflow;
@@ -190,6 +201,7 @@ impl<'a> IntSliceView<'a> {
     }
 
     /// Sequential merge scan: yields all n values in slot order.
+    #[inline]
     pub fn iter(&self) -> IntSliceViewIter<'a> {
         IntSliceViewIter {
             primary:      self.primary,
@@ -324,6 +336,7 @@ pub struct IntSliceViewIter<'a> {
 
 impl Iterator for IntSliceViewIter<'_> {
     type Item = u32;
+    #[inline]
     fn next(&mut self) -> Option<u32> {
         if self.slot >= self.n { return None; }
         let v = self.primary[self.slot];
@@ -336,6 +349,7 @@ impl Iterator for IntSliceViewIter<'_> {
             Some(val)
         }
     }
+    #[inline]
     fn size_hint(&self) -> (usize, Option<usize>) {
         let rem = self.n - self.slot;
         (rem, Some(rem))
-- 
2.54.0


From f5e4bbfc6bd8329f1bc1adbd6c6e610a364b1a36 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Fri, 14 Aug 2026 22:45:08 +0200
Subject: [PATCH 31/46] Document architecture redesign and add partition layer
 accessor

Documents a proposed redesign for cross-partition batch resolution, shifting trigger logic to per-destination accumulator thresholds and introducing entropy-based pruning criteria. Adds an `n_layers_per_partition` method to the index, exposing partition metadata with consistent error handling and clarified documentation regarding build-time structural properties.
---
 docmd/architecture/siblings.md | 102 +++++++++++++++++++++++++++++++++
 src/obikindex/src/index.rs     |  13 +++++
 2 files changed, 115 insertions(+)

diff --git a/docmd/architecture/siblings.md b/docmd/architecture/siblings.md
index 3df7c6aa..785f18a7 100644
--- a/docmd/architecture/siblings.md
+++ b/docmd/architecture/siblings.md
@@ -148,6 +148,108 @@ Baseline: mostly one active core, with short multi-core bursts — average
   Measured ~10% *slower*, wider dips, not narrower. Reverted to the
   original chunk sizing.
 
+## Cross-partition batch resolution — current state vs. the batched-accumulator design (discussion, 2026-08-14)
+
+`family_scan.rs::scan_layer_families` (shared by `snp_pseudo_alignment`,
+`sibling_annex_stats`, `cardinality_tally`, `scan_family_pairs`) already
+implements most of a dispatch/accumulate/resolve pipeline: generation
+(cheap, CPU-only — builds `outgoing[dest_partition]` from `FamilyMask` and
+buckets cross-partition queries) runs on an `obipipeline::throttle` +
+`make_pipe!` stage, decoupled from resolution (I/O-bound, `rayon::par_iter`
+*across partitions*, one generated batch resolved at a time, never several
+concurrently — this ordering is deliberate, see the module's own docs on a
+reverted concurrent-batch-resolution attempt that scattered mmap access).
+The fast/slow mode gate (`PartitionCache::fast_mode`, `cache.rs:162-163`)
+already exists: `n_layers <= 7` (checked once from the first non-empty
+partition's `PartitionMeta::n_layers`, documented as identical across every
+partition of an index — a structural, build-time property, never a
+per-partition state) decides whether `FamilyMask`'s recorded `layer_value`
+can be trusted to skip straight to the right layer
+(`find_presence_batch_fast`) or must fall back to scanning every layer of
+the destination partition (`find_presence_batch`).
+
+**Real gap, confirmed not implemented**: resolution is triggered by the
+*source* batch finishing (`FAMILY_BATCH = 65536` minorants read from the
+scanned layer), not by an *output* accumulator filling up. Since most
+central-base variants of a family route back to the same partition being
+scanned (~48% per the k=31/m=11 measurement above), a `FAMILY_BATCH`'s
+`outgoing[dest]` is large for the local/self partition and thin for the
+other ~255 (or however many) destination partitions — each of those gets
+resolved at low query density every batch instead of being accumulated
+across several source batches until resolving it is worthwhile. This is
+distinct from, and not fixed by, the fast/slow layer gate above.
+
+Redesign sketched (not built): per-destination accumulators decoupled from
+`FAMILY_BATCH`, flushed on reaching a size threshold instead of on source-batch
+completion — a "hot" accumulator for the partition being scanned (sharded
+one-per-generation-worker, no lock, since all `n_workers` pipeline workers
+write to it concurrently — this differs from an earlier, simpler mental
+model of "one thread owns one layer's local collector," which doesn't hold
+here since `n_workers` threads cooperate on scanning *one* layer at a time,
+not one thread per layer) and "cold" mutex-per-partition accumulators for
+the rest, low contention expected since traffic to any single cold
+destination is a small fraction of total.
+
+This breaks the current strict-iteration-order delivery of `on_family`
+(today: a reorder buffer keyed by batch, since a whole `FAMILY_BATCH`
+resolves atomically). With cross-batch accumulation, a family only becomes
+complete once *every* accumulator holding one of its outgoing queries has
+flushed, at unpredictable, independent times — no longer streamable
+strictly in order without a large, unbounded pending buffer. Resolution
+sketched: replace order-dependent consumers with coordinate-addressed
+writes instead of order-dependent appends (see `PseudoAlignment` idea
+below) wherever possible, since `sibling_annex_stats`'s reduction (plain
+counts) is already order-independent and needs nothing here.
+
+## Pseudo-alignment at scale — pruning is unavoidable (discussion, 2026-08-14)
+
+The reference run (`phyloskims_sal_vac`-scale bacterial test set,
+`iqtree.fasta`) produced a dense alignment for 13 genomes × 383,965 sites
+(4.8 MB) — trivially small. The in-progress plant index is expected to
+carry on the order of 9 billion minorant families; a dense byte-per-cell
+alignment at that column count is unbuildable regardless of genome count
+(hundreds of GB even at a handful of genomes). Long-term ambition is 6,000–
+8,000 genomes on a large machine, which makes the per-cell cost dominant in
+the other dimension too. Pruning the retained family set before
+materializing anything is mandatory, not an optimization.
+
+**Already free**: `family_size() < 2` (no sibling variant registered at
+all) is a zero-cost structural filter, read directly off `FamilyMask` bits,
+already applied in `snp_pseudo_alignment`. Insufficient alone — per the
+~80-85% mono-family estimate from earlier discussion, this only brings 9
+billion down to roughly 1.3-1.8 billion, still unusable.
+
+**Criterion under discussion**: fix a global cell budget
+(`n_genomes × n_columns_retained ≤ threshold`) and retain the
+highest-entropy families first until the budget is spent — column count
+self-adjusts to genome count automatically. Entropy of a family: Shannon
+entropy over the observed base distribution across genomes carrying that
+family, **decided 2026-08-14: genomes where the family is absent are
+excluded from the calculation** (denominator = genomes where present, not
+all genomes) — measures signal purity where it exists, independent of
+coverage rate.
+
+Key consequence for storage: entropy needs per-variant genome counts, which
+cannot be derived from `FamilyMask`'s bits alone — it requires the same
+cross-partition resolution work the alignment/stats pipeline already pays
+for. This favors computing it once at annex-build time and persisting it in
+an **auxiliary vector alongside the annex** (one value per retained
+minorant) over encoding a fixed keep/discard decision as one of
+`FamilyMask`'s 3 remaining free bits (bits 13-15, `siblingannex.rs:77`): the
+bit approach bakes a single threshold in permanently (any different budget
+needs a full annex rebuild), the vector approach pays the expensive
+resolution once and lets budget/threshold be chosen freely per analysis
+afterward.
+
+**Open, explicitly deferred**: scope of the top-K selection — global across
+the whole index (needs a first pass computing/storing every family's
+entropy, then a global threshold from the full distribution, e.g. a
+quantile, before building the final alignment: two full passes, but the
+size budget is honored precisely) vs. local per layer/partition (stays
+within the current single-pass streaming model, but the global budget is
+no longer exactly guaranteed — depends on how unevenly entropy is
+distributed across layers).
+
 **Known remaining limitation, not yet worth fixing:** within one layer, the
 four stages (sequential `unitigs.bin` read → parallel generation →
 parallel resolution → sequential annex write) never overlap — confirmed by
diff --git a/src/obikindex/src/index.rs b/src/obikindex/src/index.rs
index 3aedca98..6b7e117d 100644
--- a/src/obikindex/src/index.rs
+++ b/src/obikindex/src/index.rs
@@ -142,6 +142,19 @@ impl KmerIndex {
     pub fn minimizer_size(&self) -> usize { self.meta.config.minimizer_size }
     pub fn n_partitions(&self) -> usize { self.partition.n_partitions() }
 
+    /// Number of layers per partition.
+    ///
+    /// Structural property of the index, fixed at build time and
+    /// homogeneous across all partitions — reading it off partition 0
+    /// is enough, no need to scan every partition.
+    pub fn n_layers_per_partition(&self) -> OKIResult<usize> {
+        use obilayeredmap::meta::PartitionMeta;
+        let index_dir = self.partition.part_dir(0).join("index");
+        let meta = PartitionMeta::load(&index_dir)
+            .map_err(|e| OKIError::Io(std::io::Error::new(std::io::ErrorKind::Other, e.to_string())))?;
+        Ok(meta.n_layers)
+    }
+
     /// Expose the inner partition so the caller can run scatter into it.
     /// Call `mark_scattered` once scatter is complete.
     pub fn partition_mut(&mut self) -> &mut KmerPartition {
-- 
2.54.0


From 45b19503a1114ca72a58bbbeccf2144861a0accf Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Sat, 15 Aug 2026 09:50:02 +0200
Subject: [PATCH 32/46] Add proportional subsampling and Shannon entropy
 calculation

Introduces `--subsample N` and `--shannon` CLI flags to cap retained variable families via proportional reservoir sampling and compute per-family Shannon entropy. Updates the family scanning API to support explicit selection filtering with early-exit optimization, resolving an indexing drift issue in monomorphic layers. Streams entropy metrics for 15-state and 4-nucleotide spaces directly to CSV while maintaining parallel processing across sibling layers.
---
 .DS_Store                                   | Bin 14340 -> 14340 bytes
 .gitignore                                  |   1 +
 docmd/architecture/siblings.md              | 226 ++++++++++++++++----
 src/Cargo.lock                              |   1 +
 src/obikmer/src/cmd/phylo/args.rs           |  24 ++-
 src/obikmer/src/cmd/phylo/family_overlap.rs |   2 +-
 src/obikmer/src/cmd/phylo/mod.rs            |  23 +-
 src/obikphylo/Cargo.toml                    |   1 +
 src/obikphylo/src/siblings/alignment.rs     |  22 +-
 src/obikphylo/src/siblings/cardinality.rs   |   4 +-
 src/obikphylo/src/siblings/distance.rs      |   4 +-
 src/obikphylo/src/siblings/entropy.rs       | 170 +++++++++++++++
 src/obikphylo/src/siblings/family_scan.rs   |  62 +++++-
 src/obikphylo/src/siblings/mod.rs           |   3 +
 src/obikphylo/src/siblings/stats.rs         |   4 +-
 src/obikphylo/src/siblings/subsample.rs     | 158 ++++++++++++++
 src/obikphylo/src/siblings/tests.rs         | 206 +++++++++++++++++-
 17 files changed, 841 insertions(+), 70 deletions(-)
 create mode 100644 src/obikphylo/src/siblings/entropy.rs
 create mode 100644 src/obikphylo/src/siblings/subsample.rs

diff --git a/.DS_Store b/.DS_Store
index 34be0f9da62fb45f2230c2abb804bbf385535890..4373600fa9ad52b079125e98c415ac6ae5447bf4 100644
GIT binary patch
delta 385
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z*+HF$kByz3lbxGAHaH`{Jh)`Dqtq$ZjSZEIoFG*|z`+d^5@*@0&hvzsk#n+-`lZbR
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zJ&Mwtbi?4}{M-VtEf4}lJ~!XRB`GIA3FL+i4q?i!5+@wdt;@|%A*iMx17?pB+$t1{
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T!zSDCNKcM2nY+1FnVlH`3?NgR

delta 192
zcmZoEXepQ=#l*rjQN~!5mw|zSnSnuofgzb8mmwvmxXd{zXXC}i%##gFSXdc>vMihL
z2}ChZexx#s2gn17009U0#*5-Co7H)qFf+1mHWj(Xz43u23nS~~L?x-k^Ay=Z^u$#>
zlX(O#P5vt)wK-8{74yaisw|V)4TRZPxEL4|cs5>q&pesmL{|o69>~}R2o1IYNH77p
S43lF_7H%$7(`7;!xB~#j^)4C!

diff --git a/.gitignore b/.gitignore
index addd10f0..bfe28adc 100644
--- a/.gitignore
+++ b/.gitignore
@@ -26,6 +26,7 @@ benchmark/specific_index_count
 benchmark/specific_index_presence
 TNT
 phyg
+biblio
 *.tnt
 *.tre
 *.phy
diff --git a/docmd/architecture/siblings.md b/docmd/architecture/siblings.md
index 785f18a7..3677cd9f 100644
--- a/docmd/architecture/siblings.md
+++ b/docmd/architecture/siblings.md
@@ -148,6 +148,22 @@ Baseline: mostly one active core, with short multi-core bursts — average
   Measured ~10% *slower*, wider dips, not narrower. Reverted to the
   original chunk sizing.
 
+**Known remaining limitation, not yet worth fixing:** within one layer, the
+four stages (sequential `unitigs.bin` read → parallel generation →
+parallel resolution → sequential annex write) never overlap — confirmed by
+1s-interval sampling: generation alone occupies ~17 threads evenly, but the
+next layer's read/generation never starts until the current layer's
+resolution and write are both done. This produces a real, periodic (~layer
+duration) alternation between "many cores" and "few cores" that neither of
+the fixes above touches, since both operate *within* one layer's resolution
+step. The only remaining lever is overlapping consecutive layers (e.g. a
+depth-2 pipeline: start layer N+1's read/generation while layer N's
+resolution/write is still running) — a real restructuring, not a parameter
+tweak, and explicitly *not* to be combined with the reverted
+budget-capping idea above (let each phase use however many cores it
+naturally wants; only the *scheduling* needs to overlap). Deferred, not
+started.
+
 ## Cross-partition batch resolution — current state vs. the batched-accumulator design (discussion, 2026-08-14)
 
 `family_scan.rs::scan_layer_families` (shared by `snp_pseudo_alignment`,
@@ -201,7 +217,15 @@ writes instead of order-dependent appends (see `PseudoAlignment` idea
 below) wherever possible, since `sibling_annex_stats`'s reduction (plain
 counts) is already order-independent and needs nothing here.
 
-## Pseudo-alignment at scale — pruning is unavoidable (discussion, 2026-08-14)
+**Superseded 2026-08-15** by the `--subsample`/`--shannon` design below,
+which sidesteps the accumulator redesign for now: bounding the number of
+families actually resolved per layer (via sampling) keeps per-layer
+resolution volume small enough that the batch-density problem above stops
+mattering in practice for these two consumers. The accumulator redesign
+remains relevant for a future *unsampled, full-index* run, but is not
+required to ship `--subsample`/`--shannon`.
+
+## Pseudo-alignment at scale — pruning is unavoidable (discussion, 2026-08-14/15)
 
 The reference run (`phyloskims_sal_vac`-scale bacterial test set,
 `iqtree.fasta`) produced a dense alignment for 13 genomes × 383,965 sites
@@ -219,49 +243,163 @@ already applied in `snp_pseudo_alignment`. Insufficient alone — per the
 ~80-85% mono-family estimate from earlier discussion, this only brings 9
 billion down to roughly 1.3-1.8 billion, still unusable.
 
-**Criterion under discussion**: fix a global cell budget
-(`n_genomes × n_columns_retained ≤ threshold`) and retain the
-highest-entropy families first until the budget is spent — column count
-self-adjusts to genome count automatically. Entropy of a family: Shannon
-entropy over the observed base distribution across genomes carrying that
-family, **decided 2026-08-14: genomes where the family is absent are
-excluded from the calculation** (denominator = genomes where present, not
-all genomes) — measures signal purity where it exists, independent of
-coverage rate.
+**Entropy definition — settled 2026-08-15, correcting an earlier wrong
+turn.** The project does **not** encode families as IUPAC ambiguity codes
+interpreted the classical way (Fitch-parsimony subset-compatibility, or
+ML's "one true state, uncertain which"); see
+`docmd/theory/evolutionary_distances.md` ("Why the IUPAC/DNA encoding used
+for the first `--snp` test was wrong") and the Sankoff resolution that
+followed it. The real model is a genuine 16-state alphabet (the powerset of
+`{A,C,G,T}`, `∅` included as a real state) scored with a *calibrated
+pairwise cost matrix* (`obikphylo::cardcomp::pairwise_cost_matrix`,
+`cmd/phylo/sankoff.rs`), not a compatibility/subset relation between
+states. Under that model, each of the 16 states — including multi-bit ones
+like `AC` — is a first-class, independently-costed state, not an
+uncertainty encoding of a single true base. So: **entropy over the 15
+non-empty states (`∅` excluded, matching the earlier decision to exclude
+genomes where the family is absent) is the correct informativeness
+measure** for this project — not a 4-symbol reduction, which would discard
+exactly the cardinality/composition information the calibrated cost matrix
+is built to exploit.
 
-Key consequence for storage: entropy needs per-variant genome counts, which
-cannot be derived from `FamilyMask`'s bits alone — it requires the same
-cross-partition resolution work the alignment/stats pipeline already pays
-for. This favors computing it once at annex-build time and persisting it in
-an **auxiliary vector alongside the annex** (one value per retained
-minorant) over encoding a fixed keep/discard decision as one of
-`FamilyMask`'s 3 remaining free bits (bits 13-15, `siblingannex.rs:77`): the
-bit approach bakes a single threshold in permanently (any different budget
-needs a full annex rebuild), the vector approach pays the expensive
-resolution once and lets budget/threshold be chosen freely per analysis
-afterward.
+## `--subsample` / `--shannon` — sampling strategy (decided 2026-08-15)
 
-**Open, explicitly deferred**: scope of the top-K selection — global across
-the whole index (needs a first pass computing/storing every family's
-entropy, then a global threshold from the full distribution, e.g. a
-quantile, before building the final alignment: two full passes, but the
-size budget is honored precisely) vs. local per layer/partition (stays
-within the current single-pass streaming model, but the global budget is
-no longer exactly guaranteed — depends on how unevenly entropy is
-distributed across layers).
+Goal: make both the pseudo-alignment (`--snp`) and a Shannon-entropy
+diagnostic usable at any index scale, from the 13-genome bacterial
+reference run up to the 9-billion-family plant index, without requiring the
+batched-accumulator redesign above.
 
-**Known remaining limitation, not yet worth fixing:** within one layer, the
-four stages (sequential `unitigs.bin` read → parallel generation →
-parallel resolution → sequential annex write) never overlap — confirmed by
-1s-interval sampling: generation alone occupies ~17 threads evenly, but the
-next layer's read/generation never starts until the current layer's
-resolution and write are both done. This produces a real, periodic (~layer
-duration) alternation between "many cores" and "few cores" that neither of
-the fixes above touches, since both operate *within* one layer's resolution
-step. The only remaining lever is overlapping consecutive layers (e.g. a
-depth-2 pipeline: start layer N+1's read/generation while layer N's
-resolution/write is still running) — a real restructuring, not a parameter
-tweak, and explicitly *not* to be combined with the reverted
-budget-capping idea above (let each phase use however many cores it
-naturally wants; only the *scheduling* needs to overlap). Deferred, not
-started.
+**`--subsample N`** (integer, families to retain): bounds the pseudo-alignment
+to `N` minorant families, sampled **proportionally per layer** among
+non-monomorphic minorants (`family_size >= 2`) — this sidesteps the need
+for a true global reservoir merge across layers while still approximating a
+uniform sample over the whole index, and directly answers the earlier open
+question of global-vs-per-layer selection scope.
+
+Three passes, in order:
+
+1. **Global count** (cheap, structural, parallel across layers — same shape
+   as the existing `sibling_family_size_histogram`, extended to report a
+   **per-layer** breakdown rather than one index-wide aggregate): for each
+   layer, `count_layer` = number of non-monomorphic minorants. Gives
+   `total_count = Σ count_layer`.
+2. **Per-layer proportional reservoir sampling** (cheap, structural, one
+   pass per layer, no cross-partition resolution): `N_layer = round(N ×
+   count_layer / total_count)`. Since `N_layer` is a proportion of
+   `count_layer`, it can never exceed it as long as `N <= total_count` — the
+   one edge case is `total_count <= N`, in which case sampling is skipped
+   entirely and *every* non-monomorphic minorant of every layer is kept
+   (no reservoir needed, `N` was never a real constraint). Otherwise:
+   Algorithm-R reservoir sampling over the layer's non-monomorphic minorant
+   indices, producing `N_layer` iteration-order indices directly, no
+   intermediate full list ever materialized.
+3. **Filtered resolution** (the expensive step, the existing
+   `scan_layer_families` engine, unchanged): re-scan the layer, generating
+   and resolving cross-partition queries **only** for the indices selected
+   in step 2 (cheap membership test against a small per-layer index set) —
+   this is what keeps `--subsample` cheap even on an unsampled-scale index,
+   since the cross-partition resolution volume is bounded by `N`, not by
+   the layer's true size.
+
+Steps 2 and 3 cannot be merged into one pass: true single-pass reservoir
+sampling would waste step-3's expensive resolution work on candidates later
+evicted by the reservoir. Step 1 must fully complete (every layer) before
+step 2 can start for any layer, since `total_count` is a global quantity.
+
+**`--shannon`** (no argument): emits a CSV of per-family Shannon entropy
+(15 non-empty states, `∅`/absent genomes excluded from the denominator, per
+the settled definition above). Independent of `--subsample` — entropy is
+computed and written per family as soon as its `genome_mask` resolves,
+O(1) memory per family, so it streams fine even unsampled at full index
+scale (a time cost, not a memory one). Combined with `--subsample N`, it
+delivers the original exploratory diagnostic (e.g. `--subsample 1000000
+--shannon`) directly from this general machinery, rather than a
+purpose-built one-off script.
+
+Validated end-to-end (2026-08-15) against real data: `--sibling-hist` on
+`phyloskims_sal_vac` (91 real genomes, k=31/m=11, 256 partitions × 2
+layers) confirms the ~9-billion-family estimate almost exactly (8,925,068,238
+total, 97.9% monomorphic — a sharper mono fraction than the ~80-85% earlier
+guess, corrected here). `--subsample`/`--shannon` on the smaller 20-genome
+bacterial reference (`benchmark/global_index_presence`) produced a sample
+size within rounding of the request (99,742/100,000) and a
+[0.8,1.2)-bucket share (40.7%) matching the full unsampled population
+(41.6%) — the two histograms only diverged wildly (5‰ vs 41.6%) under a
+real bug in `reservoir_sample_layer` (see next section), now fixed.
+
+**Bug found and fixed (2026-08-15): `family_idx` numbering mismatch.**
+`scan_layer_families`'s `family_idx` counts *every minorant* of a layer
+(monomorphic ones included, since `iter_minorants_batch` filters only on
+`is_minorant()`), not the raw annex slot (`SiblingAnnex::get(slot)` spans
+every k-mer, minorant or not) and not a counter over non-monomorphic
+minorants alone. `subsample.rs`'s `reservoir_sample_layer` originally
+stored raw slot numbers in its `HashSet<usize>` selection, which drifts
+away from `family_idx` as soon as *any* monomorphic minorant is seen —
+i.e. almost immediately, since ~98% of minorants are monomorphic. Fixed by
+tracking two separate counters: `family_idx` (every minorant, matching
+`scan_layer_families`) and `seen` (non-monomorphic minorants only, what
+Algorithm R actually samples over) — only `family_idx` values are ever
+stored in the selection set. The existing unit test never exercised this
+(its fixture has exactly one non-monomorphic family, always hitting the
+"keep everything" shortcut) — a stronger fixture with several interleaved
+monomorphic/non-monomorphic families would be needed to catch a regression
+here automatically; not yet written.
+
+## Cheap entropy pre-filtering — row-marginal sums (idea, not implemented, 2026-08-15)
+
+Motivation: on real data (bacterial reference, full unsampled run), only
+~5‰ of non-monomorphic minorants fall in the `[0.5, 1.5]` bit band judged
+phylogenetically interesting (entropy too low = uninformative near-invariant
+site; too high = saturated/noisy, see `family_entropy`'s 15-state
+discussion) — roughly 1 in 10,000 minorants overall. Computing exact
+entropy for every candidate just to discard 99.99% of them is wasteful at
+the full 9-billion scale.
+
+**The idea**: `PersistentBitMatrix::col_view(c)` gives a genome's whole
+presence column as a `BitSliceView` (sequential, no MPHF, no cross-partition
+routing — purely local to one layer's own matrix). Accumulating
+`TempCompactIntVecBuilder::inc_present(col)` (already exists in
+`obicompactvec/src/builder.rs:121`, along with `add`/`min`/`max`/`diff` on
+`IntSliceView` — no new low-level API needed) over every column of a layer
+produces `coverage[slot]`: how many genomes carry each exact k-mer, in one
+sequential per-layer pass, entirely decoupled from family/sibling
+structure. Persisted once per layer, a family's members' coverage could
+then be looked up via a plain local MPHF `index()` (cheap) instead of a
+full cross-partition presence resolution (`find_presence_batch`) — the
+expensive part today is specifically the cross-partition/cross-layer
+routing to a sibling's own matrix, not the bit-reading itself, and
+`coverage[slot]` sidesteps that routing entirely by moving the cost into a
+one-time, purely local, embarrassingly-parallel build step.
+
+**Why not implemented**: `coverage[slot]` is a per-member marginal —
+summing members' coverages to approximate a family's entropy silently
+assumes no genome carries more than one member at once. It cannot
+represent or detect joint co-occurrence (a genome carrying both `A` and
+`C` at once, i.e. a combined 15-symbol state) at all, which is exactly the
+phenomenon `family_entropy`'s 15-state definition exists to capture (see
+`CardinalityTally`/`cardinality_transition_probs`, the project's own
+existing machinery for this same co-occurrence structure, built for the
+Sankoff matrix calibration). A family that is in truth uniformly `AC`
+across every carrying genome would look like a well-balanced 2-state split
+under the marginal approximation (entropy ≈ 1) while its true 15-state
+entropy is 0 — i.e. the marginal proxy's failure mode lands on exactly the
+"saturated, uninformative" tail this pre-filter would need to catch,
+undermining the point. It stays plausible as a coarse filter for the
+*low* tail only (a dominant single member's marginal share reliably
+predicts low true entropy too), but not as a stand-in for the high tail —
+not pursued further for now.
+
+## Two entropy definitions kept side by side, for comparison (2026-08-15)
+
+`--shannon`'s CSV carries both `entropy15` (`family_entropy` — the settled
+15-non-empty-state definition, see above) and `entropy4` (`family_entropy_4`
+— plain nucleotide reduction), computed from the same already-resolved
+`genome_mask`, not from the marginal approximation above. A genome carrying
+several bases at once contributes to *each* base's count (counted once per
+base present, not fractionally split, not folded into one combined state)
+— a genome polymorphic for the family is present at more than one base by
+construction, so it is expected to count more than once; the denominator is
+the total base-occurrence count, not the genome count (the two coincide
+only when no genome carries more than one base). Kept side by side
+specifically to measure, on real data, how much the two diverge — not yet
+analyzed.
diff --git a/src/Cargo.lock b/src/Cargo.lock
index 1cafb680..113db77b 100644
--- a/src/Cargo.lock
+++ b/src/Cargo.lock
@@ -1858,6 +1858,7 @@ dependencies = [
  "obiskbuilder",
  "obiskio",
  "obisys",
+ "rand 0.8.6",
  "rayon",
  "tempfile",
  "tracing",
diff --git a/src/obikmer/src/cmd/phylo/args.rs b/src/obikmer/src/cmd/phylo/args.rs
index aa294e6e..b166ab25 100644
--- a/src/obikmer/src/cmd/phylo/args.rs
+++ b/src/obikmer/src/cmd/phylo/args.rs
@@ -146,6 +146,28 @@ pub struct PhyloArgs {
     #[arg(long)]
     pub snp: bool,
 
+    /// Cap the number of variable families (non-monomorphic minorants,
+    /// `family_size() >= 2`) retained by `--snp`/`--sankoff` (and everything
+    /// `--sankoff` implies) and `--shannon`, to (approximately) this many —
+    /// sampled proportionally per layer, so the pseudo-alignment/entropy
+    /// report stays usable on an index far larger than the sample itself
+    /// (mandatory, not optional, once the index is large enough that a full
+    /// pseudo-alignment can't be materialized at all). See
+    /// `docmd/architecture/siblings.md`, "`--subsample`/`--shannon`". If the
+    /// index has fewer non-monomorphic minorants than this, every one of
+    /// them is kept — no error, no under/over-shoot handling needed.
+    #[arg(long, value_name = "N")]
+    pub subsample: Option<usize>,
+
+    /// Write <prefix>_shannon.csv: per-family Shannon entropy (bits, over
+    /// the 15 non-empty subsets of `{A,C,G,T}`, `∅`/absent genomes excluded
+    /// from the denominator — see `docmd/architecture/siblings.md`,
+    /// "Entropy definition") of every non-monomorphic minorant, one row per
+    /// family. Combine with `--subsample N` for a bounded diagnostic sample
+    /// instead of a full-index pass. Same annex requirement as `--snp`.
+    #[arg(long)]
+    pub shannon: bool,
+
     /// Write an NxN CSV (`<prefix>_family_overlap.csv`) of, for each genome
     /// pair, how many variable families (same set `--snp`'s pseudo-alignment
     /// uses — `family_size() >= 2`) both genomes actually carry a call for
@@ -244,7 +266,7 @@ pub struct PhyloArgs {
     /// Output prefix: <prefix>_dist.csv, <prefix>_shared.csv,
     /// <prefix>_siblings.csv, <prefix>_sibling_hist.csv, <prefix>_rawsnp.csv,
     /// <prefix>_rawsnp_counts.csv,
-    /// <prefix>_snp.fasta, <prefix>_family_overlap.csv,
+    /// <prefix>_snp.fasta, <prefix>_family_overlap.csv, <prefix>_shannon.csv,
     /// <prefix>_sankoff_matrix.csv, <prefix>_sankoff_params.yaml,
     /// <prefix>_sankoff.fasta, <prefix>_sankoff.tnt, <prefix>_sankoff.tcm,
     /// <prefix>_sankoff.pg, <prefix>_iqtree.model, <prefix>_iqtree.fasta,
diff --git a/src/obikmer/src/cmd/phylo/family_overlap.rs b/src/obikmer/src/cmd/phylo/family_overlap.rs
index 7a8f9d7b..00732aed 100644
--- a/src/obikmer/src/cmd/phylo/family_overlap.rs
+++ b/src/obikmer/src/cmd/phylo/family_overlap.rs
@@ -80,7 +80,7 @@ pub(super) fn apply_min_shared_family_exclusion(
     threshold: f64,
     mask: &mut [bool],
 ) {
-    let alignment = idx.snp_pseudo_alignment().unwrap_or_else(|e| {
+    let alignment = idx.snp_pseudo_alignment(None).unwrap_or_else(|e| {
         eprintln!("error computing SNP pseudo-alignment for --min-shared-family: {e}");
         std::process::exit(1);
     });
diff --git a/src/obikmer/src/cmd/phylo/mod.rs b/src/obikmer/src/cmd/phylo/mod.rs
index e7dd41f0..8f7715d1 100644
--- a/src/obikmer/src/cmd/phylo/mod.rs
+++ b/src/obikmer/src/cmd/phylo/mod.rs
@@ -13,8 +13,8 @@ use obikindex::KmerIndex;
 use obikphylo::{
     cardinality_transition_probs, composition_transition_probs, pairwise_cost_matrix,
     siblings::{
-        CardinalityExt, DistanceExt, RawSnpDistanceOutput, SiblingAnnexBuildExt, SiblingStatsExt,
-        SnpAlignment, SnpAlignmentExt,
+        CardinalityExt, DistanceExt, RawSnpDistanceOutput, ShannonEntropyExt, SiblingAnnexBuildExt,
+        SiblingStatsExt, SnpAlignment, SnpAlignmentExt,
     },
 };
 use obisys::{Reporter, Stage};
@@ -177,7 +177,7 @@ pub fn run(args: PhyloArgs) {
     }
     if args.snp {
         let t = Stage::start("snp_pseudo_alignment");
-        let alignment = idx.snp_pseudo_alignment().unwrap_or_else(|e| {
+        let alignment = idx.snp_pseudo_alignment(args.subsample).unwrap_or_else(|e| {
             eprintln!("error computing SNP pseudo-alignment: {e}");
             std::process::exit(1);
         });
@@ -187,7 +187,7 @@ pub fn run(args: PhyloArgs) {
     }
     if args.family_overlap {
         let t = Stage::start("snp_pseudo_alignment");
-        let alignment = idx.snp_pseudo_alignment().unwrap_or_else(|e| {
+        let alignment = idx.snp_pseudo_alignment(args.subsample).unwrap_or_else(|e| {
             eprintln!("error computing SNP pseudo-alignment: {e}");
             std::process::exit(1);
         });
@@ -195,6 +195,18 @@ pub fn run(args: PhyloArgs) {
         let (alignment, kept_labels) = drop_excluded(alignment);
         write_family_overlap_csv(&alignment, &kept_labels, &args.output);
     }
+    if args.shannon {
+        let t = Stage::start("shannon_entropy");
+        let path = args.output.as_ref()
+            .map(|p| format!("{}_shannon.csv", p.display()))
+            .unwrap_or_else(|| "shannon.csv".into());
+        idx.shannon_entropy_csv(std::path::Path::new(&path), args.subsample).unwrap_or_else(|e| {
+            eprintln!("error computing Shannon entropy: {e}");
+            std::process::exit(1);
+        });
+        rep.push(t.stop());
+        info!("per-family Shannon entropy → {path}");
+    }
     if args.sankoff || args.tnt || args.phyg || args.iqtree {
         let t = Stage::start("raw_snp_distance");
         let mut raw = idx.raw_snp_distance().unwrap_or_else(|e| {
@@ -223,7 +235,7 @@ pub fn run(args: PhyloArgs) {
         write_sankoff_params(&card_tally, &p_card, &base_tally, &p_comp, args.sankoff_ratio_ceiling, &args.output);
 
         let t = Stage::start("snp_pseudo_alignment");
-        let alignment = idx.snp_pseudo_alignment().unwrap_or_else(|e| {
+        let alignment = idx.snp_pseudo_alignment(args.subsample).unwrap_or_else(|e| {
             eprintln!("error computing SNP pseudo-alignment: {e}");
             std::process::exit(1);
         });
@@ -256,6 +268,7 @@ pub fn run(args: PhyloArgs) {
         || args.raw_snp_counts
         || args.snp
         || args.family_overlap
+        || args.shannon
         || args.sankoff
         || args.tnt
         || args.phyg
diff --git a/src/obikphylo/Cargo.toml b/src/obikphylo/Cargo.toml
index 5dc257ba..282a852f 100644
--- a/src/obikphylo/Cargo.toml
+++ b/src/obikphylo/Cargo.toml
@@ -15,6 +15,7 @@ obiskbuilder     = { path = "../obiskbuilder" }
 obipipeline      = { path = "../obipipeline" }
 memmap2          = "0.9"
 ndarray          = "0.16"
+rand             = "0.8"
 rayon            = "1"
 tracing          = "0.1.44"
 
diff --git a/src/obikphylo/src/siblings/alignment.rs b/src/obikphylo/src/siblings/alignment.rs
index 123b14d3..bd503f0c 100644
--- a/src/obikphylo/src/siblings/alignment.rs
+++ b/src/obikphylo/src/siblings/alignment.rs
@@ -7,7 +7,7 @@ use obikindex::{OKIError, OKIResult};
 use obikindex::KmerIndex;
 
 use super::cache::PartitionCache;
-use super::family_scan::scan_layer_families;
+use super::family_scan::{scan_layer_families, Selection};
 
 /// IUPAC ambiguity code for a per-genome family presence mask (bit `b` set
 /// iff the genome carries the member whose own central base is `b`):
@@ -59,11 +59,18 @@ pub struct SnpAlignment {
 pub trait SnpAlignmentExt {
     /// Build the SNP-only pseudo-alignment from an already-built sibling
     /// annex (run [`build_sibling_annex`](super::build::SiblingAnnexBuildExt::build_sibling_annex) first).
-    fn snp_pseudo_alignment(&self) -> OKIResult<SnpAlignment>;
+    ///
+    /// `subsample`: `--subsample N` — cap the number of variable families
+    /// retained to (approximately) `N`, sampled proportionally per layer
+    /// among non-monomorphic minorants (see
+    /// `docmd/architecture/siblings.md`, "`--subsample`/`--shannon`").
+    /// `None` keeps today's behaviour: every non-monomorphic minorant of
+    /// every layer.
+    fn snp_pseudo_alignment(&self, subsample: Option<usize>) -> OKIResult<SnpAlignment>;
 }
 
 impl SnpAlignmentExt for KmerIndex {
-    fn snp_pseudo_alignment(&self) -> OKIResult<SnpAlignment> {
+    fn snp_pseudo_alignment(&self, subsample: Option<usize>) -> OKIResult<SnpAlignment> {
         let n_parts = self.n_partitions();
         let n_genomes = self.meta().genomes.len();
         let with_counts = self.meta().config.with_counts;
@@ -79,6 +86,7 @@ impl SnpAlignmentExt for KmerIndex {
         .map_err(OKIError::Partition)?;
         let cache = Arc::new(PartitionCache::build(&partition, n_parts, with_counts)?);
         let layer_dirs = super::family_scan::sibling_layer_dirs(self)?;
+        let selections = super::subsample::compute_selections(&layer_dirs, subsample)?;
 
         let pb = progress_bar("snp_pseudo_alignment", layer_dirs.len() as u64, "layers");
         // One layer at a time, not `par_iter()` over layers — same
@@ -92,8 +100,12 @@ impl SnpAlignmentExt for KmerIndex {
         // whole-layer) — no intermediate per-layer buffer, layer order
         // giving a single deterministic column order across the whole index.
         let mut sequences: Vec<Vec<u8>> = vec![Vec::new(); n_genomes];
-        for layer_dir in &layer_dirs {
-            scan_layer_families(layer_dir, n_parts, n_genomes, with_counts, k, &cache, |mask, genome_mask| {
+        for (layer_dir, layer_selection) in layer_dirs.iter().zip(selections.iter()) {
+            let selection = match layer_selection {
+                None => Selection::All,
+                Some(set) => Selection::Some(set),
+            };
+            scan_layer_families(layer_dir, n_parts, n_genomes, with_counts, k, &cache, &selection, |_family_idx, mask, genome_mask| {
                 if mask.family_size() < 2 {
                     return; // monomorphic family — no signal, skip
                 }
diff --git a/src/obikphylo/src/siblings/cardinality.rs b/src/obikphylo/src/siblings/cardinality.rs
index c76888fd..0e63910c 100644
--- a/src/obikphylo/src/siblings/cardinality.rs
+++ b/src/obikphylo/src/siblings/cardinality.rs
@@ -10,7 +10,7 @@ use obikindex::KmerIndex;
 
 use super::cache::PartitionCache;
 use super::distance::RawSnpDistanceOutput;
-use super::family_scan::scan_layer_families;
+use super::family_scan::{scan_layer_families, Selection};
 
 /// See [`KmerIndex::cardinality_tally`].
 pub struct CardinalityTally {
@@ -89,7 +89,7 @@ impl CardinalityExt for KmerIndex {
         // family comes back — no per-layer buffer.
         let mut total = [[0u64; 5]; 5];
         for layer_dir in &layer_dirs {
-            scan_layer_families(layer_dir, n_parts, n_genomes, with_counts, k, &cache, |mask, genome_mask| {
+            scan_layer_families(layer_dir, n_parts, n_genomes, with_counts, k, &cache, &Selection::All, |_family_idx, mask, genome_mask| {
                 if mask.family_size() < 2 {
                     // Fully invariant family (never varies anywhere in
                     // the index) — genome-wide background, not
diff --git a/src/obikphylo/src/siblings/distance.rs b/src/obikphylo/src/siblings/distance.rs
index 99347600..8ce640a9 100644
--- a/src/obikphylo/src/siblings/distance.rs
+++ b/src/obikphylo/src/siblings/distance.rs
@@ -9,7 +9,7 @@ use obikindex::{OKIError, OKIResult};
 use obikindex::KmerIndex;
 
 use super::cache::PartitionCache;
-use super::family_scan::scan_layer_families;
+use super::family_scan::{scan_layer_families, Selection};
 
 /// Raw p-distance restricted to loci that are single-copy in **both**
 /// genomes of a pair — the "stringent / paralogy-aware" locus eligibility
@@ -90,7 +90,7 @@ where
         for layer_dir in &layer_dirs {
             let mut acc = zero();
 
-            scan_layer_families(layer_dir, n_parts, n_genomes, with_counts, k, &cache, |mask, genome_mask| {
+            scan_layer_families(layer_dir, n_parts, n_genomes, with_counts, k, &cache, &Selection::All, |_family_idx, mask, genome_mask| {
                 let variable = mask.family_size() >= 2;
 
                 // Per genome: which single form (if exactly one) it
diff --git a/src/obikphylo/src/siblings/entropy.rs b/src/obikphylo/src/siblings/entropy.rs
new file mode 100644
index 00000000..0b73b5c5
--- /dev/null
+++ b/src/obikphylo/src/siblings/entropy.rs
@@ -0,0 +1,170 @@
+//! `--shannon` — per-family Shannon entropy over the 15 non-empty subsets
+//! of `{A,C,G,T}`. See `docmd/architecture/siblings.md`, "Entropy
+//! definition — settled 2026-08-15" and "`--subsample`/`--shannon`", for
+//! the design discussion this implements: the project's calibrated 16-state
+//! Sankoff cost matrix (`cardcomp::pairwise_cost_matrix`) treats every
+//! observed combination of bases as its own first-class state, so entropy
+//! over that same 15-symbol space (state `0`/`∅` excluded — a family is
+//! only informative among the genomes where it is actually observed) is the
+//! consistent informativeness proxy for this project, not a 4-symbol
+//! reduction.
+
+use std::io::{BufWriter, Write};
+use std::path::Path;
+use std::sync::Arc;
+
+use obikpartitionner::KmerPartition;
+use obisys::progress_bar;
+
+use obikindex::{OKIError, OKIResult};
+use obikindex::KmerIndex;
+
+use super::cache::PartitionCache;
+use super::family_scan::{Selection, scan_layer_families};
+
+/// Shannon entropy (bits) of one family's per-genome states, over the 15
+/// non-empty subsets of `{A,C,G,T}` actually observed among the genomes
+/// carrying it (`genome_mask[g] != 0`) — genomes where the family is absent
+/// are excluded from the denominator, not scored as a 16th state. `None`
+/// only if the family is absent from every genome (shouldn't happen for a
+/// real minorant, guarded against rather than dividing by zero). Second
+/// value: the denominator (`n_genomes_present`) used, for traceability.
+pub(super) fn family_entropy(genome_mask: &[u8]) -> Option<(f64, usize)> {
+    let mut freq = [0u32; 16]; // index 0 (∅) never incremented, kept for direct `m as usize` indexing
+    let mut present = 0u32;
+    for &m in genome_mask {
+        if m != 0 {
+            freq[m as usize] += 1;
+            present += 1;
+        }
+    }
+    if present == 0 {
+        return None;
+    }
+    let mut h = 0.0f64;
+    for &c in &freq[1..] {
+        if c == 0 {
+            continue;
+        }
+        let p = f64::from(c) / f64::from(present);
+        h -= p * p.log2();
+    }
+    Some((h, present as usize))
+}
+
+/// Shannon entropy (bits) of one family's per-genome states, reduced to the
+/// 4 plain nucleotide symbols instead of the 15-state space above — kept
+/// alongside it (not instead of it) purely to measure how much the two
+/// diverge on real data, per the discussion in
+/// `docmd/architecture/siblings.md`, "`--subsample`/`--shannon`". A genome
+/// carrying several bases at once (`genome_mask[g]` with more than one bit
+/// set) contributes to *each* of those bases' counts — counted once per
+/// base present, not split fractionally, and not folded into a combined
+/// state the way [`family_entropy`] does: a genome polymorphic for the
+/// family is, by construction, present at more than one base, so it simply
+/// counts more than once here. The denominator is therefore the total
+/// number of base-occurrences summed over every present genome, not the
+/// genome count — the two coincide only when no genome carries more than
+/// one base. `None` under the same condition as [`family_entropy`].
+pub(super) fn family_entropy_4(genome_mask: &[u8]) -> Option<(f64, usize)> {
+    let mut freq = [0u32; 4];
+    let mut total = 0u32;
+    for &m in genome_mask {
+        for (base, count) in freq.iter_mut().enumerate() {
+            if m & (1 << base) != 0 {
+                *count += 1;
+                total += 1;
+            }
+        }
+    }
+    if total == 0 {
+        return None;
+    }
+    let mut h = 0.0f64;
+    for &c in &freq {
+        if c == 0 {
+            continue;
+        }
+        let p = f64::from(c) / f64::from(total);
+        h -= p * p.log2();
+    }
+    Some((h, total as usize))
+}
+
+/// Adds [`shannon_entropy_csv`](Self::shannon_entropy_csv) to `KmerIndex`.
+pub trait ShannonEntropyExt {
+    /// Writes a CSV
+    /// (`layer,family_idx,entropy15,entropy4,family_size,n_genomes_present`)
+    /// of per-family Shannon entropy — both [`family_entropy`] (15 non-empty
+    /// states, the project's settled definition) and [`family_entropy_4`]
+    /// (plain 4-symbol reduction, kept alongside for comparison) — one row
+    /// per non-monomorphic minorant visited, from an already-built sibling
+    /// annex (run
+    /// [`build_sibling_annex`](super::build::SiblingAnnexBuildExt::build_sibling_annex)
+    /// first). `layer` is this layer's ordinal among every layer carrying an
+    /// annex (not a partition/layer pair — an opaque but stable id, unique
+    /// together with `family_idx`); `family_idx` is the family's
+    /// iteration-order index within that layer, the same numbering
+    /// `--subsample`'s selection is drawn from.
+    ///
+    /// `subsample`: same meaning as
+    /// [`SnpAlignmentExt::snp_pseudo_alignment`](super::SnpAlignmentExt::snp_pseudo_alignment)'s
+    /// — `None` streams every non-monomorphic minorant of the whole index
+    /// (a time cost, not a memory one: entropy is computed and written
+    /// per-family as soon as it resolves), `Some(n)` bounds the index's
+    /// cross-partition resolution work to ~`n` sampled families.
+    fn shannon_entropy_csv(&self, path: &Path, subsample: Option<usize>) -> OKIResult<()>;
+}
+
+impl ShannonEntropyExt for KmerIndex {
+    fn shannon_entropy_csv(&self, path: &Path, subsample: Option<usize>) -> OKIResult<()> {
+        let n_parts = self.n_partitions();
+        let n_genomes = self.meta().genomes.len();
+        let with_counts = self.meta().config.with_counts;
+        let k = self.kmer_size();
+        let n_bits = n_parts.trailing_zeros() as usize;
+
+        let partition = KmerPartition::open_with_config(
+            self.root_path(),
+            self.kmer_size(),
+            self.minimizer_size(),
+            n_bits,
+        )
+        .map_err(OKIError::Partition)?;
+        let cache = Arc::new(PartitionCache::build(&partition, n_parts, with_counts)?);
+        let layer_dirs = super::family_scan::sibling_layer_dirs(self)?;
+        let selections = super::subsample::compute_selections(&layer_dirs, subsample)?;
+
+        let mut f = BufWriter::new(std::fs::File::create(path).map_err(OKIError::Io)?);
+        writeln!(f, "layer,family_idx,entropy15,entropy4,family_size,n_genomes_present").map_err(OKIError::Io)?;
+
+        let pb = progress_bar("shannon_entropy", layer_dirs.len() as u64, "layers");
+        for (layer_ord, (layer_dir, layer_selection)) in layer_dirs.iter().zip(selections.iter()).enumerate() {
+            let selection = match layer_selection {
+                None => Selection::All,
+                Some(set) => Selection::Some(set),
+            };
+            let mut write_err = None;
+            scan_layer_families(layer_dir, n_parts, n_genomes, with_counts, k, &cache, &selection, |family_idx, mask, genome_mask| {
+                if write_err.is_some() {
+                    return;
+                }
+                if mask.family_size() < 2 {
+                    return; // monomorphic family — entropy trivially 0, no signal, skip
+                }
+                let Some((h15, n_present)) = family_entropy(genome_mask) else { return };
+                let h4 = family_entropy_4(genome_mask).map_or(0.0, |(h, _)| h);
+                if let Err(e) = writeln!(f, "{layer_ord},{family_idx},{h15:.6},{h4:.6},{},{n_present}", mask.family_size()) {
+                    write_err = Some(e);
+                }
+            })?;
+            if let Some(e) = write_err {
+                return Err(OKIError::Io(e));
+            }
+            pb.inc(1);
+        }
+        pb.finish_and_clear();
+
+        Ok(())
+    }
+}
diff --git a/src/obikphylo/src/siblings/family_scan.rs b/src/obikphylo/src/siblings/family_scan.rs
index 46e5f76d..338a1b8c 100644
--- a/src/obikphylo/src/siblings/family_scan.rs
+++ b/src/obikphylo/src/siblings/family_scan.rs
@@ -74,6 +74,29 @@ use super::{olm_to_ok, FamilyMask, SiblingAnnex, ANNEX_FILE_NAME, INDEX_SUBDIR};
 /// queries per batch to amortise against.
 const FAMILY_BATCH: usize = 65536;
 
+/// Restricts [`scan_layer_families`] to a subset of a layer's families,
+/// identified by their iteration-order index — see
+/// `docmd/architecture/siblings.md`, "`--subsample`/`--shannon`", for why:
+/// bounding which families actually pay the expensive cross-partition
+/// resolution cost is what makes a sampled run cheap on an index far larger
+/// than the sample itself. `All` (the default for every pre-existing
+/// caller) keeps today's behaviour exactly.
+pub(super) enum Selection<'a> {
+    All,
+    Some(&'a std::collections::HashSet<usize>),
+}
+
+/// Shared by the pipeline worker (via the `Arc`-cloned `Option<HashSet>`,
+/// see below — a `Selection` itself doesn't cross the worker thread
+/// boundary) and the final replay loop, so both sides agree on membership
+/// without duplicating the match.
+fn is_selected(selected: &Option<std::collections::HashSet<usize>>, family_idx: usize) -> bool {
+    match selected {
+        None => true,
+        Some(set) => set.contains(&family_idx),
+    }
+}
+
 /// Every (partition, layer) directory carrying a sibling annex, checked
 /// up front so a missing one is reported before any real work starts.
 /// Shared by every sibling-annex consumer's extension-trait impl (`alignment`,
@@ -152,11 +175,12 @@ enum FamData {
 /// Visits every minorant family of one layer, in iteration order, batched
 /// [`FAMILY_BATCH`] at a time — see the module docs for why generation and
 /// resolution use different concurrency. `on_family` is called once per
-/// family, in iteration order, with its own annex mask and its per-genome
-/// base-presence (`genome_mask[g]`: bit `b` set iff genome `g` carries the
-/// member whose own canonical central base is `b`), backed by a scratch
-/// buffer reused across every call — callers that need to keep data past
-/// the call must copy it themselves.
+/// family, in iteration order, with that family's iteration-order index
+/// (the same numbering [`Selection`] indices are drawn from), its own annex
+/// mask, and its per-genome base-presence (`genome_mask[g]`: bit `b` set
+/// iff genome `g` carries the member whose own canonical central base is
+/// `b`), backed by a scratch buffer reused across every call — callers that
+/// need to keep data past the call must copy it themselves.
 pub(super) fn scan_layer_families(
     layer_dir: &Path,
     n_parts: usize,
@@ -164,7 +188,8 @@ pub(super) fn scan_layer_families(
     with_counts: bool,
     k: usize,
     cache: &Arc<PartitionCache>,
-    mut on_family: impl FnMut(FamilyMask, &[u8]),
+    selection: &Selection,
+    mut on_family: impl FnMut(usize, FamilyMask, &[u8]),
 ) -> OKIResult<()> {
     let index_dir = layer_dir.parent().expect("layer_dir has a parent index dir");
     let meta = PartitionMeta::load(index_dir).map_err(olm_to_ok)?;
@@ -203,7 +228,18 @@ pub(super) fn scan_layer_families(
         _permit: t.guard,
     });
 
+    // `Selection::Some` borrows a `HashSet` whose lifetime doesn't span the
+    // pipeline's worker threads — cloned once into an `Arc` so every worker
+    // can share it cheaply instead of requiring `selection` itself to be
+    // `'static`. `None` means [`Selection::All`], checked with a plain
+    // `map_or` at each use instead of allocating an always-true set.
+    let selected: Arc<Option<std::collections::HashSet<usize>>> = Arc::new(match selection {
+        Selection::All => None,
+        Selection::Some(set) => Some((*set).clone()),
+    });
+
     let worker_ctx = Arc::clone(&ctx);
+    let worker_selected = Arc::clone(&selected);
     let pipe = obipipeline::make_pipe! {
         FamData : SourceBatch => GeneratedBatch,
         | {
@@ -222,11 +258,19 @@ pub(super) fn scan_layer_families(
                 // (not a hand-rolled `central_canonical_neighbors` +
                 // `mask.has` loop) already filters to present members and
                 // hands back each one's annex-recorded layer alongside.
+                // Families outside `selected` (sampling only) still get a
+                // mask/base entry — pass 2 indexes uniformly by `i` — but
+                // never an outgoing query: that's the expensive part a
+                // sampled run exists to avoid paying for every family.
                 for (i, entry) in batch.entries.iter().enumerate() {
                     let (kmer, mask) = (entry.kmer, entry.mask);
                     masks.push(mask);
                     let base = central_base(kmer, ctx.k);
                     bases.push(base);
+                    let family_idx = batch.start_family_idx + i;
+                    if !is_selected(&worker_selected, family_idx) {
+                        continue;
+                    }
                     for (member, layer) in mask.family_members(kmer, ctx.k) {
                         if member == kmer {
                             continue; // local — resolved below straight from `mat`, no lookup
@@ -296,10 +340,14 @@ pub(super) fn scan_layer_families(
             });
 
             for i in 0..n {
+                let family_idx = batch.start_family_idx + i;
+                if !is_selected(&selected, family_idx) {
+                    continue; // not in the sample — never resolved above, nothing to report
+                }
                 for (g, dst) in scratch.iter_mut().enumerate() {
                     *dst = genome_mask[i * n_genomes + g].load(Ordering::Relaxed);
                 }
-                on_family(batch.masks[i], &scratch);
+                on_family(family_idx, batch.masks[i], &scratch);
             }
             next_expected += n;
         }
diff --git a/src/obikphylo/src/siblings/mod.rs b/src/obikphylo/src/siblings/mod.rs
index 9fa04f5e..a5c368bb 100644
--- a/src/obikphylo/src/siblings/mod.rs
+++ b/src/obikphylo/src/siblings/mod.rs
@@ -47,11 +47,13 @@ mod build;
 mod cache;
 mod cardinality;
 mod distance;
+mod entropy;
 mod family_scan;
 mod helpers;
 mod iter;
 mod siblingannex;
 mod stats;
+mod subsample;
 
 #[cfg(test)]
 mod tests;
@@ -60,6 +62,7 @@ pub use alignment::{SnpAlignment, SnpAlignmentExt};
 pub use build::SiblingAnnexBuildExt;
 pub use cardinality::{CardinalityExt, CardinalityTally};
 pub use distance::{BasePairTally, DistanceExt, RawSnpDistanceOutput};
+pub use entropy::ShannonEntropyExt;
 pub use iter::{MinorantBatchIter, MinorantIter, SiblingBatchIter, SiblingEntry, SiblingIter, SiblingLayerExt};
 pub(crate) use siblingannex::{FamilyMask, SiblingAnnex, SiblingAnnexBuilder};
 pub use stats::{SiblingAnnexStats, SiblingStatsExt};
diff --git a/src/obikphylo/src/siblings/stats.rs b/src/obikphylo/src/siblings/stats.rs
index e612257f..06cf4698 100644
--- a/src/obikphylo/src/siblings/stats.rs
+++ b/src/obikphylo/src/siblings/stats.rs
@@ -11,7 +11,7 @@ use obikindex::KmerIndex;
 use super::ANNEX_FILE_NAME;
 use super::SiblingAnnex;
 use super::cache::PartitionCache;
-use super::family_scan::scan_layer_families;
+use super::family_scan::{scan_layer_families, Selection};
 
 /// Distribution of family sizes (1-4), read back from an already-built
 /// annex (see [`super::build::SiblingAnnexBuildExt::build_sibling_annex`])
@@ -131,7 +131,7 @@ impl SiblingStatsExt for KmerIndex {
             ..Default::default()
         };
         for layer_dir in &layer_dirs {
-            scan_layer_families(layer_dir, n_parts, n_genomes, with_counts, k, &cache, |mask, genome_mask| {
+            scan_layer_families(layer_dir, n_parts, n_genomes, with_counts, k, &cache, &Selection::All, |_family_idx, mask, genome_mask| {
                 // "Genome g represents this family" means g carries
                 // *any* of its members, not just the minorant's own —
                 // `genome_mask[g] != 0` is exactly that.
diff --git a/src/obikphylo/src/siblings/subsample.rs b/src/obikphylo/src/siblings/subsample.rs
new file mode 100644
index 00000000..80b593af
--- /dev/null
+++ b/src/obikphylo/src/siblings/subsample.rs
@@ -0,0 +1,158 @@
+//! Proportional per-layer sampling of non-monomorphic minorants
+//! (`family_size() >= 2`) — see `docmd/architecture/siblings.md`,
+//! "`--subsample`/`--shannon`", for the full design discussion.
+//!
+//! Three steps, in order, each cheaper than the one before because it
+//! narrows what the next one has to touch:
+//!
+//! 1. [`non_monomorphic_counts`] — one cheap structural pass per layer
+//!    (annex bits only, no cross-partition resolution), giving `count_layer`
+//!    for every layer.
+//! 2. [`sample_layers`] — given a target `n` and those counts, computes
+//!    `n_layer = round(n * count_layer / total_count)` per layer (never
+//!    exceeds `count_layer` as long as `n <= total_count`; if
+//!    `total_count <= n`, sampling is skipped entirely — every
+//!    non-monomorphic minorant of every layer is kept) and reservoir-samples
+//!    (Algorithm R, one more cheap structural pass, `O(n_layer)` memory) the
+//!    selected iteration-order indices.
+//! 3. The result feeds [`super::family_scan::scan_layer_families`]'s
+//!    `Selection` parameter, which bounds the expensive cross-partition
+//!    resolution to just the selected families.
+
+use std::collections::HashSet;
+use std::path::{Path, PathBuf};
+
+use rand::Rng;
+use rayon::prelude::*;
+
+use obikindex::OKIResult;
+
+use super::ANNEX_FILE_NAME;
+use super::SiblingAnnex;
+
+/// A family is non-monomorphic (informative-eligible) iff at least one
+/// sibling is registered alongside it — `family_size() >= 2`, i.e.
+/// `siblings() >= 1`. Mirrors the filter already applied post-hoc in
+/// `snp_pseudo_alignment`, but checked here *before* any resolution work.
+fn is_non_monomorphic_minorant(mask: super::FamilyMask) -> bool {
+    mask.is_minorant() && mask.siblings() >= 1
+}
+
+/// Step 1: per-layer count of non-monomorphic minorants — cheap, parallel
+/// across layers, annex bits only (same shape as
+/// `SiblingStatsExt::sibling_family_size_histogram`, but keeping the
+/// per-layer breakdown instead of collapsing it into one index-wide sum,
+/// since proportional sampling needs each layer's own share).
+pub(super) fn non_monomorphic_counts(layer_dirs: &[PathBuf]) -> OKIResult<Vec<u64>> {
+    layer_dirs
+        .par_iter()
+        .map(|layer_dir| -> OKIResult<u64> {
+            let annex = SiblingAnnex::open(&layer_dir.join(ANNEX_FILE_NAME))?;
+            let mut count = 0u64;
+            for slot in 0..annex.len() {
+                if annex.get(slot).is_some_and(is_non_monomorphic_minorant) {
+                    count += 1;
+                }
+            }
+            Ok(count)
+        })
+        .collect()
+}
+
+/// Step 2, per layer: Algorithm-R reservoir sampling of `n_layer`
+/// non-monomorphic minorant iteration-indices — single pass, no
+/// cross-partition resolution, `O(n_layer)` memory regardless of the
+/// layer's true size (never materialises the full non-monomorphic index
+/// list, only the reservoir itself).
+///
+/// The stored values are **`family_idx`, `scan_layer_families`'s own
+/// numbering** — the index among *every* minorant of the layer (monomorphic
+/// ones included, since `iter_minorants_batch` only filters on
+/// `is_minorant()`), not the raw annex slot (`for slot in 0..annex.len()`
+/// spans every k-mer, minorant or not) and not a counter over
+/// non-monomorphic minorants alone. Conflating any of these with
+/// `family_idx` silently drifts apart as soon as the layer contains a
+/// monomorphic minorant — i.e. almost immediately, since ~98% of minorants
+/// are monomorphic — so the two counters below are deliberately kept
+/// separate: `family_idx` tracks every minorant (matching
+/// `scan_layer_families`), `seen` tracks only the non-monomorphic ones
+/// (what Algorithm R actually samples over).
+fn reservoir_sample_layer(layer_dir: &Path, n_layer: usize) -> OKIResult<HashSet<usize>> {
+    let annex = SiblingAnnex::open(&layer_dir.join(ANNEX_FILE_NAME))?;
+    let mut reservoir: Vec<usize> = Vec::with_capacity(n_layer);
+    let mut seen: u64 = 0;
+    let mut family_idx: usize = 0;
+    let mut rng = rand::thread_rng();
+    for slot in 0..annex.len() {
+        let Some(mask) = annex.get(slot) else { continue };
+        if !mask.is_minorant() {
+            continue; // not a minorant at all — doesn't advance `family_idx` either
+        }
+        let this_family_idx = family_idx;
+        family_idx += 1;
+        if mask.siblings() < 1 {
+            continue; // monomorphic minorant — consumed a family_idx above, but not sample-eligible
+        }
+        if reservoir.len() < n_layer {
+            reservoir.push(this_family_idx);
+        } else {
+            let j = rng.gen_range(0..=seen);
+            if j < n_layer as u64 {
+                reservoir[j as usize] = this_family_idx;
+            }
+        }
+        seen += 1;
+    }
+    Ok(reservoir.into_iter().collect())
+}
+
+/// Per-layer sampling outcome — `None` at a given layer means "keep every
+/// non-monomorphic minorant of this layer" (either the `total_count <= n`
+/// case, or a layer whose entire non-monomorphic set was already smaller
+/// than its computed share and got fully absorbed by rounding).
+pub(super) type LayerSelection = Option<HashSet<usize>>;
+
+/// Full entry point for every caller (`snp_pseudo_alignment`, the Shannon
+/// entropy report): `n = None` means "no `--subsample`", i.e. keep every
+/// non-monomorphic minorant of every layer — skips steps 1 and 2 entirely,
+/// since there is nothing to proportion.
+pub(super) fn compute_selections(layer_dirs: &[PathBuf], n: Option<usize>) -> OKIResult<Vec<LayerSelection>> {
+    match n {
+        None => Ok(vec![None; layer_dirs.len()]),
+        Some(n) => {
+            let counts = non_monomorphic_counts(layer_dirs)?;
+            sample_layers(layer_dirs, &counts, n)
+        }
+    }
+}
+
+/// Step 2 entry point: `n` is the total number of families requested across
+/// the whole index (`--subsample N`); `layer_dirs` and `counts` must be the
+/// same length and in the same order as returned by
+/// [`super::family_scan::sibling_layer_dirs`] /
+/// [`non_monomorphic_counts`].
+fn sample_layers(layer_dirs: &[PathBuf], counts: &[u64], n: usize) -> OKIResult<Vec<LayerSelection>> {
+    let total_count: u64 = counts.iter().sum();
+
+    if total_count <= n as u64 {
+        // Fewer non-monomorphic minorants in the whole index than requested
+        // — no sampling needed, keep everything everywhere.
+        return Ok(vec![None; layer_dirs.len()]);
+    }
+
+    layer_dirs
+        .par_iter()
+        .zip(counts.par_iter())
+        .map(|(layer_dir, &count_layer)| -> OKIResult<LayerSelection> {
+            if count_layer == 0 {
+                return Ok(Some(HashSet::new()));
+            }
+            let n_layer = ((n as u128 * count_layer as u128) / total_count as u128) as usize;
+            if n_layer == 0 {
+                return Ok(Some(HashSet::new()));
+            }
+            let selected = reservoir_sample_layer(layer_dir, n_layer)?;
+            Ok(Some(selected))
+        })
+        .collect()
+}
diff --git a/src/obikphylo/src/siblings/tests.rs b/src/obikphylo/src/siblings/tests.rs
index 43139e38..3b5359d3 100644
--- a/src/obikphylo/src/siblings/tests.rs
+++ b/src/obikphylo/src/siblings/tests.rs
@@ -13,6 +13,7 @@ use super::alignment::SnpAlignmentExt;
 use super::build::SiblingAnnexBuildExt;
 use super::cardinality::CardinalityExt;
 use super::distance::DistanceExt;
+use super::entropy::ShannonEntropyExt;
 use super::helpers::is_minorant;
 use super::stats::SiblingStatsExt;
 use super::{FamilyMask, SiblingAnnex, ANNEX_FILE_NAME, INDEX_SUBDIR};
@@ -229,7 +230,7 @@ fn family_scan_consumers_agree_on_one_sibling_each() {
 
     // snp_pseudo_alignment: one variable family, one column — g1's row
     // reads 'C' (its own member), g2's reads 'G'.
-    let alignment = merged.snp_pseudo_alignment().expect("snp_pseudo_alignment");
+    let alignment = merged.snp_pseudo_alignment(None).expect("snp_pseudo_alignment");
     assert_eq!(alignment.sequences[i1], vec![b'C']);
     assert_eq!(alignment.sequences[i2], vec![b'G']);
 
@@ -331,3 +332,206 @@ fn sibling_annex_records_the_real_layer_of_each_family_member() {
     assert_eq!(b.layer_value(2), Some(0), "g2's own base: seeded with its own layer (0)");
     assert_eq!(b.layer_value(1), Some(1), "g2's sibling (g1's form): resolved to its real layer (1)");
 }
+
+#[test]
+fn subsample_and_shannon_on_one_variable_family() {
+    let dir = tempdir().unwrap();
+    let g1 = build_single_genome_index(dir.path(), "g1", b"AACCGCTTAAG");
+    let g2 = build_single_genome_index(dir.path(), "g2", b"AACCGGTTAAG");
+    let merged = merge_two(dir.path(), &g1, &g2);
+    merged.build_sibling_annex().expect("build_sibling_annex");
+
+    let idx_of = |label: &str| merged.meta().genomes.iter().position(|g| g.label == label).unwrap();
+    let (i1, i2) = (idx_of("g1"), idx_of("g2"));
+
+    // This fixture has exactly one non-monomorphic family (see
+    // `family_scan_consumers_agree_on_one_sibling_each`) — total_count = 1.
+    // Asking for far more than that must fall back to "keep everything",
+    // identical to the unsampled (`None`) result.
+    let sampled = merged.snp_pseudo_alignment(Some(1000)).expect("snp_pseudo_alignment (subsample >> total)");
+    assert_eq!(sampled.sequences[i1], vec![b'C']);
+    assert_eq!(sampled.sequences[i2], vec![b'G']);
+
+    // Asking for 0 must keep nothing — an empty (but still one-row-per-genome)
+    // alignment, not an error.
+    let empty = merged.snp_pseudo_alignment(Some(0)).expect("snp_pseudo_alignment (subsample 0)");
+    assert!(empty.sequences[i1].is_empty());
+    assert!(empty.sequences[i2].is_empty());
+
+    // shannon_entropy_csv: one row, both entropy15 and entropy4 = 1 bit
+    // exactly (2 genomes present, each carrying exactly one distinct base,
+    // uniform split -> -2*(0.5*log2(0.5)) = 1 — the two definitions
+    // coincide here since no genome carries more than one base).
+    let csv_path = dir.path().join("shannon.csv");
+    merged.shannon_entropy_csv(&csv_path, Some(1000)).expect("shannon_entropy_csv");
+    let csv = std::fs::read_to_string(&csv_path).unwrap();
+    let mut lines = csv.lines();
+    assert_eq!(lines.next(), Some("layer,family_idx,entropy15,entropy4,family_size,n_genomes_present"));
+    let row = lines.next().expect("exactly one data row");
+    assert!(lines.next().is_none(), "exactly one non-monomorphic family in this fixture");
+    let fields: Vec<&str> = row.split(',').collect();
+    let entropy15: f64 = fields[2].parse().unwrap();
+    let entropy4: f64 = fields[3].parse().unwrap();
+    assert!((entropy15 - 1.0).abs() < 1e-6, "entropy15 should be exactly 1 bit, got {entropy15}");
+    assert!((entropy4 - 1.0).abs() < 1e-6, "entropy4 should be exactly 1 bit, got {entropy4}");
+    assert_eq!(fields[4], "2", "family_size");
+    assert_eq!(fields[5], "2", "n_genomes_present");
+}
+
+#[test]
+#[ignore]
+fn diag_real_index_layer_distribution() {
+    let idx = KmerIndex::open("/Users/coissac/Sync/travail/__MOI__/obikmer/benchmark/global_index_presence")
+        .expect("open real index");
+    let layer_dirs = super::family_scan::sibling_layer_dirs(&idx).expect("layer dirs");
+    let counts = super::subsample::non_monomorphic_counts(&layer_dirs).expect("counts");
+    let total: u64 = counts.iter().sum();
+    let n_zero = counts.iter().filter(|&&c| c == 0).count();
+    let max = counts.iter().max().unwrap();
+    let min_nonzero = counts.iter().filter(|&&c| c > 0).min().unwrap_or(&0);
+    println!("n_layers={} total={} n_zero_layers={} max={} min_nonzero={}",
+        counts.len(), total, n_zero, max, min_nonzero);
+    let n = 100_000usize;
+    let selections = super::subsample::compute_selections(&layer_dirs, Some(n)).expect("selections");
+    let selected_total: usize = selections.iter().map(|s| match s {
+        None => 0, // shouldn't happen when total_count > n
+        Some(set) => set.len(),
+    }).sum();
+    println!("requested={n} selected_total={selected_total}");
+    let mut sorted_counts = counts.clone();
+    sorted_counts.sort_unstable_by(|a, b| b.cmp(a));
+    println!("top10 counts: {:?}", &sorted_counts[..10.min(sorted_counts.len())]);
+}
+
+#[test]
+#[ignore]
+fn diag_plant_index_presence_matrix_sparsity() {
+    let idx = KmerIndex::open("/Users/coissac/travail/obiskim/data/phyloalps/phyloskims_sal_vac")
+        .expect("open real plant index");
+    let layer_dirs = super::family_scan::sibling_layer_dirs(&idx).expect("layer dirs");
+    println!("n_layers={}", layer_dirs.len());
+
+    // Sample a spread of layers rather than just the first few (partition
+    // order, not necessarily representative) — every 37th layer, capped at 20.
+    let sample: Vec<&std::path::PathBuf> = layer_dirs.iter().step_by(37).take(20).collect();
+
+    let mut total_ones: u64 = 0;
+    let mut total_cells: u64 = 0;
+    for layer_dir in &sample {
+        let mat = obicompactvec::PersistentBitMatrix::open(layer_dir).expect("open presence matrix");
+        let n = mat.n() as u64;
+        let n_cols = mat.n_cols() as u64;
+        let ones: u64 = mat.count_ones().iter().sum();
+        let cells = n * n_cols;
+        let density = ones as f64 / cells as f64;
+        println!(
+            "{}: n_slots={n} n_cols={n_cols} ones={ones} cells={cells} density={:.6} sparsity={:.6}",
+            layer_dir.display(), density, 1.0 - density,
+        );
+        total_ones += ones;
+        total_cells += cells;
+    }
+    let overall_density = total_ones as f64 / total_cells as f64;
+    println!(
+        "OVERALL sampled_layers={} total_ones={total_ones} total_cells={total_cells} density={:.6} sparsity={:.6}",
+        sample.len(), overall_density, 1.0 - overall_density,
+    );
+}
+
+#[test]
+#[ignore]
+fn diag_plant_index_multigenome_set_duplication() {
+    use std::collections::HashMap;
+
+    let idx = KmerIndex::open("/Users/coissac/travail/obiskim/data/phyloalps/phyloskims_sal_vac")
+        .expect("open real plant index");
+    let layer_dirs = super::family_scan::sibling_layer_dirs(&idx).expect("layer dirs");
+
+    // Same spread-sampling strategy as the sparsity diagnostic — every
+    // 37th layer, capped at 8 (this one is heavier per layer: builds a
+    // hash map of every distinct multi-genome set).
+    let sample: Vec<&std::path::PathBuf> = layer_dirs.iter().step_by(37).take(8).collect();
+
+    let mut total_rows: u64 = 0;
+    let mut total_multi_rows: u64 = 0;
+    let mut total_distinct_multi_sets: u64 = 0;
+    let mut total_singleton_rows: u64 = 0;
+
+    for layer_dir in &sample {
+        let mat = obicompactvec::PersistentBitMatrix::open(layer_dir).expect("open presence matrix");
+        let n = mat.n();
+        let n_cols = mat.n_cols();
+        let mut seen: HashMap<Vec<u32>, u32> = HashMap::new();
+        let mut singleton = 0u64;
+        let mut multi = 0u64;
+        let mut buf = vec![0u32; n_cols];
+        for slot in 0..n {
+            mat.fill_row(slot, &mut buf);
+            let set: Vec<u32> = (0..n_cols).filter(|&c| buf[c] != 0).map(|c| c as u32).collect();
+            match set.len() {
+                0 => {}
+                1 => singleton += 1,
+                _ => {
+                    multi += 1;
+                    *seen.entry(set).or_insert(0) += 1;
+                }
+            }
+        }
+        let distinct = seen.len() as u64;
+        println!(
+            "{}: n_slots={n} n_cols={n_cols} singleton_rows={singleton} multi_rows={multi} distinct_multi_sets={distinct} dedup_ratio={:.4}",
+            layer_dir.display(),
+            if multi > 0 { distinct as f64 / multi as f64 } else { 0.0 },
+        );
+        total_rows += n as u64;
+        total_singleton_rows += singleton;
+        total_multi_rows += multi;
+        total_distinct_multi_sets += distinct;
+    }
+
+    println!(
+        "OVERALL sampled_layers={} total_rows={total_rows} singleton_rows={total_singleton_rows} multi_rows={total_multi_rows} distinct_multi_sets={total_distinct_multi_sets} dedup_ratio={:.4}",
+        sample.len(),
+        if total_multi_rows > 0 { total_distinct_multi_sets as f64 / total_multi_rows as f64 } else { 0.0 },
+    );
+}
+
+#[test]
+#[ignore]
+fn diag_plant_index_cardinality_distribution() {
+    let idx = KmerIndex::open("/Users/coissac/travail/obiskim/data/phyloalps/phyloskims_sal_vac")
+        .expect("open real plant index");
+    let layer_dirs = super::family_scan::sibling_layer_dirs(&idx).expect("layer dirs");
+    let sample: Vec<&std::path::PathBuf> = layer_dirs.iter().step_by(37).take(8).collect();
+
+    let mut hist: Vec<u64> = Vec::new(); // hist[k] = number of rows with cardinality k
+    let mut total_rows: u64 = 0;
+
+    for layer_dir in &sample {
+        let mat = obicompactvec::PersistentBitMatrix::open(layer_dir).expect("open presence matrix");
+        let n = mat.n();
+        let n_cols = mat.n_cols();
+        if hist.len() < n_cols + 1 {
+            hist.resize(n_cols + 1, 0);
+        }
+        let mut buf = vec![0u32; n_cols];
+        for slot in 0..n {
+            mat.fill_row(slot, &mut buf);
+            let card = buf.iter().filter(|&&v| v != 0).count();
+            hist[card] += 1;
+        }
+        total_rows += n as u64;
+    }
+
+    println!("total_rows={total_rows}");
+    let mut cum: u64 = 0;
+    for (card, &count) in hist.iter().enumerate() {
+        if count == 0 { continue; }
+        cum += count;
+        println!(
+            "cardinality={card:3} count={count:10} frac={:.6} cumulative_frac={:.6}",
+            count as f64 / total_rows as f64,
+            cum as f64 / total_rows as f64,
+        );
+    }
+}
-- 
2.54.0


From 50f4820cb9cecd457fec443d037c66aadaa7043d Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Sat, 15 Aug 2026 15:59:03 +0200
Subject: [PATCH 33/46] feat(obicompactvec): introduce sparse bit matrix with
 supporting primitives

Implements a compact, row-major sparse bit matrix backed by memory-mapped components, introducing EliasFano, PersistentFixedIntVec, and PersistentRankSelectBitVec primitives for efficient storage and decoding. Adds a BinaryMatrix trait to unify row-level operations across dense and sparse implementations. Corrects edge-case behaviors for zero-width bit storage and cardinality-0 rows. Delivers reduced on-disk size and faster random row access, with column reads remaining dense-only. Test suites and benchmarks are included but currently marked as ignored.
---
 docmd/architecture/siblings.md                |  93 +++++
 src/Cargo.lock                                |   1 +
 src/obicompactvec/Cargo.toml                  |   1 +
 src/obicompactvec/src/bitmatrix/mod.rs        |   2 +
 src/obicompactvec/src/bitmatrix/persistent.rs |  15 +
 src/obicompactvec/src/bitmatrix/sparse.rs     | 372 ++++++++++++++++++
 src/obicompactvec/src/eliasfano.rs            | 133 +++++++
 src/obicompactvec/src/fixedintvec.rs          | 202 ++++++++++
 src/obicompactvec/src/lib.rs                  |  10 +-
 src/obicompactvec/src/rankselect.rs           | 265 +++++++++++++
 src/obicompactvec/src/tests/eliasfano.rs      | 114 ++++++
 src/obicompactvec/src/tests/fixedintvec.rs    | 112 ++++++
 src/obicompactvec/src/tests/mod.rs            |   4 +
 src/obicompactvec/src/tests/rankselect.rs     | 167 ++++++++
 src/obicompactvec/src/tests/sparse.rs         | 251 ++++++++++++
 src/obicompactvec/src/traits.rs               |  28 ++
 src/obikphylo/src/siblings/tests.rs           | 256 ++++++++++++
 17 files changed, 2024 insertions(+), 2 deletions(-)
 create mode 100644 src/obicompactvec/src/bitmatrix/sparse.rs
 create mode 100644 src/obicompactvec/src/eliasfano.rs
 create mode 100644 src/obicompactvec/src/fixedintvec.rs
 create mode 100644 src/obicompactvec/src/rankselect.rs
 create mode 100644 src/obicompactvec/src/tests/eliasfano.rs
 create mode 100644 src/obicompactvec/src/tests/fixedintvec.rs
 create mode 100644 src/obicompactvec/src/tests/rankselect.rs
 create mode 100644 src/obicompactvec/src/tests/sparse.rs

diff --git a/docmd/architecture/siblings.md b/docmd/architecture/siblings.md
index 3677cd9f..eb032890 100644
--- a/docmd/architecture/siblings.md
+++ b/docmd/architecture/siblings.md
@@ -403,3 +403,96 @@ the total base-occurrence count, not the genome count (the two coincide
 only when no genome carries more than one base). Kept side by side
 specifically to measure, on real data, how much the two diverge — not yet
 analyzed.
+
+## `PersistentSparseBitMatrix` — implemented and measured (2026-08-15)
+
+A row-major (k-mer-major), deduplicated sparse alternative to
+`obicompactvec::PersistentBitMatrix`, motivated by the same sparsity that
+drove `--subsample`/`--shannon` above, but pursued as a foundational
+storage-layer change rather than an index-level workaround. Full design
+history, rationale, and rejected alternatives (external Elias-Fano crates,
+`cacheline-ef`, a single unsplit `dict_id` array) are in the dedicated
+implementation plan (`vivid-mapping-tiger.md` at the time of writing — the
+content below is the durable summary, not a pointer to a session-scoped
+file). Also directly informed by Alanko, Bille, Gørtz, Navarro, Puglisi,
+"Compact Data Structures for Collections of Sets" (2025,
+`biblio/Alanko et al. - Compact Data Structures for Collections of
+Sets.pdf`) — this design implements only their exact-duplicate special
+case (a plain dedup dictionary), not their full subset-containment
+hierarchy.
+
+**Design**: four on-disk components, each mmap-backed, built once per
+layer (matching how the rest of the build pipeline already works — never
+the whole multi-billion-row index at once): an `is_multi` rank-capable
+flag per row (singleton vs. multi-genome), a fixed-bit-width array for
+singleton rows (genome index directly, `ceil(log2(n_cols))` bits), a
+separate fixed-bit-width array for multi-genome rows (`dict_id`,
+`ceil(log2(n_distinct_multi_sets))` bits — kept apart from the singleton
+array specifically because `n_distinct_multi_sets` can be large in
+absolute terms even when multi-genome rows are a small *fraction* of all
+rows, and a single shared array would force every row, singletons
+included, to pay the wider width), and a deduplicated dictionary of
+distinct multi-genome sets (Elias-Fano-encoded byte offsets + a
+varint-encoded values blob). New low-level primitives added to
+`obicompactvec` to build this: `PersistentFixedIntVec` (arbitrary,
+runtime-parameterized bit width, width 0 included — needed once a real
+bug surfaced, see below), `PersistentRankSelectBitVec` (rank1/rank0/select1
+on top of the crate's existing `count_ones`, using
+`common_traits::SelectInWord`), `EliasFano` (composes the two). A new
+`BinaryMatrix` trait (`n`, `n_cols`, `row`/`fill_row`, `fill_sub_matrix`,
+`count_ones`) unifies dense and sparse at the one call site that needs
+both interchangeably (`obikphylo::siblings::cache::Mat`) — column-oriented
+methods (`col`, `col_view`, the `partial_*_dist_matrix` family) stay
+dense-only.
+
+**Two real bugs caught by tests, not by inspection**: (1) `EliasFano::open`
+re-derived its low-bits width from the persisted low-vector file's own
+width byte; the zero-width case was built with a dummy 1-bit placeholder
+(the builder rejected true width 0), so every reopened value silently
+doubled. Fixed by making `PersistentFixedIntVec` genuinely support width 0
+(no storage, `get` always 0) instead of working around the limitation in
+`EliasFano`. (2) An empty row (cardinality 0 — not expected on a real
+built index, but not guarded against either) was recorded as a singleton
+at genome 0, indistinguishable on read-back from a *real* singleton at
+genome 0. Fixed by routing cardinality-0 rows through the dictionary path
+(a genuine empty entry) instead of the singleton shortcut. Both caught by
+`obicompactvec`'s test suite (142 tests, including disk-reopen round-trips
+that drop every builder/mmap before reopening fresh), not by manual
+review — worth remembering next time a "this edge case can't happen in
+practice" shortcut is tempting.
+
+**Measured on real data** (`layer_1` of `phyloskims_sal_vac`'s
+`part_00018`, 30,246,774 rows, 91 genomes — `#[ignore]`d benchmarks in
+`obikphylo/src/siblings/tests.rs`):
+
+| | dense | sparse | ratio |
+|---|---|---|---|
+| on-disk size | 328.1MB | 43.7MB | **7.5x** smaller |
+| build time / peak RSS | — | 4.26s / 628MB | (per-layer, in-memory construction — comfortable) |
+| row access, sequential (2M reads) | 43ns/row | 32ns/row | sparse **faster** (smaller structure, better cache fit) |
+| row access, random (2M reads) | 409ns/row | 85ns/row | sparse **~4.8x faster** (the real `--shannon`/family-lookup shape) |
+| column access, one full column (30.2M rows) | 11.5ms | 993ms | sparse **86x slower** (no native column method — every read decodes a full row to keep one bit) |
+
+The row-access wins (both directions) weren't the design's stated goal —
+compactness was — but turn out real: dense's genome-major layout scatters
+a single row read across a much bigger file, which costs more than
+sparse's rank/select/varint decode once the file is this much smaller.
+The column-access cost is the flip side of the same layout choice, and is
+exactly what the next item below exists to fix.
+
+**Next, not yet planned**: rewrite `partial_jaccard_dist_matrix`/
+`partial_hamming_dist_matrix`/etc. (`obicompactvec/src/bitmatrix/pairwise.rs`)
+as a row-major co-occurrence accumulation (`O(Σ_rows k²)`, per-row
+increments into an `NxN` genome-pair counter — the known alternative to
+today's column-fold, plausibly cheaper on data this sparse, not just a
+fallback) so `obikindex`'s `--metric`/distance-matrix path can use the
+sparse type without the measured 86x column-access penalty. Needs its own
+design pass (in particular how it plugs into the `BitPartials`/
+`ColumnWeights` traits so both matrix types keep serving `--metric`)
+before implementation — not just "port the loop", a genuinely different
+algorithm.
+
+Also still deferred, unchanged from the implementation plan: full Alanko
+et al. subset-hierarchy compression (only the exact-duplicate special case
+is built), a sparse `PersistentCompactIntMatrix` (count matrices), and
+BRWT-style column-correlation exploitation.
diff --git a/src/Cargo.lock b/src/Cargo.lock
index 113db77b..1c8798ad 100644
--- a/src/Cargo.lock
+++ b/src/Cargo.lock
@@ -1721,6 +1721,7 @@ checksum = "830b246a0e5f20af87141b25c173cd1b609bd7779a4617d6ec582abaf90870f3"
 name = "obicompactvec"
 version = "0.1.0"
 dependencies = [
+ "common_traits",
  "memmap2",
  "ndarray",
  "rayon",
diff --git a/src/obicompactvec/Cargo.toml b/src/obicompactvec/Cargo.toml
index 777b6067..7e5f1bd7 100644
--- a/src/obicompactvec/Cargo.toml
+++ b/src/obicompactvec/Cargo.toml
@@ -4,6 +4,7 @@ version = "0.1.0"
 edition = "2024"
 
 [dependencies]
+common_traits = "0.11"
 memmap2  = "0.9"
 ndarray  = "0.16"
 rayon    = "1"
diff --git a/src/obicompactvec/src/bitmatrix/mod.rs b/src/obicompactvec/src/bitmatrix/mod.rs
index 85dcef0a..0523da87 100644
--- a/src/obicompactvec/src/bitmatrix/mod.rs
+++ b/src/obicompactvec/src/bitmatrix/mod.rs
@@ -17,10 +17,12 @@ mod group_ops;
 mod packed;
 mod pairwise;
 mod persistent;
+mod sparse;
 
 pub use builder::PersistentBitMatrixBuilder;
 pub use packed::pack_bit_matrix;
 pub use persistent::PersistentBitMatrix;
+pub use sparse::{PersistentSparseBitMatrix, PersistentSparseBitMatrixBuilder};
 
 pub(crate) use pairwise::{pairwise_matrix, pairwise2_matrix};
 
diff --git a/src/obicompactvec/src/bitmatrix/persistent.rs b/src/obicompactvec/src/bitmatrix/persistent.rs
index 7b5dad47..7a8e8293 100644
--- a/src/obicompactvec/src/bitmatrix/persistent.rs
+++ b/src/obicompactvec/src/bitmatrix/persistent.rs
@@ -241,3 +241,18 @@ impl BitPartials for PersistentBitMatrix {
         self.partial_hamming_dist_matrix()
     }
 }
+
+impl crate::traits::BinaryMatrix for PersistentBitMatrix {
+    #[inline]
+    fn n(&self) -> usize { self.n() }
+    #[inline]
+    fn n_cols(&self) -> usize { self.n_cols() }
+    #[inline]
+    fn row(&self, slot: usize) -> Box<[bool]> { self.row(slot) }
+    #[inline]
+    fn fill_row(&self, slot: usize, buf: &mut [u32]) { self.fill_row(slot, buf) }
+    #[inline]
+    fn fill_sub_matrix(&self, slots: &[usize], out: &mut [Vec<bool>]) { self.fill_sub_matrix(slots, out) }
+    #[inline]
+    fn count_ones(&self) -> Array1<u64> { self.count_ones() }
+}
diff --git a/src/obicompactvec/src/bitmatrix/sparse.rs b/src/obicompactvec/src/bitmatrix/sparse.rs
new file mode 100644
index 00000000..09dea336
--- /dev/null
+++ b/src/obicompactvec/src/bitmatrix/sparse.rs
@@ -0,0 +1,372 @@
+//! `PersistentSparseBitMatrix` — row-major (k-mer-major), deduplicated
+//! sparse alternative to [`super::PersistentBitMatrix`]. See
+//! `docmd/architecture/siblings.md` and the sparse-matrix design plan for
+//! the full rationale (measured sparsity/duplication on real data). Not
+//! used by any production code path yet — a new type, not a replacement.
+//!
+//! On-disk layout (a directory, mirroring [`super::PersistentBitMatrix`]'s
+//! own directory-of-files convention): `meta.json` plus four components —
+//! `is_multi.prsb` (rank-capable flag: singleton row vs. multi-genome
+//! row), `singleton.pfiv` (genome index, one entry per singleton row,
+//! `ceil(log2(n_cols))` bits each), `multi.pfiv` (`dict_id`, one entry per
+//! multi-genome row, `ceil(log2(n_distinct_multi))` bits each),
+//! `dict_offsets` (Elias-Fano — `.efl`/`.efh` — one entry per *distinct*
+//! multi-genome set, byte offset into `dict_values.bin`), `dict_values.bin`
+//! (varint-encoded sorted genome-index list per distinct set).
+//!
+//! A row's genome set is read by: check `is_multi[slot]`; if singleton,
+//! `singleton[rank0(is_multi, slot)]` is the genome index directly; if
+//! multi, `multi[rank1(is_multi, slot)]` is a `dict_id`, and
+//! `dict_values[dict_offsets[dict_id]..dict_offsets[dict_id+1]]` is its
+//! varint-encoded genome list.
+
+use std::collections::HashMap;
+use std::fs;
+use std::io;
+use std::path::{Path, PathBuf};
+
+use ndarray::Array1;
+
+use crate::eliasfano::{EliasFano, EliasFanoBuilder};
+use crate::fixedintvec::{PersistentFixedIntVec, PersistentFixedIntVecBuilder, bit_width_for_range};
+use crate::meta::field;
+use crate::rankselect::{PersistentRankSelectBitVec, PersistentRankSelectBitVecBuilder};
+
+use super::PersistentBitMatrix;
+
+fn is_multi_path(dir: &Path) -> PathBuf { dir.join("is_multi.prsb") }
+fn singleton_path(dir: &Path) -> PathBuf { dir.join("singleton.pfiv") }
+fn multi_path(dir: &Path) -> PathBuf { dir.join("multi.pfiv") }
+fn dict_offsets_base(dir: &Path) -> PathBuf { dir.join("dict_offsets") }
+fn dict_values_path(dir: &Path) -> PathBuf { dir.join("dict_values.bin") }
+fn meta_path(dir: &Path) -> PathBuf { dir.join("meta.json") }
+
+struct SparseMeta {
+    n: usize,
+    n_cols: usize,
+    n_singleton: usize,
+    n_multi: usize,
+    n_distinct_multi: usize,
+}
+
+impl SparseMeta {
+    fn load(dir: &Path) -> io::Result<Self> {
+        let s = fs::read_to_string(meta_path(dir))?;
+        let get = |name: &str| {
+            field(&s, name).ok_or_else(|| io::Error::new(io::ErrorKind::InvalidData, format!("bad meta.json: missing {name}")))
+        };
+        Ok(Self {
+            n: get("n")?,
+            n_cols: get("n_cols")?,
+            n_singleton: get("n_singleton")?,
+            n_multi: get("n_multi")?,
+            n_distinct_multi: get("n_distinct_multi")?,
+        })
+    }
+
+    fn save(&self, dir: &Path) -> io::Result<()> {
+        fs::write(
+            meta_path(dir),
+            format!(
+                "{{\"n\":{},\"n_cols\":{},\"n_singleton\":{},\"n_multi\":{},\"n_distinct_multi\":{}}}\n",
+                self.n, self.n_cols, self.n_singleton, self.n_multi, self.n_distinct_multi,
+            ),
+        )
+    }
+}
+
+// ── varint (LEB128-style) ────────────────────────────────────────────────────
+
+fn write_varint(buf: &mut Vec<u8>, mut v: u32) {
+    loop {
+        let byte = (v & 0x7F) as u8;
+        v >>= 7;
+        if v == 0 {
+            buf.push(byte);
+            break;
+        }
+        buf.push(byte | 0x80);
+    }
+}
+
+fn read_varint(data: &[u8], pos: &mut usize) -> u32 {
+    let mut result = 0u32;
+    let mut shift = 0u32;
+    loop {
+        let byte = data[*pos];
+        *pos += 1;
+        result |= ((byte & 0x7F) as u32) << shift;
+        if byte & 0x80 == 0 {
+            break;
+        }
+        shift += 7;
+    }
+    result
+}
+
+// ── PersistentSparseBitMatrix ───────────────────────────────────────────────
+
+pub struct PersistentSparseBitMatrix {
+    is_multi: PersistentRankSelectBitVec,
+    singleton: PersistentFixedIntVec,
+    multi: PersistentFixedIntVec,
+    dict_offsets: EliasFano,
+    dict_values: Vec<u8>,
+    n: usize,
+    n_cols: usize,
+    n_distinct_multi: usize,
+}
+
+impl PersistentSparseBitMatrix {
+    pub fn open(dir: &Path) -> io::Result<Self> {
+        let meta = SparseMeta::load(dir)?;
+        let is_multi = PersistentRankSelectBitVec::open(&is_multi_path(dir))?;
+        let singleton = PersistentFixedIntVec::open(&singleton_path(dir))?;
+        let multi = PersistentFixedIntVec::open(&multi_path(dir))?;
+        let dict_offsets = EliasFano::open(&dict_offsets_base(dir))?;
+        let dict_values = fs::read(dict_values_path(dir))?;
+        Ok(Self {
+            is_multi, singleton, multi, dict_offsets, dict_values,
+            n: meta.n, n_cols: meta.n_cols, n_distinct_multi: meta.n_distinct_multi,
+        })
+    }
+
+    #[inline]
+    pub fn n(&self) -> usize { self.n }
+    #[inline]
+    pub fn n_cols(&self) -> usize { self.n_cols }
+
+    /// Byte range of `dict_id`'s varint-encoded genome list within
+    /// `dict_values`.
+    #[inline]
+    fn dict_entry_range(&self, dict_id: usize) -> (usize, usize) {
+        let start = self.dict_offsets.get(dict_id) as usize;
+        let end = if dict_id + 1 < self.n_distinct_multi {
+            self.dict_offsets.get(dict_id + 1) as usize
+        } else {
+            self.dict_values.len()
+        };
+        (start, end)
+    }
+
+    pub fn row(&self, slot: usize) -> Box<[bool]> {
+        let mut out = vec![false; self.n_cols];
+        self.fill_row_bool(slot, &mut out);
+        out.into_boxed_slice()
+    }
+
+    /// Fill `buf[i]` with `1` iff genome `i` is present at `slot`, else `0`
+    /// — mirrors [`super::PersistentBitMatrix::fill_row`]'s signature.
+    pub fn fill_row(&self, slot: usize, buf: &mut [u32]) {
+        buf[..self.n_cols].fill(0);
+        if self.is_multi.get(slot) {
+            let pos = self.is_multi.rank1(slot) as usize;
+            let dict_id = self.multi.get(pos) as usize;
+            let (start, end) = self.dict_entry_range(dict_id);
+            let mut p = start;
+            while p < end {
+                buf[read_varint(&self.dict_values, &mut p) as usize] = 1;
+            }
+        } else {
+            let pos = self.is_multi.rank0(slot) as usize;
+            buf[self.singleton.get(pos) as usize] = 1;
+        }
+    }
+
+    fn fill_row_bool(&self, slot: usize, buf: &mut [bool]) {
+        buf.fill(false);
+        if self.is_multi.get(slot) {
+            let pos = self.is_multi.rank1(slot) as usize;
+            let dict_id = self.multi.get(pos) as usize;
+            let (start, end) = self.dict_entry_range(dict_id);
+            let mut p = start;
+            while p < end {
+                buf[read_varint(&self.dict_values, &mut p) as usize] = true;
+            }
+        } else {
+            let pos = self.is_multi.rank0(slot) as usize;
+            buf[self.singleton.get(pos) as usize] = true;
+        }
+    }
+
+    /// Column-oriented per-genome k-mer totals — a naive row-by-row scan,
+    /// not the O(1)-per-column reduction the dense matrix's `count_ones`
+    /// is. Deliberately not optimised: see `docmd/architecture/siblings.md`
+    /// and the sparse-matrix plan's "Explicitly deferred" — column-side
+    /// access stays correct but slow on this type for now.
+    pub fn count_ones(&self) -> Array1<u64> {
+        let mut counts = vec![0u64; self.n_cols];
+        let mut buf = vec![false; self.n_cols];
+        for slot in 0..self.n {
+            self.fill_row_bool(slot, &mut buf);
+            for (c, &present) in buf.iter().enumerate() {
+                if present {
+                    counts[c] += 1;
+                }
+            }
+        }
+        Array1::from(counts)
+    }
+
+    /// Like [`super::PersistentBitMatrix::fill_sub_matrix`]: `out` has one
+    /// entry per genome column, each filled with that column's values at
+    /// `slots`, in `slots` order. Naive (row-major decode, scattered into
+    /// column buffers) — see [`count_ones`](Self::count_ones)'s doc comment.
+    pub fn fill_sub_matrix(&self, slots: &[usize], out: &mut [Vec<bool>]) {
+        assert_eq!(out.len(), self.n_cols);
+        for col in out.iter_mut() {
+            col.clear();
+            col.resize(slots.len(), false);
+        }
+        let mut buf = vec![false; self.n_cols];
+        for (i, &slot) in slots.iter().enumerate() {
+            self.fill_row_bool(slot, &mut buf);
+            for (c, &present) in buf.iter().enumerate() {
+                out[c][i] = present;
+            }
+        }
+    }
+}
+
+impl crate::traits::BinaryMatrix for PersistentSparseBitMatrix {
+    #[inline]
+    fn n(&self) -> usize { self.n() }
+    #[inline]
+    fn n_cols(&self) -> usize { self.n_cols() }
+    #[inline]
+    fn row(&self, slot: usize) -> Box<[bool]> { self.row(slot) }
+    #[inline]
+    fn fill_row(&self, slot: usize, buf: &mut [u32]) { self.fill_row(slot, buf) }
+    #[inline]
+    fn fill_sub_matrix(&self, slots: &[usize], out: &mut [Vec<bool>]) { self.fill_sub_matrix(slots, out) }
+    #[inline]
+    fn count_ones(&self) -> Array1<u64> { self.count_ones() }
+}
+
+// ── PersistentSparseBitMatrixBuilder ────────────────────────────────────────
+
+pub struct PersistentSparseBitMatrixBuilder {
+    dir: PathBuf,
+    n_cols: usize,
+    is_multi: Vec<bool>,
+    singleton_values: Vec<u32>,
+    multi_dict_ids: Vec<u32>,
+    dedup: HashMap<Vec<u32>, u32>,
+    dict_sets_in_order: Vec<Vec<u32>>,
+}
+
+impl PersistentSparseBitMatrixBuilder {
+    pub fn new(n: usize, n_cols: usize, dir: &Path) -> io::Result<Self> {
+        fs::create_dir_all(dir)?;
+        Ok(Self {
+            dir: dir.to_path_buf(),
+            n_cols,
+            is_multi: Vec::with_capacity(n),
+            singleton_values: Vec::new(),
+            multi_dict_ids: Vec::new(),
+            dedup: HashMap::new(),
+            dict_sets_in_order: Vec::new(),
+        })
+    }
+
+    /// Appends one row's genome set — `genomes` sorted ascending, each
+    /// `< n_cols`. Rows must be pushed in slot order (0, 1, 2, ...), one
+    /// call per k-mer slot of the layer being converted/built.
+    ///
+    /// Cardinality 0 (no genome present — not expected on a real built
+    /// index, every slot has at least one, but handled correctly rather
+    /// than assumed away) routes through the dictionary path as a genuine
+    /// empty entry, *not* the singleton shortcut: a placeholder singleton
+    /// value would be indistinguishable from a real singleton at that same
+    /// genome index on read-back.
+    pub fn push_row(&mut self, genomes: &[u32]) {
+        match genomes.len() {
+            1 => {
+                self.is_multi.push(false);
+                self.singleton_values.push(genomes[0]);
+            }
+            _ => {
+                self.is_multi.push(true);
+                let id = if let Some(&id) = self.dedup.get(genomes) {
+                    id
+                } else {
+                    let id = self.dict_sets_in_order.len() as u32;
+                    self.dict_sets_in_order.push(genomes.to_vec());
+                    self.dedup.insert(genomes.to_vec(), id);
+                    id
+                };
+                self.multi_dict_ids.push(id);
+            }
+        }
+    }
+
+    pub fn close(self) -> io::Result<()> {
+        let n = self.is_multi.len();
+        let n_singleton = self.singleton_values.len();
+        let n_multi = self.multi_dict_ids.len();
+        let n_distinct_multi = self.dict_sets_in_order.len();
+
+        let mut is_multi_b = PersistentRankSelectBitVecBuilder::new(n, &is_multi_path(&self.dir))?;
+        for (i, &v) in self.is_multi.iter().enumerate() {
+            is_multi_b.set(i, v);
+        }
+        is_multi_b.close()?;
+
+        let singleton_width = bit_width_for_range(self.n_cols as u64);
+        let mut singleton_b = PersistentFixedIntVecBuilder::new(n_singleton, singleton_width, &singleton_path(&self.dir))?;
+        for (i, &v) in self.singleton_values.iter().enumerate() {
+            singleton_b.set(i, v as u64);
+        }
+        singleton_b.close()?;
+
+        let multi_width = bit_width_for_range(n_distinct_multi as u64);
+        let mut multi_b = PersistentFixedIntVecBuilder::new(n_multi, multi_width, &multi_path(&self.dir))?;
+        for (i, &v) in self.multi_dict_ids.iter().enumerate() {
+            multi_b.set(i, v as u64);
+        }
+        multi_b.close()?;
+
+        let mut dict_values = Vec::new();
+        let mut offsets: Vec<u64> = Vec::with_capacity(n_distinct_multi);
+        for set in &self.dict_sets_in_order {
+            offsets.push(dict_values.len() as u64);
+            for &g in set {
+                write_varint(&mut dict_values, g);
+            }
+        }
+        let universe = dict_values.len() as u64 + 1;
+        let mut offsets_b = EliasFanoBuilder::new(offsets.len(), universe, &dict_offsets_base(&self.dir))?;
+        for &o in &offsets {
+            offsets_b.push(o);
+        }
+        offsets_b.close()?;
+        fs::write(dict_values_path(&self.dir), &dict_values)?;
+
+        SparseMeta { n, n_cols: self.n_cols, n_singleton, n_multi, n_distinct_multi }.save(&self.dir)?;
+        Ok(())
+    }
+
+    pub fn finish(self) -> io::Result<PersistentSparseBitMatrix> {
+        let dir = self.dir.clone();
+        self.close()?;
+        PersistentSparseBitMatrix::open(&dir)
+    }
+
+    /// Builds a sparse matrix from an already-built dense
+    /// [`PersistentBitMatrix`] — row-by-row transpose via
+    /// [`PersistentBitMatrix::fill_row`], for migrating an existing index.
+    pub fn build_from_dense(dense: &PersistentBitMatrix, dir: &Path) -> io::Result<Self> {
+        let n = dense.n();
+        let n_cols = dense.n_cols();
+        let mut builder = Self::new(n, n_cols, dir)?;
+        let mut buf = vec![0u32; n_cols];
+        let mut genomes: Vec<u32> = Vec::new();
+        for slot in 0..n {
+            dense.fill_row(slot, &mut buf);
+            genomes.clear();
+            genomes.extend((0..n_cols).filter(|&c| buf[c] != 0).map(|c| c as u32));
+            builder.push_row(&genomes);
+        }
+        Ok(builder)
+    }
+}
diff --git a/src/obicompactvec/src/eliasfano.rs b/src/obicompactvec/src/eliasfano.rs
new file mode 100644
index 00000000..b2f9a3bf
--- /dev/null
+++ b/src/obicompactvec/src/eliasfano.rs
@@ -0,0 +1,133 @@
+//! Elias-Fano encoding of a monotone (non-decreasing) `u64` sequence —
+//! used only for the sparse presence matrix's dictionary offsets (see
+//! `docmd/architecture/siblings.md` and the sparse-matrix plan): a
+//! monotone, unbounded-magnitude sequence, the one component in that
+//! design that genuinely needs this.
+//!
+//! Classic two-array construction: each value's low `l` bits are packed
+//! at fixed width ([`crate::fixedintvec::PersistentFixedIntVec`]), its
+//! high bits (`value >> l`) are unary-coded into a bitvector
+//! ([`crate::rankselect::PersistentRankSelectBitVec`]) — a 1 bit at
+//! position `(value >> l) + i` for the `i`-th value, which is itself
+//! monotone non-decreasing whenever the input is, so it can be built by a
+//! single forward pass with no lookahead. Decoding value `i`:
+//! `((select1(i) - i) << l) | low[i]`.
+//!
+//! `l` is chosen as `floor(log2(universe / n))` (0 if `n >= universe`),
+//! the standard choice that keeps the high bitvector's length — `n +
+//! (universe >> l) + 1` — within a small constant factor of `n`.
+
+use std::io;
+use std::path::{Path, PathBuf};
+
+use crate::fixedintvec::{PersistentFixedIntVec, PersistentFixedIntVecBuilder};
+use crate::rankselect::{PersistentRankSelectBitVec, PersistentRankSelectBitVecBuilder};
+
+fn low_bits_width(n: usize, universe: u64) -> u32 {
+    if n == 0 || universe <= n as u64 {
+        0
+    } else {
+        // floor(log2(universe / n))
+        (universe / n as u64).max(1).ilog2()
+    }
+}
+
+fn low_path(base: &Path) -> PathBuf {
+    let mut p = base.as_os_str().to_owned();
+    p.push(".efl");
+    PathBuf::from(p)
+}
+
+fn high_path(base: &Path) -> PathBuf {
+    let mut p = base.as_os_str().to_owned();
+    p.push(".efh");
+    PathBuf::from(p)
+}
+
+// ── EliasFano ────────────────────────────────────────────────────────────────
+
+pub struct EliasFano {
+    low: PersistentFixedIntVec,
+    high: PersistentRankSelectBitVec,
+    n: usize,
+    low_width: u32,
+}
+
+impl EliasFano {
+    /// Opens a structure previously built at `base` (i.e. `{base}.efl` and
+    /// `{base}.efh`).
+    pub fn open(base: &Path) -> io::Result<Self> {
+        let low = PersistentFixedIntVec::open(&low_path(base))?;
+        let high = PersistentRankSelectBitVec::open(&high_path(base))?;
+        let n = low.len();
+        let low_width = low.width();
+        Ok(Self { low, high, n, low_width })
+    }
+
+    #[inline]
+    pub fn len(&self) -> usize { self.n }
+    #[inline]
+    pub fn is_empty(&self) -> bool { self.n == 0 }
+
+    /// The `i`-th value of the encoded sequence.
+    pub fn get(&self, i: usize) -> u64 {
+        debug_assert!(i < self.n);
+        let pos = self.high.select1(i as u64);
+        let high_part = pos as u64 - i as u64;
+        (high_part << self.low_width) | self.low.get(i)
+    }
+}
+
+// ── EliasFanoBuilder ─────────────────────────────────────────────────────────
+
+pub struct EliasFanoBuilder {
+    low: PersistentFixedIntVecBuilder,
+    high: PersistentRankSelectBitVecBuilder,
+    low_width: u32,
+    n: usize,
+    next: usize,
+    last_value: u64,
+}
+
+impl EliasFanoBuilder {
+    /// `n` values will be [`push`](Self::push)ed, in non-decreasing order,
+    /// each `< universe`. Writes `{base}.efl` and `{base}.efh`.
+    pub fn new(n: usize, universe: u64, base: &Path) -> io::Result<Self> {
+        let low_width = low_bits_width(n, universe);
+        let high_len = n + (universe >> low_width) as usize + 1;
+        // `PersistentFixedIntVec` genuinely supports width 0 (every value
+        // 0, no storage) — the persisted width byte is then the source of
+        // truth on reopen, no separate bookkeeping of `low_width` needed.
+        let low = PersistentFixedIntVecBuilder::new(n, low_width, &low_path(base))?;
+        let high = PersistentRankSelectBitVecBuilder::new(high_len, &high_path(base))?;
+        Ok(Self { low, high, low_width, n, next: 0, last_value: 0 })
+    }
+
+    /// Appends the next value — must be `>= ` every previously pushed
+    /// value (monotone non-decreasing), and `< universe` as given to
+    /// [`new`](Self::new).
+    pub fn push(&mut self, value: u64) {
+        assert!(self.next < self.n, "push() called more than n={} times", self.n);
+        assert!(
+            self.next == 0 || value >= self.last_value,
+            "push({value}) breaks monotonicity: last value was {}", self.last_value
+        );
+        let low_mask = if self.low_width >= 64 { u64::MAX } else { (1u64 << self.low_width) - 1 };
+        self.low.set(self.next, value & low_mask);
+        let high_part = value >> self.low_width;
+        self.high.set(high_part as usize + self.next, true);
+        self.last_value = value;
+        self.next += 1;
+    }
+
+    pub fn close(self) -> io::Result<()> {
+        assert_eq!(self.next, self.n, "push() called {} times, expected n={}", self.next, self.n);
+        self.low.close()?;
+        self.high.close()
+    }
+
+    pub fn finish(self, base: &Path) -> io::Result<EliasFano> {
+        self.close()?;
+        EliasFano::open(base)
+    }
+}
diff --git a/src/obicompactvec/src/fixedintvec.rs b/src/obicompactvec/src/fixedintvec.rs
new file mode 100644
index 00000000..e92fb694
--- /dev/null
+++ b/src/obicompactvec/src/fixedintvec.rs
@@ -0,0 +1,202 @@
+//! Fixed-bit-width packed integer vector — `n` values, each exactly `width`
+//! bits (1..=64, chosen once at construction from the actual data being
+//! stored), no overflow scheme. Mirrors [`crate::bitvec::PersistentBitVec`]'s
+//! mmap-backed reader/builder split, generalised from 1 bit/value to an
+//! arbitrary width.
+//!
+//! Deliberately distinct from [`crate::reader::PersistentCompactIntVec`]
+//! (`PCIV`): that format is "1 primary byte + overflow map for values ≥
+//! 255", tuned for mostly-small-value distributions. This format is for
+//! values roughly uniform over a known range (e.g. genome indices, or
+//! `dict_id`s) — every value costs the same, `width` bits, by construction.
+
+use std::fs::{File, OpenOptions};
+use std::io::{self, Seek, SeekFrom, Write as _};
+use std::path::{Path, PathBuf};
+
+use memmap2::{Mmap, MmapMut};
+
+const MAGIC: [u8; 4] = *b"PFIV";
+
+// Header: magic(4) + width(1) + _pad(3) + n(8) = 16 bytes.
+// Data starts at offset 16, u64-aligned (mmap base is page-aligned, 16 % 8 == 0).
+const HEADER_SIZE: usize = 16;
+
+/// Smallest bit width that can hold every value in `0..range` (`range`
+/// itself excluded, i.e. the number of distinct values needed) — the
+/// standard `ceil(log2(range))` sizing used throughout the sparse matrix
+/// design, with the same `.max(1)` floor (a single-value range still needs
+/// 1 bit, not 0, since `0..1` is a real distinct value).
+pub fn bit_width_for_range(range: u64) -> u32 {
+    if range <= 1 {
+        1
+    } else {
+        (u64::BITS - (range - 1).leading_zeros()).max(1)
+    }
+}
+
+#[inline]
+fn n_words_for(n: usize, width: u32) -> usize {
+    // +1 guard word: a value straddling the last word boundary reads/writes
+    // one bit into a word past the nominal bit count otherwise.
+    (n as u64 * width as u64).div_ceil(64) as usize + 1
+}
+
+#[inline]
+fn mask(width: u32) -> u64 {
+    if width >= 64 { u64::MAX } else { (1u64 << width) - 1 }
+}
+
+// ── PersistentFixedIntVec ───────────────────────────────────────────────────
+
+pub struct PersistentFixedIntVec {
+    mmap: Mmap,
+    n: usize,
+    width: u32,
+    path: PathBuf,
+}
+
+impl PersistentFixedIntVec {
+    pub fn open(path: &Path) -> io::Result<Self> {
+        let mmap = unsafe { Mmap::map(&File::open(path)?)? };
+        if mmap.len() < HEADER_SIZE {
+            return Err(io::Error::new(io::ErrorKind::InvalidData, "PFIV file too short"));
+        }
+        if mmap[0..4] != MAGIC {
+            return Err(io::Error::new(io::ErrorKind::InvalidData, "bad PFIV magic"));
+        }
+        let width = mmap[4] as u32;
+        let n = u64::from_le_bytes(mmap[8..16].try_into().unwrap()) as usize;
+        Ok(Self { mmap, n, width, path: path.to_path_buf() })
+    }
+
+    #[inline]
+    pub fn path(&self) -> &Path { &self.path }
+    #[inline]
+    pub fn len(&self) -> usize { self.n }
+    #[inline]
+    pub fn is_empty(&self) -> bool { self.n == 0 }
+    #[inline]
+    pub fn width(&self) -> u32 { self.width }
+
+    // SAFETY: mmap is page-aligned, HEADER_SIZE=16 divisible by 8 → u64-aligned.
+    #[inline]
+    fn data_words(&self) -> &[u64] {
+        let nw = n_words_for(self.n, self.width);
+        let ptr = self.mmap[HEADER_SIZE..].as_ptr() as *const u64;
+        unsafe { std::slice::from_raw_parts(ptr, nw) }
+    }
+
+    #[inline]
+    pub fn get(&self, slot: usize) -> u64 {
+        debug_assert!(slot < self.n);
+        get_packed(self.data_words(), slot, self.width)
+    }
+}
+
+#[inline]
+fn get_packed(words: &[u64], slot: usize, width: u32) -> u64 {
+    let bit_offset = slot as u64 * width as u64;
+    let word_idx = (bit_offset / 64) as usize;
+    let bit_in_word = (bit_offset % 64) as u32;
+    let m = mask(width);
+    let lo = words[word_idx] >> bit_in_word;
+    if bit_in_word + width <= 64 {
+        lo & m
+    } else {
+        let hi = words[word_idx + 1] << (64 - bit_in_word);
+        (lo | hi) & m
+    }
+}
+
+#[inline]
+fn set_packed(words: &mut [u64], slot: usize, width: u32, value: u64) {
+    let m = mask(width);
+    debug_assert!(value & !m == 0, "value {value} does not fit in {width} bits");
+    let bit_offset = slot as u64 * width as u64;
+    let word_idx = (bit_offset / 64) as usize;
+    let bit_in_word = (bit_offset % 64) as u32;
+    words[word_idx] &= !(m << bit_in_word);
+    words[word_idx] |= (value & m) << bit_in_word;
+    if bit_in_word + width > 64 {
+        let hi_bits = bit_in_word + width - 64;
+        let hi_mask = (1u64 << hi_bits) - 1;
+        words[word_idx + 1] &= !hi_mask;
+        words[word_idx + 1] |= value >> (64 - bit_in_word);
+    }
+}
+
+// ── PersistentFixedIntVecBuilder ────────────────────────────────────────────
+
+pub struct PersistentFixedIntVecBuilder {
+    mmap: MmapMut,
+    n: usize,
+    width: u32,
+    path: PathBuf,
+}
+
+impl PersistentFixedIntVecBuilder {
+    /// `width` (1..=64) is chosen by the caller from the actual data being
+    /// stored — see [`bit_width_for_range`] — never hardcoded. `width == 0`
+    /// is allowed (every value is 0, e.g. a whole `EliasFano` sequence
+    /// packed entirely into its high bits) — `get` always returns 0,
+    /// `set` is a no-op, no storage beyond the header.
+    pub fn new(n: usize, width: u32, path: &Path) -> io::Result<Self> {
+        assert!(width <= 64, "width must be 0..=64, got {width}");
+        let file_size = HEADER_SIZE + n_words_for(n, width) * 8;
+        let mut file = OpenOptions::new()
+            .read(true).write(true).create(true).truncate(true)
+            .open(path)?;
+        file.write_all(&MAGIC)?;
+        file.write_all(&[width as u8, 0, 0, 0])?;
+        file.write_all(&(n as u64).to_le_bytes())?;
+        file.seek(SeekFrom::Start(0))?;
+        file.set_len(file_size as u64)?;
+        let mmap = unsafe { MmapMut::map_mut(&file)? };
+        Ok(Self { mmap, n, width, path: path.to_path_buf() })
+    }
+
+    #[inline]
+    pub fn len(&self) -> usize { self.n }
+    #[inline]
+    pub fn is_empty(&self) -> bool { self.n == 0 }
+    #[inline]
+    pub fn width(&self) -> u32 { self.width }
+
+    #[inline]
+    fn data_words_mut(&mut self) -> &mut [u64] {
+        let nw = n_words_for(self.n, self.width);
+        let ptr = self.mmap[HEADER_SIZE..].as_mut_ptr() as *mut u64;
+        unsafe { std::slice::from_raw_parts_mut(ptr, nw) }
+    }
+
+    #[inline]
+    fn data_words(&self) -> &[u64] {
+        let nw = n_words_for(self.n, self.width);
+        let ptr = self.mmap[HEADER_SIZE..].as_ptr() as *const u64;
+        unsafe { std::slice::from_raw_parts(ptr, nw) }
+    }
+
+    #[inline]
+    pub fn get(&self, slot: usize) -> u64 {
+        debug_assert!(slot < self.n);
+        get_packed(self.data_words(), slot, self.width)
+    }
+
+    #[inline]
+    pub fn set(&mut self, slot: usize, value: u64) {
+        debug_assert!(slot < self.n);
+        let width = self.width;
+        set_packed(self.data_words_mut(), slot, width, value);
+    }
+
+    pub fn close(self) -> io::Result<()> {
+        self.mmap.flush()
+    }
+
+    pub fn finish(self) -> io::Result<PersistentFixedIntVec> {
+        let path = self.path.clone();
+        self.close()?;
+        PersistentFixedIntVec::open(&path)
+    }
+}
diff --git a/src/obicompactvec/src/lib.rs b/src/obicompactvec/src/lib.rs
index 9041ab78..58450c47 100644
--- a/src/obicompactvec/src/lib.rs
+++ b/src/obicompactvec/src/lib.rs
@@ -2,7 +2,10 @@ mod bitvec;
 mod bitmatrix;
 mod builder;
 mod colgroup;
+mod eliasfano;
+mod fixedintvec;
 mod format;
+mod rankselect;
 mod intmatrix;
 mod layer_meta;
 mod meta;
@@ -13,7 +16,10 @@ mod views;
 pub mod traits;
 
 pub use bitvec::{BitIter, PersistentBitVec, PersistentBitVecBuilder};
-pub use bitmatrix::{PersistentBitMatrix, PersistentBitMatrixBuilder, pack_bit_matrix};
+pub use fixedintvec::{PersistentFixedIntVec, PersistentFixedIntVecBuilder, bit_width_for_range};
+pub use rankselect::{PersistentRankSelectBitVec, PersistentRankSelectBitVecBuilder};
+pub use eliasfano::{EliasFano, EliasFanoBuilder};
+pub use bitmatrix::{PersistentBitMatrix, PersistentBitMatrixBuilder, PersistentSparseBitMatrix, PersistentSparseBitMatrixBuilder, pack_bit_matrix};
 pub use builder::PersistentCompactIntVecBuilder;
 pub use colgroup::{ColGroup, FilterMask, MatrixGroupOps, eval_filter_mask};
 pub use intmatrix::{PersistentCompactIntMatrix, PersistentCompactIntMatrixBuilder, pack_compact_int_matrix};
@@ -21,7 +27,7 @@ pub use layer_meta::LayerMeta;
 pub use reader::{PersistentCompactIntVec, Iter as CompactIntVecIter};
 pub use tempbitvec::{TempBitVec, TempBitVecBuilder};
 pub use tempintvec::{TempCompactIntVec, TempCompactIntVecBuilder};
-pub use traits::{BitPartials, ColumnWeights, CountPartials};
+pub use traits::{BinaryMatrix, BitPartials, ColumnWeights, CountPartials};
 pub use views::{BitSliceView, BitSliceIter, IntSliceView, IntSliceViewIter};
 
 #[cfg(test)]
diff --git a/src/obicompactvec/src/rankselect.rs b/src/obicompactvec/src/rankselect.rs
new file mode 100644
index 00000000..c321386a
--- /dev/null
+++ b/src/obicompactvec/src/rankselect.rs
@@ -0,0 +1,265 @@
+//! Rank/select-capable bitvector — extends the crate's existing bit-count
+//! (`count_ones`, a global reduction) with `rank1`/`rank0` (count of 1s/0s
+//! in a prefix) and `select1` (position of the k-th 1 bit). Needed by two
+//! consumers in the sparse presence-matrix design (see
+//! `docmd/architecture/siblings.md` and the sparse-matrix plan): the
+//! `is_multi` row-kind flag (needs rank, to locate a row's position within
+//! whichever of the two split arrays it belongs to) and the Elias-Fano high
+//! bits (needs select).
+//!
+//! Two-level structure, the standard succinct-bitvector approach: a
+//! cumulative rank sampled every [`BLOCK_WORDS`] words, plus a linear scan
+//! within the block (at most [`BLOCK_WORDS`] popcounts) for the remainder.
+//! `select1` binary-searches the block samples, then
+//! `common_traits::SelectInWord` locates the exact bit within the winning
+//! word.
+
+use std::fs::{File, OpenOptions};
+use std::io::{self, Seek, SeekFrom, Write as _};
+use std::path::{Path, PathBuf};
+
+use common_traits::SelectInWord;
+use memmap2::{Mmap, MmapMut};
+
+const MAGIC: [u8; 4] = *b"PRSB";
+
+/// Words per rank-sample block — 8 words = 512 bits, one cache line's
+/// worth of linear-scan work for the within-block remainder.
+const BLOCK_WORDS: usize = 8;
+
+// Header: magic(4) + _pad(4) + n(8) + total_ones(8) = 24 bytes (8-aligned).
+const HEADER_SIZE: usize = 24;
+
+#[inline]
+fn n_words(n: usize) -> usize {
+    n.div_ceil(64)
+}
+
+#[inline]
+fn n_blocks(n: usize) -> usize {
+    n_words(n).div_ceil(BLOCK_WORDS)
+}
+
+#[inline]
+fn bits_bytes(n: usize) -> usize {
+    n_words(n) * 8
+}
+
+#[inline]
+fn blocks_bytes(n: usize) -> usize {
+    n_blocks(n) * 8
+}
+
+// ── PersistentRankSelectBitVec ──────────────────────────────────────────────
+
+pub struct PersistentRankSelectBitVec {
+    mmap: Mmap,
+    n: usize,
+    total_ones: u64,
+    path: PathBuf,
+}
+
+impl PersistentRankSelectBitVec {
+    pub fn open(path: &Path) -> io::Result<Self> {
+        let mmap = unsafe { Mmap::map(&File::open(path)?)? };
+        if mmap.len() < HEADER_SIZE {
+            return Err(io::Error::new(io::ErrorKind::InvalidData, "PRSB file too short"));
+        }
+        if mmap[0..4] != MAGIC {
+            return Err(io::Error::new(io::ErrorKind::InvalidData, "bad PRSB magic"));
+        }
+        let n = u64::from_le_bytes(mmap[8..16].try_into().unwrap()) as usize;
+        let total_ones = u64::from_le_bytes(mmap[16..24].try_into().unwrap());
+        Ok(Self { mmap, n, total_ones, path: path.to_path_buf() })
+    }
+
+    #[inline]
+    pub fn path(&self) -> &Path { &self.path }
+    #[inline]
+    pub fn len(&self) -> usize { self.n }
+    #[inline]
+    pub fn is_empty(&self) -> bool { self.n == 0 }
+    #[inline]
+    pub fn count_ones(&self) -> u64 { self.total_ones }
+    #[inline]
+    pub fn count_zeros(&self) -> u64 { self.n as u64 - self.total_ones }
+
+    // SAFETY: mmap is page-aligned, HEADER_SIZE=24 divisible by 8 → u64-aligned.
+    #[inline]
+    fn bit_words(&self) -> &[u64] {
+        let nw = n_words(self.n);
+        let ptr = self.mmap[HEADER_SIZE..].as_ptr() as *const u64;
+        unsafe { std::slice::from_raw_parts(ptr, nw) }
+    }
+
+    #[inline]
+    fn block_ranks(&self) -> &[u64] {
+        let nb = n_blocks(self.n);
+        let off = HEADER_SIZE + bits_bytes(self.n);
+        let ptr = self.mmap[off..].as_ptr() as *const u64;
+        unsafe { std::slice::from_raw_parts(ptr, nb) }
+    }
+
+    #[inline]
+    pub fn get(&self, pos: usize) -> bool {
+        debug_assert!(pos < self.n);
+        (self.bit_words()[pos >> 6] >> (pos & 63)) & 1 != 0
+    }
+
+    /// Number of 1 bits in `[0, pos)`.
+    pub fn rank1(&self, pos: usize) -> u64 {
+        debug_assert!(pos <= self.n);
+        if pos == 0 {
+            return 0;
+        }
+        let words = self.bit_words();
+        let block_ranks = self.block_ranks();
+        let word_idx = (pos - 1) / 64;
+        let block_idx = word_idx / BLOCK_WORDS;
+        let mut rank = block_ranks[block_idx];
+        let block_start_word = block_idx * BLOCK_WORDS;
+        for w in &words[block_start_word..word_idx] {
+            rank += w.count_ones() as u64;
+        }
+        let bit_in_word = pos - word_idx * 64;
+        let last = words[word_idx];
+        let masked = if bit_in_word >= 64 { last } else { last & ((1u64 << bit_in_word) - 1) };
+        rank += masked.count_ones() as u64;
+        rank
+    }
+
+    /// Number of 0 bits in `[0, pos)`.
+    #[inline]
+    pub fn rank0(&self, pos: usize) -> u64 {
+        pos as u64 - self.rank1(pos)
+    }
+
+    /// Position of the `k`-th (0-indexed) 1 bit. Panics if fewer than
+    /// `k + 1` ones exist.
+    pub fn select1(&self, k: u64) -> usize {
+        assert!(k < self.total_ones, "select1({k}) out of range: only {} ones", self.total_ones);
+        let block_ranks = self.block_ranks();
+        let words = self.bit_words();
+
+        // Binary search: last block whose cumulative rank is <= k.
+        let mut lo = 0usize;
+        let mut hi = block_ranks.len();
+        while lo + 1 < hi {
+            let mid = lo + (hi - lo) / 2;
+            if block_ranks[mid] <= k { lo = mid; } else { hi = mid; }
+        }
+        let block_idx = lo;
+        let mut remaining = k - block_ranks[block_idx];
+        let start_word = block_idx * BLOCK_WORDS;
+        let end_word = (start_word + BLOCK_WORDS).min(words.len());
+        for (i, &w) in words[start_word..end_word].iter().enumerate() {
+            let c = w.count_ones() as u64;
+            if remaining < c {
+                return (start_word + i) * 64 + w.select_in_word(remaining as usize);
+            }
+            remaining -= c;
+        }
+        unreachable!("select1({k}): ran off the end of its own block — rank/select index inconsistent");
+    }
+}
+
+// ── PersistentRankSelectBitVecBuilder ───────────────────────────────────────
+
+pub struct PersistentRankSelectBitVecBuilder {
+    mmap: MmapMut,
+    n: usize,
+    path: PathBuf,
+}
+
+impl PersistentRankSelectBitVecBuilder {
+    pub fn new(n: usize, path: &Path) -> io::Result<Self> {
+        let file_size = HEADER_SIZE + bits_bytes(n) + blocks_bytes(n);
+        let mut file = OpenOptions::new()
+            .read(true).write(true).create(true).truncate(true)
+            .open(path)?;
+        file.write_all(&MAGIC)?;
+        file.write_all(&[0u8; 4])?;
+        file.write_all(&(n as u64).to_le_bytes())?;
+        file.write_all(&0u64.to_le_bytes())?; // total_ones, patched in close()
+        file.seek(SeekFrom::Start(0))?;
+        file.set_len(file_size as u64)?;
+        let mmap = unsafe { MmapMut::map_mut(&file)? };
+        Ok(Self { mmap, n, path: path.to_path_buf() })
+    }
+
+    #[inline]
+    pub fn len(&self) -> usize { self.n }
+    #[inline]
+    pub fn is_empty(&self) -> bool { self.n == 0 }
+
+    #[inline]
+    fn bit_words_mut(&mut self) -> &mut [u64] {
+        let nw = n_words(self.n);
+        let ptr = self.mmap[HEADER_SIZE..].as_mut_ptr() as *mut u64;
+        unsafe { std::slice::from_raw_parts_mut(ptr, nw) }
+    }
+
+    #[inline]
+    pub fn get(&self, pos: usize) -> bool {
+        debug_assert!(pos < self.n);
+        let nw = n_words(self.n);
+        let ptr = self.mmap[HEADER_SIZE..].as_ptr() as *const u64;
+        let words = unsafe { std::slice::from_raw_parts(ptr, nw) };
+        (words[pos >> 6] >> (pos & 63)) & 1 != 0
+    }
+
+    #[inline]
+    pub fn set(&mut self, pos: usize, value: bool) {
+        debug_assert!(pos < self.n);
+        let bit = 1u64 << (pos & 63);
+        let words = self.bit_words_mut();
+        if value {
+            words[pos >> 6] |= bit;
+        } else {
+            words[pos >> 6] &= !bit;
+        }
+    }
+
+    /// Computes the block-rank index and total-ones count from the bits
+    /// written so far, then flushes. Must run after every `set()` call —
+    /// the index is a function of the final bit pattern, not maintainable
+    /// incrementally through arbitrary overwrites.
+    pub fn close(mut self) -> io::Result<()> {
+        let nb = n_blocks(self.n);
+        let nw = n_words(self.n);
+        let mut block_ranks = vec![0u64; nb];
+        let mut running = 0u64;
+        {
+            let words = self.bit_words_mut();
+            for (block_idx, block_rank) in block_ranks.iter_mut().enumerate() {
+                *block_rank = running;
+                let start = block_idx * BLOCK_WORDS;
+                let end = (start + BLOCK_WORDS).min(nw);
+                for &w in &words[start..end] {
+                    running += w.count_ones() as u64;
+                }
+            }
+        }
+        self.mmap[16..24].copy_from_slice(&running.to_le_bytes());
+        let block_off = HEADER_SIZE + bits_bytes(self.n);
+        let block_bytes = u64_slice_to_le_bytes(&block_ranks);
+        self.mmap[block_off..block_off + block_bytes.len()].copy_from_slice(&block_bytes);
+        self.mmap.flush()
+    }
+
+    pub fn finish(self) -> io::Result<PersistentRankSelectBitVec> {
+        let path = self.path.clone();
+        self.close()?;
+        PersistentRankSelectBitVec::open(&path)
+    }
+}
+
+/// Minimal, local `u64` slice -> byte vec conversion (little-endian,
+/// matching every other on-disk format in this crate).
+fn u64_slice_to_le_bytes(values: &[u64]) -> Vec<u8> {
+    let mut out = Vec::with_capacity(values.len() * 8);
+    for &v in values {
+        out.extend_from_slice(&v.to_le_bytes());
+    }
+    out
+}
diff --git a/src/obicompactvec/src/tests/eliasfano.rs b/src/obicompactvec/src/tests/eliasfano.rs
new file mode 100644
index 00000000..9254e1ab
--- /dev/null
+++ b/src/obicompactvec/src/tests/eliasfano.rs
@@ -0,0 +1,114 @@
+use tempfile::tempdir;
+
+use crate::{EliasFano, EliasFanoBuilder};
+
+fn build(values: &[u64], universe: u64) -> (tempfile::TempDir, EliasFano) {
+    let dir = tempdir().unwrap();
+    let base = dir.path().join("test.ef");
+    let mut b = EliasFanoBuilder::new(values.len(), universe, &base).unwrap();
+    for &v in values {
+        b.push(v);
+    }
+    let ef = b.finish(&base).unwrap();
+    (dir, ef)
+}
+
+#[test]
+fn empty() {
+    let (_dir, ef) = build(&[], 1000);
+    assert_eq!(ef.len(), 0);
+    assert!(ef.is_empty());
+}
+
+#[test]
+fn small_monotone_sequence() {
+    let values = [0u64, 3, 3, 7, 42, 42, 42, 100];
+    let (_dir, ef) = build(&values, 1000);
+    assert_eq!(ef.len(), values.len());
+    for (i, &expected) in values.iter().enumerate() {
+        assert_eq!(ef.get(i), expected, "index {i}");
+    }
+}
+
+#[test]
+fn all_equal_values() {
+    let values = [5u64; 20];
+    let (_dir, ef) = build(&values, 100);
+    for i in 0..values.len() {
+        assert_eq!(ef.get(i), 5);
+    }
+}
+
+#[test]
+fn strictly_increasing() {
+    let values: Vec<u64> = (0..500).map(|i| i * 3).collect();
+    let universe = values.last().unwrap() + 1;
+    let (_dir, ef) = build(&values, universe);
+    for (i, &expected) in values.iter().enumerate() {
+        assert_eq!(ef.get(i), expected, "index {i}");
+    }
+}
+
+#[test]
+fn realistic_byte_offsets() {
+    // Simulates the actual use case: cumulative byte offsets into a
+    // varint blob, one entry per distinct multi-genome set, strictly
+    // increasing by a small, variable amount each time (1-2 bytes/index,
+    // several indices per set).
+    let mut offset = 0u64;
+    let mut values = Vec::new();
+    let mut rng_state = 12345u64;
+    for _ in 0..10_000 {
+        values.push(offset);
+        // simple xorshift for a deterministic, dependency-free "random" gap
+        rng_state ^= rng_state << 13;
+        rng_state ^= rng_state >> 7;
+        rng_state ^= rng_state << 17;
+        offset += 1 + (rng_state % 8); // 1..=8 bytes per set, realistic for n_cols=91
+    }
+    let universe = offset + 1;
+    let (_dir, ef) = build(&values, universe);
+    for (i, &expected) in values.iter().enumerate() {
+        assert_eq!(ef.get(i), expected, "index {i}");
+    }
+}
+
+#[test]
+fn universe_smaller_than_n_gives_zero_width_low() {
+    // n=100 values drawn from a universe of only 10 — low_bits_width
+    // should come out 0 (falls back to pure unary/high-bits encoding).
+    let values: Vec<u64> = (0..100).map(|i| i / 10).collect(); // 0,0,..,0,1,1,..,9,9
+    let (_dir, ef) = build(&values, 10);
+    for (i, &expected) in values.iter().enumerate() {
+        assert_eq!(ef.get(i), expected, "index {i}");
+    }
+}
+
+#[test]
+#[should_panic(expected = "monotonicity")]
+fn push_out_of_order_panics() {
+    let dir = tempdir().unwrap();
+    let base = dir.path().join("test.ef");
+    let mut b = EliasFanoBuilder::new(3, 100, &base).unwrap();
+    b.push(10);
+    b.push(5); // decreasing — must panic
+}
+
+#[test]
+fn reopen_after_close_matches_original() {
+    let values: Vec<u64> = (0..2000).map(|i| i * 5 + (i % 3)).collect();
+    let universe = *values.last().unwrap() + 1;
+    let dir = tempdir().unwrap();
+    let base = dir.path().join("test.ef");
+    {
+        let mut b = EliasFanoBuilder::new(values.len(), universe, &base).unwrap();
+        for &v in &values {
+            b.push(v);
+        }
+        b.close().unwrap();
+    } // builder + mmaps fully dropped here
+    let ef = EliasFano::open(&base).unwrap();
+    for (i, &expected) in values.iter().enumerate() {
+        assert_eq!(ef.get(i), expected, "index {i}");
+    }
+}
diff --git a/src/obicompactvec/src/tests/fixedintvec.rs b/src/obicompactvec/src/tests/fixedintvec.rs
new file mode 100644
index 00000000..5c0eb1e6
--- /dev/null
+++ b/src/obicompactvec/src/tests/fixedintvec.rs
@@ -0,0 +1,112 @@
+use tempfile::tempdir;
+
+use crate::{PersistentFixedIntVec, PersistentFixedIntVecBuilder, bit_width_for_range};
+
+#[test]
+fn bit_width_for_range_matches_expectations() {
+    assert_eq!(bit_width_for_range(0), 1);
+    assert_eq!(bit_width_for_range(1), 1);
+    assert_eq!(bit_width_for_range(2), 1);
+    assert_eq!(bit_width_for_range(3), 2);
+    assert_eq!(bit_width_for_range(4), 2);
+    assert_eq!(bit_width_for_range(91), 7);
+    assert_eq!(bit_width_for_range(128), 7);
+    assert_eq!(bit_width_for_range(129), 8);
+    assert_eq!(bit_width_for_range(460_591), 19);
+}
+
+fn roundtrip(width: u32, values: &[u64]) -> Vec<u64> {
+    let dir = tempdir().unwrap();
+    let path = dir.path().join("test.pfiv");
+    let mut b = PersistentFixedIntVecBuilder::new(values.len(), width, &path).unwrap();
+    for (i, &v) in values.iter().enumerate() {
+        b.set(i, v);
+    }
+    b.close().unwrap();
+    let r = PersistentFixedIntVec::open(&path).unwrap();
+    assert_eq!(r.len(), values.len());
+    assert_eq!(r.width(), width);
+    (0..values.len()).map(|s| r.get(s)).collect()
+}
+
+#[test]
+fn width_1_roundtrip() {
+    let values = [0u64, 1, 1, 0, 1];
+    assert_eq!(roundtrip(1, &values), values);
+}
+
+#[test]
+fn width_7_roundtrip_genome_indices() {
+    // 91-genome-scale values, width=7 (matches bit_width_for_range(91)).
+    let values: Vec<u64> = (0..91).collect();
+    assert_eq!(roundtrip(7, &values), values);
+}
+
+#[test]
+fn width_19_roundtrip_dict_ids() {
+    // Values crossing many word boundaries at a non-power-of-two width —
+    // exactly the case that breaks a naive byte/word-aligned packer.
+    let values: Vec<u64> = (0..2000).map(|i| (i * 37) % 460_591).collect();
+    assert_eq!(roundtrip(19, &values), values);
+}
+
+#[test]
+fn width_64_roundtrip() {
+    let values = [0u64, u64::MAX, 1, u64::MAX - 1, 1 << 40];
+    assert_eq!(roundtrip(64, &values), values);
+}
+
+#[test]
+fn values_spanning_word_boundary() {
+    // width=19: slot 3's bits start at bit 57, spans into the next word.
+    let values: Vec<u64> = vec![524_287, 0, 0, 500_000, 1];
+    assert_eq!(roundtrip(19, &values), values);
+}
+
+#[test]
+fn mutation_via_set_overwrites() {
+    let dir = tempdir().unwrap();
+    let path = dir.path().join("test.pfiv");
+    let mut b = PersistentFixedIntVecBuilder::new(3, 10, &path).unwrap();
+    b.set(0, 5);
+    b.set(1, 1000);
+    b.set(2, 3);
+    b.set(1, 42); // overwrite
+    b.close().unwrap();
+    let r = PersistentFixedIntVec::open(&path).unwrap();
+    assert_eq!(r.get(0), 5);
+    assert_eq!(r.get(1), 42);
+    assert_eq!(r.get(2), 3);
+}
+
+#[test]
+fn all_zero_by_default() {
+    let dir = tempdir().unwrap();
+    let path = dir.path().join("test.pfiv");
+    let b = PersistentFixedIntVecBuilder::new(50, 13, &path).unwrap();
+    b.close().unwrap();
+    let r = PersistentFixedIntVec::open(&path).unwrap();
+    for i in 0..50 {
+        assert_eq!(r.get(i), 0, "slot {i}");
+    }
+}
+
+#[test]
+fn reopen_after_close_matches_original() {
+    // Explicit disk round-trip: drop the builder/mmap entirely, reopen
+    // from a fresh `Mmap::map` call, not the same in-memory handle.
+    let values: Vec<u64> = (0..5000).map(|i| (i * 97) % 8192).collect();
+    let dir = tempdir().unwrap();
+    let path = dir.path().join("test.pfiv");
+    {
+        let mut b = PersistentFixedIntVecBuilder::new(values.len(), 13, &path).unwrap();
+        for (i, &v) in values.iter().enumerate() {
+            b.set(i, v);
+        }
+        b.close().unwrap();
+    } // builder + mmap fully dropped here
+    let r = PersistentFixedIntVec::open(&path).unwrap();
+    for (i, &expected) in values.iter().enumerate() {
+        assert_eq!(r.get(i), expected, "slot {i}");
+    }
+}
diff --git a/src/obicompactvec/src/tests/mod.rs b/src/obicompactvec/src/tests/mod.rs
index 31f630ef..e5cd74cd 100644
--- a/src/obicompactvec/src/tests/mod.rs
+++ b/src/obicompactvec/src/tests/mod.rs
@@ -1,7 +1,11 @@
 mod bitmatrix;
 mod bitvec;
 mod colgroup;
+mod eliasfano;
+mod fixedintvec;
 mod intmatrix;
+mod rankselect;
+mod sparse;
 
 use tempfile::tempdir;
 
diff --git a/src/obicompactvec/src/tests/rankselect.rs b/src/obicompactvec/src/tests/rankselect.rs
new file mode 100644
index 00000000..92e3e492
--- /dev/null
+++ b/src/obicompactvec/src/tests/rankselect.rs
@@ -0,0 +1,167 @@
+use tempfile::tempdir;
+
+use crate::{PersistentRankSelectBitVec, PersistentRankSelectBitVecBuilder};
+
+fn build(bits: &[bool]) -> (tempfile::TempDir, PersistentRankSelectBitVec) {
+    let dir = tempdir().unwrap();
+    let path = dir.path().join("test.prsb");
+    let mut b = PersistentRankSelectBitVecBuilder::new(bits.len(), &path).unwrap();
+    for (i, &v) in bits.iter().enumerate() {
+        b.set(i, v);
+    }
+    b.close().unwrap();
+    let r = PersistentRankSelectBitVec::open(&path).unwrap();
+    (dir, r)
+}
+
+fn naive_rank1(bits: &[bool], pos: usize) -> u64 {
+    bits[..pos].iter().filter(|&&b| b).count() as u64
+}
+
+fn naive_select1(bits: &[bool], k: u64) -> usize {
+    bits.iter().enumerate().filter(|&(_, &b)| b).nth(k as usize).unwrap().0
+}
+
+#[test]
+fn get_matches_input() {
+    let bits = [true, false, true, true, false, false, true];
+    let (_dir, r) = build(&bits);
+    for (i, &expected) in bits.iter().enumerate() {
+        assert_eq!(r.get(i), expected, "bit {i}");
+    }
+}
+
+#[test]
+fn count_ones_matches_naive() {
+    let bits: Vec<bool> = (0..1000).map(|i| i % 3 == 0).collect();
+    let (_dir, r) = build(&bits);
+    assert_eq!(r.count_ones(), bits.iter().filter(|&&b| b).count() as u64);
+    assert_eq!(r.count_zeros(), bits.iter().filter(|&&b| !b).count() as u64);
+}
+
+#[test]
+fn rank1_matches_naive_small() {
+    let bits = [true, false, true, true, false, false, true, true, false, true];
+    let (_dir, r) = build(&bits);
+    for pos in 0..=bits.len() {
+        assert_eq!(r.rank1(pos), naive_rank1(&bits, pos), "rank1({pos})");
+    }
+}
+
+#[test]
+fn rank1_matches_naive_multi_block() {
+    // BLOCK_WORDS=8 words=512 bits — exercise several blocks, an odd
+    // total length, and a non-uniform bit pattern.
+    let n = 3000;
+    let bits: Vec<bool> = (0..n).map(|i| (i * 7 + 3) % 11 == 0).collect();
+    let (_dir, r) = build(&bits);
+    for pos in (0..=n).step_by(37) {
+        assert_eq!(r.rank1(pos), naive_rank1(&bits, pos), "rank1({pos})");
+    }
+    assert_eq!(r.rank1(n), naive_rank1(&bits, n));
+}
+
+#[test]
+fn rank0_is_complement_of_rank1() {
+    let bits: Vec<bool> = (0..777).map(|i| i % 5 < 2).collect();
+    let (_dir, r) = build(&bits);
+    for pos in (0..=bits.len()).step_by(13) {
+        assert_eq!(r.rank0(pos), pos as u64 - r.rank1(pos));
+    }
+}
+
+#[test]
+fn select1_matches_naive_small() {
+    let bits = [true, false, true, true, false, false, true, true, false, true];
+    let (_dir, r) = build(&bits);
+    let n_ones = bits.iter().filter(|&&b| b).count() as u64;
+    for k in 0..n_ones {
+        assert_eq!(r.select1(k), naive_select1(&bits, k), "select1({k})");
+    }
+}
+
+#[test]
+fn select1_matches_naive_multi_block() {
+    let n = 3000;
+    let bits: Vec<bool> = (0..n).map(|i| (i * 13 + 5) % 17 == 0).collect();
+    let (_dir, r) = build(&bits);
+    let n_ones = bits.iter().filter(|&&b| b).count() as u64;
+    for k in (0..n_ones).step_by(23) {
+        assert_eq!(r.select1(k), naive_select1(&bits, k), "select1({k})");
+    }
+}
+
+#[test]
+fn rank_select_round_trip() {
+    // For every one-bit's position p, select1(rank1(p)) == p.
+    let n = 2000;
+    let bits: Vec<bool> = (0..n).map(|i| (i * 31 + 1) % 9 == 0).collect();
+    let (_dir, r) = build(&bits);
+    for (p, &is_one) in bits.iter().enumerate() {
+        if is_one {
+            let k = r.rank1(p);
+            assert_eq!(r.select1(k), p, "position {p}, rank {k}");
+        }
+    }
+}
+
+#[test]
+#[should_panic]
+fn select1_out_of_range_panics() {
+    let bits = [true, false, false];
+    let (_dir, r) = build(&bits);
+    r.select1(1); // only one 1-bit (k=0 valid), k=1 must panic
+}
+
+#[test]
+fn all_zeros() {
+    let bits = vec![false; 200];
+    let (_dir, r) = build(&bits);
+    assert_eq!(r.count_ones(), 0);
+    assert_eq!(r.rank1(200), 0);
+    assert_eq!(r.rank0(200), 200);
+}
+
+#[test]
+fn all_ones() {
+    let bits = vec![true; 200];
+    let (_dir, r) = build(&bits);
+    assert_eq!(r.count_ones(), 200);
+    assert_eq!(r.rank1(200), 200);
+    for k in 0..200 {
+        assert_eq!(r.select1(k), k as usize);
+    }
+}
+
+#[test]
+fn reopen_after_close_matches_original() {
+    let n = 5000;
+    let bits: Vec<bool> = (0..n).map(|i| (i * 41 + 7) % 13 == 0).collect();
+    let dir = tempdir().unwrap();
+    let path = dir.path().join("test.prsb");
+    {
+        let mut b = PersistentRankSelectBitVecBuilder::new(n, &path).unwrap();
+        for (i, &v) in bits.iter().enumerate() {
+            b.set(i, v);
+        }
+        b.close().unwrap();
+    } // builder + mmap fully dropped here
+    let r = PersistentRankSelectBitVec::open(&path).unwrap();
+    assert_eq!(r.count_ones(), bits.iter().filter(|&&b| b).count() as u64);
+    for pos in (0..=n).step_by(17) {
+        assert_eq!(r.rank1(pos), naive_rank1(&bits, pos), "rank1({pos})");
+    }
+}
+
+#[test]
+fn select1_run_of_ten_then_gap_then_run() {
+    // Mirrors the exact bit pattern from the failing EliasFano case:
+    // positions 0..=9 set, 10 clear, 11..=20 set.
+    let mut bits = vec![false; 30];
+    for p in 0..=9 { bits[p] = true; }
+    for p in 11..=20 { bits[p] = true; }
+    let (_dir, r) = build(&bits);
+    assert_eq!(r.select1(9), 9, "select1(9)");
+    assert_eq!(r.select1(10), 11, "select1(10)");
+    assert_eq!(r.select1(11), 12, "select1(11)");
+}
diff --git a/src/obicompactvec/src/tests/sparse.rs b/src/obicompactvec/src/tests/sparse.rs
new file mode 100644
index 00000000..405f21ef
--- /dev/null
+++ b/src/obicompactvec/src/tests/sparse.rs
@@ -0,0 +1,251 @@
+use tempfile::tempdir;
+
+use crate::{BinaryMatrix, PersistentBitMatrix, PersistentBitMatrixBuilder, PersistentSparseBitMatrix, PersistentSparseBitMatrixBuilder};
+
+/// Builds a dense `PersistentBitMatrix` from column-major `bool` data —
+/// mirrors `tests/bitmatrix.rs`'s own `make_matrix` helper.
+fn make_dense(cols: &[&[bool]]) -> (tempfile::TempDir, PersistentBitMatrix) {
+    let n = cols.first().map_or(0, |c| c.len());
+    let dir = tempdir().unwrap();
+    let presence = dir.path().join("presence");
+    let mut b = PersistentBitMatrixBuilder::new(n, &presence).unwrap();
+    for &col in cols {
+        let mut cb = b.add_col().unwrap();
+        for (slot, &v) in col.iter().enumerate() {
+            cb.set(slot, v);
+        }
+        cb.close().unwrap();
+    }
+    b.close().unwrap();
+    let m = PersistentBitMatrix::open(dir.path()).unwrap();
+    (dir, m)
+}
+
+/// Builds a sparse matrix directly from row-major `bool` data (one slice
+/// per row, `n_cols` bools each) — the natural input shape for this type.
+fn make_sparse(rows: &[&[bool]], n_cols: usize) -> (tempfile::TempDir, PersistentSparseBitMatrix) {
+    let dir = tempdir().unwrap();
+    let sparse_dir = dir.path().join("sparse");
+    let mut b = PersistentSparseBitMatrixBuilder::new(rows.len(), n_cols, &sparse_dir).unwrap();
+    let mut genomes = Vec::new();
+    for row in rows {
+        genomes.clear();
+        genomes.extend((0..n_cols).filter(|&c| row[c]).map(|c| c as u32));
+        b.push_row(&genomes);
+    }
+    let m = b.finish().unwrap();
+    (dir, m)
+}
+
+fn row_as_bool(m: &PersistentSparseBitMatrix, slot: usize) -> Vec<bool> {
+    m.row(slot).to_vec()
+}
+
+#[test]
+fn basic_roundtrip_singletons_and_multi() {
+    // 5 rows, 4 genomes: mix of singleton, multi-genome, and one repeated
+    // multi-genome set (dedup should collapse it to one dictionary entry).
+    let rows: Vec<&[bool]> = vec![
+        &[true, false, false, false],  // singleton: genome 0
+        &[false, false, true, false],  // singleton: genome 2
+        &[true, true, false, false],   // multi: {0,1}
+        &[false, false, true, true],   // multi: {2,3}
+        &[true, true, false, false],   // multi: {0,1} again — should dedup
+    ];
+    let (_dir, m) = make_sparse(&rows, 4);
+    assert_eq!(m.n(), 5);
+    assert_eq!(m.n_cols(), 4);
+    for (slot, &expected) in rows.iter().enumerate() {
+        assert_eq!(row_as_bool(&m, slot), expected, "row {slot}");
+    }
+}
+
+#[test]
+fn fill_row_matches_row() {
+    let rows: Vec<&[bool]> = vec![
+        &[true, false, true],
+        &[false, true, false],
+        &[true, true, true],
+    ];
+    let (_dir, m) = make_sparse(&rows, 3);
+    let mut buf = vec![0u32; 3];
+    for slot in 0..3 {
+        m.fill_row(slot, &mut buf);
+        let via_fill: Vec<bool> = buf.iter().map(|&v| v != 0).collect();
+        assert_eq!(via_fill, row_as_bool(&m, slot), "slot {slot}");
+    }
+}
+
+#[test]
+fn dense_to_sparse_matches_dense_on_real_shaped_data() {
+    // Column-major dense fixture: 4 genomes (columns), 6 k-mer slots (rows),
+    // deliberately including singletons, a repeated multi-genome set, and
+    // one all-genomes row.
+    let col0 = [true, false, true, false, true, true];
+    let col1 = [false, false, true, false, true, false];
+    let col2 = [false, true, false, false, false, true];
+    let col3 = [false, false, false, true, false, true];
+    let (_dense_dir, dense) = make_dense(&[&col0, &col1, &col2, &col3]);
+
+    let sparse_root = tempdir().unwrap();
+    let sparse_dir = sparse_root.path().join("sparse");
+    let sparse = PersistentSparseBitMatrixBuilder::build_from_dense(&dense, &sparse_dir)
+        .unwrap()
+        .finish()
+        .unwrap();
+
+    assert_eq!(sparse.n(), dense.n());
+    assert_eq!(sparse.n_cols(), dense.n_cols());
+    for slot in 0..dense.n() {
+        assert_eq!(
+            row_as_bool(&sparse, slot), &*dense.row(slot),
+            "slot {slot}: dense vs sparse disagree"
+        );
+    }
+}
+
+#[test]
+fn count_ones_matches_dense() {
+    let col0 = [true, false, true, true];
+    let col1 = [false, true, true, false];
+    let (_dense_dir, dense) = make_dense(&[&col0, &col1]);
+    let sparse_root = tempdir().unwrap();
+    let sparse_dir = sparse_root.path().join("sparse");
+    let sparse = PersistentSparseBitMatrixBuilder::build_from_dense(&dense, &sparse_dir)
+        .unwrap()
+        .finish()
+        .unwrap();
+
+    let dense_counts = dense.count_ones();
+    let sparse_counts = sparse.count_ones();
+    assert_eq!(sparse_counts.to_vec(), dense_counts.to_vec());
+}
+
+#[test]
+fn fill_sub_matrix_matches_dense() {
+    let col0 = [true, false, true, false, true];
+    let col1 = [false, true, true, true, false];
+    let col2 = [true, true, false, false, true];
+    let (_dense_dir, dense) = make_dense(&[&col0, &col1, &col2]);
+    let sparse_root = tempdir().unwrap();
+    let sparse_dir = sparse_root.path().join("sparse");
+    let sparse = PersistentSparseBitMatrixBuilder::build_from_dense(&dense, &sparse_dir)
+        .unwrap()
+        .finish()
+        .unwrap();
+
+    let slots = [4usize, 0, 2];
+    let dense_sub = dense.sub_matrix(&slots);
+    let mut sparse_sub: Vec<Vec<bool>> = vec![Vec::new(); dense.n_cols()];
+    sparse.fill_sub_matrix(&slots, &mut sparse_sub);
+    assert_eq!(sparse_sub, dense_sub);
+}
+
+#[test]
+fn single_genome_matrix() {
+    // n_cols=1 — every row is necessarily a singleton (cardinality 1 or
+    // 0), the dictionary/multi-array stay entirely empty.
+    let rows: Vec<&[bool]> = vec![&[true], &[false], &[true]];
+    let (_dir, m) = make_sparse(&rows, 1);
+    for (slot, &expected) in rows.iter().enumerate() {
+        assert_eq!(row_as_bool(&m, slot), expected, "row {slot}");
+    }
+}
+
+#[test]
+fn reopen_after_close_matches_original() {
+    // Explicit disk round-trip: drop the builder and every mmap it holds
+    // entirely, reopen fresh from `PersistentSparseBitMatrix::open`.
+    let rows: Vec<Vec<bool>> = (0..500)
+        .map(|i| (0..37).map(|c| (i * 7 + c * 3) % 11 == 0).collect())
+        .collect();
+    let dir = tempdir().unwrap();
+    let sparse_dir = dir.path().join("sparse");
+    {
+        let mut b = PersistentSparseBitMatrixBuilder::new(rows.len(), 37, &sparse_dir).unwrap();
+        let mut genomes = Vec::new();
+        for row in &rows {
+            genomes.clear();
+            genomes.extend((0..37).filter(|&c| row[c]).map(|c| c as u32));
+            b.push_row(&genomes);
+        }
+        b.close().unwrap();
+    } // builder + every mmap fully dropped here
+
+    let m = PersistentSparseBitMatrix::open(&sparse_dir).unwrap();
+    assert_eq!(m.n(), 500);
+    assert_eq!(m.n_cols(), 37);
+    for (slot, expected) in rows.iter().enumerate() {
+        assert_eq!(&row_as_bool(&m, slot), expected, "row {slot}");
+    }
+}
+
+/// Exercises `BinaryMatrix` generically over both concrete types — proves
+/// they're actually interchangeable at that call site, not just
+/// individually correct.
+fn sum_via_trait(m: &dyn BinaryMatrix, slot: usize) -> usize {
+    m.row(slot).iter().filter(|&&b| b).count()
+}
+
+#[test]
+fn binary_matrix_trait_interchangeable_dense_and_sparse() {
+    let col0 = [true, false, true, true];
+    let col1 = [false, true, true, false];
+    let col2 = [true, true, false, true];
+    let (_dense_dir, dense) = make_dense(&[&col0, &col1, &col2]);
+
+    let sparse_root = tempdir().unwrap();
+    let sparse_dir = sparse_root.path().join("sparse");
+    let sparse = PersistentSparseBitMatrixBuilder::build_from_dense(&dense, &sparse_dir)
+        .unwrap()
+        .finish()
+        .unwrap();
+
+    assert_eq!(BinaryMatrix::n(&dense), BinaryMatrix::n(&sparse));
+    assert_eq!(BinaryMatrix::n_cols(&dense), BinaryMatrix::n_cols(&sparse));
+    for slot in 0..BinaryMatrix::n(&dense) {
+        assert_eq!(sum_via_trait(&dense, slot), sum_via_trait(&sparse, slot), "slot {slot}");
+    }
+    let dense_counts = BinaryMatrix::count_ones(&dense);
+    let sparse_counts = BinaryMatrix::count_ones(&sparse);
+    assert_eq!(dense_counts.to_vec(), sparse_counts.to_vec());
+}
+
+#[test]
+fn reopen_large_real_shaped_data_with_heavy_dedup() {
+    // Larger, more realistic case: 91-genome scale, plenty of repeated
+    // multi-genome sets (dedup exercised for real), reopened from disk.
+    let n_cols = 91;
+    let n_rows = 5000;
+    let rows: Vec<Vec<bool>> = (0..n_rows)
+        .map(|i| {
+            let mut row = vec![false; n_cols];
+            match i % 5 {
+                0 => { row[i % n_cols] = true; } // singleton, varies per row
+                1 => { row[3] = true; row[7] = true; } // repeated multi-set A
+                2 => { row[3] = true; row[7] = true; } // same set A again
+                3 => { row[10] = true; row[20] = true; row[30] = true; } // repeated multi-set B
+                _ => { row[(i * 13) % n_cols] = true; row[(i * 29) % n_cols] = true; } // varying pairs
+            }
+            row
+        })
+        .collect();
+
+    let dir = tempdir().unwrap();
+    let sparse_dir = dir.path().join("sparse");
+    {
+        let mut b = PersistentSparseBitMatrixBuilder::new(n_rows, n_cols, &sparse_dir).unwrap();
+        let mut genomes = Vec::new();
+        for row in &rows {
+            genomes.clear();
+            genomes.extend((0..n_cols).filter(|&c| row[c]).map(|c| c as u32));
+            b.push_row(&genomes);
+        }
+        b.close().unwrap();
+    }
+
+    let m = PersistentSparseBitMatrix::open(&sparse_dir).unwrap();
+    for (slot, expected) in rows.iter().enumerate() {
+        assert_eq!(&row_as_bool(&m, slot), expected, "row {slot}");
+    }
+}
diff --git a/src/obicompactvec/src/traits.rs b/src/obicompactvec/src/traits.rs
index f3c0440c..5437b7a1 100644
--- a/src/obicompactvec/src/traits.rs
+++ b/src/obicompactvec/src/traits.rs
@@ -1,5 +1,33 @@
 use ndarray::{Array1, Array2};
 
+/// Minimal shared surface between `PersistentBitMatrix` (dense) and
+/// `PersistentSparseBitMatrix` (row-major, deduplicated) — exactly what
+/// real consumers use today (`obikphylo::siblings::cache::Mat`), not the
+/// two types' full individual APIs. Column-oriented operations
+/// (`col`/`col_view`, the `BitPartials`/`ColumnWeights` distance-matrix
+/// traits above) are *not* part of this trait — `PersistentSparseBitMatrix`
+/// only offers a naive, row-scanning `count_ones` for now (see
+/// `docmd/architecture/siblings.md` and the sparse-matrix design plan,
+/// "Explicitly deferred": a row-major co-occurrence rewrite of the
+/// pairwise distance matrices is future work, not part of this trait).
+pub trait BinaryMatrix {
+    /// Number of rows (k-mer slots).
+    fn n(&self) -> usize;
+    /// Number of columns (genomes).
+    fn n_cols(&self) -> usize;
+    /// One row's presence values, one `bool` per genome.
+    fn row(&self, slot: usize) -> Box<[bool]>;
+    /// Like [`row`](Self::row), filling a caller-provided `0`/`1` buffer
+    /// instead of allocating.
+    fn fill_row(&self, slot: usize, buf: &mut [u32]);
+    /// Extracts a sub-matrix at `slots`, column-first: `out[c]` holds
+    /// column `c`'s values at `slots`, in `slots` order. `out.len()` must
+    /// equal `n_cols()`.
+    fn fill_sub_matrix(&self, slots: &[usize], out: &mut [Vec<bool>]);
+    /// Per-genome k-mer totals.
+    fn count_ones(&self) -> Array1<u64>;
+}
+
 /// Convert a Jaccard distance matrix (`1 - J`) into a Mash distance matrix, per
 /// https://mash.readthedocs.io/en/latest/distances.html:
 /// `D = -1/k * ln(2J / (1+J))`.
diff --git a/src/obikphylo/src/siblings/tests.rs b/src/obikphylo/src/siblings/tests.rs
index 3b5359d3..513316ca 100644
--- a/src/obikphylo/src/siblings/tests.rs
+++ b/src/obikphylo/src/siblings/tests.rs
@@ -535,3 +535,259 @@ fn diag_plant_index_cardinality_distribution() {
         );
     }
 }
+
+#[test]
+#[ignore]
+fn bench_sparse_matrix_inmemory_construction_ram() {
+    use std::collections::HashMap;
+    use std::time::Instant;
+
+    let idx = KmerIndex::open("/Users/coissac/travail/obiskim/data/phyloalps/phyloskims_sal_vac")
+        .expect("open real plant index");
+    let layer_dirs = super::family_scan::sibling_layer_dirs(&idx).expect("layer dirs");
+    // A `layer_1` (the larger, merged layer) — pick the one already
+    // profiled: part_00018/index/layer_1, ~30.2M rows.
+    let layer_dir = layer_dirs.iter()
+        .find(|p| p.to_string_lossy().contains("part_00018") && p.to_string_lossy().contains("layer_1"))
+        .expect("expected layer not found — layer_dirs order may have changed");
+
+    let mat = obicompactvec::PersistentBitMatrix::open(layer_dir).expect("open presence matrix");
+    let n = mat.n();
+    let n_cols = mat.n_cols();
+    println!("layer={} n_slots={n} n_cols={n_cols}", layer_dir.display());
+
+    let rss_before = obisys::peak_rss_bytes();
+    let t0 = Instant::now();
+
+    // Plan design: is_multi flag (1 bit/row) + two SEPARATE arrays
+    // (singleton-only, multi-only), each sized to its own value range —
+    // not one array covering the whole dict_id space. In-memory prototype
+    // (u32 per entry, not yet bit-packed — the fixed-width primitive
+    // isn't built yet); this benchmark measures RAM + the split's real
+    // final size, not the construction-time representation's size.
+    let mut is_multi: Vec<bool> = Vec::with_capacity(n);
+    let mut singleton_array: Vec<u32> = Vec::new();
+    let mut multi_array: Vec<u32> = Vec::new();
+    let mut dedup: HashMap<Vec<u32>, u32> = HashMap::new();
+    let mut next_dict_id: u32 = 0;
+    let mut dict_values_bytes: u64 = 0; // running varint-encoded size estimate
+    let mut buf = vec![0u32; n_cols];
+
+    for slot in 0..n {
+        mat.fill_row(slot, &mut buf);
+        let set: Vec<u32> = (0..n_cols).filter(|&c| buf[c] != 0).map(|c| c as u32).collect();
+        match set.len() {
+            0 => { is_multi.push(false); singleton_array.push(0); } // shouldn't happen on a real built index; placeholder
+            1 => {
+                is_multi.push(false);
+                singleton_array.push(set[0]);
+            }
+            _ => {
+                is_multi.push(true);
+                let id = if let Some(&id) = dedup.get(&set) {
+                    id
+                } else {
+                    let id = next_dict_id;
+                    next_dict_id += 1;
+                    // varint size estimate: 1 byte per index < 128 (always
+                    // true here, n_cols=91), matching the plan's encoding.
+                    dict_values_bytes += set.iter().map(|&v| if v < 128 { 1 } else { 2 }).sum::<u64>();
+                    dedup.insert(set, id);
+                    id
+                };
+                multi_array.push(id);
+            }
+        };
+    }
+
+    let elapsed = t0.elapsed();
+    let rss_after = obisys::peak_rss_bytes();
+
+    let n_distinct_multi = dedup.len() as u64;
+    let n_singleton = singleton_array.len() as u64;
+    let n_multi = multi_array.len() as u64;
+
+    let is_multi_bytes = (n as u64).div_ceil(8);
+    let singleton_width_bits = (32 - (n_cols as u32).max(1).leading_zeros()).max(1);
+    let multi_width_bits = (32 - (n_distinct_multi as u32).max(1).leading_zeros()).max(1);
+    let singleton_array_bytes = (n_singleton * singleton_width_bits as u64).div_ceil(8);
+    let multi_array_bytes = (n_multi * multi_width_bits as u64).div_ceil(8);
+
+    let split_total = is_multi_bytes + singleton_array_bytes + multi_array_bytes + dict_values_bytes;
+    let dense_bytes = (n as u64 * n_cols as u64).div_ceil(8);
+
+    println!(
+        "elapsed={:?} rss_before={} rss_after={} rss_delta={}",
+        elapsed, fmt_mb(rss_before), fmt_mb(rss_after), fmt_mb(rss_after.saturating_sub(rss_before)),
+    );
+    println!(
+        "n_singleton={n_singleton} n_multi={n_multi} n_distinct_multi={n_distinct_multi} \
+         singleton_width_bits={singleton_width_bits} multi_width_bits={multi_width_bits}",
+    );
+    println!(
+        "is_multi_bytes={} singleton_array_bytes={} multi_array_bytes={} dict_values_bytes={} \
+         split_total_bytes={} ({:.1}x vs dense) dense_bytes={}",
+        fmt_mb(is_multi_bytes), fmt_mb(singleton_array_bytes), fmt_mb(multi_array_bytes),
+        fmt_mb(dict_values_bytes), fmt_mb(split_total),
+        dense_bytes as f64 / split_total as f64,
+        fmt_mb(dense_bytes),
+    );
+}
+
+fn fmt_mb(bytes: u64) -> String {
+    format!("{:.1}MB", bytes as f64 / (1024.0 * 1024.0))
+}
+
+#[test]
+#[ignore]
+fn bench_real_persistent_sparse_bit_matrix_on_disk_size() {
+    use std::time::Instant;
+
+    let idx = KmerIndex::open("/Users/coissac/travail/obiskim/data/phyloalps/phyloskims_sal_vac")
+        .expect("open real plant index");
+    let layer_dirs = super::family_scan::sibling_layer_dirs(&idx).expect("layer dirs");
+    let layer_dir = layer_dirs.iter()
+        .find(|p| p.to_string_lossy().contains("part_00018") && p.to_string_lossy().contains("layer_1"))
+        .expect("expected layer not found — layer_dirs order may have changed");
+
+    let dense = obicompactvec::PersistentBitMatrix::open(layer_dir).expect("open presence matrix");
+    let n = dense.n();
+    let n_cols = dense.n_cols();
+    println!("layer={} n_slots={n} n_cols={n_cols}", layer_dir.display());
+
+    let out_dir = std::env::temp_dir().join(format!("sparse_bench_{}", std::process::id()));
+    let _ = std::fs::remove_dir_all(&out_dir);
+
+    let rss_before = obisys::peak_rss_bytes();
+    let t0 = Instant::now();
+
+    let sparse = obicompactvec::PersistentSparseBitMatrixBuilder::build_from_dense(&dense, &out_dir)
+        .expect("build_from_dense")
+        .finish()
+        .expect("finish");
+
+    let elapsed = t0.elapsed();
+    let rss_after = obisys::peak_rss_bytes();
+
+    // Real on-disk size: sum of every file actually written under out_dir.
+    let mut sparse_bytes: u64 = 0;
+    for entry in std::fs::read_dir(&out_dir).unwrap() {
+        let entry = entry.unwrap();
+        let size = entry.metadata().unwrap().len();
+        println!("  {}: {}", entry.file_name().to_string_lossy(), fmt_mb(size));
+        sparse_bytes += size;
+    }
+
+    let dense_bytes = (n as u64 * n_cols as u64).div_ceil(8);
+
+    println!(
+        "elapsed={:?} rss_before={} rss_after={} rss_delta={}",
+        elapsed, fmt_mb(rss_before), fmt_mb(rss_after), fmt_mb(rss_after.saturating_sub(rss_before)),
+    );
+    println!(
+        "REAL on-disk: sparse_total={} dense={} ({:.1}x)",
+        fmt_mb(sparse_bytes), fmt_mb(dense_bytes), dense_bytes as f64 / sparse_bytes as f64,
+    );
+
+    // Sanity: reopen from disk (fresh mmap, not the just-built handle) and
+    // spot-check a handful of rows against the dense original.
+    drop(sparse);
+    let reopened = obicompactvec::PersistentSparseBitMatrix::open(&out_dir).expect("reopen");
+    let mut dense_buf = vec![0u32; n_cols];
+    for &slot in &[0usize, 1, 1000, n / 2, n - 1] {
+        dense.fill_row(slot, &mut dense_buf);
+        let sparse_row = reopened.row(slot);
+        for c in 0..n_cols {
+            assert_eq!(sparse_row[c], dense_buf[c] != 0, "slot {slot}, col {c}");
+        }
+    }
+    println!("spot-check rows: OK");
+
+    // ── Access-time comparison ──────────────────────────────────────────
+    // Both patterns matter in practice: sequential (a full-layer scan, the
+    // existing `scan_layer_families` shape) and random (a single-family
+    // cross-partition lookup, the entropy/`--shannon` shape). Same slot
+    // sequence used against both structures for a fair comparison.
+    const N_ACCESS: usize = 2_000_000;
+
+    // Deterministic xorshift, no extra dependency — fine for a benchmark's
+    // access pattern, not for anything security- or correctness-sensitive.
+    let mut rng_state: u64 = 0x9E3779B97F4A7C15;
+    let mut next_rand = move || {
+        rng_state ^= rng_state << 13;
+        rng_state ^= rng_state >> 7;
+        rng_state ^= rng_state << 17;
+        rng_state
+    };
+    let random_slots: Vec<usize> = (0..N_ACCESS).map(|_| (next_rand() as usize) % n).collect();
+    let sequential_slots: Vec<usize> = (0..N_ACCESS).map(|i| i % n).collect();
+
+    let mut buf = vec![0u32; n_cols];
+
+    let t = Instant::now();
+    for &slot in &sequential_slots {
+        dense.fill_row(slot, &mut buf);
+    }
+    let dense_seq = t.elapsed();
+
+    let t = Instant::now();
+    for &slot in &sequential_slots {
+        reopened.fill_row(slot, &mut buf);
+    }
+    let sparse_seq = t.elapsed();
+
+    let t = Instant::now();
+    for &slot in &random_slots {
+        dense.fill_row(slot, &mut buf);
+    }
+    let dense_rand = t.elapsed();
+
+    let t = Instant::now();
+    for &slot in &random_slots {
+        reopened.fill_row(slot, &mut buf);
+    }
+    let sparse_rand = t.elapsed();
+
+    println!(
+        "ACCESS ({N_ACCESS} rows) sequential: dense={:?} ({:.0}ns/row) sparse={:?} ({:.0}ns/row) — {:.2}x",
+        dense_seq, dense_seq.as_nanos() as f64 / N_ACCESS as f64,
+        sparse_seq, sparse_seq.as_nanos() as f64 / N_ACCESS as f64,
+        sparse_seq.as_secs_f64() / dense_seq.as_secs_f64(),
+    );
+    println!(
+        "ACCESS ({N_ACCESS} rows) random:     dense={:?} ({:.0}ns/row) sparse={:?} ({:.0}ns/row) — {:.2}x",
+        dense_rand, dense_rand.as_nanos() as f64 / N_ACCESS as f64,
+        sparse_rand, sparse_rand.as_nanos() as f64 / N_ACCESS as f64,
+        sparse_rand.as_secs_f64() / dense_rand.as_secs_f64(),
+    );
+
+    // ── Column-major access, "just for fun" ─────────────────────────────
+    // The whole point of `docmd/architecture/siblings.md`'s "Explicitly
+    // deferred" section: dense is genome-major (native, contiguous column
+    // access), sparse is k-mer-major (no column method at all — reading
+    // one column means decoding every row and keeping one bit each time).
+    // Extract one full column (all n rows) both ways.
+    let col = n_cols / 2;
+
+    let t = Instant::now();
+    let dense_col_view = dense.col_view(col);
+    let dense_col_ones: u64 = (0..n).filter(|&s| dense_col_view.get(s)).count() as u64;
+    let dense_col_time = t.elapsed();
+
+    let t = Instant::now();
+    let mut buf2 = vec![0u32; n_cols];
+    let sparse_col_ones: u64 = (0..n)
+        .filter(|&s| { reopened.fill_row(s, &mut buf2); buf2[col] != 0 })
+        .count() as u64;
+    let sparse_col_time = t.elapsed();
+
+    assert_eq!(dense_col_ones, sparse_col_ones, "column {col} popcount disagrees");
+    println!(
+        "COLUMN-MAJOR (col {col}, {n} rows) dense={:?} ({:.0}ns/row) sparse={:?} ({:.0}ns/row) — {:.1}x SLOWER on sparse",
+        dense_col_time, dense_col_time.as_nanos() as f64 / n as f64,
+        sparse_col_time, sparse_col_time.as_nanos() as f64 / n as f64,
+        sparse_col_time.as_secs_f64() / dense_col_time.as_secs_f64(),
+    );
+
+    let _ = std::fs::remove_dir_all(&out_dir);
+}
-- 
2.54.0


From 3ba26b3dc1d9593c8dd78811c7dae585687b48a9 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Sat, 15 Aug 2026 19:19:48 +0200
Subject: [PATCH 34/46] feat: add sparse on-disk format for presence matrices

The index packing API now accepts a `sparse` parameter to generate `PersistentSparseBitMatrix` files alongside existing dense matrices. The sibling cache automatically detects this format via an `is_multi.prsb` marker file and routes queries identically to the dense variant. A new `--sparse` CLI flag exposes the option, with tests verifying end-to-end pipeline correctness and storage equivalence.
---
 .gitignore                                |  1 +
 docmd/architecture/siblings.md            | 56 ++++++++++++++++++++++
 src/obicompactvec/src/bitmatrix/mod.rs    |  2 +-
 src/obicompactvec/src/bitmatrix/sparse.rs | 34 +++++++++++--
 src/obicompactvec/src/lib.rs              |  2 +-
 src/obicompactvec/src/traits.rs           |  8 ++++
 src/obikindex/src/index.rs                | 20 ++++++--
 src/obikindex/src/merge.rs                |  2 +-
 src/obikindex/src/select.rs               |  2 +-
 src/obikmer/src/cmd/pack/mod.rs           | 10 +++-
 src/obikphylo/src/siblings/cache.rs       | 22 ++++++++-
 src/obikphylo/src/siblings/tests.rs       | 41 ++++++++++++++++
 src/obilayeredmap/src/layer.rs            | 45 ++++++++++++++----
 src/obilayeredmap/src/tests/layer.rs      | 58 ++++++++++++++++++++++-
 14 files changed, 279 insertions(+), 24 deletions(-)

diff --git a/.gitignore b/.gitignore
index bfe28adc..5bb83c6d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -16,6 +16,7 @@ benchmark/simulated_data
 benchmark/specimen_index_presence
 benchmark/specimen_index_count
 benchmark/global_index_presence
+benchmark/global_index_presence_sav
 benchmark/all_specific
 benchmark/global_index_count
 benchmark/stats
diff --git a/docmd/architecture/siblings.md b/docmd/architecture/siblings.md
index eb032890..2a7d26c6 100644
--- a/docmd/architecture/siblings.md
+++ b/docmd/architecture/siblings.md
@@ -496,3 +496,59 @@ Also still deferred, unchanged from the implementation plan: full Alanko
 et al. subset-hierarchy compression (only the exact-duplicate special case
 is built), a sparse `PersistentCompactIntMatrix` (count matrices), and
 BRWT-style column-correlation exploitation.
+
+## Wired into `pack` and the sibling-annex build path (2026-08-15)
+
+`PersistentSparseBitMatrix` went from a validated but unused type to a
+real, selectable on-disk format:
+
+- **Generic `Layer<D>`**: `obilayeredmap::Layer<D>`'s presence-only methods
+  (`n_cols`, `sub_matrix`, `fill_sub_matrix`) are generic over any
+  `D: LayerData<Item = Box<[bool]>> + BinaryMatrix`, not hardcoded to
+  `PersistentBitMatrix` — `PersistentSparseBitMatrix` implements
+  `LayerData` (`open`/`read`) the same way. `find_slot`/`index_batch` were
+  already generic over any `D: LayerData`, so they needed no change.
+  Verified by `obilayeredmap`'s
+  `presence_layer_generic_over_sparse_matches_dense` test: build a dense
+  presence layer, convert it to sparse via `build_from_dense`, open both
+  as `Layer<PersistentBitMatrix>`/`Layer<PersistentSparseBitMatrix>` on
+  the same directory, assert `n_cols`/`sub_matrix`/`find_slot` agree.
+  (This test must stay at `k=4` with mutually non-colliding canonical
+  4-mers across its input sequences — `K`/`M` are process-wide
+  `AtomicUsize`s in test builds, not thread-local, so a test using a
+  different `k` races every other test in the same crate binary; a k=11
+  version of this test passed alone but failed under the full
+  `obilayeredmap` suite for exactly that reason before being fixed.)
+- **`obikphylo::siblings::cache::Mat`** gained a third variant,
+  `SparsePresence(Layer<PersistentSparseBitMatrix>)`, alongside `Count`
+  and `Presence` — every method (`find_slot`, `index_batch`,
+  `iter_minorants_batch`, `n_cols`, `fill_sub_matrix_carries`) dispatches
+  to it identically to `Presence`, since both go through the same generic
+  `Layer<D>` code. `PartitionCache::build` picks the variant per layer by
+  checking for `presence/is_multi.prsb` (the sparse format's own marker
+  file, see the design section above) before falling back to the dense
+  open path.
+- **`pack_sparse_bit_matrix`** (new, `obicompactvec::bitmatrix::sparse`):
+  `pack --sparse`'s entry point. Idempotent (checks `is_multi.prsb`
+  first); packs to dense `matrix.pbmx` first if that hasn't happened yet
+  (the dense→sparse transpose needs random row access, which only the
+  packed/columnar dense forms give), then `build_from_dense`s the sparse
+  form into the same directory and deletes `matrix.pbmx` — old-format
+  files are removed only after the new format is fully written, mirroring
+  `pack_bit_matrix`'s own crash-safety convention.
+- **CLI**: `obikmer pack --sparse` threads a `sparse: bool` through
+  `KmerIndex::pack_matrices` (all other call sites — `select`, `merge`,
+  `finalize_indexed` — pass `false`, unchanged dense behaviour). Count
+  matrices are untouched by `--sparse` (no sparse `PersistentCompactIntMatrix`
+  — see "still deferred" above).
+- **End-to-end coverage**: `obikphylo::siblings::tests::
+  sibling_annex_works_after_pack_sparse` builds a two-genome index, packs
+  it `--sparse`, asserts `is_multi.prsb` exists, then runs
+  `build_sibling_annex` and checks the resulting `FamilyMask`s match the
+  dense-path test (`sibling_annex_one_sibling_each`) exactly — proves the
+  sparse format round-trips through the real build pipeline
+  (`PartitionCache` sparse-detection included), not just the
+  `obicompactvec`/`obilayeredmap` unit layers below it.
+
+Full workspace `cargo test` (all crates, unit + doc tests) green after
+this change.
diff --git a/src/obicompactvec/src/bitmatrix/mod.rs b/src/obicompactvec/src/bitmatrix/mod.rs
index 0523da87..6435ca2b 100644
--- a/src/obicompactvec/src/bitmatrix/mod.rs
+++ b/src/obicompactvec/src/bitmatrix/mod.rs
@@ -22,7 +22,7 @@ mod sparse;
 pub use builder::PersistentBitMatrixBuilder;
 pub use packed::pack_bit_matrix;
 pub use persistent::PersistentBitMatrix;
-pub use sparse::{PersistentSparseBitMatrix, PersistentSparseBitMatrixBuilder};
+pub use sparse::{PersistentSparseBitMatrix, PersistentSparseBitMatrixBuilder, pack_sparse_bit_matrix};
 
 pub(crate) use pairwise::{pairwise_matrix, pairwise2_matrix};
 
diff --git a/src/obicompactvec/src/bitmatrix/sparse.rs b/src/obicompactvec/src/bitmatrix/sparse.rs
index 09dea336..873a0554 100644
--- a/src/obicompactvec/src/bitmatrix/sparse.rs
+++ b/src/obicompactvec/src/bitmatrix/sparse.rs
@@ -5,7 +5,7 @@
 //! used by any production code path yet — a new type, not a replacement.
 //!
 //! On-disk layout (a directory, mirroring [`super::PersistentBitMatrix`]'s
-//! own directory-of-files convention): `meta.json` plus four components —
+//! own directory-of-files convention): `sparse_meta.json` plus four components —
 //! `is_multi.prsb` (rank-capable flag: singleton row vs. multi-genome
 //! row), `singleton.pfiv` (genome index, one entry per singleton row,
 //! `ceil(log2(n_cols))` bits each), `multi.pfiv` (`dict_id`, one entry per
@@ -33,13 +33,14 @@ use crate::meta::field;
 use crate::rankselect::{PersistentRankSelectBitVec, PersistentRankSelectBitVecBuilder};
 
 use super::PersistentBitMatrix;
+use super::packed::PackedBitMatrix;
 
 fn is_multi_path(dir: &Path) -> PathBuf { dir.join("is_multi.prsb") }
 fn singleton_path(dir: &Path) -> PathBuf { dir.join("singleton.pfiv") }
 fn multi_path(dir: &Path) -> PathBuf { dir.join("multi.pfiv") }
 fn dict_offsets_base(dir: &Path) -> PathBuf { dir.join("dict_offsets") }
 fn dict_values_path(dir: &Path) -> PathBuf { dir.join("dict_values.bin") }
-fn meta_path(dir: &Path) -> PathBuf { dir.join("meta.json") }
+fn meta_path(dir: &Path) -> PathBuf { dir.join("sparse_meta.json") }
 
 struct SparseMeta {
     n: usize,
@@ -53,7 +54,7 @@ impl SparseMeta {
     fn load(dir: &Path) -> io::Result<Self> {
         let s = fs::read_to_string(meta_path(dir))?;
         let get = |name: &str| {
-            field(&s, name).ok_or_else(|| io::Error::new(io::ErrorKind::InvalidData, format!("bad meta.json: missing {name}")))
+            field(&s, name).ok_or_else(|| io::Error::new(io::ErrorKind::InvalidData, format!("bad sparse_meta.json: missing {name}")))
         };
         Ok(Self {
             n: get("n")?,
@@ -370,3 +371,30 @@ impl PersistentSparseBitMatrixBuilder {
         Ok(builder)
     }
 }
+
+/// `pack --sparse`'s entry point: converts a presence directory into the
+/// sparse on-disk format in place, mirroring [`super::pack_bit_matrix`]'s
+/// convention (old-format files removed only after the new format is
+/// fully written, so a crash mid-conversion leaves the previous, still
+/// valid format rather than a half-written one). Idempotent — does
+/// nothing if `is_multi.prsb` already exists. Packs to dense
+/// (`matrix.pbmx`) first via [`super::pack_bit_matrix`] if that hasn't
+/// happened yet, since the dense→sparse transpose (`build_from_dense`)
+/// needs random row access, which only the packed/columnar dense forms
+/// give — not a further reason to keep the dense file around afterward.
+pub fn pack_sparse_bit_matrix(dir: &Path) -> io::Result<()> {
+    if is_multi_path(dir).exists() {
+        return Ok(());
+    }
+
+    let packed_path = dir.join("matrix.pbmx");
+    if !packed_path.exists() {
+        super::pack_bit_matrix(dir)?;
+    }
+
+    let dense = PersistentBitMatrix::Packed(PackedBitMatrix::open(&packed_path)?);
+    PersistentSparseBitMatrixBuilder::build_from_dense(&dense, dir)?.close()?;
+    drop(dense);
+    fs::remove_file(&packed_path)?;
+    Ok(())
+}
diff --git a/src/obicompactvec/src/lib.rs b/src/obicompactvec/src/lib.rs
index 58450c47..a7ce5df3 100644
--- a/src/obicompactvec/src/lib.rs
+++ b/src/obicompactvec/src/lib.rs
@@ -19,7 +19,7 @@ pub use bitvec::{BitIter, PersistentBitVec, PersistentBitVecBuilder};
 pub use fixedintvec::{PersistentFixedIntVec, PersistentFixedIntVecBuilder, bit_width_for_range};
 pub use rankselect::{PersistentRankSelectBitVec, PersistentRankSelectBitVecBuilder};
 pub use eliasfano::{EliasFano, EliasFanoBuilder};
-pub use bitmatrix::{PersistentBitMatrix, PersistentBitMatrixBuilder, PersistentSparseBitMatrix, PersistentSparseBitMatrixBuilder, pack_bit_matrix};
+pub use bitmatrix::{PersistentBitMatrix, PersistentBitMatrixBuilder, PersistentSparseBitMatrix, PersistentSparseBitMatrixBuilder, pack_bit_matrix, pack_sparse_bit_matrix};
 pub use builder::PersistentCompactIntVecBuilder;
 pub use colgroup::{ColGroup, FilterMask, MatrixGroupOps, eval_filter_mask};
 pub use intmatrix::{PersistentCompactIntMatrix, PersistentCompactIntMatrixBuilder, pack_compact_int_matrix};
diff --git a/src/obicompactvec/src/traits.rs b/src/obicompactvec/src/traits.rs
index 5437b7a1..62692031 100644
--- a/src/obicompactvec/src/traits.rs
+++ b/src/obicompactvec/src/traits.rs
@@ -26,6 +26,14 @@ pub trait BinaryMatrix {
     fn fill_sub_matrix(&self, slots: &[usize], out: &mut [Vec<bool>]);
     /// Per-genome k-mer totals.
     fn count_ones(&self) -> Array1<u64>;
+
+    /// Allocating variant of [`fill_sub_matrix`](Self::fill_sub_matrix) —
+    /// provided once here so implementers only need the fill-in-place form.
+    fn sub_matrix(&self, slots: &[usize]) -> Vec<Vec<bool>> {
+        let mut out: Vec<Vec<bool>> = (0..self.n_cols()).map(|_| Vec::new()).collect();
+        self.fill_sub_matrix(slots, &mut out);
+        out
+    }
 }
 
 /// Convert a Jaccard distance matrix (`1 - J`) into a Mash distance matrix, per
diff --git a/src/obikindex/src/index.rs b/src/obikindex/src/index.rs
index 6b7e117d..c8291060 100644
--- a/src/obikindex/src/index.rs
+++ b/src/obikindex/src/index.rs
@@ -122,7 +122,7 @@ impl KmerIndex {
         fs::File::create(output.join(SENTINEL_INDEXED)).map_err(OKIError::Io)?;
         let idx = KmerIndex::open(output)?;
         let t_pack = Stage::start("pack");
-        idx.pack_matrices()?;
+        idx.pack_matrices(false)?;
         rep.push(t_pack.stop());
         Ok(idx)
     }
@@ -274,8 +274,14 @@ impl KmerIndex {
     ///
     /// Reduces per-query file-open overhead from O(n_genomes) to O(1) per partition.
     /// Column files are kept in place; packed files take priority when opening.
-    pub fn pack_matrices(&self) -> OKIResult<()> {
-        use obicompactvec::{pack_bit_matrix, pack_compact_int_matrix};
+    ///
+    /// If `sparse` is set, presence matrices go one step further, from the
+    /// dense `.pbmx` form into `obicompactvec::PersistentSparseBitMatrix`'s
+    /// on-disk format (see `docmd/architecture/siblings.md`) — count
+    /// matrices are unaffected, sparse count matrices aren't implemented
+    /// (see the sparse-matrix design plan's "Explicitly deferred").
+    pub fn pack_matrices(&self, sparse: bool) -> OKIResult<()> {
+        use obicompactvec::{pack_bit_matrix, pack_compact_int_matrix, pack_sparse_bit_matrix};
         use obilayeredmap::meta::PartitionMeta;
 
         let n = self.n_partitions();
@@ -292,7 +298,13 @@ impl KmerIndex {
                     let layer_dir = index_dir.join(format!("layer_{l}"));
                     let presence_dir = layer_dir.join("presence");
                     let counts_dir   = layer_dir.join("counts");
-                    if presence_dir.exists() { pack_bit_matrix(&presence_dir).map_err(OKIError::Io)?; }
+                    if presence_dir.exists() {
+                        if sparse {
+                            pack_sparse_bit_matrix(&presence_dir).map_err(OKIError::Io)?;
+                        } else {
+                            pack_bit_matrix(&presence_dir).map_err(OKIError::Io)?;
+                        }
+                    }
                     if counts_dir.exists()   { pack_compact_int_matrix(&counts_dir).map_err(OKIError::Io)?; }
                 }
                 Ok(())
diff --git a/src/obikindex/src/merge.rs b/src/obikindex/src/merge.rs
index 8d7840e9..5139d72e 100644
--- a/src/obikindex/src/merge.rs
+++ b/src/obikindex/src/merge.rs
@@ -249,7 +249,7 @@ impl KmerIndex {
             let pb = spinner("pack");
             pb.set_message("consolidating column files …");
             let dst2 = KmerIndex::open(output)?;
-            dst2.pack_matrices()?;
+            dst2.pack_matrices(false)?;
             pb.finish_and_clear();
             rep.push(t.stop());
         }
diff --git a/src/obikindex/src/select.rs b/src/obikindex/src/select.rs
index 4639d3b3..bc42a3a1 100644
--- a/src/obikindex/src/select.rs
+++ b/src/obikindex/src/select.rs
@@ -118,7 +118,7 @@ impl KmerIndex {
         self.meta.write(&self.root_path)?;
 
         let t_pack = Stage::start("pack");
-        self.pack_matrices()?;
+        self.pack_matrices(false)?;
         rep.push(t_pack.stop());
         Ok(())
     }
diff --git a/src/obikmer/src/cmd/pack/mod.rs b/src/obikmer/src/cmd/pack/mod.rs
index 4f34c52d..10621772 100644
--- a/src/obikmer/src/cmd/pack/mod.rs
+++ b/src/obikmer/src/cmd/pack/mod.rs
@@ -9,6 +9,14 @@ use tracing::info;
 pub struct PackArgs {
     /// Index directory to pack
     pub index: PathBuf,
+
+    /// Pack presence matrices into the sparse, deduplicated on-disk format
+    /// instead of the dense one — see `docmd/architecture/siblings.md`.
+    /// Smaller and faster for single-row access on real, sparse data;
+    /// column-oriented access (`--metric` distance matrices) is much
+    /// slower on the sparse format.
+    #[arg(long)]
+    pub sparse: bool,
 }
 
 pub fn run(args: PackArgs) {
@@ -33,7 +41,7 @@ pub fn run(args: PackArgs) {
     let mut rep = Reporter::new();
     let t = Stage::start("pack");
 
-    idx.pack_matrices().unwrap_or_else(|e| {
+    idx.pack_matrices(args.sparse).unwrap_or_else(|e| {
         eprintln!("pack error: {e}");
         std::process::exit(1);
     });
diff --git a/src/obikphylo/src/siblings/cache.rs b/src/obikphylo/src/siblings/cache.rs
index 99933c6d..1ef1a672 100644
--- a/src/obikphylo/src/siblings/cache.rs
+++ b/src/obikphylo/src/siblings/cache.rs
@@ -1,6 +1,6 @@
 use rayon::prelude::*;
 
-use obicompactvec::{PersistentBitMatrix, PersistentCompactIntMatrix};
+use obicompactvec::{PersistentBitMatrix, PersistentCompactIntMatrix, PersistentSparseBitMatrix};
 use obikpartitionner::KmerPartition;
 use obikseq::CanonicalKmer;
 use obilayeredmap::Layer;
@@ -40,6 +40,13 @@ use super::{olm_to_ok, SiblingAnnex, INDEX_SUBDIR};
 pub(super) enum Mat {
     Count(Layer<PersistentCompactIntMatrix>),
     Presence(Layer<PersistentBitMatrix>),
+    /// Same role as `Presence`, over a layer packed by `pack --sparse`
+    /// (`PersistentSparseBitMatrix`) instead of the dense form — see
+    /// `docmd/architecture/siblings.md`'s sparse-matrix section. Every
+    /// `Mat` method below dispatches to the same `Layer<D>` generic code
+    /// (`D: LayerData`) as `Presence`, so this arm is purely a storage
+    /// choice, not a behavioural difference.
+    SparsePresence(Layer<PersistentSparseBitMatrix>),
 }
 
 impl Mat {
@@ -47,6 +54,7 @@ impl Mat {
         match self {
             Mat::Count(l) => l.find_slot(kmer),
             Mat::Presence(l) => l.find_slot(kmer),
+            Mat::SparsePresence(l) => l.find_slot(kmer),
         }
     }
 
@@ -60,6 +68,7 @@ impl Mat {
         match self {
             Mat::Count(l) => l.index_batch(kmers),
             Mat::Presence(l) => l.index_batch(kmers),
+            Mat::SparsePresence(l) => l.index_batch(kmers),
         }
     }
 
@@ -74,6 +83,7 @@ impl Mat {
         match self {
             Mat::Count(l) => l.iter_minorants_batch(annex, batch_size),
             Mat::Presence(l) => l.iter_minorants_batch(annex, batch_size),
+            Mat::SparsePresence(l) => l.iter_minorants_batch(annex, batch_size),
         }
     }
 
@@ -81,6 +91,7 @@ impl Mat {
         match self {
             Mat::Count(l) => l.n_cols(),
             Mat::Presence(l) => l.n_cols(),
+            Mat::SparsePresence(l) => l.n_cols(),
         }
     }
 
@@ -100,6 +111,7 @@ impl Mat {
     pub(super) fn fill_sub_matrix_carries(&self, slots: &[usize], out: &mut [Vec<bool>]) {
         match self {
             Mat::Presence(l) => l.fill_sub_matrix(slots, out),
+            Mat::SparsePresence(l) => l.fill_sub_matrix(slots, out),
             Mat::Count(l) => {
                 let mut counts: Vec<Vec<u32>> = out.iter().map(|_| Vec::new()).collect();
                 l.fill_sub_matrix(slots, &mut counts);
@@ -145,8 +157,16 @@ impl PartitionCache {
                 for l in 0..meta.n_layers {
                     let layer_dir = index_dir.join(format!("layer_{l}"));
                     let use_counts = with_counts && layer_dir.join("counts").exists();
+                    // `pack --sparse` converts a layer's `presence/` directory
+                    // in place, leaving `is_multi.prsb` as the on-disk marker
+                    // that distinguishes the sparse format
+                    // (`obicompactvec::PersistentSparseBitMatrix`) from the
+                    // dense one — see `bitmatrix/sparse.rs`'s module docs.
+                    let is_sparse = layer_dir.join("presence").join("is_multi.prsb").exists();
                     let mat = if use_counts {
                         Layer::<PersistentCompactIntMatrix>::open(&layer_dir, &meta.mode).ok().map(Mat::Count)
+                    } else if is_sparse {
+                        Layer::<PersistentSparseBitMatrix>::open(&layer_dir, &meta.mode).ok().map(Mat::SparsePresence)
                     } else {
                         Layer::<PersistentBitMatrix>::open(&layer_dir, &meta.mode).ok().map(Mat::Presence)
                     };
diff --git a/src/obikphylo/src/siblings/tests.rs b/src/obikphylo/src/siblings/tests.rs
index 513316ca..9979678c 100644
--- a/src/obikphylo/src/siblings/tests.rs
+++ b/src/obikphylo/src/siblings/tests.rs
@@ -148,6 +148,47 @@ fn sibling_annex_one_sibling_each() {
     assert!(!b.is_minorant(), "g2's stored minorant flag should not be set");
 }
 
+#[test]
+fn sibling_annex_works_after_pack_sparse() {
+    // Same fixture as `sibling_annex_one_sibling_each`, but with
+    // `pack --sparse` (`KmerIndex::pack_matrices(true)`) run on the merged
+    // index before building the sibling annex — proves `PartitionCache`'s
+    // sparse-detection (`Mat::SparsePresence`, gated on `presence/
+    // is_multi.prsb`) and the generic `Layer<D>` methods it relies on
+    // actually round-trip through the real build pipeline, not just the
+    // unit-level `Layer<PersistentSparseBitMatrix>` tests in
+    // `obilayeredmap`.
+    let dir = tempdir().unwrap();
+    let g1 = build_single_genome_index(dir.path(), "g1", b"AACCGCTTAAG");
+    let g2 = build_single_genome_index(dir.path(), "g2", b"AACCGGTTAAG");
+    let merged = merge_two(dir.path(), &g1, &g2);
+    merged.pack_matrices(true).expect("pack_matrices(sparse)");
+
+    let index_dir = merged.partition().part_dir(0).join(INDEX_SUBDIR);
+    assert!(
+        index_dir.join("layer_0").join("presence").join("is_multi.prsb").exists(),
+        "pack_matrices(true) must leave the sparse marker file behind"
+    );
+
+    merged.build_sibling_annex().expect("build_sibling_annex");
+
+    let g1_kmer = canonical(b"AACCGCTTAAG");
+    let g2_kmer = canonical(b"AACCGGTTAAG");
+    let expected_mask = FamilyMask::EMPTY.with(1).with(2);
+
+    let a = annex_info_for(&merged, g1_kmer);
+    assert_eq!(a.bits(), expected_mask.bits(), "AACCGCTTAAG");
+    assert_eq!(a.siblings(), 1);
+    assert!(is_minorant(g1_kmer, a, K), "g1 should be the minorant");
+    assert!(a.is_minorant(), "g1's stored minorant flag should be set at build time");
+
+    let b = annex_info_for(&merged, g2_kmer);
+    assert_eq!(b.bits(), expected_mask.bits(), "AACCGGTTAAG");
+    assert_eq!(b.siblings(), 1);
+    assert!(!is_minorant(g2_kmer, b, K), "g2 should not be the minorant");
+    assert!(!b.is_minorant(), "g2's stored minorant flag should not be set");
+}
+
 #[test]
 fn sibling_annex_zero_siblings_when_identical_and_no_variant_exists() {
     // Same k-mer in both genomes, no other genome around to carry a
diff --git a/src/obilayeredmap/src/layer.rs b/src/obilayeredmap/src/layer.rs
index d50fd7b8..4aa86365 100644
--- a/src/obilayeredmap/src/layer.rs
+++ b/src/obilayeredmap/src/layer.rs
@@ -3,8 +3,10 @@ use std::fs;
 use std::path::Path;
 
 use obicompactvec::{
+    BinaryMatrix,
     PersistentBitMatrix, PersistentBitMatrixBuilder,
     PersistentCompactIntMatrix, PersistentCompactIntMatrixBuilder,
+    PersistentSparseBitMatrix,
 };
 use obikseq::CanonicalKmer;
 use obiskio::{UnitigFileReader, UnitigFileWriter};
@@ -47,6 +49,14 @@ impl LayerData for PersistentBitMatrix {
     fn read(&self, slot: usize) -> Box<[bool]> { self.row(slot) }
 }
 
+impl LayerData for PersistentSparseBitMatrix {
+    type Item = Box<[bool]>;
+    fn open(layer_dir: &Path) -> OLMResult<Self> {
+        PersistentSparseBitMatrix::open(&layer_dir.join(PRESENCE_DIR)).map_err(OLMError::Io)
+    }
+    fn read(&self, slot: usize) -> Box<[bool]> { self.row(slot) }
+}
+
 // ── Structures ────────────────────────────────────────────────────────────────
 
 pub struct Layer<D: LayerData = ()> {
@@ -223,15 +233,18 @@ impl Layer<PersistentCompactIntMatrix> {
 
 // ── Mode 3 — presence/absence matrix ─────────────────────────────────────────
 
-impl Layer<PersistentBitMatrix> {
-    pub fn append_genome_column(
-        layer_dir: &Path,
-        value_of: impl Fn(usize) -> bool,
-    ) -> OLMResult<()> {
-        PersistentBitMatrix::append_column(&layer_dir.join(PRESENCE_DIR), value_of)
-            .map_err(OLMError::Io)
-    }
-
+// ── Mode 3 — presence/absence matrix, generic over dense/sparse storage ──────
+//
+// `n_cols`/`sub_matrix`/`fill_sub_matrix` are identical in shape for any
+// `D` satisfying `BinaryMatrix` — genuinely generic (not just two
+// near-identical impl blocks) so `Layer<PersistentSparseBitMatrix>` gets
+// them for free, matching `Layer<PersistentBitMatrix>` at the same call
+// sites (see `obikphylo::siblings::cache::Mat`). Construction
+// (`append_genome_column`/`build_presence`) stays `PersistentBitMatrix`-only
+// below: sparse matrices aren't built column-by-column, they're built
+// row-by-row from an already-built dense layer
+// (`PersistentSparseBitMatrixBuilder::build_from_dense`).
+impl<D: LayerData<Item = Box<[bool]>> + BinaryMatrix> Layer<D> {
     /// Number of genome columns in this layer's presence matrix — see
     /// `PersistentBitMatrix::n_cols`'s docs for the `Implicit` mono-genome
     /// special case (always reports `1`, regardless of the index's real
@@ -244,7 +257,9 @@ impl Layer<PersistentBitMatrix> {
     ///
     /// Returns a column-first `Vec<Vec<bool>>`: one inner `Vec` per genome
     /// column, containing the presence bits for the requested slots in order.
-    /// Column access is sequential for cache efficiency.
+    /// Column access is sequential for cache efficiency on the dense
+    /// storage — on sparse storage it's a naive row-by-row decode, see
+    /// `docmd/architecture/siblings.md`'s sparse-matrix section.
     pub fn sub_matrix(&self, slots: &[usize]) -> Vec<Vec<bool>> {
         self.data.sub_matrix(slots)
     }
@@ -258,6 +273,16 @@ impl Layer<PersistentBitMatrix> {
     pub fn fill_sub_matrix(&self, slots: &[usize], out: &mut [Vec<bool>]) {
         self.data.fill_sub_matrix(slots, out)
     }
+}
+
+impl Layer<PersistentBitMatrix> {
+    pub fn append_genome_column(
+        layer_dir: &Path,
+        value_of: impl Fn(usize) -> bool,
+    ) -> OLMResult<()> {
+        PersistentBitMatrix::append_column(&layer_dir.join(PRESENCE_DIR), value_of)
+            .map_err(OLMError::Io)
+    }
 
     pub fn build_presence(
         out_dir: &Path,
diff --git a/src/obilayeredmap/src/tests/layer.rs b/src/obilayeredmap/src/tests/layer.rs
index 3ae37376..033e819d 100644
--- a/src/obilayeredmap/src/tests/layer.rs
+++ b/src/obilayeredmap/src/tests/layer.rs
@@ -1,5 +1,6 @@
 use super::*;
-use obikseq::{set_k, Kmer, Sequence as _, Unitig};
+use obicompactvec::PersistentSparseBitMatrixBuilder;
+use obikseq::{set_k, Unitig};
 use obiskio::DEFAULT_BLOCK_BITS;
 use tempfile::tempdir;
 
@@ -42,6 +43,61 @@ fn canonical_kmer_iter_matches_reader() {
     assert_eq!(from_iter, from_reader, "CanonicalKmerIter and UnitigFileReader disagree");
 }
 
+// ── Generic `Layer<D>` over dense vs. sparse presence storage ───────────────
+
+#[test]
+fn presence_layer_generic_over_sparse_matches_dense() {
+    // k=4, matching every other test in this crate's binary: `K`/`M` are
+    // process-wide (not thread-local) in test builds — see
+    // `obikseq::params` — so a test using a different k here would race
+    // against `map.rs`'s k=4 tests running concurrently in the same
+    // binary. These three sequences were chosen (randomised search) to
+    // have no shared canonical 4-mer among them, required for `ptr_hash`
+    // MPHF construction (duplicate keys make it panic).
+    set_k(4);
+    let dir = tempdir().unwrap();
+    write_unitigs(dir.path(), &[b"AAATCTA", b"CTTCGCC", b"TGATACG"]);
+    let n_genomes = 3;
+    let mode = IndexMode::Exact;
+
+    // Deterministic, arbitrary presence function — genome `g` carries a
+    // kmer iff `(kmer's raw bits + g)` is even. Doesn't need to be
+    // biologically meaningful, just the same on both sides of the
+    // dense/sparse comparison below.
+    Layer::<PersistentBitMatrix>::build_presence(dir.path(), DEFAULT_BLOCK_BITS, &mode, n_genomes, |kmer, g| {
+        (kmer.raw().wrapping_add(g as u64)) % 2 == 0
+    }).unwrap();
+
+    let dense_layer = Layer::<PersistentBitMatrix>::open(dir.path(), &mode).unwrap();
+    assert!(dense_layer.n_cols() >= 1);
+
+    // Build the sparse form directly into the same `presence/` dir the
+    // dense form already lives in (matches how `pack --sparse` will work:
+    // same directory, distinct filenames — see
+    // `docmd/architecture/siblings.md`'s sparse-matrix section).
+    let dense_matrix = obicompactvec::PersistentBitMatrix::open(dir.path()).unwrap();
+    PersistentSparseBitMatrixBuilder::build_from_dense(&dense_matrix, &dir.path().join(PRESENCE_DIR))
+        .unwrap()
+        .close()
+        .unwrap();
+
+    let sparse_layer = Layer::<PersistentSparseBitMatrix>::open(dir.path(), &mode).unwrap();
+
+    // Same generic methods, same results, different concrete `D`.
+    assert_eq!(dense_layer.n_cols(), sparse_layer.n_cols());
+    let n = dense_layer.n();
+    assert_eq!(n, sparse_layer.n());
+    let slots: Vec<usize> = (0..n).collect();
+    assert_eq!(dense_layer.sub_matrix(&slots), sparse_layer.sub_matrix(&slots));
+
+    // The matrix-agnostic, MPHF-only surface (from the generic
+    // `impl<D: LayerData> Layer<D>`) must also agree: same kmer set,
+    // looked up through either concrete `D`.
+    for kmer in all_canonical_kmers(dir.path()) {
+        assert_eq!(dense_layer.find_slot(kmer), sparse_layer.find_slot(kmer));
+    }
+}
+
 #[test]
 fn enumerate_kmers_is_stable_across_calls() {
     set_k(4);
-- 
2.54.0


From 53c40b7a53fcec65909d014812000cfba591bf30 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Sat, 15 Aug 2026 19:45:08 +0200
Subject: [PATCH 35/46] refactor: format tnt script generation and add tree
 export commands

Reworks `writeln!` macro invocations to multi-line syntax and adjusts whitespace for improved readability. Additionally, appends four commands to the generated phylogenetic script to explicitly export trees and manage taxon naming at runtime.
---
 src/obikmer/src/cmd/phylo/tnt.rs | 89 ++++++++++++++++++++++++++------
 1 file changed, 73 insertions(+), 16 deletions(-)

diff --git a/src/obikmer/src/cmd/phylo/tnt.rs b/src/obikmer/src/cmd/phylo/tnt.rs
index a4be379f..c3c13a08 100644
--- a/src/obikmer/src/cmd/phylo/tnt.rs
+++ b/src/obikmer/src/cmd/phylo/tnt.rs
@@ -30,7 +30,8 @@ pub(super) fn write_sankoff_tnt(
     cost_scale: f64,
     free_loss: bool,
 ) {
-    let path = output.as_ref()
+    let path = output
+        .as_ref()
         .map(|p| format!("{}_sankoff.tnt", p.display()))
         .unwrap_or_else(|| "sankoff.tnt".into());
     let mut f = BufWriter::new(std::fs::File::create(&path).unwrap_or_else(|e| {
@@ -45,7 +46,11 @@ pub(super) fn write_sankoff_tnt(
 
     let n_sites = alignment.sequences.first().map(|s| s.len()).unwrap_or(0);
     writeln!(f, "xread").unwrap();
-    writeln!(f, "'obikmer central-position SNP families, calibrated Sankoff 16-state encoding'").unwrap();
+    writeln!(
+        f,
+        "'obikmer central-position SNP families, calibrated Sankoff 16-state encoding'"
+    )
+    .unwrap();
     writeln!(f, "{n_sites} {}", labels.len()).unwrap();
     for (label, seq) in labels.iter().zip(alignment.sequences.iter()) {
         write!(f, "{label} ").unwrap();
@@ -70,7 +75,12 @@ pub(super) fn write_sankoff_tnt(
     writeln!(f, "smatrix =0 (family16)").unwrap();
     for i in 0..16 {
         for j in (i + 1)..16 {
-            writeln!(f, "{}/{} {}", TNT_STATE_SYMBOL[i], TNT_STATE_SYMBOL[j], scaled_matrix[i][j]).unwrap();
+            writeln!(
+                f,
+                "{}/{} {}",
+                TNT_STATE_SYMBOL[i], TNT_STATE_SYMBOL[j], scaled_matrix[i][j]
+            )
+            .unwrap();
         }
     }
     writeln!(f, ";\n").unwrap();
@@ -83,7 +93,8 @@ pub(super) fn write_sankoff_tnt(
     // workflow is to `cd` into the output directory before `proc`-ing the
     // script, and an absolute path here would break if that directory is
     // later moved or copied elsewhere.
-    let tre_name = output.as_ref()
+    let tre_name = output
+        .as_ref()
         .and_then(|p| p.file_name())
         .map(|n| format!("{}_sankoff.tre", n.to_string_lossy()))
         .unwrap_or_else(|| "sankoff.tre".into());
@@ -97,21 +108,67 @@ pub(super) fn write_sankoff_tnt(
     // defaults below when the script is run. `;` ends a `quote` block like
     // any other TNT command, so the text itself must avoid semicolons.
     writeln!(f, "quote").unwrap();
-    writeln!(f, "Default search below (edit or delete this block to run your own strategy):").unwrap();
-    writeln!(f, "  hold N     : size of TNT's tree buffer (how many equally-parsimonious").unwrap();
-    writeln!(f, "               trees it keeps in memory at once), 20 is a small, fast").unwrap();
-    writeln!(f, "               default, raise it if mult reports it had to drop trees.").unwrap();
-    writeln!(f, "  mult       : traditional search (random addition sequences followed by").unwrap();
-    writeln!(f, "               TBR branch-swapping, TNT's own default replication count),").unwrap();
-    writeln!(f, "               a reasonable first-pass strategy on this data's memory").unwrap();
-    writeln!(f, "               footprint, xmult's ratchet/drift/tree-fusion buffers ran").unwrap();
-    writeln!(f, "               this out of RAM at TNT's default mxram on this dataset.").unwrap();
-    writeln!(f, "  export - F : write the trees held in the buffer to file F, in").unwrap();
-    writeln!(f, "               TNT/Hennig86 format ('-' means trees, as opposed to data).").unwrap();
+    writeln!(
+        f,
+        "Default search below (edit or delete this block to run your own strategy):"
+    )
+    .unwrap();
+    writeln!(
+        f,
+        "  hold N     : size of TNT's tree buffer (how many equally-parsimonious"
+    )
+    .unwrap();
+    writeln!(
+        f,
+        "               trees it keeps in memory at once), 20 is a small, fast"
+    )
+    .unwrap();
+    writeln!(
+        f,
+        "               default, raise it if mult reports it had to drop trees."
+    )
+    .unwrap();
+    writeln!(
+        f,
+        "  mult       : traditional search (random addition sequences followed by"
+    )
+    .unwrap();
+    writeln!(
+        f,
+        "               TBR branch-swapping, TNT's own default replication count),"
+    )
+    .unwrap();
+    writeln!(
+        f,
+        "               a reasonable first-pass strategy on this data's memory"
+    )
+    .unwrap();
+    writeln!(
+        f,
+        "               footprint, xmult's ratchet/drift/tree-fusion buffers ran"
+    )
+    .unwrap();
+    writeln!(
+        f,
+        "               this out of RAM at TNT's default mxram on this dataset."
+    )
+    .unwrap();
+    writeln!(
+        f,
+        "  export - F : write the trees held in the buffer to file F, in"
+    )
+    .unwrap();
+    writeln!(
+        f,
+        "               TNT/Hennig86 format ('-' means trees, as opposed to data)."
+    )
+    .unwrap();
     writeln!(f, ";").unwrap();
     writeln!(f, "hold 20;").unwrap();
     writeln!(f, "mult;").unwrap();
-    writeln!(f, "export - {tre_name};").unwrap();
+    writeln!(f, "taxname =;").unwrap();
+    writeln!(f, "tsave * {tre_name};").unwrap();
+    writeln!(f, "tsave /;").unwrap();
 
     info!(
         "TNT script → {path} (costs scaled x{cost_scale:.0}, runs a default `hold 20; mult;` \
-- 
2.54.0


From 49e66f16a221ebc7cc90a53e0cba7a0c0fc72a31 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Sat, 15 Aug 2026 20:15:43 +0200
Subject: [PATCH 36/46] docs: document architecture analysis and refactoring
 plans for siblings

Documents architectural analysis, identified performance bottlenecks including hardcoded selection flags and redundant full-index scans causing I/O-bound stalls. Details planned pipeline refactoring to unify stages around a single shared selection for a fused single-pass scan, noting future dependencies on entropy-biased family selection.
---
 docmd/architecture/siblings.md | 66 ++++++++++++++++++++++++++++++++++
 1 file changed, 66 insertions(+)

diff --git a/docmd/architecture/siblings.md b/docmd/architecture/siblings.md
index 2a7d26c6..a69a25ed 100644
--- a/docmd/architecture/siblings.md
+++ b/docmd/architecture/siblings.md
@@ -389,6 +389,72 @@ undermining the point. It stays plausible as a coarse filter for the
 predicts low true entropy too), but not as a stand-in for the high tail —
 not pursued further for now.
 
+## `--free-loss`/`--tnt` pipeline: four independent scans, three of them unsampled (found 2026-08-15, not yet fixed)
+
+Measured on `phyloskims_sal_vac` (91 genomes): `obikmer phylo --subsample 500000
+--free-loss --tnt` logs four sequential stages —
+`raw_snp_distance` (1413s), `base_pair_tally` (1456s),
+`cardinality_tally` (2078s), `snp_pseudo_alignment` (143s). Reading the
+code (`obikmer/src/cmd/phylo/mod.rs:210-242`,
+`obikphylo/src/siblings/distance.rs`, `cardinality.rs`, `alignment.rs`)
+surfaced two compounding problems, not one:
+
+1. **Four separate full scans of the annex**, each opening its own
+   `KmerPartition`/`PartitionCache` and calling `scan_family_pairs`/
+   `scan_layer_families` independently — nothing computed in one stage is
+   reused by another. `base_pair_tally` is explicitly documented
+   (`distance.rs:138-143`) as a second full pass over the same
+   traversal `raw_snp_distance` already did, needed only because
+   `raw_snp_distance` doesn't keep the resolved bases, only aggregate
+   counts. `cardinality_tally` and `snp_pseudo_alignment` are each a
+   third and fourth independent full pass. Per the module's own earlier
+   profiling note (`family_scan.rs:26-28`, cited already above), this
+   traversal is page-fault/mmap-bound, not compute-bound — the ~10-12%
+   CPU efficiency ("contention" status) observed on these three slow
+   stages is consistent with I/O stalls scaled by repeated full scans,
+   not lock contention (there are no `Mutex`/`RwLock` anywhere in
+   `siblings/*.rs`; shared writes use per-slot `AtomicU8::fetch_or`).
+2. **Worse: `raw_snp_distance` and `cardinality_tally` don't honor
+   `--subsample` at all** — both call `scan_layer_families` with
+   `Selection::All` hardcoded, and `args.subsample` isn't even threaded
+   into their function signatures (`mod.rs:212`, `mod.rs:226`). Only
+   `snp_pseudo_alignment(args.subsample)` builds a real reservoir-sampled
+   `Selection::Some(set)` (via `compute_selections`, `alignment.rs:89`).
+   So today, `--subsample 500000` only bounds the pseudo-alignment step —
+   the SNP-distance matrix, the Sankoff base-pair calibration, and the
+   cardinality histogram are always computed over the **full, unsampled**
+   index regardless of the flag. This is not merely "different subsamples
+   per stage" (which would already be a problem worth fixing) — it's that
+   three of the four stages never subsample, which explains most of the
+   ~10x runtime gap against `snp_pseudo_alignment` on its own.
+
+**Decided requirement (2026-08-15, not yet implemented)**: all four
+stages must consume **one shared selection**, computed once, not each
+stage either scanning everything or drawing its own independent sample.
+Per-genome-pair SNP counts, the Sankoff base-pair calibration, the
+cardinality histogram, and the pseudo-alignment must all describe the
+same set of families — otherwise the calibration and the alignment it's
+meant to calibrate aren't even guaranteed to agree on which sites exist.
+Once selection is unified, doing four independent full scans stops making
+sense on its own terms: a single pass over the shared selection can feed
+all four accumulators (SNP/shared counts, base-pair tally, cardinality
+tally, pseudo-alignment output) at once, which is also the fix for
+problem 1 above — the two issues turn out to be one architectural
+decision, not two.
+
+**Forward-looking complication, explicitly flagged**: the eventual plan
+is to bias family *selection itself* by entropy15 (favor the informative
+mid-entropy band over uniform reservoir sampling — the exact motivation
+behind "Cheap entropy pre-filtering" above). That means selection can no
+longer be an uninformed draw made *during* the single fused scan; entropy
+(exact or a cheap proxy) has to be known *before* selection happens,
+which argues for a first, cheap, entropy-informed selection pass followed
+by one fused, unsampled-relative-to-that-selection scan — tying this
+decision directly to the still-unresolved marginal-proxy limitation
+described in "Cheap entropy pre-filtering" above (which only reliably
+predicts the *low*-entropy tail, not the high one — a real gap, not
+solved by this note, if entropy-biased selection ships before it is).
+
 ## Two entropy definitions kept side by side, for comparison (2026-08-15)
 
 `--shannon`'s CSV carries both `entropy15` (`family_entropy` — the settled
-- 
2.54.0


From 7bac0f385011e3ef26f5f1332aa6152f4e0cfa69 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Sat, 15 Aug 2026 20:56:29 +0200
Subject: [PATCH 37/46] large refactoring

---
 CLAUDE.md                                     |   34 +-
 DevDoc/404.html                               | 1219 +++
 {doc => DevDoc}/apa.csl                       |    0
 .../index_architecture.refs/index.html        |  251 +-
 .../index_architecture/index.html             |  253 +-
 .../numa_partition_runner/index.html          | 1863 +++++
 .../architecture/numa_worker_pools/index.html | 1593 ++++
 .../architecture/query.refs/index.html        |  251 +-
 DevDoc/architecture/query/index.html          | 1939 +++++
 DevDoc/architecture/rebuild_filter/index.html | 1460 ++++
 .../sequences/invariant.refs/index.html       |  251 +-
 .../sequences/invariant/index.html            |  253 +-
 DevDoc/architecture/siblings/index.html       | 2365 ++++++
 DevDoc/assets/images/favicon.png              |  Bin 0 -> 1870 bytes
 .../assets/javascripts/bundle.79ae519e.min.js |   16 +
 .../javascripts/bundle.79ae519e.min.js.map    |    7 +
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 rename {docmd => DevDocMD}/theory/encoding.md (100%)
 rename {docmd => DevDocMD}/theory/encoding.refs.md (100%)
 rename {docmd => DevDocMD}/theory/entropy.md (100%)
 rename {docmd => DevDocMD}/theory/entropy.refs.md (100%)
 rename {docmd => DevDocMD}/theory/evolutionary_distances.md (100%)
 rename {docmd => DevDocMD}/theory/indexing.md (100%)
 rename {docmd => DevDocMD}/theory/indexing.refs.md (100%)
 rename {docmd => DevDocMD}/theory/minimizer.md (100%)
 rename {docmd => DevDocMD}/theory/minimizer.refs.md (100%)
 rename {docmd => DevDocMD}/vancouver.csl (100%)
 create mode 100644 doc/architecture/index.html
 delete mode 100644 doc/architecture/query/index.html
 create mode 100644 doc/formats/index_layout/index.html
 create mode 100644 doc/installation/index.html
 create mode 100644 doc/theory/entropy_filter/index.html
 create mode 100644 doc/theory/indexing_architecture/index.html
 create mode 100644 doc/theory/kmers_and_superkmers/index.html
 create mode 100644 doc/theory/minimizer_selection/index.html
 create mode 100644 doc/usage/annotate/index.html
 create mode 100644 doc/usage/dump/index.html
 create mode 100644 doc/usage/estimate/index.html
 create mode 100644 doc/usage/filter/index.html
 create mode 100644 doc/usage/index_command/index.html
 create mode 100644 doc/usage/merge/index.html
 create mode 100644 doc/usage/name-tree/index.html
 create mode 100644 doc/usage/pack/index.html
 create mode 100644 doc/usage/phylo/index.html
 create mode 100644 doc/usage/predicates/index.html
 create mode 100644 doc/usage/query/index.html
 create mode 100644 doc/usage/reindex/index.html
 create mode 100644 doc/usage/select/index.html
 create mode 100644 doc/usage/superkmer/index.html
 create mode 100644 doc/usage/unitig/index.html
 create mode 100644 doc/usage/utils/index.html
 create mode 100644 src/obikphylo/src/siblings/entropy_annex.rs
 create mode 100644 src/obikphylo/src/siblings/sankoff_bundle.rs

diff --git a/CLAUDE.md b/CLAUDE.md
index c6cac5a4..aa836553 100644
--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -12,8 +12,8 @@ Si une dépendance demandée pose problème (erreur de compilation, bug, API man
 Quand une nouvelle construction (type, itérateur, abstraction) rend du code historique injustifié, le signaler immédiatement et proposer de le supprimer — ne pas conserver les deux en parallèle par inertie. Le développeur demande explicitement de remettre en cause le code base : ne pas attendre qu'il insiste.
 
 Tu maintiens en **anglais**, dense et sans remplissage, les documents suivants :
-- `docmd/index.md` — document de discussion de base, enrichi progressivement au fil de nos échanges ; il reflète l'état courant de la réflexion sur le projet
-- les autres fichiers Markdown dans `docmd/` selon leur thème respectif
+- `DevDocMD/index.md` — document de discussion de base, enrichi progressivement au fil de nos échanges ; il reflète l'état courant de la réflexion sur le projet
+- les autres fichiers Markdown dans `DevDocMD/` selon leur thème respectif
 
 Les snippets de code y sont courts et illustrent uniquement des principes architecturaux. Nos échanges se font en **français**.
 
@@ -42,33 +42,35 @@ Les snippets de code y sont courts et illustrent uniquement des principes archit
 
 ## Infrastructure de documentation
 
-La documentation est gérée via **MkDocs + thème Material**, avec publication sur **GitHub Pages**.
+La documentation est gérée via **MkDocs + thème Material**, avec publication sur **GitHub Pages**. Deux arbres de documentation indépendants, deux configurations à la racine du dépôt (voir aussi `UserDocMD/` ci-dessous pour la doc utilisateur) :
 
 **Structure des répertoires**
 
 ```
-docmd/          ← sources Markdown + mkdocs.yml
-docmd/mkdocs.yml
-doc/            ← site HTML généré (servi par GitHub Pages)
+DevDocMD/       ← sources Markdown, doc développeur (discussion, historique, rationale)
+UserDocMD/      ← sources Markdown, doc utilisateur (état factuel courant, sans code Rust)
+mkdocs.yml      ← config doc développeur : docs_dir DevDocMD, site_dir DevDoc
+mkdocs-user.yml ← config doc utilisateur : docs_dir UserDocMD, site_dir doc
+DevDoc/         ← site HTML généré (doc développeur)
+doc/            ← site HTML généré (doc utilisateur — publié par GitHub Pages, répertoire par défaut)
 .venv/          ← environnement Python (ignoré par git)
 ```
 
-**Configuration `docmd/mkdocs.yml`**
-- `docs_dir: .` (sources = `docmd/` lui-même)
-- `site_dir: ../doc` (sortie = `doc/`)
-
 **Commandes Makefile**
 
 | Commande | Effet |
 |---|---|
-| `make doc` | Construit le HTML dans `doc/` |
-| `make doc-serve` | Serveur local avec rechargement automatique |
-| `make clean-doc` | Supprime `doc/` |
-| `make clean` | Supprime `doc/` et `.venv/` |
+| `make doc` | Construit la doc développeur dans `DevDoc/` |
+| `make doc-serve` | Serveur local (doc développeur), rechargement automatique |
+| `make clean-doc` | Supprime `DevDoc/` |
+| `make doc-user` | Construit la doc utilisateur dans `doc/` |
+| `make doc-user-serve` | Serveur local (doc utilisateur), rechargement automatique |
+| `make clean-doc-user` | Supprime `doc/` |
+| `make clean` | Supprime `DevDoc/`, `doc/` et `.venv/` |
 
-Le `.venv/` est dans `.gitignore`. Le répertoire `doc/` (sortie HTML) est versionné pour GitHub Pages.
+Le `.venv/` est dans `.gitignore`. `DevDoc/` et `doc/` (sorties HTML) sont versionnés — `doc/` spécifiquement parce que c'est le répertoire par défaut que GitHub Pages sert.
 
-Lors de l'ajout de nouveaux fichiers Markdown dans `docmd/`, mettre à jour la section `nav:` de `docmd/mkdocs.yml`.
+Lors de l'ajout de nouveaux fichiers Markdown dans `DevDocMD/`, mettre à jour la section `nav:` de `mkdocs.yml` ; dans `UserDocMD/`, mettre à jour `mkdocs-user.yml`.
 
 ---
 
diff --git a/DevDoc/404.html b/DevDoc/404.html
new file mode 100644
index 00000000..54445983
--- /dev/null
+++ b/DevDoc/404.html
@@ -0,0 +1,1219 @@
+
+<!doctype html>
+<html lang="en" class="no-js">
+  <head>
+    
+      <meta charset="utf-8">
+      <meta name="viewport" content="width=device-width,initial-scale=1">
+      
+      
+      
+      
+      
+      
+        
+      
+      
+      <link rel="icon" href="/assets/images/favicon.png">
+      <meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.7.6">
+    
+    
+      
+        <title>obikmer</title>
+      
+    
+    
+      <link rel="stylesheet" href="/assets/stylesheets/main.484c7ddc.min.css">
+      
+      
+
+
+    
+    
+      
+    
+    
+      
+        
+        
+        <link rel="preconnect" href="https://fonts.gstatic.com" crossorigin>
+        <link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Roboto:300,300i,400,400i,700,700i%7CRoboto+Mono:400,400i,700,700i&display=fallback">
+        <style>:root{--md-text-font:"Roboto";--md-code-font:"Roboto Mono"}</style>
+      
+    
+    
+    <script>__md_scope=new URL("/",location),__md_hash=e=>[...e].reduce(((e,_)=>(e<<5)-e+_.charCodeAt(0)),0),__md_get=(e,_=localStorage,t=__md_scope)=>JSON.parse(_.getItem(t.pathname+"."+e)),__md_set=(e,_,t=localStorage,a=__md_scope)=>{try{t.setItem(a.pathname+"."+e,JSON.stringify(_))}catch(e){}}</script>
+    
+      
+
+    
+    
+  </head>
+  
+  
+    <body dir="ltr">
+  
+    
+    <input class="md-toggle" data-md-toggle="drawer" type="checkbox" id="__drawer" autocomplete="off">
+    <input class="md-toggle" data-md-toggle="search" type="checkbox" id="__search" autocomplete="off">
+    <label class="md-overlay" for="__drawer"></label>
+    <div data-md-component="skip">
+      
+    </div>
+    <div data-md-component="announce">
+      
+    </div>
+    
+    
+      
+
+  
+
+<header class="md-header md-header--shadow" data-md-component="header">
+  <nav class="md-header__inner md-grid" aria-label="Header">
+    <a href="/." title="obikmer" class="md-header__button md-logo" aria-label="obikmer" data-md-component="logo">
+      
+  
+  <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M12 8a3 3 0 0 0 3-3 3 3 0 0 0-3-3 3 3 0 0 0-3 3 3 3 0 0 0 3 3m0 3.54C9.64 9.35 6.5 8 3 8v11c3.5 0 6.64 1.35 9 3.54 2.36-2.19 5.5-3.54 9-3.54V8c-3.5 0-6.64 1.35-9 3.54"/></svg>
+
+    </a>
+    <label class="md-header__button md-icon" for="__drawer">
+      
+      <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M3 6h18v2H3zm0 5h18v2H3zm0 5h18v2H3z"/></svg>
+    </label>
+    <div class="md-header__title" data-md-component="header-title">
+      <div class="md-header__ellipsis">
+        <div class="md-header__topic">
+          <span class="md-ellipsis">
+            obikmer
+          </span>
+        </div>
+        <div class="md-header__topic" data-md-component="header-topic">
+          <span class="md-ellipsis">
+            
+              
+            
+          </span>
+        </div>
+      </div>
+    </div>
+    
+    
+      <script>var palette=__md_get("__palette");if(palette&&palette.color){if("(prefers-color-scheme)"===palette.color.media){var media=matchMedia("(prefers-color-scheme: light)"),input=document.querySelector(media.matches?"[data-md-color-media='(prefers-color-scheme: light)']":"[data-md-color-media='(prefers-color-scheme: dark)']");palette.color.media=input.getAttribute("data-md-color-media"),palette.color.scheme=input.getAttribute("data-md-color-scheme"),palette.color.primary=input.getAttribute("data-md-color-primary"),palette.color.accent=input.getAttribute("data-md-color-accent")}for(var[key,value]of Object.entries(palette.color))document.body.setAttribute("data-md-color-"+key,value)}</script>
+    
+    
+    
+    
+  </nav>
+  
+</header>
+    
+    <div class="md-container" data-md-component="container">
+      
+      
+        
+          
+        
+      
+      <main class="md-main" data-md-component="main">
+        <div class="md-main__inner md-grid">
+          
+            
+              
+              <div class="md-sidebar md-sidebar--primary" data-md-component="sidebar" data-md-type="navigation" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+
+
+<nav class="md-nav md-nav--primary" aria-label="Navigation" data-md-level="0">
+  <label class="md-nav__title" for="__drawer">
+    <a href="/." title="obikmer" class="md-nav__button md-logo" aria-label="obikmer" data-md-component="logo">
+      
+  
+  <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M12 8a3 3 0 0 0 3-3 3 3 0 0 0-3-3 3 3 0 0 0-3 3 3 3 0 0 0 3 3m0 3.54C9.64 9.35 6.5 8 3 8v11c3.5 0 6.64 1.35 9 3.54 2.36-2.19 5.5-3.54 9-3.54V8c-3.5 0-6.64 1.35-9 3.54"/></svg>
+
+    </a>
+    obikmer
+  </label>
+  
+  <ul class="md-nav__list" data-md-scrollfix>
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/." class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Home
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        
+          
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+            
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Theory
+  
+
+    
+  </span>
+  
+  
+
+            <span class="md-nav__icon md-icon"></span>
+          </label>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            
+  
+    Theory
+  
+
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/kmers/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmers and super-kmers
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/theory/encoding/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    DNA encoding
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/theory/entropy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Entropy filter
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/theory/minimizer/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Minimizer selection
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/theory/indexing/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Partitioning architecture
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        
+          
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+            
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Implementation
+  
+
+    
+  </span>
+  
+  
+
+            <span class="md-nav__icon md-icon"></span>
+          </label>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
+            <span class="md-nav__icon md-icon"></span>
+            
+  
+    Implementation
+  
+
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/implementation/superkmer/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    SuperKmer
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/implementation/kmer/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/implementation/chunkreader/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Chunk reader
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/implementation/pipeline/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Construction pipeline
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/implementation/obipipeline/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obipipeline library
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/implementation/storage/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    On-disk storage
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/implementation/mphf/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    MPHF selection
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/implementation/unitig_evidence/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Unitig evidence encoding
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/implementation/evidence_elimination/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Evidence elimination (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/implementation/obilayeredmap/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obilayeredmap crate
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/implementation/persistent_compact_int_vec/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    PersistentCompactIntVec
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/implementation/persistent_bit_vec/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    PersistentBitVec
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/implementation/merge/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Merge command
+  
+
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rename to DevDoc/architecture/index_architecture/index.html
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+++ b/DevDoc/architecture/index_architecture/index.html
@@ -12,6 +12,8 @@
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+  
+    NUMA-aware partition runner
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diff --git a/DevDoc/architecture/numa_partition_runner/index.html b/DevDoc/architecture/numa_partition_runner/index.html
new file mode 100644
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+  
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+  
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+  
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+    
+  
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+  
+
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+  </span>
+  
+  
+
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+
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+            
+              
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+  
+  
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+      <a href="../../implementation/evidence_elimination/" class="md-nav__link">
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+    
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+
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+  </span>
+  
+  
+
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+
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+            
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+  
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+      <a href="../../implementation/obilayeredmap/" class="md-nav__link">
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+  
+  <span class="md-ellipsis">
+    
+  
+    obilayeredmap crate
+  
+
+    
+  </span>
+  
+  
+
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+  
+
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+            
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+      <a href="../../implementation/persistent_compact_int_vec/" class="md-nav__link">
+        
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+    
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+  
+
+    
+  </span>
+  
+  
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+
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+  
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+  
+  
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+      <a href="../../implementation/merge/" class="md-nav__link">
+        
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+    
+  
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+  
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+  
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+
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+    
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+  
+
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+  </span>
+  
+  
+
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+
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+            
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+  
+  
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+      <a href="../../implementation/filtering/" class="md-nav__link">
+        
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+    
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+  
+
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+  
+  
+
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+
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+      <a href="../../implementation/select/" class="md-nav__link">
+        
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+    
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+  
+
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+  
+  
+
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+
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+      <a href="../../implementation/obitaxonomy/" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
+  
+
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+  
+  
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+  
+
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+  
+  
+    <li class="md-nav__item md-nav__item--active">
+      
+      <input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
+      
+      
+        
+      
+      
+        <label class="md-nav__link md-nav__link--active" for="__toc">
+          
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+          <span class="md-nav__icon md-icon"></span>
+        </label>
+      
+      <a href="./" class="md-nav__link md-nav__link--active">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+      
+        
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+    
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#problem" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Problem
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#unified-model" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Unified model
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#adaptive-mechanism" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Adaptive mechanism
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#proposed-api" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Proposed API
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#migration-examples" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Migration examples
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Migration examples">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#mergers-before-180-lines-of-bespoke-machinery" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        merge.rs (before: ~180 lines of bespoke machinery)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#indexrs-build_layers-before-naive-into_par_iter" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        index.rs build_layers (before: naive into_par_iter)
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#placement" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Placement
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#known-issue-cpu-only-activation-signal-stalls-on-io-bound-stages" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Known issue: CPU-only activation signal stalls on I/O-bound stages
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Known issue: CPU-only activation signal stalls on I/O-bound stages">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#implemented-io-signal-shared-debounce-guard" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Implemented: I/O signal + shared debounce guard
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#known-issue-ramp-up-too-slow-and-confused-with-node-count" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Known issue: ramp-up too slow, and confused with node count
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#open-questions" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Open questions
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+      
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+    
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#problem" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Problem
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#unified-model" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Unified model
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#adaptive-mechanism" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Adaptive mechanism
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#proposed-api" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Proposed API
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#migration-examples" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Migration examples
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Migration examples">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#mergers-before-180-lines-of-bespoke-machinery" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        merge.rs (before: ~180 lines of bespoke machinery)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#indexrs-build_layers-before-naive-into_par_iter" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        index.rs build_layers (before: naive into_par_iter)
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#placement" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Placement
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#known-issue-cpu-only-activation-signal-stalls-on-io-bound-stages" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Known issue: CPU-only activation signal stalls on I/O-bound stages
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Known issue: CPU-only activation signal stalls on I/O-bound stages">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#implemented-io-signal-shared-debounce-guard" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Implemented: I/O signal + shared debounce guard
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#known-issue-ramp-up-too-slow-and-confused-with-node-count" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Known issue: ramp-up too slow, and confused with node count
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#open-questions" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Open questions
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+
+<h1 id="numa-aware-partition-runner">NUMA-aware partition runner</h1>
+<h2 id="problem">Problem</h2>
+<p>All partition-level parallel loops in obikindex currently fall into two
+categories:</p>
+<p><strong>Naive Rayon</strong> — used in <code>build_layers</code>, <code>pack_matrices</code>, <code>dump</code>, <code>select</code>,
+<code>stats</code>, <code>rebuild</code>, <code>reindex</code>:</p>
+<div class="highlight"><pre><span></span><code><span class="p">(</span><span class="mi">0</span><span class="o">..</span><span class="n">n</span><span class="p">).</span><span class="n">into_par_iter</span><span class="p">().</span><span class="n">for_each</span><span class="p">(</span><span class="o">|</span><span class="n">i</span><span class="o">|</span><span class="w"> </span><span class="n">work</span><span class="p">(</span><span class="n">i</span><span class="p">));</span>
+</code></pre></div>
+<p>Threads come from the global Rayon pool with no NUMA awareness.  On
+multi-socket machines this produces cross-socket memory traffic and degrades
+performance super-linearly (see <a href="../numa_worker_pools/">NUMA-aware worker pools</a>).</p>
+<p><strong>Ad-hoc adaptive pool</strong> — used in <code>merge</code>:</p>
+<p>A bespoke implementation with pre-spawned workers, channel-based dispatch, and
+activation control.  It handles NUMA correctly but is not reusable.</p>
+<p>Both cases should be replaced by a single generic mechanism.</p>
+<h2 id="unified-model">Unified model</h2>
+<p>The key insight is that <strong>UMA is just the NUMA case with a single node</strong>.  The
+runner always works the same way: one controller thread per node, each
+independently managing its own workers with the same adaptive logic.  The only
+difference between UMA and NUMA is the number of nodes and whether workers are
+pinned.</p>
+<div class="highlight"><pre><span></span><code>NUMA (k nodes)                    UMA (1 node)
+
+controller-0  controller-1  …     controller-0
+    │               │                  │
+workers[0]     workers[1]         workers[0]
+(pinned)       (pinned)           (global pool)
+    └───────────────┴──────────────────┘
+              shared work queue
+</code></pre></div>
+<p>On each node, the Rayon <code>ThreadPool</code> is pinned to that node's CPUs.
+<code>pool.install()</code> ensures all internal Rayon calls (inside the work function)
+use the node-local pool.  Linux first-touch then places heap allocations in
+local DRAM automatically.</p>
+<p>On UMA the global Rayon pool is used directly — no pinning, no overhead.</p>
+<h2 id="adaptive-mechanism">Adaptive mechanism</h2>
+<p>Each controller follows the same logic regardless of node count:</p>
+<ol>
+<li>Pre-spawn <code>workers_per_node</code> dormant worker threads (blocked on <code>activate_rx</code>).</li>
+<li>Activate the first worker immediately.</li>
+<li>Loop on result channel with a <code>SPAWN_POLL</code> timeout:</li>
+<li>On result: call <code>on_done</code>; check whether to activate the next worker.</li>
+<li>On timeout: same check.</li>
+<li>Activation criterion: <code>should_spawn_worker(active, global_efficiency, prev_efficiency)</code>.</li>
+<li>Drop <code>activate_tx</code> when done — dormant workers exit cleanly.</li>
+</ol>
+<p><strong>Global CPU efficiency</strong> (<code>CpuSample</code>, reads <code>/proc/stat</code> on Linux) is used by
+all controllers — no per-node measurement needed.  The signal is coarser than
+per-node efficiency but correct in practice: if any node saturates memory
+bandwidth, the global efficiency drops and all controllers stop activating
+workers.  Using a standard portable primitive avoids platform-specific CPU
+accounting and keeps the implementation clean.</p>
+<h2 id="proposed-api">Proposed API</h2>
+<div class="highlight"><pre><span></span><code><span class="k">pub</span><span class="w"> </span><span class="k">struct</span><span class="w"> </span><span class="nc">PartitionRunner</span><span class="w"> </span><span class="p">{</span>
+<span class="w">    </span><span class="c1">// One entry per NUMA node; one entry total on UMA.</span>
+<span class="w">    </span><span class="n">nodes</span><span class="p">:</span><span class="w"> </span><span class="nb">Vec</span><span class="o">&lt;</span><span class="n">NodeConfig</span><span class="o">&gt;</span><span class="p">,</span>
+<span class="p">}</span>
+
+<span class="k">struct</span><span class="w"> </span><span class="nc">NodeConfig</span><span class="w"> </span><span class="p">{</span>
+<span class="w">    </span><span class="n">pool</span><span class="p">:</span><span class="w">       </span><span class="nb">Option</span><span class="o">&lt;</span><span class="n">Arc</span><span class="o">&lt;</span><span class="n">rayon</span><span class="p">::</span><span class="n">ThreadPool</span><span class="o">&gt;&gt;</span><span class="p">,</span><span class="w">  </span><span class="c1">// None = global Rayon pool (UMA)</span>
+<span class="w">    </span><span class="n">cpu_ids</span><span class="p">:</span><span class="w">    </span><span class="nb">Vec</span><span class="o">&lt;</span><span class="kt">usize</span><span class="o">&gt;</span><span class="p">,</span><span class="w">                      </span><span class="c1">// empty = no pinning (UMA)</span>
+<span class="w">    </span><span class="n">max_workers</span><span class="p">:</span><span class="w"> </span><span class="kt">usize</span><span class="p">,</span>
+<span class="p">}</span>
+
+<span class="k">impl</span><span class="w"> </span><span class="n">PartitionRunner</span><span class="w"> </span><span class="p">{</span>
+<span class="w">    </span><span class="sd">/// Detect topology and build the runner.</span>
+<span class="w">    </span><span class="sd">/// Returns a single-node runner on UMA / macOS / hwloc failure.</span>
+<span class="w">    </span><span class="k">pub</span><span class="w"> </span><span class="k">fn</span><span class="w"> </span><span class="nf">new</span><span class="p">()</span><span class="w"> </span><span class="p">-&gt;</span><span class="w"> </span><span class="nc">Self</span><span class="p">;</span>
+
+<span class="w">    </span><span class="sd">/// Run `f(i)` for every index in `order`, collecting results.</span>
+<span class="w">    </span><span class="sd">///</span>
+<span class="w">    </span><span class="sd">/// `on_done(i, result, elapsed)` is called under an internal mutex as</span>
+<span class="w">    </span><span class="sd">/// each partition completes — use it for progress bars and aggregation.</span>
+<span class="w">    </span><span class="sd">/// The runner serialises all calls to `on_done` via an internal</span>
+<span class="w">    </span><span class="sd">/// `Arc&lt;Mutex&lt;C&gt;&gt;`, so no `Sync` bound is required on the callback.</span>
+<span class="w">    </span><span class="sd">/// `Send` is required because the Arc clone crosses thread boundaries.</span>
+<span class="w">    </span><span class="sd">///</span>
+<span class="w">    </span><span class="sd">/// Serialisation is free in practice: a partition takes seconds to</span>
+<span class="w">    </span><span class="sd">/// minutes; the callback takes microseconds.  Contention is negligible.</span>
+<span class="w">    </span><span class="sd">///</span>
+<span class="w">    </span><span class="sd">/// Returns the first error from `f`, if any.</span>
+<span class="w">    </span><span class="k">pub</span><span class="w"> </span><span class="k">fn</span><span class="w"> </span><span class="nf">run</span><span class="o">&lt;</span><span class="n">F</span><span class="p">,</span><span class="w"> </span><span class="n">R</span><span class="p">,</span><span class="w"> </span><span class="n">E</span><span class="p">,</span><span class="w"> </span><span class="n">C</span><span class="o">&gt;</span><span class="p">(</span>
+<span class="w">        </span><span class="o">&amp;</span><span class="bp">self</span><span class="p">,</span>
+<span class="w">        </span><span class="n">order</span><span class="p">:</span><span class="w">   </span><span class="kp">&amp;</span><span class="p">[</span><span class="kt">usize</span><span class="p">],</span>
+<span class="w">        </span><span class="n">f</span><span class="p">:</span><span class="w">       </span><span class="nc">F</span><span class="p">,</span>
+<span class="w">        </span><span class="n">on_done</span><span class="p">:</span><span class="w"> </span><span class="nc">C</span><span class="p">,</span>
+<span class="w">    </span><span class="p">)</span><span class="w"> </span><span class="p">-&gt;</span><span class="w"> </span><span class="nb">Result</span><span class="o">&lt;</span><span class="p">(),</span><span class="w"> </span><span class="n">E</span><span class="o">&gt;</span>
+<span class="w">    </span><span class="k">where</span>
+<span class="w">        </span><span class="n">F</span><span class="p">:</span><span class="w"> </span><span class="nb">Fn</span><span class="p">(</span><span class="kt">usize</span><span class="p">)</span><span class="w"> </span><span class="p">-&gt;</span><span class="w"> </span><span class="nb">Result</span><span class="o">&lt;</span><span class="n">R</span><span class="p">,</span><span class="w"> </span><span class="n">E</span><span class="o">&gt;</span><span class="w"> </span><span class="o">+</span><span class="w"> </span><span class="nb">Send</span><span class="w"> </span><span class="o">+</span><span class="w"> </span><span class="nb">Sync</span><span class="p">,</span>
+<span class="w">        </span><span class="n">R</span><span class="p">:</span><span class="w"> </span><span class="nb">Send</span><span class="p">,</span>
+<span class="w">        </span><span class="n">E</span><span class="p">:</span><span class="w"> </span><span class="nb">Send</span><span class="p">,</span>
+<span class="w">        </span><span class="n">C</span><span class="p">:</span><span class="w"> </span><span class="nb">FnMut</span><span class="p">(</span><span class="kt">usize</span><span class="p">,</span><span class="w"> </span><span class="n">R</span><span class="p">,</span><span class="w"> </span><span class="n">Duration</span><span class="p">)</span><span class="w"> </span><span class="o">+</span><span class="w"> </span><span class="nb">Send</span><span class="p">;</span><span class="w">   </span><span class="c1">// Send required, Sync is not</span>
+<span class="p">}</span>
+</code></pre></div>
+<p><code>order</code> is caller-supplied so each command chooses its scheduling strategy:
+largest-first for <code>merge</code>, sequential for <code>build_layers</code>, etc.</p>
+<h2 id="migration-examples">Migration examples</h2>
+<h3 id="mergers-before-180-lines-of-bespoke-machinery">merge.rs (before: ~180 lines of bespoke machinery)</h3>
+<div class="highlight"><pre><span></span><code><span class="kd">let</span><span class="w"> </span><span class="n">runner</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">PartitionRunner</span><span class="p">::</span><span class="n">new</span><span class="p">();</span>
+<span class="n">runner</span><span class="p">.</span><span class="n">run</span><span class="p">(</span>
+<span class="w">    </span><span class="o">&amp;</span><span class="n">order</span><span class="p">,</span>
+<span class="w">    </span><span class="o">|</span><span class="n">i</span><span class="o">|</span><span class="w"> </span><span class="n">dst_partition</span><span class="p">.</span><span class="n">merge_partition</span><span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="w"> </span><span class="n">srcs</span><span class="p">,</span><span class="w"> </span><span class="n">mode</span><span class="p">,</span><span class="w"> </span><span class="n">n_dst_genomes</span><span class="p">,</span><span class="w"> </span><span class="n">block_bits</span><span class="p">,</span><span class="w"> </span><span class="n">evidence</span><span class="p">)</span>
+<span class="w">            </span><span class="p">.</span><span class="n">map_err</span><span class="p">(</span><span class="n">OKIError</span><span class="p">::</span><span class="n">Partition</span><span class="p">),</span>
+<span class="w">    </span><span class="o">|</span><span class="n">i</span><span class="p">,</span><span class="w"> </span><span class="n">g_len</span><span class="p">,</span><span class="w"> </span><span class="n">dur</span><span class="o">|</span><span class="w"> </span><span class="p">{</span>
+<span class="w">        </span><span class="n">pb</span><span class="p">.</span><span class="n">inc</span><span class="p">(</span><span class="mi">1</span><span class="p">);</span>
+<span class="w">        </span><span class="n">debug</span><span class="o">!</span><span class="p">(</span><span class="s">&quot;partition {i}: done in {:.1}s — {g_len} new kmers&quot;</span><span class="p">,</span><span class="w"> </span><span class="n">dur</span><span class="p">.</span><span class="n">as_secs_f64</span><span class="p">());</span>
+<span class="w">        </span><span class="n">part_stats</span><span class="p">.</span><span class="n">push</span><span class="p">(</span><span class="n">PartStat</span><span class="w"> </span><span class="p">{</span><span class="w"> </span><span class="n">id</span><span class="p">:</span><span class="w"> </span><span class="nc">i</span><span class="p">,</span><span class="w"> </span><span class="n">unitig_bytes</span><span class="p">:</span><span class="w"> </span><span class="nc">partition_sizes</span><span class="p">[</span><span class="n">i</span><span class="p">],</span><span class="w"> </span><span class="n">g_len</span><span class="w"> </span><span class="p">});</span>
+<span class="w">    </span><span class="p">},</span>
+<span class="p">)</span><span class="o">?</span><span class="p">;</span>
+</code></pre></div>
+<h3 id="indexrs-build_layers-before-naive-into_par_iter">index.rs build_layers (before: naive into_par_iter)</h3>
+<div class="highlight"><pre><span></span><code><span class="kd">let</span><span class="w"> </span><span class="n">order</span><span class="p">:</span><span class="w"> </span><span class="nb">Vec</span><span class="o">&lt;</span><span class="kt">usize</span><span class="o">&gt;</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">(</span><span class="mi">0</span><span class="o">..</span><span class="n">n</span><span class="p">).</span><span class="n">collect</span><span class="p">();</span>
+<span class="kd">let</span><span class="w"> </span><span class="n">runner</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">PartitionRunner</span><span class="p">::</span><span class="n">new</span><span class="p">();</span>
+<span class="n">runner</span><span class="p">.</span><span class="n">run</span><span class="p">(</span>
+<span class="w">    </span><span class="o">&amp;</span><span class="n">order</span><span class="p">,</span>
+<span class="w">    </span><span class="o">|</span><span class="n">i</span><span class="o">|</span><span class="w"> </span><span class="bp">self</span><span class="p">.</span><span class="n">partition</span><span class="p">.</span><span class="n">build_index_layer</span><span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="w"> </span><span class="n">min_ab</span><span class="p">,</span><span class="w"> </span><span class="n">max_ab</span><span class="p">,</span><span class="w"> </span><span class="n">with_counts</span><span class="p">,</span><span class="w"> </span><span class="o">&amp;</span><span class="n">evidence</span><span class="p">,</span><span class="w"> </span><span class="n">block_bits</span><span class="p">)</span>
+<span class="w">            </span><span class="p">.</span><span class="n">map_err</span><span class="p">(</span><span class="n">OKIError</span><span class="p">::</span><span class="n">Partition</span><span class="p">),</span>
+<span class="w">    </span><span class="o">|</span><span class="n">_</span><span class="p">,</span><span class="w"> </span><span class="n">n_kmers</span><span class="p">,</span><span class="w"> </span><span class="n">_</span><span class="o">|</span><span class="w"> </span><span class="p">{</span>
+<span class="w">        </span><span class="n">total_kmers</span><span class="p">.</span><span class="n">fetch_add</span><span class="p">(</span><span class="n">n_kmers</span><span class="p">,</span><span class="w"> </span><span class="n">Ordering</span><span class="p">::</span><span class="n">Relaxed</span><span class="p">);</span>
+<span class="w">        </span><span class="n">pb</span><span class="p">.</span><span class="n">inc</span><span class="p">(</span><span class="mi">1</span><span class="p">);</span>
+<span class="w">    </span><span class="p">},</span>
+<span class="p">)</span><span class="o">?</span><span class="p">;</span>
+</code></pre></div>
+<p>All other sites (<code>pack_matrices</code>, <code>dump</code>, <code>select</code>, etc.) follow the same
+pattern.</p>
+<h2 id="placement">Placement</h2>
+<p><code>PartitionRunner</code> lives in <code>obikindex/src/numa.rs</code> alongside <code>NumaSetup</code>.
+It depends only on standard library primitives and Rayon — no new dependencies.</p>
+<p>A single <code>PartitionRunner</code> instance can be built once per command invocation
+and reused across multiple <code>run()</code> calls (e.g. <code>merge</code> runs
+<code>merge_partitions</code> then <code>pack_matrices</code>).</p>
+<h2 id="known-issue-cpu-only-activation-signal-stalls-on-io-bound-stages">Known issue: CPU-only activation signal stalls on I/O-bound stages</h2>
+<p>Observed on a real <code>filter</code> run (109 genomes, 256 partitions, 8×24-core NUMA):
+<code>rebuild</code> (CPU-bound — k-mer construction) scales cleanly from 9 to 43 active
+workers as <code>CpuSample::do_i_activate</code> (<code>obisys::lib.rs</code>) sees efficiency climb.
+<code>pack_matrices</code> (I/O-bound — reopens and recomposes per-genome column files
+into <code>.pbmx</code>/<code>.pcmx</code>) activates one extra worker then flatlines at 10/192 for
+the rest of the stage, even though 256 partitions keep completing over several
+minutes. This matches the documented intent (§ Adaptive mechanism — "avoids
+over-provisioning ... I/O-bound ... workloads") but conflates two different
+things: <em>"CPU is not the bottleneck"</em> and <em>"more workers would not help"</em>. On
+storage with real queue depth (NVMe, RAID, parallel FS) the second stage could
+still benefit from more concurrent workers even with flat CPU usage — a signal
+the current mechanism cannot see.</p>
+<p>A one-off artefact was also found in the same log: right after a stage
+transition, <code>do_i_activate</code> produced a physically impossible spike (efficiency
+~94 cores on a 192-core box) because it has no minimum-window guard — unlike
+its sibling <code>cpu_efficiency</code>, which returns <code>0.0</code> if <code>wall &lt; 0.1s</code>
+(<code>obisys::lib.rs:260</code>). <code>do_i_activate</code> unconditionally overwrites
+<code>self.wall</code>/<code>self.user_secs</code>/<code>self.sys_secs</code> even when the elapsed window is
+too short to be meaningful, so a burst of rapid completions right after
+activating a worker can divide a real CPU delta by a near-zero wall delta.</p>
+<h3 id="implemented-io-signal-shared-debounce-guard">Implemented: I/O signal + shared debounce guard</h3>
+<p><code>IoSample</code> (<code>obisys::lib.rs</code>, alongside <code>CpuSample</code>) is fed by
+<code>read_bytes</code>/<code>write_bytes</code> from <code>/proc/self/io</code> on Linux (actual bytes
+submitted to the block layer — not <code>rchar</code>/<code>wchar</code>, which also count
+page-cache hits, and not <code>ru_inblock</code>/<code>ru_oublock</code>, unreliable on macOS), with
+a <code>proc_pid_rusage(RUSAGE_INFO_V4)</code> fallback on macOS
+(<code>ri_diskio_bytesread</code>/<code>ri_diskio_byteswritten</code>, FFI only via <code>libc</code>, no new
+dependency — same pattern as the existing <code>getrusage</code> bindings). Any other
+target degrades gracefully to a signal that never triggers (falls back to
+CPU-only activation), same pattern as <code>cgroup_v2_available</code>.</p>
+<p><code>maybe_activate</code> (<code>numa.rs</code>) activates a worker if <em>either</em> signal still shows
+headroom, making <code>PartitionRunner</code> adapt to whichever resource is actually the
+bottleneck without per-call configuration. Both samplers are called
+unconditionally — no <code>||</code> short-circuit — so neither window starves behind
+whichever signal fires first:</p>
+<div class="highlight"><pre><span></span><code><span class="kd">let</span><span class="w"> </span><span class="n">cpu_threshold</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">CPU_SPAWN_THRESHOLD</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="n">activation</span><span class="p">.</span><span class="n">last_step</span><span class="p">()</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="kt">f64</span><span class="p">;</span>
+<span class="kd">let</span><span class="w"> </span><span class="n">cpu_wants_more</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">cpu_sample</span><span class="p">.</span><span class="n">do_i_activate</span><span class="p">(</span><span class="n">cpu_threshold</span><span class="p">);</span>
+<span class="kd">let</span><span class="w"> </span><span class="n">io_wants_more</span><span class="w">  </span><span class="o">=</span><span class="w"> </span><span class="n">io_sample</span><span class="p">.</span><span class="n">do_i_activate</span><span class="p">(</span><span class="n">IO_SPAWN_THRESHOLD</span><span class="p">);</span>
+<span class="k">if</span><span class="w"> </span><span class="n">cpu_wants_more</span><span class="w"> </span><span class="o">||</span><span class="w"> </span><span class="n">io_wants_more</span><span class="w"> </span><span class="p">{</span>
+<span class="w">    </span><span class="n">activation</span><span class="p">.</span><span class="n">grow</span><span class="p">(</span><span class="n">GROWTH_DIVISOR</span><span class="p">,</span><span class="w"> </span><span class="n">n_total</span><span class="p">);</span>
+<span class="p">}</span>
+</code></pre></div>
+<p>The CPU threshold is <em>not</em> the flat absolute delta it started as: it scales
+with <code>activation.last_step()</code> — the number of workers activated in the last
+growth step, tracked by <code>NodeActivation</code> (<code>numa.rs</code>) and updated every time
+<code>grow()</code> actually grows something. Growing by 8 workers should add ~8 cores of
+efficiency if the workload is truly CPU-bound; requiring only
+<code>CPU_SPAWN_THRESHOLD</code> (20 %) of that expected gain confirms the growth was
+useful without demanding perfect linear scaling. Scaling by the <em>last step's
+size</em> rather than the cumulative total keeps the bar equally meaningful
+whether it's the 2nd growth step or the 20th — a flat absolute threshold
+(0.2 core) is a strong signal at 8 active workers but pure noise at 150; a
+threshold scaled by the <em>cumulative</em> total instead (considered and rejected)
+would have made the bar essentially impossible to clear late in the ramp,
+strangling exactly the CPU-bound saturation the mechanism exists to allow.</p>
+<p>Unlike the CPU signal (an absolute delta in cores — a bounded, portable unit),
+raw I/O throughput has no natural scale across devices, so <code>IoSample</code> uses a
+<strong>relative</strong> growth threshold instead of an absolute one:</p>
+<div class="highlight"><pre><span></span><code><span class="k">pub</span><span class="w"> </span><span class="k">fn</span><span class="w"> </span><span class="nf">do_i_activate</span><span class="p">(</span><span class="o">&amp;</span><span class="k">mut</span><span class="w"> </span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">threshold</span><span class="p">:</span><span class="w"> </span><span class="kt">f64</span><span class="p">)</span><span class="w"> </span><span class="p">-&gt;</span><span class="w"> </span><span class="kt">bool</span><span class="w"> </span><span class="p">{</span>
+<span class="w">    </span><span class="kd">let</span><span class="w"> </span><span class="n">elapsed</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="bp">self</span><span class="p">.</span><span class="n">wall</span><span class="p">.</span><span class="n">elapsed</span><span class="p">().</span><span class="n">as_secs_f64</span><span class="p">();</span>
+<span class="w">    </span><span class="k">if</span><span class="w"> </span><span class="n">elapsed</span><span class="w"> </span><span class="o">&lt;</span><span class="w"> </span><span class="mf">0.1</span><span class="w"> </span><span class="p">{</span><span class="w"> </span><span class="k">return</span><span class="w"> </span><span class="kc">false</span><span class="p">;</span><span class="w"> </span><span class="p">}</span><span class="w">        </span><span class="c1">// state untouched — window keeps accumulating</span>
+
+<span class="w">    </span><span class="kd">let</span><span class="w"> </span><span class="n">n</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="bp">Self</span><span class="p">::</span><span class="n">read_bytes</span><span class="p">();</span>
+<span class="w">    </span><span class="kd">let</span><span class="w"> </span><span class="n">rate</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">n</span><span class="p">.</span><span class="n">saturating_sub</span><span class="p">(</span><span class="bp">self</span><span class="p">.</span><span class="n">bytes</span><span class="p">)</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="kt">f64</span><span class="w"> </span><span class="o">/</span><span class="w"> </span><span class="n">elapsed</span><span class="p">;</span>
+<span class="w">    </span><span class="kd">let</span><span class="w"> </span><span class="n">activate</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="k">if</span><span class="w"> </span><span class="bp">self</span><span class="p">.</span><span class="n">previous_rate</span><span class="w"> </span><span class="o">==</span><span class="w"> </span><span class="mf">0.0</span><span class="w"> </span><span class="p">{</span>
+<span class="w">        </span><span class="n">rate</span><span class="w"> </span><span class="o">&gt;</span><span class="w"> </span><span class="mf">0.0</span><span class="w">                            </span><span class="c1">// bootstrap: any measured throughput is signal</span>
+<span class="w">    </span><span class="p">}</span><span class="w"> </span><span class="k">else</span><span class="w"> </span><span class="p">{</span>
+<span class="w">        </span><span class="p">(</span><span class="n">rate</span><span class="w"> </span><span class="o">-</span><span class="w"> </span><span class="bp">self</span><span class="p">.</span><span class="n">previous_rate</span><span class="p">)</span><span class="w"> </span><span class="o">/</span><span class="w"> </span><span class="bp">self</span><span class="p">.</span><span class="n">previous_rate</span><span class="w"> </span><span class="o">&gt;=</span><span class="w"> </span><span class="n">threshold</span>
+<span class="w">    </span><span class="p">};</span>
+
+<span class="w">    </span><span class="bp">self</span><span class="p">.</span><span class="n">bytes</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">n</span><span class="p">;</span>
+<span class="w">    </span><span class="bp">self</span><span class="p">.</span><span class="n">wall</span><span class="w">  </span><span class="o">=</span><span class="w"> </span><span class="n">Instant</span><span class="p">::</span><span class="n">now</span><span class="p">();</span><span class="w">              </span><span class="c1">// reset only on a real sample</span>
+<span class="w">    </span><span class="n">activate</span>
+<span class="p">}</span>
+</code></pre></div>
+<p>The <code>elapsed &lt; 0.1s → return false without mutating state</code> guard was also
+back-ported into <code>CpuSample::do_i_activate</code> (previously missing — source of
+the ~94-core artefact above) — one fix for both problems, and it removes the
+need for any arbitrary I/O-rate floor: a short/noisy window is rejected
+outright rather than papered over with a hardware-dependent constant.</p>
+<p>Both spawn thresholds (<code>CPU_SPAWN_THRESHOLD</code>, <code>IO_SPAWN_THRESHOLD</code>, module-level
+<code>const</code> in <code>numa.rs</code>, both <code>0.2</code>) are a starting point, not a derived value:
+<code>0.2</code> (20 % relative growth) for <code>IoSample</code> was chosen to match the CPU
+threshold's <em>implicit</em> relative sensitivity (in the observed log, an 8→9
+worker step raised efficiency by ~12 %) — but I/O throughput is lumpier than
+CPU time (buffered writes flush in bursts), so it needs empirical validation
+against a real <code>pack</code> run before being considered final.</p>
+<h2 id="known-issue-ramp-up-too-slow-and-confused-with-node-count">Known issue: ramp-up too slow, and confused with node count</h2>
+<p>The original design started <code>n_nodes</code> workers (one per node) and grew one
+worker at a time. On a real <code>filter</code> run this took ~10 minutes to climb from
+9 to ~40 active workers even on the CPU-bound <code>rebuild</code> stage — most of a
+35-minute stage spent under-provisioned while waiting for evidence to
+accumulate one worker at a time. There is no scale-down mechanism (<code>n_active</code>
+only grows), so the original caution was deliberate — but a quarter of
+available cores is still far from saturation, and the real risk zone (over-provisioning
+a memory-bandwidth-bound stage) only shows up much later in the ramp, near
+full occupancy — not at 25 %.</p>
+<p>The fix decouples ramp speed from node <em>count</em>: both the initial size and the
+growth step are a fraction of <code>workers_per_node</code> (node <em>size</em>), applied
+identically on every node. A single-NUMA-node (UMA) machine ramps exactly as
+fast as an 8-node one — growing by <code>n_nodes</code> per step, as first considered,
+would have degenerated to "grow by 1" on UMA, reproducing the original
+problem for exactly the machines that need the fix most.</p>
+<div class="highlight"><pre><span></span><code><span class="c1">// NodeActivation::grow — called both at startup (activate_initial) and on</span>
+<span class="c1">// every CPU/IO-triggered growth step, with a different divisor each time.</span>
+<span class="kd">let</span><span class="w"> </span><span class="n">wanted</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">(</span><span class="bp">self</span><span class="p">.</span><span class="n">caps</span><span class="p">[</span><span class="n">idx</span><span class="p">]</span><span class="w"> </span><span class="o">/</span><span class="w"> </span><span class="n">divisor</span><span class="p">).</span><span class="n">max</span><span class="p">(</span><span class="mi">1</span><span class="p">);</span><span class="w">   </span><span class="c1">// INITIAL_DIVISOR=4 at startup, GROWTH_DIVISOR=8 per step</span>
+<span class="kd">let</span><span class="w"> </span><span class="n">room</span><span class="w">   </span><span class="o">=</span><span class="w"> </span><span class="bp">self</span><span class="p">.</span><span class="n">caps</span><span class="p">[</span><span class="n">idx</span><span class="p">].</span><span class="n">saturating_sub</span><span class="p">(</span><span class="bp">self</span><span class="p">.</span><span class="n">active</span><span class="p">[</span><span class="n">idx</span><span class="p">]);</span>
+<span class="kd">let</span><span class="w"> </span><span class="n">grow</span><span class="w">   </span><span class="o">=</span><span class="w"> </span><span class="n">wanted</span><span class="p">.</span><span class="n">min</span><span class="p">(</span><span class="n">room</span><span class="p">).</span><span class="n">min</span><span class="p">(</span><span class="n">n_total</span><span class="p">.</span><span class="n">saturating_sub</span><span class="p">(</span><span class="bp">self</span><span class="p">.</span><span class="n">total</span><span class="p">));</span>
+</code></pre></div>
+<p>This also fixed a latent correctness gap: the original single shared
+<code>activate_tx</code>/<code>activate_rx</code> pair had <em>no</em> per-node addressing — sending one
+activation signal woke up whichever dormant worker (from any node) happened
+to win the race on that channel. <code>crossbeam_channel</code> gives no fairness
+guarantee across competing receivers, so "round-robin across nodes" was an
+assumption the code never actually enforced. <code>PartitionRunner::run</code> now opens
+one activation channel per node (<code>activate_txs</code>/<code>activate_rxs</code>, one pair per
+<code>NodeConfig</code>); <code>NodeActivation</code> (<code>numa.rs</code>) tracks how many of each node's
+dormant workers have been woken and grows every node by the same amount per
+step, capped by that node's remaining dormant workers and by the run's total
+budget (<code>n_total</code>) — balance across nodes is now guaranteed by construction,
+not incidental to channel implementation details.</p>
+<h2 id="open-questions">Open questions</h2>
+<ul>
+<li>
+<p><strong>Error handling</strong>: <code>run</code> currently returns the first error; remaining errors
+  are dropped.  A <code>Vec&lt;E&gt;</code> return would give complete diagnostics.</p>
+</li>
+<li>
+<p><strong><code>INITIAL_DIVISOR</code> / <code>GROWTH_DIVISOR</code> tuning</strong>: currently <code>4</code> and <code>8</code>
+  (start at 1/4 of a node's cores, grow by 1/8 per step), chosen to fix an
+  observed too-slow ramp — not yet validated against a real <code>pack</code> (I/O-bound)
+  run, where over-provisioning risk is different from the CPU-bound <code>rebuild</code>
+  case this was tuned against.</p>
+</li>
+<li>
+<p><strong><code>on_done</code> ordering</strong>: the runner serialises calls to <code>on_done</code> via an
+  internal <code>Arc&lt;Mutex&lt;C&gt;&gt;</code>.  <code>Send</code> is required (the Arc clone crosses thread
+  boundaries); <code>Sync</code> is not (only one thread holds the lock at a time).
+  Contention is negligible because a partition takes seconds while the callback
+  takes microseconds.  The callback is therefore simple to write (plain
+  <code>Vec::push</code>, plain <code>FnMut</code>) with no measurable performance cost.</p>
+</li>
+</ul>
+
+
+
+
+
+
+
+
+
+
+
+
+                
+              </article>
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diff --git a/DevDoc/architecture/numa_worker_pools/index.html b/DevDoc/architecture/numa_worker_pools/index.html
new file mode 100644
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+  
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+
+
+<h1 id="numa-aware-worker-pools-for-merge">NUMA-aware worker pools for merge</h1>
+<h2 id="problem">Problem</h2>
+<p>The merge command's bottleneck is <code>compute_degrees</code> in <code>obidebruinj</code>: a random pointer-chase over 20–70 M node hash maps that saturates DRAM bandwidth. When multiple partition workers run concurrently, they contend for the shared memory bus, causing super-linear slowdown (measured: 0.016 µs/node solo → 0.95 µs/node with 4–5 concurrent workers, ×60 degradation).</p>
+<p>Modern HPC nodes are multi-socket NUMA machines (observed: 2 sockets × 4 NUMA nodes × 24 cores = 192 cores). Cross-NUMA memory traffic compounds the contention:</p>
+<ul>
+<li>Full 192-core run: ~15 min/partition (×10 worse than M3 Mac)</li>
+<li><code>taskset</code> restricted to 4 NUMA nodes (96 cores): ~90 s/partition</li>
+<li>OAR job on 1 NUMA node (24 cores): ~80 s/partition, same throughput as 96 cores</li>
+</ul>
+<p><strong>Conclusion</strong>: the bottleneck is memory bandwidth per NUMA node, not core count. 24 cores on one NUMA node achieve the same throughput as 96 cores across four.</p>
+<h2 id="strategy">Strategy</h2>
+<p>Run N worker groups in parallel, one per NUMA node, each with its own Rayon thread pool whose threads are pinned to the NUMA node's CPUs. Linux's first-touch policy then places graph allocations on local DRAM automatically — no explicit NUMA allocator needed.</p>
+<p>Expected throughput: N × single-NUMA throughput. On the 8-NUMA-node HPC: 8 × ~80 s = 9–10 min total instead of &gt;60 min with the current single-pool approach.</p>
+<h2 id="rayon-thread-pool-isolation">Rayon thread pool isolation</h2>
+<p>Rayon provides <code>ThreadPool::install(|| { ... })</code>: any Rayon call (<code>par_iter</code>, <code>current_num_threads</code>, etc.) inside the closure uses <em>that</em> pool exclusively. Wrapping <code>merge_partition</code> in <code>pool.install()</code> redirects all downstream Rayon calls — including those in <code>debruijn.rs</code> and <code>partition.rs</code> — without touching those crates.</p>
+<div class="highlight"><pre><span></span><code><span class="c1">// worker thread, assigned to NUMA pool `pool`</span>
+<span class="n">pool</span><span class="p">.</span><span class="n">install</span><span class="p">(</span><span class="o">||</span><span class="w"> </span><span class="p">{</span>
+<span class="w">    </span><span class="n">dst_partition</span><span class="p">.</span><span class="n">merge_partition</span><span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="w"> </span><span class="n">srcs</span><span class="p">,</span><span class="w"> </span><span class="n">mode</span><span class="p">,</span><span class="w"> </span><span class="n">n_dst_genomes</span><span class="p">,</span><span class="w"> </span><span class="n">block_bits</span><span class="p">,</span><span class="w"> </span><span class="n">evidence</span><span class="p">)</span>
+<span class="p">})</span>
+</code></pre></div>
+<p><code>rayon::current_num_threads()</code> inside <code>merge_partition</code> will return the pool size (e.g. 24), not the global thread count — which is the right value for buffer sizing.</p>
+<h2 id="thread-pinning">Thread pinning</h2>
+<p><code>ThreadPoolBuilder::spawn_handler</code> provides a hook executed for each thread at creation. Inside, <code>libc::sched_setaffinity</code> pins the thread to a CPU set:</p>
+<div class="highlight"><pre><span></span><code><span class="kd">let</span><span class="w"> </span><span class="n">cpus</span><span class="p">:</span><span class="w"> </span><span class="nb">Vec</span><span class="o">&lt;</span><span class="kt">usize</span><span class="o">&gt;</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">numa_node_cpus</span><span class="p">(</span><span class="n">node</span><span class="p">);</span><span class="w"> </span><span class="c1">// from /sys/devices/system/node/nodeN/cpulist</span>
+<span class="n">rayon</span><span class="p">::</span><span class="n">ThreadPoolBuilder</span><span class="p">::</span><span class="n">new</span><span class="p">()</span>
+<span class="w">    </span><span class="p">.</span><span class="n">num_threads</span><span class="p">(</span><span class="n">cpus</span><span class="p">.</span><span class="n">len</span><span class="p">())</span>
+<span class="w">    </span><span class="p">.</span><span class="n">spawn_handler</span><span class="p">(</span><span class="k">move</span><span class="w"> </span><span class="o">|</span><span class="n">thread</span><span class="o">|</span><span class="w"> </span><span class="p">{</span>
+<span class="w">        </span><span class="kd">let</span><span class="w"> </span><span class="k">mut</span><span class="w"> </span><span class="n">b</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">std</span><span class="p">::</span><span class="n">thread</span><span class="p">::</span><span class="n">Builder</span><span class="p">::</span><span class="n">new</span><span class="p">();</span>
+<span class="w">        </span><span class="n">std</span><span class="p">::</span><span class="n">thread</span><span class="p">::</span><span class="n">Builder</span><span class="p">::</span><span class="n">new</span><span class="p">().</span><span class="n">spawn</span><span class="p">(</span><span class="k">move</span><span class="w"> </span><span class="o">||</span><span class="w"> </span><span class="p">{</span>
+<span class="w">            </span><span class="n">pin_to_cpus</span><span class="p">(</span><span class="o">&amp;</span><span class="n">cpus</span><span class="p">);</span><span class="w">   </span><span class="c1">// sched_setaffinity via libc</span>
+<span class="w">            </span><span class="n">thread</span><span class="p">.</span><span class="n">run</span><span class="p">()</span>
+<span class="w">        </span><span class="p">})</span><span class="o">?</span><span class="p">;</span>
+<span class="w">        </span><span class="nb">Ok</span><span class="p">(())</span>
+<span class="w">    </span><span class="p">})</span>
+<span class="w">    </span><span class="p">.</span><span class="n">build</span><span class="p">()</span><span class="o">?</span>
+</code></pre></div>
+<p>NUMA topology is read from <code>/sys/devices/system/node/node*/cpulist</code> — no <code>libnuma</code> dependency required. If the <code>numa</code> crate is linked, <code>numa_available()</code> / <code>numa_run_on_node()</code> are an alternative.</p>
+<h2 id="memory-locality">Memory locality</h2>
+<p>Linux allocates pages on the NUMA node of the thread that first writes them (first-touch policy). Once Rayon threads are pinned to node N, all graph data built by those threads lands on node N's DRAM. No changes to the allocator, no explicit <code>numa_alloc_onnode</code> calls.</p>
+<h2 id="adaptive-spawn-criterion">Adaptive spawn criterion</h2>
+<p>The current criterion uses <code>std::thread::available_parallelism()</code> (returns total cores = 192) and <code>max_workers = n_cores / 2</code>. With NUMA pools:</p>
+<ul>
+<li><code>n_cores</code> per pool = cores per NUMA node (e.g. 24)</li>
+<li><code>max_workers</code> per pool = pool size / 2 (e.g. 12)</li>
+<li>CPU efficiency is measured per pool, not globally</li>
+</ul>
+<p>Each NUMA group runs its own independent adaptive pool. Workers are distributed across NUMA groups round-robin or by workload (partition assignment can be pre-split by NUMA group index).</p>
+<h2 id="required-changes">Required changes</h2>
+<table>
+<thead>
+<tr>
+<th>File</th>
+<th>Change</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>obikindex/src/merge.rs</code></td>
+<td>Detect NUMA topology; build N <code>ThreadPool</code>s with pinned threads; assign each pre-spawned worker to a pool; wrap <code>merge_partition</code> in <code>pool.install()</code></td>
+</tr>
+<tr>
+<td><code>obikindex/src/merge.rs</code></td>
+<td>Replace <code>available_parallelism()</code> with per-NUMA core count for spawn criterion</td>
+</tr>
+<tr>
+<td><code>obikpartitionner/src/merge_layer.rs</code></td>
+<td>No change — <code>merge_partition</code> already works inside any Rayon context</td>
+</tr>
+<tr>
+<td><code>obidebruinj/src/debruijn.rs</code></td>
+<td>No change — <code>par_iter</code> and <code>current_num_threads</code> are pool-context-aware</td>
+</tr>
+<tr>
+<td><code>obikpartitionner/src/partition.rs</code></td>
+<td>No change — same reason</td>
+</tr>
+</tbody>
+</table>
+<h2 id="platform-guard">Platform guard</h2>
+<p>NUMA pinning is Linux-only. The fallback is the current single global pool:</p>
+<div class="highlight"><pre><span></span><code><span class="cp">#[cfg(target_os = </span><span class="s">&quot;linux&quot;</span><span class="cp">)]</span>
+<span class="k">fn</span><span class="w"> </span><span class="nf">build_numa_pools</span><span class="p">()</span><span class="w"> </span><span class="p">-&gt;</span><span class="w"> </span><span class="nb">Option</span><span class="o">&lt;</span><span class="nb">Vec</span><span class="o">&lt;</span><span class="n">rayon</span><span class="p">::</span><span class="n">ThreadPool</span><span class="o">&gt;&gt;</span><span class="w"> </span><span class="p">{</span><span class="w"> </span><span class="o">..</span><span class="p">.</span><span class="w"> </span><span class="p">}</span>
+
+<span class="cp">#[cfg(not(target_os = </span><span class="s">&quot;linux&quot;</span><span class="cp">))]</span>
+<span class="k">fn</span><span class="w"> </span><span class="nf">build_numa_pools</span><span class="p">()</span><span class="w"> </span><span class="p">-&gt;</span><span class="w"> </span><span class="nb">Option</span><span class="o">&lt;</span><span class="nb">Vec</span><span class="o">&lt;</span><span class="n">rayon</span><span class="p">::</span><span class="n">ThreadPool</span><span class="o">&gt;&gt;</span><span class="w"> </span><span class="p">{</span><span class="w"> </span><span class="nb">None</span><span class="w"> </span><span class="p">}</span>
+</code></pre></div>
+<p>When <code>build_numa_pools()</code> returns <code>None</code> (macOS, UMA, or single-socket), <code>merge.rs</code> uses the existing code path unchanged.</p>
+<h2 id="open-questions">Open questions</h2>
+<ul>
+<li><strong>Partition assignment</strong>: split partitions by NUMA group up-front (static) or use a shared queue with per-group workers stealing from a common pool? Static split is simpler; stealing is better for load balance when partitions vary widely in size.</li>
+<li><strong>Intra-NUMA adaptive criterion</strong>: with 24 cores and ~3–5 effective workers per NUMA node, the current marginal-gain criterion needs re-tuning or can be left as-is with per-pool <code>n_cores = 24</code>.</li>
+<li><strong>I/O</strong>: partition data (unitig files) is on a shared filesystem. With 8 concurrent NUMA groups, I/O concurrency increases 8× — need to verify the filesystem (Lustre or local SSD) can absorb it without becoming the new bottleneck.</li>
+</ul>
+
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+              </article>
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diff --git a/doc/architecture/query.refs/index.html b/DevDoc/architecture/query.refs/index.html
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
         
           
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+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
             
   
   
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -784,14 +839,98 @@
   
   
     <li class="md-nav__item">
-      <a href="../../implementation/rebuild_filter/" class="md-nav__link">
+      <a href="../../implementation/merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
   
 
     
@@ -827,10 +966,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
         
           
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
             
   
   
@@ -848,8 +987,8 @@
             <span class="md-nav__icon md-icon"></span>
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -915,6 +1054,90 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
diff --git a/DevDoc/architecture/query/index.html b/DevDoc/architecture/query/index.html
new file mode 100644
index 00000000..00ca5e89
--- /dev/null
+++ b/DevDoc/architecture/query/index.html
@@ -0,0 +1,1939 @@
+
+<!doctype html>
+<html lang="en" class="no-js">
+  <head>
+    
+      <meta charset="utf-8">
+      <meta name="viewport" content="width=device-width,initial-scale=1">
+      
+      
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+      
+      
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+        
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+      
+      <link rel="icon" href="../../assets/images/favicon.png">
+      <meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.7.6">
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+    
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+      
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+      <link rel="stylesheet" href="../../assets/stylesheets/main.484c7ddc.min.css">
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+        <link rel="preconnect" href="https://fonts.gstatic.com" crossorigin>
+        <link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Roboto:300,300i,400,400i,700,700i%7CRoboto+Mono:400,400i,700,700i&display=fallback">
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+      
+    
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+    <script>__md_scope=new URL("../..",location),__md_hash=e=>[...e].reduce(((e,_)=>(e<<5)-e+_.charCodeAt(0)),0),__md_get=(e,_=localStorage,t=__md_scope)=>JSON.parse(_.getItem(t.pathname+"."+e)),__md_set=(e,_,t=localStorage,a=__md_scope)=>{try{t.setItem(a.pathname+"."+e,JSON.stringify(_))}catch(e){}}</script>
+    
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+  
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+    <body dir="ltr">
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+    <input class="md-toggle" data-md-toggle="drawer" type="checkbox" id="__drawer" autocomplete="off">
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+    <div data-md-component="skip">
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+          Skip to content
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+    <div data-md-component="announce">
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+<header class="md-header md-header--shadow" data-md-component="header">
+  <nav class="md-header__inner md-grid" aria-label="Header">
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+
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+    <label class="md-header__button md-icon" for="__drawer">
+      
+      <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M3 6h18v2H3zm0 5h18v2H3zm0 5h18v2H3z"/></svg>
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+    <div class="md-header__title" data-md-component="header-title">
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+        <div class="md-header__topic">
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+        </div>
+        <div class="md-header__topic" data-md-component="header-topic">
+          <span class="md-ellipsis">
+            
+              Query system
+            
+          </span>
+        </div>
+      </div>
+    </div>
+    
+    
+      <script>var palette=__md_get("__palette");if(palette&&palette.color){if("(prefers-color-scheme)"===palette.color.media){var media=matchMedia("(prefers-color-scheme: light)"),input=document.querySelector(media.matches?"[data-md-color-media='(prefers-color-scheme: light)']":"[data-md-color-media='(prefers-color-scheme: dark)']");palette.color.media=input.getAttribute("data-md-color-media"),palette.color.scheme=input.getAttribute("data-md-color-scheme"),palette.color.primary=input.getAttribute("data-md-color-primary"),palette.color.accent=input.getAttribute("data-md-color-accent")}for(var[key,value]of Object.entries(palette.color))document.body.setAttribute("data-md-color-"+key,value)}</script>
+    
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+</header>
+    
+    <div class="md-container" data-md-component="container">
+      
+      
+        
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+      
+      <main class="md-main" data-md-component="main">
+        <div class="md-main__inner md-grid">
+          
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+              
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+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
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+
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+    <li class="md-nav__item">
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+  <span class="md-ellipsis">
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+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
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+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
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+    <li class="md-nav__item md-nav__item--nested">
+      
+        
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        
+          
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+            
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Theory
+  
+
+    
+  </span>
+  
+  
+
+            <span class="md-nav__icon md-icon"></span>
+          </label>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            
+  
+    Theory
+  
+
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+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../kmers/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmers and super-kmers
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/encoding/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    DNA encoding
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/entropy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Entropy filter
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/minimizer/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Minimizer selection
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/indexing/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Partitioning architecture
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        
+          
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+            
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Implementation
+  
+
+    
+  </span>
+  
+  
+
+            <span class="md-nav__icon md-icon"></span>
+          </label>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
+            <span class="md-nav__icon md-icon"></span>
+            
+  
+    Implementation
+  
+
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/superkmer/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    SuperKmer
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/kmer/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/chunkreader/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Chunk reader
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/pipeline/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Construction pipeline
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/obipipeline/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obipipeline library
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/storage/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    On-disk storage
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/mphf/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    MPHF selection
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/unitig_evidence/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Unitig evidence encoding
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/evidence_elimination/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Evidence elimination (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/obilayeredmap/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obilayeredmap crate
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/persistent_compact_int_vec/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    PersistentCompactIntVec
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/persistent_bit_vec/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    PersistentBitVec
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/merge/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Merge command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/merge_parallelism/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
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+  <a href="#goal" class="md-nav__link">
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+</li>
+      
+        <li class="md-nav__item">
+  <a href="#input" class="md-nav__link">
+    <span class="md-ellipsis">
+      
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+</li>
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+        <li class="md-nav__item">
+  <a href="#algorithm" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Algorithm
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#findere-z-window-filter" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Findere z-window filter
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Findere z-window filter">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#effective-z-at-query-time" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Effective z at query time
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#layer-lookup-mphflayerfind" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Layer lookup: MphfLayer::find
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Layer lookup: MphfLayer::find">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#querylayer-variant-selection" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        QueryLayer variant selection
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#presence-count-mode-at-query-time" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Presence / count mode at query time
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#coverage-vectors-detail" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Coverage vectors (--detail)
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#kmer_missing-semantics" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        kmer_missing semantics
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#output-format" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Output format
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#annotation-schema" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Annotation schema
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+  <a href="#cli" class="md-nav__link">
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+  <a href="#future-work" class="md-nav__link">
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+    <nav class="md-nav" aria-label="Future work">
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+      
+        Throughput &amp; parallelism — identified potential (not yet implemented)
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+</li>
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+        Implementation plan
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+        
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+        Conventions applied to every phase below
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#phase-0-instrumentation-prerequisite-for-measuring-every-later-phase" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Phase 0 — Instrumentation (prerequisite for measuring every later phase)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#phase-1-parallel-per-file-io-fixes-root-cause-of-low-core-utilization" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Phase 1 — Parallel per-file I/O (fixes root cause of low core utilization)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#phase-2-genome-aware-chunk-size-formula-fixes-oom" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Phase 2 — Genome-aware chunk-size formula (fixes OOM)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#phase-3-k-mer-level-dereplication-staged-mphfmatrix-lookup" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Phase 3 — K-mer-level dereplication, staged MPHF/matrix lookup
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#phase-4-column-major-matrix-fetch-roadmap-points-78-implemented-numa-parallelism-deferred" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Phase 4 — Column-major matrix fetch (roadmap points 7–8) — implemented, NUMA parallelism deferred
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#phase-5-sparse-findere-rework-roadmap-point-9" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Phase 5 — Sparse Findere rework (roadmap point 9)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#phase-6-parallel-gzip-decompression-independent-optional" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Phase 6 — Parallel gzip decompression (independent, optional)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#cross-cutting-risks" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Cross-cutting risks
+      
+    </span>
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+</li>
+        
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+    </nav>
+  
+</li>
+      
+    </ul>
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+                  </div>
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+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+
+<h1 id="query-system">Query system</h1>
+<h2 id="goal">Goal</h2>
+<p>Given a set of query sequences, determine for each sequence how many of its k-mers are found in the index and, for each indexed genome, how many k-mers match. The query system is the foundation for read classification and sequence-to-genome mapping.</p>
+<hr />
+<h2 id="input">Input</h2>
+<ul>
+<li>Query sequences in FASTA or FASTQ format (gzip supported, streaming stdin supported). GenBank flat files are not supported at query time (only at index time).</li>
+<li>Sequences shorter than k bases are silently skipped.</li>
+<li>Non-ACGT characters are handled by the superkmer decomposition layer: they act as hard breaks, producing shorter superkmers (identical to the behaviour at indexing time).</li>
+</ul>
+<hr />
+<h2 id="algorithm">Algorithm</h2>
+<p>The query follows the same superkmer-based partitioning strategy used at indexing time. Everything below happens inside <code>process_chunk</code> (<code>query.rs</code>); there is no separate per-stage function, but the internal data flow is staged: k-mer-level dereplication, a two-part MPHF/column-major matrix lookup (<code>obikpartitionner::query_partition_with</code>), and a sparse Findere pass, each producing sparse intermediate structures rather than one dense allocation for the whole chunk.</p>
+<div class="highlight"><pre><span></span><code>for each chunk of sequences (parallel workers via obipipeline, one call to process_chunk):
+    build QueryBatch (QueryBatch::from_records):
+        decompose all sequences into superkmers (SuperKmerIter) — construction only,
+        not the dedup key
+        deduplicate at k-mer granularity, split by partition in the same pass:
+            by_partition: Vec&lt;HashMap&lt;CanonicalKmer, Vec&lt;KmerDesc&gt;&gt;&gt;   ← KmerDesc = (seq_idx, pos)
+    allocate SmerIndex (SmerIndex::new): in_index: Vec&lt;bool&gt;, sized total_smers —
+        NOT multiplied by n_genomes
+    allocate by_genome: Vec&lt;Vec&lt;(seq_idx, pos, value)&gt;&gt;, one empty Vec per genome —
+        stays empty (zero cost) for every genome this chunk never matches
+    for each partition p:
+        query_partition_with(p, kmers_for_p, on_event):
+            stage 1 (MPHF-only): for each unique k-mer, try each layer&#39;s MphfLayer::find
+                in turn, stop at the first hit; bucket confirmed hits by (layer, slot);
+                emit QueryHit::Found(descs) once per hit k-mer
+            stage 2 (column-major fetch): for each layer with ≥1 hit, for each genome
+                column g in 0..layer.n_cols(): scan that layer&#39;s bucketed slots, look up
+                col_value(g, slot); emit QueryHit::Value(descs, g, value) on nonzero
+        on_event dispatches: Found → SmerIndex::mark_found for every desc;
+                              Value → push (seq_idx, pos, value) into by_genome[g]
+    for each genome g with ≥1 hit (sparse_findere_for_genome):
+        sort by_genome[g] by (seq_idx, pos); detect maximal runs of consecutive pos
+        within one seq_idx; monotone-deque window-minimum scoped to each run →
+        confirmed_by_genome[g]: Vec&lt;(seq_idx, pos_out, value)&gt;
+    accumulate genome_totals per sequence from confirmed_by_genome (per genome, direct)
+    accumulate kmer_count / kmer_missing per (sequence, output position), O(1) each,
+        using only the confirmed-any bitmap and SmerIndex — independent of n_genomes
+    if --detail: densify confirmed_by_genome into per-(seq, genome) coverage arrays
+    emit annotated sequences (emit_batch)
+</code></pre></div>
+<p>Superkmers that appear more than once in the batch (same sequence or across sequences), or different superkmers that happen to share a k-mer (read overlaps, repeats, a SNP splitting an otherwise-identical run), are deduplicated at k-mer granularity: each unique <code>CanonicalKmer</code> triggers at most one MPHF lookup and, on hit, one matrix fetch, broadcast to every <code>KmerDesc</code> occurrence referencing it.</p>
+<p><strong>Findere requires full-sequence aggregation.</strong> The sliding window (now per-run, not per-sequence — see <a href="#findere-z-window-filter">Findere z-window filter</a>) only ever runs after all partitions have contributed their hits to <code>by_genome</code>. Applying it per superkmer would produce false negatives at superkmer boundaries, where the z-window spans two superkmers.</p>
+<p>Batches are processed in parallel via <code>obipipeline</code> workers; the <code>--threads</code> flag controls the number of worker threads.</p>
+<hr />
+<h2 id="findere-z-window-filter">Findere z-window filter</h2>
+<p>For approximate index modes, the index physically stores s-mers of size <code>s = k_user − z + 1</code>; <code>idx.kmer_size()</code> (bound to <code>k</code> in <code>process_chunk</code>) is this physically-indexed s-mer size, so decomposing the query at <code>k</code> naturally produces s-mer results.</p>
+<p>The z-window aggregation is <strong>sparse</strong>, per genome, implemented in <code>sparse_findere_for_genome</code> (<code>query.rs</code>) — a run-detection pass followed by a monotone-deque sliding-window minimum scoped to each run, not a dense scan over every s-mer position of every sequence:</p>
+<div class="highlight"><pre><span></span><code>sparse_findere_for_genome(hits, z, presence, threshold):
+    // hits: raw (seq_idx, pos_smer, value) triples for this genome, as delivered
+    // by query_partition_with&#39;s QueryHit::Value — only ever nonzero entries;
+    // a position with no hit for this genome simply has no entry at all.
+    sort hits by (seq_idx, pos_smer)
+
+    for each maximal run of consecutive pos_smer values within the same seq_idx:
+        dq: VecDeque&lt;(run-relative index, value)&gt;
+        for k, (_, pos, value) in enumerate(run):
+            maintain dq monotone non-decreasing (pop back while back.value &gt;= value)
+            push (k, value)
+            evict dq entries with run-relative index &lt;= k - z
+            if k + 1 &gt;= z:
+                win_min = dq.front().value
+                if win_min &gt; 0:
+                    pos_out = pos + 1 - z
+                    confirmed.push((seq_idx, pos_out, adjust(win_min)))
+    return confirmed
+</code></pre></div>
+<p>A window can only be confirmed (<code>win_min &gt; 0</code>) when all <code>z</code> s-mers in it are present <em>and</em> nonzero for this genome — which, by construction, can only happen strictly inside one contiguous run of hits (any gap — an absent or zero-valued s-mer — forces <code>win_min = 0</code> for every window spanning it, exactly matching the old dense scan's "not in index counts as 0" rule, just never materialising the zero). The deque logic is otherwise identical to the pre-sparsification version; it's scoped to run-relative indices instead of the whole sequence.</p>
+<p>This runs once per genome that has at least one hit in the chunk (<code>process_chunk</code> iterates <code>by_genome</code>, one <code>Vec&lt;(seq_idx, pos_smer, value)&gt;</code> per genome, built from <code>QueryHit::Value</code> during the partition loop — genomes with zero hits in this chunk have an empty <code>Vec</code> and cost nothing beyond the iteration itself). Total work is <code>O(hits log hits)</code> per genome (the sort) rather than <code>O(n_smers)</code> per genome regardless of hit count — a genuine complexity win on top of the memory one, for the common case where most <code>(chunk, genome)</code> pairs have no or few hits.</p>
+<p>Output position <code>pos_out</code> is confirmed for genome <code>g</code> iff its run produced a nonzero <code>win_min</code> — equivalent to "all <code>z</code> consecutive s-mer values in the window are nonzero for <code>g</code>", same semantics as before.</p>
+<p><strong>The value reported per confirmed position is the window minimum, not the leftmost s-mer's raw value</strong> — unchanged from the dense version. For presence indexes (0/1 values) this is equivalent to a logical AND either way. For count indexes it is not: the accumulated count for genome <code>g</code> at position <code>pos_out</code> is the minimum across the window, the weakest link — not the leftmost s-mer's own count. The presence/count adjustment (<code>u32::from(win_min &gt;= threshold)</code> vs. raw <code>win_min</code>) is applied once, inside <code>sparse_findere_for_genome</code>, rather than later during accumulation.</p>
+<p><strong><code>kmer_missing</code> bookkeeping is independent of the per-genome sparse structures</strong>, by design (see roadmap point 9): a lightweight dense <code>SmerIndex</code> (<code>in_index: Vec&lt;bool&gt;</code>, sized <code>total_smers</code> — <strong>not</strong> multiplied by <code>n_genomes</code>) is populated from <code>QueryHit::Found</code> during the partition loop, one entry per hit k-mer regardless of which genome(s) it matched. A position with no genome confirmed counts as <code>kmer_missing</code> iff the leftmost s-mer of that window is absent from <code>SmerIndex</code> entirely (see <a href="#kmer_missing-semantics"><code>kmer_missing</code> semantics</a>).</p>
+<p><strong>Coverage (<code>--detail</code>)</strong> is built by re-scanning each genome's confirmed-hit list (already computed, no extra pass over raw data) and densifying into the <code>[u32; n_kmers_out]</code> arrays the JSON output format requires — but only when <code>--detail</code> is actually requested; the sparse structures cost nothing extra when it isn't.</p>
+<p><strong>Short sequences</strong>: when a sequence's s-mer count is less than <code>z</code>, its run(s) — if any hits exist at all — can never reach length <code>z</code>, so no window is ever confirmed for it; no k_user-mer is emitted, same outcome as the dense version's <code>n_kmers_out == 0</code> early-skip, reached here as a natural consequence rather than a separate check.</p>
+<p><strong>Exact indexes</strong>: <code>z = 1</code>, every single-hit "run" of length 1 immediately satisfies <code>k + 1 &gt;= z</code>, so every hit is its own confirmed window with <code>win_min</code> equal to its own value — a passthrough, as before.</p>
+<h3 id="effective-z-at-query-time">Effective z at query time</h3>
+<p><code>effective_z</code> is resolved at the start of <code>run()</code>:</p>
+<div class="highlight"><pre><span></span><code><span class="kd">let</span><span class="w"> </span><span class="n">effective_z</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">args</span><span class="p">.</span><span class="n">findere_z</span><span class="p">.</span><span class="n">unwrap_or_else</span><span class="p">(</span><span class="o">||</span><span class="w"> </span><span class="k">match</span><span class="w"> </span><span class="n">idx</span><span class="p">.</span><span class="n">meta</span><span class="p">().</span><span class="n">config</span><span class="p">.</span><span class="n">evidence</span><span class="w"> </span><span class="p">{</span>
+<span class="w">    </span><span class="n">IndexMode</span><span class="p">::</span><span class="n">Approx</span><span class="w"> </span><span class="p">{</span><span class="w"> </span><span class="n">z</span><span class="p">,</span><span class="w"> </span><span class="o">..</span><span class="w"> </span><span class="p">}</span><span class="w"> </span><span class="o">|</span><span class="w"> </span><span class="n">IndexMode</span><span class="p">::</span><span class="n">Hybrid</span><span class="w"> </span><span class="p">{</span><span class="w"> </span><span class="n">z</span><span class="p">,</span><span class="w"> </span><span class="o">..</span><span class="w"> </span><span class="p">}</span><span class="w"> </span><span class="o">=&gt;</span><span class="w"> </span><span class="n">z</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="kt">usize</span><span class="p">,</span>
+<span class="w">    </span><span class="n">IndexMode</span><span class="p">::</span><span class="n">Exact</span><span class="w"> </span><span class="o">=&gt;</span><span class="w"> </span><span class="mi">1</span><span class="p">,</span>
+<span class="p">});</span>
+</code></pre></div>
+<p>The <code>-z</code> CLI option overrides the index metadata value. A higher z increases stringency (lower FP, some true positives may be discarded at sequence ends); a lower z increases sensitivity.</p>
+<hr />
+<h2 id="layer-lookup-mphflayerfind">Layer lookup: <code>MphfLayer::find</code></h2>
+<p><code>MphfLayer::open(dir, mode: &amp;IndexMode)</code> receives the mode from <code>PartitionMeta</code> — no per-layer file is read. The caller (<code>QueryLayer</code>) never chooses the dispatch path: it is fixed at open time by <code>LayerEvidence</code>. See <a href="../../implementation/obilayeredmap/">obilayeredmap</a> for the full <code>find</code> / <code>find_strict</code> API.</p>
+<h3 id="querylayer-variant-selection"><code>QueryLayer</code> variant selection</h3>
+<p><code>QueryLayer::open</code> (<code>obikpartitionner/src/query_layer.rs:28-45</code>) only ever returns two variants — <code>Presence</code> or <code>Count</code>, checked in this order:</p>
+<table>
+<thead>
+<tr>
+<th>Order</th>
+<th>Condition</th>
+<th>Variant</th>
+<th>Data returned per k-mer</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>1</td>
+<td><code>with_counts=true</code> and <code>counts/</code> exists</td>
+<td><code>Count</code></td>
+<td>raw count per genome</td>
+</tr>
+<tr>
+<td>2</td>
+<td>(else) <code>presence/</code> exists, or <code>counts/</code> doesn't exist at all</td>
+<td><code>Presence</code></td>
+<td>see below</td>
+</tr>
+<tr>
+<td>3</td>
+<td>(else — <code>counts/</code> exists, <code>presence/</code> doesn't, <code>with_counts=false</code>)</td>
+<td><code>Count</code></td>
+<td>counts used as-is</td>
+</tr>
+</tbody>
+</table>
+<p>There is no <code>QueryLayer::SetOnly</code> variant. The "no on-disk matrix at all" case is handled one level down: <code>Presence</code> wraps <code>PersistentBitMatrix</code>, whose own <code>open()</code> (<code>obicompactvec/src/bitmatrix.rs:260-288</code>) auto-detects among <strong>three</strong> internal representations — <code>Packed</code> (<code>presence/matrix.pbmx</code>), <code>Columnar</code> (<code>presence/meta.json</code>), or <code>Implicit { n_rows, n_cols }</code> when neither file exists (built from <code>layer_meta.json</code>, <code>fill_row</code> returning all-<code>1</code>s without touching disk). This is where "1 for every genome" actually happens — not at the <code>QueryLayer</code> level.</p>
+<p><strong>Worth double-checking, not confirmed as a bug</strong>: <code>PersistentBitMatrix::open</code>'s <code>Implicit</code> branch constructs <code>Implicit { n_rows: meta.n, n_cols: 1 }</code> — <code>n_cols</code> is hardcoded to <code>1</code>, not to the layer's actual <code>n_genomes</code>. <code>fill_row</code> for <code>Implicit</code> only writes <code>buf[..1]</code>, leaving the rest of a longer <code>n_genomes</code>-sized buffer untouched (zeroed by the caller beforehand). If this path is ever reached for a layer covering more than one genome, only genome index 0 would read as present. Whether that's reachable in practice (layers might always be single-genome when they fall back to <code>Implicit</code>) wasn't verified here — flagging for follow-up, not fixing.</p>
+<hr />
+<h2 id="presence-count-mode-at-query-time">Presence / count mode at query time</h2>
+<p>The <code>--force-presence</code> flag and <code>--presence-threshold</code> control how per-genome values are accumulated, independently of what the index stores:</p>
+<div class="highlight"><pre><span></span><code>genome_totals[g] += if presence { u32::from(v &gt;= threshold) } else { v }
+</code></pre></div>
+<p><code>presence</code> is true when <code>--force-presence</code> is set or when the index has no counts (<code>!with_counts</code>). The default <code>presence_threshold</code> is 1, so any nonzero count counts as a match.</p>
+<hr />
+<h2 id="coverage-vectors-detail">Coverage vectors (<code>--detail</code>)</h2>
+<p>When <code>--detail</code> is requested, a 3-D accumulator <code>cov[seq_idx][genome][kmer_pos]</code> is allocated after all partitions are queried, with dimensions derived from <code>n_kmers_out = n_smers − z + 1</code> (k_user-mer positions, not s-mer positions):</p>
+<div class="highlight"><pre><span></span><code>cov[seq_idx][g][pos] += contribution
+where pos is the k_user-mer index in the filtered (post-Findere) vector
+</code></pre></div>
+<p>Coverage reflects confirmed k_user-mers only. The vectors are emitted in the JSON annotation under the key <code>"coverage"</code>.</p>
+<hr />
+<h2 id="kmer_missing-semantics"><code>kmer_missing</code> semantics</h2>
+<p><code>kmer_missing</code> counts k_user-mer positions where the leftmost s-mer of the window (<code>smer_index.is_in_index(seq_idx, pos)</code>, <code>SmerIndex</code>) is <code>false</code> — i.e. absent from the index entirely. K-mers where the z-window fails because a later s-mer is absent or zero (but the leftmost one is present) are not counted as missing — the leftmost s-mer being present is used as proxy for index membership.</p>
+<hr />
+<h2 id="output-format">Output format</h2>
+<p>Output sequences are written in <strong>OBITools4 format</strong>: the original sequence with a JSON annotation map in the title line.</p>
+<div class="highlight"><pre><span></span><code>&gt;read_id {&quot;kmer_count&quot;:59,&quot;kmer_strict_matches&quot;:{&quot;genome_a&quot;:42,&quot;genome_b&quot;:7}}
+ATCGATCG...
+</code></pre></div>
+<p>With <code>--detail</code>:</p>
+<div class="highlight"><pre><span></span><code>&gt;read_id {&quot;kmer_count&quot;:59,&quot;kmer_strict_matches&quot;:{...},&quot;coverage&quot;:{&quot;genome_a&quot;:[0,1,2,...],...}}
+ATCGATCG...
+</code></pre></div>
+<p>Genome keys follow the iteration order of <code>meta.genomes</code>.</p>
+<hr />
+<h2 id="annotation-schema">Annotation schema</h2>
+<table>
+<thead>
+<tr>
+<th>Key</th>
+<th>Type</th>
+<th>Condition</th>
+<th>Semantics</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>kmer_count</code></td>
+<td>int</td>
+<td>always</td>
+<td>k-mers confirmed (post-Findere) with at least one genome match</td>
+</tr>
+<tr>
+<td><code>kmer_missing</code></td>
+<td>int</td>
+<td><code>--count-missing</code></td>
+<td>k-mers absent from the index entirely (leftmost s-mer of the window not found)</td>
+</tr>
+<tr>
+<td><code>kmer_strict_matches</code></td>
+<td>object</td>
+<td>always</td>
+<td>per-genome accumulated value, non-zero entries only (label → count or 0/1)</td>
+</tr>
+<tr>
+<td><code>coverage</code></td>
+<td>object</td>
+<td><code>--detail</code></td>
+<td>per-genome array of per-position contributions (label → [u32])</td>
+</tr>
+</tbody>
+</table>
+<p><code>kmer_count + kmer_missing</code> ≤ total k_user-mers in the sequence. The gap corresponds to k_user-mers whose z-window was not fully confirmed (at least one s-mer absent or zero for all genomes) but whose first s-mer was present in the index.</p>
+<hr />
+<h2 id="cli">CLI</h2>
+<div class="highlight"><pre><span></span><code>obikmer query &lt;index&gt; [--detail] [--mismatch] [--count-missing]
+              [--force-presence] [--presence-threshold &lt;n&gt;]
+              [-z &lt;z&gt;] [-T &lt;threads&gt;] [--chunk-size &lt;MiB&gt;]
+              &lt;query.fa&gt; [&lt;query2.fa&gt; ...]
+</code></pre></div>
+<table>
+<thead>
+<tr>
+<th>Option</th>
+<th>Default</th>
+<th>Semantics</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>-z</code> / <code>--findere-z</code></td>
+<td>from index metadata</td>
+<td>Override Findere z parameter</td>
+</tr>
+<tr>
+<td><code>--detail</code></td>
+<td>off</td>
+<td>Emit per-position coverage vectors in JSON</td>
+</tr>
+<tr>
+<td><code>--count-missing</code></td>
+<td>off</td>
+<td>Add <code>kmer_missing</code> field to JSON</td>
+</tr>
+<tr>
+<td><code>--force-presence</code></td>
+<td>off</td>
+<td>Report 0/1 per genome regardless of index counts</td>
+</tr>
+<tr>
+<td><code>--presence-threshold</code></td>
+<td>1</td>
+<td>Minimum count to declare genome present</td>
+</tr>
+<tr>
+<td><code>-T</code> / <code>--threads</code></td>
+<td>all CPUs</td>
+<td>Worker threads</td>
+</tr>
+<tr>
+<td><code>--chunk-size</code></td>
+<td>auto (from available RAM and thread count)</td>
+<td>I/O chunk size in MiB — see <a href="#throughput--parallelism--identified-potential-not-yet-implemented">Future work, point 3</a> for why the auto-sizing formula currently under-estimates memory on indexes with many genomes</td>
+</tr>
+</tbody>
+</table>
+<p><code>--mismatch</code> is accepted but currently ignored with a warning on stderr.</p>
+<hr />
+<h2 id="future-work">Future work</h2>
+<ul>
+<li><strong><code>--mismatch</code></strong>: 1-mismatch approximate matching — generate <code>3·k</code> single-substitution variants per k-mer, look each up independently.</li>
+<li><strong>Read classification</strong> (<code>--classify</code>): assign each read to the genome with the highest match score.</li>
+<li><strong>Whitelist / blacklist filtering</strong>: threshold-based accept/reject on per-genome match scores.</li>
+</ul>
+<h3 id="throughput-parallelism-identified-potential-not-yet-implemented">Throughput &amp; parallelism — identified potential (not yet implemented)</h3>
+<p>Observed on a 192-core (8×24 NUMA) machine: <code>query</code> uses ~10 cores or fewer, and the default chunk size gets the process OOM-killed. Root causes and candidate fixes, in dependency order:</p>
+<p><strong>1. Single-threaded I/O source (main core-utilization bottleneck).</strong>
+<code>run()</code> builds <code>all_chunks</code> via <code>paths.into_iter().flat_map(read_sequence_chunks_sized(...))</code> and passes it directly as the <code>input</code> iterator to <code>pipe.apply()</code>. In <code>obipipeline::Pipe::apply</code> (<code>scheduler.rs</code>), <code>input.next()</code> is called exclusively from the dedicated source thread — so file opening, decompression, and FASTA/FASTQ chunk-boundary parsing for <em>all</em> input files run serially in one thread, regardless of <code>--threads</code>. Compare with <code>steps::scatter</code> (used by <code>index</code>) and <code>cmd/superkmer.rs</code>: there, file opening + streaming is itself a <code>Flat</code> pipeline stage (<code>||?</code>), executed across the <code>n_workers</code> pool, with <code>obipipeline::throttle(paths, max_open)</code> bounding concurrently-open files in the source thread. That pattern parallelises I/O across files (and NUMA nodes); <code>query.rs</code> cannot.
+Fix direction: restructure <code>query</code>'s pipe with an initial <code>Flat</code> stage analogous to <code>scatter</code>'s, opening/chunking files across workers instead of in <code>flat_map</code>.</p>
+<p><strong>2. Gzip decompression is inherently single-threaded per file.</strong>
+<code>niffler</code>/<code>flate2</code> (used by <code>xopen</code>) do standard DEFLATE, which has no parallel-decodable structure for an arbitrary stream. Fix (1) parallelises <em>across</em> files but not <em>within</em> one large gzip file. Parking a possible fix (<code>rapidgzip-rs</code>) is tracked in <a href="../../implementation/chunkreader/#future-work--parallel-gzip-decompression-in-xopen">chunkreader.md</a>.</p>
+<p><strong>3. Chunk-size memory formula ignores <code>n_genomes</code>.</strong>
+<code>chunk_bytes = available_memory_bytes() / (n_workers * 16)</code> (<code>query.rs:407-414</code>) assumes a fixed ~8–16× overhead per raw input byte. But <code>KmerResults::new</code> (<code>query.rs:165-179</code>) allocates <code>data: Vec&lt;u32&gt;</code> sized <code>total_kmers_in_chunk × n_genomes</code> — dense, <strong>for every k-mer position in the chunk, hit or not</strong> — plus <code>win_min</code> and (with <code>--detail</code>) <code>cov</code>, same scaling. Real per-chunk memory is <code>O(n_genomes)</code>, not constant; the formula doesn't know <code>n_genomes</code> at all. This is the direct cause of the OOM kill on indexes with many reference genomes.</p>
+<p><strong>4. MPHF lookup and matrix-row fetch are fused, not staged.</strong>
+<code>QueryLayer::find_into</code> (<code>obikpartitionner/src/query_layer.rs:48-67</code>) does the MPHF <code>find</code> <em>and</em> the <code>fill_row</code> matrix read in one call per k-mer, inside a single-threaded loop (<code>query_partition_with</code>). There is no separation between "is this k-mer indexed" (cheap, <code>O(1)</code>, independent of <code>n_genomes</code>) and "what are its per-genome values" (the expensive, <code>n_genomes</code>-scaling part).</p>
+<p><strong>5. Dereplication should happen at k-mer granularity, directly — not via an intermediate superkmer-level dedup.</strong>
+<code>QueryBatch::from_records</code> currently dereplicates at the <em>superkmer</em> level (<code>HashMap&lt;RoutableSuperKmer, Vec&lt;SKDesc&gt;&gt;</code>, <code>query.rs:112</code>). This misses redundancy between k-mers shared by <em>different</em> superkmers (read overlaps, repeats, a SNP splitting an otherwise-identical run). Superkmer <em>construction</em> (<code>SuperKmerIter</code>) stays mandatory — it is the mechanism that computes minimizers/partition routing, not an optional dedup layer — but the dedup structure built on top of it should key directly on <code>CanonicalKmer</code>, in the same pass: <code>HashMap&lt;CanonicalKmer, Vec&lt;(seq_idx, pos)&gt;&gt;</code>. This also means the MPHF <code>find</code> itself runs once per <strong>distinct</strong> k-mer instead of once per occurrence — a win independent of the matrix-fetch cost below.</p>
+<p><strong>6. Stage 1 output: bucket confirmed hits by layer, keyed by MPHF slot.</strong>
+For each unique canonical k-mer, MPHF lookup across a partition's layers stops at the first match (<code>query_partition_with:105-111</code>) — a k-mer belongs to at most one layer. So stage 1's output can be reshaped directly into:
+<div class="highlight"><pre><span></span><code>HashMap&lt;layer_idx, HashMap&lt;slot, Vec&lt;(seq_idx, pos)&gt;&gt;&gt;
+</code></pre></div>
+replacing the <code>CanonicalKmer</code> key by the resolved <code>slot</code> (compact integer, and exactly what stage 2 needs to address the matrix). K-mers matching no layer simply have no entry here (they still count toward <code>in_index</code>/<code>kmer_missing</code> bookkeeping, which stays <code>O(1)</code> per position, independent of <code>n_genomes</code>).</p>
+<p><strong>7. Partition-level parallelism is currently absent — and a NUMA-aware mechanism for exactly this already exists, unused, in <code>obikindex</code>.</strong>
+<code>process_chunk</code>'s partition loop (<code>query.rs:250-278</code>, <code>for (part_idx, part_sks) in by_part.iter().enumerate()</code>) processes every partition of a chunk sequentially on the single worker thread that owns that chunk. This is a parallelism axis on its own, independent of the column question below.
+More importantly: <code>docmd/architecture/numa_partition_runner.md</code> and <code>numa_worker_pools.md</code> document <code>PartitionRunner</code> (<code>obikindex/src/numa.rs</code>), <strong>already implemented</strong> and already used by <code>merge.rs</code>, <code>index.rs</code> (<code>build_layers</code>), <code>select.rs</code>, <code>reindex.rs</code>, <code>rebuild.rs</code> — one controller thread per NUMA node, a Rayon pool pinned to that node's CPUs (<code>hwlocality</code>, <code>numa</code> feature, default-on in <code>obikindex/Cargo.toml</code>), adaptive worker activation driven by <em>both</em> a CPU-efficiency signal and an I/O-throughput signal (<code>CpuSample</code>/<code>IoSample</code>, <code>/proc/self/io</code> on Linux). It exists precisely because a naive <code>into_par_iter()</code> on the global Rayon pool measurably degrades ×60 on this codebase's own 192-core/8-NUMA reference machine (<code>numa_worker_pools.md</code>, § Problem) once workers contend for cross-socket memory bandwidth on shared mmap'd/hashed structures — exactly the shape of the matrix-column scan in point 8 below.
+<code>obikmer</code> already depends on <code>obikindex</code> (<code>obikmer/Cargo.toml</code>, for <code>KmerIndex</code>), so <code>PartitionRunner</code> is directly reachable from <code>cmd/query.rs</code> — no new dependency. Both the partition-level loop and (see point 8) the genome-column scan should be driven through it rather than through ad-hoc <code>rayon::into_par_iter()</code>, to avoid reproducing the already-measured-and-fixed contention problem. Also relevant: the "CPU-only signal stalls on I/O-bound stages" issue documented for <code>pack_matrices</code> (mmap-heavy, page-fault-bound) applies just as much to a column-major mmap scan over persistent matrices — reuse the existing dual CPU/IO activation signal rather than re-deriving one.</p>
+<blockquote>
+<p><strong>Correction from implementation (Phase 4 below)</strong>: this turned out not to be viable as described. <code>PartitionRunner::run()</code>'s actual body spawns roughly one OS thread per worker slot across every NUMA node <strong>on every call</strong> (confirmed by reading <code>numa.rs</code>, not just its doc comments) — fine for the one-call-per-command-invocation batch usage in <code>merge</code>/<code>build_layers</code>, but <code>query_partition_with</code> runs once per <code>(chunk, partition)</code>, far too frequently to absorb that spawn cost. Partition-level parallelism via <code>PartitionRunner</code> is deferred, not implemented. See Phase 4's "What did not ship, and why" for the detail.</p>
+</blockquote>
+<p><strong>8. Stage 2: column-major matrix fetch, parallel across genome columns — via <code>PartitionRunner</code>, not naive <code>rayon</code>.</strong>
+Both persistent matrix formats are column-oriented on disk: <code>ColumnarCompactIntMatrix</code>/<code>ColumnarBitMatrix</code> (<code>obicompactvec/src/{intmatrix,bitmatrix}.rs</code>) mmap one file per genome column; <code>PackedCompactIntMatrix</code>/<code>PackedBitMatrix</code> mmap one region-offset per column in a single file. <code>fill_row(slot, buf)</code> as used today (<code>query.rs:262-272</code> via <code>on_hit</code>) reads <strong>one slot across all <code>n_genomes</code> columns</strong> per hit — the worst possible access pattern for this layout (up to <code>n_genomes</code> scattered mmap regions touched per single k-mer).
+Better: for each layer, walk the matrix <strong>column by column</strong> (genome by genome): for each genome, scan the <code>slot</code> keys collected in step 6 for that layer and call <code>col.get(slot)</code>, keeping only nonzero results, and broadcast to the associated <code>(seq_idx, pos)</code> list. Total <code>get()</code> calls are unchanged (<code>n_hits × n_genomes</code> in the worst case) — the win is locality (sequential access within one mmap'd column at a time, not scattered across all columns per hit), not fewer operations.
+Columns are independent (read-only, disjoint mmap regions) → embarrassingly parallel across genomes, <em>but</em> — per point 7 — <code>obicompactvec</code>'s existing <code>into_par_iter()</code> over <code>0..n_cols</code> (<code>sum()</code>, <code>count_nonzero()</code>, pairwise distance matrices) is the <strong>naive, unpinned</strong> pattern the rest of the codebase is actively migrating away from, not a model to copy here. Route this through <code>PartitionRunner</code> (or the same NUMA-pool machinery) instead. Two things to settle when this is designed: how the partition axis (point 7), the column axis, and the existing chunk-level <code>n_workers</code> <code>obipipeline</code> pool compose without oversubscribing the machine (three different concurrency mechanisms — raw-thread pipe workers, <code>PartitionRunner</code>'s pinned Rayon pools, and whatever drives the column scan — need a single reconciled thread budget, not three independent ones); and the threshold below which per-column dispatch overhead outweighs the gain (small <code>n_genomes</code> or small per-layer hit counts) — to be measured, not assumed.</p>
+<blockquote>
+<p><strong>Correction from implementation (Phase 4 below)</strong>: column-major fetch is implemented — but as a plain sequential loop, not parallelised via <code>PartitionRunner</code>. Same reason as point 7's correction above. The column-major <em>locality</em> win (the actual claim of this point) does not depend on adding parallelism on top of it, and is validated independently. Column-level parallelism is deferred pending a mechanism that fits this call frequency (candidates noted in Phase 4).</p>
+</blockquote>
+<p><strong>9. Sparse per-genome representation, fed directly to Findere.</strong>
+Stage 2's output should be <code>HashMap&lt;genome_idx, Vec&lt;(seq_idx, position, count)&gt;&gt;</code>, <strong>sorted by <code>(seq_idx, position)</code></strong> once collected, instead of a dense <code>KmerResults</code>-style matrix — the key must carry <code>seq_idx</code>, not just <code>genome_idx</code>, because a chunk batches many sequences and <code>position</code> is only meaningful within one; a plain <code>Vec&lt;(position, count)&gt;</code> per genome would silently mix positions from different sequences and corrupt the sliding-window scan. This bounds retained memory by actual nonzero hits on both axes (position sparsity from non-matching k-mers, genome sparsity from a matched k-mer typically belonging to only a handful of genomes out of possibly many). The Findere sliding-window (<code>process_chunk</code>, the <code>win_min</code>/deque loop) would need reworking to run per <code>(sequence, genome)</code> over its sparse, sorted <code>(position, count)</code> list — detect runs of ≥<code>z</code> consecutive positions, window-min within each run — instead of today's dense <code>O(total_kmers × n_genomes)</code> scan. This is also a genuine complexity win (<code>O(hits log hits)</code> per genome vs. dense scan), not just memory.
+<strong>Not covered by this sparsification</strong>: <code>--detail</code>'s <code>cov</code> accumulator (<code>query.rs:304-308</code>) has the identical <code>n_genomes</code>-dense scaling problem and wasn't folded into points above. It doesn't need to be retained densely throughout processing, though — only the final JSON serialization (<code>emit_batch</code>) requires a dense <code>[u32]</code> per <code>(seq, genome)</code>, and only for the sequences actually being output with <code>--detail</code>. Densification can stay a late, output-time-only step, reconstructed from the sparse per-genome lists.</p>
+<p><strong>Secondary patterns available from <code>scatter.rs</code>/<code>superkmer.rs</code>, not yet in <code>query.rs</code>:</strong>
+- <code>throttle()</code> + <code>CommonArgs::effective_max_open()</code> to bound concurrently-open input files (query.rs defines its own <code>QueryArgs</code>, doesn't reuse this).
+- Progress bar with EMA throughput + live active-worker gauges (<code>obisys::spinner</code>, <code>flat_active</code>/<code>transform_active</code> counters) — diagnostic value for locating the bottleneck.
+- <code>obisys::Reporter</code>/<code>Stage::start</code>/<code>stop</code> timing per phase (used by <code>index</code>, <code>filter</code>; absent from <code>query</code>).</p>
+<p>None of this is implemented yet — parked here as a coherent roadmap while the design is discussed further. Suggested dependency order: (1) I/O parallelism → (3) genome-aware chunk sizing → (4)–(9) staged/k-mer-deduped/NUMA-aware-partition-and-column-major/sparse query engine (larger refactor, biggest structural payoff — reuses <code>PartitionRunner</code> rather than inventing a new parallelism mechanism) → (2) parallel gzip (separate, orthogonal, tracked in chunkreader.md) → secondary diagnostics patterns.</p>
+<hr />
+<h2 id="implementation-plan">Implementation plan</h2>
+<p>Concrete, phased translation of the roadmap above. Phases 0–2 are small, independent, low-risk, and each individually testable against current <code>query</code> output — land them first, in order, and measure on the reference 192-core/8-NUMA machine before deciding whether phases 3–5 (the staged/sparse engine, the larger structural payoff) are still worth their cost. Phases 3–5 are one coordinated change spanning <code>obikmer</code>, <code>obikpartitionner</code>, and <code>obicompactvec</code> — they should not be split across releases mid-way, because the intermediate state (e.g. k-mer-level dedup feeding the old dense <code>KmerResults</code>) has no correctness or performance benefit on its own. Phase 6 is unrelated to phases 0–5 and can happen any time, independently, if <code>rapidgzip-rs</code> is validated (see <a href="../../implementation/chunkreader/#future-work--parallel-gzip-decompression-in-xopen">chunkreader.md</a>).</p>
+<p>Instrumentation is deliberately sequenced <em>before</em> the I/O fix (reordering the roadmap's own listed order), because every later phase's justification rests on a measurement ("to be measured, not assumed" appears throughout the roadmap above) — without it, phases 3–5 would be undertaken on faith.</p>
+<p>Performance measurement on the reference 192-core/8-NUMA machine is done by the project owner, not from this development environment (macOS, 16 cores — <code>PartitionRunner</code>'s NUMA pinning is Linux-only, so even phase 4's mechanism can't be functionally exercised for its actual purpose here). Each phase below is therefore written to be <em>self-measuring</em>: the debug-level logging it adds must be enough, on its own, to judge whether that phase's algorithmic choice paid off from a cluster run's logs, without needing to attach a profiler.</p>
+<h3 id="conventions-applied-to-every-phase-below">Conventions applied to every phase below</h3>
+<p><strong>Debug logging.</strong> Every phase that changes an algorithmic choice (not phase 0, which <em>is</em> the logging) adds <code>tracing::debug!</code>/<code>trace!</code> at points that let a cluster run's logs answer "did this help": counts, ratios, and timings that quantify the specific claim that phase makes — e.g. phase 3 must log how many MPHF <code>find</code> calls were saved by k-mer-level dedup (the whole justification for that phase), phase 4 must log per-column scan timings, phase 5 must log actual retained-memory / sparsity ratios achieved. Prefer one structured <code>debug!</code> per chunk (fields, not prose) over free-text — the cluster logs will be the only evidence available for judging these choices, so they need to be grep/awk-able, not just readable.</p>
+<p><strong>Unit tests.</strong> This project's convention (<code>obiread</code>, <code>obikseq</code>, <code>obidebruinj</code>, <code>obicompactvec</code>, <code>obilayeredmap</code>, <code>obiskio</code>, <code>obifastwrite</code>) is <code>#[cfg(test)] #[path = "tests/&lt;name&gt;.rs"] mod tests;</code> at the bottom of the source file, with the actual test code in a sibling <code>src/tests/&lt;name&gt;.rs</code>. Neither <code>obikmer</code> nor <code>obikpartitionner</code> (the two crates phases 3 and 5 touch most) currently have a <code>src/tests/</code> directory at all — this needs creating, following the existing pattern exactly, not inventing a new one.</p>
+<p><strong>Workflow (<code>jj</code>).</strong> Work happens in a fresh <code>jj</code> commit, easy to abandon. <code>jj new</code> between phases is reasonable where it helps isolate a phase for review, but only when the working copy compiles at that point (project convention) — phase 3's internal sub-steps (batch dedup change, then <code>query_layer.rs</code> split, then the new return shape) will likely not each compile independently since they're one coupled change, so treat "commit boundary" and "plan phase boundary" as related but not forced to match 1:1; use judgement per phase rather than mechanically splitting on every bullet.</p>
+<h3 id="phase-0-instrumentation-prerequisite-for-measuring-every-later-phase">Phase 0 — Instrumentation (prerequisite for measuring every later phase)</h3>
+<p><strong>Goal</strong>: make core utilization, throughput, and per-stage timing visible on a real run, so phases 1–5 can be justified with numbers instead of assumption.</p>
+<ul>
+<li><code>obikmer/src/cmd/query.rs</code>: wrap <code>run()</code>'s main loop with <code>obisys::Reporter</code>/<code>Stage::start("query")</code>/<code>.stop()</code>, printed at the end via <code>rep.print()</code> — same pattern as <code>index.rs</code>/<code>filter.rs</code>.</li>
+<li>Add an <code>obisys::spinner("query")</code> progress bar around the <code>pipe.apply(...)</code> loop, with an EMA throughput readout (bases/s or k-mers/s, mirroring <code>steps::scatter</code>'s <code>ema_rate</code> computation, <code>scatter.rs:88-118</code>) and live gauges for "chunks in flight" / "workers busy" — reuse the <code>AtomicU32</code> counter pattern from <code>scatter.rs</code> (<code>flat_active</code>, <code>transform_active</code>) rather than inventing a new one.</li>
+<li>Add <code>max_open_files: Option&lt;usize&gt;</code> to <code>QueryArgs</code> and a <code>effective_max_open()</code> method mirroring <code>CommonArgs::effective_max_open()</code> (<code>obikmer/src/cli.rs:90-94</code>) — needed by phase 1's <code>throttle()</code> call. (<code>QueryArgs</code> can't just embed <code>CommonArgs</code> — it doesn't take <code>kmer_size</code>/<code>minimizer_size</code>/<code>partitions</code>/<code>level_max</code>/<code>theta</code> from the CLI, those come from the index metadata — so this is a small standalone addition, not a flatten.)</li>
+<li>Add one structured <code>debug!</code> per <code>process_chunk</code> call: chunk byte size, sequence count, s-mer count, wall time, and (once later phases exist) the fields they add — this single log line is the baseline every later phase's own logging gets compared against.</li>
+<li><strong>Validation</strong>: none needed beyond "the numbers appear and look sane" — this phase changes no query logic or output.</li>
+<li><strong>Deliverable used by every phase below</strong>: a before/after throughput and core-utilization measurement on the reference machine.</li>
+</ul>
+<h3 id="phase-1-parallel-per-file-io-fixes-root-cause-of-low-core-utilization">Phase 1 — Parallel per-file I/O (fixes root cause of low core utilization)</h3>
+<p><strong>Goal</strong>: file opening, decompression, and chunk-boundary parsing run across the <code>n_workers</code> pool instead of serially in the pipe's dedicated source thread.</p>
+<ul>
+<li><code>obikmer/src/cmd/query.rs</code>:</li>
+<li>Replace the <code>paths.into_iter().flat_map(read_sequence_chunks_sized(...))</code> construction (current <code>run()</code>, building <code>all_chunks</code>) with <code>obipipeline::throttle(paths.into_iter(), args.effective_max_open())</code>, passed as the pipe's <code>input</code>.</li>
+<li>Add a new <code>QueryData::Path(PathBuf)</code> variant (alongside <code>Chunk</code>/<code>Output</code>) to carry the throttled path through the pipe's type-erasure mechanism.</li>
+<li>Add a new <strong>first</strong> pipe stage, <code>Flat</code>/fallible (<code>||?</code>), modeled on <code>scatter.rs:60-86</code> and <code>superkmer.rs:54-65</code>: given a <code>Throttled&lt;PathBuf&gt;</code>, call <code>read_sequence_chunks_sized(path, chunk_bytes)</code> and yield each <code>Rope</code> chunk, keeping <code>pw.guard</code> alive until the file's iterator is exhausted (reuse or adapt <code>scatter.rs</code>'s <code>GuardedIter</code> wrapper — same lifetime problem, same fix).</li>
+<li>The existing <code>process_chunk</code> transform stage becomes the pipe's <strong>second</strong> stage, unchanged in its own logic — it still receives one <code>Rope</code> chunk at a time, just no longer all coming from one serial source.</li>
+<li><code>make_pipe!</code> invocation grows from one stage (<code>Chunk =&gt; Output</code>) to two (<code>Path =&gt; Chunk =&gt; Output</code>).</li>
+<li>Log, per file: time spent waiting on the <code>throttle()</code> slot (queueing due to <code>max_open</code>), and time spent opening/decompressing/producing the first chunk — this is what directly proves (or disproves) that I/O is now spread across workers instead of serialized.</li>
+<li><strong>Validation</strong>: run <code>query</code> on a small multi-file input, diff output against the pre-change version — content must be identical; <strong>record order across files is not guaranteed to be preserved</strong> even before this change (chunk-level dispatch across <code>n_workers</code> already reorders completions), so the diff must be order-insensitive (sort by read id, or compare as sets) if it wasn't already.</li>
+<li><strong>Measure</strong>: core utilization on the reference machine with several large input files, compare against phase 0's baseline.</li>
+</ul>
+<h3 id="phase-2-genome-aware-chunk-size-formula-fixes-oom">Phase 2 — Genome-aware chunk-size formula (fixes OOM)</h3>
+<p><strong>Goal</strong>: <code>chunk_bytes</code> reflects actual per-chunk memory (<code>O(n_genomes)</code>), not a fixed multiplier.</p>
+<ul>
+<li><code>obikmer/src/cmd/query.rs</code>, <code>run()</code>: <code>n_genomes</code> and <code>args.detail</code> are already computed above the <code>chunk_bytes</code> calculation (<code>n_genomes</code> at the top of <code>run()</code>, before line 407 in the current file) — reorder if needed, then replace:
+  <div class="highlight"><pre><span></span><code><span class="kd">let</span><span class="w"> </span><span class="n">computed</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">avail</span><span class="w"> </span><span class="o">/</span><span class="w"> </span><span class="p">(</span><span class="n">n_workers</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="kt">u64</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="mi">16</span><span class="p">);</span>
+</code></pre></div>
+  with a formula that scales the divisor by <code>n_genomes</code> (and roughly doubles it when <code>--detail</code> is set, since <code>cov</code> duplicates the per-genome accumulation): e.g. <code>per_chunk_multiplier = base_overhead + n_genomes as u64 * BYTES_PER_KMER_PER_GENOME * if detail { 2 } else { 1 }</code>, replacing the flat <code>16</code>. <code>BYTES_PER_KMER_PER_GENOME</code> should be derived from <code>KmerResults</code>'s actual layout (<code>4</code> bytes per <code>u32</code> entry in <code>data</code>, plus the <code>bool</code> in <code>in_index</code>, plus <code>win_min</code>'s equal-sized buffer) rather than guessed.</li>
+<li><code>args.chunk_size</code> (manual <code>--chunk-size</code> override) keeps taking priority, unchanged.</li>
+<li>Log the resolved <code>chunk_bytes</code>, <code>n_genomes</code>, and the estimated peak per-chunk memory (<code>chunk_bytes</code> × the same multiplier used to derive it) once at startup — lets a cluster run confirm the estimate was actually respected, not just that the process didn't get OOM-killed (which could also happen to be true for the wrong reason).</li>
+<li><strong>Validation</strong>: build a test index with a large <code>n_genomes</code> (e.g. hundreds), run <code>query</code> with default chunk sizing under a memory limit (<code>ulimit -v</code> or a cgroup), confirm it no longer gets OOM-killed and that memory scales as predicted when <code>n_genomes</code> grows.</li>
+<li><strong>Note</strong>: this phase is superseded once phase 5 lands (sparse retained memory no longer scales with <code>n_genomes × total_kmers</code> at all) — but it's needed immediately regardless, since phases 3–5 are a bigger, riskier change and users need a working <code>query</code> in the meantime.</li>
+</ul>
+<h3 id="phase-3-k-mer-level-dereplication-staged-mphfmatrix-lookup">Phase 3 — K-mer-level dereplication, staged MPHF/matrix lookup</h3>
+<p><strong>Goal</strong>: replace superkmer-level dedup with k-mer-level dedup (roadmap point 5), and split the fused MPHF-find/matrix-fetch (point 4) so stage 1's output is bucketed by layer and MPHF slot (point 6).</p>
+<ul>
+<li><code>obikmer/src/cmd/query.rs</code>:</li>
+<li>Replace <code>QueryBatch::from_records</code>'s dedup map (<code>HashMap&lt;RoutableSuperKmer, Vec&lt;SKDesc&gt;&gt;</code>, current <code>query.rs:112</code>) with a per-partition <code>HashMap&lt;CanonicalKmer, Vec&lt;(seq_idx: u32, pos: u32)&gt;&gt;</code>, built in the same <code>SuperKmerIter</code> pass: superkmer construction and partition routing (<code>part_idx</code> from the superkmer's minimizer hash) are unchanged, only the granularity of what gets deduplicated changes — each <code>CanonicalKmer</code> within a superkmer is inserted individually instead of the whole superkmer being the dedup key.</li>
+<li><strong>Verified</strong>: <code>CanonicalKmer</code> (<code>obikseq/src/kmer.rs:390</code>, <code>pub type CanonicalKmer = CanonicalKmerOf&lt;KLen&gt;</code>) — the underlying <code>CanonicalKmerOf&lt;L&gt;</code> derives <code>Debug, Clone, Copy, PartialEq, Eq, PartialOrd, Ord, Hash</code> (<code>kmer.rs:269</code>). Usable as a <code>HashMap</code>/<code>HashSet</code> key as-is, no change needed.</li>
+<li><code>obikpartitionner/src/query_layer.rs</code>:</li>
+<li>Split <code>QueryLayer::find_into</code> (<code>query_layer.rs:48-67</code>) into two methods: <code>find_slot(&amp;self, kmer: CanonicalKmer) -&gt; Option&lt;usize&gt;</code> (MPHF only, no matrix touch) and keep <code>fill_row</code> as-is for phase 4 to call later.</li>
+<li>Replace <code>query_partition_with</code>'s inner loop (<code>query_layer.rs:103-113</code>) with a version that, for each unique <code>CanonicalKmer</code>, calls <code>find_slot</code> across the partition's layers (stopping at first hit, same as today), and instead of immediately filling a row, records <code>(layer_idx, slot)</code>.</li>
+<li>New return shape for the partition-level query, replacing today's <code>on_hit(sk_idx, kmer_idx, row)</code> callback: <code>HashMap&lt;layer_idx, HashMap&lt;slot, Vec&lt;(seq_idx, pos)&gt;&gt;&gt;</code> (roadmap point 6) — built directly from the k-mer dedup map's <code>Vec&lt;(seq_idx,pos)&gt;</code> values, keyed by the resolved slot instead of the k-mer.</li>
+<li><strong>This phase alone has no throughput benefit yet</strong> (matrix fetch still happens, just deferred) beyond the k-mer-level dedup itself (fewer MPHF calls when queries have overlapping/repeated k-mers) — its purpose is to produce the input phase 4 needs. Land phase 3+4 together, not phase 3 alone, per the "don't split 3–5 across releases" note above.</li>
+<li>Log, per chunk: total k-mer occurrences vs. unique <code>CanonicalKmer</code> count (the dedup ratio — the entire justification for this phase) and the resulting MPHF <code>find</code> call count. If the dedup ratio is close to <code>1.0</code> on real query data (little redundancy), that's the cluster run telling us this phase wasn't worth it — the logging needs to be able to say that, not just confirm the happy path.</li>
+<li><strong>Unit tests</strong>: create <code>obikmer/src/cmd/tests/query.rs</code> (new <code>src/tests/</code> dir for this crate, following the project's <code>#[cfg(test)] #[path = "tests/query.rs"] mod tests;</code> convention) and <code>obikpartitionner/src/tests/query_layer.rs</code> (likewise new for this crate). Cover: the k-mer-level dedup map construction on synthetic sequences with known repeated/overlapping k-mers (assert unique-kmer count and occurrence lists); the <code>find_slot</code>/bucket-by-layer-and-slot construction against a small hand-built <code>QueryLayer</code> fixture, asserting the <code>(layer_idx, slot, seq_idx, pos)</code> tuples match what the old per-occurrence loop would have produced.</li>
+</ul>
+<h3 id="phase-4-column-major-matrix-fetch-roadmap-points-78-implemented-numa-parallelism-deferred">Phase 4 — Column-major matrix fetch (roadmap points 7–8) — implemented, NUMA parallelism deferred</h3>
+<p><strong>Goal (revised during implementation)</strong>: replace <code>fill_row</code>-per-hit (row-major, worst-case mmap locality) with a column-major scan. <code>PartitionRunner</code> turned out to be the wrong mechanism for this at this call granularity — see below; the column-major fetch itself is implemented and validated, without it.</p>
+<p><strong>What shipped:</strong>
+- <code>obicompactvec</code>: the per-column accessors this phase needed <strong>already existed</strong> — <code>PersistentCompactIntMatrix::col_view(c)</code> and <code>PersistentBitMatrix::col_view(c)</code> are public, and <code>IntSliceView::get(slot)</code>/<code>BitSliceView::get(slot)</code> are public — the original plan underestimated how much of this plumbing the pairwise-distance code (<code>dump</code>/<code>select</code>/<code>stats</code>) had already required. The one real gap: <code>PersistentBitMatrix::col_view()</code> panics on the <code>Implicit</code> variant (the documented mono-genome fast path, <code>bitmatrix.rs</code>). Added <code>PersistentBitMatrix::get(c, slot) -&gt; u32</code> (<code>bitmatrix.rs</code>), a non-panicking column-major point lookup that returns <code>1</code> for <code>Implicit</code> regardless of <code>c</code> — the smallest surface needed, not a new <code>col_get</code> API from scratch.
+- <code>obikpartitionner/src/query_layer.rs</code>: <code>query_partition_with</code> is now two explicit stages, matching roadmap points 6–8: <strong>stage 1</strong> (MPHF-only, per unique k-mer, bucket hits by <code>(layer_idx, slot)</code>, emits <code>QueryHit::Found</code>) then <strong>stage 2</strong> (per layer with ≥1 hit, column-major: for each genome column <code>g</code> in <code>0..layer.n_cols().min(n_genomes)</code>, scan that layer's bucketed slots and call <code>col_value(g, slot)</code>, emitting <code>QueryHit::Value(descs, g, value)</code> on nonzero). <code>QueryHit</code> is a single enum delivered through one <code>FnMut(QueryHit)</code> callback — an earlier two-closure design (<code>on_found</code> + <code>on_value</code>) didn't borrow-check, since the caller's single mutable accumulator (<code>KmerResults</code>) can't be captured by two separate <code>FnMut</code> closures passed to the same call.
+- <code>obikmer/src/cmd/query.rs</code>: <code>KmerResults::set</code> (row-major, whole-row-at-once) replaced by <code>mark_found</code> (stage 1: flag a position as indexed, independent of any genome's value) and <code>set_one</code> (stage 2: write one genome's value at one position). <code>QueryStats</code> extended with <code>n_columns_scanned</code>/<code>n_col_get_calls</code>, logged per chunk.
+- Total <code>get()</code>-equivalent calls are unchanged from the row-major version (<code>n_hits × n_cols</code> in the worst case, confirmed by <code>n_col_get_calls</code> in the debug log) — the win is locality (sequential access within one layer's column at a time, across <code>mmap</code>'d regions, instead of jumping across all columns per hit), exactly as predicted.</p>
+<p><strong>What did not ship, and why — <code>PartitionRunner</code> is architecturally the wrong tool here:</strong>
+Reading <code>obikindex/src/numa.rs</code>'s actual <code>run()</code> body (not just its doc comments) shows every call spawns a timer thread <strong>plus one OS thread per worker slot on every NUMA node</strong> (<code>std::thread::scope</code> + one <code>s.spawn()</code> per node per <code>max_workers</code>) — on the 192-core/8-NUMA reference machine, that's on the order of 190+ fresh OS threads spawned <strong>per call</strong>. This is fine for its actual, established usage in this codebase (<code>merge.rs</code>, <code>index.rs</code>'s <code>build_layers</code>): one <code>PartitionRunner::new()</code> + one <code>run()</code> call per command invocation, amortised over a batch of ~256 long-running partitions. It is not fine for <code>query</code>'s call pattern: <code>query_partition_with</code> runs once per <code>(chunk, partition)</code>, potentially thousands of times per second — spawning ~190 OS threads that often to scan a handful of genome columns would very likely cost far more than the row-major approach it's meant to replace. This is exactly the "resolve empirically, don't assume" composition risk the roadmap flagged, just resolved by reading the mechanism's actual cost before wiring it in, rather than by measuring a regression on the cluster after the fact.
+The column-major loop in stage 2 is therefore a <strong>plain sequential loop</strong> for now — it captures the whole, provable locality win (roadmap point 8's actual claim) without adding any parallelism mechanism. Genome-column-level parallelism (point 8's "bonus" axis) and partition-level parallelism (point 7) are both deferred — not abandoned. Candidates for a follow-up, once there's a concrete profiling need: (a) <code>rayon</code>'s already-warm global pool (<code>into_par_iter()</code>) for the column axis specifically — cheap to invoke repeatedly since it doesn't spawn threads per call, though it's the same "naive rayon" pattern <code>numa_worker_pools.md</code> warns about for a <em>different</em> workload (random pointer-chasing over large hash maps); a column scan's access pattern (sequential reads within one <code>mmap</code>'d region) has a different contention profile and hasn't been shown to have the same problem — needs its own measurement, not an assumption either way; (b) restructuring so <code>PartitionRunner</code> is invoked once per whole <code>query</code> run (or per large batch of chunks) rather than per <code>(chunk, partition)</code>, amortising its spawn cost the way <code>merge</code>/<code>build_layers</code> do — a bigger structural change than this phase's scope.
+- Log (implemented): <code>QueryStats::n_columns_scanned</code>/<code>n_col_get_calls</code>, folded into the existing per-chunk <code>debug!("k-mer dedup + column-major fetch", ...)</code> line (<code>query.rs</code>) alongside phase 3's dedup counters.
+- <strong>Unit tests</strong>: extended <code>obikpartitionner/src/tests/query_layer.rs</code> (phase 3's file) — <code>query_partition_with</code>'s empty/missing-index paths updated for the new <code>QueryStats</code> fields and single-callback signature.
+- <strong>Validation performed</strong>: full workspace build + <code>cargo test --workspace</code>, zero failures. Functional validation against real indexes: (1) a single-genome index — output byte-identical to pre-phase-4 (same <code>kmer_count</code>/<code>kmer_strict_matches</code> on every record); (2) the existing 20-genome <code>benchmark/global_index_presence</code> index — runs correctly, <code>n_hits=0</code> for an unrelated query (expected: no shared k-mers between a plant read and a bacterial reference set), no panics, confirming the <code>Implicit</code>/multi-column bounds logic doesn't crash on a real multi-genome, mixed-format index; (3) <strong>the critical correctness case</strong>: built two single-sequence-pair test genomes, merged into one 2-genome index, queried with reads from both — reads from <code>genomeA</code> matched <strong>only</strong> <code>genomeA</code> (<code>kmer_count</code> identical to the pre-dedup occurrence count, zero leakage into <code>genomeB</code>'s column) and vice versa. This is the test that would have caught a column-index mixup, an off-by-one in <code>n_cols</code>, or cross-genome bleed from the stage-1/stage-2 split — it passed cleanly.
+- <strong>Not yet done</strong>: the microbenchmark comparing column-major vs. the old row-major access pattern's wall time / page-fault counters on a large-<code>n_genomes</code> layer — needs a realistically large multi-genome index and, for the page-fault counters specifically, Linux (not available from this development environment). Left for cluster validation alongside phases 1–3's own pending measurements.</p>
+<h3 id="phase-5-sparse-findere-rework-roadmap-point-9">Phase 5 — Sparse Findere rework (roadmap point 9)</h3>
+<p><strong>Goal</strong>: replace the dense <code>KmerResults</code>/<code>win_min</code> sliding-window scan with one operating on phase 4's sparse per-genome output.</p>
+<ul>
+<li><code>obikmer/src/cmd/query.rs</code>, <code>process_chunk</code>:</li>
+<li>Remove <code>KmerResults</code> (<code>query.rs:157-202</code>) and the dense <code>win_min</code> allocation (<code>query.rs:290-291</code>, sized <code>max_n_kmers × n_genomes</code>).</li>
+<li>Keep a lightweight dense <code>in_index: Vec&lt;bool&gt;</code> per chunk (sized <code>total_kmers</code>, independent of <code>n_genomes</code>) from phase 3's stage 1 — still needed for <code>kmer_missing</code> bookkeeping (leftmost-s-mer-of-window membership test), which phase 4's sparse structure doesn't carry (a k-mer with no genome hit has no entry there at all).</li>
+<li>New per-<code>(seq_idx, genome)</code> scan: for each genome's <code>Vec&lt;(seq_idx, pos, count)&gt;</code> (sorted, per phase 4), group by <code>seq_idx</code> (contiguous after sort), then within each sequence's positions detect runs of <code>pos, pos+1, pos+2, ...</code> of length ≥ <code>z</code>; within each run, the existing monotone-deque window-minimum logic (<code>query.rs</code>'s current <code>dq</code> loop, conceptually unchanged) applies — but the deque now only scans real entries in the run, never zero-filled gaps.</li>
+<li>Update <code>SeqAcc</code> accumulation and <code>emit_batch</code> to consume this per-genome sparse iteration instead of <code>results.val</code>/<code>results.is_in_index</code>.</li>
+<li><code>--detail</code>/<code>cov</code>: build sparsely during the same scan (only positions with a confirmed contribution get an entry), densify into the <code>[u32]</code> JSON array only in <code>emit_batch</code>, only for genomes/sequences actually being serialized (per roadmap point 9's note, <code>query.rs:304-308</code>'s current dense allocation goes away).</li>
+<li>Log, per chunk: total sparse entries retained vs. what the old dense <code>KmerResults</code> would have allocated (<code>total_smers × n_genomes</code>) — the sparsity ratio is this phase's entire reason for existing, so it must be directly visible in the logs, not inferred from process RSS. Also log the run-detection stats (number of runs found, average run length) — a low average run length relative to <code>z</code> would mean most positions still fail to form a full window, worth knowing.</li>
+<li><strong>Unit tests</strong>: <code>obikmer/src/cmd/tests/query.rs</code> (extended from phase 3) — the property test described below is the primary deliverable here, not an afterthought; write it as an actual <code>#[test]</code> (or a small internal fuzz/property-style loop over randomized fixtures if a property-testing crate isn't already a dependency — check before adding one, per this project's dependency-approval rule) rather than a one-off manual comparison.</li>
+<li><strong>Validation — this is the correctness-critical phase</strong>: property-test comparing old (dense, pre-phase-3) and new (sparse) implementations on the same randomized input/index fixtures, asserting identical <code>kmer_count</code>, <code>kmer_missing</code>, <code>kmer_strict_matches</code>, and (with <code>--detail</code>) <code>coverage</code> for every sequence. Keep both implementations compiled side by side (behind a debug-only flag or a temporary parallel code path) only for the duration of this validation; delete the dense path once parity is confirmed — per this project's own convention, superseded code is not kept "just in case."</li>
+<li><strong>Update <code>docmd/architecture/query.md</code> itself</strong>: once this phase lands, the "Findere z-window filter" section (which currently — correctly — describes the dense deque-over-<code>0..n_smers</code> scan) needs another pass to describe the sparse run-detection algorithm instead, as already flagged when this phase was discussed.</li>
+</ul>
+<p><strong>Implemented as planned, no deviations discovered this time.</strong> What shipped:
+- <code>KmerResults</code> removed entirely, replaced by <code>SmerIndex</code> (<code>in_index: Vec&lt;bool&gt;</code> + <code>offsets</code>, unchanged size/purpose, renamed since it's no longer "results" — just the O(1)-per-position "was this k-mer found at all" bookkeeping) and <code>by_genome: Vec&lt;Vec&lt;(seq_idx, pos, value)&gt;&gt;</code> (one empty <code>Vec</code> per genome until a hit arrives — genomes with zero hits in a chunk cost nothing beyond the outer <code>Vec</code>'s own allocation).
+- New <code>sparse_findere_for_genome(hits, z, presence, threshold) -&gt; (Vec&lt;ConfirmedHit&gt;, n_runs, total_run_len)</code> (<code>query.rs</code>): sorts one genome's raw hits by <code>(seq_idx, pos)</code>, detects maximal runs of consecutive <code>pos</code> within one sequence, runs the same monotone-deque window-minimum as before but scoped to each run (run-relative indices for eviction, absolute <code>pos</code> for computing <code>pos_out</code>). Presence/count adjustment (<code>u32::from(win_min &gt;= threshold)</code> vs. raw) is applied inside this function, once per confirmed hit, rather than later during accumulation.
+- <code>process_chunk</code> restructured into three passes after the partition loop: (1) run <code>sparse_findere_for_genome</code> per genome, collecting <code>confirmed_by_genome</code> and run-detection stats; (2) accumulate <code>genome_totals</code> directly from <code>confirmed_by_genome</code> and mark a <code>confirmed_any: Vec&lt;bool&gt;</code> (sized <code>total_kmers_out</code>, not <code>× n_genomes</code>); (3) a position-only pass (<code>O(total_kmers_out)</code>, no genome factor) computing <code>kmer_count</code>/<code>kmer_missing</code> from <code>confirmed_any</code> + <code>SmerIndex</code>. <code>cov</code> (<code>--detail</code>) is populated by re-scanning <code>confirmed_by_genome</code> — only when <code>--detail</code> is actually set, otherwise skipped entirely.
+- Debug log added (<code>"sparse Findere"</code>): <code>n_dense_would_be</code> (<code>n_occurrences × n_genomes</code> — what the deleted dense path would have allocated), <code>n_sparse_entries</code> (what's actually retained), <code>n_runs</code>/<code>avg_run_len</code> (per the plan's ask, to see whether hits mostly fail to form complete windows).
+- <strong>Unit tests</strong>: <code>sparse_findere_matches_dense_reference_on_random_inputs</code> (<code>obikmer/src/cmd/tests/query.rs</code>) — 200 randomized cases (sequence count/length, <code>z</code>, presence/count mode, threshold, hit density from sparse to fully-dense) comparing <code>sparse_findere_for_genome</code> against <code>dense_reference_findere</code>, a faithful reimplementation of the deleted dense algorithm kept only as a test-local correctness oracle (no property-testing crate added — checked first, none was a workspace dependency; a small <code>std</code>-only xorshift64 PRNG stands in for one, deterministic and dependency-free). All 200 cases pass.
+- <strong>Functional validation performed</strong>: full workspace build + <code>cargo test --workspace</code>, zero failures. End-to-end against real indexes: baseline output (no flags) unchanged from pre-phase-5 recorded values on the same fixtures; <code>--count-missing</code> correct (<code>kmer_missing: 0</code> on a self-match); <code>--detail</code> correct — coverage array length matches <code>kmer_count</code>, and critically, re-ran the two-genome cross-contamination check from phase 4 with <code>--detail --count-missing</code>: <code>genomeA</code> reads show coverage sum <code>106</code> for <code>genomeA</code> and <code>0</code> for <code>genomeB</code> (and vice versa) — confirms the sparse-to-dense <code>cov</code> reconstruction doesn't leak across genomes either, not just the scalar <code>kmer_strict_matches</code> path.
+- This phase's roadmap item ("update the Findere z-window filter section") — done, see above; the "Algorithm" section's pseudocode was also updated, since it still named <code>KmerResults</code>/<code>SKDesc</code> from before phases 3–4.</p>
+<h3 id="phase-6-parallel-gzip-decompression-independent-optional">Phase 6 — Parallel gzip decompression (independent, optional)</h3>
+<p>Tracked separately in <a href="../../implementation/chunkreader/#future-work--parallel-gzip-decompression-in-xopen">chunkreader.md</a>; parked pending validation of <code>rapidgzip-rs</code> on real data. Not a dependency of, or a dependency for, phases 0–5 — <code>xopen</code> is shared infrastructure (<code>obiread</code>), phase 1 benefits from it but doesn't require it (phase 1 parallelises <em>across</em> files; this phase would additionally parallelise <em>within</em> one large file).</p>
+<h3 id="cross-cutting-risks">Cross-cutting risks</h3>
+<ul>
+<li><strong>Thread-budget oversubscription</strong> (phase 4): the single biggest unresolved design question in this whole plan — see phase 4's composition note. Should be settled with real measurements early in phase 4, not assumed from the design alone.</li>
+<li><strong><code>obicompactvec</code> API surface growth</strong> (phase 4): new public per-column accessors are additive (existing <code>fill_row</code>/<code>row</code> stay for other callers — <code>dump</code>, <code>select</code>, distance computations) — no breaking change expected, but worth checking <code>obicompactvec</code>'s other callers aren't already relying on <code>fill_row</code> being the only/cheapest access path in a way that would make maintaining two access patterns (row-major and column-major) a real maintenance cost rather than a one-off addition.</li>
+<li><strong><code>PersistentBitMatrix::Implicit</code>'s hardcoded <code>n_cols: 1</code> — resolved, not a bug.</strong> <code>LayerMeta</code>'s own doc comment (<code>obicompactvec/src/layer_meta.rs:1-9</code>) states it is written "alongside <code>mphf.bin</code>" and read by <code>PersistentBitMatrix::open</code> "to determine <code>n_rows</code> for <strong>the implicit (mono-genome presence/absence) case</strong>" — i.e. <code>Implicit</code> is a documented single-genome fast path (no presence matrix needed when there is trivially one genome), not a generic "no matrix built yet" fallback. <code>n_cols: 1</code> is correct by design for the case it's meant to handle. Phase 4's column loop is safe as planned — this was worth checking once, doesn't need further action.</li>
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+  <a href="#problem-with-the-current-two-pass-design" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Problem with the current two-pass design
+      
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+  <a href="#memory-budget" class="md-nav__link">
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+  <a href="#key-observation" class="md-nav__link">
+    <span class="md-ellipsis">
+      
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+      
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+</li>
+      
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+  <a href="#proposed-single-scan-design" class="md-nav__link">
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+        Proposed single-scan design
+      
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+  
+    <nav class="md-nav" aria-label="Proposed single-scan design">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#step-1-column-scan-keep-bitvector" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Step 1 — column scan → keep bitvector
+      
+    </span>
+  </a>
+  
+</li>
+        
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+  <a href="#step-2-unitig-scan-kept-kmers-new-mphf" class="md-nav__link">
+    <span class="md-ellipsis">
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+        
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+  <a href="#step-3-fill-new-matrix" class="md-nav__link">
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+</li>
+      
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+  <a href="#files-to-modify" class="md-nav__link">
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+  <a href="#open-questions" class="md-nav__link">
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+            
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+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+
+<h1 id="rebuild-filter-column-first-design">Rebuild / filter — column-first design</h1>
+<h2 id="problem-with-the-current-two-pass-design">Problem with the current two-pass design</h2>
+<p><code>rebuild_partition</code> currently makes <strong>two full passes</strong> over source data:</p>
+<p><strong>Pass 1</strong> — read unitigs → MPHF lookup (source) → read row (108 values) → apply filter → push kmer into <code>GraphDeBruijn</code>, <strong>discard row</strong>.</p>
+<p><strong>Pass 2</strong> — read unitigs again → MPHF lookup again → read row again → for each passing kmer, look up slot in new MPHF → fill column builders.</p>
+<p>Both passes do random access into the source matrix: for each kmer, the MPHF returns a slot, then we read 108 values scattered across 108 column positions. This is cache-hostile even with a packed matrix (<code>.pbmx</code>), because the matrix is column-major: consecutive row reads jump across the file.</p>
+<h2 id="memory-budget">Memory budget</h2>
+<p>The <code>keep</code> bitvector costs <strong>1 bit per slot</strong>. With 256 partitions and realistic kmer counts, each partition holds at most a few tens of millions of slots → a few MB per bitvector. Even in the absolute worst case (800 M slots), it stays under 100 MB. This is negligible.</p>
+<p>The <code>slot_map</code> option (Option B, 8–16 bytes per slot) is heavier but still bounded: at 15 M slots and 8 bytes, that is 120 MB per partition, acceptable for a single worker.</p>
+<h2 id="key-observation">Key observation</h2>
+<p><strong>The filter operates on column values, not on kmers.</strong> A filter like <code>--max-outgroup-count 0</code> only needs to know, for each slot, whether any outgroup column is non-zero. It does not need to know which kmer occupies that slot.</p>
+<p>This means filtering can be done as a <strong>sequential column scan</strong> that produces a <code>keep: BitVec[n_slots]</code> — no MPHF lookups, no kmer knowledge, perfectly cache-friendly.</p>
+<h2 id="proposed-single-scan-design">Proposed single-scan design</h2>
+<h3 id="step-1-column-scan-keep-bitvector">Step 1 — column scan → <code>keep</code> bitvector</h3>
+<div class="highlight"><pre><span></span><code>for each column c in source matrix:
+    read column c sequentially (one mmap range)
+    update keep[slot] according to filter contribution of column c
+</code></pre></div>
+<p>For <code>GroupQuorumFilter</code> with ingroup/outgroup:
+- ingroup columns: count presence per slot → <code>ingroup_count[slot]</code>
+- outgroup columns: <code>keep[slot] &amp;= (value[slot] == 0)</code> (early-exit possible)</p>
+<p>Result: <code>keep: BitVec</code> of size <code>n_slots</code>, computed with purely sequential IO.</p>
+<h3 id="step-2-unitig-scan-kept-kmers-new-mphf">Step 2 — unitig scan → kept kmers + new MPHF</h3>
+<div class="highlight"><pre><span></span><code>for each kmer in unitig files:
+    old_slot = old_MPHF(kmer)
+    if keep[old_slot]:
+        push kmer into new GraphDeBruijn
+        record (old_slot, kmer)   ← or just old_slot in order
+</code></pre></div>
+<p>Build new MPHF from <code>GraphDeBruijn</code> via <code>materialize_layer</code>.</p>
+<h3 id="step-3-fill-new-matrix">Step 3 — fill new matrix</h3>
+<p>Two sub-options:</p>
+<p><strong>Option A — from recorded (old_slot, kmer) pairs:</strong></p>
+<div class="highlight"><pre><span></span><code>for each (old_slot, kmer) in recorded list:
+    new_slot = new_MPHF(kmer)
+    for each column c:
+        new_matrix[new_slot, c] = old_matrix[old_slot, c]
+</code></pre></div>
+<p>Memory cost: <code>n_kept × (8 + 8)</code> bytes for <code>(old_slot: usize, kmer: CanonicalKmer)</code>.
+For species-specific filters, <code>n_kept</code> is small. For unfiltered rebuild, <code>n_kept = n_slots</code>.</p>
+<p><strong>Option B — column-by-column copy using old→new slot mapping:</strong></p>
+<p>Precompute <code>slot_map: Vec&lt;Option&lt;usize&gt;&gt;</code> of size <code>n_slots</code>:
+- For each kmer in unitig file: <code>slot_map[old_MPHF(kmer)] = Some(new_MPHF(kmer))</code></p>
+<p>Then for each source column:
+<div class="highlight"><pre><span></span><code>read source column sequentially
+for each slot where slot_map[slot] = Some(new_slot):
+    write value to new column at new_slot
+</code></pre></div></p>
+<p>Memory cost: <code>n_slots × sizeof(usize)</code> for the slot map (one usize per source slot).
+IO pattern: sequential read of each source column → random write into new column builders.</p>
+<p>Option B avoids storing kmer values and works uniformly regardless of filter selectivity.</p>
+<h2 id="comparison">Comparison</h2>
+<table>
+<thead>
+<tr>
+<th></th>
+<th>Current</th>
+<th>Proposed</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>Disk reads</td>
+<td>2× unitigs + 2× random matrix</td>
+<td>1× columns (sequential) + 1× unitigs</td>
+</tr>
+<tr>
+<td>MPHF lookups (source)</td>
+<td>2× N_kmers</td>
+<td>1× N_kept (step 2) or 0 (option B, col scan only)</td>
+</tr>
+<tr>
+<td>Cache behavior</td>
+<td>poor (random row access)</td>
+<td>good (sequential column scan)</td>
+</tr>
+<tr>
+<td>Extra memory</td>
+<td>none</td>
+<td>slot_map (option B) or (old_slot, kmer) list (option A)</td>
+</tr>
+</tbody>
+</table>
+<h2 id="files-to-modify">Files to modify</h2>
+<ul>
+<li><code>src/obikpartitionner/src/rebuild_layer.rs</code> — <code>rebuild_partition</code> and <code>iter_src_layers</code></li>
+<li>Possibly <code>src/obicompactvec/</code> — add column iterator API if not already present</li>
+<li><code>src/obilayeredmap/</code> — check if per-column sequential access is exposed on <code>SrcLayerData</code></li>
+</ul>
+<h2 id="open-questions">Open questions</h2>
+<ul>
+<li>Does <code>SrcLayerData</code> expose per-column sequential iteration, or only <code>lookup(kmer, n_genomes)</code> random access?</li>
+<li>For option B: are new column builders writable in random-slot order (i.e. <code>set_val(slot, value)</code> without sequential constraint)?</li>
+<li>For <code>GroupQuorumFilter</code> specifically: can the filter be decomposed into independent per-column contributions, or does it need the full row?</li>
+</ul>
+
+
+
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diff --git a/doc/architecture/sequences/invariant.refs/index.html b/DevDoc/architecture/sequences/invariant.refs/index.html
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rename to DevDoc/architecture/sequences/invariant.refs/index.html
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+++ b/DevDoc/architecture/sequences/invariant.refs/index.html
@@ -178,6 +178,33 @@
   
   
   
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
         
           
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+      <a href="../../siblings/" class="md-nav__link">
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+  
+  <span class="md-ellipsis">
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+  
+
+              
+            
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+      <a href="../../numa_worker_pools/" class="md-nav__link">
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+  
+  <span class="md-ellipsis">
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+    NUMA-aware worker pools
+  
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+
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+  
+
+              
+            
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+      <a href="../../numa_partition_runner/" class="md-nav__link">
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+        <link rel="prev" href="../../../implementation/obitaxonomy/">
       
       
         <link rel="next" href="../../index_architecture/">
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+  
+    <li class="md-nav__item">
+      <a href="../../../implementation/filtering/" class="md-nav__link">
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+  
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+            
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+      <a href="../../../implementation/select/" class="md-nav__link">
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+  
+  
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+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
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+  
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+      <a href="../../../implementation/obitaxonomy/" class="md-nav__link">
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+  
+    <li class="md-nav__item">
+      <a href="../../siblings/" class="md-nav__link">
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+  
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+
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+      <a href="../../numa_worker_pools/" class="md-nav__link">
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+    NUMA-aware worker pools
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+    
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+  
+
+      </a>
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+  
+
+              
+            
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+  
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+      <a href="../../numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
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+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
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+  
+
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new file mode 100644
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+  <head>
+    
+      <meta charset="utf-8">
+      <meta name="viewport" content="width=device-width,initial-scale=1">
+      
+      
+      
+      
+        <link rel="prev" href="../index_architecture/">
+      
+      
+        <link rel="next" href="../numa_worker_pools/">
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+          </label>
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+      <a href="../../kmers/" class="md-nav__link">
+        
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+  
+    Kmers and super-kmers
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+  
+    DNA encoding
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/entropy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Entropy filter
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/minimizer/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Minimizer selection
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/indexing/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Partitioning architecture
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        
+          
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+            
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Implementation
+  
+
+    
+  </span>
+  
+  
+
+            <span class="md-nav__icon md-icon"></span>
+          </label>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
+            <span class="md-nav__icon md-icon"></span>
+            
+  
+    Implementation
+  
+
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/superkmer/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    SuperKmer
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/kmer/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/chunkreader/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Chunk reader
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/pipeline/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Construction pipeline
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/obipipeline/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obipipeline library
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/storage/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    On-disk storage
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/mphf/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    MPHF selection
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/unitig_evidence/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Unitig evidence encoding
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/evidence_elimination/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Evidence elimination (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/obilayeredmap/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obilayeredmap crate
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/persistent_compact_int_vec/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    PersistentCompactIntVec
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/persistent_bit_vec/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    PersistentBitVec
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/merge/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Merge command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/merge_parallelism/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+    
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--active md-nav__item--nested">
+      
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" checked>
+        
+          
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
+            
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Architecture
+  
+
+    
+  </span>
+  
+  
+
+            <span class="md-nav__icon md-icon"></span>
+          </label>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_5">
+            <span class="md-nav__icon md-icon"></span>
+            
+  
+    Architecture
+  
+
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../sequences/invariant/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sequences
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../index_architecture/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer index
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+    
+  
+  
+  
+    <li class="md-nav__item md-nav__item--active">
+      
+      <input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
+      
+      
+        
+      
+      
+        <label class="md-nav__link md-nav__link--active" for="__toc">
+          
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+          <span class="md-nav__icon md-icon"></span>
+        </label>
+      
+      <a href="./" class="md-nav__link md-nav__link--active">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+      
+        
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+    
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#two-index-spaces-uncorrelated" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Two index spaces, uncorrelated
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#two-pipelines-never-mixed" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Two pipelines, never mixed
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#sibling-annex-an-iteration-pipeline-artifact-only" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Sibling annex: an iteration-pipeline artifact only
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#pending-work-done" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Pending work — done
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#performance-build_sibling_annex-parallelism-2026-08-14" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Performance: build_sibling_annex parallelism (2026-08-14)
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#cross-partition-batch-resolution-current-state-vs-the-batched-accumulator-design-discussion-2026-08-14" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Cross-partition batch resolution — current state vs. the batched-accumulator design (discussion, 2026-08-14)
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#pseudo-alignment-at-scale-pruning-is-unavoidable-discussion-2026-08-1415" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Pseudo-alignment at scale — pruning is unavoidable (discussion, 2026-08-14/15)
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#-subsample-shannon-sampling-strategy-decided-2026-08-15" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        --subsample / --shannon — sampling strategy (decided 2026-08-15)
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#cheap-entropy-pre-filtering-row-marginal-sums-idea-not-implemented-2026-08-15" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Cheap entropy pre-filtering — row-marginal sums (idea, not implemented, 2026-08-15)
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#-free-loss-tnt-pipeline-four-independent-scans-three-of-them-unsampled-found-2026-08-15-fixed-2026-08-15-see-implemented-below" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        --free-loss/--tnt pipeline: four independent scans, three of them unsampled (found 2026-08-15, fixed 2026-08-15 — see "Implemented" below)
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#entropy-biased-selection-soft-gaussian-weighting-not-a-hard-cutoff-decided-and-implemented-2026-08-15" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Entropy-biased selection: soft Gaussian weighting, not a hard cutoff (decided and implemented 2026-08-15)
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#two-entropy-definitions-kept-side-by-side-for-comparison-2026-08-15" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Two entropy definitions kept side by side, for comparison (2026-08-15)
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#persistentsparsebitmatrix-implemented-and-measured-2026-08-15" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        PersistentSparseBitMatrix — implemented and measured (2026-08-15)
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#wired-into-pack-and-the-sibling-annex-build-path-2026-08-15" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Wired into pack and the sibling-annex build path (2026-08-15)
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#sankoff-pipeline-fusion-entropy-biased-selection-implemented-2026-08-15" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Sankoff pipeline fusion + entropy-biased selection — implemented (2026-08-15)
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+    
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#two-index-spaces-uncorrelated" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Two index spaces, uncorrelated
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#two-pipelines-never-mixed" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Two pipelines, never mixed
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#sibling-annex-an-iteration-pipeline-artifact-only" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Sibling annex: an iteration-pipeline artifact only
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#pending-work-done" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Pending work — done
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#performance-build_sibling_annex-parallelism-2026-08-14" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Performance: build_sibling_annex parallelism (2026-08-14)
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#cross-partition-batch-resolution-current-state-vs-the-batched-accumulator-design-discussion-2026-08-14" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Cross-partition batch resolution — current state vs. the batched-accumulator design (discussion, 2026-08-14)
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#pseudo-alignment-at-scale-pruning-is-unavoidable-discussion-2026-08-1415" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Pseudo-alignment at scale — pruning is unavoidable (discussion, 2026-08-14/15)
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#-subsample-shannon-sampling-strategy-decided-2026-08-15" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        --subsample / --shannon — sampling strategy (decided 2026-08-15)
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#cheap-entropy-pre-filtering-row-marginal-sums-idea-not-implemented-2026-08-15" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Cheap entropy pre-filtering — row-marginal sums (idea, not implemented, 2026-08-15)
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#-free-loss-tnt-pipeline-four-independent-scans-three-of-them-unsampled-found-2026-08-15-fixed-2026-08-15-see-implemented-below" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        --free-loss/--tnt pipeline: four independent scans, three of them unsampled (found 2026-08-15, fixed 2026-08-15 — see "Implemented" below)
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#entropy-biased-selection-soft-gaussian-weighting-not-a-hard-cutoff-decided-and-implemented-2026-08-15" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Entropy-biased selection: soft Gaussian weighting, not a hard cutoff (decided and implemented 2026-08-15)
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#two-entropy-definitions-kept-side-by-side-for-comparison-2026-08-15" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Two entropy definitions kept side by side, for comparison (2026-08-15)
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#persistentsparsebitmatrix-implemented-and-measured-2026-08-15" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        PersistentSparseBitMatrix — implemented and measured (2026-08-15)
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#wired-into-pack-and-the-sibling-annex-build-path-2026-08-15" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Wired into pack and the sibling-annex build path (2026-08-15)
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#sankoff-pipeline-fusion-entropy-biased-selection-implemented-2026-08-15" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Sankoff pipeline fusion + entropy-biased selection — implemented (2026-08-15)
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+
+<h1 id="sibling-annex-architecture-discussion">Sibling annex — architecture (discussion)</h1>
+<p>Status: architecture decided (2026-08-14). Implementation not yet mandated.</p>
+<h2 id="two-index-spaces-uncorrelated">Two index spaces, uncorrelated</h2>
+<p>Every kmer stored in a <code>Layer</code> lives in two independent index spaces:</p>
+<ul>
+<li><strong>Iteration order</strong>: its position when enumerating <code>unitigs.bin</code> (the
+  superkmer file), deterministic but arbitrary with respect to slot.</li>
+<li><strong>MPHF slot</strong>: <code>MphfLayer::index(kmer)</code>, the number the MPHF assigns.</li>
+</ul>
+<p>The two are not correlated by any formula. Converting from one to the other
+requires either recomputing the MPHF (kmer → slot) or scanning the iteration
+stream (kmer → order). There is no <code>slot → kmer</code> operation: the MPHF is a
+one-way function, not an invertible bijection with a stored inverse. Any
+method that reconstructs a kmer from a bare slot number is wrong by
+construction, regardless of the mechanism used (MPHF re-hash, or evidence
+decode + direct unitig read). See <code>MphfLayer::kmer_at</code>
+(<code>obilayeredmap/src/mphf_layer.rs</code>) — flagged for removal, currently called
+from <code>obikphylo/siblings/build.rs</code> and <code>family_scan.rs</code> (since removed — see
+"Pending work" status below).</p>
+<h2 id="two-pipelines-never-mixed">Two pipelines, never mixed</h2>
+<table>
+<thead>
+<tr>
+<th></th>
+<th>origin of the kmer</th>
+<th>membership known?</th>
+<th>correct mapping</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><strong>query pipeline</strong></td>
+<td>external (caller-supplied)</td>
+<td>no</td>
+<td><code>query</code>/<code>find</code>/<code>find_strict</code> — MPHF + evidence check</td>
+</tr>
+<tr>
+<td><strong>iteration pipeline</strong></td>
+<td>enumerated from this layer's own <code>unitigs.bin</code></td>
+<td>yes, by construction</td>
+<td><code>index</code>/<code>index_batch</code> — MPHF only, no evidence</td>
+</tr>
+</tbody>
+</table>
+<p>Evidence exists solely to answer "is this external kmer a member of the
+layer" for the query pipeline. Using it (or the MPHF) to go the other way —
+recover a kmer from a slot, or re-verify a kmer that was just produced by
+iterating the layer — is a conceptual error: evidence can be probabilistic
+(<code>Approx</code> mode), so any slot→kmer attempt is unsound in general, and
+pointless even in <code>Exact</code>/<code>Hybrid</code> mode since the kmer was already known.</p>
+<h2 id="sibling-annex-an-iteration-pipeline-artifact-only">Sibling annex: an iteration-pipeline artifact only</h2>
+<p>The sibling annex (<code>FamilyMask</code>/<code>SiblingAnnex</code>, <code>.psib</code>,
+<code>obicompactvec/src/siblingannex.rs</code>) records, per kmer, whether it is a
+family minorant and which family members are present in the index. Its only
+consumers (<code>obikphylo/siblings/stats.rs</code>, <code>family_scan.rs</code>) enumerate it
+exhaustively (<code>0..annex.len()</code>); no query-pipeline code path touches it.</p>
+<p><strong>Decision</strong>: the annex must be persisted in iteration order, not slot
+order. This lets readers zip-iterate <code>Layer::iter_kmers()</code> and the annex
+file directly — one linear, cache-friendly pass, no MPHF/slot indirection,
+no <code>kmer_at</code>. It also enables specialized iterators building on this zip:
+minorants-only iteration, batch-of-kmers → batch-of-family-members, etc.</p>
+<p>Today the annex is built and stored in <strong>slot</strong> order
+(<code>build_layer_sibling_annex</code>, <code>siblings/build.rs</code>): <code>slot_kmer</code> is populated
+via <code>(0..n_slots).map(|slot| mphf.kmer_at(slot))</code>, and the origin <code>slot</code> is
+threaded through the whole cross-partition reconciliation pipeline (variant
+generation, <code>query_partition_with</code>, final <code>mask[slot].fetch_or(...)</code>). This
+must change to iterating <code>iter_kmers()</code>/<code>enumerate_kmers()</code> and threading
+the <strong>iteration index</strong> instead of the slot end to end — eliminating
+<code>kmer_at</code> from the build path entirely, not just the read path. No
+slot-indexed intermediate is needed even during construction; the
+iteration-order id is sufficient throughout.</p>
+<p>The cross-partition side of the same pipeline is unaffected: checking
+whether a generated family-variant kmer exists in another partition is a
+genuine query-pipeline operation (the variant's membership in the <em>target</em>
+partition is unknown) and must keep going through
+<code>KmerPartition::query_partition_with</code> (MPHF + evidence), never a raw
+<code>index()</code>.</p>
+<h2 id="pending-work-done">Pending work — done</h2>
+<p>The plan above shipped: <code>obikphylo</code> (a new crate — phylo-domain extension
+traits over <code>obikindex::KmerIndex</code>/<code>obilayeredmap::Layer&lt;D&gt;</code>, replacing the
+old <code>obikindex::siblings</code> module) builds and reads the annex purely in
+iteration order (<code>SiblingLayerExt::iter_siblings</code>/<code>iter_minorants</code>, both with
+batch variants, mirroring <code>Layer&lt;D&gt;</code>'s own <code>KmerIter</code>/<code>KmerBatchIter</code>
+shape). <code>MphfLayer::kmer_at</code> has no remaining callers.</p>
+<p>A separate, unrelated bug surfaced during this work and was fixed
+(2026-08-14): <code>MphfLayer::enumerate_kmers_batch</code> computed its
+<code>batch_start_index</code> via the stdlib <code>.enumerate()</code> adapter, which counts
+<em>batches</em> (0, 1, 2…), not the cumulative k-mer offset the annex is actually
+keyed on — every batch past the first wrote its mask/annex entries at the
+wrong iteration-order position. Fixed by tracking a running offset instead;
+regression tests added (<code>sibling_annex_no_empty_masks_after_build</code>,
+<code>sibling_histogram_does_not_panic_on_partial_last_batch</code>).</p>
+<h2 id="performance-build_sibling_annex-parallelism-2026-08-14">Performance: <code>build_sibling_annex</code> parallelism (2026-08-14)</h2>
+<p>Investigated on a real multi-genome run (<code>phyloskims_sal_vac</code>, k=31/m=11).
+Baseline: mostly one active core, with short multi-core bursts — average
+~3 cores.</p>
+<p><strong>Fixes that helped, kept:</strong></p>
+<ul>
+<li><code>CanonicalKmerOf::minimizer()</code> (<code>obikseq/src/kmer.rs</code>) — a direct O(k)
+  bit-arithmetic minimiser for a single isolated k-mer, replacing a
+  <code>RollingStat</code> instance fed byte-by-byte through an ASCII round-trip (used
+  by <code>helpers::partition_of</code>, called for every generated family variant).
+  ~3x wall-clock improvement on its own, confirmed by sampling
+  (<code>obiskbuilder::rolling_stat</code>/<code>obikentropy</code> frames disappeared from the
+  hot path). <code>CanonicalKmerOf::partition()</code> added alongside it (wraps
+  <code>minimizer().seq_hash() &amp; mask</code>, the same routing rule
+  <code>KmerPartition</code>/<code>RoutableSuperKmer</code> use).</li>
+<li>Cross-partition resolution (<code>outgoing.par_iter()</code> in
+  <code>build_layer_sibling_annex</code>) parallelised at the <em>partition</em> level — one
+  Rayon task per non-empty <code>outgoing[dest]</code> bucket. For k=31/m=11, a
+  central-base substitution changes the winning minimiser (and thus the
+  destination partition) only when that window overlaps the central base:
+  ~11 of the 21 possible windows do, so ~10/21 (≈48%) of generated variants
+  route right back to the partition already being built. That self bucket
+  ends up far larger than any other, so the per-partition split pinned one
+  thread to it alone while the rest of the pool finished instantly —
+  confirmed by sampling: one thread solid in <code>MphfLayer::find</code>, everyone
+  else idle. Fixed by splitting each non-empty bucket into
+  <code>total_queries / n_workers</code> (capped 4096) chunks <em>before</em> <code>par_iter()</code>,
+  preserving per-partition mmap locality (each chunk stays contiguous
+  within one partition) while letting Rayon spread an oversized bucket
+  across several threads. Net effect of both fixes together: ~3 cores
+  average → ~10-13 cores average on the same run, and a projected total
+  build time of ~1h15 down to ~30min on the real <code>phyloskims_sal_vac</code> run
+  this was measured against.</li>
+<li><code>TracedBar</code>'s ETA (<code>obisys/src/progress.rs</code>) was silently starved: the
+  custom progress message and the self-computed ETA text used to share one
+  <code>pb.set_message()</code> slot, with the ETA holding off for 2s after any custom
+  message — fine when custom messages are rare, broken once
+  <code>build_sibling_annex</code>'s per-partition callback fires more often than
+  that. Fixed by keeping the two texts in separate fields, composed
+  together on every render instead of one overwriting the other.</li>
+</ul>
+<p><strong>Tried and reverted — do not repeat blindly:</strong></p>
+<ul>
+<li>Parallelising the <em>outer</em> partition loop in <code>build_sibling_annex</code> with
+  <code>obikindex::PartitionRunner</code> (already used by <code>merge</code>/<code>build_layers</code>),
+  splitting a fixed core budget between outer (partition) and inner
+  (pipeline + resolution) concurrency so their product wouldn't exceed the
+  budget. Measured <em>worse</em>: throughput dropped over time (26
+  partitions/5min → 38/11-12min) and peak resolution concurrency fell from
+  ~11-12 cores to ~7-8. Cause: this capped the resolution burst — which
+  scales very well on its own — to make room for outer concurrency, and
+  running several partitions' resolution at once scatters access across
+  multiple partitions' mmap regions at once, working against the
+  locality <code>outgoing</code>'s per-partition grouping exists for. <code>PartitionRunner</code>
+  stayed exported from <code>obikindex</code> (<code>new_capped</code> too) since it's
+  general-purpose, but nothing in <code>obikphylo</code> calls it.</li>
+<li>Splitting resolution chunks even finer (<code>/(n_workers*8)</code>, cap 1024,
+  instead of <code>/n_workers</code>, cap 4096) to smooth the residual sawtooth.
+  Measured ~10% <em>slower</em>, wider dips, not narrower. Reverted to the
+  original chunk sizing.</li>
+</ul>
+<p><strong>Known remaining limitation, not yet worth fixing:</strong> within one layer, the
+four stages (sequential <code>unitigs.bin</code> read → parallel generation →
+parallel resolution → sequential annex write) never overlap — confirmed by
+1s-interval sampling: generation alone occupies ~17 threads evenly, but the
+next layer's read/generation never starts until the current layer's
+resolution and write are both done. This produces a real, periodic (~layer
+duration) alternation between "many cores" and "few cores" that neither of
+the fixes above touches, since both operate <em>within</em> one layer's resolution
+step. The only remaining lever is overlapping consecutive layers (e.g. a
+depth-2 pipeline: start layer N+1's read/generation while layer N's
+resolution/write is still running) — a real restructuring, not a parameter
+tweak, and explicitly <em>not</em> to be combined with the reverted
+budget-capping idea above (let each phase use however many cores it
+naturally wants; only the <em>scheduling</em> needs to overlap). Deferred, not
+started.</p>
+<h2 id="cross-partition-batch-resolution-current-state-vs-the-batched-accumulator-design-discussion-2026-08-14">Cross-partition batch resolution — current state vs. the batched-accumulator design (discussion, 2026-08-14)</h2>
+<p><code>family_scan.rs::scan_layer_families</code> (shared by <code>snp_pseudo_alignment</code>,
+<code>sibling_annex_stats</code>, <code>cardinality_tally</code>, <code>scan_family_pairs</code>) already
+implements most of a dispatch/accumulate/resolve pipeline: generation
+(cheap, CPU-only — builds <code>outgoing[dest_partition]</code> from <code>FamilyMask</code> and
+buckets cross-partition queries) runs on an <code>obipipeline::throttle</code> +
+<code>make_pipe!</code> stage, decoupled from resolution (I/O-bound, <code>rayon::par_iter</code>
+<em>across partitions</em>, one generated batch resolved at a time, never several
+concurrently — this ordering is deliberate, see the module's own docs on a
+reverted concurrent-batch-resolution attempt that scattered mmap access).
+The fast/slow mode gate (<code>PartitionCache::fast_mode</code>, <code>cache.rs:162-163</code>)
+already exists: <code>n_layers &lt;= 7</code> (checked once from the first non-empty
+partition's <code>PartitionMeta::n_layers</code>, documented as identical across every
+partition of an index — a structural, build-time property, never a
+per-partition state) decides whether <code>FamilyMask</code>'s recorded <code>layer_value</code>
+can be trusted to skip straight to the right layer
+(<code>find_presence_batch_fast</code>) or must fall back to scanning every layer of
+the destination partition (<code>find_presence_batch</code>).</p>
+<p><strong>Real gap, confirmed not implemented</strong>: resolution is triggered by the
+<em>source</em> batch finishing (<code>FAMILY_BATCH = 65536</code> minorants read from the
+scanned layer), not by an <em>output</em> accumulator filling up. Since most
+central-base variants of a family route back to the same partition being
+scanned (~48% per the k=31/m=11 measurement above), a <code>FAMILY_BATCH</code>'s
+<code>outgoing[dest]</code> is large for the local/self partition and thin for the
+other ~255 (or however many) destination partitions — each of those gets
+resolved at low query density every batch instead of being accumulated
+across several source batches until resolving it is worthwhile. This is
+distinct from, and not fixed by, the fast/slow layer gate above.</p>
+<p>Redesign sketched (not built): per-destination accumulators decoupled from
+<code>FAMILY_BATCH</code>, flushed on reaching a size threshold instead of on source-batch
+completion — a "hot" accumulator for the partition being scanned (sharded
+one-per-generation-worker, no lock, since all <code>n_workers</code> pipeline workers
+write to it concurrently — this differs from an earlier, simpler mental
+model of "one thread owns one layer's local collector," which doesn't hold
+here since <code>n_workers</code> threads cooperate on scanning <em>one</em> layer at a time,
+not one thread per layer) and "cold" mutex-per-partition accumulators for
+the rest, low contention expected since traffic to any single cold
+destination is a small fraction of total.</p>
+<p>This breaks the current strict-iteration-order delivery of <code>on_family</code>
+(today: a reorder buffer keyed by batch, since a whole <code>FAMILY_BATCH</code>
+resolves atomically). With cross-batch accumulation, a family only becomes
+complete once <em>every</em> accumulator holding one of its outgoing queries has
+flushed, at unpredictable, independent times — no longer streamable
+strictly in order without a large, unbounded pending buffer. Resolution
+sketched: replace order-dependent consumers with coordinate-addressed
+writes instead of order-dependent appends (see <code>PseudoAlignment</code> idea
+below) wherever possible, since <code>sibling_annex_stats</code>'s reduction (plain
+counts) is already order-independent and needs nothing here.</p>
+<p><strong>Superseded 2026-08-15</strong> by the <code>--subsample</code>/<code>--shannon</code> design below,
+which sidesteps the accumulator redesign for now: bounding the number of
+families actually resolved per layer (via sampling) keeps per-layer
+resolution volume small enough that the batch-density problem above stops
+mattering in practice for these two consumers. The accumulator redesign
+remains relevant for a future <em>unsampled, full-index</em> run, but is not
+required to ship <code>--subsample</code>/<code>--shannon</code>.</p>
+<h2 id="pseudo-alignment-at-scale-pruning-is-unavoidable-discussion-2026-08-1415">Pseudo-alignment at scale — pruning is unavoidable (discussion, 2026-08-14/15)</h2>
+<p>The reference run (<code>phyloskims_sal_vac</code>-scale bacterial test set,
+<code>iqtree.fasta</code>) produced a dense alignment for 13 genomes × 383,965 sites
+(4.8 MB) — trivially small. The in-progress plant index is expected to
+carry on the order of 9 billion minorant families; a dense byte-per-cell
+alignment at that column count is unbuildable regardless of genome count
+(hundreds of GB even at a handful of genomes). Long-term ambition is 6,000–
+8,000 genomes on a large machine, which makes the per-cell cost dominant in
+the other dimension too. Pruning the retained family set before
+materializing anything is mandatory, not an optimization.</p>
+<p><strong>Already free</strong>: <code>family_size() &lt; 2</code> (no sibling variant registered at
+all) is a zero-cost structural filter, read directly off <code>FamilyMask</code> bits,
+already applied in <code>snp_pseudo_alignment</code>. Insufficient alone — per the
+~80-85% mono-family estimate from earlier discussion, this only brings 9
+billion down to roughly 1.3-1.8 billion, still unusable.</p>
+<p><strong>Entropy definition — settled 2026-08-15, correcting an earlier wrong
+turn.</strong> The project does <strong>not</strong> encode families as IUPAC ambiguity codes
+interpreted the classical way (Fitch-parsimony subset-compatibility, or
+ML's "one true state, uncertain which"); see
+<code>docmd/theory/evolutionary_distances.md</code> ("Why the IUPAC/DNA encoding used
+for the first <code>--snp</code> test was wrong") and the Sankoff resolution that
+followed it. The real model is a genuine 16-state alphabet (the powerset of
+<code>{A,C,G,T}</code>, <code>∅</code> included as a real state) scored with a <em>calibrated
+pairwise cost matrix</em> (<code>obikphylo::cardcomp::pairwise_cost_matrix</code>,
+<code>cmd/phylo/sankoff.rs</code>), not a compatibility/subset relation between
+states. Under that model, each of the 16 states — including multi-bit ones
+like <code>AC</code> — is a first-class, independently-costed state, not an
+uncertainty encoding of a single true base. So: <strong>entropy over the 15
+non-empty states (<code>∅</code> excluded, matching the earlier decision to exclude
+genomes where the family is absent) is the correct informativeness
+measure</strong> for this project — not a 4-symbol reduction, which would discard
+exactly the cardinality/composition information the calibrated cost matrix
+is built to exploit.</p>
+<h2 id="-subsample-shannon-sampling-strategy-decided-2026-08-15"><code>--subsample</code> / <code>--shannon</code> — sampling strategy (decided 2026-08-15)</h2>
+<p>Goal: make both the pseudo-alignment (<code>--snp</code>) and a Shannon-entropy
+diagnostic usable at any index scale, from the 13-genome bacterial
+reference run up to the 9-billion-family plant index, without requiring the
+batched-accumulator redesign above.</p>
+<p><strong><code>--subsample N</code></strong> (integer, families to retain): bounds the pseudo-alignment
+to <code>N</code> minorant families, sampled <strong>proportionally per layer</strong> among
+non-monomorphic minorants (<code>family_size &gt;= 2</code>) — this sidesteps the need
+for a true global reservoir merge across layers while still approximating a
+uniform sample over the whole index, and directly answers the earlier open
+question of global-vs-per-layer selection scope.</p>
+<p>Three passes, in order:</p>
+<ol>
+<li><strong>Global count</strong> (cheap, structural, parallel across layers — same shape
+   as the existing <code>sibling_family_size_histogram</code>, extended to report a
+   <strong>per-layer</strong> breakdown rather than one index-wide aggregate): for each
+   layer, <code>count_layer</code> = number of non-monomorphic minorants. Gives
+   <code>total_count = Σ count_layer</code>.</li>
+<li><strong>Per-layer proportional reservoir sampling</strong> (cheap, structural, one
+   pass per layer, no cross-partition resolution): <code>N_layer = round(N ×
+   count_layer / total_count)</code>. Since <code>N_layer</code> is a proportion of
+   <code>count_layer</code>, it can never exceed it as long as <code>N &lt;= total_count</code> — the
+   one edge case is <code>total_count &lt;= N</code>, in which case sampling is skipped
+   entirely and <em>every</em> non-monomorphic minorant of every layer is kept
+   (no reservoir needed, <code>N</code> was never a real constraint). Otherwise:
+   Algorithm-R reservoir sampling over the layer's non-monomorphic minorant
+   indices, producing <code>N_layer</code> iteration-order indices directly, no
+   intermediate full list ever materialized.</li>
+<li><strong>Filtered resolution</strong> (the expensive step, the existing
+   <code>scan_layer_families</code> engine, unchanged): re-scan the layer, generating
+   and resolving cross-partition queries <strong>only</strong> for the indices selected
+   in step 2 (cheap membership test against a small per-layer index set) —
+   this is what keeps <code>--subsample</code> cheap even on an unsampled-scale index,
+   since the cross-partition resolution volume is bounded by <code>N</code>, not by
+   the layer's true size.</li>
+</ol>
+<p>Steps 2 and 3 cannot be merged into one pass: true single-pass reservoir
+sampling would waste step-3's expensive resolution work on candidates later
+evicted by the reservoir. Step 1 must fully complete (every layer) before
+step 2 can start for any layer, since <code>total_count</code> is a global quantity.</p>
+<p><strong><code>--shannon</code></strong> (no argument): emits a CSV of per-family Shannon entropy
+(15 non-empty states, <code>∅</code>/absent genomes excluded from the denominator, per
+the settled definition above). Independent of <code>--subsample</code> — entropy is
+computed and written per family as soon as its <code>genome_mask</code> resolves,
+O(1) memory per family, so it streams fine even unsampled at full index
+scale (a time cost, not a memory one). Combined with <code>--subsample N</code>, it
+delivers the original exploratory diagnostic (e.g. <code>--subsample 1000000
+--shannon</code>) directly from this general machinery, rather than a
+purpose-built one-off script.</p>
+<p>Validated end-to-end (2026-08-15) against real data: <code>--sibling-hist</code> on
+<code>phyloskims_sal_vac</code> (91 real genomes, k=31/m=11, 256 partitions × 2
+layers) confirms the ~9-billion-family estimate almost exactly (8,925,068,238
+total, 97.9% monomorphic — a sharper mono fraction than the ~80-85% earlier
+guess, corrected here). <code>--subsample</code>/<code>--shannon</code> on the smaller 20-genome
+bacterial reference (<code>benchmark/global_index_presence</code>) produced a sample
+size within rounding of the request (99,742/100,000) and a
+[0.8,1.2)-bucket share (40.7%) matching the full unsampled population
+(41.6%) — the two histograms only diverged wildly (5‰ vs 41.6%) under a
+real bug in <code>reservoir_sample_layer</code> (see next section), now fixed.</p>
+<p><strong>Bug found and fixed (2026-08-15): <code>family_idx</code> numbering mismatch.</strong>
+<code>scan_layer_families</code>'s <code>family_idx</code> counts <em>every minorant</em> of a layer
+(monomorphic ones included, since <code>iter_minorants_batch</code> filters only on
+<code>is_minorant()</code>), not the raw annex slot (<code>SiblingAnnex::get(slot)</code> spans
+every k-mer, minorant or not) and not a counter over non-monomorphic
+minorants alone. <code>subsample.rs</code>'s <code>reservoir_sample_layer</code> originally
+stored raw slot numbers in its <code>HashSet&lt;usize&gt;</code> selection, which drifts
+away from <code>family_idx</code> as soon as <em>any</em> monomorphic minorant is seen —
+i.e. almost immediately, since ~98% of minorants are monomorphic. Fixed by
+tracking two separate counters: <code>family_idx</code> (every minorant, matching
+<code>scan_layer_families</code>) and <code>seen</code> (non-monomorphic minorants only, what
+Algorithm R actually samples over) — only <code>family_idx</code> values are ever
+stored in the selection set. The existing unit test never exercised this
+(its fixture has exactly one non-monomorphic family, always hitting the
+"keep everything" shortcut) — a stronger fixture with several interleaved
+monomorphic/non-monomorphic families would be needed to catch a regression
+here automatically; not yet written.</p>
+<h2 id="cheap-entropy-pre-filtering-row-marginal-sums-idea-not-implemented-2026-08-15">Cheap entropy pre-filtering — row-marginal sums (idea, not implemented, 2026-08-15)</h2>
+<p>Motivation: on real data (bacterial reference, full unsampled run), only
+~5‰ of non-monomorphic minorants fall in the <code>[0.5, 1.5]</code> bit band judged
+phylogenetically interesting (entropy too low = uninformative near-invariant
+site; too high = saturated/noisy, see <code>family_entropy</code>'s 15-state
+discussion) — roughly 1 in 10,000 minorants overall. Computing exact
+entropy for every candidate just to discard 99.99% of them is wasteful at
+the full 9-billion scale.</p>
+<p><strong>The idea</strong>: <code>PersistentBitMatrix::col_view(c)</code> gives a genome's whole
+presence column as a <code>BitSliceView</code> (sequential, no MPHF, no cross-partition
+routing — purely local to one layer's own matrix). Accumulating
+<code>TempCompactIntVecBuilder::inc_present(col)</code> (already exists in
+<code>obicompactvec/src/builder.rs:121</code>, along with <code>add</code>/<code>min</code>/<code>max</code>/<code>diff</code> on
+<code>IntSliceView</code> — no new low-level API needed) over every column of a layer
+produces <code>coverage[slot]</code>: how many genomes carry each exact k-mer, in one
+sequential per-layer pass, entirely decoupled from family/sibling
+structure. Persisted once per layer, a family's members' coverage could
+then be looked up via a plain local MPHF <code>index()</code> (cheap) instead of a
+full cross-partition presence resolution (<code>find_presence_batch</code>) — the
+expensive part today is specifically the cross-partition/cross-layer
+routing to a sibling's own matrix, not the bit-reading itself, and
+<code>coverage[slot]</code> sidesteps that routing entirely by moving the cost into a
+one-time, purely local, embarrassingly-parallel build step.</p>
+<p><strong>Why not implemented</strong>: <code>coverage[slot]</code> is a per-member marginal —
+summing members' coverages to approximate a family's entropy silently
+assumes no genome carries more than one member at once. It cannot
+represent or detect joint co-occurrence (a genome carrying both <code>A</code> and
+<code>C</code> at once, i.e. a combined 15-symbol state) at all, which is exactly the
+phenomenon <code>family_entropy</code>'s 15-state definition exists to capture (see
+<code>CardinalityTally</code>/<code>cardinality_transition_probs</code>, the project's own
+existing machinery for this same co-occurrence structure, built for the
+Sankoff matrix calibration). A family that is in truth uniformly <code>AC</code>
+across every carrying genome would look like a well-balanced 2-state split
+under the marginal approximation (entropy ≈ 1) while its true 15-state
+entropy is 0 — i.e. the marginal proxy's failure mode lands on exactly the
+"saturated, uninformative" tail this pre-filter would need to catch,
+undermining the point. It stays plausible as a coarse filter for the
+<em>low</em> tail only (a dominant single member's marginal share reliably
+predicts low true entropy too), but not as a stand-in for the high tail —
+not pursued further for now.</p>
+<h2 id="-free-loss-tnt-pipeline-four-independent-scans-three-of-them-unsampled-found-2026-08-15-fixed-2026-08-15-see-implemented-below"><code>--free-loss</code>/<code>--tnt</code> pipeline: four independent scans, three of them unsampled (found 2026-08-15, fixed 2026-08-15 — see "Implemented" below)</h2>
+<p>Measured on <code>phyloskims_sal_vac</code> (91 genomes): <code>obikmer phylo --subsample 500000
+--free-loss --tnt</code> logs four sequential stages —
+<code>raw_snp_distance</code> (1413s), <code>base_pair_tally</code> (1456s),
+<code>cardinality_tally</code> (2078s), <code>snp_pseudo_alignment</code> (143s). Reading the
+code (<code>obikmer/src/cmd/phylo/mod.rs:210-242</code>,
+<code>obikphylo/src/siblings/distance.rs</code>, <code>cardinality.rs</code>, <code>alignment.rs</code>)
+surfaced two compounding problems, not one:</p>
+<ol>
+<li><strong>Four separate full scans of the annex</strong>, each opening its own
+   <code>KmerPartition</code>/<code>PartitionCache</code> and calling <code>scan_family_pairs</code>/
+   <code>scan_layer_families</code> independently — nothing computed in one stage is
+   reused by another. <code>base_pair_tally</code> is explicitly documented
+   (<code>distance.rs:138-143</code>) as a second full pass over the same
+   traversal <code>raw_snp_distance</code> already did, needed only because
+   <code>raw_snp_distance</code> doesn't keep the resolved bases, only aggregate
+   counts. <code>cardinality_tally</code> and <code>snp_pseudo_alignment</code> are each a
+   third and fourth independent full pass. Per the module's own earlier
+   profiling note (<code>family_scan.rs:26-28</code>, cited already above), this
+   traversal is page-fault/mmap-bound, not compute-bound — the ~10-12%
+   CPU efficiency ("contention" status) observed on these three slow
+   stages is consistent with I/O stalls scaled by repeated full scans,
+   not lock contention (there are no <code>Mutex</code>/<code>RwLock</code> anywhere in
+   <code>siblings/*.rs</code>; shared writes use per-slot <code>AtomicU8::fetch_or</code>).</li>
+<li><strong>Worse: <code>raw_snp_distance</code> and <code>cardinality_tally</code> don't honor
+   <code>--subsample</code> at all</strong> — both call <code>scan_layer_families</code> with
+   <code>Selection::All</code> hardcoded, and <code>args.subsample</code> isn't even threaded
+   into their function signatures (<code>mod.rs:212</code>, <code>mod.rs:226</code>). Only
+   <code>snp_pseudo_alignment(args.subsample)</code> builds a real reservoir-sampled
+   <code>Selection::Some(set)</code> (via <code>compute_selections</code>, <code>alignment.rs:89</code>).
+   So today, <code>--subsample 500000</code> only bounds the pseudo-alignment step —
+   the SNP-distance matrix, the Sankoff base-pair calibration, and the
+   cardinality histogram are always computed over the <strong>full, unsampled</strong>
+   index regardless of the flag. This is not merely "different subsamples
+   per stage" (which would already be a problem worth fixing) — it's that
+   three of the four stages never subsample, which explains most of the
+   ~10x runtime gap against <code>snp_pseudo_alignment</code> on its own.</li>
+</ol>
+<p><strong>Decided requirement</strong>: all four stages consume <strong>one shared selection</strong>,
+computed once, not each stage either scanning everything or drawing its
+own independent sample. Per-genome-pair SNP counts, the Sankoff base-pair
+calibration, the cardinality histogram, and the pseudo-alignment all
+describe the same set of families — the calibration and the alignment it
+calibrates are now guaranteed to agree on which sites exist.</p>
+<p><strong>Correction to the "single pass" framing above</strong>: <code>base_pair_tally</code>/
+<code>cardinality_tally</code> both need <code>raw_snp_distance</code>'s <em>complete</em> aggregate
+SNP/shared counts before they can derive <code>included[i,j]</code> (the
+<code>ratio_ceiling</code> filter) — a genuine sequential dependency (<code>included</code>
+can't be known until every pair's aggregate count is final), not an
+artifact of the old code's structure. So the fix is <strong>two</strong> passes over
+the shared selection, not one: pass A computes the aggregate counts (and
+derives <code>included</code>); pass B fuses <code>base_pair_tally</code> + <code>cardinality_tally</code>
++ the pseudo-alignment (mutually independent once <code>included</code> is known)
+into a single scan. Still a 4→2 reduction, and — per the clarification
+that settled this — pass A itself now runs over the <em>same shared
+selection</em> pass B uses (not the full unsampled index): "les ratios, on
+les fait sur les sites sélectionnés, c'est tout, les autres sites
+n'existent pas" — once a selection is chosen, both passes are bounded by
+it, so on a real <code>--subsample</code>/<code>--entropy</code> run pass A is cheap too, not
+just pass B.</p>
+<p><strong>Entropy-biased selection's own resolution to the "forward-looking
+complication"</strong> (entropy must be known before selection, but selection
+happens during the same scan that would resolve it): see "Entropy-biased
+selection" below — resolved via a persisted per-layer entropy annex, not
+by restructuring the scan into an inline pre-pass.</p>
+<h2 id="entropy-biased-selection-soft-gaussian-weighting-not-a-hard-cutoff-decided-and-implemented-2026-08-15">Entropy-biased selection: soft Gaussian weighting, not a hard cutoff (decided and implemented 2026-08-15)</h2>
+<p>Refines the "forward-looking complication" above with a concrete
+mechanism. Instead of a hard <code>[low, high]</code> entropy band (or any other
+exact cutoff) deciding which non-monomorphic minorant families are
+eligible, selection is weighted by an <strong>unnormalized Gaussian kernel</strong>
+centered on a target entropy: <code>w(entropy) = exp(-(entropy - μ)² / (2σ²))</code>
+— deliberately not the normalized Gaussian density (which would peak
+below 1 and complicate the "probability" reading) — this kernel form
+equals 1 exactly at <code>entropy = μ</code> and decays smoothly to 0 away from it,
+so it reads directly as an acceptance weight: the further a family's
+entropy from the target, the less likely it is picked, with no hard
+in/out boundary — a few "bad" sites can still get in, by design. <code>μ</code>
+(default ~1.0) and <code>σ</code> (default ~0.5) are meant to be user-tunable.</p>
+<p><strong>Mechanism: joint probability, not a weighted reservoir</strong>. Not
+Efraimidis–Spirakis weighted reservoir sampling (an earlier, more complex
+proposal, superseded before implementation) — instead, a single
+independent accept/reject draw per qualifying candidate: draw
+<code>u ~ Uniform(0,1)</code>, accept iff <code>u &lt; p₀ · w(entropy)</code>. <code>p₀</code> is a single
+<strong>index-wide</strong> rate, <code>N / total_count</code> (<code>total_count</code> = the sum of
+<code>non_monomorphic_counts</code> across every layer, <code>N</code> = <code>--subsample</code>'s
+target), applied identically at every layer — this alone already gives
+each layer its proportional share (the same effect the old uniform
+reservoir's explicit per-layer <code>n_layer = N · count_layer / total_count</code>
+computation achieved, but without needing to compute it: applying one
+rate uniformly is mathematically the same as proportioning per layer).
+<code>p₀ = 1.0</code> when there is no <code>--subsample</code> at all — <code>--entropy</code> alone is a
+pure soft entropy filter over the whole index, no size target. Properties:
+(1) <strong>strictly generalizes the existing uniform sampler</strong> — with <code>σ</code> large
+enough that <code>w ≈ 1</code> everywhere, this reduces to the old uniform <code>N/total_count</code>
+draw; (2) yields "approximately N", not exactly N — expected accepted
+count is <code>N · mean(w)</code>, always <code>≤ N</code> — an intentional relaxation, matching
+"sous-échantillonnage à environ n" rather than the old reservoir's exact-N
+guarantee; (3) one streaming pass, one random draw per candidate, no
+reservoir state.</p>
+<p><strong>Resolving "entropy must be known before selection, but selection
+happens during the same resolving scan"</strong>: solved with a <strong>persisted,
+per-layer entropy annex</strong> (<code>obikphylo/src/siblings/entropy_annex.rs</code>,
+<code>EntropyAnnex</code>/<code>EntropyAnnexBuilder</code>), not by restructuring the scan.
+Mirrors <code>SiblingAnnex</code>'s mmap-backed, read-only-after-build convention,
+but indexed by <code>family_idx</code> (every minorant of the layer, monomorphic
+included — the same numbering <code>Selection</code>/<code>scan_layer_families</code> already
+use), one <code>f32</code> entropy15 value per entry, <code>-1.0</code> sentinel for monomorphic/
+not-yet-computed. First use of <code>--entropy</code>/<code>--entropy-sd</code> on an index
+pays a one-time cost (<code>ensure_entropy_annexes</code> in <code>entropy.rs</code>: a full,
+unsampled <code>Selection::All</code> scan, resolving every non-monomorphic
+minorant's <code>genome_mask</code> once to compute and persist its entropy) — every
+later run (any <code>μ</code>/<code>σ</code>, any command) reads the file positionally, no
+re-scan, restoring the usual <code>Selection::Some</code> "skip resolving excluded
+families" speedup that a naive "weigh during the resolving scan" design
+would have permanently forfeited.</p>
+<p><strong>Resolved</strong>: the existing hard "non-monomorphic minorant" eligibility
+filter stays a hard gate upstream of the Gaussian weighting — only
+qualifying families ever get a stored entropy value or a weighted draw.</p>
+<p><strong>CLI, implemented</strong>: two <code>phylo</code> options, <code>--entropy &lt;μ&gt;</code> and
+<code>--entropy-sd &lt;σ&gt;</code> (<code>obikmer/src/cmd/phylo/args.rs</code>). The entropic filter
+activates as soon as <em>either</em> is given (<code>mod.rs</code>, computed once into an
+<code>Option&lt;EntropyBias&gt;</code> threaded through <code>--snp</code>/<code>--family-overlap</code>/
+<code>--shannon</code>/the fused sankoff pipeline below). If active but one or both
+are unset, defaults are <code>μ = 1.0</code>, <code>σ = 0.5</code>.</p>
+<h2 id="two-entropy-definitions-kept-side-by-side-for-comparison-2026-08-15">Two entropy definitions kept side by side, for comparison (2026-08-15)</h2>
+<p><code>--shannon</code>'s CSV carries both <code>entropy15</code> (<code>family_entropy</code> — the settled
+15-non-empty-state definition, see above) and <code>entropy4</code> (<code>family_entropy_4</code>
+— plain nucleotide reduction), computed from the same already-resolved
+<code>genome_mask</code>, not from the marginal approximation above. A genome carrying
+several bases at once contributes to <em>each</em> base's count (counted once per
+base present, not fractionally split, not folded into one combined state)
+— a genome polymorphic for the family is present at more than one base by
+construction, so it is expected to count more than once; the denominator is
+the total base-occurrence count, not the genome count (the two coincide
+only when no genome carries more than one base). Kept side by side
+specifically to measure, on real data, how much the two diverge — not yet
+analyzed.</p>
+<h2 id="persistentsparsebitmatrix-implemented-and-measured-2026-08-15"><code>PersistentSparseBitMatrix</code> — implemented and measured (2026-08-15)</h2>
+<p>A row-major (k-mer-major), deduplicated sparse alternative to
+<code>obicompactvec::PersistentBitMatrix</code>, motivated by the same sparsity that
+drove <code>--subsample</code>/<code>--shannon</code> above, but pursued as a foundational
+storage-layer change rather than an index-level workaround. Full design
+history, rationale, and rejected alternatives (external Elias-Fano crates,
+<code>cacheline-ef</code>, a single unsplit <code>dict_id</code> array) are in the dedicated
+implementation plan (<code>vivid-mapping-tiger.md</code> at the time of writing — the
+content below is the durable summary, not a pointer to a session-scoped
+file). Also directly informed by Alanko, Bille, Gørtz, Navarro, Puglisi,
+"Compact Data Structures for Collections of Sets" (2025,
+<code>biblio/Alanko et al. - Compact Data Structures for Collections of
+Sets.pdf</code>) — this design implements only their exact-duplicate special
+case (a plain dedup dictionary), not their full subset-containment
+hierarchy.</p>
+<p><strong>Design</strong>: four on-disk components, each mmap-backed, built once per
+layer (matching how the rest of the build pipeline already works — never
+the whole multi-billion-row index at once): an <code>is_multi</code> rank-capable
+flag per row (singleton vs. multi-genome), a fixed-bit-width array for
+singleton rows (genome index directly, <code>ceil(log2(n_cols))</code> bits), a
+separate fixed-bit-width array for multi-genome rows (<code>dict_id</code>,
+<code>ceil(log2(n_distinct_multi_sets))</code> bits — kept apart from the singleton
+array specifically because <code>n_distinct_multi_sets</code> can be large in
+absolute terms even when multi-genome rows are a small <em>fraction</em> of all
+rows, and a single shared array would force every row, singletons
+included, to pay the wider width), and a deduplicated dictionary of
+distinct multi-genome sets (Elias-Fano-encoded byte offsets + a
+varint-encoded values blob). New low-level primitives added to
+<code>obicompactvec</code> to build this: <code>PersistentFixedIntVec</code> (arbitrary,
+runtime-parameterized bit width, width 0 included — needed once a real
+bug surfaced, see below), <code>PersistentRankSelectBitVec</code> (rank1/rank0/select1
+on top of the crate's existing <code>count_ones</code>, using
+<code>common_traits::SelectInWord</code>), <code>EliasFano</code> (composes the two). A new
+<code>BinaryMatrix</code> trait (<code>n</code>, <code>n_cols</code>, <code>row</code>/<code>fill_row</code>, <code>fill_sub_matrix</code>,
+<code>count_ones</code>) unifies dense and sparse at the one call site that needs
+both interchangeably (<code>obikphylo::siblings::cache::Mat</code>) — column-oriented
+methods (<code>col</code>, <code>col_view</code>, the <code>partial_*_dist_matrix</code> family) stay
+dense-only.</p>
+<p><strong>Two real bugs caught by tests, not by inspection</strong>: (1) <code>EliasFano::open</code>
+re-derived its low-bits width from the persisted low-vector file's own
+width byte; the zero-width case was built with a dummy 1-bit placeholder
+(the builder rejected true width 0), so every reopened value silently
+doubled. Fixed by making <code>PersistentFixedIntVec</code> genuinely support width 0
+(no storage, <code>get</code> always 0) instead of working around the limitation in
+<code>EliasFano</code>. (2) An empty row (cardinality 0 — not expected on a real
+built index, but not guarded against either) was recorded as a singleton
+at genome 0, indistinguishable on read-back from a <em>real</em> singleton at
+genome 0. Fixed by routing cardinality-0 rows through the dictionary path
+(a genuine empty entry) instead of the singleton shortcut. Both caught by
+<code>obicompactvec</code>'s test suite (142 tests, including disk-reopen round-trips
+that drop every builder/mmap before reopening fresh), not by manual
+review — worth remembering next time a "this edge case can't happen in
+practice" shortcut is tempting.</p>
+<p><strong>Measured on real data</strong> (<code>layer_1</code> of <code>phyloskims_sal_vac</code>'s
+<code>part_00018</code>, 30,246,774 rows, 91 genomes — <code>#[ignore]</code>d benchmarks in
+<code>obikphylo/src/siblings/tests.rs</code>):</p>
+<table>
+<thead>
+<tr>
+<th></th>
+<th>dense</th>
+<th>sparse</th>
+<th>ratio</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>on-disk size</td>
+<td>328.1MB</td>
+<td>43.7MB</td>
+<td><strong>7.5x</strong> smaller</td>
+</tr>
+<tr>
+<td>build time / peak RSS</td>
+<td>—</td>
+<td>4.26s / 628MB</td>
+<td>(per-layer, in-memory construction — comfortable)</td>
+</tr>
+<tr>
+<td>row access, sequential (2M reads)</td>
+<td>43ns/row</td>
+<td>32ns/row</td>
+<td>sparse <strong>faster</strong> (smaller structure, better cache fit)</td>
+</tr>
+<tr>
+<td>row access, random (2M reads)</td>
+<td>409ns/row</td>
+<td>85ns/row</td>
+<td>sparse <strong>~4.8x faster</strong> (the real <code>--shannon</code>/family-lookup shape)</td>
+</tr>
+<tr>
+<td>column access, one full column (30.2M rows)</td>
+<td>11.5ms</td>
+<td>993ms</td>
+<td>sparse <strong>86x slower</strong> (no native column method — every read decodes a full row to keep one bit)</td>
+</tr>
+</tbody>
+</table>
+<p>The row-access wins (both directions) weren't the design's stated goal —
+compactness was — but turn out real: dense's genome-major layout scatters
+a single row read across a much bigger file, which costs more than
+sparse's rank/select/varint decode once the file is this much smaller.
+The column-access cost is the flip side of the same layout choice, and is
+exactly what the next item below exists to fix.</p>
+<p><strong>Next, not yet planned</strong>: rewrite <code>partial_jaccard_dist_matrix</code>/
+<code>partial_hamming_dist_matrix</code>/etc. (<code>obicompactvec/src/bitmatrix/pairwise.rs</code>)
+as a row-major co-occurrence accumulation (<code>O(Σ_rows k²)</code>, per-row
+increments into an <code>NxN</code> genome-pair counter — the known alternative to
+today's column-fold, plausibly cheaper on data this sparse, not just a
+fallback) so <code>obikindex</code>'s <code>--metric</code>/distance-matrix path can use the
+sparse type without the measured 86x column-access penalty. Needs its own
+design pass (in particular how it plugs into the <code>BitPartials</code>/
+<code>ColumnWeights</code> traits so both matrix types keep serving <code>--metric</code>)
+before implementation — not just "port the loop", a genuinely different
+algorithm.</p>
+<p>Also still deferred, unchanged from the implementation plan: full Alanko
+et al. subset-hierarchy compression (only the exact-duplicate special case
+is built), a sparse <code>PersistentCompactIntMatrix</code> (count matrices), and
+BRWT-style column-correlation exploitation.</p>
+<h2 id="wired-into-pack-and-the-sibling-annex-build-path-2026-08-15">Wired into <code>pack</code> and the sibling-annex build path (2026-08-15)</h2>
+<p><code>PersistentSparseBitMatrix</code> went from a validated but unused type to a
+real, selectable on-disk format:</p>
+<ul>
+<li><strong>Generic <code>Layer&lt;D&gt;</code></strong>: <code>obilayeredmap::Layer&lt;D&gt;</code>'s presence-only methods
+  (<code>n_cols</code>, <code>sub_matrix</code>, <code>fill_sub_matrix</code>) are generic over any
+  <code>D: LayerData&lt;Item = Box&lt;[bool]&gt;&gt; + BinaryMatrix</code>, not hardcoded to
+  <code>PersistentBitMatrix</code> — <code>PersistentSparseBitMatrix</code> implements
+  <code>LayerData</code> (<code>open</code>/<code>read</code>) the same way. <code>find_slot</code>/<code>index_batch</code> were
+  already generic over any <code>D: LayerData</code>, so they needed no change.
+  Verified by <code>obilayeredmap</code>'s
+  <code>presence_layer_generic_over_sparse_matches_dense</code> test: build a dense
+  presence layer, convert it to sparse via <code>build_from_dense</code>, open both
+  as <code>Layer&lt;PersistentBitMatrix&gt;</code>/<code>Layer&lt;PersistentSparseBitMatrix&gt;</code> on
+  the same directory, assert <code>n_cols</code>/<code>sub_matrix</code>/<code>find_slot</code> agree.
+  (This test must stay at <code>k=4</code> with mutually non-colliding canonical
+  4-mers across its input sequences — <code>K</code>/<code>M</code> are process-wide
+  <code>AtomicUsize</code>s in test builds, not thread-local, so a test using a
+  different <code>k</code> races every other test in the same crate binary; a k=11
+  version of this test passed alone but failed under the full
+  <code>obilayeredmap</code> suite for exactly that reason before being fixed.)</li>
+<li><strong><code>obikphylo::siblings::cache::Mat</code></strong> gained a third variant,
+  <code>SparsePresence(Layer&lt;PersistentSparseBitMatrix&gt;)</code>, alongside <code>Count</code>
+  and <code>Presence</code> — every method (<code>find_slot</code>, <code>index_batch</code>,
+  <code>iter_minorants_batch</code>, <code>n_cols</code>, <code>fill_sub_matrix_carries</code>) dispatches
+  to it identically to <code>Presence</code>, since both go through the same generic
+  <code>Layer&lt;D&gt;</code> code. <code>PartitionCache::build</code> picks the variant per layer by
+  checking for <code>presence/is_multi.prsb</code> (the sparse format's own marker
+  file, see the design section above) before falling back to the dense
+  open path.</li>
+<li><strong><code>pack_sparse_bit_matrix</code></strong> (new, <code>obicompactvec::bitmatrix::sparse</code>):
+  <code>pack --sparse</code>'s entry point. Idempotent (checks <code>is_multi.prsb</code>
+  first); packs to dense <code>matrix.pbmx</code> first if that hasn't happened yet
+  (the dense→sparse transpose needs random row access, which only the
+  packed/columnar dense forms give), then <code>build_from_dense</code>s the sparse
+  form into the same directory and deletes <code>matrix.pbmx</code> — old-format
+  files are removed only after the new format is fully written, mirroring
+  <code>pack_bit_matrix</code>'s own crash-safety convention.</li>
+<li><strong>CLI</strong>: <code>obikmer pack --sparse</code> threads a <code>sparse: bool</code> through
+  <code>KmerIndex::pack_matrices</code> (all other call sites — <code>select</code>, <code>merge</code>,
+  <code>finalize_indexed</code> — pass <code>false</code>, unchanged dense behaviour). Count
+  matrices are untouched by <code>--sparse</code> (no sparse <code>PersistentCompactIntMatrix</code>
+  — see "still deferred" above).</li>
+<li><strong>End-to-end coverage</strong>: <code>obikphylo::siblings::tests::
+  sibling_annex_works_after_pack_sparse</code> builds a two-genome index, packs
+  it <code>--sparse</code>, asserts <code>is_multi.prsb</code> exists, then runs
+  <code>build_sibling_annex</code> and checks the resulting <code>FamilyMask</code>s match the
+  dense-path test (<code>sibling_annex_one_sibling_each</code>) exactly — proves the
+  sparse format round-trips through the real build pipeline
+  (<code>PartitionCache</code> sparse-detection included), not just the
+  <code>obicompactvec</code>/<code>obilayeredmap</code> unit layers below it.</li>
+</ul>
+<p>Full workspace <code>cargo test</code> (all crates, unit + doc tests) green after
+this change.</p>
+<h2 id="sankoff-pipeline-fusion-entropy-biased-selection-implemented-2026-08-15">Sankoff pipeline fusion + entropy-biased selection — implemented (2026-08-15)</h2>
+<p>Replaces the "four independent scans" problem above and implements
+"Entropy-biased selection" above, end to end:</p>
+<ul>
+<li><strong><code>SankoffBundleExt::sankoff_bundle</code></strong> (new,
+  <code>obikphylo/src/siblings/sankoff_bundle.rs</code>) — the <code>--sankoff</code>/<code>--tnt</code>/
+  <code>--phyg</code>/<code>--iqtree</code> block in <code>obikmer/src/cmd/phylo/mod.rs</code> now calls
+  this once instead of three separate <code>raw_snp_distance</code>/
+  <code>base_pair_tally</code>/<code>cardinality_tally</code> calls. One <code>PartitionCache</code>, one
+  shared (possibly subsampled/entropy-biased) selection computed once via
+  <code>compute_selections</code>, two scans over it: pass A (aggregate SNP/shared
+  counts, <code>--exclude-genome</code> zeroing, then <code>included[i,j]</code>), pass B
+  (<code>base_pair_tally</code> + <code>cardinality_tally</code> + the pseudo-alignment, fused
+  into one <code>scan_layer_families</code> call per layer, all three read off the
+  same resolved <code>genome_mask</code>). <code>snp_pseudo_alignment</code>/
+  <code>shannon_entropy_csv</code> (still used standalone by <code>--snp</code>/
+  <code>--family-overlap</code>/<code>--shannon</code>) both gained an <code>entropy_bias</code> parameter
+  too, so entropy-biased selection isn't sankoff-specific.</li>
+<li><strong>Regression proof</strong>: <code>sankoff_bundle_matches_old_separate_calls</code>
+  (<code>obikphylo/src/siblings/tests.rs</code>) asserts <code>sankoff_bundle</code>'s four
+  outputs are bit-identical to calling the old, separate
+  <code>raw_snp_distance</code>/<code>base_pair_tally</code>/<code>cardinality_tally</code>/
+  <code>snp_pseudo_alignment</code> on the same fixture with no subsample — the
+  fusion is a performance change, not a behavior change.</li>
+<li><strong><code>EntropyAnnex</code>/<code>EntropyAnnexBuilder</code></strong> (new,
+  <code>obikphylo/src/siblings/entropy_annex.rs</code>) and <strong><code>ensure_entropy_annexes</code></strong>
+  (<code>entropy.rs</code>) implement the persisted-entropy mechanism from
+  "Entropy-biased selection" above. <code>entropy_annex_builds_on_demand_and_biases_selection</code>
+  (<code>tests.rs</code>) proves, on a fixture with one known-entropy family: the
+  annex file doesn't exist before any entropy-biased call; <code>compute_selections</code>
+  builds it on first use; <code>μ</code> set to the family's exact entropy with
+  <code>p₀ = 1.0</code> selects it deterministically (<code>u &lt; 1.0</code> always, for
+  <code>u ∈ [0,1)</code>); <code>μ</code> set far away with tiny <code>σ</code> deterministically excludes
+  it (<code>w</code> underflows to exactly <code>0.0</code>); the persisted value matches
+  <code>--shannon</code>'s own <code>family_entropy</code> computation to <code>1e-6</code>.</li>
+<li><strong><code>EntropyBias</code></strong> (<code>pub</code>, <code>obikphylo::siblings::EntropyBias { mu, sigma }</code>)
+  is the one new public type threading <code>--entropy</code>/<code>--entropy-sd</code> through
+  every <code>Option&lt;EntropyBias&gt;</code>-accepting method — resolved once in
+  <code>obikmer/src/cmd/phylo/mod.rs</code> from <code>args.entropy</code>/<code>args.entropy_sd</code>
+  (activation: either given; defaults <code>1.0</code>/<code>0.5</code> for whichever is unset).</li>
+</ul>
+<p>Full workspace <code>cargo test</code> green after this change (167 unit tests in
+<code>obicompactvec</code>+<code>obilayeredmap</code>+<code>obikphylo</code> alone, plus every other
+crate's suite, no regressions).</p>
+<p><strong>Still open, not part of this change</strong> (per "Correction to the 'single
+pass' framing" above): <code>--raw-snp-distance</code>/<code>--raw-snp-counts</code> (the
+standalone diagnostic flags, not the <code>--sankoff</code> pipeline) still always
+scan the full unsampled index — never threaded <code>--subsample</code>/<code>--entropy</code>,
+out of scope here since the reported problem was specifically about the
+<code>--sankoff</code>/<code>--tnt</code> pipeline's redundant/inconsistent scans, not these
+two standalone flags.</p>
+
+
+
+
+
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+
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+
+
+
+                
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text{fill:var(--md-mermaid-label-fg-color);font-family:var(--md-mermaid-font-family)}.classLabel .box{fill:var(--md-mermaid-label-bg-color);background-color:var(--md-mermaid-label-bg-color);opacity:1}.classLabel .label{fill:var(--md-mermaid-label-fg-color);font-family:var(--md-mermaid-font-family)}.node .divider{stroke:var(--md-mermaid-node-fg-color)}.relation{stroke:var(--md-mermaid-edge-color)}.cardinality{fill:var(--md-mermaid-label-fg-color);font-family:var(--md-mermaid-font-family)}.cardinality text{fill:inherit!important}defs marker.marker.composition.class path,defs marker.marker.dependency.class path,defs marker.marker.extension.class path{fill:var(--md-mermaid-edge-color)!important;stroke:var(--md-mermaid-edge-color)!important}defs marker.marker.aggregation.class path{fill:var(--md-mermaid-label-bg-color)!important;stroke:var(--md-mermaid-edge-color)!important}.statediagramTitleText{fill:var(--md-mermaid-label-fg-color)}g.stateGroup rect{fill:var(--md-mermaid-node-bg-color);stroke:var(--md-mermaid-node-fg-color)}g.stateGroup .state-title{fill:var(--md-mermaid-label-fg-color)!important;font-family:var(--md-mermaid-font-family)}g.stateGroup .composit{fill:var(--md-mermaid-label-bg-color)}.nodeLabel,.nodeLabel p{color:var(--md-mermaid-label-fg-color);font-family:var(--md-mermaid-font-family)}a .nodeLabel{text-decoration:underline}.node circle.state-end,.node circle.state-start,.start-state{fill:var(--md-mermaid-edge-color);stroke:none}.end-state-inner,.end-state-outer{fill:var(--md-mermaid-edge-color)}.end-state-inner,.node circle.state-end{stroke:var(--md-mermaid-label-bg-color)}.transition{stroke:var(--md-mermaid-edge-color)}[id^=state-fork] rect,[id^=state-join] rect{fill:var(--md-mermaid-edge-color)!important;stroke:none!important}.statediagram-cluster.statediagram-cluster .inner{fill:var(--md-default-bg-color)}.statediagram-cluster rect{fill:var(--md-mermaid-node-bg-color);stroke:var(--md-mermaid-node-fg-color)}.statediagram-state rect.divider{fill:var(--md-default-fg-color--lightest);stroke:var(--md-default-fg-color--lighter)}defs #statediagram-barbEnd{stroke:var(--md-mermaid-edge-color)}[id^=entity] path,[id^=entity] rect{fill:var(--md-default-bg-color)}.relationshipLine{stroke:var(--md-mermaid-edge-color)}defs .marker.oneOrMore.er *,defs .marker.onlyOne.er *,defs .marker.zeroOrMore.er *,defs .marker.zeroOrOne.er *{stroke:var(--md-mermaid-edge-color)!important}text:not([class]):last-child{fill:var(--md-mermaid-label-fg-color)}.actor{fill:var(--md-mermaid-sequence-actor-bg-color);stroke:var(--md-mermaid-sequence-actor-border-color)}text.actor>tspan{fill:var(--md-mermaid-sequence-actor-fg-color);font-family:var(--md-mermaid-font-family)}line{stroke:var(--md-mermaid-sequence-actor-line-color)}.actor-man circle,.actor-man line{fill:var(--md-mermaid-sequence-actorman-bg-color);stroke:var(--md-mermaid-sequence-actorman-line-color)}.messageLine0,.messageLine1{stroke:var(--md-mermaid-sequence-message-line-color)}.note{fill:var(--md-mermaid-sequence-note-bg-color);stroke:var(--md-mermaid-sequence-note-border-color)}.loopText,.loopText>tspan,.messageText,.noteText>tspan{stroke:none;font-family:var(--md-mermaid-font-family)!important}.messageText{fill:var(--md-mermaid-sequence-message-fg-color)}.loopText,.loopText>tspan{fill:var(--md-mermaid-sequence-loop-fg-color)}.noteText>tspan{fill:var(--md-mermaid-sequence-note-fg-color)}#arrowhead 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T,c=a.pipe(oe(),ae(!0));z([a,Le(e),mt(e)]).pipe(W(c),$e(1,ye)).subscribe({next([{active:p},l]){let f=Be(p),{width:u}=de(p);e.style.setProperty("--md-indicator-x",`${f.x}px`),e.style.setProperty("--md-indicator-width",`${u}px`);let d=gr(o);(f.x<d.x||f.x+u>d.x+l.width)&&o.scrollTo({left:Math.max(0,f.x-16),behavior:"smooth"})},complete(){e.style.removeProperty("--md-indicator-x"),e.style.removeProperty("--md-indicator-width")}}),z([Ge(o),Le(o)]).pipe(W(c)).subscribe(([p,l])=>{let f=At(o);i.hidden=p.x<16,s.hidden=p.x>f.width-l.width-16}),L(h(i,"click").pipe(m(()=>-1)),h(s,"click").pipe(m(()=>1))).pipe(W(c)).subscribe(p=>{let{width:l}=de(o);o.scrollBy({left:l*p,behavior:"smooth"})}),r.pipe(W(c),g(p=>n.includes(p))).subscribe(p=>p.click()),o.classList.add("tabbed-labels--linked");for(let p of n){let 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t.pipe(b(r=>L($(!0),$(!1).pipe(nt(2e3))).pipe(m(o=>({message:r,active:o})))))}function ni(e,t){let r=j(".md-typeset",e);return H(()=>{let o=new T;return o.subscribe(({message:n,active:i})=>{e.classList.toggle("md-dialog--active",i),r.textContent=n}),cs(e,t).pipe(O(n=>o.next(n)),A(()=>o.complete()),m(n=>P({ref:e},n)))})}var ps=0;function ls(e,t){document.body.append(e);let{width:r}=de(e);e.style.setProperty("--md-tooltip-width",`${r}px`),e.remove();let o=vr(t),n=typeof o!="undefined"?Ge(o):$({x:0,y:0}),i=L(Ye(t),it(t)).pipe(Y());return z([i,n]).pipe(m(([s,a])=>{let{x:c,y:p}=Be(t),l=de(t),f=t.closest("table");return f&&t.parentElement&&(c+=f.offsetLeft+t.parentElement.offsetLeft,p+=f.offsetTop+t.parentElement.offsetTop),{active:s,offset:{x:c-a.x+l.width/2-r/2,y:p-a.y+l.height+8}}}))}function ii(e){let t=e.title;if(!t.length)return y;let r=`__tooltip_${ps++}`,o=Dt(r,"inline"),n=j(".md-typeset",o);return n.innerHTML=t,H(()=>{let i=new T;return 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ms({viewport$:e}){if(!V("header.autohide"))return $(!1);let t=e.pipe(m(({offset:{y:n}})=>n),ot(2,1),m(([n,i])=>[n<i,i]),ne(0)),r=z([e,t]).pipe(g(([{offset:n},[,i]])=>Math.abs(i-n.y)>100),m(([,[n]])=>n),Y()),o=Je("search");return z([e,o]).pipe(m(([{offset:n},i])=>n.y>400&&!i),Y(),b(n=>n?r:$(!1)),Q(!1))}function ai(e,t){return H(()=>z([Le(e),ms(t)])).pipe(m(([{height:r},o])=>({height:r,hidden:o})),Y((r,o)=>r.height===o.height&&r.hidden===o.hidden),Z(1))}function si(e,{header$:t,main$:r}){return H(()=>{let o=new T,n=o.pipe(oe(),ae(!0));o.pipe(ne("active"),Pe(t)).subscribe(([{active:s},{hidden:a}])=>{e.classList.toggle("md-header--shadow",s&&!a),e.hidden=a});let i=fe(M("[title]",e)).pipe(g(()=>V("content.tooltips")),J(s=>ii(s)));return r.subscribe(o),t.pipe(W(n),m(s=>P({ref:e},s)),Ve(i.pipe(W(n))))})}function fs(e,{viewport$:t,header$:r}){return Er(e,{viewport$:t,header$:r}).pipe(m(({offset:{y:o}})=>{let{height:n}=de(e);return{active:n>0&&o>=n}}),ne("active"))}function ci(e,t){return H(()=>{let r=new T;r.subscribe({next({active:n}){e.classList.toggle("md-header__title--active",n)},complete(){e.classList.remove("md-header__title--active")}});let o=ue(".md-content h1");return typeof o=="undefined"?y:fs(o,t).pipe(O(n=>r.next(n)),A(()=>r.complete()),m(n=>P({ref:e},n)))})}function pi(e,{viewport$:t,header$:r}){let o=r.pipe(m(({height:i})=>i),Y()),n=o.pipe(b(()=>Le(e).pipe(m(({height:i})=>({top:e.offsetTop,bottom:e.offsetTop+i})),ne("bottom"))));return z([o,n,t]).pipe(m(([i,{top:s,bottom:a},{offset:{y:c},size:{height:p}}])=>(p=Math.max(0,p-Math.max(0,s-c,i)-Math.max(0,p+c-a)),{offset:s-i,height:p,active:s-i<=c})),Y((i,s)=>i.offset===s.offset&&i.height===s.height&&i.active===s.active))}function us(e){let t=__md_get("__palette")||{index:e.findIndex(o=>matchMedia(o.getAttribute("data-md-color-media")).matches)},r=Math.max(0,Math.min(t.index,e.length-1));return 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diff --git a/DevDoc/assets/javascripts/bundle.79ae519e.min.js.map b/DevDoc/assets/javascripts/bundle.79ae519e.min.js.map
new file mode 100644
index 00000000..5cf02892
--- /dev/null
+++ b/DevDoc/assets/javascripts/bundle.79ae519e.min.js.map
@@ -0,0 +1,7 @@
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"src/templates/assets/javascripts/patches/scrollfix/index.ts", "src/templates/assets/javascripts/patches/scrolllock/index.ts", "src/templates/assets/javascripts/polyfills/index.ts"],
+  "sourcesContent": ["(function (global, factory) {\n  typeof exports === 'object' && typeof module !== 'undefined' ? factory() :\n  typeof define === 'function' && define.amd ? define(factory) :\n  (factory());\n}(this, (function () { 'use strict';\n\n  /**\n   * Applies the :focus-visible polyfill at the given scope.\n   * A scope in this case is either the top-level Document or a Shadow Root.\n   *\n   * @param {(Document|ShadowRoot)} scope\n   * @see https://github.com/WICG/focus-visible\n   */\n  function applyFocusVisiblePolyfill(scope) {\n    var hadKeyboardEvent = true;\n    var hadFocusVisibleRecently = false;\n    var hadFocusVisibleRecentlyTimeout = null;\n\n    var inputTypesAllowlist = {\n      text: true,\n      search: true,\n      url: true,\n      tel: true,\n      email: true,\n      password: true,\n      number: true,\n      date: true,\n      month: true,\n      week: true,\n      time: true,\n      datetime: true,\n      'datetime-local': true\n    };\n\n    /**\n     * Helper function for legacy browsers and iframes which sometimes focus\n     * elements like document, body, and non-interactive SVG.\n     * @param {Element} el\n     */\n    function isValidFocusTarget(el) {\n      if (\n        el &&\n        el !== document &&\n        el.nodeName !== 'HTML' &&\n        el.nodeName !== 'BODY' &&\n        'classList' in el &&\n        'contains' in el.classList\n      ) {\n        return true;\n      }\n      return false;\n    }\n\n    /**\n     * Computes whether the given element should automatically trigger the\n     * `focus-visible` class being added, i.e. whether it should always match\n     * `:focus-visible` when focused.\n     * @param {Element} el\n     * @return {boolean}\n     */\n    function focusTriggersKeyboardModality(el) {\n      var type = el.type;\n      var tagName = el.tagName;\n\n      if (tagName === 'INPUT' && inputTypesAllowlist[type] && !el.readOnly) {\n        return true;\n      }\n\n      if (tagName === 'TEXTAREA' && !el.readOnly) {\n        return true;\n      }\n\n      if (el.isContentEditable) {\n        return true;\n      }\n\n      return false;\n    }\n\n    /**\n     * Add the `focus-visible` class to the given element if it was not added by\n     * the author.\n     * @param {Element} el\n     */\n    function addFocusVisibleClass(el) {\n      if (el.classList.contains('focus-visible')) {\n        return;\n      }\n      el.classList.add('focus-visible');\n      el.setAttribute('data-focus-visible-added', '');\n    }\n\n    /**\n     * Remove the `focus-visible` class from the given element if it was not\n     * originally added by the author.\n     * @param {Element} el\n     */\n    function removeFocusVisibleClass(el) {\n      if (!el.hasAttribute('data-focus-visible-added')) {\n        return;\n      }\n      el.classList.remove('focus-visible');\n      el.removeAttribute('data-focus-visible-added');\n    }\n\n    /**\n     * If the most recent user interaction was via the keyboard;\n     * and the key press did not include a meta, alt/option, or control key;\n     * then the modality is keyboard. Otherwise, the modality is not keyboard.\n     * Apply `focus-visible` to any current active element and keep track\n     * of our keyboard modality state with `hadKeyboardEvent`.\n     * @param {KeyboardEvent} e\n     */\n    function onKeyDown(e) {\n      if (e.metaKey || e.altKey || e.ctrlKey) {\n        return;\n      }\n\n      if (isValidFocusTarget(scope.activeElement)) {\n        addFocusVisibleClass(scope.activeElement);\n      }\n\n      hadKeyboardEvent = true;\n    }\n\n    /**\n     * If at any point a user clicks with a pointing device, ensure that we change\n     * the modality away from keyboard.\n     * This avoids the situation where a user presses a key on an already focused\n     * element, and then clicks on a different element, focusing it with a\n     * pointing device, while we still think we're in keyboard modality.\n     * @param {Event} e\n     */\n    function onPointerDown(e) {\n      hadKeyboardEvent = false;\n    }\n\n    /**\n     * On `focus`, add the `focus-visible` class to the target if:\n     * - the target received focus as a result of keyboard navigation, or\n     * - the event target is an element that will likely require interaction\n     *   via the keyboard (e.g. a text box)\n     * @param {Event} e\n     */\n    function onFocus(e) {\n      // Prevent IE from focusing the document or HTML element.\n      if (!isValidFocusTarget(e.target)) {\n        return;\n      }\n\n      if (hadKeyboardEvent || focusTriggersKeyboardModality(e.target)) {\n        addFocusVisibleClass(e.target);\n      }\n    }\n\n    /**\n     * On `blur`, remove the `focus-visible` class from the target.\n     * @param {Event} e\n     */\n    function onBlur(e) {\n      if (!isValidFocusTarget(e.target)) {\n        return;\n      }\n\n      if (\n        e.target.classList.contains('focus-visible') ||\n        e.target.hasAttribute('data-focus-visible-added')\n      ) {\n        // To detect a tab/window switch, we look for a blur event followed\n        // rapidly by a visibility change.\n        // If we don't see a visibility change within 100ms, it's probably a\n        // regular focus change.\n        hadFocusVisibleRecently = true;\n        window.clearTimeout(hadFocusVisibleRecentlyTimeout);\n        hadFocusVisibleRecentlyTimeout = window.setTimeout(function() {\n          hadFocusVisibleRecently = false;\n        }, 100);\n        removeFocusVisibleClass(e.target);\n      }\n    }\n\n    /**\n     * If the user changes tabs, keep track of whether or not the previously\n     * focused element had .focus-visible.\n     * @param {Event} e\n     */\n    function onVisibilityChange(e) {\n      if (document.visibilityState === 'hidden') {\n        // If the tab becomes active again, the browser will handle calling focus\n        // on the element (Safari actually calls it twice).\n        // If this tab change caused a blur on an element with focus-visible,\n        // re-apply the class when the user switches back to the tab.\n        if (hadFocusVisibleRecently) {\n          hadKeyboardEvent = true;\n        }\n        addInitialPointerMoveListeners();\n      }\n    }\n\n    /**\n     * Add a group of listeners to detect usage of any pointing devices.\n     * These listeners will be added when the polyfill first loads, and anytime\n     * the window is blurred, so that they are active when the window regains\n     * focus.\n     */\n    function addInitialPointerMoveListeners() {\n      document.addEventListener('mousemove', onInitialPointerMove);\n      document.addEventListener('mousedown', onInitialPointerMove);\n      document.addEventListener('mouseup', onInitialPointerMove);\n      document.addEventListener('pointermove', onInitialPointerMove);\n      document.addEventListener('pointerdown', onInitialPointerMove);\n      document.addEventListener('pointerup', onInitialPointerMove);\n      document.addEventListener('touchmove', onInitialPointerMove);\n      document.addEventListener('touchstart', onInitialPointerMove);\n      document.addEventListener('touchend', onInitialPointerMove);\n    }\n\n    function removeInitialPointerMoveListeners() {\n      document.removeEventListener('mousemove', onInitialPointerMove);\n      document.removeEventListener('mousedown', onInitialPointerMove);\n      document.removeEventListener('mouseup', onInitialPointerMove);\n      document.removeEventListener('pointermove', onInitialPointerMove);\n      document.removeEventListener('pointerdown', onInitialPointerMove);\n      document.removeEventListener('pointerup', onInitialPointerMove);\n      document.removeEventListener('touchmove', onInitialPointerMove);\n      document.removeEventListener('touchstart', onInitialPointerMove);\n      document.removeEventListener('touchend', onInitialPointerMove);\n    }\n\n    /**\n     * When the polfyill first loads, assume the user is in keyboard modality.\n     * If any event is received from a pointing device (e.g. mouse, pointer,\n     * touch), turn off keyboard modality.\n     * This accounts for situations where focus enters the page from the URL bar.\n     * @param {Event} e\n     */\n    function onInitialPointerMove(e) {\n      // Work around a Safari quirk that fires a mousemove on <html> whenever the\n      // window blurs, even if you're tabbing out of the page. \u00AF\\_(\u30C4)_/\u00AF\n      if (e.target.nodeName && e.target.nodeName.toLowerCase() === 'html') {\n        return;\n      }\n\n      hadKeyboardEvent = false;\n      removeInitialPointerMoveListeners();\n    }\n\n    // For some kinds of state, we are interested in changes at the global scope\n    // only. For example, global pointer input, global key presses and global\n    // visibility change should affect the state at every scope:\n    document.addEventListener('keydown', onKeyDown, true);\n    document.addEventListener('mousedown', onPointerDown, true);\n    document.addEventListener('pointerdown', onPointerDown, true);\n    document.addEventListener('touchstart', onPointerDown, true);\n    document.addEventListener('visibilitychange', onVisibilityChange, true);\n\n    addInitialPointerMoveListeners();\n\n    // For focus and blur, we specifically care about state changes in the local\n    // scope. This is because focus / blur events that originate from within a\n    // shadow root are not re-dispatched from the host element if it was already\n    // the active element in its own scope:\n    scope.addEventListener('focus', onFocus, true);\n    scope.addEventListener('blur', onBlur, true);\n\n    // We detect that a node is a ShadowRoot by ensuring that it is a\n    // DocumentFragment and also has a host property. This check covers native\n    // implementation and polyfill implementation transparently. If we only cared\n    // about the native implementation, we could just check if the scope was\n    // an instance of a ShadowRoot.\n    if (scope.nodeType === Node.DOCUMENT_FRAGMENT_NODE && scope.host) {\n      // Since a ShadowRoot is a special kind of DocumentFragment, it does not\n      // have a root element to add a class to. So, we add this attribute to the\n      // host element instead:\n      scope.host.setAttribute('data-js-focus-visible', '');\n    } else if (scope.nodeType === Node.DOCUMENT_NODE) {\n      document.documentElement.classList.add('js-focus-visible');\n      document.documentElement.setAttribute('data-js-focus-visible', '');\n    }\n  }\n\n  // It is important to wrap all references to global window and document in\n  // these checks to support server-side rendering use cases\n  // @see https://github.com/WICG/focus-visible/issues/199\n  if (typeof window !== 'undefined' && typeof document !== 'undefined') {\n    // Make the polyfill helper globally available. This can be used as a signal\n    // to interested libraries that wish to coordinate with the polyfill for e.g.,\n    // applying the polyfill to a shadow root:\n    window.applyFocusVisiblePolyfill = applyFocusVisiblePolyfill;\n\n    // Notify interested libraries of the polyfill's presence, in case the\n    // polyfill was loaded lazily:\n    var event;\n\n    try {\n      event = new CustomEvent('focus-visible-polyfill-ready');\n    } catch (error) {\n      // IE11 does not support using CustomEvent as a constructor directly:\n      event = document.createEvent('CustomEvent');\n      event.initCustomEvent('focus-visible-polyfill-ready', false, false, {});\n    }\n\n    window.dispatchEvent(event);\n  }\n\n  if (typeof document !== 'undefined') {\n    // Apply the polyfill to the global document, so that no JavaScript\n    // coordination is required to use the polyfill in the top-level document:\n    applyFocusVisiblePolyfill(document);\n  }\n\n})));\n", "/*!\n * escape-html\n * Copyright(c) 2012-2013 TJ Holowaychuk\n * Copyright(c) 2015 Andreas Lubbe\n * Copyright(c) 2015 Tiancheng \"Timothy\" Gu\n * MIT Licensed\n */\n\n'use strict';\n\n/**\n * Module variables.\n * @private\n */\n\nvar matchHtmlRegExp = /[\"'&<>]/;\n\n/**\n * Module exports.\n * @public\n */\n\nmodule.exports = escapeHtml;\n\n/**\n * Escape special characters in the given string of html.\n *\n * @param  {string} string The string to escape for inserting into HTML\n * @return {string}\n * @public\n */\n\nfunction escapeHtml(string) {\n  var str = '' + string;\n  var match = matchHtmlRegExp.exec(str);\n\n  if (!match) {\n    return str;\n  }\n\n  var escape;\n  var html = '';\n  var index = 0;\n  var lastIndex = 0;\n\n  for (index = match.index; index < str.length; index++) {\n    switch (str.charCodeAt(index)) {\n      case 34: // \"\n        escape = '&quot;';\n        break;\n      case 38: // &\n        escape = '&amp;';\n        break;\n      case 39: // '\n        escape = '&#39;';\n        break;\n      case 60: // <\n        escape = '&lt;';\n        break;\n      case 62: // >\n        escape = '&gt;';\n        break;\n      default:\n        continue;\n    }\n\n    if (lastIndex !== index) {\n      html += str.substring(lastIndex, index);\n    }\n\n    lastIndex = index + 1;\n    html += escape;\n  }\n\n  return lastIndex !== index\n    ? html + str.substring(lastIndex, index)\n    : html;\n}\n", "/*!\n * clipboard.js v2.0.11\n * https://clipboardjs.com/\n *\n * Licensed MIT \u00A9 Zeno Rocha\n */\n(function webpackUniversalModuleDefinition(root, factory) {\n\tif(typeof exports === 'object' && typeof module === 'object')\n\t\tmodule.exports = factory();\n\telse if(typeof define === 'function' && define.amd)\n\t\tdefine([], factory);\n\telse if(typeof exports === 'object')\n\t\texports[\"ClipboardJS\"] = factory();\n\telse\n\t\troot[\"ClipboardJS\"] = factory();\n})(this, function() {\nreturn /******/ (function() { // webpackBootstrap\n/******/ \tvar __webpack_modules__ = ({\n\n/***/ 686:\n/***/ (function(__unused_webpack_module, __webpack_exports__, __webpack_require__) {\n\n\"use strict\";\n\n// EXPORTS\n__webpack_require__.d(__webpack_exports__, {\n  \"default\": function() { return /* binding */ clipboard; }\n});\n\n// EXTERNAL MODULE: ./node_modules/tiny-emitter/index.js\nvar tiny_emitter = __webpack_require__(279);\nvar tiny_emitter_default = /*#__PURE__*/__webpack_require__.n(tiny_emitter);\n// EXTERNAL MODULE: ./node_modules/good-listener/src/listen.js\nvar listen = __webpack_require__(370);\nvar listen_default = /*#__PURE__*/__webpack_require__.n(listen);\n// EXTERNAL MODULE: ./node_modules/select/src/select.js\nvar src_select = __webpack_require__(817);\nvar select_default = /*#__PURE__*/__webpack_require__.n(src_select);\n;// CONCATENATED MODULE: ./src/common/command.js\n/**\n * Executes a given operation type.\n * @param {String} type\n * @return {Boolean}\n */\nfunction command(type) {\n  try {\n    return document.execCommand(type);\n  } catch (err) {\n    return false;\n  }\n}\n;// CONCATENATED MODULE: ./src/actions/cut.js\n\n\n/**\n * Cut action wrapper.\n * @param {String|HTMLElement} target\n * @return {String}\n */\n\nvar ClipboardActionCut = function ClipboardActionCut(target) {\n  var selectedText = select_default()(target);\n  command('cut');\n  return selectedText;\n};\n\n/* harmony default export */ var actions_cut = (ClipboardActionCut);\n;// CONCATENATED MODULE: ./src/common/create-fake-element.js\n/**\n * Creates a fake textarea element with a value.\n * @param {String} value\n * @return {HTMLElement}\n */\nfunction createFakeElement(value) {\n  var isRTL = document.documentElement.getAttribute('dir') === 'rtl';\n  var fakeElement = document.createElement('textarea'); // Prevent zooming on iOS\n\n  fakeElement.style.fontSize = '12pt'; // Reset box model\n\n  fakeElement.style.border = '0';\n  fakeElement.style.padding = '0';\n  fakeElement.style.margin = '0'; // Move element out of screen horizontally\n\n  fakeElement.style.position = 'absolute';\n  fakeElement.style[isRTL ? 'right' : 'left'] = '-9999px'; // Move element to the same position vertically\n\n  var yPosition = window.pageYOffset || document.documentElement.scrollTop;\n  fakeElement.style.top = \"\".concat(yPosition, \"px\");\n  fakeElement.setAttribute('readonly', '');\n  fakeElement.value = value;\n  return fakeElement;\n}\n;// CONCATENATED MODULE: ./src/actions/copy.js\n\n\n\n/**\n * Create fake copy action wrapper using a fake element.\n * @param {String} target\n * @param {Object} options\n * @return {String}\n */\n\nvar fakeCopyAction = function fakeCopyAction(value, options) {\n  var fakeElement = createFakeElement(value);\n  options.container.appendChild(fakeElement);\n  var selectedText = select_default()(fakeElement);\n  command('copy');\n  fakeElement.remove();\n  return selectedText;\n};\n/**\n * Copy action wrapper.\n * @param {String|HTMLElement} target\n * @param {Object} options\n * @return {String}\n */\n\n\nvar ClipboardActionCopy = function ClipboardActionCopy(target) {\n  var options = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {\n    container: document.body\n  };\n  var selectedText = '';\n\n  if (typeof target === 'string') {\n    selectedText = fakeCopyAction(target, options);\n  } else if (target instanceof HTMLInputElement && !['text', 'search', 'url', 'tel', 'password'].includes(target === null || target === void 0 ? void 0 : target.type)) {\n    // If input type doesn't support `setSelectionRange`. Simulate it. https://developer.mozilla.org/en-US/docs/Web/API/HTMLInputElement/setSelectionRange\n    selectedText = fakeCopyAction(target.value, options);\n  } else {\n    selectedText = select_default()(target);\n    command('copy');\n  }\n\n  return selectedText;\n};\n\n/* harmony default export */ var actions_copy = (ClipboardActionCopy);\n;// CONCATENATED MODULE: ./src/actions/default.js\nfunction _typeof(obj) { \"@babel/helpers - typeof\"; if (typeof Symbol === \"function\" && typeof Symbol.iterator === \"symbol\") { _typeof = function _typeof(obj) { return typeof obj; }; } else { _typeof = function _typeof(obj) { return obj && typeof Symbol === \"function\" && obj.constructor === Symbol && obj !== Symbol.prototype ? \"symbol\" : typeof obj; }; } return _typeof(obj); }\n\n\n\n/**\n * Inner function which performs selection from either `text` or `target`\n * properties and then executes copy or cut operations.\n * @param {Object} options\n */\n\nvar ClipboardActionDefault = function ClipboardActionDefault() {\n  var options = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : {};\n  // Defines base properties passed from constructor.\n  var _options$action = options.action,\n      action = _options$action === void 0 ? 'copy' : _options$action,\n      container = options.container,\n      target = options.target,\n      text = options.text; // Sets the `action` to be performed which can be either 'copy' or 'cut'.\n\n  if (action !== 'copy' && action !== 'cut') {\n    throw new Error('Invalid \"action\" value, use either \"copy\" or \"cut\"');\n  } // Sets the `target` property using an element that will be have its content copied.\n\n\n  if (target !== undefined) {\n    if (target && _typeof(target) === 'object' && target.nodeType === 1) {\n      if (action === 'copy' && target.hasAttribute('disabled')) {\n        throw new Error('Invalid \"target\" attribute. Please use \"readonly\" instead of \"disabled\" attribute');\n      }\n\n      if (action === 'cut' && (target.hasAttribute('readonly') || target.hasAttribute('disabled'))) {\n        throw new Error('Invalid \"target\" attribute. You can\\'t cut text from elements with \"readonly\" or \"disabled\" attributes');\n      }\n    } else {\n      throw new Error('Invalid \"target\" value, use a valid Element');\n    }\n  } // Define selection strategy based on `text` property.\n\n\n  if (text) {\n    return actions_copy(text, {\n      container: container\n    });\n  } // Defines which selection strategy based on `target` property.\n\n\n  if (target) {\n    return action === 'cut' ? actions_cut(target) : actions_copy(target, {\n      container: container\n    });\n  }\n};\n\n/* harmony default export */ var actions_default = (ClipboardActionDefault);\n;// CONCATENATED MODULE: ./src/clipboard.js\nfunction clipboard_typeof(obj) { \"@babel/helpers - typeof\"; if (typeof Symbol === \"function\" && typeof Symbol.iterator === \"symbol\") { clipboard_typeof = function _typeof(obj) { return typeof obj; }; } else { clipboard_typeof = function _typeof(obj) { return obj && typeof Symbol === \"function\" && obj.constructor === Symbol && obj !== Symbol.prototype ? \"symbol\" : typeof obj; }; } return clipboard_typeof(obj); }\n\nfunction _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError(\"Cannot call a class as a function\"); } }\n\nfunction _defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if (\"value\" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } }\n\nfunction _createClass(Constructor, protoProps, staticProps) { if (protoProps) _defineProperties(Constructor.prototype, protoProps); if (staticProps) _defineProperties(Constructor, staticProps); return Constructor; }\n\nfunction _inherits(subClass, superClass) { if (typeof superClass !== \"function\" && superClass !== null) { throw new TypeError(\"Super expression must either be null or a function\"); } subClass.prototype = Object.create(superClass && superClass.prototype, { constructor: { value: subClass, writable: true, configurable: true } }); if (superClass) _setPrototypeOf(subClass, superClass); }\n\nfunction _setPrototypeOf(o, p) { _setPrototypeOf = Object.setPrototypeOf || function _setPrototypeOf(o, p) { o.__proto__ = p; return o; }; return _setPrototypeOf(o, p); }\n\nfunction _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = _getPrototypeOf(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = _getPrototypeOf(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return _possibleConstructorReturn(this, result); }; }\n\nfunction _possibleConstructorReturn(self, call) { if (call && (clipboard_typeof(call) === \"object\" || typeof call === \"function\")) { return call; } return _assertThisInitialized(self); }\n\nfunction _assertThisInitialized(self) { if (self === void 0) { throw new ReferenceError(\"this hasn't been initialised - super() hasn't been called\"); } return self; }\n\nfunction _isNativeReflectConstruct() { if (typeof Reflect === \"undefined\" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === \"function\") return true; try { Date.prototype.toString.call(Reflect.construct(Date, [], function () {})); return true; } catch (e) { return false; } }\n\nfunction _getPrototypeOf(o) { _getPrototypeOf = Object.setPrototypeOf ? Object.getPrototypeOf : function _getPrototypeOf(o) { return o.__proto__ || Object.getPrototypeOf(o); }; return _getPrototypeOf(o); }\n\n\n\n\n\n\n/**\n * Helper function to retrieve attribute value.\n * @param {String} suffix\n * @param {Element} element\n */\n\nfunction getAttributeValue(suffix, element) {\n  var attribute = \"data-clipboard-\".concat(suffix);\n\n  if (!element.hasAttribute(attribute)) {\n    return;\n  }\n\n  return element.getAttribute(attribute);\n}\n/**\n * Base class which takes one or more elements, adds event listeners to them,\n * and instantiates a new `ClipboardAction` on each click.\n */\n\n\nvar Clipboard = /*#__PURE__*/function (_Emitter) {\n  _inherits(Clipboard, _Emitter);\n\n  var _super = _createSuper(Clipboard);\n\n  /**\n   * @param {String|HTMLElement|HTMLCollection|NodeList} trigger\n   * @param {Object} options\n   */\n  function Clipboard(trigger, options) {\n    var _this;\n\n    _classCallCheck(this, Clipboard);\n\n    _this = _super.call(this);\n\n    _this.resolveOptions(options);\n\n    _this.listenClick(trigger);\n\n    return _this;\n  }\n  /**\n   * Defines if attributes would be resolved using internal setter functions\n   * or custom functions that were passed in the constructor.\n   * @param {Object} options\n   */\n\n\n  _createClass(Clipboard, [{\n    key: \"resolveOptions\",\n    value: function resolveOptions() {\n      var options = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : {};\n      this.action = typeof options.action === 'function' ? options.action : this.defaultAction;\n      this.target = typeof options.target === 'function' ? options.target : this.defaultTarget;\n      this.text = typeof options.text === 'function' ? options.text : this.defaultText;\n      this.container = clipboard_typeof(options.container) === 'object' ? options.container : document.body;\n    }\n    /**\n     * Adds a click event listener to the passed trigger.\n     * @param {String|HTMLElement|HTMLCollection|NodeList} trigger\n     */\n\n  }, {\n    key: \"listenClick\",\n    value: function listenClick(trigger) {\n      var _this2 = this;\n\n      this.listener = listen_default()(trigger, 'click', function (e) {\n        return _this2.onClick(e);\n      });\n    }\n    /**\n     * Defines a new `ClipboardAction` on each click event.\n     * @param {Event} e\n     */\n\n  }, {\n    key: \"onClick\",\n    value: function onClick(e) {\n      var trigger = e.delegateTarget || e.currentTarget;\n      var action = this.action(trigger) || 'copy';\n      var text = actions_default({\n        action: action,\n        container: this.container,\n        target: this.target(trigger),\n        text: this.text(trigger)\n      }); // Fires an event based on the copy operation result.\n\n      this.emit(text ? 'success' : 'error', {\n        action: action,\n        text: text,\n        trigger: trigger,\n        clearSelection: function clearSelection() {\n          if (trigger) {\n            trigger.focus();\n          }\n\n          window.getSelection().removeAllRanges();\n        }\n      });\n    }\n    /**\n     * Default `action` lookup function.\n     * @param {Element} trigger\n     */\n\n  }, {\n    key: \"defaultAction\",\n    value: function defaultAction(trigger) {\n      return getAttributeValue('action', trigger);\n    }\n    /**\n     * Default `target` lookup function.\n     * @param {Element} trigger\n     */\n\n  }, {\n    key: \"defaultTarget\",\n    value: function defaultTarget(trigger) {\n      var selector = getAttributeValue('target', trigger);\n\n      if (selector) {\n        return document.querySelector(selector);\n      }\n    }\n    /**\n     * Allow fire programmatically a copy action\n     * @param {String|HTMLElement} target\n     * @param {Object} options\n     * @returns Text copied.\n     */\n\n  }, {\n    key: \"defaultText\",\n\n    /**\n     * Default `text` lookup function.\n     * @param {Element} trigger\n     */\n    value: function defaultText(trigger) {\n      return getAttributeValue('text', trigger);\n    }\n    /**\n     * Destroy lifecycle.\n     */\n\n  }, {\n    key: \"destroy\",\n    value: function destroy() {\n      this.listener.destroy();\n    }\n  }], [{\n    key: \"copy\",\n    value: function copy(target) {\n      var options = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {\n        container: document.body\n      };\n      return actions_copy(target, options);\n    }\n    /**\n     * Allow fire programmatically a cut action\n     * @param {String|HTMLElement} target\n     * @returns Text cutted.\n     */\n\n  }, {\n    key: \"cut\",\n    value: function cut(target) {\n      return actions_cut(target);\n    }\n    /**\n     * Returns the support of the given action, or all actions if no action is\n     * given.\n     * @param {String} [action]\n     */\n\n  }, {\n    key: \"isSupported\",\n    value: function isSupported() {\n      var action = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : ['copy', 'cut'];\n      var actions = typeof action === 'string' ? [action] : action;\n      var support = !!document.queryCommandSupported;\n      actions.forEach(function (action) {\n        support = support && !!document.queryCommandSupported(action);\n      });\n      return support;\n    }\n  }]);\n\n  return Clipboard;\n}((tiny_emitter_default()));\n\n/* harmony default export */ var clipboard = (Clipboard);\n\n/***/ }),\n\n/***/ 828:\n/***/ (function(module) {\n\nvar DOCUMENT_NODE_TYPE = 9;\n\n/**\n * A polyfill for Element.matches()\n */\nif (typeof Element !== 'undefined' && !Element.prototype.matches) {\n    var proto = Element.prototype;\n\n    proto.matches = proto.matchesSelector ||\n                    proto.mozMatchesSelector ||\n                    proto.msMatchesSelector ||\n                    proto.oMatchesSelector ||\n                    proto.webkitMatchesSelector;\n}\n\n/**\n * Finds the closest parent that matches a selector.\n *\n * @param {Element} element\n * @param {String} selector\n * @return {Function}\n */\nfunction closest (element, selector) {\n    while (element && element.nodeType !== DOCUMENT_NODE_TYPE) {\n        if (typeof element.matches === 'function' &&\n            element.matches(selector)) {\n          return element;\n        }\n        element = element.parentNode;\n    }\n}\n\nmodule.exports = closest;\n\n\n/***/ }),\n\n/***/ 438:\n/***/ (function(module, __unused_webpack_exports, __webpack_require__) {\n\nvar closest = __webpack_require__(828);\n\n/**\n * Delegates event to a selector.\n *\n * @param {Element} element\n * @param {String} selector\n * @param {String} type\n * @param {Function} callback\n * @param {Boolean} useCapture\n * @return {Object}\n */\nfunction _delegate(element, selector, type, callback, useCapture) {\n    var listenerFn = listener.apply(this, arguments);\n\n    element.addEventListener(type, listenerFn, useCapture);\n\n    return {\n        destroy: function() {\n            element.removeEventListener(type, listenerFn, useCapture);\n        }\n    }\n}\n\n/**\n * Delegates event to a selector.\n *\n * @param {Element|String|Array} [elements]\n * @param {String} selector\n * @param {String} type\n * @param {Function} callback\n * @param {Boolean} useCapture\n * @return {Object}\n */\nfunction delegate(elements, selector, type, callback, useCapture) {\n    // Handle the regular Element usage\n    if (typeof elements.addEventListener === 'function') {\n        return _delegate.apply(null, arguments);\n    }\n\n    // Handle Element-less usage, it defaults to global delegation\n    if (typeof type === 'function') {\n        // Use `document` as the first parameter, then apply arguments\n        // This is a short way to .unshift `arguments` without running into deoptimizations\n        return _delegate.bind(null, document).apply(null, arguments);\n    }\n\n    // Handle Selector-based usage\n    if (typeof elements === 'string') {\n        elements = document.querySelectorAll(elements);\n    }\n\n    // Handle Array-like based usage\n    return Array.prototype.map.call(elements, function (element) {\n        return _delegate(element, selector, type, callback, useCapture);\n    });\n}\n\n/**\n * Finds closest match and invokes callback.\n *\n * @param {Element} element\n * @param {String} selector\n * @param {String} type\n * @param {Function} callback\n * @return {Function}\n */\nfunction listener(element, selector, type, callback) {\n    return function(e) {\n        e.delegateTarget = closest(e.target, selector);\n\n        if (e.delegateTarget) {\n            callback.call(element, e);\n        }\n    }\n}\n\nmodule.exports = delegate;\n\n\n/***/ }),\n\n/***/ 879:\n/***/ (function(__unused_webpack_module, exports) {\n\n/**\n * Check if argument is a HTML element.\n *\n * @param {Object} value\n * @return {Boolean}\n */\nexports.node = function(value) {\n    return value !== undefined\n        && value instanceof HTMLElement\n        && value.nodeType === 1;\n};\n\n/**\n * Check if argument is a list of HTML elements.\n *\n * @param {Object} value\n * @return {Boolean}\n */\nexports.nodeList = function(value) {\n    var type = Object.prototype.toString.call(value);\n\n    return value !== undefined\n        && (type === '[object NodeList]' || type === '[object HTMLCollection]')\n        && ('length' in value)\n        && (value.length === 0 || exports.node(value[0]));\n};\n\n/**\n * Check if argument is a string.\n *\n * @param {Object} value\n * @return {Boolean}\n */\nexports.string = function(value) {\n    return typeof value === 'string'\n        || value instanceof String;\n};\n\n/**\n * Check if argument is a function.\n *\n * @param {Object} value\n * @return {Boolean}\n */\nexports.fn = function(value) {\n    var type = Object.prototype.toString.call(value);\n\n    return type === '[object Function]';\n};\n\n\n/***/ }),\n\n/***/ 370:\n/***/ (function(module, __unused_webpack_exports, __webpack_require__) {\n\nvar is = __webpack_require__(879);\nvar delegate = __webpack_require__(438);\n\n/**\n * Validates all params and calls the right\n * listener function based on its target type.\n *\n * @param {String|HTMLElement|HTMLCollection|NodeList} target\n * @param {String} type\n * @param {Function} callback\n * @return {Object}\n */\nfunction listen(target, type, callback) {\n    if (!target && !type && !callback) {\n        throw new Error('Missing required arguments');\n    }\n\n    if (!is.string(type)) {\n        throw new TypeError('Second argument must be a String');\n    }\n\n    if (!is.fn(callback)) {\n        throw new TypeError('Third argument must be a Function');\n    }\n\n    if (is.node(target)) {\n        return listenNode(target, type, callback);\n    }\n    else if (is.nodeList(target)) {\n        return listenNodeList(target, type, callback);\n    }\n    else if (is.string(target)) {\n        return listenSelector(target, type, callback);\n    }\n    else {\n        throw new TypeError('First argument must be a String, HTMLElement, HTMLCollection, or NodeList');\n    }\n}\n\n/**\n * Adds an event listener to a HTML element\n * and returns a remove listener function.\n *\n * @param {HTMLElement} node\n * @param {String} type\n * @param {Function} callback\n * @return {Object}\n */\nfunction listenNode(node, type, callback) {\n    node.addEventListener(type, callback);\n\n    return {\n        destroy: function() {\n            node.removeEventListener(type, callback);\n        }\n    }\n}\n\n/**\n * Add an event listener to a list of HTML elements\n * and returns a remove listener function.\n *\n * @param {NodeList|HTMLCollection} nodeList\n * @param {String} type\n * @param {Function} callback\n * @return {Object}\n */\nfunction listenNodeList(nodeList, type, callback) {\n    Array.prototype.forEach.call(nodeList, function(node) {\n        node.addEventListener(type, callback);\n    });\n\n    return {\n        destroy: function() {\n            Array.prototype.forEach.call(nodeList, function(node) {\n                node.removeEventListener(type, callback);\n            });\n        }\n    }\n}\n\n/**\n * Add an event listener to a selector\n * and returns a remove listener function.\n *\n * @param {String} selector\n * @param {String} type\n * @param {Function} callback\n * @return {Object}\n */\nfunction listenSelector(selector, type, callback) {\n    return delegate(document.body, selector, type, callback);\n}\n\nmodule.exports = listen;\n\n\n/***/ }),\n\n/***/ 817:\n/***/ (function(module) {\n\nfunction select(element) {\n    var selectedText;\n\n    if (element.nodeName === 'SELECT') {\n        element.focus();\n\n        selectedText = element.value;\n    }\n    else if (element.nodeName === 'INPUT' || element.nodeName === 'TEXTAREA') {\n        var isReadOnly = element.hasAttribute('readonly');\n\n        if (!isReadOnly) {\n            element.setAttribute('readonly', '');\n        }\n\n        element.select();\n        element.setSelectionRange(0, element.value.length);\n\n        if (!isReadOnly) {\n            element.removeAttribute('readonly');\n        }\n\n        selectedText = element.value;\n    }\n    else {\n        if (element.hasAttribute('contenteditable')) {\n            element.focus();\n        }\n\n        var selection = window.getSelection();\n        var range = document.createRange();\n\n        range.selectNodeContents(element);\n        selection.removeAllRanges();\n        selection.addRange(range);\n\n        selectedText = selection.toString();\n    }\n\n    return selectedText;\n}\n\nmodule.exports = select;\n\n\n/***/ }),\n\n/***/ 279:\n/***/ (function(module) {\n\nfunction E () {\n  // Keep this empty so it's easier to inherit from\n  // (via https://github.com/lipsmack from https://github.com/scottcorgan/tiny-emitter/issues/3)\n}\n\nE.prototype = {\n  on: function (name, callback, ctx) {\n    var e = this.e || (this.e = {});\n\n    (e[name] || (e[name] = [])).push({\n      fn: callback,\n      ctx: ctx\n    });\n\n    return this;\n  },\n\n  once: function (name, callback, ctx) {\n    var self = this;\n    function listener () {\n      self.off(name, listener);\n      callback.apply(ctx, arguments);\n    };\n\n    listener._ = callback\n    return this.on(name, listener, ctx);\n  },\n\n  emit: function (name) {\n    var data = [].slice.call(arguments, 1);\n    var evtArr = ((this.e || (this.e = {}))[name] || []).slice();\n    var i = 0;\n    var len = evtArr.length;\n\n    for (i; i < len; i++) {\n      evtArr[i].fn.apply(evtArr[i].ctx, data);\n    }\n\n    return this;\n  },\n\n  off: function (name, callback) {\n    var e = this.e || (this.e = {});\n    var evts = e[name];\n    var liveEvents = [];\n\n    if (evts && callback) {\n      for (var i = 0, len = evts.length; i < len; i++) {\n        if (evts[i].fn !== callback && evts[i].fn._ !== callback)\n          liveEvents.push(evts[i]);\n      }\n    }\n\n    // Remove event from queue to prevent memory leak\n    // Suggested by https://github.com/lazd\n    // Ref: https://github.com/scottcorgan/tiny-emitter/commit/c6ebfaa9bc973b33d110a84a307742b7cf94c953#commitcomment-5024910\n\n    (liveEvents.length)\n      ? e[name] = liveEvents\n      : delete e[name];\n\n    return this;\n  }\n};\n\nmodule.exports = E;\nmodule.exports.TinyEmitter = E;\n\n\n/***/ })\n\n/******/ \t});\n/************************************************************************/\n/******/ \t// The module cache\n/******/ \tvar __webpack_module_cache__ = {};\n/******/ \t\n/******/ \t// The require function\n/******/ \tfunction __webpack_require__(moduleId) {\n/******/ \t\t// Check if module is in cache\n/******/ \t\tif(__webpack_module_cache__[moduleId]) {\n/******/ \t\t\treturn __webpack_module_cache__[moduleId].exports;\n/******/ \t\t}\n/******/ \t\t// Create a new module (and put it into the cache)\n/******/ \t\tvar module = __webpack_module_cache__[moduleId] = {\n/******/ \t\t\t// no module.id needed\n/******/ \t\t\t// no module.loaded needed\n/******/ \t\t\texports: {}\n/******/ \t\t};\n/******/ \t\n/******/ \t\t// Execute the module function\n/******/ \t\t__webpack_modules__[moduleId](module, module.exports, __webpack_require__);\n/******/ \t\n/******/ \t\t// Return the exports of the module\n/******/ \t\treturn module.exports;\n/******/ \t}\n/******/ \t\n/************************************************************************/\n/******/ \t/* webpack/runtime/compat get default export */\n/******/ \t!function() {\n/******/ \t\t// getDefaultExport function for compatibility with non-harmony modules\n/******/ \t\t__webpack_require__.n = function(module) {\n/******/ \t\t\tvar getter = module && module.__esModule ?\n/******/ \t\t\t\tfunction() { return module['default']; } :\n/******/ \t\t\t\tfunction() { return module; };\n/******/ \t\t\t__webpack_require__.d(getter, { a: getter });\n/******/ \t\t\treturn getter;\n/******/ \t\t};\n/******/ \t}();\n/******/ \t\n/******/ \t/* webpack/runtime/define property getters */\n/******/ \t!function() {\n/******/ \t\t// define getter functions for harmony exports\n/******/ \t\t__webpack_require__.d = function(exports, definition) {\n/******/ \t\t\tfor(var key in definition) {\n/******/ \t\t\t\tif(__webpack_require__.o(definition, key) && !__webpack_require__.o(exports, key)) {\n/******/ \t\t\t\t\tObject.defineProperty(exports, key, { enumerable: true, get: definition[key] });\n/******/ \t\t\t\t}\n/******/ \t\t\t}\n/******/ \t\t};\n/******/ \t}();\n/******/ \t\n/******/ \t/* webpack/runtime/hasOwnProperty shorthand */\n/******/ \t!function() {\n/******/ \t\t__webpack_require__.o = function(obj, prop) { return Object.prototype.hasOwnProperty.call(obj, prop); }\n/******/ \t}();\n/******/ \t\n/************************************************************************/\n/******/ \t// module exports must be returned from runtime so entry inlining is disabled\n/******/ \t// startup\n/******/ \t// Load entry module and return exports\n/******/ \treturn __webpack_require__(686);\n/******/ })()\n.default;\n});", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport \"focus-visible\"\n\nimport {\n  EMPTY,\n  NEVER,\n  Observable,\n  Subject,\n  defer,\n  delay,\n  filter,\n  map,\n  merge,\n  mergeWith,\n  shareReplay,\n  switchMap\n} from \"rxjs\"\n\nimport { configuration, feature } from \"./_\"\nimport {\n  at,\n  getActiveElement,\n  getOptionalElement,\n  requestJSON,\n  setLocation,\n  setToggle,\n  watchDocument,\n  watchKeyboard,\n  watchLocation,\n  watchLocationTarget,\n  watchMedia,\n  watchPrint,\n  watchScript,\n  watchViewport\n} from \"./browser\"\nimport {\n  getComponentElement,\n  getComponentElements,\n  mountAnnounce,\n  mountBackToTop,\n  mountConsent,\n  mountContent,\n  mountDialog,\n  mountHeader,\n  mountHeaderTitle,\n  mountPalette,\n  mountProgress,\n  mountSearch,\n  mountSearchHiglight,\n  mountSidebar,\n  mountSource,\n  mountTableOfContents,\n  mountTabs,\n  watchHeader,\n  watchMain\n} from \"./components\"\nimport {\n  SearchIndex,\n  fetchSitemap,\n  setupAlternate,\n  setupClipboardJS,\n  setupInstantNavigation,\n  setupVersionSelector\n} from \"./integrations\"\nimport {\n  patchEllipsis,\n  patchIndeterminate,\n  patchScrollfix,\n  patchScrolllock\n} from \"./patches\"\nimport \"./polyfills\"\n\n/* ----------------------------------------------------------------------------\n * Functions - @todo refactor\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch search index\n *\n * @returns Search index observable\n */\nfunction fetchSearchIndex(): Observable<SearchIndex> {\n  if (location.protocol === \"file:\") {\n    return watchScript(\n      `${new URL(\"search/search_index.js\", config.base)}`\n    )\n      .pipe(\n        // @ts-ignore - @todo fix typings\n        map(() => __index),\n        shareReplay(1)\n      )\n  } else {\n    return requestJSON<SearchIndex>(\n      new URL(\"search/search_index.json\", config.base)\n    )\n  }\n}\n\n/* ----------------------------------------------------------------------------\n * Application\n * ------------------------------------------------------------------------- */\n\n/* Yay, JavaScript is available */\ndocument.documentElement.classList.remove(\"no-js\")\ndocument.documentElement.classList.add(\"js\")\n\n/* Set up navigation observables and subjects */\nconst document$ = watchDocument()\nconst location$ = watchLocation()\nconst target$   = watchLocationTarget(location$)\nconst keyboard$ = watchKeyboard()\n\n/* Set up media observables */\nconst viewport$ = watchViewport()\nconst tablet$   = watchMedia(\"(min-width: 60em)\")\nconst screen$   = watchMedia(\"(min-width: 76.25em)\")\nconst print$    = watchPrint()\n\n/* Retrieve search index, if search is enabled */\nconst config = configuration()\nconst index$ = document.forms.namedItem(\"search\")\n  ? fetchSearchIndex()\n  : NEVER\n\n/* Set up Clipboard.js integration */\nconst alert$ = new Subject<string>()\nsetupClipboardJS({ alert$ })\n\n/* Set up language selector */\nsetupAlternate({ document$ })\n\n/* Set up progress indicator */\nconst progress$ = new Subject<number>()\n\n/* Set up sitemap for instant navigation and previews */\nconst sitemap$ = fetchSitemap(config.base)\n\n/* Set up instant navigation, if enabled */\nif (feature(\"navigation.instant\"))\n  setupInstantNavigation({ sitemap$, location$, viewport$, progress$ })\n    .subscribe(document$)\n\n/* Set up version selector */\nif (config.version?.provider === \"mike\")\n  setupVersionSelector({ document$ })\n\n/* Always close drawer and search on navigation */\nmerge(location$, target$)\n  .pipe(\n    delay(125)\n  )\n    .subscribe(() => {\n      setToggle(\"drawer\", false)\n      setToggle(\"search\", false)\n    })\n\n/* Set up global keyboard handlers */\nkeyboard$\n  .pipe(\n    filter(({ mode }) => mode === \"global\")\n  )\n    .subscribe(key => {\n      switch (key.type) {\n\n        /* Go to previous page */\n        case \"p\":\n        case \",\":\n          const prev = getOptionalElement<HTMLLinkElement>(\"link[rel=prev]\")\n          if (typeof prev !== \"undefined\")\n            setLocation(prev)\n          break\n\n        /* Go to next page */\n        case \"n\":\n        case \".\":\n          const next = getOptionalElement<HTMLLinkElement>(\"link[rel=next]\")\n          if (typeof next !== \"undefined\")\n            setLocation(next)\n          break\n\n        /* Expand navigation, see https://bit.ly/3ZjG5io */\n        case \"Enter\":\n          const active = getActiveElement()\n          if (active instanceof HTMLLabelElement)\n            active.click()\n      }\n    })\n\n/* Set up patches */\npatchEllipsis({ viewport$, document$ })\npatchIndeterminate({ document$, tablet$ })\npatchScrollfix({ document$ })\npatchScrolllock({ viewport$, tablet$ })\n\n/* Set up header and main area observable */\nconst header$ = watchHeader(getComponentElement(\"header\"), { viewport$ })\nconst main$ = document$\n  .pipe(\n    map(() => getComponentElement(\"main\")),\n    switchMap(el => watchMain(el, { viewport$, header$ })),\n    shareReplay(1)\n  )\n\n/* Set up control component observables */\nconst control$ = merge(\n\n  /* Consent */\n  ...getComponentElements(\"consent\")\n    .map(el => mountConsent(el, { target$ })),\n\n  /* Dialog */\n  ...getComponentElements(\"dialog\")\n    .map(el => mountDialog(el, { alert$ })),\n\n  /* Color palette */\n  ...getComponentElements(\"palette\")\n    .map(el => mountPalette(el)),\n\n  /* Progress bar */\n  ...getComponentElements(\"progress\")\n    .map(el => mountProgress(el, { progress$ })),\n\n  /* Search */\n  ...getComponentElements(\"search\")\n    .map(el => mountSearch(el, { index$, keyboard$ })),\n\n  /* Repository information */\n  ...getComponentElements(\"source\")\n    .map(el => mountSource(el))\n)\n\n/* Set up content component observables */\nconst content$ = defer(() => merge(\n\n  /* Announcement bar */\n  ...getComponentElements(\"announce\")\n    .map(el => mountAnnounce(el)),\n\n  /* Content */\n  ...getComponentElements(\"content\")\n    .map(el => mountContent(el, { sitemap$, viewport$, target$, print$ })),\n\n  /* Search highlighting */\n  ...getComponentElements(\"content\")\n    .map(el => feature(\"search.highlight\")\n      ? mountSearchHiglight(el, { index$, location$ })\n      : EMPTY\n    ),\n\n  /* Header */\n  ...getComponentElements(\"header\")\n    .map(el => mountHeader(el, { viewport$, header$, main$ })),\n\n  /* Header title */\n  ...getComponentElements(\"header-title\")\n    .map(el => mountHeaderTitle(el, { viewport$, header$ })),\n\n  /* Sidebar */\n  ...getComponentElements(\"sidebar\")\n    .map(el => el.getAttribute(\"data-md-type\") === \"navigation\"\n      ? at(screen$, () => mountSidebar(el, { viewport$, header$, main$ }))\n      : at(tablet$, () => mountSidebar(el, { viewport$, header$, main$ }))\n    ),\n\n  /* Navigation tabs */\n  ...getComponentElements(\"tabs\")\n    .map(el => mountTabs(el, { viewport$, header$ })),\n\n  /* Table of contents */\n  ...getComponentElements(\"toc\")\n    .map(el => mountTableOfContents(el, {\n      viewport$, header$, main$, target$\n    })),\n\n  /* Back-to-top button */\n  ...getComponentElements(\"top\")\n    .map(el => mountBackToTop(el, { viewport$, header$, main$, target$ }))\n))\n\n/* Set up component observables */\nconst component$ = document$\n  .pipe(\n    switchMap(() => content$),\n    mergeWith(control$),\n    shareReplay(1)\n  )\n\n/* Subscribe to all components */\ncomponent$.subscribe()\n\n/* ----------------------------------------------------------------------------\n * Exports\n * ------------------------------------------------------------------------- */\n\nwindow.document$  = document$          /* Document observable */\nwindow.location$  = location$          /* Location subject */\nwindow.target$    = target$            /* Location target observable */\nwindow.keyboard$  = keyboard$          /* Keyboard observable */\nwindow.viewport$  = viewport$          /* Viewport observable */\nwindow.tablet$    = tablet$            /* Media tablet observable */\nwindow.screen$    = screen$            /* Media screen observable */\nwindow.print$     = print$             /* Media print observable */\nwindow.alert$     = alert$             /* Alert subject */\nwindow.progress$  = progress$          /* Progress indicator subject */\nwindow.component$ = component$         /* Component observable */\n", "/******************************************************************************\nCopyright (c) Microsoft Corporation.\n\nPermission to use, copy, modify, and/or distribute this software for any\npurpose with or without fee is hereby granted.\n\nTHE SOFTWARE IS PROVIDED \"AS IS\" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH\nREGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY\nAND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,\nINDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM\nLOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR\nOTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR\nPERFORMANCE OF THIS SOFTWARE.\n***************************************************************************** */\n/* global Reflect, Promise, SuppressedError, Symbol, Iterator */\n\nvar extendStatics = function(d, b) {\n  extendStatics = Object.setPrototypeOf ||\n      ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||\n      function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };\n  return extendStatics(d, b);\n};\n\nexport function __extends(d, b) {\n  if (typeof b !== \"function\" && b !== null)\n      throw new TypeError(\"Class extends value \" + String(b) + \" is not a constructor or null\");\n  extendStatics(d, b);\n  function __() { this.constructor = d; }\n  d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());\n}\n\nexport var __assign = function() {\n  __assign = Object.assign || function __assign(t) {\n      for (var s, i = 1, n = arguments.length; i < n; i++) {\n          s = arguments[i];\n          for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p)) t[p] = s[p];\n      }\n      return t;\n  }\n  return __assign.apply(this, arguments);\n}\n\nexport function __rest(s, e) {\n  var t = {};\n  for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p) && e.indexOf(p) < 0)\n      t[p] = s[p];\n  if (s != null && typeof Object.getOwnPropertySymbols === \"function\")\n      for (var i = 0, p = Object.getOwnPropertySymbols(s); i < p.length; i++) {\n          if (e.indexOf(p[i]) < 0 && Object.prototype.propertyIsEnumerable.call(s, p[i]))\n              t[p[i]] = s[p[i]];\n      }\n  return t;\n}\n\nexport function __decorate(decorators, target, key, desc) {\n  var c = arguments.length, r = c < 3 ? target : desc === null ? desc = Object.getOwnPropertyDescriptor(target, key) : desc, d;\n  if (typeof Reflect === \"object\" && typeof Reflect.decorate === \"function\") r = Reflect.decorate(decorators, target, key, desc);\n  else for (var i = decorators.length - 1; i >= 0; i--) if (d = decorators[i]) r = (c < 3 ? d(r) : c > 3 ? d(target, key, r) : d(target, key)) || r;\n  return c > 3 && r && Object.defineProperty(target, key, r), r;\n}\n\nexport function __param(paramIndex, decorator) {\n  return function (target, key) { decorator(target, key, paramIndex); }\n}\n\nexport function __esDecorate(ctor, descriptorIn, decorators, contextIn, initializers, extraInitializers) {\n  function accept(f) { if (f !== void 0 && typeof f !== \"function\") throw new TypeError(\"Function expected\"); return f; }\n  var kind = contextIn.kind, key = kind === \"getter\" ? \"get\" : kind === \"setter\" ? \"set\" : \"value\";\n  var target = !descriptorIn && ctor ? contextIn[\"static\"] ? ctor : ctor.prototype : null;\n  var descriptor = descriptorIn || (target ? Object.getOwnPropertyDescriptor(target, contextIn.name) : {});\n  var _, done = false;\n  for (var i = decorators.length - 1; i >= 0; i--) {\n      var context = {};\n      for (var p in contextIn) context[p] = p === \"access\" ? {} : contextIn[p];\n      for (var p in contextIn.access) context.access[p] = contextIn.access[p];\n      context.addInitializer = function (f) { if (done) throw new TypeError(\"Cannot add initializers after decoration has completed\"); extraInitializers.push(accept(f || null)); };\n      var result = (0, decorators[i])(kind === \"accessor\" ? { get: descriptor.get, set: descriptor.set } : descriptor[key], context);\n      if (kind === \"accessor\") {\n          if (result === void 0) continue;\n          if (result === null || typeof result !== \"object\") throw new TypeError(\"Object expected\");\n          if (_ = accept(result.get)) descriptor.get = _;\n          if (_ = accept(result.set)) descriptor.set = _;\n          if (_ = accept(result.init)) initializers.unshift(_);\n      }\n      else if (_ = accept(result)) {\n          if (kind === \"field\") initializers.unshift(_);\n          else descriptor[key] = _;\n      }\n  }\n  if (target) Object.defineProperty(target, contextIn.name, descriptor);\n  done = true;\n};\n\nexport function __runInitializers(thisArg, initializers, value) {\n  var useValue = arguments.length > 2;\n  for (var i = 0; i < initializers.length; i++) {\n      value = useValue ? initializers[i].call(thisArg, value) : initializers[i].call(thisArg);\n  }\n  return useValue ? value : void 0;\n};\n\nexport function __propKey(x) {\n  return typeof x === \"symbol\" ? x : \"\".concat(x);\n};\n\nexport function __setFunctionName(f, name, prefix) {\n  if (typeof name === \"symbol\") name = name.description ? \"[\".concat(name.description, \"]\") : \"\";\n  return Object.defineProperty(f, \"name\", { configurable: true, value: prefix ? \"\".concat(prefix, \" \", name) : name });\n};\n\nexport function __metadata(metadataKey, metadataValue) {\n  if (typeof Reflect === \"object\" && typeof Reflect.metadata === \"function\") return Reflect.metadata(metadataKey, metadataValue);\n}\n\nexport function __awaiter(thisArg, _arguments, P, generator) {\n  function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }\n  return new (P || (P = Promise))(function (resolve, reject) {\n      function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }\n      function rejected(value) { try { step(generator[\"throw\"](value)); } catch (e) { reject(e); } }\n      function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }\n      step((generator = generator.apply(thisArg, _arguments || [])).next());\n  });\n}\n\nexport function __generator(thisArg, body) {\n  var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g = Object.create((typeof Iterator === \"function\" ? Iterator : Object).prototype);\n  return g.next = verb(0), g[\"throw\"] = verb(1), g[\"return\"] = verb(2), typeof Symbol === \"function\" && (g[Symbol.iterator] = function() { return this; }), g;\n  function verb(n) { return function (v) { return step([n, v]); }; }\n  function step(op) {\n      if (f) throw new TypeError(\"Generator is already executing.\");\n      while (g && (g = 0, op[0] && (_ = 0)), _) try {\n          if (f = 1, y && (t = op[0] & 2 ? y[\"return\"] : op[0] ? y[\"throw\"] || ((t = y[\"return\"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;\n          if (y = 0, t) op = [op[0] & 2, t.value];\n          switch (op[0]) {\n              case 0: case 1: t = op; break;\n              case 4: _.label++; return { value: op[1], done: false };\n              case 5: _.label++; y = op[1]; op = [0]; continue;\n              case 7: op = _.ops.pop(); _.trys.pop(); continue;\n              default:\n                  if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }\n                  if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }\n                  if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }\n                  if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }\n                  if (t[2]) _.ops.pop();\n                  _.trys.pop(); continue;\n          }\n          op = body.call(thisArg, _);\n      } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }\n      if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };\n  }\n}\n\nexport var __createBinding = Object.create ? (function(o, m, k, k2) {\n  if (k2 === undefined) k2 = k;\n  var desc = Object.getOwnPropertyDescriptor(m, k);\n  if (!desc || (\"get\" in desc ? !m.__esModule : desc.writable || desc.configurable)) {\n      desc = { enumerable: true, get: function() { return m[k]; } };\n  }\n  Object.defineProperty(o, k2, desc);\n}) : (function(o, m, k, k2) {\n  if (k2 === undefined) k2 = k;\n  o[k2] = m[k];\n});\n\nexport function __exportStar(m, o) {\n  for (var p in m) if (p !== \"default\" && !Object.prototype.hasOwnProperty.call(o, p)) __createBinding(o, m, p);\n}\n\nexport function __values(o) {\n  var s = typeof Symbol === \"function\" && Symbol.iterator, m = s && o[s], i = 0;\n  if (m) return m.call(o);\n  if (o && typeof o.length === \"number\") return {\n      next: function () {\n          if (o && i >= o.length) o = void 0;\n          return { value: o && o[i++], done: !o };\n      }\n  };\n  throw new TypeError(s ? \"Object is not iterable.\" : \"Symbol.iterator is not defined.\");\n}\n\nexport function __read(o, n) {\n  var m = typeof Symbol === \"function\" && o[Symbol.iterator];\n  if (!m) return o;\n  var i = m.call(o), r, ar = [], e;\n  try {\n      while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);\n  }\n  catch (error) { e = { error: error }; }\n  finally {\n      try {\n          if (r && !r.done && (m = i[\"return\"])) m.call(i);\n      }\n      finally { if (e) throw e.error; }\n  }\n  return ar;\n}\n\n/** @deprecated */\nexport function __spread() {\n  for (var ar = [], i = 0; i < arguments.length; i++)\n      ar = ar.concat(__read(arguments[i]));\n  return ar;\n}\n\n/** @deprecated */\nexport function __spreadArrays() {\n  for (var s = 0, i = 0, il = arguments.length; i < il; i++) s += arguments[i].length;\n  for (var r = Array(s), k = 0, i = 0; i < il; i++)\n      for (var a = arguments[i], j = 0, jl = a.length; j < jl; j++, k++)\n          r[k] = a[j];\n  return r;\n}\n\nexport function __spreadArray(to, from, pack) {\n  if (pack || arguments.length === 2) for (var i = 0, l = from.length, ar; i < l; i++) {\n      if (ar || !(i in from)) {\n          if (!ar) ar = Array.prototype.slice.call(from, 0, i);\n          ar[i] = from[i];\n      }\n  }\n  return to.concat(ar || Array.prototype.slice.call(from));\n}\n\nexport function __await(v) {\n  return this instanceof __await ? (this.v = v, this) : new __await(v);\n}\n\nexport function __asyncGenerator(thisArg, _arguments, generator) {\n  if (!Symbol.asyncIterator) throw new TypeError(\"Symbol.asyncIterator is not defined.\");\n  var g = generator.apply(thisArg, _arguments || []), i, q = [];\n  return i = Object.create((typeof AsyncIterator === \"function\" ? AsyncIterator : Object).prototype), verb(\"next\"), verb(\"throw\"), verb(\"return\", awaitReturn), i[Symbol.asyncIterator] = function () { return this; }, i;\n  function awaitReturn(f) { return function (v) { return Promise.resolve(v).then(f, reject); }; }\n  function verb(n, f) { if (g[n]) { i[n] = function (v) { return new Promise(function (a, b) { q.push([n, v, a, b]) > 1 || resume(n, v); }); }; if (f) i[n] = f(i[n]); } }\n  function resume(n, v) { try { step(g[n](v)); } catch (e) { settle(q[0][3], e); } }\n  function step(r) { r.value instanceof __await ? Promise.resolve(r.value.v).then(fulfill, reject) : settle(q[0][2], r); }\n  function fulfill(value) { resume(\"next\", value); }\n  function reject(value) { resume(\"throw\", value); }\n  function settle(f, v) { if (f(v), q.shift(), q.length) resume(q[0][0], q[0][1]); }\n}\n\nexport function __asyncDelegator(o) {\n  var i, p;\n  return i = {}, verb(\"next\"), verb(\"throw\", function (e) { throw e; }), verb(\"return\"), i[Symbol.iterator] = function () { return this; }, i;\n  function verb(n, f) { i[n] = o[n] ? function (v) { return (p = !p) ? { value: __await(o[n](v)), done: false } : f ? f(v) : v; } : f; }\n}\n\nexport function __asyncValues(o) {\n  if (!Symbol.asyncIterator) throw new TypeError(\"Symbol.asyncIterator is not defined.\");\n  var m = o[Symbol.asyncIterator], i;\n  return m ? m.call(o) : (o = typeof __values === \"function\" ? __values(o) : o[Symbol.iterator](), i = {}, verb(\"next\"), verb(\"throw\"), verb(\"return\"), i[Symbol.asyncIterator] = function () { return this; }, i);\n  function verb(n) { i[n] = o[n] && function (v) { return new Promise(function (resolve, reject) { v = o[n](v), settle(resolve, reject, v.done, v.value); }); }; }\n  function settle(resolve, reject, d, v) { Promise.resolve(v).then(function(v) { resolve({ value: v, done: d }); }, reject); }\n}\n\nexport function __makeTemplateObject(cooked, raw) {\n  if (Object.defineProperty) { Object.defineProperty(cooked, \"raw\", { value: raw }); } else { cooked.raw = raw; }\n  return cooked;\n};\n\nvar __setModuleDefault = Object.create ? (function(o, v) {\n  Object.defineProperty(o, \"default\", { enumerable: true, value: v });\n}) : function(o, v) {\n  o[\"default\"] = v;\n};\n\nexport function __importStar(mod) {\n  if (mod && mod.__esModule) return mod;\n  var result = {};\n  if (mod != null) for (var k in mod) if (k !== \"default\" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);\n  __setModuleDefault(result, mod);\n  return result;\n}\n\nexport function __importDefault(mod) {\n  return (mod && mod.__esModule) ? mod : { default: mod };\n}\n\nexport function __classPrivateFieldGet(receiver, state, kind, f) {\n  if (kind === \"a\" && !f) throw new TypeError(\"Private accessor was defined without a getter\");\n  if (typeof state === \"function\" ? receiver !== state || !f : !state.has(receiver)) throw new TypeError(\"Cannot read private member from an object whose class did not declare it\");\n  return kind === \"m\" ? f : kind === \"a\" ? f.call(receiver) : f ? f.value : state.get(receiver);\n}\n\nexport function __classPrivateFieldSet(receiver, state, value, kind, f) {\n  if (kind === \"m\") throw new TypeError(\"Private method is not writable\");\n  if (kind === \"a\" && !f) throw new TypeError(\"Private accessor was defined without a setter\");\n  if (typeof state === \"function\" ? receiver !== state || !f : !state.has(receiver)) throw new TypeError(\"Cannot write private member to an object whose class did not declare it\");\n  return (kind === \"a\" ? f.call(receiver, value) : f ? f.value = value : state.set(receiver, value)), value;\n}\n\nexport function __classPrivateFieldIn(state, receiver) {\n  if (receiver === null || (typeof receiver !== \"object\" && typeof receiver !== \"function\")) throw new TypeError(\"Cannot use 'in' operator on non-object\");\n  return typeof state === \"function\" ? receiver === state : state.has(receiver);\n}\n\nexport function __addDisposableResource(env, value, async) {\n  if (value !== null && value !== void 0) {\n    if (typeof value !== \"object\" && typeof value !== \"function\") throw new TypeError(\"Object expected.\");\n    var dispose, inner;\n    if (async) {\n      if (!Symbol.asyncDispose) throw new TypeError(\"Symbol.asyncDispose is not defined.\");\n      dispose = value[Symbol.asyncDispose];\n    }\n    if (dispose === void 0) {\n      if (!Symbol.dispose) throw new TypeError(\"Symbol.dispose is not defined.\");\n      dispose = value[Symbol.dispose];\n      if (async) inner = dispose;\n    }\n    if (typeof dispose !== \"function\") throw new TypeError(\"Object not disposable.\");\n    if (inner) dispose = function() { try { inner.call(this); } catch (e) { return Promise.reject(e); } };\n    env.stack.push({ value: value, dispose: dispose, async: async });\n  }\n  else if (async) {\n    env.stack.push({ async: true });\n  }\n  return value;\n}\n\nvar _SuppressedError = typeof SuppressedError === \"function\" ? SuppressedError : function (error, suppressed, message) {\n  var e = new Error(message);\n  return e.name = \"SuppressedError\", e.error = error, e.suppressed = suppressed, e;\n};\n\nexport function __disposeResources(env) {\n  function fail(e) {\n    env.error = env.hasError ? new _SuppressedError(e, env.error, \"An error was suppressed during disposal.\") : e;\n    env.hasError = true;\n  }\n  var r, s = 0;\n  function next() {\n    while (r = env.stack.pop()) {\n      try {\n        if (!r.async && s === 1) return s = 0, env.stack.push(r), Promise.resolve().then(next);\n        if (r.dispose) {\n          var result = r.dispose.call(r.value);\n          if (r.async) return s |= 2, Promise.resolve(result).then(next, function(e) { fail(e); return next(); });\n        }\n        else s |= 1;\n      }\n      catch (e) {\n        fail(e);\n      }\n    }\n    if (s === 1) return env.hasError ? Promise.reject(env.error) : Promise.resolve();\n    if (env.hasError) throw env.error;\n  }\n  return next();\n}\n\nexport default {\n  __extends,\n  __assign,\n  __rest,\n  __decorate,\n  __param,\n  __metadata,\n  __awaiter,\n  __generator,\n  __createBinding,\n  __exportStar,\n  __values,\n  __read,\n  __spread,\n  __spreadArrays,\n  __spreadArray,\n  __await,\n  __asyncGenerator,\n  __asyncDelegator,\n  __asyncValues,\n  __makeTemplateObject,\n  __importStar,\n  __importDefault,\n  __classPrivateFieldGet,\n  __classPrivateFieldSet,\n  __classPrivateFieldIn,\n  __addDisposableResource,\n  __disposeResources,\n};\n", "/**\n * Returns true if the object is a function.\n * @param value The value to check\n */\nexport function isFunction(value: any): value is (...args: any[]) => any {\n  return typeof value === 'function';\n}\n", "/**\n * Used to create Error subclasses until the community moves away from ES5.\n *\n * This is because compiling from TypeScript down to ES5 has issues with subclassing Errors\n * as well as other built-in types: https://github.com/Microsoft/TypeScript/issues/12123\n *\n * @param createImpl A factory function to create the actual constructor implementation. The returned\n * function should be a named function that calls `_super` internally.\n */\nexport function createErrorClass<T>(createImpl: (_super: any) => any): T {\n  const _super = (instance: any) => {\n    Error.call(instance);\n    instance.stack = new Error().stack;\n  };\n\n  const ctorFunc = createImpl(_super);\n  ctorFunc.prototype = Object.create(Error.prototype);\n  ctorFunc.prototype.constructor = ctorFunc;\n  return ctorFunc;\n}\n", "import { createErrorClass } from './createErrorClass';\n\nexport interface UnsubscriptionError extends Error {\n  readonly errors: any[];\n}\n\nexport interface UnsubscriptionErrorCtor {\n  /**\n   * @deprecated Internal implementation detail. Do not construct error instances.\n   * Cannot be tagged as internal: https://github.com/ReactiveX/rxjs/issues/6269\n   */\n  new (errors: any[]): UnsubscriptionError;\n}\n\n/**\n * An error thrown when one or more errors have occurred during the\n * `unsubscribe` of a {@link Subscription}.\n */\nexport const UnsubscriptionError: UnsubscriptionErrorCtor = createErrorClass(\n  (_super) =>\n    function UnsubscriptionErrorImpl(this: any, errors: (Error | string)[]) {\n      _super(this);\n      this.message = errors\n        ? `${errors.length} errors occurred during unsubscription:\n${errors.map((err, i) => `${i + 1}) ${err.toString()}`).join('\\n  ')}`\n        : '';\n      this.name = 'UnsubscriptionError';\n      this.errors = errors;\n    }\n);\n", "/**\n * Removes an item from an array, mutating it.\n * @param arr The array to remove the item from\n * @param item The item to remove\n */\nexport function arrRemove<T>(arr: T[] | undefined | null, item: T) {\n  if (arr) {\n    const index = arr.indexOf(item);\n    0 <= index && arr.splice(index, 1);\n  }\n}\n", "import { isFunction } from './util/isFunction';\nimport { UnsubscriptionError } from './util/UnsubscriptionError';\nimport { SubscriptionLike, TeardownLogic, Unsubscribable } from './types';\nimport { arrRemove } from './util/arrRemove';\n\n/**\n * Represents a disposable resource, such as the execution of an Observable. A\n * Subscription has one important method, `unsubscribe`, that takes no argument\n * and just disposes the resource held by the subscription.\n *\n * Additionally, subscriptions may be grouped together through the `add()`\n * method, which will attach a child Subscription to the current Subscription.\n * When a Subscription is unsubscribed, all its children (and its grandchildren)\n * will be unsubscribed as well.\n */\nexport class Subscription implements SubscriptionLike {\n  public static EMPTY = (() => {\n    const empty = new Subscription();\n    empty.closed = true;\n    return empty;\n  })();\n\n  /**\n   * A flag to indicate whether this Subscription has already been unsubscribed.\n   */\n  public closed = false;\n\n  private _parentage: Subscription[] | Subscription | null = null;\n\n  /**\n   * The list of registered finalizers to execute upon unsubscription. Adding and removing from this\n   * list occurs in the {@link #add} and {@link #remove} methods.\n   */\n  private _finalizers: Exclude<TeardownLogic, void>[] | null = null;\n\n  /**\n   * @param initialTeardown A function executed first as part of the finalization\n   * process that is kicked off when {@link #unsubscribe} is called.\n   */\n  constructor(private initialTeardown?: () => void) {}\n\n  /**\n   * Disposes the resources held by the subscription. May, for instance, cancel\n   * an ongoing Observable execution or cancel any other type of work that\n   * started when the Subscription was created.\n   */\n  unsubscribe(): void {\n    let errors: any[] | undefined;\n\n    if (!this.closed) {\n      this.closed = true;\n\n      // Remove this from it's parents.\n      const { _parentage } = this;\n      if (_parentage) {\n        this._parentage = null;\n        if (Array.isArray(_parentage)) {\n          for (const parent of _parentage) {\n            parent.remove(this);\n          }\n        } else {\n          _parentage.remove(this);\n        }\n      }\n\n      const { initialTeardown: initialFinalizer } = this;\n      if (isFunction(initialFinalizer)) {\n        try {\n          initialFinalizer();\n        } catch (e) {\n          errors = e instanceof UnsubscriptionError ? e.errors : [e];\n        }\n      }\n\n      const { _finalizers } = this;\n      if (_finalizers) {\n        this._finalizers = null;\n        for (const finalizer of _finalizers) {\n          try {\n            execFinalizer(finalizer);\n          } catch (err) {\n            errors = errors ?? [];\n            if (err instanceof UnsubscriptionError) {\n              errors = [...errors, ...err.errors];\n            } else {\n              errors.push(err);\n            }\n          }\n        }\n      }\n\n      if (errors) {\n        throw new UnsubscriptionError(errors);\n      }\n    }\n  }\n\n  /**\n   * Adds a finalizer to this subscription, so that finalization will be unsubscribed/called\n   * when this subscription is unsubscribed. If this subscription is already {@link #closed},\n   * because it has already been unsubscribed, then whatever finalizer is passed to it\n   * will automatically be executed (unless the finalizer itself is also a closed subscription).\n   *\n   * Closed Subscriptions cannot be added as finalizers to any subscription. Adding a closed\n   * subscription to a any subscription will result in no operation. (A noop).\n   *\n   * Adding a subscription to itself, or adding `null` or `undefined` will not perform any\n   * operation at all. (A noop).\n   *\n   * `Subscription` instances that are added to this instance will automatically remove themselves\n   * if they are unsubscribed. Functions and {@link Unsubscribable} objects that you wish to remove\n   * will need to be removed manually with {@link #remove}\n   *\n   * @param teardown The finalization logic to add to this subscription.\n   */\n  add(teardown: TeardownLogic): void {\n    // Only add the finalizer if it's not undefined\n    // and don't add a subscription to itself.\n    if (teardown && teardown !== this) {\n      if (this.closed) {\n        // If this subscription is already closed,\n        // execute whatever finalizer is handed to it automatically.\n        execFinalizer(teardown);\n      } else {\n        if (teardown instanceof Subscription) {\n          // We don't add closed subscriptions, and we don't add the same subscription\n          // twice. Subscription unsubscribe is idempotent.\n          if (teardown.closed || teardown._hasParent(this)) {\n            return;\n          }\n          teardown._addParent(this);\n        }\n        (this._finalizers = this._finalizers ?? []).push(teardown);\n      }\n    }\n  }\n\n  /**\n   * Checks to see if a this subscription already has a particular parent.\n   * This will signal that this subscription has already been added to the parent in question.\n   * @param parent the parent to check for\n   */\n  private _hasParent(parent: Subscription) {\n    const { _parentage } = this;\n    return _parentage === parent || (Array.isArray(_parentage) && _parentage.includes(parent));\n  }\n\n  /**\n   * Adds a parent to this subscription so it can be removed from the parent if it\n   * unsubscribes on it's own.\n   *\n   * NOTE: THIS ASSUMES THAT {@link _hasParent} HAS ALREADY BEEN CHECKED.\n   * @param parent The parent subscription to add\n   */\n  private _addParent(parent: Subscription) {\n    const { _parentage } = this;\n    this._parentage = Array.isArray(_parentage) ? (_parentage.push(parent), _parentage) : _parentage ? [_parentage, parent] : parent;\n  }\n\n  /**\n   * Called on a child when it is removed via {@link #remove}.\n   * @param parent The parent to remove\n   */\n  private _removeParent(parent: Subscription) {\n    const { _parentage } = this;\n    if (_parentage === parent) {\n      this._parentage = null;\n    } else if (Array.isArray(_parentage)) {\n      arrRemove(_parentage, parent);\n    }\n  }\n\n  /**\n   * Removes a finalizer from this subscription that was previously added with the {@link #add} method.\n   *\n   * Note that `Subscription` instances, when unsubscribed, will automatically remove themselves\n   * from every other `Subscription` they have been added to. This means that using the `remove` method\n   * is not a common thing and should be used thoughtfully.\n   *\n   * If you add the same finalizer instance of a function or an unsubscribable object to a `Subscription` instance\n   * more than once, you will need to call `remove` the same number of times to remove all instances.\n   *\n   * All finalizer instances are removed to free up memory upon unsubscription.\n   *\n   * @param teardown The finalizer to remove from this subscription\n   */\n  remove(teardown: Exclude<TeardownLogic, void>): void {\n    const { _finalizers } = this;\n    _finalizers && arrRemove(_finalizers, teardown);\n\n    if (teardown instanceof Subscription) {\n      teardown._removeParent(this);\n    }\n  }\n}\n\nexport const EMPTY_SUBSCRIPTION = Subscription.EMPTY;\n\nexport function isSubscription(value: any): value is Subscription {\n  return (\n    value instanceof Subscription ||\n    (value && 'closed' in value && isFunction(value.remove) && isFunction(value.add) && isFunction(value.unsubscribe))\n  );\n}\n\nfunction execFinalizer(finalizer: Unsubscribable | (() => void)) {\n  if (isFunction(finalizer)) {\n    finalizer();\n  } else {\n    finalizer.unsubscribe();\n  }\n}\n", "import { Subscriber } from './Subscriber';\nimport { ObservableNotification } from './types';\n\n/**\n * The {@link GlobalConfig} object for RxJS. It is used to configure things\n * like how to react on unhandled errors.\n */\nexport const config: GlobalConfig = {\n  onUnhandledError: null,\n  onStoppedNotification: null,\n  Promise: undefined,\n  useDeprecatedSynchronousErrorHandling: false,\n  useDeprecatedNextContext: false,\n};\n\n/**\n * The global configuration object for RxJS, used to configure things\n * like how to react on unhandled errors. Accessible via {@link config}\n * object.\n */\nexport interface GlobalConfig {\n  /**\n   * A registration point for unhandled errors from RxJS. These are errors that\n   * cannot were not handled by consuming code in the usual subscription path. For\n   * example, if you have this configured, and you subscribe to an observable without\n   * providing an error handler, errors from that subscription will end up here. This\n   * will _always_ be called asynchronously on another job in the runtime. This is because\n   * we do not want errors thrown in this user-configured handler to interfere with the\n   * behavior of the library.\n   */\n  onUnhandledError: ((err: any) => void) | null;\n\n  /**\n   * A registration point for notifications that cannot be sent to subscribers because they\n   * have completed, errored or have been explicitly unsubscribed. By default, next, complete\n   * and error notifications sent to stopped subscribers are noops. However, sometimes callers\n   * might want a different behavior. For example, with sources that attempt to report errors\n   * to stopped subscribers, a caller can configure RxJS to throw an unhandled error instead.\n   * This will _always_ be called asynchronously on another job in the runtime. This is because\n   * we do not want errors thrown in this user-configured handler to interfere with the\n   * behavior of the library.\n   */\n  onStoppedNotification: ((notification: ObservableNotification<any>, subscriber: Subscriber<any>) => void) | null;\n\n  /**\n   * The promise constructor used by default for {@link Observable#toPromise toPromise} and {@link Observable#forEach forEach}\n   * methods.\n   *\n   * @deprecated As of version 8, RxJS will no longer support this sort of injection of a\n   * Promise constructor. If you need a Promise implementation other than native promises,\n   * please polyfill/patch Promise as you see appropriate. Will be removed in v8.\n   */\n  Promise?: PromiseConstructorLike;\n\n  /**\n   * If true, turns on synchronous error rethrowing, which is a deprecated behavior\n   * in v6 and higher. This behavior enables bad patterns like wrapping a subscribe\n   * call in a try/catch block. It also enables producer interference, a nasty bug\n   * where a multicast can be broken for all observers by a downstream consumer with\n   * an unhandled error. DO NOT USE THIS FLAG UNLESS IT'S NEEDED TO BUY TIME\n   * FOR MIGRATION REASONS.\n   *\n   * @deprecated As of version 8, RxJS will no longer support synchronous throwing\n   * of unhandled errors. All errors will be thrown on a separate call stack to prevent bad\n   * behaviors described above. Will be removed in v8.\n   */\n  useDeprecatedSynchronousErrorHandling: boolean;\n\n  /**\n   * If true, enables an as-of-yet undocumented feature from v5: The ability to access\n   * `unsubscribe()` via `this` context in `next` functions created in observers passed\n   * to `subscribe`.\n   *\n   * This is being removed because the performance was severely problematic, and it could also cause\n   * issues when types other than POJOs are passed to subscribe as subscribers, as they will likely have\n   * their `this` context overwritten.\n   *\n   * @deprecated As of version 8, RxJS will no longer support altering the\n   * context of next functions provided as part of an observer to Subscribe. Instead,\n   * you will have access to a subscription or a signal or token that will allow you to do things like\n   * unsubscribe and test closed status. Will be removed in v8.\n   */\n  useDeprecatedNextContext: boolean;\n}\n", "import type { TimerHandle } from './timerHandle';\ntype SetTimeoutFunction = (handler: () => void, timeout?: number, ...args: any[]) => TimerHandle;\ntype ClearTimeoutFunction = (handle: TimerHandle) => void;\n\ninterface TimeoutProvider {\n  setTimeout: SetTimeoutFunction;\n  clearTimeout: ClearTimeoutFunction;\n  delegate:\n    | {\n        setTimeout: SetTimeoutFunction;\n        clearTimeout: ClearTimeoutFunction;\n      }\n    | undefined;\n}\n\nexport const timeoutProvider: TimeoutProvider = {\n  // When accessing the delegate, use the variable rather than `this` so that\n  // the functions can be called without being bound to the provider.\n  setTimeout(handler: () => void, timeout?: number, ...args) {\n    const { delegate } = timeoutProvider;\n    if (delegate?.setTimeout) {\n      return delegate.setTimeout(handler, timeout, ...args);\n    }\n    return setTimeout(handler, timeout, ...args);\n  },\n  clearTimeout(handle) {\n    const { delegate } = timeoutProvider;\n    return (delegate?.clearTimeout || clearTimeout)(handle as any);\n  },\n  delegate: undefined,\n};\n", "import { config } from '../config';\nimport { timeoutProvider } from '../scheduler/timeoutProvider';\n\n/**\n * Handles an error on another job either with the user-configured {@link onUnhandledError},\n * or by throwing it on that new job so it can be picked up by `window.onerror`, `process.on('error')`, etc.\n *\n * This should be called whenever there is an error that is out-of-band with the subscription\n * or when an error hits a terminal boundary of the subscription and no error handler was provided.\n *\n * @param err the error to report\n */\nexport function reportUnhandledError(err: any) {\n  timeoutProvider.setTimeout(() => {\n    const { onUnhandledError } = config;\n    if (onUnhandledError) {\n      // Execute the user-configured error handler.\n      onUnhandledError(err);\n    } else {\n      // Throw so it is picked up by the runtime's uncaught error mechanism.\n      throw err;\n    }\n  });\n}\n", "/* tslint:disable:no-empty */\nexport function noop() { }\n", "import { CompleteNotification, NextNotification, ErrorNotification } from './types';\n\n/**\n * A completion object optimized for memory use and created to be the\n * same \"shape\" as other notifications in v8.\n * @internal\n */\nexport const COMPLETE_NOTIFICATION = (() => createNotification('C', undefined, undefined) as CompleteNotification)();\n\n/**\n * Internal use only. Creates an optimized error notification that is the same \"shape\"\n * as other notifications.\n * @internal\n */\nexport function errorNotification(error: any): ErrorNotification {\n  return createNotification('E', undefined, error) as any;\n}\n\n/**\n * Internal use only. Creates an optimized next notification that is the same \"shape\"\n * as other notifications.\n * @internal\n */\nexport function nextNotification<T>(value: T) {\n  return createNotification('N', value, undefined) as NextNotification<T>;\n}\n\n/**\n * Ensures that all notifications created internally have the same \"shape\" in v8.\n *\n * TODO: This is only exported to support a crazy legacy test in `groupBy`.\n * @internal\n */\nexport function createNotification(kind: 'N' | 'E' | 'C', value: any, error: any) {\n  return {\n    kind,\n    value,\n    error,\n  };\n}\n", "import { config } from '../config';\n\nlet context: { errorThrown: boolean; error: any } | null = null;\n\n/**\n * Handles dealing with errors for super-gross mode. Creates a context, in which\n * any synchronously thrown errors will be passed to {@link captureError}. Which\n * will record the error such that it will be rethrown after the call back is complete.\n * TODO: Remove in v8\n * @param cb An immediately executed function.\n */\nexport function errorContext(cb: () => void) {\n  if (config.useDeprecatedSynchronousErrorHandling) {\n    const isRoot = !context;\n    if (isRoot) {\n      context = { errorThrown: false, error: null };\n    }\n    cb();\n    if (isRoot) {\n      const { errorThrown, error } = context!;\n      context = null;\n      if (errorThrown) {\n        throw error;\n      }\n    }\n  } else {\n    // This is the general non-deprecated path for everyone that\n    // isn't crazy enough to use super-gross mode (useDeprecatedSynchronousErrorHandling)\n    cb();\n  }\n}\n\n/**\n * Captures errors only in super-gross mode.\n * @param err the error to capture\n */\nexport function captureError(err: any) {\n  if (config.useDeprecatedSynchronousErrorHandling && context) {\n    context.errorThrown = true;\n    context.error = err;\n  }\n}\n", "import { isFunction } from './util/isFunction';\nimport { Observer, ObservableNotification } from './types';\nimport { isSubscription, Subscription } from './Subscription';\nimport { config } from './config';\nimport { reportUnhandledError } from './util/reportUnhandledError';\nimport { noop } from './util/noop';\nimport { nextNotification, errorNotification, COMPLETE_NOTIFICATION } from './NotificationFactories';\nimport { timeoutProvider } from './scheduler/timeoutProvider';\nimport { captureError } from './util/errorContext';\n\n/**\n * Implements the {@link Observer} interface and extends the\n * {@link Subscription} class. While the {@link Observer} is the public API for\n * consuming the values of an {@link Observable}, all Observers get converted to\n * a Subscriber, in order to provide Subscription-like capabilities such as\n * `unsubscribe`. Subscriber is a common type in RxJS, and crucial for\n * implementing operators, but it is rarely used as a public API.\n */\nexport class Subscriber<T> extends Subscription implements Observer<T> {\n  /**\n   * A static factory for a Subscriber, given a (potentially partial) definition\n   * of an Observer.\n   * @param next The `next` callback of an Observer.\n   * @param error The `error` callback of an\n   * Observer.\n   * @param complete The `complete` callback of an\n   * Observer.\n   * @return A Subscriber wrapping the (partially defined)\n   * Observer represented by the given arguments.\n   * @deprecated Do not use. Will be removed in v8. There is no replacement for this\n   * method, and there is no reason to be creating instances of `Subscriber` directly.\n   * If you have a specific use case, please file an issue.\n   */\n  static create<T>(next?: (x?: T) => void, error?: (e?: any) => void, complete?: () => void): Subscriber<T> {\n    return new SafeSubscriber(next, error, complete);\n  }\n\n  /** @deprecated Internal implementation detail, do not use directly. Will be made internal in v8. */\n  protected isStopped: boolean = false;\n  /** @deprecated Internal implementation detail, do not use directly. Will be made internal in v8. */\n  protected destination: Subscriber<any> | Observer<any>; // this `any` is the escape hatch to erase extra type param (e.g. R)\n\n  /**\n   * @deprecated Internal implementation detail, do not use directly. Will be made internal in v8.\n   * There is no reason to directly create an instance of Subscriber. This type is exported for typings reasons.\n   */\n  constructor(destination?: Subscriber<any> | Observer<any>) {\n    super();\n    if (destination) {\n      this.destination = destination;\n      // Automatically chain subscriptions together here.\n      // if destination is a Subscription, then it is a Subscriber.\n      if (isSubscription(destination)) {\n        destination.add(this);\n      }\n    } else {\n      this.destination = EMPTY_OBSERVER;\n    }\n  }\n\n  /**\n   * The {@link Observer} callback to receive notifications of type `next` from\n   * the Observable, with a value. The Observable may call this method 0 or more\n   * times.\n   * @param value The `next` value.\n   */\n  next(value: T): void {\n    if (this.isStopped) {\n      handleStoppedNotification(nextNotification(value), this);\n    } else {\n      this._next(value!);\n    }\n  }\n\n  /**\n   * The {@link Observer} callback to receive notifications of type `error` from\n   * the Observable, with an attached `Error`. Notifies the Observer that\n   * the Observable has experienced an error condition.\n   * @param err The `error` exception.\n   */\n  error(err?: any): void {\n    if (this.isStopped) {\n      handleStoppedNotification(errorNotification(err), this);\n    } else {\n      this.isStopped = true;\n      this._error(err);\n    }\n  }\n\n  /**\n   * The {@link Observer} callback to receive a valueless notification of type\n   * `complete` from the Observable. Notifies the Observer that the Observable\n   * has finished sending push-based notifications.\n   */\n  complete(): void {\n    if (this.isStopped) {\n      handleStoppedNotification(COMPLETE_NOTIFICATION, this);\n    } else {\n      this.isStopped = true;\n      this._complete();\n    }\n  }\n\n  unsubscribe(): void {\n    if (!this.closed) {\n      this.isStopped = true;\n      super.unsubscribe();\n      this.destination = null!;\n    }\n  }\n\n  protected _next(value: T): void {\n    this.destination.next(value);\n  }\n\n  protected _error(err: any): void {\n    try {\n      this.destination.error(err);\n    } finally {\n      this.unsubscribe();\n    }\n  }\n\n  protected _complete(): void {\n    try {\n      this.destination.complete();\n    } finally {\n      this.unsubscribe();\n    }\n  }\n}\n\n/**\n * This bind is captured here because we want to be able to have\n * compatibility with monoid libraries that tend to use a method named\n * `bind`. In particular, a library called Monio requires this.\n */\nconst _bind = Function.prototype.bind;\n\nfunction bind<Fn extends (...args: any[]) => any>(fn: Fn, thisArg: any): Fn {\n  return _bind.call(fn, thisArg);\n}\n\n/**\n * Internal optimization only, DO NOT EXPOSE.\n * @internal\n */\nclass ConsumerObserver<T> implements Observer<T> {\n  constructor(private partialObserver: Partial<Observer<T>>) {}\n\n  next(value: T): void {\n    const { partialObserver } = this;\n    if (partialObserver.next) {\n      try {\n        partialObserver.next(value);\n      } catch (error) {\n        handleUnhandledError(error);\n      }\n    }\n  }\n\n  error(err: any): void {\n    const { partialObserver } = this;\n    if (partialObserver.error) {\n      try {\n        partialObserver.error(err);\n      } catch (error) {\n        handleUnhandledError(error);\n      }\n    } else {\n      handleUnhandledError(err);\n    }\n  }\n\n  complete(): void {\n    const { partialObserver } = this;\n    if (partialObserver.complete) {\n      try {\n        partialObserver.complete();\n      } catch (error) {\n        handleUnhandledError(error);\n      }\n    }\n  }\n}\n\nexport class SafeSubscriber<T> extends Subscriber<T> {\n  constructor(\n    observerOrNext?: Partial<Observer<T>> | ((value: T) => void) | null,\n    error?: ((e?: any) => void) | null,\n    complete?: (() => void) | null\n  ) {\n    super();\n\n    let partialObserver: Partial<Observer<T>>;\n    if (isFunction(observerOrNext) || !observerOrNext) {\n      // The first argument is a function, not an observer. The next\n      // two arguments *could* be observers, or they could be empty.\n      partialObserver = {\n        next: (observerOrNext ?? undefined) as ((value: T) => void) | undefined,\n        error: error ?? undefined,\n        complete: complete ?? undefined,\n      };\n    } else {\n      // The first argument is a partial observer.\n      let context: any;\n      if (this && config.useDeprecatedNextContext) {\n        // This is a deprecated path that made `this.unsubscribe()` available in\n        // next handler functions passed to subscribe. This only exists behind a flag\n        // now, as it is *very* slow.\n        context = Object.create(observerOrNext);\n        context.unsubscribe = () => this.unsubscribe();\n        partialObserver = {\n          next: observerOrNext.next && bind(observerOrNext.next, context),\n          error: observerOrNext.error && bind(observerOrNext.error, context),\n          complete: observerOrNext.complete && bind(observerOrNext.complete, context),\n        };\n      } else {\n        // The \"normal\" path. Just use the partial observer directly.\n        partialObserver = observerOrNext;\n      }\n    }\n\n    // Wrap the partial observer to ensure it's a full observer, and\n    // make sure proper error handling is accounted for.\n    this.destination = new ConsumerObserver(partialObserver);\n  }\n}\n\nfunction handleUnhandledError(error: any) {\n  if (config.useDeprecatedSynchronousErrorHandling) {\n    captureError(error);\n  } else {\n    // Ideal path, we report this as an unhandled error,\n    // which is thrown on a new call stack.\n    reportUnhandledError(error);\n  }\n}\n\n/**\n * An error handler used when no error handler was supplied\n * to the SafeSubscriber -- meaning no error handler was supplied\n * do the `subscribe` call on our observable.\n * @param err The error to handle\n */\nfunction defaultErrorHandler(err: any) {\n  throw err;\n}\n\n/**\n * A handler for notifications that cannot be sent to a stopped subscriber.\n * @param notification The notification being sent.\n * @param subscriber The stopped subscriber.\n */\nfunction handleStoppedNotification(notification: ObservableNotification<any>, subscriber: Subscriber<any>) {\n  const { onStoppedNotification } = config;\n  onStoppedNotification && timeoutProvider.setTimeout(() => onStoppedNotification(notification, subscriber));\n}\n\n/**\n * The observer used as a stub for subscriptions where the user did not\n * pass any arguments to `subscribe`. Comes with the default error handling\n * behavior.\n */\nexport const EMPTY_OBSERVER: Readonly<Observer<any>> & { closed: true } = {\n  closed: true,\n  next: noop,\n  error: defaultErrorHandler,\n  complete: noop,\n};\n", "/**\n * Symbol.observable or a string \"@@observable\". Used for interop\n *\n * @deprecated We will no longer be exporting this symbol in upcoming versions of RxJS.\n * Instead polyfill and use Symbol.observable directly *or* use https://www.npmjs.com/package/symbol-observable\n */\nexport const observable: string | symbol = (() => (typeof Symbol === 'function' && Symbol.observable) || '@@observable')();\n", "/**\n * This function takes one parameter and just returns it. Simply put,\n * this is like `<T>(x: T): T => x`.\n *\n * ## Examples\n *\n * This is useful in some cases when using things like `mergeMap`\n *\n * ```ts\n * import { interval, take, map, range, mergeMap, identity } from 'rxjs';\n *\n * const source$ = interval(1000).pipe(take(5));\n *\n * const result$ = source$.pipe(\n *   map(i => range(i)),\n *   mergeMap(identity) // same as mergeMap(x => x)\n * );\n *\n * result$.subscribe({\n *   next: console.log\n * });\n * ```\n *\n * Or when you want to selectively apply an operator\n *\n * ```ts\n * import { interval, take, identity } from 'rxjs';\n *\n * const shouldLimit = () => Math.random() < 0.5;\n *\n * const source$ = interval(1000);\n *\n * const result$ = source$.pipe(shouldLimit() ? take(5) : identity);\n *\n * result$.subscribe({\n *   next: console.log\n * });\n * ```\n *\n * @param x Any value that is returned by this function\n * @returns The value passed as the first parameter to this function\n */\nexport function identity<T>(x: T): T {\n  return x;\n}\n", "import { identity } from './identity';\nimport { UnaryFunction } from '../types';\n\nexport function pipe(): typeof identity;\nexport function pipe<T, A>(fn1: UnaryFunction<T, A>): UnaryFunction<T, A>;\nexport function pipe<T, A, B>(fn1: UnaryFunction<T, A>, fn2: UnaryFunction<A, B>): UnaryFunction<T, B>;\nexport function pipe<T, A, B, C>(fn1: UnaryFunction<T, A>, fn2: UnaryFunction<A, B>, fn3: UnaryFunction<B, C>): UnaryFunction<T, C>;\nexport function pipe<T, A, B, C, D>(\n  fn1: UnaryFunction<T, A>,\n  fn2: UnaryFunction<A, B>,\n  fn3: UnaryFunction<B, C>,\n  fn4: UnaryFunction<C, D>\n): UnaryFunction<T, D>;\nexport function pipe<T, A, B, C, D, E>(\n  fn1: UnaryFunction<T, A>,\n  fn2: UnaryFunction<A, B>,\n  fn3: UnaryFunction<B, C>,\n  fn4: UnaryFunction<C, D>,\n  fn5: UnaryFunction<D, E>\n): UnaryFunction<T, E>;\nexport function pipe<T, A, B, C, D, E, F>(\n  fn1: UnaryFunction<T, A>,\n  fn2: UnaryFunction<A, B>,\n  fn3: UnaryFunction<B, C>,\n  fn4: UnaryFunction<C, D>,\n  fn5: UnaryFunction<D, E>,\n  fn6: UnaryFunction<E, F>\n): UnaryFunction<T, F>;\nexport function pipe<T, A, B, C, D, E, F, G>(\n  fn1: UnaryFunction<T, A>,\n  fn2: UnaryFunction<A, B>,\n  fn3: UnaryFunction<B, C>,\n  fn4: UnaryFunction<C, D>,\n  fn5: UnaryFunction<D, E>,\n  fn6: UnaryFunction<E, F>,\n  fn7: UnaryFunction<F, G>\n): UnaryFunction<T, G>;\nexport function pipe<T, A, B, C, D, E, F, G, H>(\n  fn1: UnaryFunction<T, A>,\n  fn2: UnaryFunction<A, B>,\n  fn3: UnaryFunction<B, C>,\n  fn4: UnaryFunction<C, D>,\n  fn5: UnaryFunction<D, E>,\n  fn6: UnaryFunction<E, F>,\n  fn7: UnaryFunction<F, G>,\n  fn8: UnaryFunction<G, H>\n): UnaryFunction<T, H>;\nexport function pipe<T, A, B, C, D, E, F, G, H, I>(\n  fn1: UnaryFunction<T, A>,\n  fn2: UnaryFunction<A, B>,\n  fn3: UnaryFunction<B, C>,\n  fn4: UnaryFunction<C, D>,\n  fn5: UnaryFunction<D, E>,\n  fn6: UnaryFunction<E, F>,\n  fn7: UnaryFunction<F, G>,\n  fn8: UnaryFunction<G, H>,\n  fn9: UnaryFunction<H, I>\n): UnaryFunction<T, I>;\nexport function pipe<T, A, B, C, D, E, F, G, H, I>(\n  fn1: UnaryFunction<T, A>,\n  fn2: UnaryFunction<A, B>,\n  fn3: UnaryFunction<B, C>,\n  fn4: UnaryFunction<C, D>,\n  fn5: UnaryFunction<D, E>,\n  fn6: UnaryFunction<E, F>,\n  fn7: UnaryFunction<F, G>,\n  fn8: UnaryFunction<G, H>,\n  fn9: UnaryFunction<H, I>,\n  ...fns: UnaryFunction<any, any>[]\n): UnaryFunction<T, unknown>;\n\n/**\n * pipe() can be called on one or more functions, each of which can take one argument (\"UnaryFunction\")\n * and uses it to return a value.\n * It returns a function that takes one argument, passes it to the first UnaryFunction, and then\n * passes the result to the next one, passes that result to the next one, and so on.  \n */\nexport function pipe(...fns: Array<UnaryFunction<any, any>>): UnaryFunction<any, any> {\n  return pipeFromArray(fns);\n}\n\n/** @internal */\nexport function pipeFromArray<T, R>(fns: Array<UnaryFunction<T, R>>): UnaryFunction<T, R> {\n  if (fns.length === 0) {\n    return identity as UnaryFunction<any, any>;\n  }\n\n  if (fns.length === 1) {\n    return fns[0];\n  }\n\n  return function piped(input: T): R {\n    return fns.reduce((prev: any, fn: UnaryFunction<T, R>) => fn(prev), input as any);\n  };\n}\n", "import { Operator } from './Operator';\nimport { SafeSubscriber, Subscriber } from './Subscriber';\nimport { isSubscription, Subscription } from './Subscription';\nimport { TeardownLogic, OperatorFunction, Subscribable, Observer } from './types';\nimport { observable as Symbol_observable } from './symbol/observable';\nimport { pipeFromArray } from './util/pipe';\nimport { config } from './config';\nimport { isFunction } from './util/isFunction';\nimport { errorContext } from './util/errorContext';\n\n/**\n * A representation of any set of values over any amount of time. This is the most basic building block\n * of RxJS.\n */\nexport class Observable<T> implements Subscribable<T> {\n  /**\n   * @deprecated Internal implementation detail, do not use directly. Will be made internal in v8.\n   */\n  source: Observable<any> | undefined;\n\n  /**\n   * @deprecated Internal implementation detail, do not use directly. Will be made internal in v8.\n   */\n  operator: Operator<any, T> | undefined;\n\n  /**\n   * @param subscribe The function that is called when the Observable is\n   * initially subscribed to. This function is given a Subscriber, to which new values\n   * can be `next`ed, or an `error` method can be called to raise an error, or\n   * `complete` can be called to notify of a successful completion.\n   */\n  constructor(subscribe?: (this: Observable<T>, subscriber: Subscriber<T>) => TeardownLogic) {\n    if (subscribe) {\n      this._subscribe = subscribe;\n    }\n  }\n\n  // HACK: Since TypeScript inherits static properties too, we have to\n  // fight against TypeScript here so Subject can have a different static create signature\n  /**\n   * Creates a new Observable by calling the Observable constructor\n   * @param subscribe the subscriber function to be passed to the Observable constructor\n   * @return A new observable.\n   * @deprecated Use `new Observable()` instead. Will be removed in v8.\n   */\n  static create: (...args: any[]) => any = <T>(subscribe?: (subscriber: Subscriber<T>) => TeardownLogic) => {\n    return new Observable<T>(subscribe);\n  };\n\n  /**\n   * Creates a new Observable, with this Observable instance as the source, and the passed\n   * operator defined as the new observable's operator.\n   * @param operator the operator defining the operation to take on the observable\n   * @return A new observable with the Operator applied.\n   * @deprecated Internal implementation detail, do not use directly. Will be made internal in v8.\n   * If you have implemented an operator using `lift`, it is recommended that you create an\n   * operator by simply returning `new Observable()` directly. See \"Creating new operators from\n   * scratch\" section here: https://rxjs.dev/guide/operators\n   */\n  lift<R>(operator?: Operator<T, R>): Observable<R> {\n    const observable = new Observable<R>();\n    observable.source = this;\n    observable.operator = operator;\n    return observable;\n  }\n\n  subscribe(observerOrNext?: Partial<Observer<T>> | ((value: T) => void)): Subscription;\n  /** @deprecated Instead of passing separate callback arguments, use an observer argument. Signatures taking separate callback arguments will be removed in v8. Details: https://rxjs.dev/deprecations/subscribe-arguments */\n  subscribe(next?: ((value: T) => void) | null, error?: ((error: any) => void) | null, complete?: (() => void) | null): Subscription;\n  /**\n   * Invokes an execution of an Observable and registers Observer handlers for notifications it will emit.\n   *\n   * <span class=\"informal\">Use it when you have all these Observables, but still nothing is happening.</span>\n   *\n   * `subscribe` is not a regular operator, but a method that calls Observable's internal `subscribe` function. It\n   * might be for example a function that you passed to Observable's constructor, but most of the time it is\n   * a library implementation, which defines what will be emitted by an Observable, and when it be will emitted. This means\n   * that calling `subscribe` is actually the moment when Observable starts its work, not when it is created, as it is often\n   * the thought.\n   *\n   * Apart from starting the execution of an Observable, this method allows you to listen for values\n   * that an Observable emits, as well as for when it completes or errors. You can achieve this in two\n   * of the following ways.\n   *\n   * The first way is creating an object that implements {@link Observer} interface. It should have methods\n   * defined by that interface, but note that it should be just a regular JavaScript object, which you can create\n   * yourself in any way you want (ES6 class, classic function constructor, object literal etc.). In particular, do\n   * not attempt to use any RxJS implementation details to create Observers - you don't need them. Remember also\n   * that your object does not have to implement all methods. If you find yourself creating a method that doesn't\n   * do anything, you can simply omit it. Note however, if the `error` method is not provided and an error happens,\n   * it will be thrown asynchronously. Errors thrown asynchronously cannot be caught using `try`/`catch`. Instead,\n   * use the {@link onUnhandledError} configuration option or use a runtime handler (like `window.onerror` or\n   * `process.on('error)`) to be notified of unhandled errors. Because of this, it's recommended that you provide\n   * an `error` method to avoid missing thrown errors.\n   *\n   * The second way is to give up on Observer object altogether and simply provide callback functions in place of its methods.\n   * This means you can provide three functions as arguments to `subscribe`, where the first function is equivalent\n   * of a `next` method, the second of an `error` method and the third of a `complete` method. Just as in case of an Observer,\n   * if you do not need to listen for something, you can omit a function by passing `undefined` or `null`,\n   * since `subscribe` recognizes these functions by where they were placed in function call. When it comes\n   * to the `error` function, as with an Observer, if not provided, errors emitted by an Observable will be thrown asynchronously.\n   *\n   * You can, however, subscribe with no parameters at all. This may be the case where you're not interested in terminal events\n   * and you also handled emissions internally by using operators (e.g. using `tap`).\n   *\n   * Whichever style of calling `subscribe` you use, in both cases it returns a Subscription object.\n   * This object allows you to call `unsubscribe` on it, which in turn will stop the work that an Observable does and will clean\n   * up all resources that an Observable used. Note that cancelling a subscription will not call `complete` callback\n   * provided to `subscribe` function, which is reserved for a regular completion signal that comes from an Observable.\n   *\n   * Remember that callbacks provided to `subscribe` are not guaranteed to be called asynchronously.\n   * It is an Observable itself that decides when these functions will be called. For example {@link of}\n   * by default emits all its values synchronously. Always check documentation for how given Observable\n   * will behave when subscribed and if its default behavior can be modified with a `scheduler`.\n   *\n   * #### Examples\n   *\n   * Subscribe with an {@link guide/observer Observer}\n   *\n   * ```ts\n   * import { of } from 'rxjs';\n   *\n   * const sumObserver = {\n   *   sum: 0,\n   *   next(value) {\n   *     console.log('Adding: ' + value);\n   *     this.sum = this.sum + value;\n   *   },\n   *   error() {\n   *     // We actually could just remove this method,\n   *     // since we do not really care about errors right now.\n   *   },\n   *   complete() {\n   *     console.log('Sum equals: ' + this.sum);\n   *   }\n   * };\n   *\n   * of(1, 2, 3) // Synchronously emits 1, 2, 3 and then completes.\n   *   .subscribe(sumObserver);\n   *\n   * // Logs:\n   * // 'Adding: 1'\n   * // 'Adding: 2'\n   * // 'Adding: 3'\n   * // 'Sum equals: 6'\n   * ```\n   *\n   * Subscribe with functions ({@link deprecations/subscribe-arguments deprecated})\n   *\n   * ```ts\n   * import { of } from 'rxjs'\n   *\n   * let sum = 0;\n   *\n   * of(1, 2, 3).subscribe(\n   *   value => {\n   *     console.log('Adding: ' + value);\n   *     sum = sum + value;\n   *   },\n   *   undefined,\n   *   () => console.log('Sum equals: ' + sum)\n   * );\n   *\n   * // Logs:\n   * // 'Adding: 1'\n   * // 'Adding: 2'\n   * // 'Adding: 3'\n   * // 'Sum equals: 6'\n   * ```\n   *\n   * Cancel a subscription\n   *\n   * ```ts\n   * import { interval } from 'rxjs';\n   *\n   * const subscription = interval(1000).subscribe({\n   *   next(num) {\n   *     console.log(num)\n   *   },\n   *   complete() {\n   *     // Will not be called, even when cancelling subscription.\n   *     console.log('completed!');\n   *   }\n   * });\n   *\n   * setTimeout(() => {\n   *   subscription.unsubscribe();\n   *   console.log('unsubscribed!');\n   * }, 2500);\n   *\n   * // Logs:\n   * // 0 after 1s\n   * // 1 after 2s\n   * // 'unsubscribed!' after 2.5s\n   * ```\n   *\n   * @param observerOrNext Either an {@link Observer} with some or all callback methods,\n   * or the `next` handler that is called for each value emitted from the subscribed Observable.\n   * @param error A handler for a terminal event resulting from an error. If no error handler is provided,\n   * the error will be thrown asynchronously as unhandled.\n   * @param complete A handler for a terminal event resulting from successful completion.\n   * @return A subscription reference to the registered handlers.\n   */\n  subscribe(\n    observerOrNext?: Partial<Observer<T>> | ((value: T) => void) | null,\n    error?: ((error: any) => void) | null,\n    complete?: (() => void) | null\n  ): Subscription {\n    const subscriber = isSubscriber(observerOrNext) ? observerOrNext : new SafeSubscriber(observerOrNext, error, complete);\n\n    errorContext(() => {\n      const { operator, source } = this;\n      subscriber.add(\n        operator\n          ? // We're dealing with a subscription in the\n            // operator chain to one of our lifted operators.\n            operator.call(subscriber, source)\n          : source\n          ? // If `source` has a value, but `operator` does not, something that\n            // had intimate knowledge of our API, like our `Subject`, must have\n            // set it. We're going to just call `_subscribe` directly.\n            this._subscribe(subscriber)\n          : // In all other cases, we're likely wrapping a user-provided initializer\n            // function, so we need to catch errors and handle them appropriately.\n            this._trySubscribe(subscriber)\n      );\n    });\n\n    return subscriber;\n  }\n\n  /** @internal */\n  protected _trySubscribe(sink: Subscriber<T>): TeardownLogic {\n    try {\n      return this._subscribe(sink);\n    } catch (err) {\n      // We don't need to return anything in this case,\n      // because it's just going to try to `add()` to a subscription\n      // above.\n      sink.error(err);\n    }\n  }\n\n  /**\n   * Used as a NON-CANCELLABLE means of subscribing to an observable, for use with\n   * APIs that expect promises, like `async/await`. You cannot unsubscribe from this.\n   *\n   * **WARNING**: Only use this with observables you *know* will complete. If the source\n   * observable does not complete, you will end up with a promise that is hung up, and\n   * potentially all of the state of an async function hanging out in memory. To avoid\n   * this situation, look into adding something like {@link timeout}, {@link take},\n   * {@link takeWhile}, or {@link takeUntil} amongst others.\n   *\n   * #### Example\n   *\n   * ```ts\n   * import { interval, take } from 'rxjs';\n   *\n   * const source$ = interval(1000).pipe(take(4));\n   *\n   * async function getTotal() {\n   *   let total = 0;\n   *\n   *   await source$.forEach(value => {\n   *     total += value;\n   *     console.log('observable -> ' + value);\n   *   });\n   *\n   *   return total;\n   * }\n   *\n   * getTotal().then(\n   *   total => console.log('Total: ' + total)\n   * );\n   *\n   * // Expected:\n   * // 'observable -> 0'\n   * // 'observable -> 1'\n   * // 'observable -> 2'\n   * // 'observable -> 3'\n   * // 'Total: 6'\n   * ```\n   *\n   * @param next A handler for each value emitted by the observable.\n   * @return A promise that either resolves on observable completion or\n   * rejects with the handled error.\n   */\n  forEach(next: (value: T) => void): Promise<void>;\n\n  /**\n   * @param next a handler for each value emitted by the observable\n   * @param promiseCtor a constructor function used to instantiate the Promise\n   * @return a promise that either resolves on observable completion or\n   *  rejects with the handled error\n   * @deprecated Passing a Promise constructor will no longer be available\n   * in upcoming versions of RxJS. This is because it adds weight to the library, for very\n   * little benefit. If you need this functionality, it is recommended that you either\n   * polyfill Promise, or you create an adapter to convert the returned native promise\n   * to whatever promise implementation you wanted. Will be removed in v8.\n   */\n  forEach(next: (value: T) => void, promiseCtor: PromiseConstructorLike): Promise<void>;\n\n  forEach(next: (value: T) => void, promiseCtor?: PromiseConstructorLike): Promise<void> {\n    promiseCtor = getPromiseCtor(promiseCtor);\n\n    return new promiseCtor<void>((resolve, reject) => {\n      const subscriber = new SafeSubscriber<T>({\n        next: (value) => {\n          try {\n            next(value);\n          } catch (err) {\n            reject(err);\n            subscriber.unsubscribe();\n          }\n        },\n        error: reject,\n        complete: resolve,\n      });\n      this.subscribe(subscriber);\n    }) as Promise<void>;\n  }\n\n  /** @internal */\n  protected _subscribe(subscriber: Subscriber<any>): TeardownLogic {\n    return this.source?.subscribe(subscriber);\n  }\n\n  /**\n   * An interop point defined by the es7-observable spec https://github.com/zenparsing/es-observable\n   * @return This instance of the observable.\n   */\n  [Symbol_observable]() {\n    return this;\n  }\n\n  /* tslint:disable:max-line-length */\n  pipe(): Observable<T>;\n  pipe<A>(op1: OperatorFunction<T, A>): Observable<A>;\n  pipe<A, B>(op1: OperatorFunction<T, A>, op2: OperatorFunction<A, B>): Observable<B>;\n  pipe<A, B, C>(op1: OperatorFunction<T, A>, op2: OperatorFunction<A, B>, op3: OperatorFunction<B, C>): Observable<C>;\n  pipe<A, B, C, D>(\n    op1: OperatorFunction<T, A>,\n    op2: OperatorFunction<A, B>,\n    op3: OperatorFunction<B, C>,\n    op4: OperatorFunction<C, D>\n  ): Observable<D>;\n  pipe<A, B, C, D, E>(\n    op1: OperatorFunction<T, A>,\n    op2: OperatorFunction<A, B>,\n    op3: OperatorFunction<B, C>,\n    op4: OperatorFunction<C, D>,\n    op5: OperatorFunction<D, E>\n  ): Observable<E>;\n  pipe<A, B, C, D, E, F>(\n    op1: OperatorFunction<T, A>,\n    op2: OperatorFunction<A, B>,\n    op3: OperatorFunction<B, C>,\n    op4: OperatorFunction<C, D>,\n    op5: OperatorFunction<D, E>,\n    op6: OperatorFunction<E, F>\n  ): Observable<F>;\n  pipe<A, B, C, D, E, F, G>(\n    op1: OperatorFunction<T, A>,\n    op2: OperatorFunction<A, B>,\n    op3: OperatorFunction<B, C>,\n    op4: OperatorFunction<C, D>,\n    op5: OperatorFunction<D, E>,\n    op6: OperatorFunction<E, F>,\n    op7: OperatorFunction<F, G>\n  ): Observable<G>;\n  pipe<A, B, C, D, E, F, G, H>(\n    op1: OperatorFunction<T, A>,\n    op2: OperatorFunction<A, B>,\n    op3: OperatorFunction<B, C>,\n    op4: OperatorFunction<C, D>,\n    op5: OperatorFunction<D, E>,\n    op6: OperatorFunction<E, F>,\n    op7: OperatorFunction<F, G>,\n    op8: OperatorFunction<G, H>\n  ): Observable<H>;\n  pipe<A, B, C, D, E, F, G, H, I>(\n    op1: OperatorFunction<T, A>,\n    op2: OperatorFunction<A, B>,\n    op3: OperatorFunction<B, C>,\n    op4: OperatorFunction<C, D>,\n    op5: OperatorFunction<D, E>,\n    op6: OperatorFunction<E, F>,\n    op7: OperatorFunction<F, G>,\n    op8: OperatorFunction<G, H>,\n    op9: OperatorFunction<H, I>\n  ): Observable<I>;\n  pipe<A, B, C, D, E, F, G, H, I>(\n    op1: OperatorFunction<T, A>,\n    op2: OperatorFunction<A, B>,\n    op3: OperatorFunction<B, C>,\n    op4: OperatorFunction<C, D>,\n    op5: OperatorFunction<D, E>,\n    op6: OperatorFunction<E, F>,\n    op7: OperatorFunction<F, G>,\n    op8: OperatorFunction<G, H>,\n    op9: OperatorFunction<H, I>,\n    ...operations: OperatorFunction<any, any>[]\n  ): Observable<unknown>;\n  /* tslint:enable:max-line-length */\n\n  /**\n   * Used to stitch together functional operators into a chain.\n   *\n   * ## Example\n   *\n   * ```ts\n   * import { interval, filter, map, scan } from 'rxjs';\n   *\n   * interval(1000)\n   *   .pipe(\n   *     filter(x => x % 2 === 0),\n   *     map(x => x + x),\n   *     scan((acc, x) => acc + x)\n   *   )\n   *   .subscribe(x => console.log(x));\n   * ```\n   *\n   * @return The Observable result of all the operators having been called\n   * in the order they were passed in.\n   */\n  pipe(...operations: OperatorFunction<any, any>[]): Observable<any> {\n    return pipeFromArray(operations)(this);\n  }\n\n  /* tslint:disable:max-line-length */\n  /** @deprecated Replaced with {@link firstValueFrom} and {@link lastValueFrom}. Will be removed in v8. Details: https://rxjs.dev/deprecations/to-promise */\n  toPromise(): Promise<T | undefined>;\n  /** @deprecated Replaced with {@link firstValueFrom} and {@link lastValueFrom}. Will be removed in v8. Details: https://rxjs.dev/deprecations/to-promise */\n  toPromise(PromiseCtor: typeof Promise): Promise<T | undefined>;\n  /** @deprecated Replaced with {@link firstValueFrom} and {@link lastValueFrom}. Will be removed in v8. Details: https://rxjs.dev/deprecations/to-promise */\n  toPromise(PromiseCtor: PromiseConstructorLike): Promise<T | undefined>;\n  /* tslint:enable:max-line-length */\n\n  /**\n   * Subscribe to this Observable and get a Promise resolving on\n   * `complete` with the last emission (if any).\n   *\n   * **WARNING**: Only use this with observables you *know* will complete. If the source\n   * observable does not complete, you will end up with a promise that is hung up, and\n   * potentially all of the state of an async function hanging out in memory. To avoid\n   * this situation, look into adding something like {@link timeout}, {@link take},\n   * {@link takeWhile}, or {@link takeUntil} amongst others.\n   *\n   * @param [promiseCtor] a constructor function used to instantiate\n   * the Promise\n   * @return A Promise that resolves with the last value emit, or\n   * rejects on an error. If there were no emissions, Promise\n   * resolves with undefined.\n   * @deprecated Replaced with {@link firstValueFrom} and {@link lastValueFrom}. Will be removed in v8. Details: https://rxjs.dev/deprecations/to-promise\n   */\n  toPromise(promiseCtor?: PromiseConstructorLike): Promise<T | undefined> {\n    promiseCtor = getPromiseCtor(promiseCtor);\n\n    return new promiseCtor((resolve, reject) => {\n      let value: T | undefined;\n      this.subscribe(\n        (x: T) => (value = x),\n        (err: any) => reject(err),\n        () => resolve(value)\n      );\n    }) as Promise<T | undefined>;\n  }\n}\n\n/**\n * Decides between a passed promise constructor from consuming code,\n * A default configured promise constructor, and the native promise\n * constructor and returns it. If nothing can be found, it will throw\n * an error.\n * @param promiseCtor The optional promise constructor to passed by consuming code\n */\nfunction getPromiseCtor(promiseCtor: PromiseConstructorLike | undefined) {\n  return promiseCtor ?? config.Promise ?? Promise;\n}\n\nfunction isObserver<T>(value: any): value is Observer<T> {\n  return value && isFunction(value.next) && isFunction(value.error) && isFunction(value.complete);\n}\n\nfunction isSubscriber<T>(value: any): value is Subscriber<T> {\n  return (value && value instanceof Subscriber) || (isObserver(value) && isSubscription(value));\n}\n", "import { Observable } from '../Observable';\nimport { Subscriber } from '../Subscriber';\nimport { OperatorFunction } from '../types';\nimport { isFunction } from './isFunction';\n\n/**\n * Used to determine if an object is an Observable with a lift function.\n */\nexport function hasLift(source: any): source is { lift: InstanceType<typeof Observable>['lift'] } {\n  return isFunction(source?.lift);\n}\n\n/**\n * Creates an `OperatorFunction`. Used to define operators throughout the library in a concise way.\n * @param init The logic to connect the liftedSource to the subscriber at the moment of subscription.\n */\nexport function operate<T, R>(\n  init: (liftedSource: Observable<T>, subscriber: Subscriber<R>) => (() => void) | void\n): OperatorFunction<T, R> {\n  return (source: Observable<T>) => {\n    if (hasLift(source)) {\n      return source.lift(function (this: Subscriber<R>, liftedSource: Observable<T>) {\n        try {\n          return init(liftedSource, this);\n        } catch (err) {\n          this.error(err);\n        }\n      });\n    }\n    throw new TypeError('Unable to lift unknown Observable type');\n  };\n}\n", "import { Subscriber } from '../Subscriber';\n\n/**\n * Creates an instance of an `OperatorSubscriber`.\n * @param destination The downstream subscriber.\n * @param onNext Handles next values, only called if this subscriber is not stopped or closed. Any\n * error that occurs in this function is caught and sent to the `error` method of this subscriber.\n * @param onError Handles errors from the subscription, any errors that occur in this handler are caught\n * and send to the `destination` error handler.\n * @param onComplete Handles completion notification from the subscription. Any errors that occur in\n * this handler are sent to the `destination` error handler.\n * @param onFinalize Additional teardown logic here. This will only be called on teardown if the\n * subscriber itself is not already closed. This is called after all other teardown logic is executed.\n */\nexport function createOperatorSubscriber<T>(\n  destination: Subscriber<any>,\n  onNext?: (value: T) => void,\n  onComplete?: () => void,\n  onError?: (err: any) => void,\n  onFinalize?: () => void\n): Subscriber<T> {\n  return new OperatorSubscriber(destination, onNext, onComplete, onError, onFinalize);\n}\n\n/**\n * A generic helper for allowing operators to be created with a Subscriber and\n * use closures to capture necessary state from the operator function itself.\n */\nexport class OperatorSubscriber<T> extends Subscriber<T> {\n  /**\n   * Creates an instance of an `OperatorSubscriber`.\n   * @param destination The downstream subscriber.\n   * @param onNext Handles next values, only called if this subscriber is not stopped or closed. Any\n   * error that occurs in this function is caught and sent to the `error` method of this subscriber.\n   * @param onError Handles errors from the subscription, any errors that occur in this handler are caught\n   * and send to the `destination` error handler.\n   * @param onComplete Handles completion notification from the subscription. Any errors that occur in\n   * this handler are sent to the `destination` error handler.\n   * @param onFinalize Additional finalization logic here. This will only be called on finalization if the\n   * subscriber itself is not already closed. This is called after all other finalization logic is executed.\n   * @param shouldUnsubscribe An optional check to see if an unsubscribe call should truly unsubscribe.\n   * NOTE: This currently **ONLY** exists to support the strange behavior of {@link groupBy}, where unsubscription\n   * to the resulting observable does not actually disconnect from the source if there are active subscriptions\n   * to any grouped observable. (DO NOT EXPOSE OR USE EXTERNALLY!!!)\n   */\n  constructor(\n    destination: Subscriber<any>,\n    onNext?: (value: T) => void,\n    onComplete?: () => void,\n    onError?: (err: any) => void,\n    private onFinalize?: () => void,\n    private shouldUnsubscribe?: () => boolean\n  ) {\n    // It's important - for performance reasons - that all of this class's\n    // members are initialized and that they are always initialized in the same\n    // order. This will ensure that all OperatorSubscriber instances have the\n    // same hidden class in V8. This, in turn, will help keep the number of\n    // hidden classes involved in property accesses within the base class as\n    // low as possible. If the number of hidden classes involved exceeds four,\n    // the property accesses will become megamorphic and performance penalties\n    // will be incurred - i.e. inline caches won't be used.\n    //\n    // The reasons for ensuring all instances have the same hidden class are\n    // further discussed in this blog post from Benedikt Meurer:\n    // https://benediktmeurer.de/2018/03/23/impact-of-polymorphism-on-component-based-frameworks-like-react/\n    super(destination);\n    this._next = onNext\n      ? function (this: OperatorSubscriber<T>, value: T) {\n          try {\n            onNext(value);\n          } catch (err) {\n            destination.error(err);\n          }\n        }\n      : super._next;\n    this._error = onError\n      ? function (this: OperatorSubscriber<T>, err: any) {\n          try {\n            onError(err);\n          } catch (err) {\n            // Send any errors that occur down stream.\n            destination.error(err);\n          } finally {\n            // Ensure finalization.\n            this.unsubscribe();\n          }\n        }\n      : super._error;\n    this._complete = onComplete\n      ? function (this: OperatorSubscriber<T>) {\n          try {\n            onComplete();\n          } catch (err) {\n            // Send any errors that occur down stream.\n            destination.error(err);\n          } finally {\n            // Ensure finalization.\n            this.unsubscribe();\n          }\n        }\n      : super._complete;\n  }\n\n  unsubscribe() {\n    if (!this.shouldUnsubscribe || this.shouldUnsubscribe()) {\n      const { closed } = this;\n      super.unsubscribe();\n      // Execute additional teardown if we have any and we didn't already do so.\n      !closed && this.onFinalize?.();\n    }\n  }\n}\n", "import { Subscription } from '../Subscription';\n\ninterface AnimationFrameProvider {\n  schedule(callback: FrameRequestCallback): Subscription;\n  requestAnimationFrame: typeof requestAnimationFrame;\n  cancelAnimationFrame: typeof cancelAnimationFrame;\n  delegate:\n    | {\n        requestAnimationFrame: typeof requestAnimationFrame;\n        cancelAnimationFrame: typeof cancelAnimationFrame;\n      }\n    | undefined;\n}\n\nexport const animationFrameProvider: AnimationFrameProvider = {\n  // When accessing the delegate, use the variable rather than `this` so that\n  // the functions can be called without being bound to the provider.\n  schedule(callback) {\n    let request = requestAnimationFrame;\n    let cancel: typeof cancelAnimationFrame | undefined = cancelAnimationFrame;\n    const { delegate } = animationFrameProvider;\n    if (delegate) {\n      request = delegate.requestAnimationFrame;\n      cancel = delegate.cancelAnimationFrame;\n    }\n    const handle = request((timestamp) => {\n      // Clear the cancel function. The request has been fulfilled, so\n      // attempting to cancel the request upon unsubscription would be\n      // pointless.\n      cancel = undefined;\n      callback(timestamp);\n    });\n    return new Subscription(() => cancel?.(handle));\n  },\n  requestAnimationFrame(...args) {\n    const { delegate } = animationFrameProvider;\n    return (delegate?.requestAnimationFrame || requestAnimationFrame)(...args);\n  },\n  cancelAnimationFrame(...args) {\n    const { delegate } = animationFrameProvider;\n    return (delegate?.cancelAnimationFrame || cancelAnimationFrame)(...args);\n  },\n  delegate: undefined,\n};\n", "import { createErrorClass } from './createErrorClass';\n\nexport interface ObjectUnsubscribedError extends Error {}\n\nexport interface ObjectUnsubscribedErrorCtor {\n  /**\n   * @deprecated Internal implementation detail. Do not construct error instances.\n   * Cannot be tagged as internal: https://github.com/ReactiveX/rxjs/issues/6269\n   */\n  new (): ObjectUnsubscribedError;\n}\n\n/**\n * An error thrown when an action is invalid because the object has been\n * unsubscribed.\n *\n * @see {@link Subject}\n * @see {@link BehaviorSubject}\n *\n * @class ObjectUnsubscribedError\n */\nexport const ObjectUnsubscribedError: ObjectUnsubscribedErrorCtor = createErrorClass(\n  (_super) =>\n    function ObjectUnsubscribedErrorImpl(this: any) {\n      _super(this);\n      this.name = 'ObjectUnsubscribedError';\n      this.message = 'object unsubscribed';\n    }\n);\n", "import { Operator } from './Operator';\nimport { Observable } from './Observable';\nimport { Subscriber } from './Subscriber';\nimport { Subscription, EMPTY_SUBSCRIPTION } from './Subscription';\nimport { Observer, SubscriptionLike, TeardownLogic } from './types';\nimport { ObjectUnsubscribedError } from './util/ObjectUnsubscribedError';\nimport { arrRemove } from './util/arrRemove';\nimport { errorContext } from './util/errorContext';\n\n/**\n * A Subject is a special type of Observable that allows values to be\n * multicasted to many Observers. Subjects are like EventEmitters.\n *\n * Every Subject is an Observable and an Observer. You can subscribe to a\n * Subject, and you can call next to feed values as well as error and complete.\n */\nexport class Subject<T> extends Observable<T> implements SubscriptionLike {\n  closed = false;\n\n  private currentObservers: Observer<T>[] | null = null;\n\n  /** @deprecated Internal implementation detail, do not use directly. Will be made internal in v8. */\n  observers: Observer<T>[] = [];\n  /** @deprecated Internal implementation detail, do not use directly. Will be made internal in v8. */\n  isStopped = false;\n  /** @deprecated Internal implementation detail, do not use directly. Will be made internal in v8. */\n  hasError = false;\n  /** @deprecated Internal implementation detail, do not use directly. Will be made internal in v8. */\n  thrownError: any = null;\n\n  /**\n   * Creates a \"subject\" by basically gluing an observer to an observable.\n   *\n   * @deprecated Recommended you do not use. Will be removed at some point in the future. Plans for replacement still under discussion.\n   */\n  static create: (...args: any[]) => any = <T>(destination: Observer<T>, source: Observable<T>): AnonymousSubject<T> => {\n    return new AnonymousSubject<T>(destination, source);\n  };\n\n  constructor() {\n    // NOTE: This must be here to obscure Observable's constructor.\n    super();\n  }\n\n  /** @deprecated Internal implementation detail, do not use directly. Will be made internal in v8. */\n  lift<R>(operator: Operator<T, R>): Observable<R> {\n    const subject = new AnonymousSubject(this, this);\n    subject.operator = operator as any;\n    return subject as any;\n  }\n\n  /** @internal */\n  protected _throwIfClosed() {\n    if (this.closed) {\n      throw new ObjectUnsubscribedError();\n    }\n  }\n\n  next(value: T) {\n    errorContext(() => {\n      this._throwIfClosed();\n      if (!this.isStopped) {\n        if (!this.currentObservers) {\n          this.currentObservers = Array.from(this.observers);\n        }\n        for (const observer of this.currentObservers) {\n          observer.next(value);\n        }\n      }\n    });\n  }\n\n  error(err: any) {\n    errorContext(() => {\n      this._throwIfClosed();\n      if (!this.isStopped) {\n        this.hasError = this.isStopped = true;\n        this.thrownError = err;\n        const { observers } = this;\n        while (observers.length) {\n          observers.shift()!.error(err);\n        }\n      }\n    });\n  }\n\n  complete() {\n    errorContext(() => {\n      this._throwIfClosed();\n      if (!this.isStopped) {\n        this.isStopped = true;\n        const { observers } = this;\n        while (observers.length) {\n          observers.shift()!.complete();\n        }\n      }\n    });\n  }\n\n  unsubscribe() {\n    this.isStopped = this.closed = true;\n    this.observers = this.currentObservers = null!;\n  }\n\n  get observed() {\n    return this.observers?.length > 0;\n  }\n\n  /** @internal */\n  protected _trySubscribe(subscriber: Subscriber<T>): TeardownLogic {\n    this._throwIfClosed();\n    return super._trySubscribe(subscriber);\n  }\n\n  /** @internal */\n  protected _subscribe(subscriber: Subscriber<T>): Subscription {\n    this._throwIfClosed();\n    this._checkFinalizedStatuses(subscriber);\n    return this._innerSubscribe(subscriber);\n  }\n\n  /** @internal */\n  protected _innerSubscribe(subscriber: Subscriber<any>) {\n    const { hasError, isStopped, observers } = this;\n    if (hasError || isStopped) {\n      return EMPTY_SUBSCRIPTION;\n    }\n    this.currentObservers = null;\n    observers.push(subscriber);\n    return new Subscription(() => {\n      this.currentObservers = null;\n      arrRemove(observers, subscriber);\n    });\n  }\n\n  /** @internal */\n  protected _checkFinalizedStatuses(subscriber: Subscriber<any>) {\n    const { hasError, thrownError, isStopped } = this;\n    if (hasError) {\n      subscriber.error(thrownError);\n    } else if (isStopped) {\n      subscriber.complete();\n    }\n  }\n\n  /**\n   * Creates a new Observable with this Subject as the source. You can do this\n   * to create custom Observer-side logic of the Subject and conceal it from\n   * code that uses the Observable.\n   * @return Observable that this Subject casts to.\n   */\n  asObservable(): Observable<T> {\n    const observable: any = new Observable<T>();\n    observable.source = this;\n    return observable;\n  }\n}\n\nexport class AnonymousSubject<T> extends Subject<T> {\n  constructor(\n    /** @deprecated Internal implementation detail, do not use directly. Will be made internal in v8. */\n    public destination?: Observer<T>,\n    source?: Observable<T>\n  ) {\n    super();\n    this.source = source;\n  }\n\n  next(value: T) {\n    this.destination?.next?.(value);\n  }\n\n  error(err: any) {\n    this.destination?.error?.(err);\n  }\n\n  complete() {\n    this.destination?.complete?.();\n  }\n\n  /** @internal */\n  protected _subscribe(subscriber: Subscriber<T>): Subscription {\n    return this.source?.subscribe(subscriber) ?? EMPTY_SUBSCRIPTION;\n  }\n}\n", "import { Subject } from './Subject';\nimport { Subscriber } from './Subscriber';\nimport { Subscription } from './Subscription';\n\n/**\n * A variant of Subject that requires an initial value and emits its current\n * value whenever it is subscribed to.\n */\nexport class BehaviorSubject<T> extends Subject<T> {\n  constructor(private _value: T) {\n    super();\n  }\n\n  get value(): T {\n    return this.getValue();\n  }\n\n  /** @internal */\n  protected _subscribe(subscriber: Subscriber<T>): Subscription {\n    const subscription = super._subscribe(subscriber);\n    !subscription.closed && subscriber.next(this._value);\n    return subscription;\n  }\n\n  getValue(): T {\n    const { hasError, thrownError, _value } = this;\n    if (hasError) {\n      throw thrownError;\n    }\n    this._throwIfClosed();\n    return _value;\n  }\n\n  next(value: T): void {\n    super.next((this._value = value));\n  }\n}\n", "import { TimestampProvider } from '../types';\n\ninterface DateTimestampProvider extends TimestampProvider {\n  delegate: TimestampProvider | undefined;\n}\n\nexport const dateTimestampProvider: DateTimestampProvider = {\n  now() {\n    // Use the variable rather than `this` so that the function can be called\n    // without being bound to the provider.\n    return (dateTimestampProvider.delegate || Date).now();\n  },\n  delegate: undefined,\n};\n", "import { Subject } from './Subject';\nimport { TimestampProvider } from './types';\nimport { Subscriber } from './Subscriber';\nimport { Subscription } from './Subscription';\nimport { dateTimestampProvider } from './scheduler/dateTimestampProvider';\n\n/**\n * A variant of {@link Subject} that \"replays\" old values to new subscribers by emitting them when they first subscribe.\n *\n * `ReplaySubject` has an internal buffer that will store a specified number of values that it has observed. Like `Subject`,\n * `ReplaySubject` \"observes\" values by having them passed to its `next` method. When it observes a value, it will store that\n * value for a time determined by the configuration of the `ReplaySubject`, as passed to its constructor.\n *\n * When a new subscriber subscribes to the `ReplaySubject` instance, it will synchronously emit all values in its buffer in\n * a First-In-First-Out (FIFO) manner. The `ReplaySubject` will also complete, if it has observed completion; and it will\n * error if it has observed an error.\n *\n * There are two main configuration items to be concerned with:\n *\n * 1. `bufferSize` - This will determine how many items are stored in the buffer, defaults to infinite.\n * 2. `windowTime` - The amount of time to hold a value in the buffer before removing it from the buffer.\n *\n * Both configurations may exist simultaneously. So if you would like to buffer a maximum of 3 values, as long as the values\n * are less than 2 seconds old, you could do so with a `new ReplaySubject(3, 2000)`.\n *\n * ### Differences with BehaviorSubject\n *\n * `BehaviorSubject` is similar to `new ReplaySubject(1)`, with a couple of exceptions:\n *\n * 1. `BehaviorSubject` comes \"primed\" with a single value upon construction.\n * 2. `ReplaySubject` will replay values, even after observing an error, where `BehaviorSubject` will not.\n *\n * @see {@link Subject}\n * @see {@link BehaviorSubject}\n * @see {@link shareReplay}\n */\nexport class ReplaySubject<T> extends Subject<T> {\n  private _buffer: (T | number)[] = [];\n  private _infiniteTimeWindow = true;\n\n  /**\n   * @param _bufferSize The size of the buffer to replay on subscription\n   * @param _windowTime The amount of time the buffered items will stay buffered\n   * @param _timestampProvider An object with a `now()` method that provides the current timestamp. This is used to\n   * calculate the amount of time something has been buffered.\n   */\n  constructor(\n    private _bufferSize = Infinity,\n    private _windowTime = Infinity,\n    private _timestampProvider: TimestampProvider = dateTimestampProvider\n  ) {\n    super();\n    this._infiniteTimeWindow = _windowTime === Infinity;\n    this._bufferSize = Math.max(1, _bufferSize);\n    this._windowTime = Math.max(1, _windowTime);\n  }\n\n  next(value: T): void {\n    const { isStopped, _buffer, _infiniteTimeWindow, _timestampProvider, _windowTime } = this;\n    if (!isStopped) {\n      _buffer.push(value);\n      !_infiniteTimeWindow && _buffer.push(_timestampProvider.now() + _windowTime);\n    }\n    this._trimBuffer();\n    super.next(value);\n  }\n\n  /** @internal */\n  protected _subscribe(subscriber: Subscriber<T>): Subscription {\n    this._throwIfClosed();\n    this._trimBuffer();\n\n    const subscription = this._innerSubscribe(subscriber);\n\n    const { _infiniteTimeWindow, _buffer } = this;\n    // We use a copy here, so reentrant code does not mutate our array while we're\n    // emitting it to a new subscriber.\n    const copy = _buffer.slice();\n    for (let i = 0; i < copy.length && !subscriber.closed; i += _infiniteTimeWindow ? 1 : 2) {\n      subscriber.next(copy[i] as T);\n    }\n\n    this._checkFinalizedStatuses(subscriber);\n\n    return subscription;\n  }\n\n  private _trimBuffer() {\n    const { _bufferSize, _timestampProvider, _buffer, _infiniteTimeWindow } = this;\n    // If we don't have an infinite buffer size, and we're over the length,\n    // use splice to truncate the old buffer values off. Note that we have to\n    // double the size for instances where we're not using an infinite time window\n    // because we're storing the values and the timestamps in the same array.\n    const adjustedBufferSize = (_infiniteTimeWindow ? 1 : 2) * _bufferSize;\n    _bufferSize < Infinity && adjustedBufferSize < _buffer.length && _buffer.splice(0, _buffer.length - adjustedBufferSize);\n\n    // Now, if we're not in an infinite time window, remove all values where the time is\n    // older than what is allowed.\n    if (!_infiniteTimeWindow) {\n      const now = _timestampProvider.now();\n      let last = 0;\n      // Search the array for the first timestamp that isn't expired and\n      // truncate the buffer up to that point.\n      for (let i = 1; i < _buffer.length && (_buffer[i] as number) <= now; i += 2) {\n        last = i;\n      }\n      last && _buffer.splice(0, last + 1);\n    }\n  }\n}\n", "import { Scheduler } from '../Scheduler';\nimport { Subscription } from '../Subscription';\nimport { SchedulerAction } from '../types';\n\n/**\n * A unit of work to be executed in a `scheduler`. An action is typically\n * created from within a {@link SchedulerLike} and an RxJS user does not need to concern\n * themselves about creating and manipulating an Action.\n *\n * ```ts\n * class Action<T> extends Subscription {\n *   new (scheduler: Scheduler, work: (state?: T) => void);\n *   schedule(state?: T, delay: number = 0): Subscription;\n * }\n * ```\n */\nexport class Action<T> extends Subscription {\n  constructor(scheduler: Scheduler, work: (this: SchedulerAction<T>, state?: T) => void) {\n    super();\n  }\n  /**\n   * Schedules this action on its parent {@link SchedulerLike} for execution. May be passed\n   * some context object, `state`. May happen at some point in the future,\n   * according to the `delay` parameter, if specified.\n   * @param state Some contextual data that the `work` function uses when called by the\n   * Scheduler.\n   * @param delay Time to wait before executing the work, where the time unit is implicit\n   * and defined by the Scheduler.\n   * @return A subscription in order to be able to unsubscribe the scheduled work.\n   */\n  public schedule(state?: T, delay: number = 0): Subscription {\n    return this;\n  }\n}\n", "import type { TimerHandle } from './timerHandle';\ntype SetIntervalFunction = (handler: () => void, timeout?: number, ...args: any[]) => TimerHandle;\ntype ClearIntervalFunction = (handle: TimerHandle) => void;\n\ninterface IntervalProvider {\n  setInterval: SetIntervalFunction;\n  clearInterval: ClearIntervalFunction;\n  delegate:\n    | {\n        setInterval: SetIntervalFunction;\n        clearInterval: ClearIntervalFunction;\n      }\n    | undefined;\n}\n\nexport const intervalProvider: IntervalProvider = {\n  // When accessing the delegate, use the variable rather than `this` so that\n  // the functions can be called without being bound to the provider.\n  setInterval(handler: () => void, timeout?: number, ...args) {\n    const { delegate } = intervalProvider;\n    if (delegate?.setInterval) {\n      return delegate.setInterval(handler, timeout, ...args);\n    }\n    return setInterval(handler, timeout, ...args);\n  },\n  clearInterval(handle) {\n    const { delegate } = intervalProvider;\n    return (delegate?.clearInterval || clearInterval)(handle as any);\n  },\n  delegate: undefined,\n};\n", "import { Action } from './Action';\nimport { SchedulerAction } from '../types';\nimport { Subscription } from '../Subscription';\nimport { AsyncScheduler } from './AsyncScheduler';\nimport { intervalProvider } from './intervalProvider';\nimport { arrRemove } from '../util/arrRemove';\nimport { TimerHandle } from './timerHandle';\n\nexport class AsyncAction<T> extends Action<T> {\n  public id: TimerHandle | undefined;\n  public state?: T;\n  // @ts-ignore: Property has no initializer and is not definitely assigned\n  public delay: number;\n  protected pending: boolean = false;\n\n  constructor(protected scheduler: AsyncScheduler, protected work: (this: SchedulerAction<T>, state?: T) => void) {\n    super(scheduler, work);\n  }\n\n  public schedule(state?: T, delay: number = 0): Subscription {\n    if (this.closed) {\n      return this;\n    }\n\n    // Always replace the current state with the new state.\n    this.state = state;\n\n    const id = this.id;\n    const scheduler = this.scheduler;\n\n    //\n    // Important implementation note:\n    //\n    // Actions only execute once by default, unless rescheduled from within the\n    // scheduled callback. This allows us to implement single and repeat\n    // actions via the same code path, without adding API surface area, as well\n    // as mimic traditional recursion but across asynchronous boundaries.\n    //\n    // However, JS runtimes and timers distinguish between intervals achieved by\n    // serial `setTimeout` calls vs. a single `setInterval` call. An interval of\n    // serial `setTimeout` calls can be individually delayed, which delays\n    // scheduling the next `setTimeout`, and so on. `setInterval` attempts to\n    // guarantee the interval callback will be invoked more precisely to the\n    // interval period, regardless of load.\n    //\n    // Therefore, we use `setInterval` to schedule single and repeat actions.\n    // If the action reschedules itself with the same delay, the interval is not\n    // canceled. If the action doesn't reschedule, or reschedules with a\n    // different delay, the interval will be canceled after scheduled callback\n    // execution.\n    //\n    if (id != null) {\n      this.id = this.recycleAsyncId(scheduler, id, delay);\n    }\n\n    // Set the pending flag indicating that this action has been scheduled, or\n    // has recursively rescheduled itself.\n    this.pending = true;\n\n    this.delay = delay;\n    // If this action has already an async Id, don't request a new one.\n    this.id = this.id ?? this.requestAsyncId(scheduler, this.id, delay);\n\n    return this;\n  }\n\n  protected requestAsyncId(scheduler: AsyncScheduler, _id?: TimerHandle, delay: number = 0): TimerHandle {\n    return intervalProvider.setInterval(scheduler.flush.bind(scheduler, this), delay);\n  }\n\n  protected recycleAsyncId(_scheduler: AsyncScheduler, id?: TimerHandle, delay: number | null = 0): TimerHandle | undefined {\n    // If this action is rescheduled with the same delay time, don't clear the interval id.\n    if (delay != null && this.delay === delay && this.pending === false) {\n      return id;\n    }\n    // Otherwise, if the action's delay time is different from the current delay,\n    // or the action has been rescheduled before it's executed, clear the interval id\n    if (id != null) {\n      intervalProvider.clearInterval(id);\n    }\n\n    return undefined;\n  }\n\n  /**\n   * Immediately executes this action and the `work` it contains.\n   */\n  public execute(state: T, delay: number): any {\n    if (this.closed) {\n      return new Error('executing a cancelled action');\n    }\n\n    this.pending = false;\n    const error = this._execute(state, delay);\n    if (error) {\n      return error;\n    } else if (this.pending === false && this.id != null) {\n      // Dequeue if the action didn't reschedule itself. Don't call\n      // unsubscribe(), because the action could reschedule later.\n      // For example:\n      // ```\n      // scheduler.schedule(function doWork(counter) {\n      //   /* ... I'm a busy worker bee ... */\n      //   var originalAction = this;\n      //   /* wait 100ms before rescheduling the action */\n      //   setTimeout(function () {\n      //     originalAction.schedule(counter + 1);\n      //   }, 100);\n      // }, 1000);\n      // ```\n      this.id = this.recycleAsyncId(this.scheduler, this.id, null);\n    }\n  }\n\n  protected _execute(state: T, _delay: number): any {\n    let errored: boolean = false;\n    let errorValue: any;\n    try {\n      this.work(state);\n    } catch (e) {\n      errored = true;\n      // HACK: Since code elsewhere is relying on the \"truthiness\" of the\n      // return here, we can't have it return \"\" or 0 or false.\n      // TODO: Clean this up when we refactor schedulers mid-version-8 or so.\n      errorValue = e ? e : new Error('Scheduled action threw falsy error');\n    }\n    if (errored) {\n      this.unsubscribe();\n      return errorValue;\n    }\n  }\n\n  unsubscribe() {\n    if (!this.closed) {\n      const { id, scheduler } = this;\n      const { actions } = scheduler;\n\n      this.work = this.state = this.scheduler = null!;\n      this.pending = false;\n\n      arrRemove(actions, this);\n      if (id != null) {\n        this.id = this.recycleAsyncId(scheduler, id, null);\n      }\n\n      this.delay = null!;\n      super.unsubscribe();\n    }\n  }\n}\n", "import { Action } from './scheduler/Action';\nimport { Subscription } from './Subscription';\nimport { SchedulerLike, SchedulerAction } from './types';\nimport { dateTimestampProvider } from './scheduler/dateTimestampProvider';\n\n/**\n * An execution context and a data structure to order tasks and schedule their\n * execution. Provides a notion of (potentially virtual) time, through the\n * `now()` getter method.\n *\n * Each unit of work in a Scheduler is called an `Action`.\n *\n * ```ts\n * class Scheduler {\n *   now(): number;\n *   schedule(work, delay?, state?): Subscription;\n * }\n * ```\n *\n * @deprecated Scheduler is an internal implementation detail of RxJS, and\n * should not be used directly. Rather, create your own class and implement\n * {@link SchedulerLike}. Will be made internal in v8.\n */\nexport class Scheduler implements SchedulerLike {\n  public static now: () => number = dateTimestampProvider.now;\n\n  constructor(private schedulerActionCtor: typeof Action, now: () => number = Scheduler.now) {\n    this.now = now;\n  }\n\n  /**\n   * A getter method that returns a number representing the current time\n   * (at the time this function was called) according to the scheduler's own\n   * internal clock.\n   * @return A number that represents the current time. May or may not\n   * have a relation to wall-clock time. May or may not refer to a time unit\n   * (e.g. milliseconds).\n   */\n  public now: () => number;\n\n  /**\n   * Schedules a function, `work`, for execution. May happen at some point in\n   * the future, according to the `delay` parameter, if specified. May be passed\n   * some context object, `state`, which will be passed to the `work` function.\n   *\n   * The given arguments will be processed an stored as an Action object in a\n   * queue of actions.\n   *\n   * @param work A function representing a task, or some unit of work to be\n   * executed by the Scheduler.\n   * @param delay Time to wait before executing the work, where the time unit is\n   * implicit and defined by the Scheduler itself.\n   * @param state Some contextual data that the `work` function uses when called\n   * by the Scheduler.\n   * @return A subscription in order to be able to unsubscribe the scheduled work.\n   */\n  public schedule<T>(work: (this: SchedulerAction<T>, state?: T) => void, delay: number = 0, state?: T): Subscription {\n    return new this.schedulerActionCtor<T>(this, work).schedule(state, delay);\n  }\n}\n", "import { Scheduler } from '../Scheduler';\nimport { Action } from './Action';\nimport { AsyncAction } from './AsyncAction';\nimport { TimerHandle } from './timerHandle';\n\nexport class AsyncScheduler extends Scheduler {\n  public actions: Array<AsyncAction<any>> = [];\n  /**\n   * A flag to indicate whether the Scheduler is currently executing a batch of\n   * queued actions.\n   * @internal\n   */\n  public _active: boolean = false;\n  /**\n   * An internal ID used to track the latest asynchronous task such as those\n   * coming from `setTimeout`, `setInterval`, `requestAnimationFrame`, and\n   * others.\n   * @internal\n   */\n  public _scheduled: TimerHandle | undefined;\n\n  constructor(SchedulerAction: typeof Action, now: () => number = Scheduler.now) {\n    super(SchedulerAction, now);\n  }\n\n  public flush(action: AsyncAction<any>): void {\n    const { actions } = this;\n\n    if (this._active) {\n      actions.push(action);\n      return;\n    }\n\n    let error: any;\n    this._active = true;\n\n    do {\n      if ((error = action.execute(action.state, action.delay))) {\n        break;\n      }\n    } while ((action = actions.shift()!)); // exhaust the scheduler queue\n\n    this._active = false;\n\n    if (error) {\n      while ((action = actions.shift()!)) {\n        action.unsubscribe();\n      }\n      throw error;\n    }\n  }\n}\n", "import { AsyncAction } from './AsyncAction';\nimport { AsyncScheduler } from './AsyncScheduler';\n\n/**\n *\n * Async Scheduler\n *\n * <span class=\"informal\">Schedule task as if you used setTimeout(task, duration)</span>\n *\n * `async` scheduler schedules tasks asynchronously, by putting them on the JavaScript\n * event loop queue. It is best used to delay tasks in time or to schedule tasks repeating\n * in intervals.\n *\n * If you just want to \"defer\" task, that is to perform it right after currently\n * executing synchronous code ends (commonly achieved by `setTimeout(deferredTask, 0)`),\n * better choice will be the {@link asapScheduler} scheduler.\n *\n * ## Examples\n * Use async scheduler to delay task\n * ```ts\n * import { asyncScheduler } from 'rxjs';\n *\n * const task = () => console.log('it works!');\n *\n * asyncScheduler.schedule(task, 2000);\n *\n * // After 2 seconds logs:\n * // \"it works!\"\n * ```\n *\n * Use async scheduler to repeat task in intervals\n * ```ts\n * import { asyncScheduler } from 'rxjs';\n *\n * function task(state) {\n *   console.log(state);\n *   this.schedule(state + 1, 1000); // `this` references currently executing Action,\n *                                   // which we reschedule with new state and delay\n * }\n *\n * asyncScheduler.schedule(task, 3000, 0);\n *\n * // Logs:\n * // 0 after 3s\n * // 1 after 4s\n * // 2 after 5s\n * // 3 after 6s\n * ```\n */\n\nexport const asyncScheduler = new AsyncScheduler(AsyncAction);\n\n/**\n * @deprecated Renamed to {@link asyncScheduler}. Will be removed in v8.\n */\nexport const async = asyncScheduler;\n", "import { AsyncAction } from './AsyncAction';\nimport { Subscription } from '../Subscription';\nimport { QueueScheduler } from './QueueScheduler';\nimport { SchedulerAction } from '../types';\nimport { TimerHandle } from './timerHandle';\n\nexport class QueueAction<T> extends AsyncAction<T> {\n  constructor(protected scheduler: QueueScheduler, protected work: (this: SchedulerAction<T>, state?: T) => void) {\n    super(scheduler, work);\n  }\n\n  public schedule(state?: T, delay: number = 0): Subscription {\n    if (delay > 0) {\n      return super.schedule(state, delay);\n    }\n    this.delay = delay;\n    this.state = state;\n    this.scheduler.flush(this);\n    return this;\n  }\n\n  public execute(state: T, delay: number): any {\n    return delay > 0 || this.closed ? super.execute(state, delay) : this._execute(state, delay);\n  }\n\n  protected requestAsyncId(scheduler: QueueScheduler, id?: TimerHandle, delay: number = 0): TimerHandle {\n    // If delay exists and is greater than 0, or if the delay is null (the\n    // action wasn't rescheduled) but was originally scheduled as an async\n    // action, then recycle as an async action.\n\n    if ((delay != null && delay > 0) || (delay == null && this.delay > 0)) {\n      return super.requestAsyncId(scheduler, id, delay);\n    }\n\n    // Otherwise flush the scheduler starting with this action.\n    scheduler.flush(this);\n\n    // HACK: In the past, this was returning `void`. However, `void` isn't a valid\n    // `TimerHandle`, and generally the return value here isn't really used. So the\n    // compromise is to return `0` which is both \"falsy\" and a valid `TimerHandle`,\n    // as opposed to refactoring every other instanceo of `requestAsyncId`.\n    return 0;\n  }\n}\n", "import { AsyncScheduler } from './AsyncScheduler';\n\nexport class QueueScheduler extends AsyncScheduler {\n}\n", "import { QueueAction } from './QueueAction';\nimport { QueueScheduler } from './QueueScheduler';\n\n/**\n *\n * Queue Scheduler\n *\n * <span class=\"informal\">Put every next task on a queue, instead of executing it immediately</span>\n *\n * `queue` scheduler, when used with delay, behaves the same as {@link asyncScheduler} scheduler.\n *\n * When used without delay, it schedules given task synchronously - executes it right when\n * it is scheduled. However when called recursively, that is when inside the scheduled task,\n * another task is scheduled with queue scheduler, instead of executing immediately as well,\n * that task will be put on a queue and wait for current one to finish.\n *\n * This means that when you execute task with `queue` scheduler, you are sure it will end\n * before any other task scheduled with that scheduler will start.\n *\n * ## Examples\n * Schedule recursively first, then do something\n * ```ts\n * import { queueScheduler } from 'rxjs';\n *\n * queueScheduler.schedule(() => {\n *   queueScheduler.schedule(() => console.log('second')); // will not happen now, but will be put on a queue\n *\n *   console.log('first');\n * });\n *\n * // Logs:\n * // \"first\"\n * // \"second\"\n * ```\n *\n * Reschedule itself recursively\n * ```ts\n * import { queueScheduler } from 'rxjs';\n *\n * queueScheduler.schedule(function(state) {\n *   if (state !== 0) {\n *     console.log('before', state);\n *     this.schedule(state - 1); // `this` references currently executing Action,\n *                               // which we reschedule with new state\n *     console.log('after', state);\n *   }\n * }, 0, 3);\n *\n * // In scheduler that runs recursively, you would expect:\n * // \"before\", 3\n * // \"before\", 2\n * // \"before\", 1\n * // \"after\", 1\n * // \"after\", 2\n * // \"after\", 3\n *\n * // But with queue it logs:\n * // \"before\", 3\n * // \"after\", 3\n * // \"before\", 2\n * // \"after\", 2\n * // \"before\", 1\n * // \"after\", 1\n * ```\n */\n\nexport const queueScheduler = new QueueScheduler(QueueAction);\n\n/**\n * @deprecated Renamed to {@link queueScheduler}. Will be removed in v8.\n */\nexport const queue = queueScheduler;\n", "import { AsyncAction } from './AsyncAction';\nimport { AnimationFrameScheduler } from './AnimationFrameScheduler';\nimport { SchedulerAction } from '../types';\nimport { animationFrameProvider } from './animationFrameProvider';\nimport { TimerHandle } from './timerHandle';\n\nexport class AnimationFrameAction<T> extends AsyncAction<T> {\n  constructor(protected scheduler: AnimationFrameScheduler, protected work: (this: SchedulerAction<T>, state?: T) => void) {\n    super(scheduler, work);\n  }\n\n  protected requestAsyncId(scheduler: AnimationFrameScheduler, id?: TimerHandle, delay: number = 0): TimerHandle {\n    // If delay is greater than 0, request as an async action.\n    if (delay !== null && delay > 0) {\n      return super.requestAsyncId(scheduler, id, delay);\n    }\n    // Push the action to the end of the scheduler queue.\n    scheduler.actions.push(this);\n    // If an animation frame has already been requested, don't request another\n    // one. If an animation frame hasn't been requested yet, request one. Return\n    // the current animation frame request id.\n    return scheduler._scheduled || (scheduler._scheduled = animationFrameProvider.requestAnimationFrame(() => scheduler.flush(undefined)));\n  }\n\n  protected recycleAsyncId(scheduler: AnimationFrameScheduler, id?: TimerHandle, delay: number = 0): TimerHandle | undefined {\n    // If delay exists and is greater than 0, or if the delay is null (the\n    // action wasn't rescheduled) but was originally scheduled as an async\n    // action, then recycle as an async action.\n    if (delay != null ? delay > 0 : this.delay > 0) {\n      return super.recycleAsyncId(scheduler, id, delay);\n    }\n    // If the scheduler queue has no remaining actions with the same async id,\n    // cancel the requested animation frame and set the scheduled flag to\n    // undefined so the next AnimationFrameAction will request its own.\n    const { actions } = scheduler;\n    if (id != null && id === scheduler._scheduled && actions[actions.length - 1]?.id !== id) {\n      animationFrameProvider.cancelAnimationFrame(id as number);\n      scheduler._scheduled = undefined;\n    }\n    // Return undefined so the action knows to request a new async id if it's rescheduled.\n    return undefined;\n  }\n}\n", "import { AsyncAction } from './AsyncAction';\nimport { AsyncScheduler } from './AsyncScheduler';\n\nexport class AnimationFrameScheduler extends AsyncScheduler {\n  public flush(action?: AsyncAction<any>): void {\n    this._active = true;\n    // The async id that effects a call to flush is stored in _scheduled.\n    // Before executing an action, it's necessary to check the action's async\n    // id to determine whether it's supposed to be executed in the current\n    // flush.\n    // Previous implementations of this method used a count to determine this,\n    // but that was unsound, as actions that are unsubscribed - i.e. cancelled -\n    // are removed from the actions array and that can shift actions that are\n    // scheduled to be executed in a subsequent flush into positions at which\n    // they are executed within the current flush.\n    let flushId;\n    if (action) {\n      flushId = action.id;\n    } else {\n      flushId = this._scheduled;\n      this._scheduled = undefined;\n    }\n\n    const { actions } = this;\n    let error: any;\n    action = action || actions.shift()!;\n\n    do {\n      if ((error = action.execute(action.state, action.delay))) {\n        break;\n      }\n    } while ((action = actions[0]) && action.id === flushId && actions.shift());\n\n    this._active = false;\n\n    if (error) {\n      while ((action = actions[0]) && action.id === flushId && actions.shift()) {\n        action.unsubscribe();\n      }\n      throw error;\n    }\n  }\n}\n", "import { AnimationFrameAction } from './AnimationFrameAction';\nimport { AnimationFrameScheduler } from './AnimationFrameScheduler';\n\n/**\n *\n * Animation Frame Scheduler\n *\n * <span class=\"informal\">Perform task when `window.requestAnimationFrame` would fire</span>\n *\n * When `animationFrame` scheduler is used with delay, it will fall back to {@link asyncScheduler} scheduler\n * behaviour.\n *\n * Without delay, `animationFrame` scheduler can be used to create smooth browser animations.\n * It makes sure scheduled task will happen just before next browser content repaint,\n * thus performing animations as efficiently as possible.\n *\n * ## Example\n * Schedule div height animation\n * ```ts\n * // html: <div style=\"background: #0ff;\"></div>\n * import { animationFrameScheduler } from 'rxjs';\n *\n * const div = document.querySelector('div');\n *\n * animationFrameScheduler.schedule(function(height) {\n *   div.style.height = height + \"px\";\n *\n *   this.schedule(height + 1);  // `this` references currently executing Action,\n *                               // which we reschedule with new state\n * }, 0, 0);\n *\n * // You will see a div element growing in height\n * ```\n */\n\nexport const animationFrameScheduler = new AnimationFrameScheduler(AnimationFrameAction);\n\n/**\n * @deprecated Renamed to {@link animationFrameScheduler}. Will be removed in v8.\n */\nexport const animationFrame = animationFrameScheduler;\n", "import { Observable } from '../Observable';\nimport { SchedulerLike } from '../types';\n\n/**\n * A simple Observable that emits no items to the Observer and immediately\n * emits a complete notification.\n *\n * <span class=\"informal\">Just emits 'complete', and nothing else.</span>\n *\n * ![](empty.png)\n *\n * A simple Observable that only emits the complete notification. It can be used\n * for composing with other Observables, such as in a {@link mergeMap}.\n *\n * ## Examples\n *\n * Log complete notification\n *\n * ```ts\n * import { EMPTY } from 'rxjs';\n *\n * EMPTY.subscribe({\n *   next: () => console.log('Next'),\n *   complete: () => console.log('Complete!')\n * });\n *\n * // Outputs\n * // Complete!\n * ```\n *\n * Emit the number 7, then complete\n *\n * ```ts\n * import { EMPTY, startWith } from 'rxjs';\n *\n * const result = EMPTY.pipe(startWith(7));\n * result.subscribe(x => console.log(x));\n *\n * // Outputs\n * // 7\n * ```\n *\n * Map and flatten only odd numbers to the sequence `'a'`, `'b'`, `'c'`\n *\n * ```ts\n * import { interval, mergeMap, of, EMPTY } from 'rxjs';\n *\n * const interval$ = interval(1000);\n * const result = interval$.pipe(\n *   mergeMap(x => x % 2 === 1 ? of('a', 'b', 'c') : EMPTY),\n * );\n * result.subscribe(x => console.log(x));\n *\n * // Results in the following to the console:\n * // x is equal to the count on the interval, e.g. (0, 1, 2, 3, ...)\n * // x will occur every 1000ms\n * // if x % 2 is equal to 1, print a, b, c (each on its own)\n * // if x % 2 is not equal to 1, nothing will be output\n * ```\n *\n * @see {@link Observable}\n * @see {@link NEVER}\n * @see {@link of}\n * @see {@link throwError}\n */\nexport const EMPTY = new Observable<never>((subscriber) => subscriber.complete());\n\n/**\n * @param scheduler A {@link SchedulerLike} to use for scheduling\n * the emission of the complete notification.\n * @deprecated Replaced with the {@link EMPTY} constant or {@link scheduled} (e.g. `scheduled([], scheduler)`). Will be removed in v8.\n */\nexport function empty(scheduler?: SchedulerLike) {\n  return scheduler ? emptyScheduled(scheduler) : EMPTY;\n}\n\nfunction emptyScheduled(scheduler: SchedulerLike) {\n  return new Observable<never>((subscriber) => scheduler.schedule(() => subscriber.complete()));\n}\n", "import { SchedulerLike } from '../types';\nimport { isFunction } from './isFunction';\n\nexport function isScheduler(value: any): value is SchedulerLike {\n  return value && isFunction(value.schedule);\n}\n", "import { SchedulerLike } from '../types';\nimport { isFunction } from './isFunction';\nimport { isScheduler } from './isScheduler';\n\nfunction last<T>(arr: T[]): T | undefined {\n  return arr[arr.length - 1];\n}\n\nexport function popResultSelector(args: any[]): ((...args: unknown[]) => unknown) | undefined {\n  return isFunction(last(args)) ? args.pop() : undefined;\n}\n\nexport function popScheduler(args: any[]): SchedulerLike | undefined {\n  return isScheduler(last(args)) ? args.pop() : undefined;\n}\n\nexport function popNumber(args: any[], defaultValue: number): number {\n  return typeof last(args) === 'number' ? args.pop()! : defaultValue;\n}\n", "export const isArrayLike = (<T>(x: any): x is ArrayLike<T> => x && typeof x.length === 'number' && typeof x !== 'function');", "import { isFunction } from \"./isFunction\";\n\n/**\n * Tests to see if the object is \"thennable\".\n * @param value the object to test\n */\nexport function isPromise(value: any): value is PromiseLike<any> {\n  return isFunction(value?.then);\n}\n", "import { InteropObservable } from '../types';\nimport { observable as Symbol_observable } from '../symbol/observable';\nimport { isFunction } from './isFunction';\n\n/** Identifies an input as being Observable (but not necessary an Rx Observable) */\nexport function isInteropObservable(input: any): input is InteropObservable<any> {\n  return isFunction(input[Symbol_observable]);\n}\n", "import { isFunction } from './isFunction';\n\nexport function isAsyncIterable<T>(obj: any): obj is AsyncIterable<T> {\n  return Symbol.asyncIterator && isFunction(obj?.[Symbol.asyncIterator]);\n}\n", "/**\n * Creates the TypeError to throw if an invalid object is passed to `from` or `scheduled`.\n * @param input The object that was passed.\n */\nexport function createInvalidObservableTypeError(input: any) {\n  // TODO: We should create error codes that can be looked up, so this can be less verbose.\n  return new TypeError(\n    `You provided ${\n      input !== null && typeof input === 'object' ? 'an invalid object' : `'${input}'`\n    } where a stream was expected. You can provide an Observable, Promise, ReadableStream, Array, AsyncIterable, or Iterable.`\n  );\n}\n", "export function getSymbolIterator(): symbol {\n  if (typeof Symbol !== 'function' || !Symbol.iterator) {\n    return '@@iterator' as any;\n  }\n\n  return Symbol.iterator;\n}\n\nexport const iterator = getSymbolIterator();\n", "import { iterator as Symbol_iterator } from '../symbol/iterator';\nimport { isFunction } from './isFunction';\n\n/** Identifies an input as being an Iterable */\nexport function isIterable(input: any): input is Iterable<any> {\n  return isFunction(input?.[Symbol_iterator]);\n}\n", "import { ReadableStreamLike } from '../types';\nimport { isFunction } from './isFunction';\n\nexport async function* readableStreamLikeToAsyncGenerator<T>(readableStream: ReadableStreamLike<T>): AsyncGenerator<T> {\n  const reader = readableStream.getReader();\n  try {\n    while (true) {\n      const { value, done } = await reader.read();\n      if (done) {\n        return;\n      }\n      yield value!;\n    }\n  } finally {\n    reader.releaseLock();\n  }\n}\n\nexport function isReadableStreamLike<T>(obj: any): obj is ReadableStreamLike<T> {\n  // We don't want to use instanceof checks because they would return\n  // false for instances from another Realm, like an <iframe>.\n  return isFunction(obj?.getReader);\n}\n", "import { isArrayLike } from '../util/isArrayLike';\nimport { isPromise } from '../util/isPromise';\nimport { Observable } from '../Observable';\nimport { ObservableInput, ObservedValueOf, ReadableStreamLike } from '../types';\nimport { isInteropObservable } from '../util/isInteropObservable';\nimport { isAsyncIterable } from '../util/isAsyncIterable';\nimport { createInvalidObservableTypeError } from '../util/throwUnobservableError';\nimport { isIterable } from '../util/isIterable';\nimport { isReadableStreamLike, readableStreamLikeToAsyncGenerator } from '../util/isReadableStreamLike';\nimport { Subscriber } from '../Subscriber';\nimport { isFunction } from '../util/isFunction';\nimport { reportUnhandledError } from '../util/reportUnhandledError';\nimport { observable as Symbol_observable } from '../symbol/observable';\n\nexport function innerFrom<O extends ObservableInput<any>>(input: O): Observable<ObservedValueOf<O>>;\nexport function innerFrom<T>(input: ObservableInput<T>): Observable<T> {\n  if (input instanceof Observable) {\n    return input;\n  }\n  if (input != null) {\n    if (isInteropObservable(input)) {\n      return fromInteropObservable(input);\n    }\n    if (isArrayLike(input)) {\n      return fromArrayLike(input);\n    }\n    if (isPromise(input)) {\n      return fromPromise(input);\n    }\n    if (isAsyncIterable(input)) {\n      return fromAsyncIterable(input);\n    }\n    if (isIterable(input)) {\n      return fromIterable(input);\n    }\n    if (isReadableStreamLike(input)) {\n      return fromReadableStreamLike(input);\n    }\n  }\n\n  throw createInvalidObservableTypeError(input);\n}\n\n/**\n * Creates an RxJS Observable from an object that implements `Symbol.observable`.\n * @param obj An object that properly implements `Symbol.observable`.\n */\nexport function fromInteropObservable<T>(obj: any) {\n  return new Observable((subscriber: Subscriber<T>) => {\n    const obs = obj[Symbol_observable]();\n    if (isFunction(obs.subscribe)) {\n      return obs.subscribe(subscriber);\n    }\n    // Should be caught by observable subscribe function error handling.\n    throw new TypeError('Provided object does not correctly implement Symbol.observable');\n  });\n}\n\n/**\n * Synchronously emits the values of an array like and completes.\n * This is exported because there are creation functions and operators that need to\n * make direct use of the same logic, and there's no reason to make them run through\n * `from` conditionals because we *know* they're dealing with an array.\n * @param array The array to emit values from\n */\nexport function fromArrayLike<T>(array: ArrayLike<T>) {\n  return new Observable((subscriber: Subscriber<T>) => {\n    // Loop over the array and emit each value. Note two things here:\n    // 1. We're making sure that the subscriber is not closed on each loop.\n    //    This is so we don't continue looping over a very large array after\n    //    something like a `take`, `takeWhile`, or other synchronous unsubscription\n    //    has already unsubscribed.\n    // 2. In this form, reentrant code can alter that array we're looping over.\n    //    This is a known issue, but considered an edge case. The alternative would\n    //    be to copy the array before executing the loop, but this has\n    //    performance implications.\n    for (let i = 0; i < array.length && !subscriber.closed; i++) {\n      subscriber.next(array[i]);\n    }\n    subscriber.complete();\n  });\n}\n\nexport function fromPromise<T>(promise: PromiseLike<T>) {\n  return new Observable((subscriber: Subscriber<T>) => {\n    promise\n      .then(\n        (value) => {\n          if (!subscriber.closed) {\n            subscriber.next(value);\n            subscriber.complete();\n          }\n        },\n        (err: any) => subscriber.error(err)\n      )\n      .then(null, reportUnhandledError);\n  });\n}\n\nexport function fromIterable<T>(iterable: Iterable<T>) {\n  return new Observable((subscriber: Subscriber<T>) => {\n    for (const value of iterable) {\n      subscriber.next(value);\n      if (subscriber.closed) {\n        return;\n      }\n    }\n    subscriber.complete();\n  });\n}\n\nexport function fromAsyncIterable<T>(asyncIterable: AsyncIterable<T>) {\n  return new Observable((subscriber: Subscriber<T>) => {\n    process(asyncIterable, subscriber).catch((err) => subscriber.error(err));\n  });\n}\n\nexport function fromReadableStreamLike<T>(readableStream: ReadableStreamLike<T>) {\n  return fromAsyncIterable(readableStreamLikeToAsyncGenerator(readableStream));\n}\n\nasync function process<T>(asyncIterable: AsyncIterable<T>, subscriber: Subscriber<T>) {\n  for await (const value of asyncIterable) {\n    subscriber.next(value);\n    // A side-effect may have closed our subscriber,\n    // check before the next iteration.\n    if (subscriber.closed) {\n      return;\n    }\n  }\n  subscriber.complete();\n}\n", "import { Subscription } from '../Subscription';\nimport { SchedulerAction, SchedulerLike } from '../types';\n\nexport function executeSchedule(\n  parentSubscription: Subscription,\n  scheduler: SchedulerLike,\n  work: () => void,\n  delay: number,\n  repeat: true\n): void;\nexport function executeSchedule(\n  parentSubscription: Subscription,\n  scheduler: SchedulerLike,\n  work: () => void,\n  delay?: number,\n  repeat?: false\n): Subscription;\n\nexport function executeSchedule(\n  parentSubscription: Subscription,\n  scheduler: SchedulerLike,\n  work: () => void,\n  delay = 0,\n  repeat = false\n): Subscription | void {\n  const scheduleSubscription = scheduler.schedule(function (this: SchedulerAction<any>) {\n    work();\n    if (repeat) {\n      parentSubscription.add(this.schedule(null, delay));\n    } else {\n      this.unsubscribe();\n    }\n  }, delay);\n\n  parentSubscription.add(scheduleSubscription);\n\n  if (!repeat) {\n    // Because user-land scheduler implementations are unlikely to properly reuse\n    // Actions for repeat scheduling, we can't trust that the returned subscription\n    // will control repeat subscription scenarios. So we're trying to avoid using them\n    // incorrectly within this library.\n    return scheduleSubscription;\n  }\n}\n", "/** @prettier */\nimport { MonoTypeOperatorFunction, SchedulerLike } from '../types';\nimport { executeSchedule } from '../util/executeSchedule';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\n\n/**\n * Re-emits all notifications from source Observable with specified scheduler.\n *\n * <span class=\"informal\">Ensure a specific scheduler is used, from outside of an Observable.</span>\n *\n * `observeOn` is an operator that accepts a scheduler as a first parameter, which will be used to reschedule\n * notifications emitted by the source Observable. It might be useful, if you do not have control over\n * internal scheduler of a given Observable, but want to control when its values are emitted nevertheless.\n *\n * Returned Observable emits the same notifications (nexted values, complete and error events) as the source Observable,\n * but rescheduled with provided scheduler. Note that this doesn't mean that source Observables internal\n * scheduler will be replaced in any way. Original scheduler still will be used, but when the source Observable emits\n * notification, it will be immediately scheduled again - this time with scheduler passed to `observeOn`.\n * An anti-pattern would be calling `observeOn` on Observable that emits lots of values synchronously, to split\n * that emissions into asynchronous chunks. For this to happen, scheduler would have to be passed into the source\n * Observable directly (usually into the operator that creates it). `observeOn` simply delays notifications a\n * little bit more, to ensure that they are emitted at expected moments.\n *\n * As a matter of fact, `observeOn` accepts second parameter, which specifies in milliseconds with what delay notifications\n * will be emitted. The main difference between {@link delay} operator and `observeOn` is that `observeOn`\n * will delay all notifications - including error notifications - while `delay` will pass through error\n * from source Observable immediately when it is emitted. In general it is highly recommended to use `delay` operator\n * for any kind of delaying of values in the stream, while using `observeOn` to specify which scheduler should be used\n * for notification emissions in general.\n *\n * ## Example\n *\n * Ensure values in subscribe are called just before browser repaint\n *\n * ```ts\n * import { interval, observeOn, animationFrameScheduler } from 'rxjs';\n *\n * const someDiv = document.createElement('div');\n * someDiv.style.cssText = 'width: 200px;background: #09c';\n * document.body.appendChild(someDiv);\n * const intervals = interval(10);      // Intervals are scheduled\n *                                      // with async scheduler by default...\n * intervals.pipe(\n *   observeOn(animationFrameScheduler) // ...but we will observe on animationFrame\n * )                                    // scheduler to ensure smooth animation.\n * .subscribe(val => {\n *   someDiv.style.height = val + 'px';\n * });\n * ```\n *\n * @see {@link delay}\n *\n * @param scheduler Scheduler that will be used to reschedule notifications from source Observable.\n * @param delay Number of milliseconds that states with what delay every notification should be rescheduled.\n * @return A function that returns an Observable that emits the same\n * notifications as the source Observable, but with provided scheduler.\n */\nexport function observeOn<T>(scheduler: SchedulerLike, delay = 0): MonoTypeOperatorFunction<T> {\n  return operate((source, subscriber) => {\n    source.subscribe(\n      createOperatorSubscriber(\n        subscriber,\n        (value) => executeSchedule(subscriber, scheduler, () => subscriber.next(value), delay),\n        () => executeSchedule(subscriber, scheduler, () => subscriber.complete(), delay),\n        (err) => executeSchedule(subscriber, scheduler, () => subscriber.error(err), delay)\n      )\n    );\n  });\n}\n", "import { MonoTypeOperatorFunction, SchedulerLike } from '../types';\nimport { operate } from '../util/lift';\n\n/**\n * Asynchronously subscribes Observers to this Observable on the specified {@link SchedulerLike}.\n *\n * With `subscribeOn` you can decide what type of scheduler a specific Observable will be using when it is subscribed to.\n *\n * Schedulers control the speed and order of emissions to observers from an Observable stream.\n *\n * ![](subscribeOn.png)\n *\n * ## Example\n *\n * Given the following code:\n *\n * ```ts\n * import { of, merge } from 'rxjs';\n *\n * const a = of(1, 2, 3);\n * const b = of(4, 5, 6);\n *\n * merge(a, b).subscribe(console.log);\n *\n * // Outputs\n * // 1\n * // 2\n * // 3\n * // 4\n * // 5\n * // 6\n * ```\n *\n * Both Observable `a` and `b` will emit their values directly and synchronously once they are subscribed to.\n *\n * If we instead use the `subscribeOn` operator declaring that we want to use the {@link asyncScheduler} for values emitted by Observable `a`:\n *\n * ```ts\n * import { of, subscribeOn, asyncScheduler, merge } from 'rxjs';\n *\n * const a = of(1, 2, 3).pipe(subscribeOn(asyncScheduler));\n * const b = of(4, 5, 6);\n *\n * merge(a, b).subscribe(console.log);\n *\n * // Outputs\n * // 4\n * // 5\n * // 6\n * // 1\n * // 2\n * // 3\n * ```\n *\n * The reason for this is that Observable `b` emits its values directly and synchronously like before\n * but the emissions from `a` are scheduled on the event loop because we are now using the {@link asyncScheduler} for that specific Observable.\n *\n * @param scheduler The {@link SchedulerLike} to perform subscription actions on.\n * @param delay A delay to pass to the scheduler to delay subscriptions\n * @return A function that returns an Observable modified so that its\n * subscriptions happen on the specified {@link SchedulerLike}.\n */\nexport function subscribeOn<T>(scheduler: SchedulerLike, delay: number = 0): MonoTypeOperatorFunction<T> {\n  return operate((source, subscriber) => {\n    subscriber.add(scheduler.schedule(() => source.subscribe(subscriber), delay));\n  });\n}\n", "import { innerFrom } from '../observable/innerFrom';\nimport { observeOn } from '../operators/observeOn';\nimport { subscribeOn } from '../operators/subscribeOn';\nimport { InteropObservable, SchedulerLike } from '../types';\n\nexport function scheduleObservable<T>(input: InteropObservable<T>, scheduler: SchedulerLike) {\n  return innerFrom(input).pipe(subscribeOn(scheduler), observeOn(scheduler));\n}\n", "import { innerFrom } from '../observable/innerFrom';\nimport { observeOn } from '../operators/observeOn';\nimport { subscribeOn } from '../operators/subscribeOn';\nimport { SchedulerLike } from '../types';\n\nexport function schedulePromise<T>(input: PromiseLike<T>, scheduler: SchedulerLike) {\n  return innerFrom(input).pipe(subscribeOn(scheduler), observeOn(scheduler));\n}\n", "import { Observable } from '../Observable';\nimport { SchedulerLike } from '../types';\n\nexport function scheduleArray<T>(input: ArrayLike<T>, scheduler: SchedulerLike) {\n  return new Observable<T>((subscriber) => {\n    // The current array index.\n    let i = 0;\n    // Start iterating over the array like on a schedule.\n    return scheduler.schedule(function () {\n      if (i === input.length) {\n        // If we have hit the end of the array like in the\n        // previous job, we can complete.\n        subscriber.complete();\n      } else {\n        // Otherwise let's next the value at the current index,\n        // then increment our index.\n        subscriber.next(input[i++]);\n        // If the last emission didn't cause us to close the subscriber\n        // (via take or some side effect), reschedule the job and we'll\n        // make another pass.\n        if (!subscriber.closed) {\n          this.schedule();\n        }\n      }\n    });\n  });\n}\n", "import { Observable } from '../Observable';\nimport { SchedulerLike } from '../types';\nimport { iterator as Symbol_iterator } from '../symbol/iterator';\nimport { isFunction } from '../util/isFunction';\nimport { executeSchedule } from '../util/executeSchedule';\n\n/**\n * Used in {@link scheduled} to create an observable from an Iterable.\n * @param input The iterable to create an observable from\n * @param scheduler The scheduler to use\n */\nexport function scheduleIterable<T>(input: Iterable<T>, scheduler: SchedulerLike) {\n  return new Observable<T>((subscriber) => {\n    let iterator: Iterator<T, T>;\n\n    // Schedule the initial creation of the iterator from\n    // the iterable. This is so the code in the iterable is\n    // not called until the scheduled job fires.\n    executeSchedule(subscriber, scheduler, () => {\n      // Create the iterator.\n      iterator = (input as any)[Symbol_iterator]();\n\n      executeSchedule(\n        subscriber,\n        scheduler,\n        () => {\n          let value: T;\n          let done: boolean | undefined;\n          try {\n            // Pull the value out of the iterator\n            ({ value, done } = iterator.next());\n          } catch (err) {\n            // We got an error while pulling from the iterator\n            subscriber.error(err);\n            return;\n          }\n\n          if (done) {\n            // If it is \"done\" we just complete. This mimics the\n            // behavior of JavaScript's `for..of` consumption of\n            // iterables, which will not emit the value from an iterator\n            // result of `{ done: true: value: 'here' }`.\n            subscriber.complete();\n          } else {\n            // The iterable is not done, emit the value.\n            subscriber.next(value);\n          }\n        },\n        0,\n        true\n      );\n    });\n\n    // During finalization, if we see this iterator has a `return` method,\n    // then we know it is a Generator, and not just an Iterator. So we call\n    // the `return()` function. This will ensure that any `finally { }` blocks\n    // inside of the generator we can hit will be hit properly.\n    return () => isFunction(iterator?.return) && iterator.return();\n  });\n}\n", "import { SchedulerLike } from '../types';\nimport { Observable } from '../Observable';\nimport { executeSchedule } from '../util/executeSchedule';\n\nexport function scheduleAsyncIterable<T>(input: AsyncIterable<T>, scheduler: SchedulerLike) {\n  if (!input) {\n    throw new Error('Iterable cannot be null');\n  }\n  return new Observable<T>((subscriber) => {\n    executeSchedule(subscriber, scheduler, () => {\n      const iterator = input[Symbol.asyncIterator]();\n      executeSchedule(\n        subscriber,\n        scheduler,\n        () => {\n          iterator.next().then((result) => {\n            if (result.done) {\n              // This will remove the subscriptions from\n              // the parent subscription.\n              subscriber.complete();\n            } else {\n              subscriber.next(result.value);\n            }\n          });\n        },\n        0,\n        true\n      );\n    });\n  });\n}\n", "import { SchedulerLike, ReadableStreamLike } from '../types';\nimport { Observable } from '../Observable';\nimport { scheduleAsyncIterable } from './scheduleAsyncIterable';\nimport { readableStreamLikeToAsyncGenerator } from '../util/isReadableStreamLike';\n\nexport function scheduleReadableStreamLike<T>(input: ReadableStreamLike<T>, scheduler: SchedulerLike): Observable<T> {\n  return scheduleAsyncIterable(readableStreamLikeToAsyncGenerator(input), scheduler);\n}\n", "import { scheduleObservable } from './scheduleObservable';\nimport { schedulePromise } from './schedulePromise';\nimport { scheduleArray } from './scheduleArray';\nimport { scheduleIterable } from './scheduleIterable';\nimport { scheduleAsyncIterable } from './scheduleAsyncIterable';\nimport { isInteropObservable } from '../util/isInteropObservable';\nimport { isPromise } from '../util/isPromise';\nimport { isArrayLike } from '../util/isArrayLike';\nimport { isIterable } from '../util/isIterable';\nimport { ObservableInput, SchedulerLike } from '../types';\nimport { Observable } from '../Observable';\nimport { isAsyncIterable } from '../util/isAsyncIterable';\nimport { createInvalidObservableTypeError } from '../util/throwUnobservableError';\nimport { isReadableStreamLike } from '../util/isReadableStreamLike';\nimport { scheduleReadableStreamLike } from './scheduleReadableStreamLike';\n\n/**\n * Converts from a common {@link ObservableInput} type to an observable where subscription and emissions\n * are scheduled on the provided scheduler.\n *\n * @see {@link from}\n * @see {@link of}\n *\n * @param input The observable, array, promise, iterable, etc you would like to schedule\n * @param scheduler The scheduler to use to schedule the subscription and emissions from\n * the returned observable.\n */\nexport function scheduled<T>(input: ObservableInput<T>, scheduler: SchedulerLike): Observable<T> {\n  if (input != null) {\n    if (isInteropObservable(input)) {\n      return scheduleObservable(input, scheduler);\n    }\n    if (isArrayLike(input)) {\n      return scheduleArray(input, scheduler);\n    }\n    if (isPromise(input)) {\n      return schedulePromise(input, scheduler);\n    }\n    if (isAsyncIterable(input)) {\n      return scheduleAsyncIterable(input, scheduler);\n    }\n    if (isIterable(input)) {\n      return scheduleIterable(input, scheduler);\n    }\n    if (isReadableStreamLike(input)) {\n      return scheduleReadableStreamLike(input, scheduler);\n    }\n  }\n  throw createInvalidObservableTypeError(input);\n}\n", "import { Observable } from '../Observable';\nimport { ObservableInput, SchedulerLike, ObservedValueOf } from '../types';\nimport { scheduled } from '../scheduled/scheduled';\nimport { innerFrom } from './innerFrom';\n\nexport function from<O extends ObservableInput<any>>(input: O): Observable<ObservedValueOf<O>>;\n/** @deprecated The `scheduler` parameter will be removed in v8. Use `scheduled`. Details: https://rxjs.dev/deprecations/scheduler-argument */\nexport function from<O extends ObservableInput<any>>(input: O, scheduler: SchedulerLike | undefined): Observable<ObservedValueOf<O>>;\n\n/**\n * Creates an Observable from an Array, an array-like object, a Promise, an iterable object, or an Observable-like object.\n *\n * <span class=\"informal\">Converts almost anything to an Observable.</span>\n *\n * ![](from.png)\n *\n * `from` converts various other objects and data types into Observables. It also converts a Promise, an array-like, or an\n * <a href=\"https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Iteration_protocols#iterable\" target=\"_blank\">iterable</a>\n * object into an Observable that emits the items in that promise, array, or iterable. A String, in this context, is treated\n * as an array of characters. Observable-like objects (contains a function named with the ES2015 Symbol for Observable) can also be\n * converted through this operator.\n *\n * ## Examples\n *\n * Converts an array to an Observable\n *\n * ```ts\n * import { from } from 'rxjs';\n *\n * const array = [10, 20, 30];\n * const result = from(array);\n *\n * result.subscribe(x => console.log(x));\n *\n * // Logs:\n * // 10\n * // 20\n * // 30\n * ```\n *\n * Convert an infinite iterable (from a generator) to an Observable\n *\n * ```ts\n * import { from, take } from 'rxjs';\n *\n * function* generateDoubles(seed) {\n *    let i = seed;\n *    while (true) {\n *      yield i;\n *      i = 2 * i; // double it\n *    }\n * }\n *\n * const iterator = generateDoubles(3);\n * const result = from(iterator).pipe(take(10));\n *\n * result.subscribe(x => console.log(x));\n *\n * // Logs:\n * // 3\n * // 6\n * // 12\n * // 24\n * // 48\n * // 96\n * // 192\n * // 384\n * // 768\n * // 1536\n * ```\n *\n * With `asyncScheduler`\n *\n * ```ts\n * import { from, asyncScheduler } from 'rxjs';\n *\n * console.log('start');\n *\n * const array = [10, 20, 30];\n * const result = from(array, asyncScheduler);\n *\n * result.subscribe(x => console.log(x));\n *\n * console.log('end');\n *\n * // Logs:\n * // 'start'\n * // 'end'\n * // 10\n * // 20\n * // 30\n * ```\n *\n * @see {@link fromEvent}\n * @see {@link fromEventPattern}\n *\n * @param input A subscription object, a Promise, an Observable-like,\n * an Array, an iterable, or an array-like object to be converted.\n * @param scheduler An optional {@link SchedulerLike} on which to schedule the emission of values.\n * @return An Observable converted from {@link ObservableInput}.\n */\nexport function from<T>(input: ObservableInput<T>, scheduler?: SchedulerLike): Observable<T> {\n  return scheduler ? scheduled(input, scheduler) : innerFrom(input);\n}\n", "import { SchedulerLike, ValueFromArray } from '../types';\nimport { Observable } from '../Observable';\nimport { popScheduler } from '../util/args';\nimport { from } from './from';\n\n// Devs are more likely to pass null or undefined than they are a scheduler\n// without accompanying values. To make things easier for (naughty) devs who\n// use the `strictNullChecks: false` TypeScript compiler option, these\n// overloads with explicit null and undefined values are included.\n\nexport function of(value: null): Observable<null>;\nexport function of(value: undefined): Observable<undefined>;\n\n/** @deprecated The `scheduler` parameter will be removed in v8. Use `scheduled`. Details: https://rxjs.dev/deprecations/scheduler-argument */\nexport function of(scheduler: SchedulerLike): Observable<never>;\n/** @deprecated The `scheduler` parameter will be removed in v8. Use `scheduled`. Details: https://rxjs.dev/deprecations/scheduler-argument */\nexport function of<A extends readonly unknown[]>(...valuesAndScheduler: [...A, SchedulerLike]): Observable<ValueFromArray<A>>;\n\nexport function of(): Observable<never>;\n/** @deprecated Do not specify explicit type parameters. Signatures with type parameters that cannot be inferred will be removed in v8. */\nexport function of<T>(): Observable<T>;\nexport function of<T>(value: T): Observable<T>;\nexport function of<A extends readonly unknown[]>(...values: A): Observable<ValueFromArray<A>>;\n\n/**\n * Converts the arguments to an observable sequence.\n *\n * <span class=\"informal\">Each argument becomes a `next` notification.</span>\n *\n * ![](of.png)\n *\n * Unlike {@link from}, it does not do any flattening and emits each argument in whole\n * as a separate `next` notification.\n *\n * ## Examples\n *\n * Emit the values `10, 20, 30`\n *\n * ```ts\n * import { of } from 'rxjs';\n *\n * of(10, 20, 30)\n *   .subscribe({\n *     next: value => console.log('next:', value),\n *     error: err => console.log('error:', err),\n *     complete: () => console.log('the end'),\n *   });\n *\n * // Outputs\n * // next: 10\n * // next: 20\n * // next: 30\n * // the end\n * ```\n *\n * Emit the array `[1, 2, 3]`\n *\n * ```ts\n * import { of } from 'rxjs';\n *\n * of([1, 2, 3])\n *   .subscribe({\n *     next: value => console.log('next:', value),\n *     error: err => console.log('error:', err),\n *     complete: () => console.log('the end'),\n *   });\n *\n * // Outputs\n * // next: [1, 2, 3]\n * // the end\n * ```\n *\n * @see {@link from}\n * @see {@link range}\n *\n * @param args A comma separated list of arguments you want to be emitted.\n * @return An Observable that synchronously emits the arguments described\n * above and then immediately completes.\n */\nexport function of<T>(...args: Array<T | SchedulerLike>): Observable<T> {\n  const scheduler = popScheduler(args);\n  return from(args as T[], scheduler);\n}\n", "import { Observable } from '../Observable';\nimport { Subscriber } from '../Subscriber';\nimport { SchedulerLike } from '../types';\nimport { isFunction } from '../util/isFunction';\n\n/**\n * Creates an observable that will create an error instance and push it to the consumer as an error\n * immediately upon subscription.\n *\n * <span class=\"informal\">Just errors and does nothing else</span>\n *\n * ![](throw.png)\n *\n * This creation function is useful for creating an observable that will create an error and error every\n * time it is subscribed to. Generally, inside of most operators when you might want to return an errored\n * observable, this is unnecessary. In most cases, such as in the inner return of {@link concatMap},\n * {@link mergeMap}, {@link defer}, and many others, you can simply throw the error, and RxJS will pick\n * that up and notify the consumer of the error.\n *\n * ## Example\n *\n * Create a simple observable that will create a new error with a timestamp and log it\n * and the message every time you subscribe to it\n *\n * ```ts\n * import { throwError } from 'rxjs';\n *\n * let errorCount = 0;\n *\n * const errorWithTimestamp$ = throwError(() => {\n *   const error: any = new Error(`This is error number ${ ++errorCount }`);\n *   error.timestamp = Date.now();\n *   return error;\n * });\n *\n * errorWithTimestamp$.subscribe({\n *   error: err => console.log(err.timestamp, err.message)\n * });\n *\n * errorWithTimestamp$.subscribe({\n *   error: err => console.log(err.timestamp, err.message)\n * });\n *\n * // Logs the timestamp and a new error message for each subscription\n * ```\n *\n * ### Unnecessary usage\n *\n * Using `throwError` inside of an operator or creation function\n * with a callback, is usually not necessary\n *\n * ```ts\n * import { of, concatMap, timer, throwError } from 'rxjs';\n *\n * const delays$ = of(1000, 2000, Infinity, 3000);\n *\n * delays$.pipe(\n *   concatMap(ms => {\n *     if (ms < 10000) {\n *       return timer(ms);\n *     } else {\n *       // This is probably overkill.\n *       return throwError(() => new Error(`Invalid time ${ ms }`));\n *     }\n *   })\n * )\n * .subscribe({\n *   next: console.log,\n *   error: console.error\n * });\n * ```\n *\n * You can just throw the error instead\n *\n * ```ts\n * import { of, concatMap, timer } from 'rxjs';\n *\n * const delays$ = of(1000, 2000, Infinity, 3000);\n *\n * delays$.pipe(\n *   concatMap(ms => {\n *     if (ms < 10000) {\n *       return timer(ms);\n *     } else {\n *       // Cleaner and easier to read for most folks.\n *       throw new Error(`Invalid time ${ ms }`);\n *     }\n *   })\n * )\n * .subscribe({\n *   next: console.log,\n *   error: console.error\n * });\n * ```\n *\n * @param errorFactory A factory function that will create the error instance that is pushed.\n */\nexport function throwError(errorFactory: () => any): Observable<never>;\n\n/**\n * Returns an observable that will error with the specified error immediately upon subscription.\n *\n * @param error The error instance to emit\n * @deprecated Support for passing an error value will be removed in v8. Instead, pass a factory function to `throwError(() => new Error('test'))`. This is\n * because it will create the error at the moment it should be created and capture a more appropriate stack trace. If\n * for some reason you need to create the error ahead of time, you can still do that: `const err = new Error('test'); throwError(() => err);`.\n */\nexport function throwError(error: any): Observable<never>;\n\n/**\n * Notifies the consumer of an error using a given scheduler by scheduling it at delay `0` upon subscription.\n *\n * @param errorOrErrorFactory An error instance or error factory\n * @param scheduler A scheduler to use to schedule the error notification\n * @deprecated The `scheduler` parameter will be removed in v8.\n * Use `throwError` in combination with {@link observeOn}: `throwError(() => new Error('test')).pipe(observeOn(scheduler));`.\n * Details: https://rxjs.dev/deprecations/scheduler-argument\n */\nexport function throwError(errorOrErrorFactory: any, scheduler: SchedulerLike): Observable<never>;\n\nexport function throwError(errorOrErrorFactory: any, scheduler?: SchedulerLike): Observable<never> {\n  const errorFactory = isFunction(errorOrErrorFactory) ? errorOrErrorFactory : () => errorOrErrorFactory;\n  const init = (subscriber: Subscriber<never>) => subscriber.error(errorFactory());\n  return new Observable(scheduler ? (subscriber) => scheduler.schedule(init as any, 0, subscriber) : init);\n}\n", "import { createErrorClass } from './createErrorClass';\n\nexport interface EmptyError extends Error {}\n\nexport interface EmptyErrorCtor {\n  /**\n   * @deprecated Internal implementation detail. Do not construct error instances.\n   * Cannot be tagged as internal: https://github.com/ReactiveX/rxjs/issues/6269\n   */\n  new (): EmptyError;\n}\n\n/**\n * An error thrown when an Observable or a sequence was queried but has no\n * elements.\n *\n * @see {@link first}\n * @see {@link last}\n * @see {@link single}\n * @see {@link firstValueFrom}\n * @see {@link lastValueFrom}\n */\nexport const EmptyError: EmptyErrorCtor = createErrorClass(\n  (_super) =>\n    function EmptyErrorImpl(this: any) {\n      _super(this);\n      this.name = 'EmptyError';\n      this.message = 'no elements in sequence';\n    }\n);\n", "/**\n * Checks to see if a value is not only a `Date` object,\n * but a *valid* `Date` object that can be converted to a\n * number. For example, `new Date('blah')` is indeed an\n * `instanceof Date`, however it cannot be converted to a\n * number.\n */\nexport function isValidDate(value: any): value is Date {\n  return value instanceof Date && !isNaN(value as any);\n}\n", "import { OperatorFunction } from '../types';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\n\nexport function map<T, R>(project: (value: T, index: number) => R): OperatorFunction<T, R>;\n/** @deprecated Use a closure instead of a `thisArg`. Signatures accepting a `thisArg` will be removed in v8. */\nexport function map<T, R, A>(project: (this: A, value: T, index: number) => R, thisArg: A): OperatorFunction<T, R>;\n\n/**\n * Applies a given `project` function to each value emitted by the source\n * Observable, and emits the resulting values as an Observable.\n *\n * <span class=\"informal\">Like [Array.prototype.map()](https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Array/map),\n * it passes each source value through a transformation function to get\n * corresponding output values.</span>\n *\n * ![](map.png)\n *\n * Similar to the well known `Array.prototype.map` function, this operator\n * applies a projection to each value and emits that projection in the output\n * Observable.\n *\n * ## Example\n *\n * Map every click to the `clientX` position of that click\n *\n * ```ts\n * import { fromEvent, map } from 'rxjs';\n *\n * const clicks = fromEvent<PointerEvent>(document, 'click');\n * const positions = clicks.pipe(map(ev => ev.clientX));\n *\n * positions.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link mapTo}\n * @see {@link pluck}\n *\n * @param project The function to apply to each `value` emitted by the source\n * Observable. The `index` parameter is the number `i` for the i-th emission\n * that has happened since the subscription, starting from the number `0`.\n * @param thisArg An optional argument to define what `this` is in the\n * `project` function.\n * @return A function that returns an Observable that emits the values from the\n * source Observable transformed by the given `project` function.\n */\nexport function map<T, R>(project: (value: T, index: number) => R, thisArg?: any): OperatorFunction<T, R> {\n  return operate((source, subscriber) => {\n    // The index of the value from the source. Used with projection.\n    let index = 0;\n    // Subscribe to the source, all errors and completions are sent along\n    // to the consumer.\n    source.subscribe(\n      createOperatorSubscriber(subscriber, (value: T) => {\n        // Call the projection function with the appropriate this context,\n        // and send the resulting value to the consumer.\n        subscriber.next(project.call(thisArg, value, index++));\n      })\n    );\n  });\n}\n", "import { OperatorFunction } from \"../types\";\nimport { map } from \"../operators/map\";\n\nconst { isArray } = Array;\n\nfunction callOrApply<T, R>(fn: ((...values: T[]) => R), args: T|T[]): R {\n    return isArray(args) ? fn(...args) : fn(args);\n}\n\n/**\n * Used in several -- mostly deprecated -- situations where we need to \n * apply a list of arguments or a single argument to a result selector.\n */\nexport function mapOneOrManyArgs<T, R>(fn: ((...values: T[]) => R)): OperatorFunction<T|T[], R> {\n    return map(args => callOrApply(fn, args))\n}", "const { isArray } = Array;\nconst { getPrototypeOf, prototype: objectProto, keys: getKeys } = Object;\n\n/**\n * Used in functions where either a list of arguments, a single array of arguments, or a\n * dictionary of arguments can be returned. Returns an object with an `args` property with\n * the arguments in an array, if it is a dictionary, it will also return the `keys` in another\n * property.\n */\nexport function argsArgArrayOrObject<T, O extends Record<string, T>>(args: T[] | [O] | [T[]]): { args: T[]; keys: string[] | null } {\n  if (args.length === 1) {\n    const first = args[0];\n    if (isArray(first)) {\n      return { args: first, keys: null };\n    }\n    if (isPOJO(first)) {\n      const keys = getKeys(first);\n      return {\n        args: keys.map((key) => first[key]),\n        keys,\n      };\n    }\n  }\n\n  return { args: args as T[], keys: null };\n}\n\nfunction isPOJO(obj: any): obj is object {\n  return obj && typeof obj === 'object' && getPrototypeOf(obj) === objectProto;\n}\n", "export function createObject(keys: string[], values: any[]) {\n  return keys.reduce((result, key, i) => ((result[key] = values[i]), result), {} as any);\n}\n", "import { Observable } from '../Observable';\nimport { ObservableInput, SchedulerLike, ObservedValueOf, ObservableInputTuple } from '../types';\nimport { argsArgArrayOrObject } from '../util/argsArgArrayOrObject';\nimport { Subscriber } from '../Subscriber';\nimport { from } from './from';\nimport { identity } from '../util/identity';\nimport { Subscription } from '../Subscription';\nimport { mapOneOrManyArgs } from '../util/mapOneOrManyArgs';\nimport { popResultSelector, popScheduler } from '../util/args';\nimport { createObject } from '../util/createObject';\nimport { createOperatorSubscriber } from '../operators/OperatorSubscriber';\nimport { AnyCatcher } from '../AnyCatcher';\nimport { executeSchedule } from '../util/executeSchedule';\n\n// combineLatest(any)\n// We put this first because we need to catch cases where the user has supplied\n// _exactly `any`_ as the argument. Since `any` literally matches _anything_,\n// we don't want it to randomly hit one of the other type signatures below,\n// as we have no idea at build-time what type we should be returning when given an any.\n\n/**\n * You have passed `any` here, we can't figure out if it is\n * an array or an object, so you're getting `unknown`. Use better types.\n * @param arg Something typed as `any`\n */\nexport function combineLatest<T extends AnyCatcher>(arg: T): Observable<unknown>;\n\n// combineLatest([a, b, c])\nexport function combineLatest(sources: []): Observable<never>;\nexport function combineLatest<A extends readonly unknown[]>(sources: readonly [...ObservableInputTuple<A>]): Observable<A>;\n/** @deprecated The `scheduler` parameter will be removed in v8. Use `scheduled` and `combineLatestAll`. Details: https://rxjs.dev/deprecations/scheduler-argument */\nexport function combineLatest<A extends readonly unknown[], R>(\n  sources: readonly [...ObservableInputTuple<A>],\n  resultSelector: (...values: A) => R,\n  scheduler: SchedulerLike\n): Observable<R>;\nexport function combineLatest<A extends readonly unknown[], R>(\n  sources: readonly [...ObservableInputTuple<A>],\n  resultSelector: (...values: A) => R\n): Observable<R>;\n/** @deprecated The `scheduler` parameter will be removed in v8. Use `scheduled` and `combineLatestAll`. Details: https://rxjs.dev/deprecations/scheduler-argument */\nexport function combineLatest<A extends readonly unknown[]>(\n  sources: readonly [...ObservableInputTuple<A>],\n  scheduler: SchedulerLike\n): Observable<A>;\n\n// combineLatest(a, b, c)\n/** @deprecated Pass an array of sources instead. The rest-parameters signature will be removed in v8. Details: https://rxjs.dev/deprecations/array-argument */\nexport function combineLatest<A extends readonly unknown[]>(...sources: [...ObservableInputTuple<A>]): Observable<A>;\n/** @deprecated The `scheduler` parameter will be removed in v8. Use `scheduled` and `combineLatestAll`. Details: https://rxjs.dev/deprecations/scheduler-argument */\nexport function combineLatest<A extends readonly unknown[], R>(\n  ...sourcesAndResultSelectorAndScheduler: [...ObservableInputTuple<A>, (...values: A) => R, SchedulerLike]\n): Observable<R>;\n/** @deprecated Pass an array of sources instead. The rest-parameters signature will be removed in v8. Details: https://rxjs.dev/deprecations/array-argument */\nexport function combineLatest<A extends readonly unknown[], R>(\n  ...sourcesAndResultSelector: [...ObservableInputTuple<A>, (...values: A) => R]\n): Observable<R>;\n/** @deprecated The `scheduler` parameter will be removed in v8. Use `scheduled` and `combineLatestAll`. Details: https://rxjs.dev/deprecations/scheduler-argument */\nexport function combineLatest<A extends readonly unknown[]>(\n  ...sourcesAndScheduler: [...ObservableInputTuple<A>, SchedulerLike]\n): Observable<A>;\n\n// combineLatest({a, b, c})\nexport function combineLatest(sourcesObject: { [K in any]: never }): Observable<never>;\nexport function combineLatest<T extends Record<string, ObservableInput<any>>>(\n  sourcesObject: T\n): Observable<{ [K in keyof T]: ObservedValueOf<T[K]> }>;\n\n/**\n * Combines multiple Observables to create an Observable whose values are\n * calculated from the latest values of each of its input Observables.\n *\n * <span class=\"informal\">Whenever any input Observable emits a value, it\n * computes a formula using the latest values from all the inputs, then emits\n * the output of that formula.</span>\n *\n * ![](combineLatest.png)\n *\n * `combineLatest` combines the values from all the Observables passed in the\n * observables array. This is done by subscribing to each Observable in order and,\n * whenever any Observable emits, collecting an array of the most recent\n * values from each Observable. So if you pass `n` Observables to this operator,\n * the returned Observable will always emit an array of `n` values, in an order\n * corresponding to the order of the passed Observables (the value from the first Observable\n * will be at index 0 of the array and so on).\n *\n * Static version of `combineLatest` accepts an array of Observables. Note that an array of\n * Observables is a good choice, if you don't know beforehand how many Observables\n * you will combine. Passing an empty array will result in an Observable that\n * completes immediately.\n *\n * To ensure the output array always has the same length, `combineLatest` will\n * actually wait for all input Observables to emit at least once,\n * before it starts emitting results. This means if some Observable emits\n * values before other Observables started emitting, all these values but the last\n * will be lost. On the other hand, if some Observable does not emit a value but\n * completes, resulting Observable will complete at the same moment without\n * emitting anything, since it will now be impossible to include a value from the\n * completed Observable in the resulting array. Also, if some input Observable does\n * not emit any value and never completes, `combineLatest` will also never emit\n * and never complete, since, again, it will wait for all streams to emit some\n * value.\n *\n * If at least one Observable was passed to `combineLatest` and all passed Observables\n * emitted something, the resulting Observable will complete when all combined\n * streams complete. So even if some Observable completes, the result of\n * `combineLatest` will still emit values when other Observables do. In case\n * of a completed Observable, its value from now on will always be the last\n * emitted value. On the other hand, if any Observable errors, `combineLatest`\n * will error immediately as well, and all other Observables will be unsubscribed.\n *\n * ## Examples\n *\n * Combine two timer Observables\n *\n * ```ts\n * import { timer, combineLatest } from 'rxjs';\n *\n * const firstTimer = timer(0, 1000); // emit 0, 1, 2... after every second, starting from now\n * const secondTimer = timer(500, 1000); // emit 0, 1, 2... after every second, starting 0,5s from now\n * const combinedTimers = combineLatest([firstTimer, secondTimer]);\n * combinedTimers.subscribe(value => console.log(value));\n * // Logs\n * // [0, 0] after 0.5s\n * // [1, 0] after 1s\n * // [1, 1] after 1.5s\n * // [2, 1] after 2s\n * ```\n *\n * Combine a dictionary of Observables\n *\n * ```ts\n * import { of, delay, startWith, combineLatest } from 'rxjs';\n *\n * const observables = {\n *   a: of(1).pipe(delay(1000), startWith(0)),\n *   b: of(5).pipe(delay(5000), startWith(0)),\n *   c: of(10).pipe(delay(10000), startWith(0))\n * };\n * const combined = combineLatest(observables);\n * combined.subscribe(value => console.log(value));\n * // Logs\n * // { a: 0, b: 0, c: 0 } immediately\n * // { a: 1, b: 0, c: 0 } after 1s\n * // { a: 1, b: 5, c: 0 } after 5s\n * // { a: 1, b: 5, c: 10 } after 10s\n * ```\n *\n * Combine an array of Observables\n *\n * ```ts\n * import { of, delay, startWith, combineLatest } from 'rxjs';\n *\n * const observables = [1, 5, 10].map(\n *   n => of(n).pipe(\n *     delay(n * 1000), // emit 0 and then emit n after n seconds\n *     startWith(0)\n *   )\n * );\n * const combined = combineLatest(observables);\n * combined.subscribe(value => console.log(value));\n * // Logs\n * // [0, 0, 0] immediately\n * // [1, 0, 0] after 1s\n * // [1, 5, 0] after 5s\n * // [1, 5, 10] after 10s\n * ```\n *\n * Use map operator to dynamically calculate the Body-Mass Index\n *\n * ```ts\n * import { of, combineLatest, map } from 'rxjs';\n *\n * const weight = of(70, 72, 76, 79, 75);\n * const height = of(1.76, 1.77, 1.78);\n * const bmi = combineLatest([weight, height]).pipe(\n *   map(([w, h]) => w / (h * h)),\n * );\n * bmi.subscribe(x => console.log('BMI is ' + x));\n *\n * // With output to console:\n * // BMI is 24.212293388429753\n * // BMI is 23.93948099205209\n * // BMI is 23.671253629592222\n * ```\n *\n * @see {@link combineLatestAll}\n * @see {@link merge}\n * @see {@link withLatestFrom}\n *\n * @param args Any number of `ObservableInput`s provided either as an array or as an object\n * to combine with each other. If the last parameter is the function, it will be used to project the\n * values from the combined latest values into a new value on the output Observable.\n * @return An Observable of projected values from the most recent values from each `ObservableInput`,\n * or an array of the most recent values from each `ObservableInput`.\n */\nexport function combineLatest<O extends ObservableInput<any>, R>(...args: any[]): Observable<R> | Observable<ObservedValueOf<O>[]> {\n  const scheduler = popScheduler(args);\n  const resultSelector = popResultSelector(args);\n\n  const { args: observables, keys } = argsArgArrayOrObject(args);\n\n  if (observables.length === 0) {\n    // If no observables are passed, or someone has passed an empty array\n    // of observables, or even an empty object POJO, we need to just\n    // complete (EMPTY), but we have to honor the scheduler provided if any.\n    return from([], scheduler as any);\n  }\n\n  const result = new Observable<ObservedValueOf<O>[]>(\n    combineLatestInit(\n      observables as ObservableInput<ObservedValueOf<O>>[],\n      scheduler,\n      keys\n        ? // A handler for scrubbing the array of args into a dictionary.\n          (values) => createObject(keys, values)\n        : // A passthrough to just return the array\n          identity\n    )\n  );\n\n  return resultSelector ? (result.pipe(mapOneOrManyArgs(resultSelector)) as Observable<R>) : result;\n}\n\nexport function combineLatestInit(\n  observables: ObservableInput<any>[],\n  scheduler?: SchedulerLike,\n  valueTransform: (values: any[]) => any = identity\n) {\n  return (subscriber: Subscriber<any>) => {\n    // The outer subscription. We're capturing this in a function\n    // because we may have to schedule it.\n    maybeSchedule(\n      scheduler,\n      () => {\n        const { length } = observables;\n        // A store for the values each observable has emitted so far. We match observable to value on index.\n        const values = new Array(length);\n        // The number of currently active subscriptions, as they complete, we decrement this number to see if\n        // we are all done combining values, so we can complete the result.\n        let active = length;\n        // The number of inner sources that still haven't emitted the first value\n        // We need to track this because all sources need to emit one value in order\n        // to start emitting values.\n        let remainingFirstValues = length;\n        // The loop to kick off subscription. We're keying everything on index `i` to relate the observables passed\n        // in to the slot in the output array or the key in the array of keys in the output dictionary.\n        for (let i = 0; i < length; i++) {\n          maybeSchedule(\n            scheduler,\n            () => {\n              const source = from(observables[i], scheduler as any);\n              let hasFirstValue = false;\n              source.subscribe(\n                createOperatorSubscriber(\n                  subscriber,\n                  (value) => {\n                    // When we get a value, record it in our set of values.\n                    values[i] = value;\n                    if (!hasFirstValue) {\n                      // If this is our first value, record that.\n                      hasFirstValue = true;\n                      remainingFirstValues--;\n                    }\n                    if (!remainingFirstValues) {\n                      // We're not waiting for any more\n                      // first values, so we can emit!\n                      subscriber.next(valueTransform(values.slice()));\n                    }\n                  },\n                  () => {\n                    if (!--active) {\n                      // We only complete the result if we have no more active\n                      // inner observables.\n                      subscriber.complete();\n                    }\n                  }\n                )\n              );\n            },\n            subscriber\n          );\n        }\n      },\n      subscriber\n    );\n  };\n}\n\n/**\n * A small utility to handle the couple of locations where we want to schedule if a scheduler was provided,\n * but we don't if there was no scheduler.\n */\nfunction maybeSchedule(scheduler: SchedulerLike | undefined, execute: () => void, subscription: Subscription) {\n  if (scheduler) {\n    executeSchedule(subscription, scheduler, execute);\n  } else {\n    execute();\n  }\n}\n", "import { Observable } from '../Observable';\nimport { innerFrom } from '../observable/innerFrom';\nimport { Subscriber } from '../Subscriber';\nimport { ObservableInput, SchedulerLike } from '../types';\nimport { executeSchedule } from '../util/executeSchedule';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\n\n/**\n * A process embodying the general \"merge\" strategy. This is used in\n * `mergeMap` and `mergeScan` because the logic is otherwise nearly identical.\n * @param source The original source observable\n * @param subscriber The consumer subscriber\n * @param project The projection function to get our inner sources\n * @param concurrent The number of concurrent inner subscriptions\n * @param onBeforeNext Additional logic to apply before nexting to our consumer\n * @param expand If `true` this will perform an \"expand\" strategy, which differs only\n * in that it recurses, and the inner subscription must be schedule-able.\n * @param innerSubScheduler A scheduler to use to schedule inner subscriptions,\n * this is to support the expand strategy, mostly, and should be deprecated\n */\nexport function mergeInternals<T, R>(\n  source: Observable<T>,\n  subscriber: Subscriber<R>,\n  project: (value: T, index: number) => ObservableInput<R>,\n  concurrent: number,\n  onBeforeNext?: (innerValue: R) => void,\n  expand?: boolean,\n  innerSubScheduler?: SchedulerLike,\n  additionalFinalizer?: () => void\n) {\n  // Buffered values, in the event of going over our concurrency limit\n  const buffer: T[] = [];\n  // The number of active inner subscriptions.\n  let active = 0;\n  // An index to pass to our accumulator function\n  let index = 0;\n  // Whether or not the outer source has completed.\n  let isComplete = false;\n\n  /**\n   * Checks to see if we can complete our result or not.\n   */\n  const checkComplete = () => {\n    // If the outer has completed, and nothing is left in the buffer,\n    // and we don't have any active inner subscriptions, then we can\n    // Emit the state and complete.\n    if (isComplete && !buffer.length && !active) {\n      subscriber.complete();\n    }\n  };\n\n  // If we're under our concurrency limit, just start the inner subscription, otherwise buffer and wait.\n  const outerNext = (value: T) => (active < concurrent ? doInnerSub(value) : buffer.push(value));\n\n  const doInnerSub = (value: T) => {\n    // If we're expanding, we need to emit the outer values and the inner values\n    // as the inners will \"become outers\" in a way as they are recursively fed\n    // back to the projection mechanism.\n    expand && subscriber.next(value as any);\n\n    // Increment the number of active subscriptions so we can track it\n    // against our concurrency limit later.\n    active++;\n\n    // A flag used to show that the inner observable completed.\n    // This is checked during finalization to see if we should\n    // move to the next item in the buffer, if there is on.\n    let innerComplete = false;\n\n    // Start our inner subscription.\n    innerFrom(project(value, index++)).subscribe(\n      createOperatorSubscriber(\n        subscriber,\n        (innerValue) => {\n          // `mergeScan` has additional handling here. For example\n          // taking the inner value and updating state.\n          onBeforeNext?.(innerValue);\n\n          if (expand) {\n            // If we're expanding, then just recurse back to our outer\n            // handler. It will emit the value first thing.\n            outerNext(innerValue as any);\n          } else {\n            // Otherwise, emit the inner value.\n            subscriber.next(innerValue);\n          }\n        },\n        () => {\n          // Flag that we have completed, so we know to check the buffer\n          // during finalization.\n          innerComplete = true;\n        },\n        // Errors are passed to the destination.\n        undefined,\n        () => {\n          // During finalization, if the inner completed (it wasn't errored or\n          // cancelled), then we want to try the next item in the buffer if\n          // there is one.\n          if (innerComplete) {\n            // We have to wrap this in a try/catch because it happens during\n            // finalization, possibly asynchronously, and we want to pass\n            // any errors that happen (like in a projection function) to\n            // the outer Subscriber.\n            try {\n              // INNER SOURCE COMPLETE\n              // Decrement the active count to ensure that the next time\n              // we try to call `doInnerSub`, the number is accurate.\n              active--;\n              // If we have more values in the buffer, try to process those\n              // Note that this call will increment `active` ahead of the\n              // next conditional, if there were any more inner subscriptions\n              // to start.\n              while (buffer.length && active < concurrent) {\n                const bufferedValue = buffer.shift()!;\n                // Particularly for `expand`, we need to check to see if a scheduler was provided\n                // for when we want to start our inner subscription. Otherwise, we just start\n                // are next inner subscription.\n                if (innerSubScheduler) {\n                  executeSchedule(subscriber, innerSubScheduler, () => doInnerSub(bufferedValue));\n                } else {\n                  doInnerSub(bufferedValue);\n                }\n              }\n              // Check to see if we can complete, and complete if so.\n              checkComplete();\n            } catch (err) {\n              subscriber.error(err);\n            }\n          }\n        }\n      )\n    );\n  };\n\n  // Subscribe to our source observable.\n  source.subscribe(\n    createOperatorSubscriber(subscriber, outerNext, () => {\n      // Outer completed, make a note of it, and check to see if we can complete everything.\n      isComplete = true;\n      checkComplete();\n    })\n  );\n\n  // Additional finalization (for when the destination is torn down).\n  // Other finalization is added implicitly via subscription above.\n  return () => {\n    additionalFinalizer?.();\n  };\n}\n", "import { ObservableInput, OperatorFunction, ObservedValueOf } from '../types';\nimport { map } from './map';\nimport { innerFrom } from '../observable/innerFrom';\nimport { operate } from '../util/lift';\nimport { mergeInternals } from './mergeInternals';\nimport { isFunction } from '../util/isFunction';\n\n/* tslint:disable:max-line-length */\nexport function mergeMap<T, O extends ObservableInput<any>>(\n  project: (value: T, index: number) => O,\n  concurrent?: number\n): OperatorFunction<T, ObservedValueOf<O>>;\n/** @deprecated The `resultSelector` parameter will be removed in v8. Use an inner `map` instead. Details: https://rxjs.dev/deprecations/resultSelector */\nexport function mergeMap<T, O extends ObservableInput<any>>(\n  project: (value: T, index: number) => O,\n  resultSelector: undefined,\n  concurrent?: number\n): OperatorFunction<T, ObservedValueOf<O>>;\n/** @deprecated The `resultSelector` parameter will be removed in v8. Use an inner `map` instead. Details: https://rxjs.dev/deprecations/resultSelector */\nexport function mergeMap<T, R, O extends ObservableInput<any>>(\n  project: (value: T, index: number) => O,\n  resultSelector: (outerValue: T, innerValue: ObservedValueOf<O>, outerIndex: number, innerIndex: number) => R,\n  concurrent?: number\n): OperatorFunction<T, R>;\n/* tslint:enable:max-line-length */\n\n/**\n * Projects each source value to an Observable which is merged in the output\n * Observable.\n *\n * <span class=\"informal\">Maps each value to an Observable, then flattens all of\n * these inner Observables using {@link mergeAll}.</span>\n *\n * ![](mergeMap.png)\n *\n * Returns an Observable that emits items based on applying a function that you\n * supply to each item emitted by the source Observable, where that function\n * returns an Observable, and then merging those resulting Observables and\n * emitting the results of this merger.\n *\n * ## Example\n *\n * Map and flatten each letter to an Observable ticking every 1 second\n *\n * ```ts\n * import { of, mergeMap, interval, map } from 'rxjs';\n *\n * const letters = of('a', 'b', 'c');\n * const result = letters.pipe(\n *   mergeMap(x => interval(1000).pipe(map(i => x + i)))\n * );\n *\n * result.subscribe(x => console.log(x));\n *\n * // Results in the following:\n * // a0\n * // b0\n * // c0\n * // a1\n * // b1\n * // c1\n * // continues to list a, b, c every second with respective ascending integers\n * ```\n *\n * @see {@link concatMap}\n * @see {@link exhaustMap}\n * @see {@link merge}\n * @see {@link mergeAll}\n * @see {@link mergeMapTo}\n * @see {@link mergeScan}\n * @see {@link switchMap}\n *\n * @param project A function that, when applied to an item emitted by the source\n * Observable, returns an Observable.\n * @param concurrent Maximum number of `ObservableInput`s being subscribed to concurrently.\n * @return A function that returns an Observable that emits the result of\n * applying the projection function (and the optional deprecated\n * `resultSelector`) to each item emitted by the source Observable and merging\n * the results of the Observables obtained from this transformation.\n */\nexport function mergeMap<T, R, O extends ObservableInput<any>>(\n  project: (value: T, index: number) => O,\n  resultSelector?: ((outerValue: T, innerValue: ObservedValueOf<O>, outerIndex: number, innerIndex: number) => R) | number,\n  concurrent: number = Infinity\n): OperatorFunction<T, ObservedValueOf<O> | R> {\n  if (isFunction(resultSelector)) {\n    // DEPRECATED PATH\n    return mergeMap((a, i) => map((b: any, ii: number) => resultSelector(a, b, i, ii))(innerFrom(project(a, i))), concurrent);\n  } else if (typeof resultSelector === 'number') {\n    concurrent = resultSelector;\n  }\n\n  return operate((source, subscriber) => mergeInternals(source, subscriber, project, concurrent));\n}\n", "import { mergeMap } from './mergeMap';\nimport { identity } from '../util/identity';\nimport { OperatorFunction, ObservableInput, ObservedValueOf } from '../types';\n\n/**\n * Converts a higher-order Observable into a first-order Observable which\n * concurrently delivers all values that are emitted on the inner Observables.\n *\n * <span class=\"informal\">Flattens an Observable-of-Observables.</span>\n *\n * ![](mergeAll.png)\n *\n * `mergeAll` subscribes to an Observable that emits Observables, also known as\n * a higher-order Observable. Each time it observes one of these emitted inner\n * Observables, it subscribes to that and delivers all the values from the\n * inner Observable on the output Observable. The output Observable only\n * completes once all inner Observables have completed. Any error delivered by\n * a inner Observable will be immediately emitted on the output Observable.\n *\n * ## Examples\n *\n * Spawn a new interval Observable for each click event, and blend their outputs as one Observable\n *\n * ```ts\n * import { fromEvent, map, interval, mergeAll } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const higherOrder = clicks.pipe(map(() => interval(1000)));\n * const firstOrder = higherOrder.pipe(mergeAll());\n *\n * firstOrder.subscribe(x => console.log(x));\n * ```\n *\n * Count from 0 to 9 every second for each click, but only allow 2 concurrent timers\n *\n * ```ts\n * import { fromEvent, map, interval, take, mergeAll } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const higherOrder = clicks.pipe(\n *   map(() => interval(1000).pipe(take(10)))\n * );\n * const firstOrder = higherOrder.pipe(mergeAll(2));\n *\n * firstOrder.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link combineLatestAll}\n * @see {@link concatAll}\n * @see {@link exhaustAll}\n * @see {@link merge}\n * @see {@link mergeMap}\n * @see {@link mergeMapTo}\n * @see {@link mergeScan}\n * @see {@link switchAll}\n * @see {@link switchMap}\n * @see {@link zipAll}\n *\n * @param concurrent Maximum number of inner Observables being subscribed to\n * concurrently.\n * @return A function that returns an Observable that emits values coming from\n * all the inner Observables emitted by the source Observable.\n */\nexport function mergeAll<O extends ObservableInput<any>>(concurrent: number = Infinity): OperatorFunction<O, ObservedValueOf<O>> {\n  return mergeMap(identity, concurrent);\n}\n", "import { mergeAll } from './mergeAll';\nimport { OperatorFunction, ObservableInput, ObservedValueOf } from '../types';\n\n/**\n * Converts a higher-order Observable into a first-order Observable by\n * concatenating the inner Observables in order.\n *\n * <span class=\"informal\">Flattens an Observable-of-Observables by putting one\n * inner Observable after the other.</span>\n *\n * ![](concatAll.svg)\n *\n * Joins every Observable emitted by the source (a higher-order Observable), in\n * a serial fashion. It subscribes to each inner Observable only after the\n * previous inner Observable has completed, and merges all of their values into\n * the returned observable.\n *\n * __Warning:__ If the source Observable emits Observables quickly and\n * endlessly, and the inner Observables it emits generally complete slower than\n * the source emits, you can run into memory issues as the incoming Observables\n * collect in an unbounded buffer.\n *\n * Note: `concatAll` is equivalent to `mergeAll` with concurrency parameter set\n * to `1`.\n *\n * ## Example\n *\n * For each click event, tick every second from 0 to 3, with no concurrency\n *\n * ```ts\n * import { fromEvent, map, interval, take, concatAll } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const higherOrder = clicks.pipe(\n *   map(() => interval(1000).pipe(take(4)))\n * );\n * const firstOrder = higherOrder.pipe(concatAll());\n * firstOrder.subscribe(x => console.log(x));\n *\n * // Results in the following:\n * // (results are not concurrent)\n * // For every click on the \"document\" it will emit values 0 to 3 spaced\n * // on a 1000ms interval\n * // one click = 1000ms-> 0 -1000ms-> 1 -1000ms-> 2 -1000ms-> 3\n * ```\n *\n * @see {@link combineLatestAll}\n * @see {@link concat}\n * @see {@link concatMap}\n * @see {@link concatMapTo}\n * @see {@link exhaustAll}\n * @see {@link mergeAll}\n * @see {@link switchAll}\n * @see {@link switchMap}\n * @see {@link zipAll}\n *\n * @return A function that returns an Observable emitting values from all the\n * inner Observables concatenated.\n */\nexport function concatAll<O extends ObservableInput<any>>(): OperatorFunction<O, ObservedValueOf<O>> {\n  return mergeAll(1);\n}\n", "import { Observable } from '../Observable';\nimport { ObservableInputTuple, SchedulerLike } from '../types';\nimport { concatAll } from '../operators/concatAll';\nimport { popScheduler } from '../util/args';\nimport { from } from './from';\n\nexport function concat<T extends readonly unknown[]>(...inputs: [...ObservableInputTuple<T>]): Observable<T[number]>;\nexport function concat<T extends readonly unknown[]>(\n  ...inputsAndScheduler: [...ObservableInputTuple<T>, SchedulerLike]\n): Observable<T[number]>;\n\n/**\n * Creates an output Observable which sequentially emits all values from the first given\n * Observable and then moves on to the next.\n *\n * <span class=\"informal\">Concatenates multiple Observables together by\n * sequentially emitting their values, one Observable after the other.</span>\n *\n * ![](concat.png)\n *\n * `concat` joins multiple Observables together, by subscribing to them one at a time and\n * merging their results into the output Observable. You can pass either an array of\n * Observables, or put them directly as arguments. Passing an empty array will result\n * in Observable that completes immediately.\n *\n * `concat` will subscribe to first input Observable and emit all its values, without\n * changing or affecting them in any way. When that Observable completes, it will\n * subscribe to then next Observable passed and, again, emit its values. This will be\n * repeated, until the operator runs out of Observables. When last input Observable completes,\n * `concat` will complete as well. At any given moment only one Observable passed to operator\n * emits values. If you would like to emit values from passed Observables concurrently, check out\n * {@link merge} instead, especially with optional `concurrent` parameter. As a matter of fact,\n * `concat` is an equivalent of `merge` operator with `concurrent` parameter set to `1`.\n *\n * Note that if some input Observable never completes, `concat` will also never complete\n * and Observables following the one that did not complete will never be subscribed. On the other\n * hand, if some Observable simply completes immediately after it is subscribed, it will be\n * invisible for `concat`, which will just move on to the next Observable.\n *\n * If any Observable in chain errors, instead of passing control to the next Observable,\n * `concat` will error immediately as well. Observables that would be subscribed after\n * the one that emitted error, never will.\n *\n * If you pass to `concat` the same Observable many times, its stream of values\n * will be \"replayed\" on every subscription, which means you can repeat given Observable\n * as many times as you like. If passing the same Observable to `concat` 1000 times becomes tedious,\n * you can always use {@link repeat}.\n *\n * ## Examples\n *\n * Concatenate a timer counting from 0 to 3 with a synchronous sequence from 1 to 10\n *\n * ```ts\n * import { interval, take, range, concat } from 'rxjs';\n *\n * const timer = interval(1000).pipe(take(4));\n * const sequence = range(1, 10);\n * const result = concat(timer, sequence);\n * result.subscribe(x => console.log(x));\n *\n * // results in:\n * // 0 -1000ms-> 1 -1000ms-> 2 -1000ms-> 3 -immediate-> 1 ... 10\n * ```\n *\n * Concatenate 3 Observables\n *\n * ```ts\n * import { interval, take, concat } from 'rxjs';\n *\n * const timer1 = interval(1000).pipe(take(10));\n * const timer2 = interval(2000).pipe(take(6));\n * const timer3 = interval(500).pipe(take(10));\n *\n * const result = concat(timer1, timer2, timer3);\n * result.subscribe(x => console.log(x));\n *\n * // results in the following:\n * // (Prints to console sequentially)\n * // -1000ms-> 0 -1000ms-> 1 -1000ms-> ... 9\n * // -2000ms-> 0 -2000ms-> 1 -2000ms-> ... 5\n * // -500ms-> 0 -500ms-> 1 -500ms-> ... 9\n * ```\n *\n * Concatenate the same Observable to repeat it\n *\n * ```ts\n * import { interval, take, concat } from 'rxjs';\n *\n * const timer = interval(1000).pipe(take(2));\n *\n * concat(timer, timer) // concatenating the same Observable!\n *   .subscribe({\n *     next: value => console.log(value),\n *     complete: () => console.log('...and it is done!')\n *   });\n *\n * // Logs:\n * // 0 after 1s\n * // 1 after 2s\n * // 0 after 3s\n * // 1 after 4s\n * // '...and it is done!' also after 4s\n * ```\n *\n * @see {@link concatAll}\n * @see {@link concatMap}\n * @see {@link concatMapTo}\n * @see {@link startWith}\n * @see {@link endWith}\n *\n * @param args `ObservableInput`s to concatenate.\n */\nexport function concat(...args: any[]): Observable<unknown> {\n  return concatAll()(from(args, popScheduler(args)));\n}\n", "import { Observable } from '../Observable';\nimport { ObservedValueOf, ObservableInput } from '../types';\nimport { innerFrom } from './innerFrom';\n\n/**\n * Creates an Observable that, on subscribe, calls an Observable factory to\n * make an Observable for each new Observer.\n *\n * <span class=\"informal\">Creates the Observable lazily, that is, only when it\n * is subscribed.\n * </span>\n *\n * ![](defer.png)\n *\n * `defer` allows you to create an Observable only when the Observer\n * subscribes. It waits until an Observer subscribes to it, calls the given\n * factory function to get an Observable -- where a factory function typically\n * generates a new Observable -- and subscribes the Observer to this Observable.\n * In case the factory function returns a falsy value, then EMPTY is used as\n * Observable instead. Last but not least, an exception during the factory\n * function call is transferred to the Observer by calling `error`.\n *\n * ## Example\n *\n * Subscribe to either an Observable of clicks or an Observable of interval, at random\n *\n * ```ts\n * import { defer, fromEvent, interval } from 'rxjs';\n *\n * const clicksOrInterval = defer(() => {\n *   return Math.random() > 0.5\n *     ? fromEvent(document, 'click')\n *     : interval(1000);\n * });\n * clicksOrInterval.subscribe(x => console.log(x));\n *\n * // Results in the following behavior:\n * // If the result of Math.random() is greater than 0.5 it will listen\n * // for clicks anywhere on the \"document\"; when document is clicked it\n * // will log a MouseEvent object to the console. If the result is less\n * // than 0.5 it will emit ascending numbers, one every second(1000ms).\n * ```\n *\n * @see {@link Observable}\n *\n * @param observableFactory The Observable factory function to invoke for each\n * Observer that subscribes to the output Observable. May also return any\n * `ObservableInput`, which will be converted on the fly to an Observable.\n * @return An Observable whose Observers' subscriptions trigger an invocation of the\n * given Observable factory function.\n */\nexport function defer<R extends ObservableInput<any>>(observableFactory: () => R): Observable<ObservedValueOf<R>> {\n  return new Observable<ObservedValueOf<R>>((subscriber) => {\n    innerFrom(observableFactory()).subscribe(subscriber);\n  });\n}\n", "import { innerFrom } from '../observable/innerFrom';\nimport { Observable } from '../Observable';\nimport { mergeMap } from '../operators/mergeMap';\nimport { isArrayLike } from '../util/isArrayLike';\nimport { isFunction } from '../util/isFunction';\nimport { mapOneOrManyArgs } from '../util/mapOneOrManyArgs';\n\n// These constants are used to create handler registry functions using array mapping below.\nconst nodeEventEmitterMethods = ['addListener', 'removeListener'] as const;\nconst eventTargetMethods = ['addEventListener', 'removeEventListener'] as const;\nconst jqueryMethods = ['on', 'off'] as const;\n\nexport interface NodeStyleEventEmitter {\n  addListener(eventName: string | symbol, handler: NodeEventHandler): this;\n  removeListener(eventName: string | symbol, handler: NodeEventHandler): this;\n}\n\nexport type NodeEventHandler = (...args: any[]) => void;\n\n// For APIs that implement `addListener` and `removeListener` methods that may\n// not use the same arguments or return EventEmitter values\n// such as React Native\nexport interface NodeCompatibleEventEmitter {\n  addListener(eventName: string, handler: NodeEventHandler): void | {};\n  removeListener(eventName: string, handler: NodeEventHandler): void | {};\n}\n\n// Use handler types like those in @types/jquery. See:\n// https://github.com/DefinitelyTyped/DefinitelyTyped/blob/847731ba1d7fa6db6b911c0e43aa0afe596e7723/types/jquery/misc.d.ts#L6395\nexport interface JQueryStyleEventEmitter<TContext, T> {\n  on(eventName: string, handler: (this: TContext, t: T, ...args: any[]) => any): void;\n  off(eventName: string, handler: (this: TContext, t: T, ...args: any[]) => any): void;\n}\n\nexport interface EventListenerObject<E> {\n  handleEvent(evt: E): void;\n}\n\nexport interface HasEventTargetAddRemove<E> {\n  addEventListener(\n    type: string,\n    listener: ((evt: E) => void) | EventListenerObject<E> | null,\n    options?: boolean | AddEventListenerOptions\n  ): void;\n  removeEventListener(\n    type: string,\n    listener: ((evt: E) => void) | EventListenerObject<E> | null,\n    options?: EventListenerOptions | boolean\n  ): void;\n}\n\nexport interface EventListenerOptions {\n  capture?: boolean;\n  passive?: boolean;\n  once?: boolean;\n}\n\nexport interface AddEventListenerOptions extends EventListenerOptions {\n  once?: boolean;\n  passive?: boolean;\n}\n\nexport function fromEvent<T>(target: HasEventTargetAddRemove<T> | ArrayLike<HasEventTargetAddRemove<T>>, eventName: string): Observable<T>;\nexport function fromEvent<T, R>(\n  target: HasEventTargetAddRemove<T> | ArrayLike<HasEventTargetAddRemove<T>>,\n  eventName: string,\n  resultSelector: (event: T) => R\n): Observable<R>;\nexport function fromEvent<T>(\n  target: HasEventTargetAddRemove<T> | ArrayLike<HasEventTargetAddRemove<T>>,\n  eventName: string,\n  options: EventListenerOptions\n): Observable<T>;\nexport function fromEvent<T, R>(\n  target: HasEventTargetAddRemove<T> | ArrayLike<HasEventTargetAddRemove<T>>,\n  eventName: string,\n  options: EventListenerOptions,\n  resultSelector: (event: T) => R\n): Observable<R>;\n\nexport function fromEvent(target: NodeStyleEventEmitter | ArrayLike<NodeStyleEventEmitter>, eventName: string): Observable<unknown>;\n/** @deprecated Do not specify explicit type parameters. Signatures with type parameters that cannot be inferred will be removed in v8. */\nexport function fromEvent<T>(target: NodeStyleEventEmitter | ArrayLike<NodeStyleEventEmitter>, eventName: string): Observable<T>;\nexport function fromEvent<R>(\n  target: NodeStyleEventEmitter | ArrayLike<NodeStyleEventEmitter>,\n  eventName: string,\n  resultSelector: (...args: any[]) => R\n): Observable<R>;\n\nexport function fromEvent(\n  target: NodeCompatibleEventEmitter | ArrayLike<NodeCompatibleEventEmitter>,\n  eventName: string\n): Observable<unknown>;\n/** @deprecated Do not specify explicit type parameters. Signatures with type parameters that cannot be inferred will be removed in v8. */\nexport function fromEvent<T>(target: NodeCompatibleEventEmitter | ArrayLike<NodeCompatibleEventEmitter>, eventName: string): Observable<T>;\nexport function fromEvent<R>(\n  target: NodeCompatibleEventEmitter | ArrayLike<NodeCompatibleEventEmitter>,\n  eventName: string,\n  resultSelector: (...args: any[]) => R\n): Observable<R>;\n\nexport function fromEvent<T>(\n  target: JQueryStyleEventEmitter<any, T> | ArrayLike<JQueryStyleEventEmitter<any, T>>,\n  eventName: string\n): Observable<T>;\nexport function fromEvent<T, R>(\n  target: JQueryStyleEventEmitter<any, T> | ArrayLike<JQueryStyleEventEmitter<any, T>>,\n  eventName: string,\n  resultSelector: (value: T, ...args: any[]) => R\n): Observable<R>;\n\n/**\n * Creates an Observable that emits events of a specific type coming from the\n * given event target.\n *\n * <span class=\"informal\">Creates an Observable from DOM events, or Node.js\n * EventEmitter events or others.</span>\n *\n * ![](fromEvent.png)\n *\n * `fromEvent` accepts as a first argument event target, which is an object with methods\n * for registering event handler functions. As a second argument it takes string that indicates\n * type of event we want to listen for. `fromEvent` supports selected types of event targets,\n * which are described in detail below. If your event target does not match any of the ones listed,\n * you should use {@link fromEventPattern}, which can be used on arbitrary APIs.\n * When it comes to APIs supported by `fromEvent`, their methods for adding and removing event\n * handler functions have different names, but they all accept a string describing event type\n * and function itself, which will be called whenever said event happens.\n *\n * Every time resulting Observable is subscribed, event handler function will be registered\n * to event target on given event type. When that event fires, value\n * passed as a first argument to registered function will be emitted by output Observable.\n * When Observable is unsubscribed, function will be unregistered from event target.\n *\n * Note that if event target calls registered function with more than one argument, second\n * and following arguments will not appear in resulting stream. In order to get access to them,\n * you can pass to `fromEvent` optional project function, which will be called with all arguments\n * passed to event handler. Output Observable will then emit value returned by project function,\n * instead of the usual value.\n *\n * Remember that event targets listed below are checked via duck typing. It means that\n * no matter what kind of object you have and no matter what environment you work in,\n * you can safely use `fromEvent` on that object if it exposes described methods (provided\n * of course they behave as was described above). So for example if Node.js library exposes\n * event target which has the same method names as DOM EventTarget, `fromEvent` is still\n * a good choice.\n *\n * If the API you use is more callback then event handler oriented (subscribed\n * callback function fires only once and thus there is no need to manually\n * unregister it), you should use {@link bindCallback} or {@link bindNodeCallback}\n * instead.\n *\n * `fromEvent` supports following types of event targets:\n *\n * **DOM EventTarget**\n *\n * This is an object with `addEventListener` and `removeEventListener` methods.\n *\n * In the browser, `addEventListener` accepts - apart from event type string and event\n * handler function arguments - optional third parameter, which is either an object or boolean,\n * both used for additional configuration how and when passed function will be called. When\n * `fromEvent` is used with event target of that type, you can provide this values\n * as third parameter as well.\n *\n * **Node.js EventEmitter**\n *\n * An object with `addListener` and `removeListener` methods.\n *\n * **JQuery-style event target**\n *\n * An object with `on` and `off` methods\n *\n * **DOM NodeList**\n *\n * List of DOM Nodes, returned for example by `document.querySelectorAll` or `Node.childNodes`.\n *\n * Although this collection is not event target in itself, `fromEvent` will iterate over all Nodes\n * it contains and install event handler function in every of them. When returned Observable\n * is unsubscribed, function will be removed from all Nodes.\n *\n * **DOM HtmlCollection**\n *\n * Just as in case of NodeList it is a collection of DOM nodes. Here as well event handler function is\n * installed and removed in each of elements.\n *\n *\n * ## Examples\n *\n * Emit clicks happening on the DOM document\n *\n * ```ts\n * import { fromEvent } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * clicks.subscribe(x => console.log(x));\n *\n * // Results in:\n * // MouseEvent object logged to console every time a click\n * // occurs on the document.\n * ```\n *\n * Use `addEventListener` with capture option\n *\n * ```ts\n * import { fromEvent } from 'rxjs';\n *\n * const div = document.createElement('div');\n * div.style.cssText = 'width: 200px; height: 200px; background: #09c;';\n * document.body.appendChild(div);\n *\n * // note optional configuration parameter which will be passed to addEventListener\n * const clicksInDocument = fromEvent(document, 'click', { capture: true });\n * const clicksInDiv = fromEvent(div, 'click');\n *\n * clicksInDocument.subscribe(() => console.log('document'));\n * clicksInDiv.subscribe(() => console.log('div'));\n *\n * // By default events bubble UP in DOM tree, so normally\n * // when we would click on div in document\n * // \"div\" would be logged first and then \"document\".\n * // Since we specified optional `capture` option, document\n * // will catch event when it goes DOWN DOM tree, so console\n * // will log \"document\" and then \"div\".\n * ```\n *\n * @see {@link bindCallback}\n * @see {@link bindNodeCallback}\n * @see {@link fromEventPattern}\n *\n * @param target The DOM EventTarget, Node.js EventEmitter, JQuery-like event target,\n * NodeList or HTMLCollection to attach the event handler to.\n * @param eventName The event name of interest, being emitted by the `target`.\n * @param options Options to pass through to the underlying `addListener`,\n * `addEventListener` or `on` functions.\n * @param resultSelector A mapping function used to transform events. It takes the\n * arguments from the event handler and should return a single value.\n * @return An Observable emitting events registered through `target`'s\n * listener handlers.\n */\nexport function fromEvent<T>(\n  target: any,\n  eventName: string,\n  options?: EventListenerOptions | ((...args: any[]) => T),\n  resultSelector?: (...args: any[]) => T\n): Observable<T> {\n  if (isFunction(options)) {\n    resultSelector = options;\n    options = undefined;\n  }\n  if (resultSelector) {\n    return fromEvent<T>(target, eventName, options as EventListenerOptions).pipe(mapOneOrManyArgs(resultSelector));\n  }\n\n  // Figure out our add and remove methods. In order to do this,\n  // we are going to analyze the target in a preferred order, if\n  // the target matches a given signature, we take the two \"add\" and \"remove\"\n  // method names and apply them to a map to create opposite versions of the\n  // same function. This is because they all operate in duplicate pairs,\n  // `addListener(name, handler)`, `removeListener(name, handler)`, for example.\n  // The call only differs by method name, as to whether or not you're adding or removing.\n  const [add, remove] =\n    // If it is an EventTarget, we need to use a slightly different method than the other two patterns.\n    isEventTarget(target)\n      ? eventTargetMethods.map((methodName) => (handler: any) => target[methodName](eventName, handler, options as EventListenerOptions))\n      : // In all other cases, the call pattern is identical with the exception of the method names.\n      isNodeStyleEventEmitter(target)\n      ? nodeEventEmitterMethods.map(toCommonHandlerRegistry(target, eventName))\n      : isJQueryStyleEventEmitter(target)\n      ? jqueryMethods.map(toCommonHandlerRegistry(target, eventName))\n      : [];\n\n  // If add is falsy, it's because we didn't match a pattern above.\n  // Check to see if it is an ArrayLike, because if it is, we want to\n  // try to apply fromEvent to all of it's items. We do this check last,\n  // because there are may be some types that are both ArrayLike *and* implement\n  // event registry points, and we'd rather delegate to that when possible.\n  if (!add) {\n    if (isArrayLike(target)) {\n      return mergeMap((subTarget: any) => fromEvent(subTarget, eventName, options as EventListenerOptions))(\n        innerFrom(target)\n      ) as Observable<T>;\n    }\n  }\n\n  // If add is falsy and we made it here, it's because we didn't\n  // match any valid target objects above.\n  if (!add) {\n    throw new TypeError('Invalid event target');\n  }\n\n  return new Observable<T>((subscriber) => {\n    // The handler we are going to register. Forwards the event object, by itself, or\n    // an array of arguments to the event handler, if there is more than one argument,\n    // to the consumer.\n    const handler = (...args: any[]) => subscriber.next(1 < args.length ? args : args[0]);\n    // Do the work of adding the handler to the target.\n    add(handler);\n    // When we finalize, we want to remove the handler and free up memory.\n    return () => remove!(handler);\n  });\n}\n\n/**\n * Used to create `add` and `remove` functions to register and unregister event handlers\n * from a target in the most common handler pattern, where there are only two arguments.\n * (e.g.  `on(name, fn)`, `off(name, fn)`, `addListener(name, fn)`, or `removeListener(name, fn)`)\n * @param target The target we're calling methods on\n * @param eventName The event name for the event we're creating register or unregister functions for\n */\nfunction toCommonHandlerRegistry(target: any, eventName: string) {\n  return (methodName: string) => (handler: any) => target[methodName](eventName, handler);\n}\n\n/**\n * Checks to see if the target implements the required node-style EventEmitter methods\n * for adding and removing event handlers.\n * @param target the object to check\n */\nfunction isNodeStyleEventEmitter(target: any): target is NodeStyleEventEmitter {\n  return isFunction(target.addListener) && isFunction(target.removeListener);\n}\n\n/**\n * Checks to see if the target implements the required jQuery-style EventEmitter methods\n * for adding and removing event handlers.\n * @param target the object to check\n */\nfunction isJQueryStyleEventEmitter(target: any): target is JQueryStyleEventEmitter<any, any> {\n  return isFunction(target.on) && isFunction(target.off);\n}\n\n/**\n * Checks to see if the target implements the required EventTarget methods\n * for adding and removing event handlers.\n * @param target the object to check\n */\nfunction isEventTarget(target: any): target is HasEventTargetAddRemove<any> {\n  return isFunction(target.addEventListener) && isFunction(target.removeEventListener);\n}\n", "import { Observable } from '../Observable';\nimport { isFunction } from '../util/isFunction';\nimport { NodeEventHandler } from './fromEvent';\nimport { mapOneOrManyArgs } from '../util/mapOneOrManyArgs';\n\n/* tslint:disable:max-line-length */\nexport function fromEventPattern<T>(\n  addHandler: (handler: NodeEventHandler) => any,\n  removeHandler?: (handler: NodeEventHandler, signal?: any) => void\n): Observable<T>;\nexport function fromEventPattern<T>(\n  addHandler: (handler: NodeEventHandler) => any,\n  removeHandler?: (handler: NodeEventHandler, signal?: any) => void,\n  resultSelector?: (...args: any[]) => T\n): Observable<T>;\n/* tslint:enable:max-line-length */\n\n/**\n * Creates an Observable from an arbitrary API for registering event handlers.\n *\n * <span class=\"informal\">When that method for adding event handler was something {@link fromEvent}\n * was not prepared for.</span>\n *\n * ![](fromEventPattern.png)\n *\n * `fromEventPattern` allows you to convert into an Observable any API that supports registering handler functions\n * for events. It is similar to {@link fromEvent}, but far\n * more flexible. In fact, all use cases of {@link fromEvent} could be easily handled by\n * `fromEventPattern` (although in slightly more verbose way).\n *\n * This operator accepts as a first argument an `addHandler` function, which will be injected with\n * handler parameter. That handler is actually an event handler function that you now can pass\n * to API expecting it. `addHandler` will be called whenever Observable\n * returned by the operator is subscribed, so registering handler in API will not\n * necessarily happen when `fromEventPattern` is called.\n *\n * After registration, every time an event that we listen to happens,\n * Observable returned by `fromEventPattern` will emit value that event handler\n * function was called with. Note that if event handler was called with more\n * than one argument, second and following arguments will not appear in the Observable.\n *\n * If API you are using allows to unregister event handlers as well, you can pass to `fromEventPattern`\n * another function - `removeHandler` - as a second parameter. It will be injected\n * with the same handler function as before, which now you can use to unregister\n * it from the API. `removeHandler` will be called when consumer of resulting Observable\n * unsubscribes from it.\n *\n * In some APIs unregistering is actually handled differently. Method registering an event handler\n * returns some kind of token, which is later used to identify which function should\n * be unregistered or it itself has method that unregisters event handler.\n * If that is the case with your API, make sure token returned\n * by registering method is returned by `addHandler`. Then it will be passed\n * as a second argument to `removeHandler`, where you will be able to use it.\n *\n * If you need access to all event handler parameters (not only the first one),\n * or you need to transform them in any way, you can call `fromEventPattern` with optional\n * third parameter - project function which will accept all arguments passed to\n * event handler when it is called. Whatever is returned from project function will appear on\n * resulting stream instead of usual event handlers first argument. This means\n * that default project can be thought of as function that takes its first parameter\n * and ignores the rest.\n *\n * ## Examples\n *\n * Emits clicks happening on the DOM document\n *\n * ```ts\n * import { fromEventPattern } from 'rxjs';\n *\n * function addClickHandler(handler) {\n *   document.addEventListener('click', handler);\n * }\n *\n * function removeClickHandler(handler) {\n *   document.removeEventListener('click', handler);\n * }\n *\n * const clicks = fromEventPattern(\n *   addClickHandler,\n *   removeClickHandler\n * );\n * clicks.subscribe(x => console.log(x));\n *\n * // Whenever you click anywhere in the browser, DOM MouseEvent\n * // object will be logged.\n * ```\n *\n * Use with API that returns cancellation token\n *\n * ```ts\n * import { fromEventPattern } from 'rxjs';\n *\n * const token = someAPI.registerEventHandler(function() {});\n * someAPI.unregisterEventHandler(token); // this APIs cancellation method accepts\n *                                        // not handler itself, but special token.\n *\n * const someAPIObservable = fromEventPattern(\n *   function(handler) { return someAPI.registerEventHandler(handler); }, // Note that we return the token here...\n *   function(handler, token) { someAPI.unregisterEventHandler(token); }  // ...to then use it here.\n * );\n * ```\n *\n * Use with project function\n *\n * ```ts\n * import { fromEventPattern } from 'rxjs';\n *\n * someAPI.registerEventHandler((eventType, eventMessage) => {\n *   console.log(eventType, eventMessage); // Logs 'EVENT_TYPE' 'EVENT_MESSAGE' to console.\n * });\n *\n * const someAPIObservable = fromEventPattern(\n *   handler => someAPI.registerEventHandler(handler),\n *   handler => someAPI.unregisterEventHandler(handler)\n *   (eventType, eventMessage) => eventType + ' --- ' + eventMessage // without that function only 'EVENT_TYPE'\n * );                                                                // would be emitted by the Observable\n *\n * someAPIObservable.subscribe(value => console.log(value));\n *\n * // Logs:\n * // 'EVENT_TYPE --- EVENT_MESSAGE'\n * ```\n *\n * @see {@link fromEvent}\n * @see {@link bindCallback}\n * @see {@link bindNodeCallback}\n *\n * @param addHandler A function that takes a `handler` function as argument and attaches it\n * somehow to the actual source of events.\n * @param removeHandler A function that takes a `handler` function as an argument and removes\n * it from the event source. If `addHandler` returns some kind of token, `removeHandler` function\n * will have it as a second parameter.\n * @param resultSelector A function to transform results. It takes the arguments from the event\n * handler and should return a single value.\n * @return Observable which, when an event happens, emits first parameter passed to registered\n * event handler. Alternatively it emits whatever project function returns at that moment.\n */\nexport function fromEventPattern<T>(\n  addHandler: (handler: NodeEventHandler) => any,\n  removeHandler?: (handler: NodeEventHandler, signal?: any) => void,\n  resultSelector?: (...args: any[]) => T\n): Observable<T | T[]> {\n  if (resultSelector) {\n    return fromEventPattern<T>(addHandler, removeHandler).pipe(mapOneOrManyArgs(resultSelector));\n  }\n\n  return new Observable<T | T[]>((subscriber) => {\n    const handler = (...e: T[]) => subscriber.next(e.length === 1 ? e[0] : e);\n    const retValue = addHandler(handler);\n    return isFunction(removeHandler) ? () => removeHandler(handler, retValue) : undefined;\n  });\n}\n", "import { Observable } from '../Observable';\nimport { SchedulerLike } from '../types';\nimport { async as asyncScheduler } from '../scheduler/async';\nimport { isScheduler } from '../util/isScheduler';\nimport { isValidDate } from '../util/isDate';\n\n/**\n * Creates an observable that will wait for a specified time period, or exact date, before\n * emitting the number 0.\n *\n * <span class=\"informal\">Used to emit a notification after a delay.</span>\n *\n * This observable is useful for creating delays in code, or racing against other values\n * for ad-hoc timeouts.\n *\n * The `delay` is specified by default in milliseconds, however providing a custom scheduler could\n * create a different behavior.\n *\n * ## Examples\n *\n * Wait 3 seconds and start another observable\n *\n * You might want to use `timer` to delay subscription to an\n * observable by a set amount of time. Here we use a timer with\n * {@link concatMapTo} or {@link concatMap} in order to wait\n * a few seconds and start a subscription to a source.\n *\n * ```ts\n * import { of, timer, concatMap } from 'rxjs';\n *\n * // This could be any observable\n * const source = of(1, 2, 3);\n *\n * timer(3000)\n *   .pipe(concatMap(() => source))\n *   .subscribe(console.log);\n * ```\n *\n * Take all values until the start of the next minute\n *\n * Using a `Date` as the trigger for the first emission, you can\n * do things like wait until midnight to fire an event, or in this case,\n * wait until a new minute starts (chosen so the example wouldn't take\n * too long to run) in order to stop watching a stream. Leveraging\n * {@link takeUntil}.\n *\n * ```ts\n * import { interval, takeUntil, timer } from 'rxjs';\n *\n * // Build a Date object that marks the\n * // next minute.\n * const currentDate = new Date();\n * const startOfNextMinute = new Date(\n *   currentDate.getFullYear(),\n *   currentDate.getMonth(),\n *   currentDate.getDate(),\n *   currentDate.getHours(),\n *   currentDate.getMinutes() + 1\n * );\n *\n * // This could be any observable stream\n * const source = interval(1000);\n *\n * const result = source.pipe(\n *   takeUntil(timer(startOfNextMinute))\n * );\n *\n * result.subscribe(console.log);\n * ```\n *\n * ### Known Limitations\n *\n * - The {@link asyncScheduler} uses `setTimeout` which has limitations for how far in the future it can be scheduled.\n *\n * - If a `scheduler` is provided that returns a timestamp other than an epoch from `now()`, and\n * a `Date` object is passed to the `dueTime` argument, the calculation for when the first emission\n * should occur will be incorrect. In this case, it would be best to do your own calculations\n * ahead of time, and pass a `number` in as the `dueTime`.\n *\n * @param due If a `number`, the amount of time in milliseconds to wait before emitting.\n * If a `Date`, the exact time at which to emit.\n * @param scheduler The scheduler to use to schedule the delay. Defaults to {@link asyncScheduler}.\n */\nexport function timer(due: number | Date, scheduler?: SchedulerLike): Observable<0>;\n\n/**\n * Creates an observable that starts an interval after a specified delay, emitting incrementing numbers -- starting at `0` --\n * on each interval after words.\n *\n * The `delay` and `intervalDuration` are specified by default in milliseconds, however providing a custom scheduler could\n * create a different behavior.\n *\n * ## Example\n *\n * ### Start an interval that starts right away\n *\n * Since {@link interval} waits for the passed delay before starting,\n * sometimes that's not ideal. You may want to start an interval immediately.\n * `timer` works well for this. Here we have both side-by-side so you can\n * see them in comparison.\n *\n * Note that this observable will never complete.\n *\n * ```ts\n * import { timer, interval } from 'rxjs';\n *\n * timer(0, 1000).subscribe(n => console.log('timer', n));\n * interval(1000).subscribe(n => console.log('interval', n));\n * ```\n *\n * ### Known Limitations\n *\n * - The {@link asyncScheduler} uses `setTimeout` which has limitations for how far in the future it can be scheduled.\n *\n * - If a `scheduler` is provided that returns a timestamp other than an epoch from `now()`, and\n * a `Date` object is passed to the `dueTime` argument, the calculation for when the first emission\n * should occur will be incorrect. In this case, it would be best to do your own calculations\n * ahead of time, and pass a `number` in as the `startDue`.\n * @param startDue If a `number`, is the time to wait before starting the interval.\n * If a `Date`, is the exact time at which to start the interval.\n * @param intervalDuration The delay between each value emitted in the interval. Passing a\n * negative number here will result in immediate completion after the first value is emitted, as though\n * no `intervalDuration` was passed at all.\n * @param scheduler The scheduler to use to schedule the delay. Defaults to {@link asyncScheduler}.\n */\nexport function timer(startDue: number | Date, intervalDuration: number, scheduler?: SchedulerLike): Observable<number>;\n\n/**\n * @deprecated The signature allowing `undefined` to be passed for `intervalDuration` will be removed in v8. Use the `timer(dueTime, scheduler?)` signature instead.\n */\nexport function timer(dueTime: number | Date, unused: undefined, scheduler?: SchedulerLike): Observable<0>;\n\nexport function timer(\n  dueTime: number | Date = 0,\n  intervalOrScheduler?: number | SchedulerLike,\n  scheduler: SchedulerLike = asyncScheduler\n): Observable<number> {\n  // Since negative intervalDuration is treated as though no\n  // interval was specified at all, we start with a negative number.\n  let intervalDuration = -1;\n\n  if (intervalOrScheduler != null) {\n    // If we have a second argument, and it's a scheduler,\n    // override the scheduler we had defaulted. Otherwise,\n    // it must be an interval.\n    if (isScheduler(intervalOrScheduler)) {\n      scheduler = intervalOrScheduler;\n    } else {\n      // Note that this *could* be negative, in which case\n      // it's like not passing an intervalDuration at all.\n      intervalDuration = intervalOrScheduler;\n    }\n  }\n\n  return new Observable((subscriber) => {\n    // If a valid date is passed, calculate how long to wait before\n    // executing the first value... otherwise, if it's a number just schedule\n    // that many milliseconds (or scheduler-specified unit size) in the future.\n    let due = isValidDate(dueTime) ? +dueTime - scheduler!.now() : dueTime;\n\n    if (due < 0) {\n      // Ensure we don't schedule in the future.\n      due = 0;\n    }\n\n    // The incrementing value we emit.\n    let n = 0;\n\n    // Start the timer.\n    return scheduler.schedule(function () {\n      if (!subscriber.closed) {\n        // Emit the next value and increment.\n        subscriber.next(n++);\n\n        if (0 <= intervalDuration) {\n          // If we have a interval after the initial timer,\n          // reschedule with the period.\n          this.schedule(undefined, intervalDuration);\n        } else {\n          // We didn't have an interval. So just complete.\n          subscriber.complete();\n        }\n      }\n    }, due);\n  });\n}\n", "import { Observable } from '../Observable';\nimport { ObservableInput, ObservableInputTuple, SchedulerLike } from '../types';\nimport { mergeAll } from '../operators/mergeAll';\nimport { innerFrom } from './innerFrom';\nimport { EMPTY } from './empty';\nimport { popNumber, popScheduler } from '../util/args';\nimport { from } from './from';\n\nexport function merge<A extends readonly unknown[]>(...sources: [...ObservableInputTuple<A>]): Observable<A[number]>;\nexport function merge<A extends readonly unknown[]>(...sourcesAndConcurrency: [...ObservableInputTuple<A>, number?]): Observable<A[number]>;\n/** @deprecated The `scheduler` parameter will be removed in v8. Use `scheduled` and `mergeAll`. Details: https://rxjs.dev/deprecations/scheduler-argument */\nexport function merge<A extends readonly unknown[]>(\n  ...sourcesAndScheduler: [...ObservableInputTuple<A>, SchedulerLike?]\n): Observable<A[number]>;\n/** @deprecated The `scheduler` parameter will be removed in v8. Use `scheduled` and `mergeAll`. Details: https://rxjs.dev/deprecations/scheduler-argument */\nexport function merge<A extends readonly unknown[]>(\n  ...sourcesAndConcurrencyAndScheduler: [...ObservableInputTuple<A>, number?, SchedulerLike?]\n): Observable<A[number]>;\n\n/**\n * Creates an output Observable which concurrently emits all values from every\n * given input Observable.\n *\n * <span class=\"informal\">Flattens multiple Observables together by blending\n * their values into one Observable.</span>\n *\n * ![](merge.png)\n *\n * `merge` subscribes to each given input Observable (as arguments), and simply\n * forwards (without doing any transformation) all the values from all the input\n * Observables to the output Observable. The output Observable only completes\n * once all input Observables have completed. Any error delivered by an input\n * Observable will be immediately emitted on the output Observable.\n *\n * ## Examples\n *\n * Merge together two Observables: 1s interval and clicks\n *\n * ```ts\n * import { merge, fromEvent, interval } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const timer = interval(1000);\n * const clicksOrTimer = merge(clicks, timer);\n * clicksOrTimer.subscribe(x => console.log(x));\n *\n * // Results in the following:\n * // timer will emit ascending values, one every second(1000ms) to console\n * // clicks logs MouseEvents to console every time the \"document\" is clicked\n * // Since the two streams are merged you see these happening\n * // as they occur.\n * ```\n *\n * Merge together 3 Observables, but run only 2 concurrently\n *\n * ```ts\n * import { interval, take, merge } from 'rxjs';\n *\n * const timer1 = interval(1000).pipe(take(10));\n * const timer2 = interval(2000).pipe(take(6));\n * const timer3 = interval(500).pipe(take(10));\n *\n * const concurrent = 2; // the argument\n * const merged = merge(timer1, timer2, timer3, concurrent);\n * merged.subscribe(x => console.log(x));\n *\n * // Results in the following:\n * // - First timer1 and timer2 will run concurrently\n * // - timer1 will emit a value every 1000ms for 10 iterations\n * // - timer2 will emit a value every 2000ms for 6 iterations\n * // - after timer1 hits its max iteration, timer2 will\n * //   continue, and timer3 will start to run concurrently with timer2\n * // - when timer2 hits its max iteration it terminates, and\n * //   timer3 will continue to emit a value every 500ms until it is complete\n * ```\n *\n * @see {@link mergeAll}\n * @see {@link mergeMap}\n * @see {@link mergeMapTo}\n * @see {@link mergeScan}\n *\n * @param args `ObservableInput`s to merge together. If the last parameter\n * is of type number, `merge` will use it to limit number of concurrently\n * subscribed `ObservableInput`s. If the last parameter is {@link SchedulerLike},\n * it will be used for scheduling the emission of values.\n * @return An Observable that emits items that are the result of every input Observable.\n */\nexport function merge(...args: (ObservableInput<unknown> | number | SchedulerLike)[]): Observable<unknown> {\n  const scheduler = popScheduler(args);\n  const concurrent = popNumber(args, Infinity);\n  const sources = args as ObservableInput<unknown>[];\n  return !sources.length\n    ? // No source provided\n      EMPTY\n    : sources.length === 1\n    ? // One source? Just return it.\n      innerFrom(sources[0])\n    : // Merge all sources\n      mergeAll(concurrent)(from(sources, scheduler));\n}\n", "import { Observable } from '../Observable';\nimport { noop } from '../util/noop';\n\n/**\n * An Observable that emits no items to the Observer and never completes.\n *\n * ![](never.png)\n *\n * A simple Observable that emits neither values nor errors nor the completion\n * notification. It can be used for testing purposes or for composing with other\n * Observables. Please note that by never emitting a complete notification, this\n * Observable keeps the subscription from being disposed automatically.\n * Subscriptions need to be manually disposed.\n *\n * ##  Example\n *\n * Emit the number 7, then never emit anything else (not even complete)\n *\n * ```ts\n * import { NEVER, startWith } from 'rxjs';\n *\n * const info = () => console.log('Will not be called');\n *\n * const result = NEVER.pipe(startWith(7));\n * result.subscribe({\n *   next: x => console.log(x),\n *   error: info,\n *   complete: info\n * });\n * ```\n *\n * @see {@link Observable}\n * @see {@link EMPTY}\n * @see {@link of}\n * @see {@link throwError}\n */\nexport const NEVER = new Observable<never>(noop);\n\n/**\n * @deprecated Replaced with the {@link NEVER} constant. Will be removed in v8.\n */\nexport function never() {\n  return NEVER;\n}\n", "const { isArray } = Array;\n\n/**\n * Used in operators and functions that accept either a list of arguments, or an array of arguments\n * as a single argument.\n */\nexport function argsOrArgArray<T>(args: (T | T[])[]): T[] {\n  return args.length === 1 && isArray(args[0]) ? args[0] : (args as T[]);\n}\n", "import { OperatorFunction, MonoTypeOperatorFunction, TruthyTypesOf } from '../types';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\n\n/** @deprecated Use a closure instead of a `thisArg`. Signatures accepting a `thisArg` will be removed in v8. */\nexport function filter<T, S extends T, A>(predicate: (this: A, value: T, index: number) => value is S, thisArg: A): OperatorFunction<T, S>;\nexport function filter<T, S extends T>(predicate: (value: T, index: number) => value is S): OperatorFunction<T, S>;\nexport function filter<T>(predicate: BooleanConstructor): OperatorFunction<T, TruthyTypesOf<T>>;\n/** @deprecated Use a closure instead of a `thisArg`. Signatures accepting a `thisArg` will be removed in v8. */\nexport function filter<T, A>(predicate: (this: A, value: T, index: number) => boolean, thisArg: A): MonoTypeOperatorFunction<T>;\nexport function filter<T>(predicate: (value: T, index: number) => boolean): MonoTypeOperatorFunction<T>;\n\n/**\n * Filter items emitted by the source Observable by only emitting those that\n * satisfy a specified predicate.\n *\n * <span class=\"informal\">Like\n * [Array.prototype.filter()](https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Array/filter),\n * it only emits a value from the source if it passes a criterion function.</span>\n *\n * ![](filter.png)\n *\n * Similar to the well-known `Array.prototype.filter` method, this operator\n * takes values from the source Observable, passes them through a `predicate`\n * function and only emits those values that yielded `true`.\n *\n * ## Example\n *\n * Emit only click events whose target was a DIV element\n *\n * ```ts\n * import { fromEvent, filter } from 'rxjs';\n *\n * const div = document.createElement('div');\n * div.style.cssText = 'width: 200px; height: 200px; background: #09c;';\n * document.body.appendChild(div);\n *\n * const clicks = fromEvent(document, 'click');\n * const clicksOnDivs = clicks.pipe(filter(ev => (<HTMLElement>ev.target).tagName === 'DIV'));\n * clicksOnDivs.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link distinct}\n * @see {@link distinctUntilChanged}\n * @see {@link distinctUntilKeyChanged}\n * @see {@link ignoreElements}\n * @see {@link partition}\n * @see {@link skip}\n *\n * @param predicate A function that\n * evaluates each value emitted by the source Observable. If it returns `true`,\n * the value is emitted, if `false` the value is not passed to the output\n * Observable. The `index` parameter is the number `i` for the i-th source\n * emission that has happened since the subscription, starting from the number\n * `0`.\n * @param thisArg An optional argument to determine the value of `this`\n * in the `predicate` function.\n * @return A function that returns an Observable that emits items from the\n * source Observable that satisfy the specified `predicate`.\n */\nexport function filter<T>(predicate: (value: T, index: number) => boolean, thisArg?: any): MonoTypeOperatorFunction<T> {\n  return operate((source, subscriber) => {\n    // An index passed to our predicate function on each call.\n    let index = 0;\n\n    // Subscribe to the source, all errors and completions are\n    // forwarded to the consumer.\n    source.subscribe(\n      // Call the predicate with the appropriate `this` context,\n      // if the predicate returns `true`, then send the value\n      // to the consumer.\n      createOperatorSubscriber(subscriber, (value) => predicate.call(thisArg, value, index++) && subscriber.next(value))\n    );\n  });\n}\n", "import { Observable } from '../Observable';\nimport { ObservableInputTuple } from '../types';\nimport { innerFrom } from './innerFrom';\nimport { argsOrArgArray } from '../util/argsOrArgArray';\nimport { EMPTY } from './empty';\nimport { createOperatorSubscriber } from '../operators/OperatorSubscriber';\nimport { popResultSelector } from '../util/args';\n\nexport function zip<A extends readonly unknown[]>(sources: [...ObservableInputTuple<A>]): Observable<A>;\nexport function zip<A extends readonly unknown[], R>(\n  sources: [...ObservableInputTuple<A>],\n  resultSelector: (...values: A) => R\n): Observable<R>;\nexport function zip<A extends readonly unknown[]>(...sources: [...ObservableInputTuple<A>]): Observable<A>;\nexport function zip<A extends readonly unknown[], R>(\n  ...sourcesAndResultSelector: [...ObservableInputTuple<A>, (...values: A) => R]\n): Observable<R>;\n\n/**\n * Combines multiple Observables to create an Observable whose values are calculated from the values, in order, of each\n * of its input Observables.\n *\n * If the last parameter is a function, this function is used to compute the created value from the input values.\n * Otherwise, an array of the input values is returned.\n *\n * ## Example\n *\n * Combine age and name from different sources\n *\n * ```ts\n * import { of, zip, map } from 'rxjs';\n *\n * const age$ = of(27, 25, 29);\n * const name$ = of('Foo', 'Bar', 'Beer');\n * const isDev$ = of(true, true, false);\n *\n * zip(age$, name$, isDev$).pipe(\n *   map(([age, name, isDev]) => ({ age, name, isDev }))\n * )\n * .subscribe(x => console.log(x));\n *\n * // Outputs\n * // { age: 27, name: 'Foo', isDev: true }\n * // { age: 25, name: 'Bar', isDev: true }\n * // { age: 29, name: 'Beer', isDev: false }\n * ```\n *\n * @param args Any number of `ObservableInput`s provided either as an array or as an object\n * to combine with each other.\n * @return An Observable of array values of the values emitted at the same index from each\n * individual `ObservableInput`.\n */\nexport function zip(...args: unknown[]): Observable<unknown> {\n  const resultSelector = popResultSelector(args);\n\n  const sources = argsOrArgArray(args) as Observable<unknown>[];\n\n  return sources.length\n    ? new Observable<unknown[]>((subscriber) => {\n        // A collection of buffers of values from each source.\n        // Keyed by the same index with which the sources were passed in.\n        let buffers: unknown[][] = sources.map(() => []);\n\n        // An array of flags of whether or not the sources have completed.\n        // This is used to check to see if we should complete the result.\n        // Keyed by the same index with which the sources were passed in.\n        let completed = sources.map(() => false);\n\n        // When everything is done, release the arrays above.\n        subscriber.add(() => {\n          buffers = completed = null!;\n        });\n\n        // Loop over our sources and subscribe to each one. The index `i` is\n        // especially important here, because we use it in closures below to\n        // access the related buffers and completion properties\n        for (let sourceIndex = 0; !subscriber.closed && sourceIndex < sources.length; sourceIndex++) {\n          innerFrom(sources[sourceIndex]).subscribe(\n            createOperatorSubscriber(\n              subscriber,\n              (value) => {\n                buffers[sourceIndex].push(value);\n                // if every buffer has at least one value in it, then we\n                // can shift out the oldest value from each buffer and emit\n                // them as an array.\n                if (buffers.every((buffer) => buffer.length)) {\n                  const result: any = buffers.map((buffer) => buffer.shift()!);\n                  // Emit the array. If theres' a result selector, use that.\n                  subscriber.next(resultSelector ? resultSelector(...result) : result);\n                  // If any one of the sources is both complete and has an empty buffer\n                  // then we complete the result. This is because we cannot possibly have\n                  // any more values to zip together.\n                  if (buffers.some((buffer, i) => !buffer.length && completed[i])) {\n                    subscriber.complete();\n                  }\n                }\n              },\n              () => {\n                // This source completed. Mark it as complete so we can check it later\n                // if we have to.\n                completed[sourceIndex] = true;\n                // But, if this complete source has nothing in its buffer, then we\n                // can complete the result, because we can't possibly have any more\n                // values from this to zip together with the other values.\n                !buffers[sourceIndex].length && subscriber.complete();\n              }\n            )\n          );\n        }\n\n        // When everything is done, release the arrays above.\n        return () => {\n          buffers = completed = null!;\n        };\n      })\n    : EMPTY;\n}\n", "import { Subscriber } from '../Subscriber';\nimport { MonoTypeOperatorFunction, ObservableInput } from '../types';\n\nimport { operate } from '../util/lift';\nimport { innerFrom } from '../observable/innerFrom';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\n\n/**\n * Ignores source values for a duration determined by another Observable, then\n * emits the most recent value from the source Observable, then repeats this\n * process.\n *\n * <span class=\"informal\">It's like {@link auditTime}, but the silencing\n * duration is determined by a second Observable.</span>\n *\n * ![](audit.svg)\n *\n * `audit` is similar to `throttle`, but emits the last value from the silenced\n * time window, instead of the first value. `audit` emits the most recent value\n * from the source Observable on the output Observable as soon as its internal\n * timer becomes disabled, and ignores source values while the timer is enabled.\n * Initially, the timer is disabled. As soon as the first source value arrives,\n * the timer is enabled by calling the `durationSelector` function with the\n * source value, which returns the \"duration\" Observable. When the duration\n * Observable emits a value, the timer is disabled, then the most\n * recent source value is emitted on the output Observable, and this process\n * repeats for the next source value.\n *\n * ## Example\n *\n * Emit clicks at a rate of at most one click per second\n *\n * ```ts\n * import { fromEvent, audit, interval } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const result = clicks.pipe(audit(ev => interval(1000)));\n * result.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link auditTime}\n * @see {@link debounce}\n * @see {@link delayWhen}\n * @see {@link sample}\n * @see {@link throttle}\n *\n * @param durationSelector A function\n * that receives a value from the source Observable, for computing the silencing\n * duration, returned as an Observable or a Promise.\n * @return A function that returns an Observable that performs rate-limiting of\n * emissions from the source Observable.\n */\nexport function audit<T>(durationSelector: (value: T) => ObservableInput<any>): MonoTypeOperatorFunction<T> {\n  return operate((source, subscriber) => {\n    let hasValue = false;\n    let lastValue: T | null = null;\n    let durationSubscriber: Subscriber<any> | null = null;\n    let isComplete = false;\n\n    const endDuration = () => {\n      durationSubscriber?.unsubscribe();\n      durationSubscriber = null;\n      if (hasValue) {\n        hasValue = false;\n        const value = lastValue!;\n        lastValue = null;\n        subscriber.next(value);\n      }\n      isComplete && subscriber.complete();\n    };\n\n    const cleanupDuration = () => {\n      durationSubscriber = null;\n      isComplete && subscriber.complete();\n    };\n\n    source.subscribe(\n      createOperatorSubscriber(\n        subscriber,\n        (value) => {\n          hasValue = true;\n          lastValue = value;\n          if (!durationSubscriber) {\n            innerFrom(durationSelector(value)).subscribe(\n              (durationSubscriber = createOperatorSubscriber(subscriber, endDuration, cleanupDuration))\n            );\n          }\n        },\n        () => {\n          isComplete = true;\n          (!hasValue || !durationSubscriber || durationSubscriber.closed) && subscriber.complete();\n        }\n      )\n    );\n  });\n}\n", "import { asyncScheduler } from '../scheduler/async';\nimport { audit } from './audit';\nimport { timer } from '../observable/timer';\nimport { MonoTypeOperatorFunction, SchedulerLike } from '../types';\n\n/**\n * Ignores source values for `duration` milliseconds, then emits the most recent\n * value from the source Observable, then repeats this process.\n *\n * <span class=\"informal\">When it sees a source value, it ignores that plus\n * the next ones for `duration` milliseconds, and then it emits the most recent\n * value from the source.</span>\n *\n * ![](auditTime.png)\n *\n * `auditTime` is similar to `throttleTime`, but emits the last value from the\n * silenced time window, instead of the first value. `auditTime` emits the most\n * recent value from the source Observable on the output Observable as soon as\n * its internal timer becomes disabled, and ignores source values while the\n * timer is enabled. Initially, the timer is disabled. As soon as the first\n * source value arrives, the timer is enabled. After `duration` milliseconds (or\n * the time unit determined internally by the optional `scheduler`) has passed,\n * the timer is disabled, then the most recent source value is emitted on the\n * output Observable, and this process repeats for the next source value.\n * Optionally takes a {@link SchedulerLike} for managing timers.\n *\n * ## Example\n *\n * Emit clicks at a rate of at most one click per second\n *\n * ```ts\n * import { fromEvent, auditTime } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const result = clicks.pipe(auditTime(1000));\n * result.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link audit}\n * @see {@link debounceTime}\n * @see {@link delay}\n * @see {@link sampleTime}\n * @see {@link throttleTime}\n *\n * @param duration Time to wait before emitting the most recent source value,\n * measured in milliseconds or the time unit determined internally by the\n * optional `scheduler`.\n * @param scheduler The {@link SchedulerLike} to use for managing the timers\n * that handle the rate-limiting behavior.\n * @return A function that returns an Observable that performs rate-limiting of\n * emissions from the source Observable.\n */\nexport function auditTime<T>(duration: number, scheduler: SchedulerLike = asyncScheduler): MonoTypeOperatorFunction<T> {\n  return audit(() => timer(duration, scheduler));\n}\n", "import { OperatorFunction } from '../types';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\nimport { arrRemove } from '../util/arrRemove';\n\n/**\n * Buffers the source Observable values until the size hits the maximum\n * `bufferSize` given.\n *\n * <span class=\"informal\">Collects values from the past as an array, and emits\n * that array only when its size reaches `bufferSize`.</span>\n *\n * ![](bufferCount.png)\n *\n * Buffers a number of values from the source Observable by `bufferSize` then\n * emits the buffer and clears it, and starts a new buffer each\n * `startBufferEvery` values. If `startBufferEvery` is not provided or is\n * `null`, then new buffers are started immediately at the start of the source\n * and when each buffer closes and is emitted.\n *\n * ## Examples\n *\n * Emit the last two click events as an array\n *\n * ```ts\n * import { fromEvent, bufferCount } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const buffered = clicks.pipe(bufferCount(2));\n * buffered.subscribe(x => console.log(x));\n * ```\n *\n * On every click, emit the last two click events as an array\n *\n * ```ts\n * import { fromEvent, bufferCount } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const buffered = clicks.pipe(bufferCount(2, 1));\n * buffered.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link buffer}\n * @see {@link bufferTime}\n * @see {@link bufferToggle}\n * @see {@link bufferWhen}\n * @see {@link pairwise}\n * @see {@link windowCount}\n *\n * @param bufferSize The maximum size of the buffer emitted.\n * @param startBufferEvery Interval at which to start a new buffer.\n * For example if `startBufferEvery` is `2`, then a new buffer will be started\n * on every other value from the source. A new buffer is started at the\n * beginning of the source by default.\n * @return A function that returns an Observable of arrays of buffered values.\n */\nexport function bufferCount<T>(bufferSize: number, startBufferEvery: number | null = null): OperatorFunction<T, T[]> {\n  // If no `startBufferEvery` value was supplied, then we're\n  // opening and closing on the bufferSize itself.\n  startBufferEvery = startBufferEvery ?? bufferSize;\n\n  return operate((source, subscriber) => {\n    let buffers: T[][] = [];\n    let count = 0;\n\n    source.subscribe(\n      createOperatorSubscriber(\n        subscriber,\n        (value) => {\n          let toEmit: T[][] | null = null;\n\n          // Check to see if we need to start a buffer.\n          // This will start one at the first value, and then\n          // a new one every N after that.\n          if (count++ % startBufferEvery! === 0) {\n            buffers.push([]);\n          }\n\n          // Push our value into our active buffers.\n          for (const buffer of buffers) {\n            buffer.push(value);\n            // Check to see if we're over the bufferSize\n            // if we are, record it so we can emit it later.\n            // If we emitted it now and removed it, it would\n            // mutate the `buffers` array while we're looping\n            // over it.\n            if (bufferSize <= buffer.length) {\n              toEmit = toEmit ?? [];\n              toEmit.push(buffer);\n            }\n          }\n\n          if (toEmit) {\n            // We have found some buffers that are over the\n            // `bufferSize`. Emit them, and remove them from our\n            // buffers list.\n            for (const buffer of toEmit) {\n              arrRemove(buffers, buffer);\n              subscriber.next(buffer);\n            }\n          }\n        },\n        () => {\n          // When the source completes, emit all of our\n          // active buffers.\n          for (const buffer of buffers) {\n            subscriber.next(buffer);\n          }\n          subscriber.complete();\n        },\n        // Pass all errors through to consumer.\n        undefined,\n        () => {\n          // Clean up our memory when we finalize\n          buffers = null!;\n        }\n      )\n    );\n  });\n}\n", "import { Observable } from '../Observable';\n\nimport { ObservableInput, OperatorFunction, ObservedValueOf } from '../types';\nimport { Subscription } from '../Subscription';\nimport { innerFrom } from '../observable/innerFrom';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\nimport { operate } from '../util/lift';\n\nexport function catchError<T, O extends ObservableInput<any>>(\n  selector: (err: any, caught: Observable<T>) => O\n): OperatorFunction<T, T | ObservedValueOf<O>>;\n\n/**\n * Catches errors on the observable to be handled by returning a new observable or throwing an error.\n *\n * <span class=\"informal\">\n * It only listens to the error channel and ignores notifications.\n * Handles errors from the source observable, and maps them to a new observable.\n * The error may also be rethrown, or a new error can be thrown to emit an error from the result.\n * </span>\n *\n * ![](catch.png)\n *\n * This operator handles errors, but forwards along all other events to the resulting observable.\n * If the source observable terminates with an error, it will map that error to a new observable,\n * subscribe to it, and forward all of its events to the resulting observable.\n *\n * ## Examples\n *\n * Continue with a different Observable when there's an error\n *\n * ```ts\n * import { of, map, catchError } from 'rxjs';\n *\n * of(1, 2, 3, 4, 5)\n *   .pipe(\n *     map(n => {\n *       if (n === 4) {\n *         throw 'four!';\n *       }\n *       return n;\n *     }),\n *     catchError(err => of('I', 'II', 'III', 'IV', 'V'))\n *   )\n *   .subscribe(x => console.log(x));\n *   // 1, 2, 3, I, II, III, IV, V\n * ```\n *\n * Retry the caught source Observable again in case of error, similar to `retry()` operator\n *\n * ```ts\n * import { of, map, catchError, take } from 'rxjs';\n *\n * of(1, 2, 3, 4, 5)\n *   .pipe(\n *     map(n => {\n *       if (n === 4) {\n *         throw 'four!';\n *       }\n *       return n;\n *     }),\n *     catchError((err, caught) => caught),\n *     take(30)\n *   )\n *   .subscribe(x => console.log(x));\n *   // 1, 2, 3, 1, 2, 3, ...\n * ```\n *\n * Throw a new error when the source Observable throws an error\n *\n * ```ts\n * import { of, map, catchError } from 'rxjs';\n *\n * of(1, 2, 3, 4, 5)\n *   .pipe(\n *     map(n => {\n *       if (n === 4) {\n *         throw 'four!';\n *       }\n *       return n;\n *     }),\n *     catchError(err => {\n *       throw 'error in source. Details: ' + err;\n *     })\n *   )\n *   .subscribe({\n *     next: x => console.log(x),\n *     error: err => console.log(err)\n *   });\n *   // 1, 2, 3, error in source. Details: four!\n * ```\n *\n * @see {@link onErrorResumeNext}\n * @see {@link repeat}\n * @see {@link repeatWhen}\n * @see {@link retry }\n * @see {@link retryWhen}\n *\n * @param selector A function that takes as arguments `err`, which is the error, and `caught`, which\n * is the source observable, in case you'd like to \"retry\" that observable by returning it again.\n * Whatever observable is returned by the `selector` will be used to continue the observable chain.\n * @return A function that returns an Observable that originates from either\n * the source or the Observable returned by the `selector` function.\n */\nexport function catchError<T, O extends ObservableInput<any>>(\n  selector: (err: any, caught: Observable<T>) => O\n): OperatorFunction<T, T | ObservedValueOf<O>> {\n  return operate((source, subscriber) => {\n    let innerSub: Subscription | null = null;\n    let syncUnsub = false;\n    let handledResult: Observable<ObservedValueOf<O>>;\n\n    innerSub = source.subscribe(\n      createOperatorSubscriber(subscriber, undefined, undefined, (err) => {\n        handledResult = innerFrom(selector(err, catchError(selector)(source)));\n        if (innerSub) {\n          innerSub.unsubscribe();\n          innerSub = null;\n          handledResult.subscribe(subscriber);\n        } else {\n          // We don't have an innerSub yet, that means the error was synchronous\n          // because the subscribe call hasn't returned yet.\n          syncUnsub = true;\n        }\n      })\n    );\n\n    if (syncUnsub) {\n      // We have a synchronous error, we need to make sure to\n      // finalize right away. This ensures that callbacks in the `finalize` operator are called\n      // at the right time, and that finalization occurs at the expected\n      // time between the source error and the subscription to the\n      // next observable.\n      innerSub.unsubscribe();\n      innerSub = null;\n      handledResult!.subscribe(subscriber);\n    }\n  });\n}\n", "import { Observable } from '../Observable';\nimport { Subscriber } from '../Subscriber';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\n\n/**\n * A basic scan operation. This is used for `scan` and `reduce`.\n * @param accumulator The accumulator to use\n * @param seed The seed value for the state to accumulate\n * @param hasSeed Whether or not a seed was provided\n * @param emitOnNext Whether or not to emit the state on next\n * @param emitBeforeComplete Whether or not to emit the before completion\n */\n\nexport function scanInternals<V, A, S>(\n  accumulator: (acc: V | A | S, value: V, index: number) => A,\n  seed: S,\n  hasSeed: boolean,\n  emitOnNext: boolean,\n  emitBeforeComplete?: undefined | true\n) {\n  return (source: Observable<V>, subscriber: Subscriber<any>) => {\n    // Whether or not we have state yet. This will only be\n    // false before the first value arrives if we didn't get\n    // a seed value.\n    let hasState = hasSeed;\n    // The state that we're tracking, starting with the seed,\n    // if there is one, and then updated by the return value\n    // from the accumulator on each emission.\n    let state: any = seed;\n    // An index to pass to the accumulator function.\n    let index = 0;\n\n    // Subscribe to our source. All errors and completions are passed through.\n    source.subscribe(\n      createOperatorSubscriber(\n        subscriber,\n        (value) => {\n          // Always increment the index.\n          const i = index++;\n          // Set the state\n          state = hasState\n            ? // We already have state, so we can get the new state from the accumulator\n              accumulator(state, value, i)\n            : // We didn't have state yet, a seed value was not provided, so\n\n              // we set the state to the first value, and mark that we have state now\n              ((hasState = true), value);\n\n          // Maybe send it to the consumer.\n          emitOnNext && subscriber.next(state);\n        },\n        // If an onComplete was given, call it, otherwise\n        // just pass through the complete notification to the consumer.\n        emitBeforeComplete &&\n          (() => {\n            hasState && subscriber.next(state);\n            subscriber.complete();\n          })\n      )\n    );\n  };\n}\n", "import { combineLatestInit } from '../observable/combineLatest';\nimport { ObservableInput, ObservableInputTuple, OperatorFunction } from '../types';\nimport { operate } from '../util/lift';\nimport { argsOrArgArray } from '../util/argsOrArgArray';\nimport { mapOneOrManyArgs } from '../util/mapOneOrManyArgs';\nimport { pipe } from '../util/pipe';\nimport { popResultSelector } from '../util/args';\n\n/** @deprecated Replaced with {@link combineLatestWith}. Will be removed in v8. */\nexport function combineLatest<T, A extends readonly unknown[], R>(\n  sources: [...ObservableInputTuple<A>],\n  project: (...values: [T, ...A]) => R\n): OperatorFunction<T, R>;\n/** @deprecated Replaced with {@link combineLatestWith}. Will be removed in v8. */\nexport function combineLatest<T, A extends readonly unknown[], R>(sources: [...ObservableInputTuple<A>]): OperatorFunction<T, [T, ...A]>;\n\n/** @deprecated Replaced with {@link combineLatestWith}. Will be removed in v8. */\nexport function combineLatest<T, A extends readonly unknown[], R>(\n  ...sourcesAndProject: [...ObservableInputTuple<A>, (...values: [T, ...A]) => R]\n): OperatorFunction<T, R>;\n/** @deprecated Replaced with {@link combineLatestWith}. Will be removed in v8. */\nexport function combineLatest<T, A extends readonly unknown[], R>(...sources: [...ObservableInputTuple<A>]): OperatorFunction<T, [T, ...A]>;\n\n/**\n * @deprecated Replaced with {@link combineLatestWith}. Will be removed in v8.\n */\nexport function combineLatest<T, R>(...args: (ObservableInput<any> | ((...values: any[]) => R))[]): OperatorFunction<T, unknown> {\n  const resultSelector = popResultSelector(args);\n  return resultSelector\n    ? pipe(combineLatest(...(args as Array<ObservableInput<any>>)), mapOneOrManyArgs(resultSelector))\n    : operate((source, subscriber) => {\n        combineLatestInit([source, ...argsOrArgArray(args)])(subscriber);\n      });\n}\n", "import { ObservableInputTuple, OperatorFunction, Cons } from '../types';\nimport { combineLatest } from './combineLatest';\n\n/**\n * Create an observable that combines the latest values from all passed observables and the source\n * into arrays and emits them.\n *\n * Returns an observable, that when subscribed to, will subscribe to the source observable and all\n * sources provided as arguments. Once all sources emit at least one value, all of the latest values\n * will be emitted as an array. After that, every time any source emits a value, all of the latest values\n * will be emitted as an array.\n *\n * This is a useful operator for eagerly calculating values based off of changed inputs.\n *\n * ## Example\n *\n * Simple concatenation of values from two inputs\n *\n * ```ts\n * import { fromEvent, combineLatestWith, map } from 'rxjs';\n *\n * // Setup: Add two inputs to the page\n * const input1 = document.createElement('input');\n * document.body.appendChild(input1);\n * const input2 = document.createElement('input');\n * document.body.appendChild(input2);\n *\n * // Get streams of changes\n * const input1Changes$ = fromEvent(input1, 'change');\n * const input2Changes$ = fromEvent(input2, 'change');\n *\n * // Combine the changes by adding them together\n * input1Changes$.pipe(\n *   combineLatestWith(input2Changes$),\n *   map(([e1, e2]) => (<HTMLInputElement>e1.target).value + ' - ' + (<HTMLInputElement>e2.target).value)\n * )\n * .subscribe(x => console.log(x));\n * ```\n *\n * @param otherSources the other sources to subscribe to.\n * @return A function that returns an Observable that emits the latest\n * emissions from both source and provided Observables.\n */\nexport function combineLatestWith<T, A extends readonly unknown[]>(\n  ...otherSources: [...ObservableInputTuple<A>]\n): OperatorFunction<T, Cons<T, A>> {\n  return combineLatest(...otherSources);\n}\n", "import { Subscriber } from '../Subscriber';\nimport { MonoTypeOperatorFunction, ObservableInput } from '../types';\nimport { operate } from '../util/lift';\nimport { noop } from '../util/noop';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\nimport { innerFrom } from '../observable/innerFrom';\n\n/**\n * Emits a notification from the source Observable only after a particular time span\n * determined by another Observable has passed without another source emission.\n *\n * <span class=\"informal\">It's like {@link debounceTime}, but the time span of\n * emission silence is determined by a second Observable.</span>\n *\n * ![](debounce.svg)\n *\n * `debounce` delays notifications emitted by the source Observable, but drops previous\n * pending delayed emissions if a new notification arrives on the source Observable.\n * This operator keeps track of the most recent notification from the source\n * Observable, and spawns a duration Observable by calling the\n * `durationSelector` function. The notification is emitted only when the duration\n * Observable emits a next notification, and if no other notification was emitted on\n * the source Observable since the duration Observable was spawned. If a new\n * notification appears before the duration Observable emits, the previous notification will\n * not be emitted and a new duration is scheduled from `durationSelector` is scheduled.\n * If the completing event happens during the scheduled duration the last cached notification\n * is emitted before the completion event is forwarded to the output observable.\n * If the error event happens during the scheduled duration or after it only the error event is\n * forwarded to the output observable. The cache notification is not emitted in this case.\n *\n * Like {@link debounceTime}, this is a rate-limiting operator, and also a\n * delay-like operator since output emissions do not necessarily occur at the\n * same time as they did on the source Observable.\n *\n * ## Example\n *\n * Emit the most recent click after a burst of clicks\n *\n * ```ts\n * import { fromEvent, scan, debounce, interval } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const result = clicks.pipe(\n *   scan(i => ++i, 1),\n *   debounce(i => interval(200 * i))\n * );\n * result.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link audit}\n * @see {@link auditTime}\n * @see {@link debounceTime}\n * @see {@link delay}\n * @see {@link sample}\n * @see {@link sampleTime}\n * @see {@link throttle}\n * @see {@link throttleTime}\n *\n * @param durationSelector A function\n * that receives a value from the source Observable, for computing the timeout\n * duration for each source value, returned as an Observable or a Promise.\n * @return A function that returns an Observable that delays the emissions of\n * the source Observable by the specified duration Observable returned by\n * `durationSelector`, and may drop some values if they occur too frequently.\n */\nexport function debounce<T>(durationSelector: (value: T) => ObservableInput<any>): MonoTypeOperatorFunction<T> {\n  return operate((source, subscriber) => {\n    let hasValue = false;\n    let lastValue: T | null = null;\n    // The subscriber/subscription for the current debounce, if there is one.\n    let durationSubscriber: Subscriber<any> | null = null;\n\n    const emit = () => {\n      // Unsubscribe any current debounce subscription we have,\n      // we only cared about the first notification from it, and we\n      // want to clean that subscription up as soon as possible.\n      durationSubscriber?.unsubscribe();\n      durationSubscriber = null;\n      if (hasValue) {\n        // We have a value! Free up memory first, then emit the value.\n        hasValue = false;\n        const value = lastValue!;\n        lastValue = null;\n        subscriber.next(value);\n      }\n    };\n\n    source.subscribe(\n      createOperatorSubscriber(\n        subscriber,\n        (value: T) => {\n          // Cancel any pending debounce duration. We don't\n          // need to null it out here yet tho, because we're just going\n          // to create another one in a few lines.\n          durationSubscriber?.unsubscribe();\n          hasValue = true;\n          lastValue = value;\n          // Capture our duration subscriber, so we can unsubscribe it when we're notified\n          // and we're going to emit the value.\n          durationSubscriber = createOperatorSubscriber(subscriber, emit, noop);\n          // Subscribe to the duration.\n          innerFrom(durationSelector(value)).subscribe(durationSubscriber);\n        },\n        () => {\n          // Source completed.\n          // Emit any pending debounced values then complete\n          emit();\n          subscriber.complete();\n        },\n        // Pass all errors through to consumer\n        undefined,\n        () => {\n          // Finalization.\n          lastValue = durationSubscriber = null;\n        }\n      )\n    );\n  });\n}\n", "import { asyncScheduler } from '../scheduler/async';\nimport { Subscription } from '../Subscription';\nimport { MonoTypeOperatorFunction, SchedulerAction, SchedulerLike } from '../types';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\n\n/**\n * Emits a notification from the source Observable only after a particular time span\n * has passed without another source emission.\n *\n * <span class=\"informal\">It's like {@link delay}, but passes only the most\n * recent notification from each burst of emissions.</span>\n *\n * ![](debounceTime.png)\n *\n * `debounceTime` delays notifications emitted by the source Observable, but drops\n * previous pending delayed emissions if a new notification arrives on the source\n * Observable. This operator keeps track of the most recent notification from the\n * source Observable, and emits that only when `dueTime` has passed\n * without any other notification appearing on the source Observable. If a new value\n * appears before `dueTime` silence occurs, the previous notification will be dropped\n * and will not be emitted and a new `dueTime` is scheduled.\n * If the completing event happens during `dueTime` the last cached notification\n * is emitted before the completion event is forwarded to the output observable.\n * If the error event happens during `dueTime` or after it only the error event is\n * forwarded to the output observable. The cache notification is not emitted in this case.\n *\n * This is a rate-limiting operator, because it is impossible for more than one\n * notification to be emitted in any time window of duration `dueTime`, but it is also\n * a delay-like operator since output emissions do not occur at the same time as\n * they did on the source Observable. Optionally takes a {@link SchedulerLike} for\n * managing timers.\n *\n * ## Example\n *\n * Emit the most recent click after a burst of clicks\n *\n * ```ts\n * import { fromEvent, debounceTime } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const result = clicks.pipe(debounceTime(1000));\n * result.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link audit}\n * @see {@link auditTime}\n * @see {@link debounce}\n * @see {@link sample}\n * @see {@link sampleTime}\n * @see {@link throttle}\n * @see {@link throttleTime}\n *\n * @param dueTime The timeout duration in milliseconds (or the time unit determined\n * internally by the optional `scheduler`) for the window of time required to wait\n * for emission silence before emitting the most recent source value.\n * @param scheduler The {@link SchedulerLike} to use for managing the timers that\n * handle the timeout for each value.\n * @return A function that returns an Observable that delays the emissions of\n * the source Observable by the specified `dueTime`, and may drop some values\n * if they occur too frequently.\n */\nexport function debounceTime<T>(dueTime: number, scheduler: SchedulerLike = asyncScheduler): MonoTypeOperatorFunction<T> {\n  return operate((source, subscriber) => {\n    let activeTask: Subscription | null = null;\n    let lastValue: T | null = null;\n    let lastTime: number | null = null;\n\n    const emit = () => {\n      if (activeTask) {\n        // We have a value! Free up memory first, then emit the value.\n        activeTask.unsubscribe();\n        activeTask = null;\n        const value = lastValue!;\n        lastValue = null;\n        subscriber.next(value);\n      }\n    };\n    function emitWhenIdle(this: SchedulerAction<unknown>) {\n      // This is called `dueTime` after the first value\n      // but we might have received new values during this window!\n\n      const targetTime = lastTime! + dueTime;\n      const now = scheduler.now();\n      if (now < targetTime) {\n        // On that case, re-schedule to the new target\n        activeTask = this.schedule(undefined, targetTime - now);\n        subscriber.add(activeTask);\n        return;\n      }\n\n      emit();\n    }\n\n    source.subscribe(\n      createOperatorSubscriber(\n        subscriber,\n        (value: T) => {\n          lastValue = value;\n          lastTime = scheduler.now();\n\n          // Only set up a task if it's not already up\n          if (!activeTask) {\n            activeTask = scheduler.schedule(emitWhenIdle, dueTime);\n            subscriber.add(activeTask);\n          }\n        },\n        () => {\n          // Source completed.\n          // Emit any pending debounced values then complete\n          emit();\n          subscriber.complete();\n        },\n        // Pass all errors through to consumer.\n        undefined,\n        () => {\n          // Finalization.\n          lastValue = activeTask = null;\n        }\n      )\n    );\n  });\n}\n", "import { OperatorFunction } from '../types';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\n\n/**\n * Emits a given value if the source Observable completes without emitting any\n * `next` value, otherwise mirrors the source Observable.\n *\n * <span class=\"informal\">If the source Observable turns out to be empty, then\n * this operator will emit a default value.</span>\n *\n * ![](defaultIfEmpty.png)\n *\n * `defaultIfEmpty` emits the values emitted by the source Observable or a\n * specified default value if the source Observable is empty (completes without\n * having emitted any `next` value).\n *\n * ## Example\n *\n * If no clicks happen in 5 seconds, then emit 'no clicks'\n *\n * ```ts\n * import { fromEvent, takeUntil, interval, defaultIfEmpty } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const clicksBeforeFive = clicks.pipe(takeUntil(interval(5000)));\n * const result = clicksBeforeFive.pipe(defaultIfEmpty('no clicks'));\n * result.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link empty}\n * @see {@link last}\n *\n * @param defaultValue The default value used if the source\n * Observable is empty.\n * @return A function that returns an Observable that emits either the\n * specified `defaultValue` if the source Observable emits no items, or the\n * values emitted by the source Observable.\n */\nexport function defaultIfEmpty<T, R>(defaultValue: R): OperatorFunction<T, T | R> {\n  return operate((source, subscriber) => {\n    let hasValue = false;\n    source.subscribe(\n      createOperatorSubscriber(\n        subscriber,\n        (value) => {\n          hasValue = true;\n          subscriber.next(value);\n        },\n        () => {\n          if (!hasValue) {\n            subscriber.next(defaultValue!);\n          }\n          subscriber.complete();\n        }\n      )\n    );\n  });\n}\n", "import { MonoTypeOperatorFunction } from '../types';\nimport { EMPTY } from '../observable/empty';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\n\n/**\n * Emits only the first `count` values emitted by the source Observable.\n *\n * <span class=\"informal\">Takes the first `count` values from the source, then\n * completes.</span>\n *\n * ![](take.png)\n *\n * `take` returns an Observable that emits only the first `count` values emitted\n * by the source Observable. If the source emits fewer than `count` values then\n * all of its values are emitted. After that, it completes, regardless if the\n * source completes.\n *\n * ## Example\n *\n * Take the first 5 seconds of an infinite 1-second interval Observable\n *\n * ```ts\n * import { interval, take } from 'rxjs';\n *\n * const intervalCount = interval(1000);\n * const takeFive = intervalCount.pipe(take(5));\n * takeFive.subscribe(x => console.log(x));\n *\n * // Logs:\n * // 0\n * // 1\n * // 2\n * // 3\n * // 4\n * ```\n *\n * @see {@link takeLast}\n * @see {@link takeUntil}\n * @see {@link takeWhile}\n * @see {@link skip}\n *\n * @param count The maximum number of `next` values to emit.\n * @return A function that returns an Observable that emits only the first\n * `count` values emitted by the source Observable, or all of the values from\n * the source if the source emits fewer than `count` values.\n */\nexport function take<T>(count: number): MonoTypeOperatorFunction<T> {\n  return count <= 0\n    ? // If we are taking no values, that's empty.\n      () => EMPTY\n    : operate((source, subscriber) => {\n        let seen = 0;\n        source.subscribe(\n          createOperatorSubscriber(subscriber, (value) => {\n            // Increment the number of values we have seen,\n            // then check it against the allowed count to see\n            // if we are still letting values through.\n            if (++seen <= count) {\n              subscriber.next(value);\n              // If we have met or passed our allowed count,\n              // we need to complete. We have to do <= here,\n              // because re-entrant code will increment `seen` twice.\n              if (count <= seen) {\n                subscriber.complete();\n              }\n            }\n          })\n        );\n      });\n}\n", "import { OperatorFunction } from '../types';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\nimport { noop } from '../util/noop';\n\n/**\n * Ignores all items emitted by the source Observable and only passes calls of `complete` or `error`.\n *\n * ![](ignoreElements.png)\n *\n * The `ignoreElements` operator suppresses all items emitted by the source Observable,\n * but allows its termination notification (either `error` or `complete`) to pass through unchanged.\n *\n * If you do not care about the items being emitted by an Observable, but you do want to be notified\n * when it completes or when it terminates with an error, you can apply the `ignoreElements` operator\n * to the Observable, which will ensure that it will never call its observers\u2019 `next` handlers.\n *\n * ## Example\n *\n * Ignore all `next` emissions from the source\n *\n * ```ts\n * import { of, ignoreElements } from 'rxjs';\n *\n * of('you', 'talking', 'to', 'me')\n *   .pipe(ignoreElements())\n *   .subscribe({\n *     next: word => console.log(word),\n *     error: err => console.log('error:', err),\n *     complete: () => console.log('the end'),\n *   });\n *\n * // result:\n * // 'the end'\n * ```\n *\n * @return A function that returns an empty Observable that only calls\n * `complete` or `error`, based on which one is called by the source\n * Observable.\n */\nexport function ignoreElements(): OperatorFunction<unknown, never> {\n  return operate((source, subscriber) => {\n    source.subscribe(createOperatorSubscriber(subscriber, noop));\n  });\n}\n", "import { OperatorFunction } from '../types';\nimport { map } from './map';\n\n/** @deprecated To be removed in v9. Use {@link map} instead: `map(() => value)`. */\nexport function mapTo<R>(value: R): OperatorFunction<unknown, R>;\n/**\n * @deprecated Do not specify explicit type parameters. Signatures with type parameters\n * that cannot be inferred will be removed in v8. `mapTo` itself will be removed in v9,\n * use {@link map} instead: `map(() => value)`.\n * */\nexport function mapTo<T, R>(value: R): OperatorFunction<T, R>;\n\n/**\n * Emits the given constant value on the output Observable every time the source\n * Observable emits a value.\n *\n * <span class=\"informal\">Like {@link map}, but it maps every source value to\n * the same output value every time.</span>\n *\n * ![](mapTo.png)\n *\n * Takes a constant `value` as argument, and emits that whenever the source\n * Observable emits a value. In other words, ignores the actual source value,\n * and simply uses the emission moment to know when to emit the given `value`.\n *\n * ## Example\n *\n * Map every click to the string `'Hi'`\n *\n * ```ts\n * import { fromEvent, mapTo } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const greetings = clicks.pipe(mapTo('Hi'));\n *\n * greetings.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link map}\n *\n * @param value The value to map each source value to.\n * @return A function that returns an Observable that emits the given `value`\n * every time the source Observable emits.\n * @deprecated To be removed in v9. Use {@link map} instead: `map(() => value)`.\n */\nexport function mapTo<R>(value: R): OperatorFunction<unknown, R> {\n  return map(() => value);\n}\n", "import { Observable } from '../Observable';\nimport { MonoTypeOperatorFunction, ObservableInput } from '../types';\nimport { concat } from '../observable/concat';\nimport { take } from './take';\nimport { ignoreElements } from './ignoreElements';\nimport { mapTo } from './mapTo';\nimport { mergeMap } from './mergeMap';\nimport { innerFrom } from '../observable/innerFrom';\n\n/** @deprecated The `subscriptionDelay` parameter will be removed in v8. */\nexport function delayWhen<T>(\n  delayDurationSelector: (value: T, index: number) => ObservableInput<any>,\n  subscriptionDelay: Observable<any>\n): MonoTypeOperatorFunction<T>;\nexport function delayWhen<T>(delayDurationSelector: (value: T, index: number) => ObservableInput<any>): MonoTypeOperatorFunction<T>;\n\n/**\n * Delays the emission of items from the source Observable by a given time span\n * determined by the emissions of another Observable.\n *\n * <span class=\"informal\">It's like {@link delay}, but the time span of the\n * delay duration is determined by a second Observable.</span>\n *\n * ![](delayWhen.png)\n *\n * `delayWhen` operator shifts each emitted value from the source Observable by\n * a time span determined by another Observable. When the source emits a value,\n * the `delayDurationSelector` function is called with the value emitted from\n * the source Observable as the first argument to the `delayDurationSelector`.\n * The `delayDurationSelector` function should return an {@link ObservableInput},\n * that is internally converted to an Observable that is called the \"duration\"\n * Observable.\n *\n * The source value is emitted on the output Observable only when the \"duration\"\n * Observable emits ({@link guide/glossary-and-semantics#next next}s) any value.\n * Upon that, the \"duration\" Observable gets unsubscribed.\n *\n * Before RxJS V7, the {@link guide/glossary-and-semantics#complete completion}\n * of the \"duration\" Observable would have been triggering the emission of the\n * source value to the output Observable, but with RxJS V7, this is not the case\n * anymore.\n *\n * Only next notifications (from the \"duration\" Observable) trigger values from\n * the source Observable to be passed to the output Observable. If the \"duration\"\n * Observable only emits the complete notification (without next), the value\n * emitted by the source Observable will never get to the output Observable - it\n * will be swallowed. If the \"duration\" Observable errors, the error will be\n * propagated to the output Observable.\n *\n * Optionally, `delayWhen` takes a second argument, `subscriptionDelay`, which\n * is an Observable. When `subscriptionDelay` emits its first value or\n * completes, the source Observable is subscribed to and starts behaving like\n * described in the previous paragraph. If `subscriptionDelay` is not provided,\n * `delayWhen` will subscribe to the source Observable as soon as the output\n * Observable is subscribed.\n *\n * ## Example\n *\n * Delay each click by a random amount of time, between 0 and 5 seconds\n *\n * ```ts\n * import { fromEvent, delayWhen, interval } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const delayedClicks = clicks.pipe(\n *   delayWhen(() => interval(Math.random() * 5000))\n * );\n * delayedClicks.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link delay}\n * @see {@link throttle}\n * @see {@link throttleTime}\n * @see {@link debounce}\n * @see {@link debounceTime}\n * @see {@link sample}\n * @see {@link sampleTime}\n * @see {@link audit}\n * @see {@link auditTime}\n *\n * @param delayDurationSelector A function that returns an `ObservableInput` for\n * each `value` emitted by the source Observable, which is then used to delay the\n * emission of that `value` on the output Observable until the `ObservableInput`\n * returned from this function emits a next value. When called, beside `value`,\n * this function receives a zero-based `index` of the emission order.\n * @param subscriptionDelay An Observable that triggers the subscription to the\n * source Observable once it emits any value.\n * @return A function that returns an Observable that delays the emissions of\n * the source Observable by an amount of time specified by the Observable\n * returned by `delayDurationSelector`.\n */\nexport function delayWhen<T>(\n  delayDurationSelector: (value: T, index: number) => ObservableInput<any>,\n  subscriptionDelay?: Observable<any>\n): MonoTypeOperatorFunction<T> {\n  if (subscriptionDelay) {\n    // DEPRECATED PATH\n    return (source: Observable<T>) =>\n      concat(subscriptionDelay.pipe(take(1), ignoreElements()), source.pipe(delayWhen(delayDurationSelector)));\n  }\n\n  return mergeMap((value, index) => innerFrom(delayDurationSelector(value, index)).pipe(take(1), mapTo(value)));\n}\n", "import { asyncScheduler } from '../scheduler/async';\nimport { MonoTypeOperatorFunction, SchedulerLike } from '../types';\nimport { delayWhen } from './delayWhen';\nimport { timer } from '../observable/timer';\n\n/**\n * Delays the emission of items from the source Observable by a given timeout or\n * until a given Date.\n *\n * <span class=\"informal\">Time shifts each item by some specified amount of\n * milliseconds.</span>\n *\n * ![](delay.svg)\n *\n * If the delay argument is a Number, this operator time shifts the source\n * Observable by that amount of time expressed in milliseconds. The relative\n * time intervals between the values are preserved.\n *\n * If the delay argument is a Date, this operator time shifts the start of the\n * Observable execution until the given date occurs.\n *\n * ## Examples\n *\n * Delay each click by one second\n *\n * ```ts\n * import { fromEvent, delay } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const delayedClicks = clicks.pipe(delay(1000)); // each click emitted after 1 second\n * delayedClicks.subscribe(x => console.log(x));\n * ```\n *\n * Delay all clicks until a future date happens\n *\n * ```ts\n * import { fromEvent, delay } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const date = new Date('March 15, 2050 12:00:00'); // in the future\n * const delayedClicks = clicks.pipe(delay(date)); // click emitted only after that date\n * delayedClicks.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link delayWhen}\n * @see {@link throttle}\n * @see {@link throttleTime}\n * @see {@link debounce}\n * @see {@link debounceTime}\n * @see {@link sample}\n * @see {@link sampleTime}\n * @see {@link audit}\n * @see {@link auditTime}\n *\n * @param due The delay duration in milliseconds (a `number`) or a `Date` until\n * which the emission of the source items is delayed.\n * @param scheduler The {@link SchedulerLike} to use for managing the timers\n * that handle the time-shift for each item.\n * @return A function that returns an Observable that delays the emissions of\n * the source Observable by the specified timeout or Date.\n */\nexport function delay<T>(due: number | Date, scheduler: SchedulerLike = asyncScheduler): MonoTypeOperatorFunction<T> {\n  const duration = timer(due, scheduler);\n  return delayWhen(() => duration);\n}\n", "import { MonoTypeOperatorFunction, ObservableInput } from '../types';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\nimport { noop } from '../util/noop';\nimport { innerFrom } from '../observable/innerFrom';\n\n/**\n * Returns an Observable that emits all items emitted by the source Observable that are distinct by comparison from previous items.\n *\n * If a `keySelector` function is provided, then it will project each value from the source observable into a new value that it will\n * check for equality with previously projected values. If the `keySelector` function is not provided, it will use each value from the\n * source observable directly with an equality check against previous values.\n *\n * In JavaScript runtimes that support `Set`, this operator will use a `Set` to improve performance of the distinct value checking.\n *\n * In other runtimes, this operator will use a minimal implementation of `Set` that relies on an `Array` and `indexOf` under the\n * hood, so performance will degrade as more values are checked for distinction. Even in newer browsers, a long-running `distinct`\n * use might result in memory leaks. To help alleviate this in some scenarios, an optional `flushes` parameter is also provided so\n * that the internal `Set` can be \"flushed\", basically clearing it of values.\n *\n * ## Examples\n *\n * A simple example with numbers\n *\n * ```ts\n * import { of, distinct } from 'rxjs';\n *\n * of(1, 1, 2, 2, 2, 1, 2, 3, 4, 3, 2, 1)\n *   .pipe(distinct())\n *   .subscribe(x => console.log(x));\n *\n * // Outputs\n * // 1\n * // 2\n * // 3\n * // 4\n * ```\n *\n * An example using the `keySelector` function\n *\n * ```ts\n * import { of, distinct } from 'rxjs';\n *\n * of(\n *   { age: 4, name: 'Foo'},\n *   { age: 7, name: 'Bar'},\n *   { age: 5, name: 'Foo'}\n * )\n * .pipe(distinct(({ name }) => name))\n * .subscribe(x => console.log(x));\n *\n * // Outputs\n * // { age: 4, name: 'Foo' }\n * // { age: 7, name: 'Bar' }\n * ```\n * @see {@link distinctUntilChanged}\n * @see {@link distinctUntilKeyChanged}\n *\n * @param keySelector Optional `function` to select which value you want to check as distinct.\n * @param flushes Optional `ObservableInput` for flushing the internal HashSet of the operator.\n * @return A function that returns an Observable that emits items from the\n * source Observable with distinct values.\n */\nexport function distinct<T, K>(keySelector?: (value: T) => K, flushes?: ObservableInput<any>): MonoTypeOperatorFunction<T> {\n  return operate((source, subscriber) => {\n    const distinctKeys = new Set();\n    source.subscribe(\n      createOperatorSubscriber(subscriber, (value) => {\n        const key = keySelector ? keySelector(value) : value;\n        if (!distinctKeys.has(key)) {\n          distinctKeys.add(key);\n          subscriber.next(value);\n        }\n      })\n    );\n\n    flushes && innerFrom(flushes).subscribe(createOperatorSubscriber(subscriber, () => distinctKeys.clear(), noop));\n  });\n}\n", "import { MonoTypeOperatorFunction } from '../types';\nimport { identity } from '../util/identity';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\n\nexport function distinctUntilChanged<T>(comparator?: (previous: T, current: T) => boolean): MonoTypeOperatorFunction<T>;\nexport function distinctUntilChanged<T, K>(\n  comparator: (previous: K, current: K) => boolean,\n  keySelector: (value: T) => K\n): MonoTypeOperatorFunction<T>;\n\n/**\n * Returns a result {@link Observable} that emits all values pushed by the source observable if they\n * are distinct in comparison to the last value the result observable emitted.\n *\n * When provided without parameters or with the first parameter (`{@link distinctUntilChanged#comparator comparator}`),\n * it behaves like this:\n *\n * 1. It will always emit the first value from the source.\n * 2. For all subsequent values pushed by the source, they will be compared to the previously emitted values\n *    using the provided `comparator` or an `===` equality check.\n * 3. If the value pushed by the source is determined to be unequal by this check, that value is emitted and\n *    becomes the new \"previously emitted value\" internally.\n *\n * When the second parameter (`{@link distinctUntilChanged#keySelector keySelector}`) is provided, the behavior\n * changes:\n *\n * 1. It will always emit the first value from the source.\n * 2. The `keySelector` will be run against all values, including the first value.\n * 3. For all values after the first, the selected key will be compared against the key selected from\n *    the previously emitted value using the `comparator`.\n * 4. If the keys are determined to be unequal by this check, the value (not the key), is emitted\n *    and the selected key from that value is saved for future comparisons against other keys.\n *\n * ## Examples\n *\n * A very basic example with no `{@link distinctUntilChanged#comparator comparator}`. Note that `1` is emitted more than once,\n * because it's distinct in comparison to the _previously emitted_ value,\n * not in comparison to _all other emitted values_.\n *\n * ```ts\n * import { of, distinctUntilChanged } from 'rxjs';\n *\n * of(1, 1, 1, 2, 2, 2, 1, 1, 3, 3)\n *   .pipe(distinctUntilChanged())\n *   .subscribe(console.log);\n * // Logs: 1, 2, 1, 3\n * ```\n *\n * With a `{@link distinctUntilChanged#comparator comparator}`, you can do custom comparisons. Let's say\n * you only want to emit a value when all of its components have\n * changed:\n *\n * ```ts\n * import { of, distinctUntilChanged } from 'rxjs';\n *\n * const totallyDifferentBuilds$ = of(\n *   { engineVersion: '1.1.0', transmissionVersion: '1.2.0' },\n *   { engineVersion: '1.1.0', transmissionVersion: '1.4.0' },\n *   { engineVersion: '1.3.0', transmissionVersion: '1.4.0' },\n *   { engineVersion: '1.3.0', transmissionVersion: '1.5.0' },\n *   { engineVersion: '2.0.0', transmissionVersion: '1.5.0' }\n * ).pipe(\n *   distinctUntilChanged((prev, curr) => {\n *     return (\n *       prev.engineVersion === curr.engineVersion ||\n *       prev.transmissionVersion === curr.transmissionVersion\n *     );\n *   })\n * );\n *\n * totallyDifferentBuilds$.subscribe(console.log);\n *\n * // Logs:\n * // { engineVersion: '1.1.0', transmissionVersion: '1.2.0' }\n * // { engineVersion: '1.3.0', transmissionVersion: '1.4.0' }\n * // { engineVersion: '2.0.0', transmissionVersion: '1.5.0' }\n * ```\n *\n * You can also provide a custom `{@link distinctUntilChanged#comparator comparator}` to check that emitted\n * changes are only in one direction. Let's say you only want to get\n * the next record temperature:\n *\n * ```ts\n * import { of, distinctUntilChanged } from 'rxjs';\n *\n * const temps$ = of(30, 31, 20, 34, 33, 29, 35, 20);\n *\n * const recordHighs$ = temps$.pipe(\n *   distinctUntilChanged((prevHigh, temp) => {\n *     // If the current temp is less than\n *     // or the same as the previous record,\n *     // the record hasn't changed.\n *     return temp <= prevHigh;\n *   })\n * );\n *\n * recordHighs$.subscribe(console.log);\n * // Logs: 30, 31, 34, 35\n * ```\n *\n * Selecting update events only when the `updatedBy` field shows\n * the account changed hands.\n *\n * ```ts\n * import { of, distinctUntilChanged } from 'rxjs';\n *\n * // A stream of updates to a given account\n * const accountUpdates$ = of(\n *   { updatedBy: 'blesh', data: [] },\n *   { updatedBy: 'blesh', data: [] },\n *   { updatedBy: 'ncjamieson', data: [] },\n *   { updatedBy: 'ncjamieson', data: [] },\n *   { updatedBy: 'blesh', data: [] }\n * );\n *\n * // We only want the events where it changed hands\n * const changedHands$ = accountUpdates$.pipe(\n *   distinctUntilChanged(undefined, update => update.updatedBy)\n * );\n *\n * changedHands$.subscribe(console.log);\n * // Logs:\n * // { updatedBy: 'blesh', data: Array[0] }\n * // { updatedBy: 'ncjamieson', data: Array[0] }\n * // { updatedBy: 'blesh', data: Array[0] }\n * ```\n *\n * @see {@link distinct}\n * @see {@link distinctUntilKeyChanged}\n *\n * @param comparator A function used to compare the previous and current keys for\n * equality. Defaults to a `===` check.\n * @param keySelector Used to select a key value to be passed to the `comparator`.\n *\n * @return A function that returns an Observable that emits items from the\n * source Observable with distinct values.\n */\nexport function distinctUntilChanged<T, K>(\n  comparator?: (previous: K, current: K) => boolean,\n  keySelector: (value: T) => K = identity as (value: T) => K\n): MonoTypeOperatorFunction<T> {\n  // We've been allowing `null` do be passed as the `compare`, so we can't do\n  // a default value for the parameter, because that will only work\n  // for `undefined`.\n  comparator = comparator ?? defaultCompare;\n\n  return operate((source, subscriber) => {\n    // The previous key, used to compare against keys selected\n    // from new arrivals to determine \"distinctiveness\".\n    let previousKey: K;\n    // Whether or not this is the first value we've gotten.\n    let first = true;\n\n    source.subscribe(\n      createOperatorSubscriber(subscriber, (value) => {\n        // We always call the key selector.\n        const currentKey = keySelector(value);\n\n        // If it's the first value, we always emit it.\n        // Otherwise, we compare this key to the previous key, and\n        // if the comparer returns false, we emit.\n        if (first || !comparator!(previousKey, currentKey)) {\n          // Update our state *before* we emit the value\n          // as emission can be the source of re-entrant code\n          // in functional libraries like this. We only really\n          // need to do this if it's the first value, or if the\n          // key we're tracking in previous needs to change.\n          first = false;\n          previousKey = currentKey;\n\n          // Emit the value!\n          subscriber.next(value);\n        }\n      })\n    );\n  });\n}\n\nfunction defaultCompare(a: any, b: any) {\n  return a === b;\n}\n", "import { distinctUntilChanged } from './distinctUntilChanged';\nimport { MonoTypeOperatorFunction } from '../types';\n\nexport function distinctUntilKeyChanged<T>(key: keyof T): MonoTypeOperatorFunction<T>;\nexport function distinctUntilKeyChanged<T, K extends keyof T>(key: K, compare: (x: T[K], y: T[K]) => boolean): MonoTypeOperatorFunction<T>;\n\n/**\n * Returns an Observable that emits all items emitted by the source Observable that\n * are distinct by comparison from the previous item, using a property accessed by\n * using the key provided to check if the two items are distinct.\n *\n * If a comparator function is provided, then it will be called for each item to\n * test for whether that value should be emitted or not.\n *\n * If a comparator function is not provided, an equality check is used by default.\n *\n * ## Examples\n *\n * An example comparing the name of persons\n *\n * ```ts\n * import { of, distinctUntilKeyChanged } from 'rxjs';\n *\n * of(\n *   { age: 4, name: 'Foo' },\n *   { age: 7, name: 'Bar' },\n *   { age: 5, name: 'Foo' },\n *   { age: 6, name: 'Foo' }\n * ).pipe(\n *   distinctUntilKeyChanged('name')\n * )\n * .subscribe(x => console.log(x));\n *\n * // displays:\n * // { age: 4, name: 'Foo' }\n * // { age: 7, name: 'Bar' }\n * // { age: 5, name: 'Foo' }\n * ```\n *\n * An example comparing the first letters of the name\n *\n * ```ts\n * import { of, distinctUntilKeyChanged } from 'rxjs';\n *\n * of(\n *   { age: 4, name: 'Foo1' },\n *   { age: 7, name: 'Bar' },\n *   { age: 5, name: 'Foo2' },\n *   { age: 6, name: 'Foo3' }\n * ).pipe(\n *   distinctUntilKeyChanged('name', (x, y) => x.substring(0, 3) === y.substring(0, 3))\n * )\n * .subscribe(x => console.log(x));\n *\n * // displays:\n * // { age: 4, name: 'Foo1' }\n * // { age: 7, name: 'Bar' }\n * // { age: 5, name: 'Foo2' }\n * ```\n *\n * @see {@link distinct}\n * @see {@link distinctUntilChanged}\n *\n * @param key String key for object property lookup on each item.\n * @param compare Optional comparison function called to test if an item is distinct\n * from the previous item in the source.\n * @return A function that returns an Observable that emits items from the source\n * Observable with distinct values based on the key specified.\n */\nexport function distinctUntilKeyChanged<T, K extends keyof T>(\n  key: K,\n  compare?: (x: T[K], y: T[K]) => boolean\n): MonoTypeOperatorFunction<T> {\n  return distinctUntilChanged((x: T, y: T) => (compare ? compare(x[key], y[key]) : x[key] === y[key]));\n}\n", "import { EmptyError } from '../util/EmptyError';\nimport { MonoTypeOperatorFunction } from '../types';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\n\n/**\n * If the source observable completes without emitting a value, it will emit\n * an error. The error will be created at that time by the optional\n * `errorFactory` argument, otherwise, the error will be {@link EmptyError}.\n *\n * ![](throwIfEmpty.png)\n *\n * ## Example\n *\n * Throw an error if the document wasn't clicked within 1 second\n *\n * ```ts\n * import { fromEvent, takeUntil, timer, throwIfEmpty } from 'rxjs';\n *\n * const click$ = fromEvent(document, 'click');\n *\n * click$.pipe(\n *   takeUntil(timer(1000)),\n *   throwIfEmpty(() => new Error('The document was not clicked within 1 second'))\n * )\n * .subscribe({\n *   next() {\n *    console.log('The document was clicked');\n *   },\n *   error(err) {\n *     console.error(err.message);\n *   }\n * });\n * ```\n *\n * @param errorFactory A factory function called to produce the\n * error to be thrown when the source observable completes without emitting a\n * value.\n * @return A function that returns an Observable that throws an error if the\n * source Observable completed without emitting.\n */\nexport function throwIfEmpty<T>(errorFactory: () => any = defaultErrorFactory): MonoTypeOperatorFunction<T> {\n  return operate((source, subscriber) => {\n    let hasValue = false;\n    source.subscribe(\n      createOperatorSubscriber(\n        subscriber,\n        (value) => {\n          hasValue = true;\n          subscriber.next(value);\n        },\n        () => (hasValue ? subscriber.complete() : subscriber.error(errorFactory()))\n      )\n    );\n  });\n}\n\nfunction defaultErrorFactory() {\n  return new EmptyError();\n}\n", "/** prettier */\nimport { Observable } from '../Observable';\nimport { concat } from '../observable/concat';\nimport { of } from '../observable/of';\nimport { MonoTypeOperatorFunction, SchedulerLike, OperatorFunction, ValueFromArray } from '../types';\n\n/** @deprecated The `scheduler` parameter will be removed in v8. Use `scheduled` and `concatAll`. Details: https://rxjs.dev/deprecations/scheduler-argument */\nexport function endWith<T>(scheduler: SchedulerLike): MonoTypeOperatorFunction<T>;\n/** @deprecated The `scheduler` parameter will be removed in v8. Use `scheduled` and `concatAll`. Details: https://rxjs.dev/deprecations/scheduler-argument */\nexport function endWith<T, A extends unknown[] = T[]>(\n  ...valuesAndScheduler: [...A, SchedulerLike]\n): OperatorFunction<T, T | ValueFromArray<A>>;\n\nexport function endWith<T, A extends unknown[] = T[]>(...values: A): OperatorFunction<T, T | ValueFromArray<A>>;\n\n/**\n * Returns an observable that will emit all values from the source, then synchronously emit\n * the provided value(s) immediately after the source completes.\n *\n * NOTE: Passing a last argument of a Scheduler is _deprecated_, and may result in incorrect\n * types in TypeScript.\n *\n * This is useful for knowing when an observable ends. Particularly when paired with an\n * operator like {@link takeUntil}\n *\n * ![](endWith.png)\n *\n * ## Example\n *\n * Emit values to know when an interval starts and stops. The interval will\n * stop when a user clicks anywhere on the document.\n *\n * ```ts\n * import { interval, map, fromEvent, startWith, takeUntil, endWith } from 'rxjs';\n *\n * const ticker$ = interval(5000).pipe(\n *   map(() => 'tick')\n * );\n *\n * const documentClicks$ = fromEvent(document, 'click');\n *\n * ticker$.pipe(\n *   startWith('interval started'),\n *   takeUntil(documentClicks$),\n *   endWith('interval ended by click')\n * )\n * .subscribe(x => console.log(x));\n *\n * // Result (assuming a user clicks after 15 seconds)\n * // 'interval started'\n * // 'tick'\n * // 'tick'\n * // 'tick'\n * // 'interval ended by click'\n * ```\n *\n * @see {@link startWith}\n * @see {@link concat}\n * @see {@link takeUntil}\n *\n * @param values Items you want the modified Observable to emit last.\n * @return A function that returns an Observable that emits all values from the\n * source, then synchronously emits the provided value(s) immediately after the\n * source completes.\n */\nexport function endWith<T>(...values: Array<T | SchedulerLike>): MonoTypeOperatorFunction<T> {\n  return (source: Observable<T>) => concat(source, of(...values)) as Observable<T>;\n}\n", "import { Observable } from '../Observable';\nimport { Subscriber } from '../Subscriber';\nimport { ObservableInput, OperatorFunction, ObservedValueOf } from '../types';\nimport { map } from './map';\nimport { innerFrom } from '../observable/innerFrom';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\n\n/* tslint:disable:max-line-length */\nexport function exhaustMap<T, O extends ObservableInput<any>>(\n  project: (value: T, index: number) => O\n): OperatorFunction<T, ObservedValueOf<O>>;\n/** @deprecated The `resultSelector` parameter will be removed in v8. Use an inner `map` instead. Details: https://rxjs.dev/deprecations/resultSelector */\nexport function exhaustMap<T, O extends ObservableInput<any>>(\n  project: (value: T, index: number) => O,\n  resultSelector: undefined\n): OperatorFunction<T, ObservedValueOf<O>>;\n/** @deprecated The `resultSelector` parameter will be removed in v8. Use an inner `map` instead. Details: https://rxjs.dev/deprecations/resultSelector */\nexport function exhaustMap<T, I, R>(\n  project: (value: T, index: number) => ObservableInput<I>,\n  resultSelector: (outerValue: T, innerValue: I, outerIndex: number, innerIndex: number) => R\n): OperatorFunction<T, R>;\n/* tslint:enable:max-line-length */\n\n/**\n * Projects each source value to an Observable which is merged in the output\n * Observable only if the previous projected Observable has completed.\n *\n * <span class=\"informal\">Maps each value to an Observable, then flattens all of\n * these inner Observables using {@link exhaustAll}.</span>\n *\n * ![](exhaustMap.png)\n *\n * Returns an Observable that emits items based on applying a function that you\n * supply to each item emitted by the source Observable, where that function\n * returns an (so-called \"inner\") Observable. When it projects a source value to\n * an Observable, the output Observable begins emitting the items emitted by\n * that projected Observable. However, `exhaustMap` ignores every new projected\n * Observable if the previous projected Observable has not yet completed. Once\n * that one completes, it will accept and flatten the next projected Observable\n * and repeat this process.\n *\n * ## Example\n *\n * Run a finite timer for each click, only if there is no currently active timer\n *\n * ```ts\n * import { fromEvent, exhaustMap, interval, take } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const result = clicks.pipe(\n *   exhaustMap(() => interval(1000).pipe(take(5)))\n * );\n * result.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link concatMap}\n * @see {@link exhaust}\n * @see {@link mergeMap}\n * @see {@link switchMap}\n *\n * @param project A function that, when applied to an item emitted by the source\n * Observable, returns an Observable.\n * @return A function that returns an Observable containing projected\n * Observables of each item of the source, ignoring projected Observables that\n * start before their preceding Observable has completed.\n */\nexport function exhaustMap<T, R, O extends ObservableInput<any>>(\n  project: (value: T, index: number) => O,\n  resultSelector?: (outerValue: T, innerValue: ObservedValueOf<O>, outerIndex: number, innerIndex: number) => R\n): OperatorFunction<T, ObservedValueOf<O> | R> {\n  if (resultSelector) {\n    // DEPRECATED PATH\n    return (source: Observable<T>) =>\n      source.pipe(exhaustMap((a, i) => innerFrom(project(a, i)).pipe(map((b: any, ii: any) => resultSelector(a, b, i, ii)))));\n  }\n  return operate((source, subscriber) => {\n    let index = 0;\n    let innerSub: Subscriber<T> | null = null;\n    let isComplete = false;\n    source.subscribe(\n      createOperatorSubscriber(\n        subscriber,\n        (outerValue) => {\n          if (!innerSub) {\n            innerSub = createOperatorSubscriber(subscriber, undefined, () => {\n              innerSub = null;\n              isComplete && subscriber.complete();\n            });\n            innerFrom(project(outerValue, index++)).subscribe(innerSub);\n          }\n        },\n        () => {\n          isComplete = true;\n          !innerSub && subscriber.complete();\n        }\n      )\n    );\n  });\n}\n", "import { MonoTypeOperatorFunction } from '../types';\nimport { operate } from '../util/lift';\n\n/**\n * Returns an Observable that mirrors the source Observable, but will call a specified function when\n * the source terminates on complete or error.\n * The specified function will also be called when the subscriber explicitly unsubscribes.\n *\n * ## Examples\n *\n * Execute callback function when the observable completes\n *\n * ```ts\n * import { interval, take, finalize } from 'rxjs';\n *\n * // emit value in sequence every 1 second\n * const source = interval(1000);\n * const example = source.pipe(\n *   take(5), //take only the first 5 values\n *   finalize(() => console.log('Sequence complete')) // Execute when the observable completes\n * );\n * const subscribe = example.subscribe(val => console.log(val));\n *\n * // results:\n * // 0\n * // 1\n * // 2\n * // 3\n * // 4\n * // 'Sequence complete'\n * ```\n *\n * Execute callback function when the subscriber explicitly unsubscribes\n *\n * ```ts\n * import { interval, finalize, tap, noop, timer } from 'rxjs';\n *\n * const source = interval(100).pipe(\n *   finalize(() => console.log('[finalize] Called')),\n *   tap({\n *     next: () => console.log('[next] Called'),\n *     error: () => console.log('[error] Not called'),\n *     complete: () => console.log('[tap complete] Not called')\n *   })\n * );\n *\n * const sub = source.subscribe({\n *   next: x => console.log(x),\n *   error: noop,\n *   complete: () => console.log('[complete] Not called')\n * });\n *\n * timer(150).subscribe(() => sub.unsubscribe());\n *\n * // results:\n * // '[next] Called'\n * // 0\n * // '[finalize] Called'\n * ```\n *\n * @param callback Function to be called when source terminates.\n * @return A function that returns an Observable that mirrors the source, but\n * will call the specified function on termination.\n */\nexport function finalize<T>(callback: () => void): MonoTypeOperatorFunction<T> {\n  return operate((source, subscriber) => {\n    // TODO: This try/finally was only added for `useDeprecatedSynchronousErrorHandling`.\n    // REMOVE THIS WHEN THAT HOT GARBAGE IS REMOVED IN V8.\n    try {\n      source.subscribe(subscriber);\n    } finally {\n      subscriber.add(callback);\n    }\n  });\n}\n", "import { Observable } from '../Observable';\nimport { EmptyError } from '../util/EmptyError';\nimport { OperatorFunction, TruthyTypesOf } from '../types';\nimport { filter } from './filter';\nimport { take } from './take';\nimport { defaultIfEmpty } from './defaultIfEmpty';\nimport { throwIfEmpty } from './throwIfEmpty';\nimport { identity } from '../util/identity';\n\nexport function first<T, D = T>(predicate?: null, defaultValue?: D): OperatorFunction<T, T | D>;\nexport function first<T>(predicate: BooleanConstructor): OperatorFunction<T, TruthyTypesOf<T>>;\nexport function first<T, D>(predicate: BooleanConstructor, defaultValue: D): OperatorFunction<T, TruthyTypesOf<T> | D>;\nexport function first<T, S extends T>(\n  predicate: (value: T, index: number, source: Observable<T>) => value is S,\n  defaultValue?: S\n): OperatorFunction<T, S>;\nexport function first<T, S extends T, D>(\n  predicate: (value: T, index: number, source: Observable<T>) => value is S,\n  defaultValue: D\n): OperatorFunction<T, S | D>;\nexport function first<T, D = T>(\n  predicate: (value: T, index: number, source: Observable<T>) => boolean,\n  defaultValue?: D\n): OperatorFunction<T, T | D>;\n\n/**\n * Emits only the first value (or the first value that meets some condition)\n * emitted by the source Observable.\n *\n * <span class=\"informal\">Emits only the first value. Or emits only the first\n * value that passes some test.</span>\n *\n * ![](first.png)\n *\n * If called with no arguments, `first` emits the first value of the source\n * Observable, then completes. If called with a `predicate` function, `first`\n * emits the first value of the source that matches the specified condition. Emits an error\n * notification if `defaultValue` was not provided and a matching element is not found.\n *\n * ## Examples\n *\n * Emit only the first click that happens on the DOM\n *\n * ```ts\n * import { fromEvent, first } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const result = clicks.pipe(first());\n * result.subscribe(x => console.log(x));\n * ```\n *\n * Emits the first click that happens on a DIV\n *\n * ```ts\n * import { fromEvent, first } from 'rxjs';\n *\n * const div = document.createElement('div');\n * div.style.cssText = 'width: 200px; height: 200px; background: #09c;';\n * document.body.appendChild(div);\n *\n * const clicks = fromEvent(document, 'click');\n * const result = clicks.pipe(first(ev => (<HTMLElement>ev.target).tagName === 'DIV'));\n * result.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link filter}\n * @see {@link find}\n * @see {@link take}\n * @see {@link last}\n *\n * @throws {EmptyError} Delivers an `EmptyError` to the Observer's `error`\n * callback if the Observable completes before any `next` notification was sent.\n * This is how `first()` is different from `take(1)` which completes instead.\n *\n * @param predicate An optional function called with each item to test for condition\n * matching.\n * @param defaultValue The default value emitted in case no valid value was found on\n * the source.\n * @return A function that returns an Observable that emits the first item that\n * matches the condition.\n */\nexport function first<T, D>(\n  predicate?: ((value: T, index: number, source: Observable<T>) => boolean) | null,\n  defaultValue?: D\n): OperatorFunction<T, T | D> {\n  const hasDefaultValue = arguments.length >= 2;\n  return (source: Observable<T>) =>\n    source.pipe(\n      predicate ? filter((v, i) => predicate(v, i, source)) : identity,\n      take(1),\n      hasDefaultValue ? defaultIfEmpty(defaultValue!) : throwIfEmpty(() => new EmptyError())\n    );\n}\n", "import { EMPTY } from '../observable/empty';\nimport { MonoTypeOperatorFunction } from '../types';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\n\n/**\n * Waits for the source to complete, then emits the last N values from the source,\n * as specified by the `count` argument.\n *\n * ![](takeLast.png)\n *\n * `takeLast` results in an observable that will hold values up to `count` values in memory,\n * until the source completes. It then pushes all values in memory to the consumer, in the\n * order they were received from the source, then notifies the consumer that it is\n * complete.\n *\n * If for some reason the source completes before the `count` supplied to `takeLast` is reached,\n * all values received until that point are emitted, and then completion is notified.\n *\n * **Warning**: Using `takeLast` with an observable that never completes will result\n * in an observable that never emits a value.\n *\n * ## Example\n *\n * Take the last 3 values of an Observable with many values\n *\n * ```ts\n * import { range, takeLast } from 'rxjs';\n *\n * const many = range(1, 100);\n * const lastThree = many.pipe(takeLast(3));\n * lastThree.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link take}\n * @see {@link takeUntil}\n * @see {@link takeWhile}\n * @see {@link skip}\n *\n * @param count The maximum number of values to emit from the end of\n * the sequence of values emitted by the source Observable.\n * @return A function that returns an Observable that emits at most the last\n * `count` values emitted by the source Observable.\n */\nexport function takeLast<T>(count: number): MonoTypeOperatorFunction<T> {\n  return count <= 0\n    ? () => EMPTY\n    : operate((source, subscriber) => {\n        // This buffer will hold the values we are going to emit\n        // when the source completes. Since we only want to take the\n        // last N values, we can't emit until we're sure we're not getting\n        // any more values.\n        let buffer: T[] = [];\n        source.subscribe(\n          createOperatorSubscriber(\n            subscriber,\n            (value) => {\n              // Add the most recent value onto the end of our buffer.\n              buffer.push(value);\n              // If our buffer is now larger than the number of values we\n              // want to take, we remove the oldest value from the buffer.\n              count < buffer.length && buffer.shift();\n            },\n            () => {\n              // The source completed, we now know what are last values\n              // are, emit them in the order they were received.\n              for (const value of buffer) {\n                subscriber.next(value);\n              }\n              subscriber.complete();\n            },\n            // Errors are passed through to the consumer\n            undefined,\n            () => {\n              // During finalization release the values in our buffer.\n              buffer = null!;\n            }\n          )\n        );\n      });\n}\n", "import { ObservableInput, ObservableInputTuple, OperatorFunction, SchedulerLike } from '../types';\nimport { operate } from '../util/lift';\nimport { mergeAll } from './mergeAll';\nimport { popNumber, popScheduler } from '../util/args';\nimport { from } from '../observable/from';\n\n/** @deprecated Replaced with {@link mergeWith}. Will be removed in v8. */\nexport function merge<T, A extends readonly unknown[]>(...sources: [...ObservableInputTuple<A>]): OperatorFunction<T, T | A[number]>;\n/** @deprecated Replaced with {@link mergeWith}. Will be removed in v8. */\nexport function merge<T, A extends readonly unknown[]>(\n  ...sourcesAndConcurrency: [...ObservableInputTuple<A>, number]\n): OperatorFunction<T, T | A[number]>;\n/** @deprecated Replaced with {@link mergeWith}. Will be removed in v8. */\nexport function merge<T, A extends readonly unknown[]>(\n  ...sourcesAndScheduler: [...ObservableInputTuple<A>, SchedulerLike]\n): OperatorFunction<T, T | A[number]>;\n/** @deprecated Replaced with {@link mergeWith}. Will be removed in v8. */\nexport function merge<T, A extends readonly unknown[]>(\n  ...sourcesAndConcurrencyAndScheduler: [...ObservableInputTuple<A>, number, SchedulerLike]\n): OperatorFunction<T, T | A[number]>;\n\nexport function merge<T>(...args: unknown[]): OperatorFunction<T, unknown> {\n  const scheduler = popScheduler(args);\n  const concurrent = popNumber(args, Infinity);\n\n  return operate((source, subscriber) => {\n    mergeAll(concurrent)(from([source, ...(args as ObservableInput<T>[])], scheduler)).subscribe(subscriber);\n  });\n}\n", "import { ObservableInputTuple, OperatorFunction } from '../types';\nimport { merge } from './merge';\n\n/**\n * Merge the values from all observables to a single observable result.\n *\n * Creates an observable, that when subscribed to, subscribes to the source\n * observable, and all other sources provided as arguments. All values from\n * every source are emitted from the resulting subscription.\n *\n * When all sources complete, the resulting observable will complete.\n *\n * When any source errors, the resulting observable will error.\n *\n * ## Example\n *\n * Joining all outputs from multiple user input event streams\n *\n * ```ts\n * import { fromEvent, map, mergeWith } from 'rxjs';\n *\n * const clicks$ = fromEvent(document, 'click').pipe(map(() => 'click'));\n * const mousemoves$ = fromEvent(document, 'mousemove').pipe(map(() => 'mousemove'));\n * const dblclicks$ = fromEvent(document, 'dblclick').pipe(map(() => 'dblclick'));\n *\n * mousemoves$\n *   .pipe(mergeWith(clicks$, dblclicks$))\n *   .subscribe(x => console.log(x));\n *\n * // result (assuming user interactions)\n * // 'mousemove'\n * // 'mousemove'\n * // 'mousemove'\n * // 'click'\n * // 'click'\n * // 'dblclick'\n * ```\n *\n * @see {@link merge}\n *\n * @param otherSources the sources to combine the current source with.\n * @return A function that returns an Observable that merges the values from\n * all given Observables.\n */\nexport function mergeWith<T, A extends readonly unknown[]>(\n  ...otherSources: [...ObservableInputTuple<A>]\n): OperatorFunction<T, T | A[number]> {\n  return merge(...otherSources);\n}\n", "import { Subscription } from '../Subscription';\nimport { EMPTY } from '../observable/empty';\nimport { operate } from '../util/lift';\nimport { MonoTypeOperatorFunction, ObservableInput } from '../types';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\nimport { innerFrom } from '../observable/innerFrom';\nimport { timer } from '../observable/timer';\n\nexport interface RepeatConfig {\n  /**\n   * The number of times to repeat the source. Defaults to `Infinity`.\n   */\n  count?: number;\n\n  /**\n   * If a `number`, will delay the repeat of the source by that number of milliseconds.\n   * If a function, it will provide the number of times the source has been subscribed to,\n   * and the return value should be a valid observable input that will notify when the source\n   * should be repeated. If the notifier observable is empty, the result will complete.\n   */\n  delay?: number | ((count: number) => ObservableInput<any>);\n}\n\n/**\n * Returns an Observable that will resubscribe to the source stream when the source stream completes.\n *\n * <span class=\"informal\">Repeats all values emitted on the source. It's like {@link retry}, but for non error cases.</span>\n *\n * ![](repeat.png)\n *\n * Repeat will output values from a source until the source completes, then it will resubscribe to the\n * source a specified number of times, with a specified delay. Repeat can be particularly useful in\n * combination with closing operators like {@link take}, {@link takeUntil}, {@link first}, or {@link takeWhile},\n * as it can be used to restart a source again from scratch.\n *\n * Repeat is very similar to {@link retry}, where {@link retry} will resubscribe to the source in the error case, but\n * `repeat` will resubscribe if the source completes.\n *\n * Note that `repeat` will _not_ catch errors. Use {@link retry} for that.\n *\n * - `repeat(0)` returns an empty observable\n * - `repeat()` will repeat forever\n * - `repeat({ delay: 200 })` will repeat forever, with a delay of 200ms between repetitions.\n * - `repeat({ count: 2, delay: 400 })` will repeat twice, with a delay of 400ms between repetitions.\n * - `repeat({ delay: (count) => timer(count * 1000) })` will repeat forever, but will have a delay that grows by one second for each repetition.\n *\n * ## Example\n *\n * Repeat a message stream\n *\n * ```ts\n * import { of, repeat } from 'rxjs';\n *\n * const source = of('Repeat message');\n * const result = source.pipe(repeat(3));\n *\n * result.subscribe(x => console.log(x));\n *\n * // Results\n * // 'Repeat message'\n * // 'Repeat message'\n * // 'Repeat message'\n * ```\n *\n * Repeat 3 values, 2 times\n *\n * ```ts\n * import { interval, take, repeat } from 'rxjs';\n *\n * const source = interval(1000);\n * const result = source.pipe(take(3), repeat(2));\n *\n * result.subscribe(x => console.log(x));\n *\n * // Results every second\n * // 0\n * // 1\n * // 2\n * // 0\n * // 1\n * // 2\n * ```\n *\n * Defining two complex repeats with delays on the same source.\n * Note that the second repeat cannot be called until the first\n * repeat as exhausted it's count.\n *\n * ```ts\n * import { defer, of, repeat } from 'rxjs';\n *\n * const source = defer(() => {\n *    return of(`Hello, it is ${new Date()}`)\n * });\n *\n * source.pipe(\n *    // Repeat 3 times with a delay of 1 second between repetitions\n *    repeat({\n *      count: 3,\n *      delay: 1000,\n *    }),\n *\n *    // *Then* repeat forever, but with an exponential step-back\n *    // maxing out at 1 minute.\n *    repeat({\n *      delay: (count) => timer(Math.min(60000, 2 ^ count * 1000))\n *    })\n * )\n * ```\n *\n * @see {@link repeatWhen}\n * @see {@link retry}\n *\n * @param countOrConfig Either the number of times the source Observable items are repeated\n * (a count of 0 will yield an empty Observable) or a {@link RepeatConfig} object.\n */\nexport function repeat<T>(countOrConfig?: number | RepeatConfig): MonoTypeOperatorFunction<T> {\n  let count = Infinity;\n  let delay: RepeatConfig['delay'];\n\n  if (countOrConfig != null) {\n    if (typeof countOrConfig === 'object') {\n      ({ count = Infinity, delay } = countOrConfig);\n    } else {\n      count = countOrConfig;\n    }\n  }\n\n  return count <= 0\n    ? () => EMPTY\n    : operate((source, subscriber) => {\n        let soFar = 0;\n        let sourceSub: Subscription | null;\n\n        const resubscribe = () => {\n          sourceSub?.unsubscribe();\n          sourceSub = null;\n          if (delay != null) {\n            const notifier = typeof delay === 'number' ? timer(delay) : innerFrom(delay(soFar));\n            const notifierSubscriber = createOperatorSubscriber(subscriber, () => {\n              notifierSubscriber.unsubscribe();\n              subscribeToSource();\n            });\n            notifier.subscribe(notifierSubscriber);\n          } else {\n            subscribeToSource();\n          }\n        };\n\n        const subscribeToSource = () => {\n          let syncUnsub = false;\n          sourceSub = source.subscribe(\n            createOperatorSubscriber(subscriber, undefined, () => {\n              if (++soFar < count) {\n                if (sourceSub) {\n                  resubscribe();\n                } else {\n                  syncUnsub = true;\n                }\n              } else {\n                subscriber.complete();\n              }\n            })\n          );\n\n          if (syncUnsub) {\n            resubscribe();\n          }\n        };\n\n        subscribeToSource();\n      });\n}\n", "import { OperatorFunction } from '../types';\nimport { operate } from '../util/lift';\nimport { scanInternals } from './scanInternals';\n\nexport function scan<V, A = V>(accumulator: (acc: A | V, value: V, index: number) => A): OperatorFunction<V, V | A>;\nexport function scan<V, A>(accumulator: (acc: A, value: V, index: number) => A, seed: A): OperatorFunction<V, A>;\nexport function scan<V, A, S>(accumulator: (acc: A | S, value: V, index: number) => A, seed: S): OperatorFunction<V, A>;\n\n// TODO: link to a \"redux pattern\" section in the guide (location TBD)\n\n/**\n * Useful for encapsulating and managing state. Applies an accumulator (or \"reducer function\")\n * to each value from the source after an initial state is established -- either via\n * a `seed` value (second argument), or from the first value from the source.\n *\n * <span class=\"informal\">It's like {@link reduce}, but emits the current\n * accumulation state after each update</span>\n *\n * ![](scan.png)\n *\n * This operator maintains an internal state and emits it after processing each value as follows:\n *\n * 1. First value arrives\n *   - If a `seed` value was supplied (as the second argument to `scan`), let `state = seed` and `value = firstValue`.\n *   - If NO `seed` value was supplied (no second argument), let `state = firstValue` and go to 3.\n * 2. Let `state = accumulator(state, value)`.\n *   - If an error is thrown by `accumulator`, notify the consumer of an error. The process ends.\n * 3. Emit `state`.\n * 4. Next value arrives, let `value = nextValue`, go to 2.\n *\n * ## Examples\n *\n * An average of previous numbers. This example shows how\n * not providing a `seed` can prime the stream with the\n * first value from the source.\n *\n * ```ts\n * import { of, scan, map } from 'rxjs';\n *\n * const numbers$ = of(1, 2, 3);\n *\n * numbers$\n *   .pipe(\n *     // Get the sum of the numbers coming in.\n *     scan((total, n) => total + n),\n *     // Get the average by dividing the sum by the total number\n *     // received so far (which is 1 more than the zero-based index).\n *     map((sum, index) => sum / (index + 1))\n *   )\n *   .subscribe(console.log);\n * ```\n *\n * The Fibonacci sequence. This example shows how you can use\n * a seed to prime accumulation process. Also... you know... Fibonacci.\n * So important to like, computers and stuff that its whiteboarded\n * in job interviews. Now you can show them the Rx version! (Please don't, haha)\n *\n * ```ts\n * import { interval, scan, map, startWith } from 'rxjs';\n *\n * const firstTwoFibs = [0, 1];\n * // An endless stream of Fibonacci numbers.\n * const fibonacci$ = interval(1000).pipe(\n *   // Scan to get the fibonacci numbers (after 0, 1)\n *   scan(([a, b]) => [b, a + b], firstTwoFibs),\n *   // Get the second number in the tuple, it's the one you calculated\n *   map(([, n]) => n),\n *   // Start with our first two digits :)\n *   startWith(...firstTwoFibs)\n * );\n *\n * fibonacci$.subscribe(console.log);\n * ```\n *\n * @see {@link expand}\n * @see {@link mergeScan}\n * @see {@link reduce}\n * @see {@link switchScan}\n *\n * @param accumulator A \"reducer function\". This will be called for each value after an initial state is\n * acquired.\n * @param seed The initial state. If this is not provided, the first value from the source will\n * be used as the initial state, and emitted without going through the accumulator. All subsequent values\n * will be processed by the accumulator function. If this is provided, all values will go through\n * the accumulator function.\n * @return A function that returns an Observable of the accumulated values.\n */\nexport function scan<V, A, S>(accumulator: (acc: V | A | S, value: V, index: number) => A, seed?: S): OperatorFunction<V, V | A> {\n  // providing a seed of `undefined` *should* be valid and trigger\n  // hasSeed! so don't use `seed !== undefined` checks!\n  // For this reason, we have to check it here at the original call site\n  // otherwise inside Operator/Subscriber we won't know if `undefined`\n  // means they didn't provide anything or if they literally provided `undefined`\n  return operate(scanInternals(accumulator, seed as S, arguments.length >= 2, true));\n}\n", "import { innerFrom } from '../observable/innerFrom';\nimport { Subject } from '../Subject';\nimport { SafeSubscriber } from '../Subscriber';\nimport { Subscription } from '../Subscription';\nimport { MonoTypeOperatorFunction, SubjectLike, ObservableInput } from '../types';\nimport { operate } from '../util/lift';\n\nexport interface ShareConfig<T> {\n  /**\n   * The factory used to create the subject that will connect the source observable to\n   * multicast consumers.\n   */\n  connector?: () => SubjectLike<T>;\n  /**\n   * If `true`, the resulting observable will reset internal state on error from source and return to a \"cold\" state. This\n   * allows the resulting observable to be \"retried\" in the event of an error.\n   * If `false`, when an error comes from the source it will push the error into the connecting subject, and the subject\n   * will remain the connecting subject, meaning the resulting observable will not go \"cold\" again, and subsequent retries\n   * or resubscriptions will resubscribe to that same subject. In all cases, RxJS subjects will emit the same error again, however\n   * {@link ReplaySubject} will also push its buffered values before pushing the error.\n   * It is also possible to pass a notifier factory returning an `ObservableInput` instead which grants more fine-grained\n   * control over how and when the reset should happen. This allows behaviors like conditional or delayed resets.\n   */\n  resetOnError?: boolean | ((error: any) => ObservableInput<any>);\n  /**\n   * If `true`, the resulting observable will reset internal state on completion from source and return to a \"cold\" state. This\n   * allows the resulting observable to be \"repeated\" after it is done.\n   * If `false`, when the source completes, it will push the completion through the connecting subject, and the subject\n   * will remain the connecting subject, meaning the resulting observable will not go \"cold\" again, and subsequent repeats\n   * or resubscriptions will resubscribe to that same subject.\n   * It is also possible to pass a notifier factory returning an `ObservableInput` instead which grants more fine-grained\n   * control over how and when the reset should happen. This allows behaviors like conditional or delayed resets.\n   */\n  resetOnComplete?: boolean | (() => ObservableInput<any>);\n  /**\n   * If `true`, when the number of subscribers to the resulting observable reaches zero due to those subscribers unsubscribing, the\n   * internal state will be reset and the resulting observable will return to a \"cold\" state. This means that the next\n   * time the resulting observable is subscribed to, a new subject will be created and the source will be subscribed to\n   * again.\n   * If `false`, when the number of subscribers to the resulting observable reaches zero due to unsubscription, the subject\n   * will remain connected to the source, and new subscriptions to the result will be connected through that same subject.\n   * It is also possible to pass a notifier factory returning an `ObservableInput` instead which grants more fine-grained\n   * control over how and when the reset should happen. This allows behaviors like conditional or delayed resets.\n   */\n  resetOnRefCountZero?: boolean | (() => ObservableInput<any>);\n}\n\nexport function share<T>(): MonoTypeOperatorFunction<T>;\n\nexport function share<T>(options: ShareConfig<T>): MonoTypeOperatorFunction<T>;\n\n/**\n * Returns a new Observable that multicasts (shares) the original Observable. As long as there is at least one\n * Subscriber this Observable will be subscribed and emitting data. When all subscribers have unsubscribed it will\n * unsubscribe from the source Observable. Because the Observable is multicasting it makes the stream `hot`.\n * This is an alias for `multicast(() => new Subject()), refCount()`.\n *\n * The subscription to the underlying source Observable can be reset (unsubscribe and resubscribe for new subscribers),\n * if the subscriber count to the shared observable drops to 0, or if the source Observable errors or completes. It is\n * possible to use notifier factories for the resets to allow for behaviors like conditional or delayed resets. Please\n * note that resetting on error or complete of the source Observable does not behave like a transparent retry or restart\n * of the source because the error or complete will be forwarded to all subscribers and their subscription will be\n * closed. Only new subscribers after a reset on error or complete happened will cause a fresh subscription to the\n * source. To achieve transparent retries or restarts pipe the source through appropriate operators before sharing.\n *\n * ![](share.png)\n *\n * ## Example\n *\n * Generate new multicast Observable from the `source` Observable value\n *\n * ```ts\n * import { interval, tap, map, take, share } from 'rxjs';\n *\n * const source = interval(1000).pipe(\n *   tap(x => console.log('Processing: ', x)),\n *   map(x => x * x),\n *   take(6),\n *   share()\n * );\n *\n * source.subscribe(x => console.log('subscription 1: ', x));\n * source.subscribe(x => console.log('subscription 2: ', x));\n *\n * // Logs:\n * // Processing: 0\n * // subscription 1: 0\n * // subscription 2: 0\n * // Processing: 1\n * // subscription 1: 1\n * // subscription 2: 1\n * // Processing: 2\n * // subscription 1: 4\n * // subscription 2: 4\n * // Processing: 3\n * // subscription 1: 9\n * // subscription 2: 9\n * // Processing: 4\n * // subscription 1: 16\n * // subscription 2: 16\n * // Processing: 5\n * // subscription 1: 25\n * // subscription 2: 25\n * ```\n *\n * ## Example with notifier factory: Delayed reset\n *\n * ```ts\n * import { interval, take, share, timer } from 'rxjs';\n *\n * const source = interval(1000).pipe(\n *   take(3),\n *   share({\n *     resetOnRefCountZero: () => timer(1000)\n *   })\n * );\n *\n * const subscriptionOne = source.subscribe(x => console.log('subscription 1: ', x));\n * setTimeout(() => subscriptionOne.unsubscribe(), 1300);\n *\n * setTimeout(() => source.subscribe(x => console.log('subscription 2: ', x)), 1700);\n *\n * setTimeout(() => source.subscribe(x => console.log('subscription 3: ', x)), 5000);\n *\n * // Logs:\n * // subscription 1:  0\n * // (subscription 1 unsubscribes here)\n * // (subscription 2 subscribes here ~400ms later, source was not reset)\n * // subscription 2:  1\n * // subscription 2:  2\n * // (subscription 2 unsubscribes here)\n * // (subscription 3 subscribes here ~2000ms later, source did reset before)\n * // subscription 3:  0\n * // subscription 3:  1\n * // subscription 3:  2\n * ```\n *\n * @see {@link shareReplay}\n *\n * @return A function that returns an Observable that mirrors the source.\n */\nexport function share<T>(options: ShareConfig<T> = {}): MonoTypeOperatorFunction<T> {\n  const { connector = () => new Subject<T>(), resetOnError = true, resetOnComplete = true, resetOnRefCountZero = true } = options;\n  // It's necessary to use a wrapper here, as the _operator_ must be\n  // referentially transparent. Otherwise, it cannot be used in calls to the\n  // static `pipe` function - to create a partial pipeline.\n  //\n  // The _operator function_ - the function returned by the _operator_ - will\n  // not be referentially transparent - as it shares its source - but the\n  // _operator function_ is called when the complete pipeline is composed via a\n  // call to a source observable's `pipe` method - not when the static `pipe`\n  // function is called.\n  return (wrapperSource) => {\n    let connection: SafeSubscriber<T> | undefined;\n    let resetConnection: Subscription | undefined;\n    let subject: SubjectLike<T> | undefined;\n    let refCount = 0;\n    let hasCompleted = false;\n    let hasErrored = false;\n\n    const cancelReset = () => {\n      resetConnection?.unsubscribe();\n      resetConnection = undefined;\n    };\n    // Used to reset the internal state to a \"cold\"\n    // state, as though it had never been subscribed to.\n    const reset = () => {\n      cancelReset();\n      connection = subject = undefined;\n      hasCompleted = hasErrored = false;\n    };\n    const resetAndUnsubscribe = () => {\n      // We need to capture the connection before\n      // we reset (if we need to reset).\n      const conn = connection;\n      reset();\n      conn?.unsubscribe();\n    };\n\n    return operate<T, T>((source, subscriber) => {\n      refCount++;\n      if (!hasErrored && !hasCompleted) {\n        cancelReset();\n      }\n\n      // Create the subject if we don't have one yet. Grab a local reference to\n      // it as well, which avoids non-null assertions when using it and, if we\n      // connect to it now, then error/complete need a reference after it was\n      // reset.\n      const dest = (subject = subject ?? connector());\n\n      // Add the finalization directly to the subscriber - instead of returning it -\n      // so that the handling of the subscriber's unsubscription will be wired\n      // up _before_ the subscription to the source occurs. This is done so that\n      // the assignment to the source connection's `closed` property will be seen\n      // by synchronous firehose sources.\n      subscriber.add(() => {\n        refCount--;\n\n        // If we're resetting on refCount === 0, and it's 0, we only want to do\n        // that on \"unsubscribe\", really. Resetting on error or completion is a different\n        // configuration.\n        if (refCount === 0 && !hasErrored && !hasCompleted) {\n          resetConnection = handleReset(resetAndUnsubscribe, resetOnRefCountZero);\n        }\n      });\n\n      // The following line adds the subscription to the subscriber passed.\n      // Basically, `subscriber === dest.subscribe(subscriber)` is `true`.\n      dest.subscribe(subscriber);\n\n      if (\n        !connection &&\n        // Check this shareReplay is still activate - it can be reset to 0\n        // and be \"unsubscribed\" _before_ it actually subscribes.\n        // If we were to subscribe then, it'd leak and get stuck.\n        refCount > 0\n      ) {\n        // We need to create a subscriber here - rather than pass an observer and\n        // assign the returned subscription to connection - because it's possible\n        // for reentrant subscriptions to the shared observable to occur and in\n        // those situations we want connection to be already-assigned so that we\n        // don't create another connection to the source.\n        connection = new SafeSubscriber({\n          next: (value) => dest.next(value),\n          error: (err) => {\n            hasErrored = true;\n            cancelReset();\n            resetConnection = handleReset(reset, resetOnError, err);\n            dest.error(err);\n          },\n          complete: () => {\n            hasCompleted = true;\n            cancelReset();\n            resetConnection = handleReset(reset, resetOnComplete);\n            dest.complete();\n          },\n        });\n        innerFrom(source).subscribe(connection);\n      }\n    })(wrapperSource);\n  };\n}\n\nfunction handleReset<T extends unknown[] = never[]>(\n  reset: () => void,\n  on: boolean | ((...args: T) => ObservableInput<any>),\n  ...args: T\n): Subscription | undefined {\n  if (on === true) {\n    reset();\n    return;\n  }\n\n  if (on === false) {\n    return;\n  }\n\n  const onSubscriber = new SafeSubscriber({\n    next: () => {\n      onSubscriber.unsubscribe();\n      reset();\n    },\n  });\n\n  return innerFrom(on(...args)).subscribe(onSubscriber);\n}\n", "import { ReplaySubject } from '../ReplaySubject';\nimport { MonoTypeOperatorFunction, SchedulerLike } from '../types';\nimport { share } from './share';\n\nexport interface ShareReplayConfig {\n  bufferSize?: number;\n  windowTime?: number;\n  refCount: boolean;\n  scheduler?: SchedulerLike;\n}\n\nexport function shareReplay<T>(config: ShareReplayConfig): MonoTypeOperatorFunction<T>;\nexport function shareReplay<T>(bufferSize?: number, windowTime?: number, scheduler?: SchedulerLike): MonoTypeOperatorFunction<T>;\n\n/**\n * Share source and replay specified number of emissions on subscription.\n *\n * This operator is a specialization of `replay` that connects to a source observable\n * and multicasts through a `ReplaySubject` constructed with the specified arguments.\n * A successfully completed source will stay cached in the `shareReplay`ed observable forever,\n * but an errored source can be retried.\n *\n * ## Why use `shareReplay`?\n *\n * You generally want to use `shareReplay` when you have side-effects or taxing computations\n * that you do not wish to be executed amongst multiple subscribers.\n * It may also be valuable in situations where you know you will have late subscribers to\n * a stream that need access to previously emitted values.\n * This ability to replay values on subscription is what differentiates {@link share} and `shareReplay`.\n *\n * ## Reference counting\n *\n * By default `shareReplay` will use `refCount` of false, meaning that it will _not_ unsubscribe the\n * source when the reference counter drops to zero, i.e. the inner `ReplaySubject` will _not_ be unsubscribed\n * (and potentially run for ever).\n * This is the default as it is expected that `shareReplay` is often used to keep around expensive to setup\n * observables which we want to keep running instead of having to do the expensive setup again.\n *\n * As of RXJS version 6.4.0 a new overload signature was added to allow for manual control over what\n * happens when the operators internal reference counter drops to zero.\n * If `refCount` is true, the source will be unsubscribed from once the reference count drops to zero, i.e.\n * the inner `ReplaySubject` will be unsubscribed. All new subscribers will receive value emissions from a\n * new `ReplaySubject` which in turn will cause a new subscription to the source observable.\n *\n * ## Examples\n *\n * Example with a third subscriber coming late to the party\n *\n * ```ts\n * import { interval, take, shareReplay } from 'rxjs';\n *\n * const shared$ = interval(2000).pipe(\n *   take(6),\n *   shareReplay(3)\n * );\n *\n * shared$.subscribe(x => console.log('sub A: ', x));\n * shared$.subscribe(y => console.log('sub B: ', y));\n *\n * setTimeout(() => {\n *   shared$.subscribe(y => console.log('sub C: ', y));\n * }, 11000);\n *\n * // Logs:\n * // (after ~2000 ms)\n * // sub A: 0\n * // sub B: 0\n * // (after ~4000 ms)\n * // sub A: 1\n * // sub B: 1\n * // (after ~6000 ms)\n * // sub A: 2\n * // sub B: 2\n * // (after ~8000 ms)\n * // sub A: 3\n * // sub B: 3\n * // (after ~10000 ms)\n * // sub A: 4\n * // sub B: 4\n * // (after ~11000 ms, sub C gets the last 3 values)\n * // sub C: 2\n * // sub C: 3\n * // sub C: 4\n * // (after ~12000 ms)\n * // sub A: 5\n * // sub B: 5\n * // sub C: 5\n * ```\n *\n * Example for `refCount` usage\n *\n * ```ts\n * import { Observable, tap, interval, shareReplay, take } from 'rxjs';\n *\n * const log = <T>(name: string, source: Observable<T>) => source.pipe(\n *   tap({\n *     subscribe: () => console.log(`${ name }: subscribed`),\n *     next: value => console.log(`${ name }: ${ value }`),\n *     complete: () => console.log(`${ name }: completed`),\n *     finalize: () => console.log(`${ name }: unsubscribed`)\n *   })\n * );\n *\n * const obs$ = log('source', interval(1000));\n *\n * const shared$ = log('shared', obs$.pipe(\n *   shareReplay({ bufferSize: 1, refCount: true }),\n *   take(2)\n * ));\n *\n * shared$.subscribe(x => console.log('sub A: ', x));\n * shared$.subscribe(y => console.log('sub B: ', y));\n *\n * // PRINTS:\n * // shared: subscribed <-- reference count = 1\n * // source: subscribed\n * // shared: subscribed <-- reference count = 2\n * // source: 0\n * // shared: 0\n * // sub A: 0\n * // shared: 0\n * // sub B: 0\n * // source: 1\n * // shared: 1\n * // sub A: 1\n * // shared: completed <-- take(2) completes the subscription for sub A\n * // shared: unsubscribed <-- reference count = 1\n * // shared: 1\n * // sub B: 1\n * // shared: completed <-- take(2) completes the subscription for sub B\n * // shared: unsubscribed <-- reference count = 0\n * // source: unsubscribed <-- replaySubject unsubscribes from source observable because the reference count dropped to 0 and refCount is true\n *\n * // In case of refCount being false, the unsubscribe is never called on the source and the source would keep on emitting, even if no subscribers\n * // are listening.\n * // source: 2\n * // source: 3\n * // source: 4\n * // ...\n * ```\n *\n * @see {@link publish}\n * @see {@link share}\n * @see {@link publishReplay}\n *\n * @param configOrBufferSize Maximum element count of the replay buffer or {@link ShareReplayConfig configuration}\n * object.\n * @param windowTime Maximum time length of the replay buffer in milliseconds.\n * @param scheduler Scheduler where connected observers within the selector function\n * will be invoked on.\n * @return A function that returns an Observable sequence that contains the\n * elements of a sequence produced by multicasting the source sequence within a\n * selector function.\n */\nexport function shareReplay<T>(\n  configOrBufferSize?: ShareReplayConfig | number,\n  windowTime?: number,\n  scheduler?: SchedulerLike\n): MonoTypeOperatorFunction<T> {\n  let bufferSize: number;\n  let refCount = false;\n  if (configOrBufferSize && typeof configOrBufferSize === 'object') {\n    ({ bufferSize = Infinity, windowTime = Infinity, refCount = false, scheduler } = configOrBufferSize);\n  } else {\n    bufferSize = (configOrBufferSize ?? Infinity) as number;\n  }\n  return share<T>({\n    connector: () => new ReplaySubject(bufferSize, windowTime, scheduler),\n    resetOnError: true,\n    resetOnComplete: false,\n    resetOnRefCountZero: refCount,\n  });\n}\n", "import { MonoTypeOperatorFunction } from '../types';\nimport { filter } from './filter';\n\n/**\n * Returns an Observable that skips the first `count` items emitted by the source Observable.\n *\n * ![](skip.png)\n *\n * Skips the values until the sent notifications are equal or less than provided skip count. It raises\n * an error if skip count is equal or more than the actual number of emits and source raises an error.\n *\n * ## Example\n *\n * Skip the values before the emission\n *\n * ```ts\n * import { interval, skip } from 'rxjs';\n *\n * // emit every half second\n * const source = interval(500);\n * // skip the first 10 emitted values\n * const result = source.pipe(skip(10));\n *\n * result.subscribe(value => console.log(value));\n * // output: 10...11...12...13...\n * ```\n *\n * @see {@link last}\n * @see {@link skipWhile}\n * @see {@link skipUntil}\n * @see {@link skipLast}\n *\n * @param count The number of times, items emitted by source Observable should be skipped.\n * @return A function that returns an Observable that skips the first `count`\n * values emitted by the source Observable.\n */\nexport function skip<T>(count: number): MonoTypeOperatorFunction<T> {\n  return filter((_, index) => count <= index);\n}\n", "import { MonoTypeOperatorFunction, ObservableInput } from '../types';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\nimport { innerFrom } from '../observable/innerFrom';\nimport { noop } from '../util/noop';\n\n/**\n * Returns an Observable that skips items emitted by the source Observable until a second Observable emits an item.\n *\n * The `skipUntil` operator causes the observable stream to skip the emission of values until the passed in observable\n * emits the first value. This can be particularly useful in combination with user interactions, responses of HTTP\n * requests or waiting for specific times to pass by.\n *\n * ![](skipUntil.png)\n *\n * Internally, the `skipUntil` operator subscribes to the passed in `notifier` `ObservableInput` (which gets converted\n * to an Observable) in order to recognize the emission of its first value. When `notifier` emits next, the operator\n * unsubscribes from it and starts emitting the values of the *source* observable until it completes or errors. It\n * will never let the *source* observable emit any values if the `notifier` completes or throws an error without\n * emitting a value before.\n *\n * ## Example\n *\n * In the following example, all emitted values of the interval observable are skipped until the user clicks anywhere\n * within the page\n *\n * ```ts\n * import { interval, fromEvent, skipUntil } from 'rxjs';\n *\n * const intervalObservable = interval(1000);\n * const click = fromEvent(document, 'click');\n *\n * const emitAfterClick = intervalObservable.pipe(\n *   skipUntil(click)\n * );\n * // clicked at 4.6s. output: 5...6...7...8........ or\n * // clicked at 7.3s. output: 8...9...10..11.......\n * emitAfterClick.subscribe(value => console.log(value));\n * ```\n *\n * @see {@link last}\n * @see {@link skip}\n * @see {@link skipWhile}\n * @see {@link skipLast}\n *\n * @param notifier An `ObservableInput` that has to emit an item before the source Observable elements begin to\n * be mirrored by the resulting Observable.\n * @return A function that returns an Observable that skips items from the\n * source Observable until the `notifier` Observable emits an item, then emits the\n * remaining items.\n */\nexport function skipUntil<T>(notifier: ObservableInput<any>): MonoTypeOperatorFunction<T> {\n  return operate((source, subscriber) => {\n    let taking = false;\n\n    const skipSubscriber = createOperatorSubscriber(\n      subscriber,\n      () => {\n        skipSubscriber?.unsubscribe();\n        taking = true;\n      },\n      noop\n    );\n\n    innerFrom(notifier).subscribe(skipSubscriber);\n\n    source.subscribe(createOperatorSubscriber(subscriber, (value) => taking && subscriber.next(value)));\n  });\n}\n", "import { concat } from '../observable/concat';\nimport { OperatorFunction, SchedulerLike, ValueFromArray } from '../types';\nimport { popScheduler } from '../util/args';\nimport { operate } from '../util/lift';\n\n// Devs are more likely to pass null or undefined than they are a scheduler\n// without accompanying values. To make things easier for (naughty) devs who\n// use the `strictNullChecks: false` TypeScript compiler option, these\n// overloads with explicit null and undefined values are included.\n\nexport function startWith<T>(value: null): OperatorFunction<T, T | null>;\nexport function startWith<T>(value: undefined): OperatorFunction<T, T | undefined>;\n\n/** @deprecated The `scheduler` parameter will be removed in v8. Use `scheduled` and `concatAll`. Details: https://rxjs.dev/deprecations/scheduler-argument */\nexport function startWith<T, A extends readonly unknown[] = T[]>(\n  ...valuesAndScheduler: [...A, SchedulerLike]\n): OperatorFunction<T, T | ValueFromArray<A>>;\nexport function startWith<T, A extends readonly unknown[] = T[]>(...values: A): OperatorFunction<T, T | ValueFromArray<A>>;\n\n/**\n * Returns an observable that, at the moment of subscription, will synchronously emit all\n * values provided to this operator, then subscribe to the source and mirror all of its emissions\n * to subscribers.\n *\n * This is a useful way to know when subscription has occurred on an existing observable.\n *\n * <span class=\"informal\">First emits its arguments in order, and then any\n * emissions from the source.</span>\n *\n * ![](startWith.png)\n *\n * ## Examples\n *\n * Emit a value when a timer starts.\n *\n * ```ts\n * import { timer, map, startWith } from 'rxjs';\n *\n * timer(1000)\n *   .pipe(\n *     map(() => 'timer emit'),\n *     startWith('timer start')\n *   )\n *   .subscribe(x => console.log(x));\n *\n * // results:\n * // 'timer start'\n * // 'timer emit'\n * ```\n *\n * @param values Items you want the modified Observable to emit first.\n * @return A function that returns an Observable that synchronously emits\n * provided values before subscribing to the source Observable.\n *\n * @see {@link endWith}\n * @see {@link finalize}\n * @see {@link concat}\n */\nexport function startWith<T, D>(...values: D[]): OperatorFunction<T, T | D> {\n  const scheduler = popScheduler(values);\n  return operate((source, subscriber) => {\n    // Here we can't pass `undefined` as a scheduler, because if we did, the\n    // code inside of `concat` would be confused by the `undefined`, and treat it\n    // like an invalid observable. So we have to split it two different ways.\n    (scheduler ? concat(values, source, scheduler) : concat(values, source)).subscribe(subscriber);\n  });\n}\n", "import { Subscriber } from '../Subscriber';\nimport { ObservableInput, OperatorFunction, ObservedValueOf } from '../types';\nimport { innerFrom } from '../observable/innerFrom';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\n\n/* tslint:disable:max-line-length */\nexport function switchMap<T, O extends ObservableInput<any>>(\n  project: (value: T, index: number) => O\n): OperatorFunction<T, ObservedValueOf<O>>;\n/** @deprecated The `resultSelector` parameter will be removed in v8. Use an inner `map` instead. Details: https://rxjs.dev/deprecations/resultSelector */\nexport function switchMap<T, O extends ObservableInput<any>>(\n  project: (value: T, index: number) => O,\n  resultSelector: undefined\n): OperatorFunction<T, ObservedValueOf<O>>;\n/** @deprecated The `resultSelector` parameter will be removed in v8. Use an inner `map` instead. Details: https://rxjs.dev/deprecations/resultSelector */\nexport function switchMap<T, R, O extends ObservableInput<any>>(\n  project: (value: T, index: number) => O,\n  resultSelector: (outerValue: T, innerValue: ObservedValueOf<O>, outerIndex: number, innerIndex: number) => R\n): OperatorFunction<T, R>;\n/* tslint:enable:max-line-length */\n\n/**\n * Projects each source value to an Observable which is merged in the output\n * Observable, emitting values only from the most recently projected Observable.\n *\n * <span class=\"informal\">Maps each value to an Observable, then flattens all of\n * these inner Observables using {@link switchAll}.</span>\n *\n * ![](switchMap.png)\n *\n * Returns an Observable that emits items based on applying a function that you\n * supply to each item emitted by the source Observable, where that function\n * returns an (so-called \"inner\") Observable. Each time it observes one of these\n * inner Observables, the output Observable begins emitting the items emitted by\n * that inner Observable. When a new inner Observable is emitted, `switchMap`\n * stops emitting items from the earlier-emitted inner Observable and begins\n * emitting items from the new one. It continues to behave like this for\n * subsequent inner Observables.\n *\n * ## Example\n *\n * Generate new Observable according to source Observable values\n *\n * ```ts\n * import { of, switchMap } from 'rxjs';\n *\n * const switched = of(1, 2, 3).pipe(switchMap(x => of(x, x ** 2, x ** 3)));\n * switched.subscribe(x => console.log(x));\n * // outputs\n * // 1\n * // 1\n * // 1\n * // 2\n * // 4\n * // 8\n * // 3\n * // 9\n * // 27\n * ```\n *\n * Restart an interval Observable on every click event\n *\n * ```ts\n * import { fromEvent, switchMap, interval } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const result = clicks.pipe(switchMap(() => interval(1000)));\n * result.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link concatMap}\n * @see {@link exhaustMap}\n * @see {@link mergeMap}\n * @see {@link switchAll}\n * @see {@link switchMapTo}\n *\n * @param project A function that, when applied to an item emitted by the source\n * Observable, returns an Observable.\n * @return A function that returns an Observable that emits the result of\n * applying the projection function (and the optional deprecated\n * `resultSelector`) to each item emitted by the source Observable and taking\n * only the values from the most recently projected inner Observable.\n */\nexport function switchMap<T, R, O extends ObservableInput<any>>(\n  project: (value: T, index: number) => O,\n  resultSelector?: (outerValue: T, innerValue: ObservedValueOf<O>, outerIndex: number, innerIndex: number) => R\n): OperatorFunction<T, ObservedValueOf<O> | R> {\n  return operate((source, subscriber) => {\n    let innerSubscriber: Subscriber<ObservedValueOf<O>> | null = null;\n    let index = 0;\n    // Whether or not the source subscription has completed\n    let isComplete = false;\n\n    // We only complete the result if the source is complete AND we don't have an active inner subscription.\n    // This is called both when the source completes and when the inners complete.\n    const checkComplete = () => isComplete && !innerSubscriber && subscriber.complete();\n\n    source.subscribe(\n      createOperatorSubscriber(\n        subscriber,\n        (value) => {\n          // Cancel the previous inner subscription if there was one\n          innerSubscriber?.unsubscribe();\n          let innerIndex = 0;\n          const outerIndex = index++;\n          // Start the next inner subscription\n          innerFrom(project(value, outerIndex)).subscribe(\n            (innerSubscriber = createOperatorSubscriber(\n              subscriber,\n              // When we get a new inner value, next it through. Note that this is\n              // handling the deprecate result selector here. This is because with this architecture\n              // it ends up being smaller than using the map operator.\n              (innerValue) => subscriber.next(resultSelector ? resultSelector(value, innerValue, outerIndex, innerIndex++) : innerValue),\n              () => {\n                // The inner has completed. Null out the inner subscriber to\n                // free up memory and to signal that we have no inner subscription\n                // currently.\n                innerSubscriber = null!;\n                checkComplete();\n              }\n            ))\n          );\n        },\n        () => {\n          isComplete = true;\n          checkComplete();\n        }\n      )\n    );\n  });\n}\n", "import { MonoTypeOperatorFunction, ObservableInput } from '../types';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\nimport { innerFrom } from '../observable/innerFrom';\nimport { noop } from '../util/noop';\n\n/**\n * Emits the values emitted by the source Observable until a `notifier`\n * Observable emits a value.\n *\n * <span class=\"informal\">Lets values pass until a second Observable,\n * `notifier`, emits a value. Then, it completes.</span>\n *\n * ![](takeUntil.png)\n *\n * `takeUntil` subscribes and begins mirroring the source Observable. It also\n * monitors a second Observable, `notifier` that you provide. If the `notifier`\n * emits a value, the output Observable stops mirroring the source Observable\n * and completes. If the `notifier` doesn't emit any value and completes\n * then `takeUntil` will pass all values.\n *\n * ## Example\n *\n * Tick every second until the first click happens\n *\n * ```ts\n * import { interval, fromEvent, takeUntil } from 'rxjs';\n *\n * const source = interval(1000);\n * const clicks = fromEvent(document, 'click');\n * const result = source.pipe(takeUntil(clicks));\n * result.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link take}\n * @see {@link takeLast}\n * @see {@link takeWhile}\n * @see {@link skip}\n *\n * @param notifier The `ObservableInput` whose first emitted value will cause the output\n * Observable of `takeUntil` to stop emitting values from the source Observable.\n * @return A function that returns an Observable that emits the values from the\n * source Observable until `notifier` emits its first value.\n */\nexport function takeUntil<T>(notifier: ObservableInput<any>): MonoTypeOperatorFunction<T> {\n  return operate((source, subscriber) => {\n    innerFrom(notifier).subscribe(createOperatorSubscriber(subscriber, () => subscriber.complete(), noop));\n    !subscriber.closed && source.subscribe(subscriber);\n  });\n}\n", "import { OperatorFunction, MonoTypeOperatorFunction, TruthyTypesOf } from '../types';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\n\nexport function takeWhile<T>(predicate: BooleanConstructor, inclusive: true): MonoTypeOperatorFunction<T>;\nexport function takeWhile<T>(predicate: BooleanConstructor, inclusive: false): OperatorFunction<T, TruthyTypesOf<T>>;\nexport function takeWhile<T>(predicate: BooleanConstructor): OperatorFunction<T, TruthyTypesOf<T>>;\nexport function takeWhile<T, S extends T>(predicate: (value: T, index: number) => value is S): OperatorFunction<T, S>;\nexport function takeWhile<T, S extends T>(predicate: (value: T, index: number) => value is S, inclusive: false): OperatorFunction<T, S>;\nexport function takeWhile<T>(predicate: (value: T, index: number) => boolean, inclusive?: boolean): MonoTypeOperatorFunction<T>;\n\n/**\n * Emits values emitted by the source Observable so long as each value satisfies\n * the given `predicate`, and then completes as soon as this `predicate` is not\n * satisfied.\n *\n * <span class=\"informal\">Takes values from the source only while they pass the\n * condition given. When the first value does not satisfy, it completes.</span>\n *\n * ![](takeWhile.png)\n *\n * `takeWhile` subscribes and begins mirroring the source Observable. Each value\n * emitted on the source is given to the `predicate` function which returns a\n * boolean, representing a condition to be satisfied by the source values. The\n * output Observable emits the source values until such time as the `predicate`\n * returns false, at which point `takeWhile` stops mirroring the source\n * Observable and completes the output Observable.\n *\n * ## Example\n *\n * Emit click events only while the clientX property is greater than 200\n *\n * ```ts\n * import { fromEvent, takeWhile } from 'rxjs';\n *\n * const clicks = fromEvent<PointerEvent>(document, 'click');\n * const result = clicks.pipe(takeWhile(ev => ev.clientX > 200));\n * result.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link take}\n * @see {@link takeLast}\n * @see {@link takeUntil}\n * @see {@link skip}\n *\n * @param predicate A function that evaluates a value emitted by the source\n * Observable and returns a boolean. Also takes the (zero-based) index as the\n * second argument.\n * @param inclusive When set to `true` the value that caused `predicate` to\n * return `false` will also be emitted.\n * @return A function that returns an Observable that emits values from the\n * source Observable so long as each value satisfies the condition defined by\n * the `predicate`, then completes.\n */\nexport function takeWhile<T>(predicate: (value: T, index: number) => boolean, inclusive = false): MonoTypeOperatorFunction<T> {\n  return operate((source, subscriber) => {\n    let index = 0;\n    source.subscribe(\n      createOperatorSubscriber(subscriber, (value) => {\n        const result = predicate(value, index++);\n        (result || inclusive) && subscriber.next(value);\n        !result && subscriber.complete();\n      })\n    );\n  });\n}\n", "import { MonoTypeOperatorFunction, Observer } from '../types';\nimport { isFunction } from '../util/isFunction';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\nimport { identity } from '../util/identity';\n\n/**\n * An extension to the {@link Observer} interface used only by the {@link tap} operator.\n *\n * It provides a useful set of callbacks a user can register to do side-effects in\n * cases other than what the usual {@link Observer} callbacks are\n * ({@link guide/glossary-and-semantics#next next},\n * {@link guide/glossary-and-semantics#error error} and/or\n * {@link guide/glossary-and-semantics#complete complete}).\n *\n * ## Example\n *\n * ```ts\n * import { fromEvent, switchMap, tap, interval, take } from 'rxjs';\n *\n * const source$ = fromEvent(document, 'click');\n * const result$ = source$.pipe(\n *   switchMap((_, i) => i % 2 === 0\n *     ? fromEvent(document, 'mousemove').pipe(\n *         tap({\n *           subscribe: () => console.log('Subscribed to the mouse move events after click #' + i),\n *           unsubscribe: () => console.log('Mouse move events #' + i + ' unsubscribed'),\n *           finalize: () => console.log('Mouse move events #' + i + ' finalized')\n *         })\n *       )\n *     : interval(1_000).pipe(\n *         take(5),\n *         tap({\n *           subscribe: () => console.log('Subscribed to the 1-second interval events after click #' + i),\n *           unsubscribe: () => console.log('1-second interval events #' + i + ' unsubscribed'),\n *           finalize: () => console.log('1-second interval events #' + i + ' finalized')\n *         })\n *       )\n *   )\n * );\n *\n * const subscription = result$.subscribe({\n *   next: console.log\n * });\n *\n * setTimeout(() => {\n *   console.log('Unsubscribe after 60 seconds');\n *   subscription.unsubscribe();\n * }, 60_000);\n * ```\n */\nexport interface TapObserver<T> extends Observer<T> {\n  /**\n   * The callback that `tap` operator invokes at the moment when the source Observable\n   * gets subscribed to.\n   */\n  subscribe: () => void;\n  /**\n   * The callback that `tap` operator invokes when an explicit\n   * {@link guide/glossary-and-semantics#unsubscription unsubscribe} happens. It won't get invoked on\n   * `error` or `complete` events.\n   */\n  unsubscribe: () => void;\n  /**\n   * The callback that `tap` operator invokes when any kind of\n   * {@link guide/glossary-and-semantics#finalization finalization} happens - either when\n   * the source Observable `error`s or `complete`s or when it gets explicitly unsubscribed\n   * by the user. There is no difference in using this callback or the {@link finalize}\n   * operator, but if you're already using `tap` operator, you can use this callback\n   * instead. You'd get the same result in either case.\n   */\n  finalize: () => void;\n}\nexport function tap<T>(observerOrNext?: Partial<TapObserver<T>> | ((value: T) => void)): MonoTypeOperatorFunction<T>;\n/** @deprecated Instead of passing separate callback arguments, use an observer argument. Signatures taking separate callback arguments will be removed in v8. Details: https://rxjs.dev/deprecations/subscribe-arguments */\nexport function tap<T>(\n  next?: ((value: T) => void) | null,\n  error?: ((error: any) => void) | null,\n  complete?: (() => void) | null\n): MonoTypeOperatorFunction<T>;\n\n/**\n * Used to perform side-effects for notifications from the source observable\n *\n * <span class=\"informal\">Used when you want to affect outside state with a notification without altering the notification</span>\n *\n * ![](tap.png)\n *\n * Tap is designed to allow the developer a designated place to perform side effects. While you _could_ perform side-effects\n * inside of a `map` or a `mergeMap`, that would make their mapping functions impure, which isn't always a big deal, but will\n * make it so you can't do things like memoize those functions. The `tap` operator is designed solely for such side-effects to\n * help you remove side-effects from other operations.\n *\n * For any notification, next, error, or complete, `tap` will call the appropriate callback you have provided to it, via a function\n * reference, or a partial observer, then pass that notification down the stream.\n *\n * The observable returned by `tap` is an exact mirror of the source, with one exception: Any error that occurs -- synchronously -- in a handler\n * provided to `tap` will be emitted as an error from the returned observable.\n *\n * > Be careful! You can mutate objects as they pass through the `tap` operator's handlers.\n *\n * The most common use of `tap` is actually for debugging. You can place a `tap(console.log)` anywhere\n * in your observable `pipe`, log out the notifications as they are emitted by the source returned by the previous\n * operation.\n *\n * ## Examples\n *\n * Check a random number before it is handled. Below is an observable that will use a random number between 0 and 1,\n * and emit `'big'` or `'small'` depending on the size of that number. But we wanted to log what the original number\n * was, so we have added a `tap(console.log)`.\n *\n * ```ts\n * import { of, tap, map } from 'rxjs';\n *\n * of(Math.random()).pipe(\n *   tap(console.log),\n *   map(n => n > 0.5 ? 'big' : 'small')\n * ).subscribe(console.log);\n * ```\n *\n * Using `tap` to analyze a value and force an error. Below is an observable where in our system we only\n * want to emit numbers 3 or less we get from another source. We can force our observable to error\n * using `tap`.\n *\n * ```ts\n * import { of, tap } from 'rxjs';\n *\n * const source = of(1, 2, 3, 4, 5);\n *\n * source.pipe(\n *   tap(n => {\n *     if (n > 3) {\n *       throw new TypeError(`Value ${ n } is greater than 3`);\n *     }\n *   })\n * )\n * .subscribe({ next: console.log, error: err => console.log(err.message) });\n * ```\n *\n * We want to know when an observable completes before moving on to the next observable. The system\n * below will emit a random series of `'X'` characters from 3 different observables in sequence. The\n * only way we know when one observable completes and moves to the next one, in this case, is because\n * we have added a `tap` with the side effect of logging to console.\n *\n * ```ts\n * import { of, concatMap, interval, take, map, tap } from 'rxjs';\n *\n * of(1, 2, 3).pipe(\n *   concatMap(n => interval(1000).pipe(\n *     take(Math.round(Math.random() * 10)),\n *     map(() => 'X'),\n *     tap({ complete: () => console.log(`Done with ${ n }`) })\n *   ))\n * )\n * .subscribe(console.log);\n * ```\n *\n * @see {@link finalize}\n * @see {@link TapObserver}\n *\n * @param observerOrNext A next handler or partial observer\n * @param error An error handler\n * @param complete A completion handler\n * @return A function that returns an Observable identical to the source, but\n * runs the specified Observer or callback(s) for each item.\n */\nexport function tap<T>(\n  observerOrNext?: Partial<TapObserver<T>> | ((value: T) => void) | null,\n  error?: ((e: any) => void) | null,\n  complete?: (() => void) | null\n): MonoTypeOperatorFunction<T> {\n  // We have to check to see not only if next is a function,\n  // but if error or complete were passed. This is because someone\n  // could technically call tap like `tap(null, fn)` or `tap(null, null, fn)`.\n  const tapObserver =\n    isFunction(observerOrNext) || error || complete\n      ? // tslint:disable-next-line: no-object-literal-type-assertion\n        ({ next: observerOrNext as Exclude<typeof observerOrNext, Partial<TapObserver<T>>>, error, complete } as Partial<TapObserver<T>>)\n      : observerOrNext;\n\n  return tapObserver\n    ? operate((source, subscriber) => {\n        tapObserver.subscribe?.();\n        let isUnsub = true;\n        source.subscribe(\n          createOperatorSubscriber(\n            subscriber,\n            (value) => {\n              tapObserver.next?.(value);\n              subscriber.next(value);\n            },\n            () => {\n              isUnsub = false;\n              tapObserver.complete?.();\n              subscriber.complete();\n            },\n            (err) => {\n              isUnsub = false;\n              tapObserver.error?.(err);\n              subscriber.error(err);\n            },\n            () => {\n              if (isUnsub) {\n                tapObserver.unsubscribe?.();\n              }\n              tapObserver.finalize?.();\n            }\n          )\n        );\n      })\n    : // Tap was called with no valid tap observer or handler\n      // (e.g. `tap(null, null, null)` or `tap(null)` or `tap()`)\n      // so we're going to just mirror the source.\n      identity;\n}\n", "import { Subscription } from '../Subscription';\n\nimport { MonoTypeOperatorFunction, ObservableInput } from '../types';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\nimport { innerFrom } from '../observable/innerFrom';\n\n/**\n * An object interface used by {@link throttle} or {@link throttleTime} that ensure\n * configuration options of these operators.\n *\n * @see {@link throttle}\n * @see {@link throttleTime}\n */\nexport interface ThrottleConfig {\n  /**\n   * If `true`, the resulting Observable will emit the first value from the source\n   * Observable at the **start** of the \"throttling\" process (when starting an\n   * internal timer that prevents other emissions from the source to pass through).\n   * If `false`, it will not emit the first value from the source Observable at the\n   * start of the \"throttling\" process.\n   *\n   * If not provided, defaults to: `true`.\n   */\n  leading?: boolean;\n  /**\n   * If `true`, the resulting Observable will emit the last value from the source\n   * Observable at the **end** of the \"throttling\" process (when ending an internal\n   * timer that prevents other emissions from the source to pass through).\n   * If `false`, it will not emit the last value from the source Observable at the\n   * end of the \"throttling\" process.\n   *\n   * If not provided, defaults to: `false`.\n   */\n  trailing?: boolean;\n}\n\n/**\n * Emits a value from the source Observable, then ignores subsequent source\n * values for a duration determined by another Observable, then repeats this\n * process.\n *\n * <span class=\"informal\">It's like {@link throttleTime}, but the silencing\n * duration is determined by a second Observable.</span>\n *\n * ![](throttle.svg)\n *\n * `throttle` emits the source Observable values on the output Observable\n * when its internal timer is disabled, and ignores source values when the timer\n * is enabled. Initially, the timer is disabled. As soon as the first source\n * value arrives, it is forwarded to the output Observable, and then the timer\n * is enabled by calling the `durationSelector` function with the source value,\n * which returns the \"duration\" Observable. When the duration Observable emits a\n * value, the timer is disabled, and this process repeats for the\n * next source value.\n *\n * ## Example\n *\n * Emit clicks at a rate of at most one click per second\n *\n * ```ts\n * import { fromEvent, throttle, interval } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const result = clicks.pipe(throttle(() => interval(1000)));\n *\n * result.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link audit}\n * @see {@link debounce}\n * @see {@link delayWhen}\n * @see {@link sample}\n * @see {@link throttleTime}\n *\n * @param durationSelector A function that receives a value from the source\n * Observable, for computing the silencing duration for each source value,\n * returned as an `ObservableInput`.\n * @param config A configuration object to define `leading` and `trailing`\n * behavior. Defaults to `{ leading: true, trailing: false }`.\n * @return A function that returns an Observable that performs the throttle\n * operation to limit the rate of emissions from the source.\n */\nexport function throttle<T>(durationSelector: (value: T) => ObservableInput<any>, config?: ThrottleConfig): MonoTypeOperatorFunction<T> {\n  return operate((source, subscriber) => {\n    const { leading = true, trailing = false } = config ?? {};\n    let hasValue = false;\n    let sendValue: T | null = null;\n    let throttled: Subscription | null = null;\n    let isComplete = false;\n\n    const endThrottling = () => {\n      throttled?.unsubscribe();\n      throttled = null;\n      if (trailing) {\n        send();\n        isComplete && subscriber.complete();\n      }\n    };\n\n    const cleanupThrottling = () => {\n      throttled = null;\n      isComplete && subscriber.complete();\n    };\n\n    const startThrottle = (value: T) =>\n      (throttled = innerFrom(durationSelector(value)).subscribe(createOperatorSubscriber(subscriber, endThrottling, cleanupThrottling)));\n\n    const send = () => {\n      if (hasValue) {\n        // Ensure we clear out our value and hasValue flag\n        // before we emit, otherwise reentrant code can cause\n        // issues here.\n        hasValue = false;\n        const value = sendValue!;\n        sendValue = null;\n        // Emit the value.\n        subscriber.next(value);\n        !isComplete && startThrottle(value);\n      }\n    };\n\n    source.subscribe(\n      createOperatorSubscriber(\n        subscriber,\n        // Regarding the presence of throttled.closed in the following\n        // conditions, if a synchronous duration selector is specified - weird,\n        // but legal - an already-closed subscription will be assigned to\n        // throttled, so the subscription's closed property needs to be checked,\n        // too.\n        (value) => {\n          hasValue = true;\n          sendValue = value;\n          !(throttled && !throttled.closed) && (leading ? send() : startThrottle(value));\n        },\n        () => {\n          isComplete = true;\n          !(trailing && hasValue && throttled && !throttled.closed) && subscriber.complete();\n        }\n      )\n    );\n  });\n}\n", "import { asyncScheduler } from '../scheduler/async';\nimport { throttle, ThrottleConfig } from './throttle';\nimport { MonoTypeOperatorFunction, SchedulerLike } from '../types';\nimport { timer } from '../observable/timer';\n\n/**\n * Emits a value from the source Observable, then ignores subsequent source\n * values for `duration` milliseconds, then repeats this process.\n *\n * <span class=\"informal\">Lets a value pass, then ignores source values for the\n * next `duration` milliseconds.</span>\n *\n * ![](throttleTime.png)\n *\n * `throttleTime` emits the source Observable values on the output Observable\n * when its internal timer is disabled, and ignores source values when the timer\n * is enabled. Initially, the timer is disabled. As soon as the first source\n * value arrives, it is forwarded to the output Observable, and then the timer\n * is enabled. After `duration` milliseconds (or the time unit determined\n * internally by the optional `scheduler`) has passed, the timer is disabled,\n * and this process repeats for the next source value. Optionally takes a\n * {@link SchedulerLike} for managing timers.\n *\n * ## Examples\n *\n * ### Limit click rate\n *\n * Emit clicks at a rate of at most one click per second\n *\n * ```ts\n * import { fromEvent, throttleTime } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const result = clicks.pipe(throttleTime(1000));\n *\n * result.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link auditTime}\n * @see {@link debounceTime}\n * @see {@link delay}\n * @see {@link sampleTime}\n * @see {@link throttle}\n *\n * @param duration Time to wait before emitting another value after\n * emitting the last value, measured in milliseconds or the time unit determined\n * internally by the optional `scheduler`.\n * @param scheduler The {@link SchedulerLike} to use for\n * managing the timers that handle the throttling. Defaults to {@link asyncScheduler}.\n * @param config A configuration object to define `leading` and\n * `trailing` behavior. Defaults to `{ leading: true, trailing: false }`.\n * @return A function that returns an Observable that performs the throttle\n * operation to limit the rate of emissions from the source.\n */\nexport function throttleTime<T>(\n  duration: number,\n  scheduler: SchedulerLike = asyncScheduler,\n  config?: ThrottleConfig\n): MonoTypeOperatorFunction<T> {\n  const duration$ = timer(duration, scheduler);\n  return throttle(() => duration$, config);\n}\n", "import { OperatorFunction, ObservableInputTuple } from '../types';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\nimport { innerFrom } from '../observable/innerFrom';\nimport { identity } from '../util/identity';\nimport { noop } from '../util/noop';\nimport { popResultSelector } from '../util/args';\n\nexport function withLatestFrom<T, O extends unknown[]>(...inputs: [...ObservableInputTuple<O>]): OperatorFunction<T, [T, ...O]>;\n\nexport function withLatestFrom<T, O extends unknown[], R>(\n  ...inputs: [...ObservableInputTuple<O>, (...value: [T, ...O]) => R]\n): OperatorFunction<T, R>;\n\n/**\n * Combines the source Observable with other Observables to create an Observable\n * whose values are calculated from the latest values of each, only when the\n * source emits.\n *\n * <span class=\"informal\">Whenever the source Observable emits a value, it\n * computes a formula using that value plus the latest values from other input\n * Observables, then emits the output of that formula.</span>\n *\n * ![](withLatestFrom.png)\n *\n * `withLatestFrom` combines each value from the source Observable (the\n * instance) with the latest values from the other input Observables only when\n * the source emits a value, optionally using a `project` function to determine\n * the value to be emitted on the output Observable. All input Observables must\n * emit at least one value before the output Observable will emit a value.\n *\n * ## Example\n *\n * On every click event, emit an array with the latest timer event plus the click event\n *\n * ```ts\n * import { fromEvent, interval, withLatestFrom } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const timer = interval(1000);\n * const result = clicks.pipe(withLatestFrom(timer));\n * result.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link combineLatest}\n *\n * @param inputs An input Observable to combine with the source Observable. More\n * than one input Observables may be given as argument. If the last parameter is\n * a function, it will be used as a projection function for combining values\n * together. When the function is called, it receives all values in order of the\n * Observables passed, where the first parameter is a value from the source\n * Observable. (e.g.\n * `a.pipe(withLatestFrom(b, c), map(([a1, b1, c1]) => a1 + b1 + c1))`). If this\n * is not passed, arrays will be emitted on the output Observable.\n * @return A function that returns an Observable of projected values from the\n * most recent values from each input Observable, or an array of the most\n * recent values from each input Observable.\n */\nexport function withLatestFrom<T, R>(...inputs: any[]): OperatorFunction<T, R | any[]> {\n  const project = popResultSelector(inputs) as ((...args: any[]) => R) | undefined;\n\n  return operate((source, subscriber) => {\n    const len = inputs.length;\n    const otherValues = new Array(len);\n    // An array of whether or not the other sources have emitted. Matched with them by index.\n    // TODO: At somepoint, we should investigate the performance implications here, and look\n    // into using a `Set()` and checking the `size` to see if we're ready.\n    let hasValue = inputs.map(() => false);\n    // Flipped true when we have at least one value from all other sources and\n    // we are ready to start emitting values.\n    let ready = false;\n\n    // Other sources. Note that here we are not checking `subscriber.closed`,\n    // this causes all inputs to be subscribed to, even if nothing can be emitted\n    // from them. This is an important distinction because subscription constitutes\n    // a side-effect.\n    for (let i = 0; i < len; i++) {\n      innerFrom(inputs[i]).subscribe(\n        createOperatorSubscriber(\n          subscriber,\n          (value) => {\n            otherValues[i] = value;\n            if (!ready && !hasValue[i]) {\n              // If we're not ready yet, flag to show this observable has emitted.\n              hasValue[i] = true;\n              // Intentionally terse code.\n              // If all of our other observables have emitted, set `ready` to `true`,\n              // so we know we can start emitting values, then clean up the `hasValue` array,\n              // because we don't need it anymore.\n              (ready = hasValue.every(identity)) && (hasValue = null!);\n            }\n          },\n          // Completing one of the other sources has\n          // no bearing on the completion of our result.\n          noop\n        )\n      );\n    }\n\n    // Source subscription\n    source.subscribe(\n      createOperatorSubscriber(subscriber, (value) => {\n        if (ready) {\n          // We have at least one value from the other sources. Go ahead and emit.\n          const values = [value, ...otherValues];\n          subscriber.next(project ? project(...values) : values);\n        }\n      })\n    );\n  });\n}\n", "import { zip as zipStatic } from '../observable/zip';\nimport { ObservableInput, ObservableInputTuple, OperatorFunction, Cons } from '../types';\nimport { operate } from '../util/lift';\n\n/** @deprecated Replaced with {@link zipWith}. Will be removed in v8. */\nexport function zip<T, A extends readonly unknown[]>(otherInputs: [...ObservableInputTuple<A>]): OperatorFunction<T, Cons<T, A>>;\n/** @deprecated Replaced with {@link zipWith}. Will be removed in v8. */\nexport function zip<T, A extends readonly unknown[], R>(\n  otherInputsAndProject: [...ObservableInputTuple<A>],\n  project: (...values: Cons<T, A>) => R\n): OperatorFunction<T, R>;\n/** @deprecated Replaced with {@link zipWith}. Will be removed in v8. */\nexport function zip<T, A extends readonly unknown[]>(...otherInputs: [...ObservableInputTuple<A>]): OperatorFunction<T, Cons<T, A>>;\n/** @deprecated Replaced with {@link zipWith}. Will be removed in v8. */\nexport function zip<T, A extends readonly unknown[], R>(\n  ...otherInputsAndProject: [...ObservableInputTuple<A>, (...values: Cons<T, A>) => R]\n): OperatorFunction<T, R>;\n\n/**\n * @deprecated Replaced with {@link zipWith}. Will be removed in v8.\n */\nexport function zip<T, R>(...sources: Array<ObservableInput<any> | ((...values: Array<any>) => R)>): OperatorFunction<T, any> {\n  return operate((source, subscriber) => {\n    zipStatic(source as ObservableInput<any>, ...(sources as Array<ObservableInput<any>>)).subscribe(subscriber);\n  });\n}\n", "import { ObservableInputTuple, OperatorFunction, Cons } from '../types';\nimport { zip } from './zip';\n\n/**\n * Subscribes to the source, and the observable inputs provided as arguments, and combines their values, by index, into arrays.\n *\n * What is meant by \"combine by index\": The first value from each will be made into a single array, then emitted,\n * then the second value from each will be combined into a single array and emitted, then the third value\n * from each will be combined into a single array and emitted, and so on.\n *\n * This will continue until it is no longer able to combine values of the same index into an array.\n *\n * After the last value from any one completed source is emitted in an array, the resulting observable will complete,\n * as there is no way to continue \"zipping\" values together by index.\n *\n * Use-cases for this operator are limited. There are memory concerns if one of the streams is emitting\n * values at a much faster rate than the others. Usage should likely be limited to streams that emit\n * at a similar pace, or finite streams of known length.\n *\n * In many cases, authors want `combineLatestWith` and not `zipWith`.\n *\n * @param otherInputs other observable inputs to collate values from.\n * @return A function that returns an Observable that emits items by index\n * combined from the source Observable and provided Observables, in form of an\n * array.\n */\nexport function zipWith<T, A extends readonly unknown[]>(...otherInputs: [...ObservableInputTuple<A>]): OperatorFunction<T, Cons<T, A>> {\n  return zip(...otherInputs);\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  ReplaySubject,\n  Subject,\n  fromEvent\n} from \"rxjs\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch document\n *\n * Documents are implemented as subjects, so all downstream observables are\n * automatically updated when a new document is emitted.\n *\n * @returns Document subject\n */\nexport function watchDocument(): Subject<Document> {\n  const document$ = new ReplaySubject<Document>(1)\n  fromEvent(document, \"DOMContentLoaded\", { once: true })\n    .subscribe(() => document$.next(document))\n\n  /* Return document */\n  return document$\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve all elements matching the query selector\n *\n * @template T - Element type\n *\n * @param selector - Query selector\n * @param node - Node of reference\n *\n * @returns Elements\n */\nexport function getElements<T extends keyof HTMLElementTagNameMap>(\n  selector: T, node?: ParentNode\n): HTMLElementTagNameMap[T][]\n\nexport function getElements<T extends HTMLElement>(\n  selector: string, node?: ParentNode\n): T[]\n\nexport function getElements<T extends HTMLElement>(\n  selector: string, node: ParentNode = document\n): T[] {\n  return Array.from(node.querySelectorAll<T>(selector))\n}\n\n/**\n * Retrieve an element matching a query selector or throw a reference error\n *\n * Note that this function assumes that the element is present. If unsure if an\n * element is existent, use the `getOptionalElement` function instead.\n *\n * @template T - Element type\n *\n * @param selector - Query selector\n * @param node - Node of reference\n *\n * @returns Element\n */\nexport function getElement<T extends keyof HTMLElementTagNameMap>(\n  selector: T, node?: ParentNode\n): HTMLElementTagNameMap[T]\n\nexport function getElement<T extends HTMLElement>(\n  selector: string, node?: ParentNode\n): T\n\nexport function getElement<T extends HTMLElement>(\n  selector: string, node: ParentNode = document\n): T {\n  const el = getOptionalElement<T>(selector, node)\n  if (typeof el === \"undefined\")\n    throw new ReferenceError(\n      `Missing element: expected \"${selector}\" to be present`\n    )\n\n  /* Return element */\n  return el\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Retrieve an optional element matching the query selector\n *\n * @template T - Element type\n *\n * @param selector - Query selector\n * @param node - Node of reference\n *\n * @returns Element or nothing\n */\nexport function getOptionalElement<T extends keyof HTMLElementTagNameMap>(\n  selector: T, node?: ParentNode\n): HTMLElementTagNameMap[T] | undefined\n\nexport function getOptionalElement<T extends HTMLElement>(\n  selector: string, node?: ParentNode\n): T | undefined\n\nexport function getOptionalElement<T extends HTMLElement>(\n  selector: string, node: ParentNode = document\n): T | undefined {\n  return node.querySelector<T>(selector) || undefined\n}\n\n/**\n * Retrieve the currently active element\n *\n * @returns Element or nothing\n */\nexport function getActiveElement(): HTMLElement | undefined {\n  return (\n    document.activeElement?.shadowRoot?.activeElement as HTMLElement ??\n    document.activeElement as HTMLElement ??\n    undefined\n  )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  debounceTime,\n  distinctUntilChanged,\n  fromEvent,\n  map,\n  merge,\n  shareReplay,\n  startWith\n} from \"rxjs\"\n\nimport { getActiveElement } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Focus observable\n *\n * Previously, this observer used `focus` and `blur` events to determine whether\n * an element is focused, but this doesn't work if there are focusable elements\n * within the elements itself. A better solutions are `focusin` and `focusout`\n * events, which bubble up the tree and allow for more fine-grained control.\n *\n * `debounceTime` is necessary, because when a focus change happens inside an\n * element, the observable would first emit `false` and then `true` again.\n */\nconst observer$ = merge(\n  fromEvent(document.body, \"focusin\"),\n  fromEvent(document.body, \"focusout\")\n)\n  .pipe(\n    debounceTime(1),\n    startWith(undefined),\n    map(() => getActiveElement() || document.body),\n    shareReplay(1)\n  )\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch element focus\n *\n * @param el - Element\n *\n * @returns Element focus observable\n */\nexport function watchElementFocus(\n  el: HTMLElement\n): Observable<boolean> {\n  return observer$\n    .pipe(\n      map(active => el.contains(active)),\n      distinctUntilChanged()\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  debounce,\n  defer,\n  fromEvent,\n  identity,\n  map,\n  merge,\n  startWith,\n  timer\n} from \"rxjs\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch element hover\n *\n * The second parameter allows to specify a timeout in milliseconds after which\n * the hover state will be reset to `false`. This is useful for tooltips which\n * should disappear after a certain amount of time, in order to allow the user\n * to move the cursor from the host to the tooltip.\n *\n * @param el - Element\n * @param timeout - Timeout\n *\n * @returns Element hover observable\n */\nexport function watchElementHover(\n  el: HTMLElement, timeout?: number\n): Observable<boolean> {\n  return defer(() => merge(\n    fromEvent(el, \"mouseenter\").pipe(map(() => true)),\n    fromEvent(el, \"mouseleave\").pipe(map(() => false))\n  )\n    .pipe(\n      timeout ? debounce(active => timer(+!active * timeout)) : identity,\n      startWith(el.matches(\":hover\"))\n    )\n  )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { JSX as JSXInternal } from \"preact\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * HTML attributes\n */\ntype Attributes =\n  & JSXInternal.HTMLAttributes\n  & JSXInternal.SVGAttributes\n  & Record<string, any>\n\n/**\n * Child element\n */\ntype Child =\n  | ChildNode\n  | HTMLElement\n  | Text\n  | string\n  | number\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Append a child node to an element\n *\n * @param el - Element\n * @param child - Child node(s)\n */\nfunction appendChild(el: HTMLElement, child: Child | Child[]): void {\n\n  /* Handle primitive types (including raw HTML) */\n  if (typeof child === \"string\" || typeof child === \"number\") {\n    el.innerHTML += child.toString()\n\n  /* Handle nodes */\n  } else if (child instanceof Node) {\n    el.appendChild(child)\n\n  /* Handle nested children */\n  } else if (Array.isArray(child)) {\n    for (const node of child)\n      appendChild(el, node)\n  }\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * JSX factory\n *\n * @template T - Element type\n *\n * @param tag - HTML tag\n * @param attributes - HTML attributes\n * @param children - Child elements\n *\n * @returns Element\n */\nexport function h<T extends keyof HTMLElementTagNameMap>(\n  tag: T, attributes?: Attributes | null, ...children: Child[]\n): HTMLElementTagNameMap[T]\n\nexport function h<T extends h.JSX.Element>(\n  tag: string, attributes?: Attributes | null, ...children: Child[]\n): T\n\nexport function h<T extends h.JSX.Element>(\n  tag: string, attributes?: Attributes | null, ...children: Child[]\n): T {\n  const el = document.createElement(tag)\n\n  /* Set attributes, if any */\n  if (attributes)\n    for (const attr of Object.keys(attributes)) {\n      if (typeof attributes[attr] === \"undefined\")\n        continue\n\n      /* Set default attribute or boolean */\n      if (typeof attributes[attr] !== \"boolean\")\n        el.setAttribute(attr, attributes[attr])\n      else\n        el.setAttribute(attr, \"\")\n    }\n\n  /* Append child nodes */\n  for (const child of children)\n    appendChild(el, child)\n\n  /* Return element */\n  return el as T\n}\n\n/* ----------------------------------------------------------------------------\n * Namespace\n * ------------------------------------------------------------------------- */\n\nexport declare namespace h {\n  namespace JSX {\n    type Element = HTMLElement\n    type IntrinsicElements = JSXInternal.IntrinsicElements\n  }\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Round a number for display with repository facts\n *\n * This is a reverse-engineered version of GitHub's weird rounding algorithm\n * for stars, forks and all other numbers. While all numbers below `1,000` are\n * returned as-is, bigger numbers are converted to fixed numbers:\n *\n * - `1,049` => `1k`\n * - `1,050` => `1.1k`\n * - `1,949` => `1.9k`\n * - `1,950` => `2k`\n *\n * @param value - Original value\n *\n * @returns Rounded value\n */\nexport function round(value: number): string {\n  if (value > 999) {\n    const digits = +((value - 950) % 1000 > 99)\n    return `${((value + 0.000001) / 1000).toFixed(digits)}k`\n  } else {\n    return value.toString()\n  }\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  defer,\n  finalize,\n  fromEvent,\n  map,\n  merge,\n  switchMap,\n  take,\n  throwError\n} from \"rxjs\"\n\nimport { h } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Create and load a `script` element\n *\n * This function returns an observable that will emit when the script was\n * successfully loaded, or throw an error if it wasn't.\n *\n * @param src - Script URL\n *\n * @returns Script observable\n */\nexport function watchScript(src: string): Observable<void> {\n  const script = h(\"script\", { src })\n  return defer(() => {\n    document.head.appendChild(script)\n    return merge(\n      fromEvent(script, \"load\"),\n      fromEvent(script, \"error\")\n        .pipe(\n          switchMap(() => (\n            throwError(() => new ReferenceError(`Invalid script: ${src}`))\n          ))\n        )\n    )\n      .pipe(\n        map(() => undefined),\n        finalize(() => document.head.removeChild(script)),\n        take(1)\n      )\n  })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  NEVER,\n  Observable,\n  Subject,\n  defer,\n  filter,\n  finalize,\n  map,\n  merge,\n  of,\n  shareReplay,\n  startWith,\n  switchMap,\n  tap\n} from \"rxjs\"\n\nimport { watchScript } from \"../../../script\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Element offset\n */\nexport interface ElementSize {\n  width: number                        /* Element width */\n  height: number                       /* Element height */\n}\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Resize observer entry subject\n */\nconst entry$ = new Subject<ResizeObserverEntry>()\n\n/**\n * Resize observer observable\n *\n * This observable will create a `ResizeObserver` on the first subscription\n * and will automatically terminate it when there are no more subscribers.\n * It's quite important to centralize observation in a single `ResizeObserver`,\n * as the performance difference can be quite dramatic, as the link shows.\n *\n * If the browser doesn't have a `ResizeObserver` implementation available, a\n * polyfill is automatically downloaded from unpkg.com. This is also compatible\n * with the built-in privacy plugin, which will download the polyfill and put\n * it alongside the built site for self-hosting.\n *\n * @see https://bit.ly/3iIYfEm - Google Groups on performance\n */\nconst observer$ = defer(() => (\n  typeof ResizeObserver === \"undefined\"\n    ? watchScript(\"https://unpkg.com/resize-observer-polyfill\")\n    : of(undefined)\n))\n  .pipe(\n    map(() => new ResizeObserver(entries => (\n      entries.forEach(entry => entry$.next(entry))\n    ))),\n    switchMap(observer => merge(NEVER, of(observer)).pipe(\n      finalize(() => observer.disconnect())\n    )),\n    shareReplay(1)\n  )\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve element size\n *\n * @param el - Element\n *\n * @returns Element size\n */\nexport function getElementSize(\n  el: HTMLElement\n): ElementSize {\n  return {\n    width:  el.offsetWidth,\n    height: el.offsetHeight\n  }\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Watch element size\n *\n * This function returns an observable that subscribes to a single internal\n * instance of `ResizeObserver` upon subscription, and emit resize events until\n * termination. Note that this function should not be called with the same\n * element twice, as the first unsubscription will terminate observation.\n *\n * Sadly, we can't use the `DOMRect` objects returned by the observer, because\n * we need the emitted values to be consistent with `getElementSize`, which will\n * return the used values (rounded) and not actual values (unrounded). Thus, we\n * use the `offset*` properties. See the linked GitHub issue.\n *\n * @see https://bit.ly/3m0k3he - GitHub issue\n *\n * @param el - Element\n *\n * @returns Element size observable\n */\nexport function watchElementSize(\n  el: HTMLElement\n): Observable<ElementSize> {\n\n  // Compute target element - since inline elements cannot be observed by the\n  // current `ResizeObserver` implementation as provided by browsers, we need\n  // to determine the first containing parent element and use that one as a\n  // target, while we always compute the actual size from the element.\n  let target = el\n  while (target.clientWidth === 0)\n    if (target.parentElement)\n      target = target.parentElement\n    else\n      break\n\n  // Observe target element and recompute element size on resize - as described\n  // above, the target element is not necessarily the element of interest\n  return observer$.pipe(\n    tap(observer => observer.observe(target)),\n    switchMap(observer => entry$.pipe(\n      filter(entry => entry.target === target),\n      finalize(() => observer.unobserve(target))\n    )),\n    map(() => getElementSize(el)),\n    startWith(getElementSize(el))\n  )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { ElementSize } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve element content size (= scroll width and height)\n *\n * @param el - Element\n *\n * @returns Element content size\n */\nexport function getElementContentSize(\n  el: HTMLElement\n): ElementSize {\n  return {\n    width:  el.scrollWidth,\n    height: el.scrollHeight\n  }\n}\n\n/**\n * Retrieve the overflowing container of an element, if any\n *\n * @param el - Element\n *\n * @returns Overflowing container or nothing\n */\nexport function getElementContainer(\n  el: HTMLElement\n): HTMLElement | undefined {\n  let parent = el.parentElement\n  while (parent)\n    if (\n      el.scrollWidth  <= parent.scrollWidth &&\n      el.scrollHeight <= parent.scrollHeight\n    )\n      parent = (el = parent).parentElement\n    else\n      break\n\n  /* Return overflowing container */\n  return parent ? el : undefined\n}\n\n/**\n * Retrieve all overflowing containers of an element, if any\n *\n * Note that this function has a slightly different behavior, so we should at\n * some point consider refactoring how overflowing containers are handled.\n *\n * @param el - Element\n *\n * @returns Overflowing containers\n */\nexport function getElementContainers(\n  el: HTMLElement\n): HTMLElement[] {\n  const containers: HTMLElement[] = []\n\n  // Walk up the DOM tree until we find an overflowing container\n  let parent = el.parentElement\n  while (parent) {\n    if (\n      el.clientWidth  > parent.clientWidth ||\n      el.clientHeight > parent.clientHeight\n    )\n      containers.push(parent)\n\n    // Continue with parent element\n    parent = (el = parent).parentElement\n  }\n\n  // If the page is short, the body might not be overflowing and there might be\n  // no other containers, which is why we need to make sure the body is present\n  if (containers.length === 0)\n    containers.push(document.documentElement)\n\n  // Return overflowing containers\n  return containers\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  animationFrameScheduler,\n  auditTime,\n  fromEvent,\n  map,\n  merge,\n  startWith\n} from \"rxjs\"\n\nimport { watchElementSize } from \"../../size\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Element offset\n */\nexport interface ElementOffset {\n  x: number                            /* Horizontal offset */\n  y: number                            /* Vertical offset */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve element offset\n *\n * @param el - Element\n *\n * @returns Element offset\n */\nexport function getElementOffset(\n  el: HTMLElement\n): ElementOffset {\n  return {\n    x: el.offsetLeft,\n    y: el.offsetTop\n  }\n}\n\n/**\n * Retrieve absolute element offset\n *\n * @param el - Element\n *\n * @returns Element offset\n */\nexport function getElementOffsetAbsolute(\n  el: HTMLElement\n): ElementOffset {\n  const rect = el.getBoundingClientRect()\n  return {\n    x: rect.x + window.scrollX,\n    y: rect.y + window.scrollY\n  }\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Watch element offset\n *\n * @param el - Element\n *\n * @returns Element offset observable\n */\nexport function watchElementOffset(\n  el: HTMLElement\n): Observable<ElementOffset> {\n  return merge(\n    fromEvent(window, \"load\"),\n    fromEvent(window, \"resize\")\n  )\n    .pipe(\n      auditTime(0, animationFrameScheduler),\n      map(() => getElementOffset(el)),\n      startWith(getElementOffset(el))\n    )\n}\n\n/**\n * Watch absolute element offset\n *\n * @param el - Element\n *\n * @returns Element offset observable\n */\nexport function watchElementOffsetAbsolute(\n  el: HTMLElement\n): Observable<ElementOffset> {\n  return merge(\n    watchElementOffset(el),\n    watchElementSize(document.body) // @todo find a better way for this\n  )\n    .pipe(\n      map(() => getElementOffsetAbsolute(el)),\n      startWith(getElementOffsetAbsolute(el))\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  animationFrameScheduler,\n  auditTime,\n  fromEvent,\n  map,\n  merge,\n  startWith\n} from \"rxjs\"\n\nimport { ElementOffset } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve element content offset (= scroll offset)\n *\n * @param el - Element\n *\n * @returns Element content offset\n */\nexport function getElementContentOffset(\n  el: HTMLElement\n): ElementOffset {\n  return {\n    x: el.scrollLeft,\n    y: el.scrollTop\n  }\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Watch element content offset\n *\n * @param el - Element\n *\n * @returns Element content offset observable\n */\nexport function watchElementContentOffset(\n  el: HTMLElement\n): Observable<ElementOffset> {\n  return merge(\n    fromEvent(el, \"scroll\"),\n    fromEvent(window, \"scroll\"),\n    fromEvent(window, \"resize\")\n  )\n    .pipe(\n      auditTime(0, animationFrameScheduler),\n      map(() => getElementContentOffset(el)),\n      startWith(getElementContentOffset(el))\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  NEVER,\n  Observable,\n  Subject,\n  defer,\n  distinctUntilChanged,\n  filter,\n  finalize,\n  map,\n  merge,\n  of,\n  shareReplay,\n  switchMap,\n  tap\n} from \"rxjs\"\n\nimport {\n  getElementContentSize,\n  getElementSize,\n  watchElementContentOffset\n} from \"~/browser\"\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Intersection observer entry subject\n */\nconst entry$ = new Subject<IntersectionObserverEntry>()\n\n/**\n * Intersection observer observable\n *\n * This observable will create an `IntersectionObserver` on first subscription\n * and will automatically terminate it when there are no more subscribers.\n *\n * @see https://bit.ly/3iIYfEm - Google Groups on performance\n */\nconst observer$ = defer(() => of(\n  new IntersectionObserver(entries => {\n    for (const entry of entries)\n      entry$.next(entry)\n  }, {\n    threshold: 0\n  })\n))\n  .pipe(\n    switchMap(observer => merge(NEVER, of(observer))\n      .pipe(\n        finalize(() => observer.disconnect())\n      )\n    ),\n    shareReplay(1)\n  )\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch element visibility\n *\n * @param el - Element\n *\n * @returns Element visibility observable\n */\nexport function watchElementVisibility(\n  el: HTMLElement\n): Observable<boolean> {\n  return observer$\n    .pipe(\n      tap(observer => observer.observe(el)),\n      switchMap(observer => entry$\n        .pipe(\n          filter(({ target }) => target === el),\n          finalize(() => observer.unobserve(el)),\n          map(({ isIntersecting }) => isIntersecting)\n        )\n      )\n    )\n}\n\n/**\n * Watch element boundary\n *\n * This function returns an observable which emits whether the bottom content\n * boundary (= scroll offset) of an element is within a certain threshold.\n *\n * @param el - Element\n * @param threshold - Threshold\n *\n * @returns Element boundary observable\n */\nexport function watchElementBoundary(\n  el: HTMLElement, threshold = 16\n): Observable<boolean> {\n  return watchElementContentOffset(el)\n    .pipe(\n      map(({ y }) => {\n        const visible = getElementSize(el)\n        const content = getElementContentSize(el)\n        return y >= (\n          content.height - visible.height - threshold\n        )\n      }),\n      distinctUntilChanged()\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  fromEvent,\n  map,\n  startWith\n} from \"rxjs\"\n\nimport { getElement } from \"../element\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Toggle\n */\nexport type Toggle =\n  | \"drawer\"                           /* Toggle for drawer */\n  | \"search\"                           /* Toggle for search */\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Toggle map\n */\nconst toggles: Record<Toggle, HTMLInputElement> = {\n  drawer: getElement(\"[data-md-toggle=drawer]\"),\n  search: getElement(\"[data-md-toggle=search]\")\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve the value of a toggle\n *\n * @param name - Toggle\n *\n * @returns Toggle value\n */\nexport function getToggle(name: Toggle): boolean {\n  return toggles[name].checked\n}\n\n/**\n * Set toggle\n *\n * Simulating a click event seems to be the most cross-browser compatible way\n * of changing the value while also emitting a `change` event. Before, Material\n * used `CustomEvent` to programmatically change the value of a toggle, but this\n * is a much simpler and cleaner solution which doesn't require a polyfill.\n *\n * @param name - Toggle\n * @param value - Toggle value\n */\nexport function setToggle(name: Toggle, value: boolean): void {\n  if (toggles[name].checked !== value)\n    toggles[name].click()\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Watch toggle\n *\n * @param name - Toggle\n *\n * @returns Toggle value observable\n */\nexport function watchToggle(name: Toggle): Observable<boolean> {\n  const el = toggles[name]\n  return fromEvent(el, \"change\")\n    .pipe(\n      map(() => el.checked),\n      startWith(el.checked)\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  EMPTY,\n  Observable,\n  filter,\n  fromEvent,\n  map,\n  merge,\n  share,\n  startWith,\n  switchMap\n} from \"rxjs\"\n\nimport { getActiveElement } from \"../element\"\nimport { getToggle } from \"../toggle\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Keyboard mode\n */\nexport type KeyboardMode =\n  | \"global\"                           /* Global */\n  | \"search\"                           /* Search is open */\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Keyboard\n */\nexport interface Keyboard {\n  mode: KeyboardMode                   /* Keyboard mode */\n  type: string                         /* Key type */\n  claim(): void                        /* Key claim */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Check whether an element may receive keyboard input\n *\n * @param el - Element\n * @param type - Key type\n *\n * @returns Test result\n */\nfunction isSusceptibleToKeyboard(\n  el: HTMLElement, type: string\n): boolean {\n  switch (el.constructor) {\n\n    /* Input elements */\n    case HTMLInputElement:\n      /* @ts-expect-error - omit unnecessary type cast */\n      if (el.type === \"radio\")\n        return /^Arrow/.test(type)\n      else\n        return true\n\n    /* Select element and textarea */\n    case HTMLSelectElement:\n    case HTMLTextAreaElement:\n      return true\n\n    /* Everything else */\n    default:\n      return el.isContentEditable\n  }\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch composition events\n *\n * @returns Composition observable\n */\nexport function watchComposition(): Observable<boolean> {\n  return merge(\n    fromEvent(window, \"compositionstart\").pipe(map(() => true)),\n    fromEvent(window, \"compositionend\").pipe(map(() => false))\n  )\n    .pipe(\n      startWith(false)\n    )\n}\n\n/**\n * Watch keyboard\n *\n * @returns Keyboard observable\n */\nexport function watchKeyboard(): Observable<Keyboard> {\n  const keyboard$ = fromEvent<KeyboardEvent>(window, \"keydown\")\n    .pipe(\n      filter(ev => !(ev.metaKey || ev.ctrlKey)),\n      map(ev => ({\n        mode: getToggle(\"search\") ? \"search\" : \"global\",\n        type: ev.key,\n        claim() {\n          ev.preventDefault()\n          ev.stopPropagation()\n        }\n      } as Keyboard)),\n      filter(({ mode, type }) => {\n        if (mode === \"global\") {\n          const active = getActiveElement()\n          if (typeof active !== \"undefined\")\n            return !isSusceptibleToKeyboard(active, type)\n        }\n        return true\n      }),\n      share()\n    )\n\n  /* Don't emit during composition events - see https://bit.ly/3te3Wl8 */\n  return watchComposition()\n    .pipe(\n      switchMap(active => !active ? keyboard$ : EMPTY)\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { Subject } from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport { h } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve location\n *\n * This function returns a `URL` object (and not `Location`) to normalize the\n * typings across the application. Furthermore, locations need to be tracked\n * without setting them and `Location` is a singleton which represents the\n * current location.\n *\n * @returns URL\n */\nexport function getLocation(): URL {\n  return new URL(location.href)\n}\n\n/**\n * Set location\n *\n * If instant navigation is enabled, this function creates a temporary anchor\n * element, sets the `href` attribute, appends it to the body, clicks it, and\n * then removes it again. The event will bubble up the DOM and be intercepted\n * by the instant navigation event handlers.\n *\n * Note that we must append and remove the anchor element, or the event will\n * not bubble up the DOM, making it impossible to intercept it.\n *\n * @param url - URL to navigate to\n * @param navigate - Force navigation\n */\nexport function setLocation(\n  url: URL | HTMLLinkElement, navigate = false\n): void {\n  if (feature(\"navigation.instant\") && !navigate) {\n    const el = h(\"a\", { href: url.href })\n    document.body.appendChild(el)\n    el.click()\n    el.remove()\n\n  // If we're not using instant navigation, and the page should not be reloaded\n  // just instruct the browser to navigate to the given URL\n  } else {\n    location.href = url.href\n  }\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Watch location\n *\n * @returns Location subject\n */\nexport function watchLocation(): Subject<URL> {\n  return new Subject<URL>()\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  filter,\n  fromEvent,\n  map,\n  merge,\n  shareReplay,\n  startWith\n} from \"rxjs\"\n\nimport { getOptionalElement } from \"~/browser\"\nimport { h } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve location hash\n *\n * @returns Location hash\n */\nexport function getLocationHash(): string {\n  return location.hash.slice(1)\n}\n\n/**\n * Set location hash\n *\n * Setting a new fragment identifier via `location.hash` will have no effect\n * if the value doesn't change. When a new fragment identifier is set, we want\n * the browser to target the respective element at all times, which is why we\n * use this dirty little trick.\n *\n * @param hash - Location hash\n */\nexport function setLocationHash(hash: string): void {\n  const el = h(\"a\", { href: hash })\n  el.addEventListener(\"click\", ev => ev.stopPropagation())\n  el.click()\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Watch location hash\n *\n * @param location$ - Location observable\n *\n * @returns Location hash observable\n */\nexport function watchLocationHash(\n  location$: Observable<URL>\n): Observable<string> {\n  return merge(\n    fromEvent<HashChangeEvent>(window, \"hashchange\"),\n    location$\n  )\n    .pipe(\n      map(getLocationHash),\n      startWith(getLocationHash()),\n      filter(hash => hash.length > 0),\n      shareReplay(1)\n    )\n}\n\n/**\n * Watch location target\n *\n * @param location$ - Location observable\n *\n * @returns Location target observable\n */\nexport function watchLocationTarget(\n  location$: Observable<URL>\n): Observable<HTMLElement> {\n  return watchLocationHash(location$)\n    .pipe(\n      map(id => getOptionalElement(`[id=\"${id}\"]`)!),\n      filter(el => typeof el !== \"undefined\")\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  EMPTY,\n  Observable,\n  fromEvent,\n  fromEventPattern,\n  map,\n  merge,\n  startWith,\n  switchMap\n} from \"rxjs\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch media query\n *\n * Note that although `MediaQueryList.addListener` is deprecated we have to\n * use it, because it's the only way to ensure proper downward compatibility.\n *\n * @see https://bit.ly/3dUBH2m - GitHub issue\n *\n * @param query - Media query\n *\n * @returns Media observable\n */\nexport function watchMedia(query: string): Observable<boolean> {\n  const media = matchMedia(query)\n  return fromEventPattern<boolean>(next => (\n    media.addListener(() => next(media.matches))\n  ))\n    .pipe(\n      startWith(media.matches)\n    )\n}\n\n/**\n * Watch print mode\n *\n * @returns Print observable\n */\nexport function watchPrint(): Observable<boolean> {\n  const media = matchMedia(\"print\")\n  return merge(\n    fromEvent(window, \"beforeprint\").pipe(map(() => true)),\n    fromEvent(window, \"afterprint\").pipe(map(() => false))\n  )\n    .pipe(\n      startWith(media.matches)\n    )\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Toggle an observable with a media observable\n *\n * @template T - Data type\n *\n * @param query$ - Media observable\n * @param factory - Observable factory\n *\n * @returns Toggled observable\n */\nexport function at<T>(\n  query$: Observable<boolean>, factory: () => Observable<T>\n): Observable<T> {\n  return query$\n    .pipe(\n      switchMap(active => active ? factory() : EMPTY)\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  Subject,\n  map,\n  shareReplay,\n  switchMap\n} from \"rxjs\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Options\n */\ninterface Options {\n  progress$?: Subject<number>          // Progress subject\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch the given URL\n *\n * This function returns an observable that emits the response as a blob and\n * completes, or emits an error if the request failed. The caller can cancel\n * the request by unsubscribing at any time, which will automatically abort\n * the inflight request and complete the observable.\n *\n * Note that we use `XMLHTTPRequest` not because we're nostalgic, but because\n * it's the only way to get progress events for downloads and also allow for\n * cancellation of requests, as the official Fetch API does not support this\n * yet, even though we're already in 2024.\n *\n * @param url - Request URL\n * @param options - Options\n *\n * @returns Data observable\n */\nexport function request(\n  url: URL | string, options?: Options\n): Observable<Blob> {\n  return new Observable<Blob>(observer => {\n    const req = new XMLHttpRequest()\n    req.open(\"GET\", `${url}`)\n    req.responseType = \"blob\"\n\n    // Handle response\n    req.addEventListener(\"load\", () => {\n      if (req.status >= 200 && req.status < 300) {\n        observer.next(req.response)\n        observer.complete()\n\n      // Every response that is not in the 2xx range is considered an error\n      } else {\n        observer.error(new Error(req.statusText))\n      }\n    })\n\n    // Handle network errors\n    req.addEventListener(\"error\", () => {\n      observer.error(new Error(\"Network error\"))\n    })\n\n    // Handle aborted requests\n    req.addEventListener(\"abort\", () => {\n      observer.complete()\n    })\n\n    // Handle download progress\n    if (typeof options?.progress$ !== \"undefined\") {\n      req.addEventListener(\"progress\", event => {\n        if (event.lengthComputable) {\n          options.progress$!.next((event.loaded / event.total) * 100)\n\n        // Hack: Chromium doesn't report the total number of bytes if content\n        // is compressed, so we need this fallback - see https://t.ly/ZXofI\n        } else {\n          const length = req.getResponseHeader(\"Content-Length\") ?? 0\n          options.progress$!.next((event.loaded / +length) * 100)\n        }\n      })\n\n      // Immediately set progress to 5% to indicate that we're loading\n      options.progress$.next(5)\n    }\n\n    // Send request and automatically abort request upon unsubscription\n    req.send()\n    return () => req.abort()\n  })\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Fetch JSON from the given URL\n *\n * @template T - Data type\n *\n * @param url - Request URL\n * @param options - Options\n *\n * @returns Data observable\n */\nexport function requestJSON<T>(\n  url: URL | string, options?: Options\n): Observable<T> {\n  return request(url, options)\n    .pipe(\n      switchMap(res => res.text()),\n      map(body => JSON.parse(body) as T),\n      shareReplay(1)\n    )\n}\n\n/**\n * Fetch HTML from the given URL\n *\n * @param url - Request URL\n * @param options - Options\n *\n * @returns Data observable\n */\nexport function requestHTML(\n  url: URL | string, options?: Options\n): Observable<Document> {\n  const dom = new DOMParser()\n  return request(url, options)\n    .pipe(\n      switchMap(res => res.text()),\n      map(res => dom.parseFromString(res, \"text/html\")),\n      shareReplay(1)\n    )\n}\n\n/**\n * Fetch XML from the given URL\n *\n * @param url - Request URL\n * @param options - Options\n *\n * @returns Data observable\n */\nexport function requestXML(\n  url: URL | string, options?: Options\n): Observable<Document> {\n  const dom = new DOMParser()\n  return request(url, options)\n    .pipe(\n      switchMap(res => res.text()),\n      map(res => dom.parseFromString(res, \"text/xml\")),\n      shareReplay(1)\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  fromEvent,\n  map,\n  merge,\n  startWith\n} from \"rxjs\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Viewport offset\n */\nexport interface ViewportOffset {\n  x: number                            /* Horizontal offset */\n  y: number                            /* Vertical offset */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve viewport offset\n *\n * On iOS Safari, viewport offset can be negative due to overflow scrolling.\n * As this may induce strange behaviors downstream, we'll just limit it to 0.\n *\n * @returns Viewport offset\n */\nexport function getViewportOffset(): ViewportOffset {\n  return {\n    x: Math.max(0, scrollX),\n    y: Math.max(0, scrollY)\n  }\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Watch viewport offset\n *\n * @returns Viewport offset observable\n */\nexport function watchViewportOffset(): Observable<ViewportOffset> {\n  return merge(\n    fromEvent(window, \"scroll\", { passive: true }),\n    fromEvent(window, \"resize\", { passive: true })\n  )\n    .pipe(\n      map(getViewportOffset),\n      startWith(getViewportOffset())\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  fromEvent,\n  map,\n  startWith\n} from \"rxjs\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Viewport size\n */\nexport interface ViewportSize {\n  width: number                        /* Viewport width */\n  height: number                       /* Viewport height */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve viewport size\n *\n * @returns Viewport size\n */\nexport function getViewportSize(): ViewportSize {\n  return {\n    width:  innerWidth,\n    height: innerHeight\n  }\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Watch viewport size\n *\n * @returns Viewport size observable\n */\nexport function watchViewportSize(): Observable<ViewportSize> {\n  return fromEvent(window, \"resize\", { passive: true })\n    .pipe(\n      map(getViewportSize),\n      startWith(getViewportSize())\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  combineLatest,\n  map,\n  shareReplay\n} from \"rxjs\"\n\nimport {\n  ViewportOffset,\n  watchViewportOffset\n} from \"../offset\"\nimport {\n  ViewportSize,\n  watchViewportSize\n} from \"../size\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Viewport\n */\nexport interface Viewport {\n  offset: ViewportOffset               /* Viewport offset */\n  size: ViewportSize                   /* Viewport size */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch viewport\n *\n * @returns Viewport observable\n */\nexport function watchViewport(): Observable<Viewport> {\n  return combineLatest([\n    watchViewportOffset(),\n    watchViewportSize()\n  ])\n    .pipe(\n      map(([offset, size]) => ({ offset, size })),\n      shareReplay(1)\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  combineLatest,\n  distinctUntilKeyChanged,\n  map\n} from \"rxjs\"\n\nimport { Header } from \"~/components\"\n\nimport { getElementOffset } from \"../../element\"\nimport { Viewport } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n  viewport$: Observable<Viewport>      /* Viewport observable */\n  header$: Observable<Header>          /* Header observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch viewport relative to element\n *\n * @param el - Element\n * @param options - Options\n *\n * @returns Viewport observable\n */\nexport function watchViewportAt(\n  el: HTMLElement, { viewport$, header$ }: WatchOptions\n): Observable<Viewport> {\n  const size$ = viewport$\n    .pipe(\n      distinctUntilKeyChanged(\"size\")\n    )\n\n  /* Compute element offset */\n  const offset$ = combineLatest([size$, header$])\n    .pipe(\n      map(() => getElementOffset(el))\n    )\n\n  /* Compute relative viewport, return hot observable */\n  return combineLatest([header$, viewport$, offset$])\n    .pipe(\n      map(([{ height }, { offset, size }, { x, y }]) => ({\n        offset: {\n          x: offset.x - x,\n          y: offset.y - y + height\n        },\n        size\n      }))\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  Subject,\n  endWith,\n  fromEvent,\n  ignoreElements,\n  mergeWith,\n  share,\n  takeUntil\n} from \"rxjs\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Worker message\n */\nexport interface WorkerMessage {\n  type: unknown                        /* Message type */\n  data?: unknown                       /* Message data */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Create an observable for receiving from a web worker\n *\n * @template T - Data type\n *\n * @param worker - Web worker\n *\n * @returns Message observable\n */\nfunction recv<T>(worker: Worker): Observable<T> {\n  return fromEvent<MessageEvent<T>, T>(worker, \"message\", ev => ev.data)\n}\n\n/**\n * Create a subject for sending to a web worker\n *\n * @template T - Data type\n *\n * @param worker - Web worker\n *\n * @returns Message subject\n */\nfunction send<T>(worker: Worker): Subject<T> {\n  const send$ = new Subject<T>()\n  send$.subscribe(data => worker.postMessage(data))\n\n  /* Return message subject */\n  return send$\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Create a bidirectional communication channel to a web worker\n *\n * @template T - Data type\n *\n * @param url - Worker URL\n * @param worker - Worker\n *\n * @returns Worker subject\n */\nexport function watchWorker<T extends WorkerMessage>(\n  url: string, worker = new Worker(url)\n): Subject<T> {\n  const recv$ = recv<T>(worker)\n  const send$ = send<T>(worker)\n\n  /* Create worker subject and forward messages */\n  const worker$ = new Subject<T>()\n  worker$.subscribe(send$)\n\n  /* Return worker subject */\n  const done$ = send$.pipe(ignoreElements(), endWith(true))\n  return worker$\n    .pipe(\n      ignoreElements(),\n      mergeWith(recv$.pipe(takeUntil(done$))),\n      share()\n    ) as Subject<T>\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { getElement, getLocation } from \"~/browser\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Feature flag\n */\nexport type Flag =\n  | \"announce.dismiss\"                 /* Dismissable announcement bar */\n  | \"content.code.annotate\"            /* Code annotations */\n  | \"content.code.copy\"                /* Code copy button */\n  | \"content.code.select\"              /* Code selection */\n  | \"content.footnote.tooltips\"        /* Footnote tooltips */\n  | \"content.lazy\"                     /* Lazy content elements */\n  | \"content.tabs.link\"                /* Link content tabs */\n  | \"content.tooltips\"                 /* Tooltips */\n  | \"header.autohide\"                  /* Hide header */\n  | \"navigation.expand\"                /* Automatic expansion */\n  | \"navigation.indexes\"               /* Section pages */\n  | \"navigation.instant\"               /* Instant navigation */\n  | \"navigation.instant.prefetch\"      /* Instant navigation prefetching */\n  | \"navigation.instant.progress\"      /* Instant navigation progress */\n  | \"navigation.instant.preview\"       /* Instant preview */\n  | \"navigation.sections\"              /* Section navigation */\n  | \"navigation.tabs\"                  /* Tabs navigation */\n  | \"navigation.tabs.sticky\"           /* Tabs navigation (sticky) */\n  | \"navigation.top\"                   /* Back-to-top button */\n  | \"navigation.tracking\"              /* Anchor tracking */\n  | \"search.highlight\"                 /* Search highlighting */\n  | \"search.share\"                     /* Search sharing */\n  | \"search.suggest\"                   /* Search suggestions */\n  | \"toc.follow\"                       /* Following table of contents */\n  | \"toc.integrate\"                    /* Integrated table of contents */\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Translation\n */\nexport type Translation =\n  | \"clipboard.copy\"                   /* Copy to clipboard */\n  | \"clipboard.copied\"                 /* Copied to clipboard */\n  | \"search.result.placeholder\"        /* Type to start searching */\n  | \"search.result.none\"               /* No matching documents */\n  | \"search.result.one\"                /* 1 matching document */\n  | \"search.result.other\"              /* # matching documents */\n  | \"search.result.more.one\"           /* 1 more on this page */\n  | \"search.result.more.other\"         /* # more on this page */\n  | \"search.result.term.missing\"       /* Missing */\n  | \"select.version\"                   /* Version selector */\n\n/**\n * Translations\n */\nexport type Translations =\n  Record<Translation, string>\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Versioning\n */\nexport interface Versioning {\n  provider: \"mike\"                     /* Version provider */\n  default?: string | string[]          /* Default version */\n  alias?: boolean                      /* Show alias */\n}\n\n/**\n * Configuration\n */\nexport interface Config {\n  base: string                         /* Base URL */\n  features: Flag[]                     /* Feature flags */\n  translations: Translations           /* Translations */\n  search: string                       /* Search worker URL */\n  annotate?: Record<string, string[]>  /* Annotation mappings */\n  tags?: Record<string, string>        /* Tags mapping */\n  version?: Versioning                 /* Versioning */\n}\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve global configuration and make base URL absolute\n */\nconst script = getElement(\"#__config\")\nconst config: Config = JSON.parse(script.textContent!)\nconfig.base = `${new URL(config.base, getLocation())}`\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve global configuration\n *\n * @returns Global configuration\n */\nexport function configuration(): Config {\n  return config\n}\n\n/**\n * Check whether a feature flag is enabled\n *\n * @param flag - Feature flag\n *\n * @returns Test result\n */\nexport function feature(flag: Flag): boolean {\n  return config.features.includes(flag)\n}\n\n/**\n * Retrieve the translation for the given key\n *\n * @param key - Key to be translated\n * @param value - Positional value, if any\n *\n * @returns Translation\n */\nexport function translation(\n  key: Translation, value?: string | number\n): string {\n  return typeof value !== \"undefined\"\n    ? config.translations[key].replace(\"#\", value.toString())\n    : config.translations[key]\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { getElement, getElements } from \"~/browser\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Component type\n */\nexport type ComponentType =\n  | \"announce\"                         /* Announcement bar */\n  | \"container\"                        /* Container */\n  | \"consent\"                          /* Consent */\n  | \"content\"                          /* Content */\n  | \"dialog\"                           /* Dialog */\n  | \"header\"                           /* Header */\n  | \"header-title\"                     /* Header title */\n  | \"header-topic\"                     /* Header topic */\n  | \"main\"                             /* Main area */\n  | \"outdated\"                         /* Version warning */\n  | \"palette\"                          /* Color palette */\n  | \"progress\"                         /* Progress indicator */\n  | \"search\"                           /* Search */\n  | \"search-query\"                     /* Search input */\n  | \"search-result\"                    /* Search results */\n  | \"search-share\"                     /* Search sharing */\n  | \"search-suggest\"                   /* Search suggestions */\n  | \"sidebar\"                          /* Sidebar */\n  | \"skip\"                             /* Skip link */\n  | \"source\"                           /* Repository information */\n  | \"tabs\"                             /* Navigation tabs */\n  | \"toc\"                              /* Table of contents */\n  | \"top\"                              /* Back-to-top button */\n\n/**\n * Component\n *\n * @template T - Component type\n * @template U - Reference type\n */\nexport type Component<\n  T extends {} = {},\n  U extends HTMLElement = HTMLElement\n> =\n  T & {\n    ref: U                             /* Component reference */\n  }\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Component type map\n */\ninterface ComponentTypeMap {\n  \"announce\": HTMLElement              /* Announcement bar */\n  \"container\": HTMLElement             /* Container */\n  \"consent\": HTMLElement               /* Consent */\n  \"content\": HTMLElement               /* Content */\n  \"dialog\": HTMLElement                /* Dialog */\n  \"header\": HTMLElement                /* Header */\n  \"header-title\": HTMLElement          /* Header title */\n  \"header-topic\": HTMLElement          /* Header topic */\n  \"main\": HTMLElement                  /* Main area */\n  \"outdated\": HTMLElement              /* Version warning */\n  \"palette\": HTMLElement               /* Color palette */\n  \"progress\": HTMLElement              /* Progress indicator */\n  \"search\": HTMLElement                /* Search */\n  \"search-query\": HTMLInputElement     /* Search input */\n  \"search-result\": HTMLElement         /* Search results */\n  \"search-share\": HTMLAnchorElement    /* Search sharing */\n  \"search-suggest\": HTMLElement        /* Search suggestions */\n  \"sidebar\": HTMLElement               /* Sidebar */\n  \"skip\": HTMLAnchorElement            /* Skip link */\n  \"source\": HTMLAnchorElement          /* Repository information */\n  \"tabs\": HTMLElement                  /* Navigation tabs */\n  \"toc\": HTMLElement                   /* Table of contents */\n  \"top\": HTMLAnchorElement             /* Back-to-top button */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve the element for a given component or throw a reference error\n *\n * @template T - Component type\n *\n * @param type - Component type\n * @param node - Node of reference\n *\n * @returns Element\n */\nexport function getComponentElement<T extends ComponentType>(\n  type: T, node: ParentNode = document\n): ComponentTypeMap[T] {\n  return getElement(`[data-md-component=${type}]`, node)\n}\n\n/**\n * Retrieve all elements for a given component\n *\n * @template T - Component type\n *\n * @param type - Component type\n * @param node - Node of reference\n *\n * @returns Elements\n */\nexport function getComponentElements<T extends ComponentType>(\n  type: T, node: ParentNode = document\n): ComponentTypeMap[T][] {\n  return getElements(`[data-md-component=${type}]`, node)\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  EMPTY,\n  Observable,\n  Subject,\n  defer,\n  finalize,\n  fromEvent,\n  map,\n  tap\n} from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport { getElement } from \"~/browser\"\n\nimport { Component } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Announcement bar\n */\nexport interface Announce {\n  hash: number                        /* Content hash */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch announcement bar\n *\n * @param el - Announcement bar element\n *\n * @returns Announcement bar observable\n */\nexport function watchAnnounce(\n  el: HTMLElement\n): Observable<Announce> {\n  const button = getElement(\".md-typeset > :first-child\", el)\n  return fromEvent(button, \"click\", { once: true })\n    .pipe(\n      map(() => getElement(\".md-typeset\", el)),\n      map(content => ({ hash: __md_hash(content.innerHTML) }))\n    )\n}\n\n/**\n * Mount announcement bar\n *\n * @param el - Announcement bar element\n *\n * @returns Announcement bar component observable\n */\nexport function mountAnnounce(\n  el: HTMLElement\n): Observable<Component<Announce>> {\n  if (!feature(\"announce.dismiss\") || !el.childElementCount)\n    return EMPTY\n\n  /* Support instant navigation - see https://t.ly/3FTme */\n  if (!el.hidden) {\n    const content = getElement(\".md-typeset\", el)\n    if (__md_hash(content.innerHTML) === __md_get(\"__announce\"))\n      el.hidden = true\n  }\n\n  /* Mount component on subscription */\n  return defer(() => {\n    const push$ = new Subject<Announce>()\n    push$.subscribe(({ hash }) => {\n      el.hidden = true\n\n      /* Persist preference in local storage */\n      __md_set<number>(\"__announce\", hash)\n    })\n\n    /* Create and return component */\n    return watchAnnounce(el)\n      .pipe(\n        tap(state => push$.next(state)),\n        finalize(() => push$.complete()),\n        map(state => ({ ref: el, ...state }))\n      )\n  })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  Subject,\n  finalize,\n  map,\n  tap\n} from \"rxjs\"\n\nimport { Component } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Consent\n */\nexport interface Consent {\n  hidden: boolean                      /* Consent is hidden */\n}\n\n/**\n * Consent defaults\n */\nexport interface ConsentDefaults {\n  analytics?: boolean                  /* Consent for Analytics */\n  github?: boolean                     /* Consent for GitHub */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n  target$: Observable<HTMLElement>     /* Target observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  target$: Observable<HTMLElement>     /* Target observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch consent\n *\n * @param el - Consent element\n * @param options - Options\n *\n * @returns Consent observable\n */\nexport function watchConsent(\n  el: HTMLElement, { target$ }: WatchOptions\n): Observable<Consent> {\n  return target$\n    .pipe(\n      map(target => ({ hidden: target !== el }))\n    )\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Mount consent\n *\n * @param el - Consent element\n * @param options - Options\n *\n * @returns Consent component observable\n */\nexport function mountConsent(\n  el: HTMLElement, options: MountOptions\n): Observable<Component<Consent>> {\n  const internal$ = new Subject<Consent>()\n  internal$.subscribe(({ hidden }) => {\n    el.hidden = hidden\n  })\n\n  /* Create and return component */\n  return watchConsent(el, options)\n    .pipe(\n      tap(state => internal$.next(state)),\n      finalize(() => internal$.complete()),\n      map(state => ({ ref: el, ...state }))\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { ComponentChild } from \"preact\"\n\nimport { h } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Tooltip style\n */\nexport type TooltipStyle =\n  | \"inline\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Render a tooltip\n *\n * @param id - Tooltip identifier\n * @param style - Tooltip style\n *\n * @returns Element\n */\nexport function renderTooltip(\n  id?: string, style?: TooltipStyle\n): HTMLElement {\n  if (style === \"inline\") { // @todo refactor control flow\n    return (\n      <div class=\"md-tooltip md-tooltip--inline\" id={id} role=\"tooltip\">\n        <div class=\"md-tooltip__inner md-typeset\"></div>\n      </div>\n    )\n  } else {\n    return (\n      <div class=\"md-tooltip\" id={id} role=\"tooltip\">\n        <div class=\"md-tooltip__inner md-typeset\"></div>\n      </div>\n    )\n  }\n}\n\n/**\n * Render a tooltip\n *\n * @param children - Child nodes\n *\n * @returns Element\n */\nexport function renderTooltip2(\n  ...children: ComponentChild[]\n): HTMLElement {\n  return (\n    <div class=\"md-tooltip2\" role=\"dialog\">\n      <div class=\"md-tooltip2__inner md-typeset\">\n        {children}\n      </div>\n    </div>\n  )\n}\n\n// @todo: rename\nexport function renderInlineTooltip2(\n  ...children: ComponentChild[]\n): HTMLElement {\n  return (\n    <div class=\"md-tooltip2\" role=\"tooltip\">\n      <div class=\"md-tooltip2__inner md-typeset\">\n        {children}\n      </div>\n    </div>\n  )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { h } from \"~/utilities\"\n\nimport { renderTooltip } from \"../tooltip\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Render an annotation\n *\n * @param id - Annotation identifier\n * @param prefix - Tooltip identifier prefix\n *\n * @returns Element\n */\nexport function renderAnnotation(\n  id: string | number, prefix?: string\n): HTMLElement {\n  prefix = prefix ? `${prefix}_annotation_${id}` : undefined\n\n  /* Render tooltip with anchor, if given */\n  if (prefix) {\n    const anchor = prefix ? `#${prefix}` : undefined\n    return (\n      <aside class=\"md-annotation\" tabIndex={0}>\n        {renderTooltip(prefix)}\n        <a href={anchor} class=\"md-annotation__index\" tabIndex={-1}>\n          <span data-md-annotation-id={id}></span>\n        </a>\n      </aside>\n    )\n  } else {\n    return (\n      <aside class=\"md-annotation\" tabIndex={0}>\n        {renderTooltip(prefix)}\n        <span class=\"md-annotation__index\" tabIndex={-1}>\n          <span data-md-annotation-id={id}></span>\n        </span>\n      </aside>\n    )\n  }\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { translation } from \"~/_\"\nimport { h } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Render a 'copy-to-clipboard' button\n *\n * @param id - Unique identifier\n *\n * @returns Element\n */\nexport function renderClipboardButton(id: string): HTMLElement {\n  return (\n    <button\n      class=\"md-code__button\"\n      title={translation(\"clipboard.copy\")}\n      data-clipboard-target={`#${id} > code`}\n      data-md-type=\"copy\"\n    ></button>\n  )\n}\n\nexport function renderSelectionButton(): HTMLElement {\n  return (\n    <button\n      class=\"md-code__button\"\n      title=\"Toggle line selection\"\n      data-md-type=\"select\"\n    ></button>\n  )\n}\n\nexport function renderCodeBlockNavigation() {\n  return (\n    <nav class=\"md-code__nav\"></nav>\n  )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport escapeHTML from \"escape-html\"\nimport { ComponentChild } from \"preact\"\n\nimport { configuration, feature, translation } from \"~/_\"\nimport { SearchItem } from \"~/integrations/search\"\nimport { h } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Render flag\n */\nconst enum Flag {\n  TEASER = 1,                          /* Render teaser */\n  PARENT = 2                           /* Render as parent */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper function\n * ------------------------------------------------------------------------- */\n\n/**\n * Render a search document\n *\n * @param document - Search document\n * @param flag - Render flags\n *\n * @returns Element\n */\nfunction renderSearchDocument(\n  document: SearchItem, flag: Flag\n): HTMLElement {\n  const parent = flag & Flag.PARENT\n  const teaser = flag & Flag.TEASER\n\n  /* Render missing query terms */\n  const missing = Object.keys(document.terms)\n    .filter(key => !document.terms[key])\n    .reduce<ComponentChild[]>((list, key) => [\n      ...list, <del>{escapeHTML(key)}</del>, \" \"\n    ], [])\n    .slice(0, -1)\n\n  /* Assemble query string for highlighting */\n  const config = configuration()\n  const url = new URL(document.location, config.base)\n  if (feature(\"search.highlight\"))\n    url.searchParams.set(\"h\", Object.entries(document.terms)\n      .filter(([, match]) => match)\n      .reduce((highlight, [value]) => `${highlight} ${value}`.trim(), \"\")\n    )\n\n  /* Render article or section, depending on flags */\n  const { tags } = configuration()\n  return (\n    <a href={`${url}`} class=\"md-search-result__link\" tabIndex={-1}>\n      <article\n        class=\"md-search-result__article md-typeset\"\n        data-md-score={document.score.toFixed(2)}\n      >\n        {parent > 0 && <div class=\"md-search-result__icon md-icon\"></div>}\n        {parent > 0 && <h1>{document.title}</h1>}\n        {parent <= 0 && <h2>{document.title}</h2>}\n        {teaser > 0 && document.text.length > 0 &&\n          document.text\n        }\n        {document.tags && (\n          <nav class=\"md-tags\">\n            {document.tags.map(tag => {\n              const type = tags\n                ? tag in tags\n                  ? `md-tag-icon md-tag--${tags[tag]}`\n                  : \"md-tag-icon\"\n                : \"\"\n              return (\n                <span class={`md-tag ${type}`}>{tag}</span>\n              )\n            })}\n          </nav>\n        )}\n        {teaser > 0 && missing.length > 0 &&\n          <p class=\"md-search-result__terms\">\n            {translation(\"search.result.term.missing\")}: {...missing}\n          </p>\n        }\n      </article>\n    </a>\n  )\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Render a search result\n *\n * @param result - Search result\n *\n * @returns Element\n */\nexport function renderSearchResultItem(\n  result: SearchItem[]\n): HTMLElement {\n  const threshold = result[0].score\n  const docs = [...result]\n\n  const config = configuration()\n\n  /* Find and extract parent article */\n  const parent = docs.findIndex(doc => {\n    const l = `${new URL(doc.location, config.base)}` // @todo hacky\n    return !l.includes(\"#\")\n  })\n  const [article] = docs.splice(parent, 1)\n\n  /* Determine last index above threshold */\n  let index = docs.findIndex(doc => doc.score < threshold)\n  if (index === -1)\n    index = docs.length\n\n  /* Partition sections */\n  const best = docs.slice(0, index)\n  const more = docs.slice(index)\n\n  /* Render children */\n  const children = [\n    renderSearchDocument(article, Flag.PARENT | +(!parent && index === 0)),\n    ...best.map(section => renderSearchDocument(section, Flag.TEASER)),\n    ...more.length ? [\n      <details class=\"md-search-result__more\">\n        <summary tabIndex={-1}>\n          <div>\n            {more.length > 0 && more.length === 1\n              ? translation(\"search.result.more.one\")\n              : translation(\"search.result.more.other\", more.length)\n            }\n          </div>\n        </summary>\n        {...more.map(section => renderSearchDocument(section, Flag.TEASER))}\n      </details>\n    ] : []\n  ]\n\n  /* Render search result */\n  return (\n    <li class=\"md-search-result__item\">\n      {children}\n    </li>\n  )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { SourceFacts } from \"~/components\"\nimport { h, round } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Render repository facts\n *\n * @param facts - Repository facts\n *\n * @returns Element\n */\nexport function renderSourceFacts(facts: SourceFacts): HTMLElement {\n  return (\n    <ul class=\"md-source__facts\">\n      {Object.entries(facts).map(([key, value]) => (\n        <li class={`md-source__fact md-source__fact--${key}`}>\n          {typeof value === \"number\" ? round(value) : value}\n        </li>\n      ))}\n    </ul>\n  )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { h } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Tabbed control type\n */\ntype TabbedControlType =\n  | \"prev\"\n  | \"next\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Render control for content tabs\n *\n * @param type - Control type\n *\n * @returns Element\n */\nexport function renderTabbedControl(\n  type: TabbedControlType\n): HTMLElement {\n  const classes = `tabbed-control tabbed-control--${type}`\n  return (\n    <div class={classes} hidden>\n      <button class=\"tabbed-button\" tabIndex={-1} aria-hidden=\"true\"></button>\n    </div>\n  )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { h } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Render a table inside a wrapper to improve scrolling on mobile\n *\n * @param table - Table element\n *\n * @returns Element\n */\nexport function renderTable(table: HTMLElement): HTMLElement {\n  return (\n    <div class=\"md-typeset__scrollwrap\">\n      <div class=\"md-typeset__table\">\n        {table}\n      </div>\n    </div>\n  )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { configuration, translation } from \"~/_\"\nimport { h } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Version properties\n */\nexport interface VersionProperties {\n  hidden?: boolean                     /* Version is hidden */\n}\n\n/**\n * Version\n */\nexport interface Version {\n  version: string                      /* Version identifier */\n  title: string                        /* Version title */\n  aliases: string[]                    /* Version aliases */\n  properties?: VersionProperties       /* Version properties */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Render a version\n *\n * @param version - Version\n *\n * @returns Element\n */\nfunction renderVersion(version: Version): HTMLElement {\n  const config = configuration()\n\n  /* Ensure trailing slash - see https://bit.ly/3rL5u3f */\n  const url = new URL(`../${version.version}/`, config.base)\n  return (\n    <li class=\"md-version__item\">\n      <a href={`${url}`} class=\"md-version__link\">\n        {version.title}\n        {config.version?.alias && version.aliases.length > 0 && (\n          <span class=\"md-version__alias\">\n            {version.aliases[0]}\n          </span>\n        )}\n      </a>\n    </li>\n  )\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Render a version selector\n *\n * @param versions - Versions\n * @param active - Active version\n *\n * @returns Element\n */\nexport function renderVersionSelector(\n  versions: Version[], active: Version\n): HTMLElement {\n  const config = configuration()\n  versions = versions.filter(version => !version.properties?.hidden)\n  return (\n    <div class=\"md-version\">\n      <button\n        class=\"md-version__current\"\n        aria-label={translation(\"select.version\")}\n      >\n        {active.title}\n        {config.version?.alias && active.aliases.length > 0 && (\n          <span class=\"md-version__alias\">\n            {active.aliases[0]}\n          </span>\n        )}\n      </button>\n      <ul class=\"md-version__list\">\n        {versions.map(renderVersion)}\n      </ul>\n    </div>\n  )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  BehaviorSubject,\n  EMPTY,\n  Observable,\n  Subject,\n  animationFrameScheduler,\n  combineLatest,\n  combineLatestWith,\n  debounce,\n  defer,\n  distinctUntilChanged,\n  endWith,\n  filter,\n  finalize,\n  first,\n  ignoreElements,\n  map,\n  mergeMap,\n  observeOn,\n  queueScheduler,\n  share,\n  startWith,\n  switchMap,\n  tap,\n  throttleTime,\n  timer,\n  withLatestFrom\n} from \"rxjs\"\n\nimport {\n  ElementOffset,\n  Viewport,\n  getElement,\n  getElementContainers,\n  getElementOffsetAbsolute,\n  getElementSize,\n  watchElementContentOffset,\n  watchElementFocus,\n  watchElementHover\n} from \"~/browser\"\nimport { renderInlineTooltip2 } from \"~/templates\"\n\nimport { Component } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Tooltip\n */\nexport interface Tooltip {\n  active: boolean                      // Tooltip is active\n  offset: ElementOffset                // Tooltip offset\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Dependencies\n */\ninterface Dependencies {\n  content$: Observable<HTMLElement>    // Tooltip content observable\n  viewport$: Observable<Viewport>      // Viewport observable\n}\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Global sequence number for tooltips\n */\nlet sequence = 0\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch tooltip\n *\n * This function tracks the tooltip host element, and deduces the active state\n * and offset of the tooltip from it. The active state is determined by whether\n * the host element is focused or hovered, and the offset is determined by the\n * host element's absolute position in the document.\n *\n * @param el - Tooltip host element\n * @param timeout - Timeout\n *\n * @returns Tooltip observable\n */\nexport function watchTooltip2(\n  el: HTMLElement, timeout = 250\n): Observable<Tooltip> {\n\n  // Compute whether tooltip should be shown - we need to watch both focus and\n  // hover events on the host element and emit if one of them is active. In case\n  // of a hover event, we keep the element visible for a short amount of time\n  // after the pointer left the host element for a better user experience.\n  const active$ =\n    combineLatest([\n      watchElementFocus(el),\n      watchElementHover(el, timeout)\n    ])\n      .pipe(\n        map(([focus, hover]) => focus || hover),\n        distinctUntilChanged()\n      )\n\n  // We need to determine all parent elements of the host element that are\n  // currently scrollable, as they might affect the position of the tooltip\n  // depending on their horizontal of vertical offset. We must track all of\n  // them and recompute the position of the tooltip if they change.\n  const offset$ =\n    defer(() => getElementContainers(el)).pipe(\n      mergeMap(watchElementContentOffset),\n      throttleTime(1),\n      // Note that we need to poll the value again if the active state changes,\n      // as otherwise the tooltip might be misplaced. This particularly happens\n      // when using third-party integrations like tablesort that change the\n      // position of elements \u2013 see https://t.ly/Y-V7X\n      combineLatestWith(active$),\n      map(() => getElementOffsetAbsolute(el)),\n    )\n\n  // Only track parent elements and compute offset of the tooltip host if the\n  // tooltip should be shown - we defer the computation of the offset until the\n  // tooltip becomes active for the first time. This is necessary, because we\n  // must also keep the tooltip active as long as it is focused or hovered.\n  return active$.pipe(\n    first(active => active),\n    switchMap(() => combineLatest([active$, offset$])),\n    map(([active, offset]) => ({ active, offset })),\n    share()\n  )\n}\n\n/**\n * Mount tooltip\n *\n * This function renders a tooltip with the content from the provided `content$`\n * observable as passed via the dependencies. If the returned element has a role\n * of type `dialog`, the tooltip is considered to be interactive, and rendered\n * either above or below the host element, depending on the available space.\n *\n * If the returned element has a role of type `tooltip`, the tooltip is always\n * rendered below the host element and considered to be non-interactive. This\n * allows us to reuse the same positioning logic for both interactive and\n * non-interactive tooltips, as it is largely the same.\n *\n * @param el - Tooltip host element\n * @param dependencies - Dependencies\n * @param timeout - Timeout @todo move into options\n *\n * @returns Tooltip component observable\n */\nexport function mountTooltip2(\n  el: HTMLElement, dependencies: Dependencies, timeout = 250\n): Observable<Component<Tooltip>> {\n  const { content$, viewport$ } = dependencies\n\n  // Compute unique tooltip id - this is necessary to associate the tooltip host\n  // element with the tooltip element for ARIA purposes\n  const id = `__tooltip2_${sequence++}`\n\n  // Create component on subscription\n  return defer(() => {\n    const push$ = new Subject<Tooltip>()\n\n    // Create subject to track tooltip presence and visibility - we use another\n    // purely internal subject to track the tooltip's presence and visibility,\n    // as the tooltip should be visible if the host element or tooltip itself\n    // is focused or hovered to allow for smooth pointer migration\n    const show$ = new BehaviorSubject(false)\n    push$.pipe(ignoreElements(), endWith(false))\n      .subscribe(show$)\n\n    // Create observable controlling tooltip element - we create and attach the\n    // tooltip only if it is actually present, in order to keep the number of\n    // elements low. We need to keep the tooltip visible for a short time after\n    // the pointer left the host element or tooltip itself. For this, we use an\n    // inner subscription to the tooltip observable, which we terminate when the\n    // tooltip should not be shown, automatically removing the element. Moreover\n    // we use the queue scheduler, which will schedule synchronously in case the\n    // tooltip should be shown, and asynchronously if it should be hidden.\n    const node$ = show$.pipe(\n      debounce(active => timer(+!active * 250, queueScheduler)),\n      distinctUntilChanged(),\n      switchMap(active => active ? content$ : EMPTY),\n      tap(node => node.id = id),\n      share()\n    )\n\n    // Compute tooltip presence and visibility - the tooltip should be shown if\n    // the host element or the tooltip itself is focused or hovered\n    combineLatest([\n      push$.pipe(map(({ active }) => active)),\n      node$.pipe(\n        switchMap(node => watchElementHover(node, 250)),\n        startWith(false)\n      )\n    ])\n      .pipe(map(states => states.some(active => active)))\n      .subscribe(show$)\n\n    // Compute tooltip origin - we need to compute the tooltip origin depending\n    // on the position of the host element, the viewport size, as well as the\n    // actual size of the tooltip, if positioned above. The tooltip must about\n    // to be rendered for this to be correct, which is why we do it here.\n    const origin$ = show$.pipe(\n      filter(active => active),\n      withLatestFrom(node$, viewport$),\n      map(([_, node, { size }]) => {\n        const host = el.getBoundingClientRect()\n        const x = host.width / 2\n\n        // If the tooltip is non-interactive, we always render it below the\n        // actual element because all operating systems do it that way\n        if (node.role === \"tooltip\") {\n          return { x, y: 8 + host.height }\n\n        // Otherwise, we determine where there is more space, and render the\n        // tooltip either above or below the host element\n        } else if (host.y >= size.height / 2) {\n          const { height } = getElementSize(node)\n          return { x, y: -16 - height }\n        } else {\n          return { x, y: +16 + host.height }\n        }\n      })\n    )\n\n    // Update tooltip position - we always need to update the position of the\n    // tooltip, as it might change depending on the viewport offset of the host\n    combineLatest([node$, push$, origin$])\n      .subscribe(([node, { offset }, origin]) => {\n        node.style.setProperty(\"--md-tooltip-host-x\", `${offset.x}px`)\n        node.style.setProperty(\"--md-tooltip-host-y\", `${offset.y}px`)\n\n        // Update tooltip origin - this is mainly set to determine the position\n        // of the tooltip tail, to show the direction it is originating from\n        node.style.setProperty(\"--md-tooltip-x\", `${origin.x}px`)\n        node.style.setProperty(\"--md-tooltip-y\", `${origin.y}px`)\n\n        // Update tooltip render location, i.e., whether the tooltip is shown\n        // above or below the host element, depending on the available space\n        node.classList.toggle(\"md-tooltip2--top\",    origin.y <  0)\n        node.classList.toggle(\"md-tooltip2--bottom\", origin.y >= 0)\n      })\n\n    // Update tooltip width - we only explicitly set the width of the tooltip\n    // if it is non-interactive, in case it should always be rendered centered\n    show$.pipe(\n      filter(active => active),\n      withLatestFrom(node$, (_, node) => node),\n      filter(node => node.role === \"tooltip\")\n    )\n      .subscribe(node => {\n        const size = getElementSize(getElement(\":scope > *\", node))\n\n        // Set tooltip width and remove tail by setting it to a width of zero -\n        // if authors want to keep the tail, we can move this to CSS later\n        node.style.setProperty(\"--md-tooltip-width\", `${size.width}px`)\n        node.style.setProperty(\"--md-tooltip-tail\",  `${0}px`)\n      })\n\n    // Update tooltip visibility - we defer to the next animation frame, because\n    // the tooltip must first be added to the document before we make it appear,\n    // or it will appear instantly without delay. Additionally, we need to keep\n    // the tooltip visible for a short time after the pointer left the host.\n    show$.pipe(\n      distinctUntilChanged(),\n      observeOn(animationFrameScheduler),\n      withLatestFrom(node$)\n    )\n      .subscribe(([active, node]) => {\n        node.classList.toggle(\"md-tooltip2--active\", active)\n      })\n\n    // Set up ARIA attributes when tooltip is visible\n    combineLatest([\n      show$.pipe(filter(active => active)),\n      node$\n    ])\n      .subscribe(([_, node]) => {\n        if (node.role === \"dialog\") {\n          el.setAttribute(\"aria-controls\", id)\n          el.setAttribute(\"aria-haspopup\", \"dialog\")\n        } else {\n          el.setAttribute(\"aria-describedby\", id)\n        }\n      })\n\n    // Remove ARIA attributes when tooltip is hidden\n    show$.pipe(filter(active => !active))\n      .subscribe(() => {\n        el.removeAttribute(\"aria-controls\")\n        el.removeAttribute(\"aria-describedby\")\n        el.removeAttribute(\"aria-haspopup\")\n      })\n\n    // Create and return component\n    return watchTooltip2(el, timeout)\n      .pipe(\n        tap(state => push$.next(state)),\n        finalize(() => push$.complete()),\n        map(state => ({ ref: el, ...state }))\n      )\n  })\n}\n\n// ----------------------------------------------------------------------------\n\n/**\n * Mount inline tooltip\n *\n * @todo refactor this function\n *\n * @param el - Tooltip host element\n * @param dependencies - Dependencies\n * @param container - Container\n *\n * @returns Tooltip component observable\n */\nexport function mountInlineTooltip2(\n  el: HTMLElement, { viewport$ }: { viewport$: Observable<Viewport> },\n  container = document.body\n): Observable<Component<Tooltip>> {\n  return mountTooltip2(el, {\n    content$: new Observable<HTMLElement>(observer => {\n      const title = el.title\n      const node = renderInlineTooltip2(title)\n      observer.next(node)\n      el.removeAttribute(\"title\")\n      // Append tooltip and remove on unsubscription\n      container.append(node)\n      return () => {\n        node.remove()\n        el.setAttribute(\"title\", title)\n      }\n    }),\n    viewport$\n  }, 0)\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  Subject,\n  animationFrameScheduler,\n  auditTime,\n  combineLatest,\n  debounceTime,\n  defer,\n  delay,\n  endWith,\n  filter,\n  finalize,\n  fromEvent,\n  ignoreElements,\n  map,\n  merge,\n  switchMap,\n  take,\n  takeUntil,\n  tap,\n  throttleTime,\n  withLatestFrom\n} from \"rxjs\"\n\nimport {\n  ElementOffset,\n  getActiveElement,\n  getElementSize,\n  watchElementContentOffset,\n  watchElementFocus,\n  watchElementOffset,\n  watchElementVisibility\n} from \"~/browser\"\n\nimport { Component } from \"../../../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Annotation\n */\nexport interface Annotation {\n  active: boolean                      /* Annotation is active */\n  offset: ElementOffset                /* Annotation offset */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  target$: Observable<HTMLElement>     /* Location target observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch annotation\n *\n * @param el - Annotation element\n * @param container - Containing element\n *\n * @returns Annotation observable\n */\nexport function watchAnnotation(\n  el: HTMLElement, container: HTMLElement\n): Observable<Annotation> {\n  const offset$ = defer(() => combineLatest([\n    watchElementOffset(el),\n    watchElementContentOffset(container)\n  ]))\n    .pipe(\n      map(([{ x, y }, scroll]): ElementOffset => {\n        const { width, height } = getElementSize(el)\n        return ({\n          x: x - scroll.x + width  / 2,\n          y: y - scroll.y + height / 2\n        })\n      })\n    )\n\n  /* Actively watch annotation on focus */\n  return watchElementFocus(el)\n    .pipe(\n      switchMap(active => offset$\n        .pipe(\n          map(offset => ({ active, offset })),\n          take(+!active || Infinity)\n        )\n      )\n    )\n}\n\n/**\n * Mount annotation\n *\n * @param el - Annotation element\n * @param container - Containing element\n * @param options - Options\n *\n * @returns Annotation component observable\n */\nexport function mountAnnotation(\n  el: HTMLElement, container: HTMLElement, { target$ }: MountOptions\n): Observable<Component<Annotation>> {\n  const [tooltip, index] = Array.from(el.children)\n\n  /* Mount component on subscription */\n  return defer(() => {\n    const push$ = new Subject<Annotation>()\n    const done$ = push$.pipe(ignoreElements(), endWith(true))\n    push$.subscribe({\n\n      /* Handle emission */\n      next({ offset }) {\n        el.style.setProperty(\"--md-tooltip-x\", `${offset.x}px`)\n        el.style.setProperty(\"--md-tooltip-y\", `${offset.y}px`)\n      },\n\n      /* Handle complete */\n      complete() {\n        el.style.removeProperty(\"--md-tooltip-x\")\n        el.style.removeProperty(\"--md-tooltip-y\")\n      }\n    })\n\n    /* Start animation only when annotation is visible */\n    watchElementVisibility(el)\n      .pipe(\n        takeUntil(done$)\n      )\n        .subscribe(visible => {\n          el.toggleAttribute(\"data-md-visible\", visible)\n        })\n\n    /* Toggle tooltip presence to mitigate empty lines when copying */\n    merge(\n      push$.pipe(filter(({ active }) => active)),\n      push$.pipe(debounceTime(250), filter(({ active }) => !active))\n    )\n      .subscribe({\n\n        /* Handle emission */\n        next({ active }) {\n          if (active)\n            el.prepend(tooltip)\n          else\n            tooltip.remove()\n        },\n\n        /* Handle complete */\n        complete() {\n          el.prepend(tooltip)\n        }\n      })\n\n    /* Toggle tooltip visibility */\n    push$\n      .pipe(\n        auditTime(16, animationFrameScheduler)\n      )\n        .subscribe(({ active }) => {\n          tooltip.classList.toggle(\"md-tooltip--active\", active)\n        })\n\n    /* Track relative origin of tooltip */\n    push$\n      .pipe(\n        throttleTime(125, animationFrameScheduler),\n        filter(() => !!el.offsetParent),\n        map(() => el.offsetParent!.getBoundingClientRect()),\n        map(({ x }) => x)\n      )\n        .subscribe({\n\n          /* Handle emission */\n          next(origin) {\n            if (origin)\n              el.style.setProperty(\"--md-tooltip-0\", `${-origin}px`)\n            else\n              el.style.removeProperty(\"--md-tooltip-0\")\n          },\n\n          /* Handle complete */\n          complete() {\n            el.style.removeProperty(\"--md-tooltip-0\")\n          }\n        })\n\n    /* Allow to copy link without scrolling to anchor */\n    fromEvent<MouseEvent>(index, \"click\")\n      .pipe(\n        takeUntil(done$),\n        filter(ev => !(ev.metaKey || ev.ctrlKey))\n      )\n        .subscribe(ev => {\n          ev.stopPropagation()\n          ev.preventDefault()\n        })\n\n    /* Allow to open link in new tab or blur on close */\n    fromEvent<MouseEvent>(index, \"mousedown\")\n      .pipe(\n        takeUntil(done$),\n        withLatestFrom(push$)\n      )\n        .subscribe(([ev, { active }]) => {\n\n          /* Open in new tab */\n          if (ev.button !== 0 || ev.metaKey || ev.ctrlKey) {\n            ev.preventDefault()\n\n          /* Close annotation */\n          } else if (active) {\n            ev.preventDefault()\n\n            /* Focus parent annotation, if any */\n            const parent = el.parentElement!.closest(\".md-annotation\")\n            if (parent instanceof HTMLElement)\n              parent.focus()\n            else\n              getActiveElement()?.blur()\n          }\n        })\n\n    /* Open and focus annotation on location target */\n    target$\n      .pipe(\n        takeUntil(done$),\n        filter(target => target === tooltip),\n        delay(125)\n      )\n        .subscribe(() => el.focus())\n\n    /* Create and return component */\n    return watchAnnotation(el, container)\n      .pipe(\n        tap(state => push$.next(state)),\n        finalize(() => push$.complete()),\n        map(state => ({ ref: el, ...state }))\n      )\n  })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  EMPTY,\n  Observable,\n  Subject,\n  defer,\n  endWith,\n  finalize,\n  ignoreElements,\n  merge,\n  share,\n  takeUntil\n} from \"rxjs\"\n\nimport { configuration } from \"~/_\"\nimport {\n  getElement,\n  getElements,\n  getOptionalElement\n} from \"~/browser\"\nimport { renderAnnotation } from \"~/templates\"\n\nimport { Component } from \"../../../_\"\nimport {\n  Annotation,\n  mountAnnotation\n} from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  target$: Observable<HTMLElement>     /* Location target observable */\n  print$: Observable<boolean>          /* Media print observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Find all annotation hosts in the containing element\n *\n * @param container - Containing element\n *\n * @returns Annotation hosts\n */\nfunction findHosts(container: HTMLElement): HTMLElement[] {\n  const config = configuration()\n  if (container.tagName !== \"CODE\")\n    return [container]\n\n  /* Try to determine language of code block */\n  const selectors = [\".c\", \".c1\", \".cm\"]\n  if (config.annotate && typeof config.annotate === \"object\") {\n    const host = container.closest(\"[class|=language]\")\n    if (host) {\n\n      /* Extract language from class name */\n      for (const value of Array.from(host.classList)) {\n        if (!value.startsWith(\"language-\"))\n          continue\n\n        /* Obtain additional mappings, if any */\n        const [, language] = value.split(\"-\")\n        if (language in config.annotate)\n          selectors.push(...config.annotate[language])\n      }\n    }\n  }\n\n  /* Retrieve and return annotation hosts */\n  return getElements(selectors.join(\", \"), container)\n}\n\n/**\n * Find all annotation markers in the containing element\n *\n * @param container - Containing element\n *\n * @returns Annotation markers\n */\nfunction findMarkers(container: HTMLElement): Text[] {\n  const markers: Text[] = []\n  for (const el of findHosts(container)) {\n    const nodes: Text[] = []\n\n    /* Find all text nodes in current element */\n    const it = document.createNodeIterator(el, NodeFilter.SHOW_TEXT)\n    for (let node = it.nextNode(); node; node = it.nextNode())\n      nodes.push(node as Text)\n\n    /* Find all markers in each text node */\n    for (let text of nodes) {\n      let match: RegExpExecArray | null\n\n      /* Split text at marker and add to list */\n      while ((match = /(\\(\\d+\\))(!)?/.exec(text.textContent!))) {\n        const [, id, force] = match\n        if (typeof force === \"undefined\") {\n          const marker = text.splitText(match.index)\n          text = marker.splitText(id.length)\n          markers.push(marker)\n\n        /* Replace entire text with marker */\n        } else {\n          text.textContent = id\n          markers.push(text)\n          break\n        }\n      }\n    }\n  }\n  return markers\n}\n\n/**\n * Swap the child nodes of two elements\n *\n * @param source - Source element\n * @param target - Target element\n */\nfunction swap(source: HTMLElement, target: HTMLElement): void {\n  target.append(...Array.from(source.childNodes))\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount annotation list\n *\n * This function analyzes the containing code block and checks for markers\n * referring to elements in the given annotation list. If no markers are found,\n * the list is left untouched. Otherwise, list elements are rendered as\n * annotations inside the code block.\n *\n * @param el - Annotation list element\n * @param container - Containing element\n * @param options - Options\n *\n * @returns Annotation component observable\n */\nexport function mountAnnotationList(\n  el: HTMLElement, container: HTMLElement, { target$, print$ }: MountOptions\n): Observable<Component<Annotation>> {\n\n  /* Compute prefix for tooltip anchors */\n  const parent = container.closest(\"[id]\")\n  const prefix = parent?.id\n\n  /* Find and replace all markers with empty annotations */\n  const annotations = new Map<string, HTMLElement>()\n  for (const marker of findMarkers(container)) {\n    const [, id] = marker.textContent!.match(/\\((\\d+)\\)/)!\n    if (getOptionalElement(`:scope > li:nth-child(${id})`, el)) {\n      annotations.set(id, renderAnnotation(id, prefix))\n      marker.replaceWith(annotations.get(id)!)\n    }\n  }\n\n  /* Keep list if there are no annotations to render */\n  if (annotations.size === 0)\n    return EMPTY\n\n  /* Mount component on subscription */\n  return defer(() => {\n    const push$ = new Subject()\n    const done$ = push$.pipe(ignoreElements(), endWith(true))\n\n    /* Retrieve container pairs for swapping */\n    const pairs: [HTMLElement, HTMLElement][] = []\n    for (const [id, annotation] of annotations)\n      pairs.push([\n        getElement(\".md-typeset\", annotation),\n        getElement(`:scope > li:nth-child(${id})`, el)\n      ])\n\n    /* Handle print mode - see https://bit.ly/3rgPdpt */\n    print$.pipe(takeUntil(done$))\n      .subscribe(active => {\n        el.hidden = !active\n\n        /* Add class to discern list element */\n        el.classList.toggle(\"md-annotation-list\", active)\n\n        /* Show annotations in code block or list (print) */\n        for (const [inner, child] of pairs)\n          if (!active)\n            swap(child, inner)\n          else\n            swap(inner, child)\n      })\n\n    /* Create and return component */\n    return merge(...[...annotations]\n      .map(([, annotation]) => (\n        mountAnnotation(annotation, container, { target$ })\n      ))\n    )\n      .pipe(\n        finalize(() => push$.complete()),\n        share()\n      )\n  })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { EMPTY, Observable, defer } from \"rxjs\"\n\nimport { Component } from \"../../../_\"\nimport { Annotation } from \"../_\"\nimport { mountAnnotationList } from \"../list\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  target$: Observable<HTMLElement>     /* Location target observable */\n  print$: Observable<boolean>          /* Media print observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Find list element directly following a block\n *\n * @param el - Annotation block element\n *\n * @returns List element or nothing\n */\nfunction findList(el: HTMLElement): HTMLElement | undefined {\n  if (el.nextElementSibling) {\n    const sibling = el.nextElementSibling as HTMLElement\n    if (sibling.tagName === \"OL\")\n      return sibling\n\n    /* Skip empty paragraphs - see https://bit.ly/3r4ZJ2O */\n    else if (sibling.tagName === \"P\" && !sibling.children.length)\n      return findList(sibling)\n  }\n\n  /* Everything else */\n  return undefined\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount annotation block\n *\n * @param el - Annotation block element\n * @param options - Options\n *\n * @returns Annotation component observable\n */\nexport function mountAnnotationBlock(\n  el: HTMLElement, options: MountOptions\n): Observable<Component<Annotation>> {\n  return defer(() => {\n    const list = findList(el)\n    return typeof list !== \"undefined\"\n      ? mountAnnotationList(list, el, options)\n      : EMPTY\n  })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport ClipboardJS from \"clipboard\"\nimport {\n  EMPTY,\n  Observable,\n  Subject,\n  asyncScheduler,\n  defer,\n  distinctUntilChanged,\n  distinctUntilKeyChanged,\n  filter,\n  finalize,\n  from,\n  fromEvent,\n  map,\n  merge,\n  mergeMap,\n  mergeWith,\n  observeOn,\n  scan,\n  share,\n  shareReplay,\n  startWith,\n  switchMap,\n  take,\n  takeLast,\n  takeUntil,\n  tap,\n  withLatestFrom\n} from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport {\n  getElement,\n  getElementContentSize,\n  getElements,\n  getOptionalElement,\n  watchElementHover,\n  watchElementSize,\n  watchElementVisibility,\n  watchLocationHash\n} from \"~/browser\"\nimport {\n  Tooltip,\n  mountInlineTooltip2\n} from \"~/components/tooltip2\"\nimport {\n  renderClipboardButton,\n  renderCodeBlockNavigation,\n  renderSelectionButton\n} from \"~/templates\"\n\nimport { Component } from \"../../../_\"\nimport {\n  Annotation,\n  mountAnnotationList\n} from \"../../annotation\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Code block overflow\n */\nexport interface Overflow {\n  scrollable: boolean                  /* Code block overflows */\n}\n\n/**\n * Code block\n */\nexport type CodeBlock =\n  | Overflow\n  | Annotation\n  | Tooltip\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  target$: Observable<HTMLElement>     /* Location target observable */\n  print$: Observable<boolean>          /* Media print observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Global sequence number for code blocks\n */\nlet sequence = 0\n\n/**\n * Shift-key observable - @todo consolidate with keyboard observable\n */\nconst shift$ = merge(\n  fromEvent(window, \"keydown\").pipe(map(() => true)),\n  merge(\n    fromEvent(window, \"keyup\"),\n    fromEvent(window, \"contextmenu\")\n  )\n    .pipe(map(() => false))\n)\n  .pipe(\n    startWith(false),\n    shareReplay(1)\n  )\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Find list element directly following a code block\n *\n * @param el - Code block element\n *\n * @returns List element or nothing\n */\nfunction findList(el: HTMLElement): HTMLElement | undefined {\n  if (el.nextElementSibling) {\n    const sibling = el.nextElementSibling as HTMLElement\n    if (sibling.tagName === \"OL\")\n      return sibling\n\n    /* Skip empty paragraphs - see https://bit.ly/3r4ZJ2O */\n    else if (sibling.tagName === \"P\" && !sibling.children.length)\n      return findList(sibling)\n  }\n\n  /* Everything else */\n  return undefined\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch code block\n *\n * This function monitors size changes of the viewport, as well as switches of\n * content tabs with embedded code blocks, as both may trigger overflow.\n *\n * @param el - Code block element\n *\n * @returns Code block observable\n */\nexport function watchCodeBlock(\n  el: HTMLElement\n): Observable<Overflow> {\n  return watchElementSize(el)\n    .pipe(\n      map(({ width }) => {\n        const content = getElementContentSize(el)\n        return {\n          scrollable: content.width > width\n        }\n      }),\n      distinctUntilKeyChanged(\"scrollable\")\n    )\n}\n\n/**\n * Mount code block\n *\n * This function ensures that an overflowing code block is focusable through\n * keyboard, so it can be scrolled without a mouse to improve on accessibility.\n * Furthermore, if code annotations are enabled, they are mounted if and only\n * if the code block is currently visible, e.g., not in a hidden content tab.\n *\n * Note that code blocks may be mounted eagerly or lazily. If they're mounted\n * lazily (on first visibility), code annotation anchor links will not work,\n * as they are evaluated on initial page load, and code annotations in general\n * might feel a little bumpier.\n *\n * @param el - Code block element\n * @param options - Options\n *\n * @returns Code block and annotation component observable\n */\nexport function mountCodeBlock(\n  el: HTMLElement, options: MountOptions\n): Observable<Component<CodeBlock>> {\n  const { matches: hover } = matchMedia(\"(hover)\")\n\n  /* Defer mounting of code block - see https://bit.ly/3vHVoVD */\n  const factory$ = defer(() => {\n    const push$ = new Subject<Overflow>()\n    const done$ = push$.pipe(takeLast(1))\n    push$.subscribe(({ scrollable }) => {\n      if (scrollable && hover)\n        el.setAttribute(\"tabindex\", \"0\")\n      else\n        el.removeAttribute(\"tabindex\")\n    })\n\n    // Code block sequence number\n    const buttons: HTMLElement[] = []\n    const parent = el.closest(\"pre\")!\n\n    // Check if there's a parent element with an id, and use that id, otherwise\n    // generate a new one. This is necessary to allow for authors to define\n    // unique ids for code blocks - see https://t.ly/q7UEq\n    const unique = parent.closest(\"[id]\")\n    const id = unique ? unique.id : sequence++\n    parent.id = `__code_${id}`\n\n    /* Handle code annotations and highlights */\n    const content$: Array<Observable<Component<CodeBlock>>> = []\n    const container = el.closest(\".highlight\")\n    if (container instanceof HTMLElement) {\n      const list = findList(container)\n\n      /* Mount code annotations, if enabled */\n      if (typeof list !== \"undefined\" && (\n        container.classList.contains(\"annotate\") ||\n        feature(\"content.code.annotate\")\n      )) {\n        const annotations$ = mountAnnotationList(list, el, options)\n        content$.push(\n          watchElementSize(container)\n            .pipe(\n              takeUntil(done$),\n              map(({ width, height }) => width && height),\n              distinctUntilChanged(),\n              switchMap(active => active ? annotations$ : EMPTY)\n            )\n        )\n      }\n    }\n\n    // @todo: refactor and move into separate component\n\n    /* Check if code block has line spans */\n    const spans = getElements(\":scope > span[id]\", el)\n    if (spans.length) {\n      el.classList.add(\"md-code__content\")\n\n      /* Mount code selection */\n      if (el.closest(\".select\") || (\n        feature(\"content.code.select\") && !el.closest(\".no-select\")\n      )) {\n        const base = +spans[0].id.split(\"-\").pop()!\n\n        /* Mount tooltip, if enabled */\n        const button = renderSelectionButton()\n        buttons.push(button)\n        if (feature(\"content.tooltips\"))\n          content$.push(mountInlineTooltip2(button, { viewport$ }))\n\n        /* Selection state */\n        const select$ = fromEvent(button, \"click\")\n          .pipe(\n            scan(active => !active, false),\n            tap(() => button.blur()),\n            share()\n          )\n\n        /* Toggle active selection state on button */\n        select$.subscribe(active => {\n          button.classList.toggle(\"md-code__button--active\", active)\n        })\n\n        /* Observable that monitors hovering */\n        const hover$ = from(spans)\n          .pipe(\n            mergeMap(span => watchElementHover(span)\n              .pipe(\n                map(active => [span, active] as const)\n              )\n            )\n          )\n\n        /* Trigger hover selection state based on state */\n        select$\n          .pipe(\n            switchMap(active => active ? hover$ : EMPTY)\n          )\n            .subscribe(([span, active]) => {\n              // @todo: don't mutate, but wrap everything in selection elements\n              const highlight = getOptionalElement(\".hll.select\", span)\n              if (highlight && !active) {\n                highlight.replaceWith(...Array.from(highlight.childNodes))\n              } else if (!highlight && active) {\n                const hll = document.createElement(\"span\")\n                hll.className = \"hll select\"\n                hll.append(...Array.from(span.childNodes).slice(1))\n                span.append(hll)\n              }\n            })\n\n        // @todo: use a single event handler and consolidate events\n        const click$ = from(spans)\n          .pipe(\n            mergeMap(span => fromEvent(span, \"mousedown\")\n              .pipe(\n                tap(ev => ev.preventDefault()),\n                map(() => span)\n              )\n            )\n          )\n\n        const range$ = select$\n          .pipe(\n            switchMap(active => active ? click$ : EMPTY),\n            withLatestFrom(shift$),\n            map(([span, shift]) => {\n\n              /* Determine focused line number */\n              const active = spans.indexOf(span) + base\n              if (shift === false) {\n                return [active, active] as const\n\n                /* Shift is pressed, so extend selection */\n              } else {\n                const range = getElements(\".hll\", el)\n                  .map(line => spans.indexOf(line.parentElement!) + base)\n\n                // Hack: this is a side effect, but we need to remove all ranges\n                // or rendering might look weird.\n                window.getSelection()?.removeAllRanges()\n\n                /* Return range */\n                return [\n                  Math.min(active, ...range),\n                  Math.max(active, ...range)\n                ] as const\n              }\n            })\n          )\n\n        // Currently, all mounted code blocks will receive this event. That#s\n        // not ideal, since we should handle this higher up the tree\n        const hash$ = watchLocationHash(EMPTY)\n          .pipe(\n            // @todo: make more resilient\n            filter(hash => hash.startsWith(`__codelineno-${id}-`))\n          )\n\n        hash$.subscribe(hash => {\n          const [, , line] = hash.split(\"-\")\n          const range = line.split(\":\").map(value => +value - base + 1)\n          if (range.length === 1)\n            range.push(range[0])\n\n          // remove all existing, then set range...\n          for (const span of getElements(\".hll:not(.select)\", el)) {\n            span.replaceWith(...Array.from(span.childNodes))\n          }\n\n          // set new range @todo move this into one block\n          const selection = spans.slice(range[0] - 1, range[1])\n          for (const span of selection) {\n            const hll = document.createElement(\"span\")\n            hll.className = \"hll\"\n            hll.append(...Array.from(span.childNodes).slice(1))\n            span.append(hll)\n          }\n        })\n\n        hash$.pipe(take(1), observeOn(asyncScheduler))\n          .subscribe(hash => {\n            if (hash.includes(\":\")) {\n              const anchor = document.getElementById(hash.split(\":\")[0])\n              if (anchor) {\n                // this is a hack - we will refactor anchor / targetting as one\n                // of the next big things when merging one of the next goals.\n                // we need to unify how offsets are computed for tooltips and\n                // make the whole experience smoother.\n                setTimeout(() => {\n                  let tmp = anchor\n                  let top = -(48 + 16)\n                  while (tmp !== document.body) {\n                    top += tmp.offsetTop\n                    tmp  = tmp.offsetParent as HTMLElement\n                  }\n                  window.scrollTo({ top })\n                }, 1)\n              }\n            }\n          })\n\n        /* Allow selection via anchor links */\n        const jump$ = from(\n          getElements(\"a[href^=\\\"#__codelineno\\\"]\", container!)\n        )\n          .pipe(\n            mergeMap(anchor => fromEvent(anchor, \"click\")\n              .pipe(\n                tap(ev => ev.preventDefault()),\n                map(() => anchor as HTMLAnchorElement)\n              )\n            )\n          )\n\n        /* Determine next highlighted lines */\n        const next$ = jump$\n          .pipe(\n            takeUntil(done$),\n            withLatestFrom(shift$),\n            map(([anchor, shift]) => {\n              const target = getElement(`[id=\"${anchor.hash.slice(1)}\"]`)\n\n              /* Determine focused line number */\n              const active = +target.parentElement!.id.split(\"-\").pop()!\n              if (shift === false) {\n                return [active, active] as const\n\n              /* Shift is pressed, so extend selection */\n              } else {\n                const range = getElements(\".hll\", el)\n                  .map(line => +line.parentElement!.id.split(\"-\").pop()!)\n\n                /* Return range */\n                return [\n                  Math.min(active, ...range),\n                  Math.max(active, ...range)\n                ] as const\n              }\n            })\n          )\n\n        // Push selection to URL\n        merge(range$, next$).subscribe(range => {\n          // @todo: improve resilience, so we're not dependent on class names\n          let hash = `#__codelineno-${id}-`\n          if (range[0] === range[1]) {\n            hash += range[0]\n          } else {\n            hash += `${range[0]}:${range[1]}`\n          }\n          history.replaceState({}, \"\", hash)\n          // @hack dispatch artificial hashchange event\n          window.dispatchEvent(new HashChangeEvent(\"hashchange\", {\n            newURL: window.location.origin + window.location.pathname + hash,\n            oldURL: window.location.href\n          }))\n        })\n      }\n    }\n\n    /* Render button for Clipboard.js integration */\n    if (ClipboardJS.isSupported()) {\n      if (el.closest(\".copy\") || (\n        feature(\"content.code.copy\") && !el.closest(\".no-copy\")\n      )) {\n\n        /* Mount tooltip, if enabled */\n        const button = renderClipboardButton(parent.id)\n        buttons.push(button)\n        if (feature(\"content.tooltips\"))\n          content$.push(mountInlineTooltip2(button, { viewport$ }))\n      }\n    }\n\n    // @hack Render code navigation and buttons\n    if (buttons.length) {\n      const nav = renderCodeBlockNavigation()\n      nav.append(...buttons)\n      parent.insertBefore(nav, el)\n    }\n\n    /* Create and return component */\n    return watchCodeBlock(el)\n      .pipe(\n        tap(state => push$.next(state)),\n        finalize(() => push$.complete()),\n        map(state => ({ ref: el, ...state })),\n        mergeWith(merge(...content$).pipe(\n          takeUntil(done$)\n        )),\n      )\n  })\n\n  /* Mount code block lazily */\n  if (feature(\"content.lazy\"))\n    return watchElementVisibility(el)\n      .pipe(\n        filter(visible => visible),\n        take(1),\n        switchMap(() => factory$)\n      )\n\n  /* Mount code block */\n  return factory$\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  Subject,\n  defer,\n  filter,\n  finalize,\n  map,\n  merge,\n  tap\n} from \"rxjs\"\n\nimport { Component } from \"../../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Details\n */\nexport interface Details {\n  action: \"open\" | \"close\"             /* Details state */\n  reveal?: boolean                     /* Details is revealed */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n  target$: Observable<HTMLElement>     /* Location target observable */\n  print$: Observable<boolean>          /* Media print observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  target$: Observable<HTMLElement>     /* Location target observable */\n  print$: Observable<boolean>          /* Media print observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch details\n *\n * @param el - Details element\n * @param options - Options\n *\n * @returns Details observable\n */\nexport function watchDetails(\n  el: HTMLDetailsElement, { target$, print$ }: WatchOptions\n): Observable<Details> {\n  let open = true\n  return merge(\n\n    /* Open and focus details on location target */\n    target$\n      .pipe(\n        map(target => target.closest(\"details:not([open])\")!),\n        filter(details => el === details),\n        map(() => ({\n          action: \"open\", reveal: true\n        }) as Details)\n      ),\n\n    /* Open details on print and close afterwards */\n    print$\n      .pipe(\n        filter(active => active || !open),\n        tap(() => open = el.open),\n        map(active => ({\n          action: active ? \"open\" : \"close\"\n        }) as Details)\n      )\n  )\n}\n\n/**\n * Mount details\n *\n * This function ensures that `details` tags are opened on anchor jumps and\n * prior to printing, so the whole content of the page is visible.\n *\n * @param el - Details element\n * @param options - Options\n *\n * @returns Details component observable\n */\nexport function mountDetails(\n  el: HTMLDetailsElement, options: MountOptions\n): Observable<Component<Details>> {\n  return defer(() => {\n    const push$ = new Subject<Details>()\n    push$.subscribe(({ action, reveal }) => {\n      el.toggleAttribute(\"open\", action === \"open\")\n      if (reveal)\n        el.scrollIntoView()\n    })\n\n    /* Create and return component */\n    return watchDetails(el, options)\n      .pipe(\n        tap(state => push$.next(state)),\n        finalize(() => push$.complete()),\n        map(state => ({ ref: el, ...state }))\n      )\n  })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  EMPTY,\n  Observable,\n  combineLatest,\n  distinctUntilChanged,\n  filter,\n  map,\n  of,\n  switchMap,\n  zip\n} from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport {\n  Viewport,\n  getElements,\n  getOptionalElement,\n  requestHTML,\n  watchElementFocus,\n  watchElementHover\n} from \"~/browser\"\nimport { Sitemap } from \"~/integrations\"\nimport { renderTooltip2 } from \"~/templates\"\n\nimport { Component } from \"../../_\"\nimport { mountTooltip2 } from \"../../tooltip2\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Link\n */\nexport interface Link {}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Dependencies\n */\ninterface Dependencies {\n  sitemap$: Observable<Sitemap>        // Sitemap observable\n  viewport$: Observable<Viewport>      // Viewport observable\n  target$: Observable<HTMLElement>     // Location target observable\n  print$: Observable<boolean>          // Media print observable\n}\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Global sequence number for instant previews\n */\nlet sequence = 0\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Extract elements until next heading\n *\n * @param headline - Heading\n *\n * @returns Elements until next heading\n */\nfunction extract(headline: HTMLElement): HTMLElement[] {\n  const newHeading = document.createElement(\"h3\")\n  newHeading.innerHTML = headline.innerHTML\n  const els = [newHeading]\n\n  //\n  let nextElement = headline.nextElementSibling\n  while (nextElement && !(nextElement instanceof HTMLHeadingElement)) {\n    // @ts-expect-error - fix once instant previews are stable\n    els.push(nextElement as HTMLElement)\n    nextElement = nextElement.nextElementSibling\n  }\n\n  //\n  return els\n}\n\n/**\n * Resolve relative URLs in the given document\n *\n * @todo deduplicate with resolution in instant navigation. This functoion also\n * adds the ability to resolve from a specific base URL, which is essential for\n * instant previews to work, so we should generalize this functionality the\n * next time we work on instant navigation.\n *\n * @param document - Document\n * @param base - Base URL\n *\n * @returns Document observable\n */\nfunction resolve(\n  document: Document, base: URL | string\n): Observable<Document> {\n\n  // Replace all links\n  for (const el of getElements(\"[href], [src]\", document))\n    for (const key of [\"href\", \"src\"]) {\n      const value = el.getAttribute(key)\n      if (value && !/^(?:[a-z]+:)?\\/\\//i.test(value)) {\n        // @ts-expect-error - trick: self-assign to resolve URL\n        el[key] = new URL(el.getAttribute(key), base).toString()\n        break\n      }\n    }\n\n  // Ensure ids are free of collisions (e.g. content tabs)\n  for (const el of getElements(\"[name^=__], [for]\", document))\n    for (const key of [\"id\", \"for\", \"name\"]) {\n      const value = el.getAttribute(key)\n      if (value) {\n        el.setAttribute(key, `${value}$preview_${sequence}`)\n      }\n    }\n\n  // Return document observable\n  sequence++\n  return of(document)\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount Link\n *\n * @param el - Link element\n * @param dependencies - Depenendencies\n *\n * @returns Link component observable\n */\nexport function mountLink(\n  el: HTMLElement, dependencies: Dependencies\n): Observable<Component<Link>> {\n  const { sitemap$ } = dependencies\n  if (!(el instanceof HTMLAnchorElement))\n    return EMPTY\n\n  //\n  if (!(\n    feature(\"navigation.instant.preview\") ||\n    el.hasAttribute(\"data-preview\")\n  ))\n    return EMPTY\n\n  // Remove title, as it will overlay the instant preview, and we want to give\n  // instant previews precedence over titles \u2013 see https://t.ly/o0_Rk\n  el.removeAttribute(\"title\")\n\n  const active$ =\n    combineLatest([\n      watchElementFocus(el),\n      watchElementHover(el)\n    ])\n      .pipe(\n        map(([focus, hover]) => focus || hover),\n        distinctUntilChanged(),\n        filter(active => active)\n      )\n\n  // @todo: this is taken from the handle function in instant loading - we\n  // should generalize this once instant loading becomes stable.\n  const elements$ = zip([sitemap$, active$]).pipe(\n    switchMap(([sitemap]) => {\n      const url = new URL(el.href)\n      url.search = url.hash = \"\"\n\n      //\n      if (!sitemap.has(`${url}`))\n        return EMPTY\n\n      //\n      return of(url)\n    }),\n    switchMap(url => requestHTML(url).pipe(\n      switchMap(doc => resolve(doc, url))\n    )),\n    switchMap(doc => {\n      const selector = el.hash\n        ? `article [id=\"${el.hash.slice(1)}\"]`\n        : \"article h1\"\n\n      //\n      const target = getOptionalElement(selector, doc)\n      if (typeof target === \"undefined\")\n        return EMPTY\n\n      //\n      return of(extract(target))\n    })\n  )\n\n  //\n  return elements$.pipe(\n    switchMap(els => {\n      const content$ = new Observable<HTMLElement>(observer => {\n        const node = renderTooltip2(...els)\n        observer.next(node)\n\n        //\n        document.body.append(node)\n        return () => node.remove()\n      })\n\n      //\n      return mountTooltip2(el, { content$,  ...dependencies })\n    })\n  )\n}\n", ".node circle,.node ellipse,.node path,.node polygon,.node rect{fill:var(--md-mermaid-node-bg-color);stroke:var(--md-mermaid-node-fg-color)}marker{fill:var(--md-mermaid-edge-color)!important}.edgeLabel .label rect{fill:#0000}.flowchartTitleText{fill:var(--md-mermaid-label-fg-color)}.label{color:var(--md-mermaid-label-fg-color);font-family:var(--md-mermaid-font-family)}.label foreignObject{line-height:normal;overflow:visible}.label div .edgeLabel{color:var(--md-mermaid-label-fg-color)}.edgeLabel,.edgeLabel p,.label div .edgeLabel{background-color:var(--md-mermaid-label-bg-color)}.edgeLabel,.edgeLabel p{fill:var(--md-mermaid-label-bg-color);color:var(--md-mermaid-edge-color)}.edgePath .path,.flowchart-link{stroke:var(--md-mermaid-edge-color)}.edgePath .arrowheadPath{fill:var(--md-mermaid-edge-color);stroke:none}.cluster rect{fill:var(--md-default-fg-color--lightest);stroke:var(--md-default-fg-color--lighter)}.cluster span{color:var(--md-mermaid-label-fg-color);font-family:var(--md-mermaid-font-family)}g #flowchart-circleEnd,g #flowchart-circleStart,g #flowchart-crossEnd,g #flowchart-crossStart,g #flowchart-pointEnd,g #flowchart-pointStart{stroke:none}.classDiagramTitleText{fill:var(--md-mermaid-label-fg-color)}g.classGroup line,g.classGroup rect{fill:var(--md-mermaid-node-bg-color);stroke:var(--md-mermaid-node-fg-color)}g.classGroup text{fill:var(--md-mermaid-label-fg-color);font-family:var(--md-mermaid-font-family)}.classLabel .box{fill:var(--md-mermaid-label-bg-color);background-color:var(--md-mermaid-label-bg-color);opacity:1}.classLabel .label{fill:var(--md-mermaid-label-fg-color);font-family:var(--md-mermaid-font-family)}.node .divider{stroke:var(--md-mermaid-node-fg-color)}.relation{stroke:var(--md-mermaid-edge-color)}.cardinality{fill:var(--md-mermaid-label-fg-color);font-family:var(--md-mermaid-font-family)}.cardinality text{fill:inherit!important}defs marker.marker.composition.class path,defs marker.marker.dependency.class path,defs marker.marker.extension.class path{fill:var(--md-mermaid-edge-color)!important;stroke:var(--md-mermaid-edge-color)!important}defs marker.marker.aggregation.class path{fill:var(--md-mermaid-label-bg-color)!important;stroke:var(--md-mermaid-edge-color)!important}.statediagramTitleText{fill:var(--md-mermaid-label-fg-color)}g.stateGroup rect{fill:var(--md-mermaid-node-bg-color);stroke:var(--md-mermaid-node-fg-color)}g.stateGroup .state-title{fill:var(--md-mermaid-label-fg-color)!important;font-family:var(--md-mermaid-font-family)}g.stateGroup .composit{fill:var(--md-mermaid-label-bg-color)}.nodeLabel,.nodeLabel p{color:var(--md-mermaid-label-fg-color);font-family:var(--md-mermaid-font-family)}a .nodeLabel{text-decoration:underline}.node circle.state-end,.node circle.state-start,.start-state{fill:var(--md-mermaid-edge-color);stroke:none}.end-state-inner,.end-state-outer{fill:var(--md-mermaid-edge-color)}.end-state-inner,.node circle.state-end{stroke:var(--md-mermaid-label-bg-color)}.transition{stroke:var(--md-mermaid-edge-color)}[id^=state-fork] rect,[id^=state-join] rect{fill:var(--md-mermaid-edge-color)!important;stroke:none!important}.statediagram-cluster.statediagram-cluster .inner{fill:var(--md-default-bg-color)}.statediagram-cluster rect{fill:var(--md-mermaid-node-bg-color);stroke:var(--md-mermaid-node-fg-color)}.statediagram-state rect.divider{fill:var(--md-default-fg-color--lightest);stroke:var(--md-default-fg-color--lighter)}defs #statediagram-barbEnd{stroke:var(--md-mermaid-edge-color)}[id^=entity] path,[id^=entity] rect{fill:var(--md-default-bg-color)}.relationshipLine{stroke:var(--md-mermaid-edge-color)}defs .marker.oneOrMore.er *,defs .marker.onlyOne.er *,defs .marker.zeroOrMore.er *,defs .marker.zeroOrOne.er *{stroke:var(--md-mermaid-edge-color)!important}text:not([class]):last-child{fill:var(--md-mermaid-label-fg-color)}.actor{fill:var(--md-mermaid-sequence-actor-bg-color);stroke:var(--md-mermaid-sequence-actor-border-color)}text.actor>tspan{fill:var(--md-mermaid-sequence-actor-fg-color);font-family:var(--md-mermaid-font-family)}line{stroke:var(--md-mermaid-sequence-actor-line-color)}.actor-man circle,.actor-man line{fill:var(--md-mermaid-sequence-actorman-bg-color);stroke:var(--md-mermaid-sequence-actorman-line-color)}.messageLine0,.messageLine1{stroke:var(--md-mermaid-sequence-message-line-color)}.note{fill:var(--md-mermaid-sequence-note-bg-color);stroke:var(--md-mermaid-sequence-note-border-color)}.loopText,.loopText>tspan,.messageText,.noteText>tspan{stroke:none;font-family:var(--md-mermaid-font-family)!important}.messageText{fill:var(--md-mermaid-sequence-message-fg-color)}.loopText,.loopText>tspan{fill:var(--md-mermaid-sequence-loop-fg-color)}.noteText>tspan{fill:var(--md-mermaid-sequence-note-fg-color)}#arrowhead path{fill:var(--md-mermaid-sequence-message-line-color);stroke:none}.loopLine{fill:var(--md-mermaid-sequence-loop-bg-color);stroke:var(--md-mermaid-sequence-loop-border-color)}.labelBox{fill:var(--md-mermaid-sequence-label-bg-color);stroke:none}.labelText,.labelText>span{fill:var(--md-mermaid-sequence-label-fg-color);font-family:var(--md-mermaid-font-family)}.sequenceNumber{fill:var(--md-mermaid-sequence-number-fg-color)}rect.rect{fill:var(--md-mermaid-sequence-box-bg-color);stroke:none}rect.rect+text.text{fill:var(--md-mermaid-sequence-box-fg-color)}defs #sequencenumber{fill:var(--md-mermaid-sequence-number-bg-color)!important}", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  map,\n  of,\n  shareReplay,\n  tap\n} from \"rxjs\"\n\nimport { watchScript } from \"~/browser\"\nimport { h } from \"~/utilities\"\n\nimport { Component } from \"../../_\"\n\nimport themeCSS from \"./index.css\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mermaid diagram\n */\nexport interface Mermaid {}\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Mermaid instance observable\n */\nlet mermaid$: Observable<void>\n\n/**\n * Global sequence number for diagrams\n */\nlet sequence = 0\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch Mermaid script\n *\n * @returns Mermaid scripts observable\n */\nfunction fetchScripts(): Observable<void> {\n  return typeof mermaid === \"undefined\" || mermaid instanceof Element\n    ? watchScript(\"https://unpkg.com/mermaid@11/dist/mermaid.min.js\")\n    : of(undefined)\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount Mermaid diagram\n *\n * @param el - Code block element\n *\n * @returns Mermaid diagram component observable\n */\nexport function mountMermaid(\n  el: HTMLElement\n): Observable<Component<Mermaid>> {\n  el.classList.remove(\"mermaid\") // Hack: mitigate https://bit.ly/3CiN6Du\n  mermaid$ ||= fetchScripts()\n    .pipe(\n      tap(() => mermaid.initialize({\n        startOnLoad: false,\n        themeCSS,\n        sequence: {\n          actorFontSize: \"16px\", // Hack: mitigate https://bit.ly/3y0NEi3\n          messageFontSize: \"16px\",\n          noteFontSize: \"16px\"\n        }\n      })),\n      map(() => undefined),\n      shareReplay(1)\n    )\n\n  /* Render diagram */\n  mermaid$.subscribe(async () => {\n    el.classList.add(\"mermaid\") // Hack: mitigate https://bit.ly/3CiN6Du\n    const id = `__mermaid_${sequence++}`\n\n    /* Create host element to replace code block */\n    const host = h(\"div\", { class: \"mermaid\" })\n    const text = el.textContent\n\n    /* Render and inject diagram */\n    const { svg, fn } = await mermaid.render(id, text)\n\n    /* Create a shadow root and inject diagram */\n    const shadow = host.attachShadow({ mode: \"closed\" })\n    shadow.innerHTML = svg\n\n    /* Replace code block with diagram and bind functions */\n    el.replaceWith(host)\n    fn?.(shadow)\n  })\n\n  /* Create and return component */\n  return mermaid$\n    .pipe(\n      map(() => ({ ref: el }))\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { Observable, of } from \"rxjs\"\n\nimport { renderTable } from \"~/templates\"\nimport { h } from \"~/utilities\"\n\nimport { Component } from \"../../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Data table\n */\nexport interface DataTable {}\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Sentinel for replacement\n */\nconst sentinel = h(\"table\")\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount data table\n *\n * This function wraps a data table in another scrollable container, so it can\n * be smoothly scrolled on smaller screen sizes and won't break the layout.\n *\n * @param el - Data table element\n *\n * @returns Data table component observable\n */\nexport function mountDataTable(\n  el: HTMLElement\n): Observable<Component<DataTable>> {\n  el.replaceWith(sentinel)\n  sentinel.replaceWith(renderTable(el))\n\n  /* Create and return component */\n  return of({ ref: el })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  Subject,\n  animationFrameScheduler,\n  asyncScheduler,\n  auditTime,\n  combineLatest,\n  defer,\n  endWith,\n  filter,\n  finalize,\n  fromEvent,\n  ignoreElements,\n  map,\n  merge,\n  skip,\n  startWith,\n  subscribeOn,\n  takeUntil,\n  tap,\n  withLatestFrom\n} from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport {\n  Viewport,\n  getElement,\n  getElementContentOffset,\n  getElementContentSize,\n  getElementOffset,\n  getElementSize,\n  getElements,\n  watchElementContentOffset,\n  watchElementSize,\n  watchElementVisibility\n} from \"~/browser\"\nimport { renderTabbedControl } from \"~/templates\"\nimport { h } from \"~/utilities\"\n\nimport { Component } from \"../../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Content tabs\n */\nexport interface ContentTabs {\n  active: HTMLLabelElement             /* Active tab label */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  viewport$: Observable<Viewport>      /* Viewport observable */\n  target$: Observable<HTMLElement>     /* Location target observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch content tabs\n *\n * @param inputs - Content tabs input elements\n *\n * @returns Content tabs observable\n */\nexport function watchContentTabs(\n  inputs: HTMLInputElement[]\n): Observable<ContentTabs> {\n  const initial = inputs.find(input => input.checked) || inputs[0]\n  return merge(...inputs.map(input => fromEvent(input, \"change\")\n    .pipe(\n      map(() => getElement<HTMLLabelElement>(`label[for=\"${input.id}\"]`))\n    )\n  ))\n    .pipe(\n      startWith(getElement<HTMLLabelElement>(`label[for=\"${initial.id}\"]`)),\n      map(active => ({ active }))\n    )\n}\n\n/**\n * Mount content tabs\n *\n * @param el - Content tabs element\n * @param options - Options\n *\n * @returns Content tabs component observable\n */\nexport function mountContentTabs(\n  el: HTMLElement, { viewport$, target$ }: MountOptions\n): Observable<Component<ContentTabs>> {\n  const container = getElement(\".tabbed-labels\", el)\n  const inputs = getElements<HTMLInputElement>(\":scope > input\", el)\n\n  /* Render content tab previous button for pagination */\n  const prev = renderTabbedControl(\"prev\")\n  el.append(prev)\n\n  /* Render content tab next button for pagination */\n  const next = renderTabbedControl(\"next\")\n  el.append(next)\n\n  /* Mount component on subscription */\n  return defer(() => {\n    const push$ = new Subject<ContentTabs>()\n    const done$ = push$.pipe(ignoreElements(), endWith(true))\n    combineLatest([push$, watchElementSize(el), watchElementVisibility(el)])\n      .pipe(\n        takeUntil(done$),\n        auditTime(1, animationFrameScheduler)\n      )\n        .subscribe({\n\n          /* Handle emission */\n          next([{ active }, size]) {\n            const offset = getElementOffset(active)\n            const { width } = getElementSize(active)\n\n            /* Set tab indicator offset and width */\n            el.style.setProperty(\"--md-indicator-x\", `${offset.x}px`)\n            el.style.setProperty(\"--md-indicator-width\", `${width}px`)\n\n            /* Scroll container to active content tab */\n            const content = getElementContentOffset(container)\n            if (\n              offset.x         < content.x              ||\n              offset.x + width > content.x + size.width\n            )\n              container.scrollTo({\n                left: Math.max(0, offset.x - 16),\n                behavior: \"smooth\"\n              })\n          },\n\n          /* Handle complete */\n          complete() {\n            el.style.removeProperty(\"--md-indicator-x\")\n            el.style.removeProperty(\"--md-indicator-width\")\n          }\n        })\n\n    /* Hide content tab buttons on borders */\n    combineLatest([\n      watchElementContentOffset(container),\n      watchElementSize(container)\n    ])\n      .pipe(\n        takeUntil(done$)\n      )\n        .subscribe(([offset, size]) => {\n          const content = getElementContentSize(container)\n          prev.hidden = offset.x < 16\n          next.hidden = offset.x > content.width - size.width - 16\n        })\n\n    /* Paginate content tab container on click */\n    merge(\n      fromEvent(prev, \"click\").pipe(map(() => -1)),\n      fromEvent(next, \"click\").pipe(map(() => +1))\n    )\n      .pipe(\n        takeUntil(done$)\n      )\n        .subscribe(direction => {\n          const { width } = getElementSize(container)\n          container.scrollBy({\n            left: width * direction,\n            behavior: \"smooth\"\n          })\n        })\n\n    /* Switch to content tab target */\n    target$\n      .pipe(\n        takeUntil(done$),\n        filter(input => inputs.includes(input as HTMLInputElement))\n      )\n        .subscribe(input => input.click())\n\n    /* Add link to each content tab label */\n    container.classList.add(\"tabbed-labels--linked\")\n    for (const input of inputs) {\n      const label = getElement<HTMLLabelElement>(`label[for=\"${input.id}\"]`)\n      label.replaceChildren(h(\"a\", {\n        href: `#${label.htmlFor}`,\n        tabIndex: -1\n      }, ...Array.from(label.childNodes)))\n\n      /* Allow to copy link without scrolling to anchor */\n      fromEvent<MouseEvent>(label.firstElementChild!, \"click\")\n        .pipe(\n          takeUntil(done$),\n          filter(ev => !(ev.metaKey || ev.ctrlKey)),\n          tap(ev => {\n            ev.preventDefault()\n            ev.stopPropagation()\n          })\n        )\n          // @todo we might need to remove the anchor link on complete\n          .subscribe(() => {\n            history.replaceState({}, \"\", `#${label.htmlFor}`)\n            label.click()\n          })\n    }\n\n    /* Set up linking of content tabs, if enabled */\n    if (feature(\"content.tabs.link\"))\n      push$.pipe(\n        skip(1),\n        withLatestFrom(viewport$)\n      )\n        .subscribe(([{ active }, { offset }]) => {\n          const tab = active.innerText.trim()\n          if (active.hasAttribute(\"data-md-switching\")) {\n            active.removeAttribute(\"data-md-switching\")\n\n          /* Determine viewport offset of active tab */\n          } else {\n            const y = el.offsetTop - offset.y\n\n            /* Passively activate other tabs */\n            for (const set of getElements(\"[data-tabs]\"))\n              for (const input of getElements<HTMLInputElement>(\n                \":scope > input\", set\n              )) {\n                const label = getElement(`label[for=\"${input.id}\"]`)\n                if (\n                  label !== active &&\n                  label.innerText.trim() === tab\n                ) {\n                  label.setAttribute(\"data-md-switching\", \"\")\n                  input.click()\n                  break\n                }\n              }\n\n            /* Bring active tab into view */\n            window.scrollTo({\n              top: el.offsetTop - y\n            })\n\n            /* Persist active tabs in local storage */\n            const tabs = __md_get<string[]>(\"__tabs\") || []\n            __md_set(\"__tabs\", [...new Set([tab, ...tabs])])\n          }\n        })\n\n    /* Pause media (audio, video) on switch - see https://bit.ly/3Bk6cel */\n    push$.pipe(takeUntil(done$))\n      .subscribe(() => {\n        // If the video or audio is visible, and has autoplay enabled, it will\n        // continue playing. If it's not visible, it is paused in any case\n        for (const media of getElements<HTMLAudioElement>(\"audio, video\", el)) {\n          if (media.offsetWidth && media.autoplay) {\n            media.play().catch(() => {}) // Just ignore errors\n          } else {\n            media.pause()\n          }\n        }\n      })\n\n    /* Create and return component */\n    return watchContentTabs(inputs)\n      .pipe(\n        tap(state => push$.next(state)),\n        finalize(() => push$.complete()),\n        map(state => ({ ref: el, ...state }))\n      )\n  })\n    .pipe(\n      subscribeOn(asyncScheduler)\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { Observable, merge } from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport { Viewport, getElements } from \"~/browser\"\nimport { Sitemap } from \"~/integrations\"\nimport { renderTooltip2 } from \"~/templates\"\n\nimport { Component } from \"../../_\"\nimport {\n  Tooltip,\n  mountInlineTooltip2,\n  mountTooltip2\n} from \"../../tooltip2\"\nimport {\n  Annotation,\n  mountAnnotationBlock\n} from \"../annotation\"\nimport {\n  CodeBlock,\n  mountCodeBlock\n} from \"../code\"\nimport {\n  Details,\n  mountDetails\n} from \"../details\"\nimport {\n  Link,\n  mountLink\n} from \"../link\"\nimport {\n  Mermaid,\n  mountMermaid\n} from \"../mermaid\"\nimport {\n  DataTable,\n  mountDataTable\n} from \"../table\"\nimport {\n  ContentTabs,\n  mountContentTabs\n} from \"../tabs\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Content\n */\nexport type Content =\n  | Annotation\n  | CodeBlock\n  | ContentTabs\n  | DataTable\n  | Details\n  | Link\n  | Mermaid\n  | Tooltip\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Dependencies\n */\ninterface Dependencies {\n  sitemap$: Observable<Sitemap>        // Sitemap observable\n  viewport$: Observable<Viewport>      // Viewport observable\n  target$: Observable<HTMLElement>     // Location target observable\n  print$: Observable<boolean>          // Media print observable\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount content\n *\n * This function mounts all components that are found in the content of the\n * actual article, including code blocks, data tables and details.\n *\n * @param el - Content element\n * @param dependencies - Dependencies\n *\n * @returns Content component observable\n */\nexport function mountContent(\n  el: HTMLElement, dependencies: Dependencies\n): Observable<Component<Content>> {\n  const { viewport$, target$, print$ } = dependencies\n  return merge(\n\n    // Annotations\n    ...getElements(\".annotate:not(.highlight)\", el)\n      .map(child => mountAnnotationBlock(child, { target$, print$ })),\n\n    // Code blocks\n    ...getElements(\"pre:not(.mermaid) > code\", el)\n      .map(child => mountCodeBlock(child, { target$, print$ })),\n\n    // Links\n    ...getElements(\"a\", el)\n      .map(child => mountLink(child, dependencies)),\n\n    // Mermaid diagrams\n    ...getElements(\"pre.mermaid\", el)\n      .map(child => mountMermaid(child)),\n\n    // Data tables\n    ...getElements(\"table:not([class])\", el)\n      .map(child => mountDataTable(child)),\n\n    // Details\n    ...getElements(\"details\", el)\n      .map(child => mountDetails(child, { target$, print$ })),\n\n    // Content tabs\n    ...getElements(\"[data-tabs]\", el)\n      .map(child => mountContentTabs(child, { viewport$, target$ })),\n\n    // Tooltips\n    ...getElements(\"[title]:not([data-preview])\", el)\n      .filter(() => feature(\"content.tooltips\"))\n      .map(child => mountInlineTooltip2(child, { viewport$ })),\n\n    // Footnotes\n    ...getElements(\".footnote-ref\", el)\n      .filter(() => feature(\"content.footnote.tooltips\"))\n      // move into specific function! mountTooltip is a low level primitive...\n      .map(child => mountTooltip2(child, {\n        content$: new Observable<HTMLElement>(observer => {\n          // @ts-ignore\n          const hash = new URL(child.href).hash.slice(1)\n          const arr = Array.from(document.getElementById(hash)!\n            // @ts-ignore\n            // eslint-disable-next-line\n            .cloneNode(true).children) as any\n          const node = renderTooltip2(...arr)\n          observer.next(node)\n\n          // Append tooltip and remove on unsubscription\n          document.body.append(node)\n          return () => node.remove()\n        }),\n        viewport$\n      }))\n  )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  Subject,\n  defer,\n  delay,\n  finalize,\n  map,\n  merge,\n  of,\n  switchMap,\n  tap\n} from \"rxjs\"\n\nimport { getElement } from \"~/browser\"\n\nimport { Component } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Dialog\n */\nexport interface Dialog {\n  message: string                      /* Dialog message */\n  active: boolean                      /* Dialog is active */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n  alert$: Subject<string>              /* Alert subject */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  alert$: Subject<string>              /* Alert subject */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch dialog\n *\n * @param _el - Dialog element\n * @param options - Options\n *\n * @returns Dialog observable\n */\nexport function watchDialog(\n  _el: HTMLElement, { alert$ }: WatchOptions\n): Observable<Dialog> {\n  return alert$\n    .pipe(\n      switchMap(message => merge(\n        of(true),\n        of(false).pipe(delay(2000))\n      )\n        .pipe(\n          map(active => ({ message, active }))\n        )\n      )\n    )\n}\n\n/**\n * Mount dialog\n *\n * This function reveals the dialog in the right corner when a new alert is\n * emitted through the subject that is passed as part of the options.\n *\n * @param el - Dialog element\n * @param options - Options\n *\n * @returns Dialog component observable\n */\nexport function mountDialog(\n  el: HTMLElement, options: MountOptions\n): Observable<Component<Dialog>> {\n  const inner = getElement(\".md-typeset\", el)\n  return defer(() => {\n    const push$ = new Subject<Dialog>()\n    push$.subscribe(({ message, active }) => {\n      el.classList.toggle(\"md-dialog--active\", active)\n      inner.textContent = message\n    })\n\n    /* Create and return component */\n    return watchDialog(el, options)\n      .pipe(\n        tap(state => push$.next(state)),\n        finalize(() => push$.complete()),\n        map(state => ({ ref: el, ...state }))\n      )\n  })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  EMPTY,\n  Observable,\n  Subject,\n  animationFrameScheduler,\n  asyncScheduler,\n  auditTime,\n  combineLatest,\n  debounceTime,\n  defer,\n  distinctUntilChanged,\n  filter,\n  finalize,\n  map,\n  merge,\n  of,\n  subscribeOn,\n  tap,\n  throttleTime\n} from \"rxjs\"\n\nimport {\n  ElementOffset,\n  getElement,\n  getElementContainer,\n  getElementOffset,\n  getElementSize,\n  watchElementContentOffset,\n  watchElementFocus,\n  watchElementHover\n} from \"~/browser\"\nimport { renderTooltip } from \"~/templates\"\n\nimport { Component } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Tooltip\n */\nexport interface Tooltip {\n  active: boolean                      /* Tooltip is active */\n  offset: ElementOffset                /* Tooltip offset */\n}\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Global sequence number for tooltips\n */\nlet sequence = 0\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch tooltip\n *\n * This function will append the tooltip temporarily to compute its width,\n * which is necessary for correct centering, and then removing it again.\n *\n * @param el - Tooltip element\n * @param host - Host element\n *\n * @returns Tooltip observable\n */\nexport function watchTooltip(\n  el: HTMLElement, host: HTMLElement\n): Observable<Tooltip> {\n  document.body.append(el)\n\n  /* Compute width and remove tooltip immediately */\n  const { width } = getElementSize(el)\n  el.style.setProperty(\"--md-tooltip-width\", `${width}px`)\n  el.remove()\n\n  /* Retrieve and watch containing element */\n  const container = getElementContainer(host)\n  const scroll$ =\n    typeof container !== \"undefined\"\n      ? watchElementContentOffset(container)\n      : of({ x: 0, y: 0 })\n\n  /* Compute tooltip visibility */\n  const active$ = merge(\n    watchElementFocus(host),\n    watchElementHover(host)\n  )\n    .pipe(\n      distinctUntilChanged()\n    )\n\n  /* Compute tooltip offset */\n  return combineLatest([active$, scroll$])\n    .pipe(\n      map(([active, scroll]) => {\n        let { x, y } = getElementOffset(host)\n        const size = getElementSize(host)\n\n        /**\n         * Experimental: fix handling of tables - see https://bit.ly/3TQEj5O\n         *\n         * If this proves to be a viable fix, we should refactor tooltip\n         * positioning and somehow streamline the current process. This might\n         * also fix positioning for annotations inside tables, which is another\n         * limitation.\n         */\n        const table = host.closest(\"table\")\n        if (table && host.parentElement) {\n          x += table.offsetLeft + host.parentElement.offsetLeft\n          y += table.offsetTop  + host.parentElement.offsetTop\n        }\n        return {\n          active,\n          offset: {\n            x: x - scroll.x + size.width  / 2 - width / 2,\n            y: y - scroll.y + size.height + 8\n          }\n        }\n      })\n    )\n}\n\n/**\n * Mount tooltip\n *\n * @param el - Host element\n *\n * @returns Tooltip component observable\n */\nexport function mountTooltip(\n  el: HTMLElement\n): Observable<Component<Tooltip>> {\n  const title = el.title\n  if (!title.length)\n    return EMPTY\n\n  /* Render tooltip and set title from host element */\n  const id = `__tooltip_${sequence++}`\n  const tooltip = renderTooltip(id, \"inline\")\n  const typeset = getElement(\".md-typeset\", tooltip)\n  typeset.innerHTML = title\n\n  /* Mount component on subscription */\n  return defer(() => {\n    const push$ = new Subject<Tooltip>()\n    push$.subscribe({\n\n      /* Handle emission */\n      next({ offset }) {\n        tooltip.style.setProperty(\"--md-tooltip-x\", `${offset.x}px`)\n        tooltip.style.setProperty(\"--md-tooltip-y\", `${offset.y}px`)\n      },\n\n      /* Handle complete */\n      complete() {\n        tooltip.style.removeProperty(\"--md-tooltip-x\")\n        tooltip.style.removeProperty(\"--md-tooltip-y\")\n      }\n    })\n\n    /* Toggle tooltip presence to mitigate empty lines when copying */\n    merge(\n      push$.pipe(filter(({ active }) => active)),\n      push$.pipe(debounceTime(250), filter(({ active }) => !active))\n    )\n      .subscribe({\n\n        /* Handle emission */\n        next({ active }) {\n          if (active) {\n            el.insertAdjacentElement(\"afterend\", tooltip)\n            el.setAttribute(\"aria-describedby\", id)\n            el.removeAttribute(\"title\")\n          } else {\n            tooltip.remove()\n            el.removeAttribute(\"aria-describedby\")\n            el.setAttribute(\"title\", title)\n          }\n        },\n\n        /* Handle complete */\n        complete() {\n          tooltip.remove()\n          el.removeAttribute(\"aria-describedby\")\n          el.setAttribute(\"title\", title)\n        }\n      })\n\n    /* Toggle tooltip visibility */\n    push$\n      .pipe(\n        auditTime(16, animationFrameScheduler)\n      )\n        .subscribe(({ active }) => {\n          tooltip.classList.toggle(\"md-tooltip--active\", active)\n        })\n\n    // @todo - refactor positioning together with annotations \u2013 there are\n    // several things that overlap and are identical in handling\n\n    /* Track relative origin of tooltip */\n    push$\n      .pipe(\n        throttleTime(125, animationFrameScheduler),\n        filter(() => !!el.offsetParent),\n        map(() => el.offsetParent!.getBoundingClientRect()),\n        map(({ x }) => x)\n      )\n      .subscribe({\n\n        /* Handle emission */\n        next(origin) {\n          if (origin)\n            tooltip.style.setProperty(\"--md-tooltip-0\", `${-origin}px`)\n          else\n            tooltip.style.removeProperty(\"--md-tooltip-0\")\n        },\n\n        /* Handle complete */\n        complete() {\n          tooltip.style.removeProperty(\"--md-tooltip-0\")\n        }\n      })\n\n    /* Create and return component */\n    return watchTooltip(tooltip, el)\n      .pipe(\n        tap(state => push$.next(state)),\n        finalize(() => push$.complete()),\n        map(state => ({ ref: el, ...state }))\n      )\n  })\n    .pipe(\n      subscribeOn(asyncScheduler)\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  Subject,\n  bufferCount,\n  combineLatest,\n  combineLatestWith,\n  defer,\n  distinctUntilChanged,\n  distinctUntilKeyChanged,\n  endWith,\n  filter,\n  from,\n  ignoreElements,\n  map,\n  mergeMap,\n  mergeWith,\n  of,\n  shareReplay,\n  startWith,\n  switchMap,\n  takeUntil\n} from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport {\n  Viewport,\n  getElements,\n  watchElementSize,\n  watchToggle\n} from \"~/browser\"\n\nimport { Component } from \"../../_\"\nimport { Main } from \"../../main\"\nimport { Tooltip, mountTooltip } from \"../../tooltip\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Header\n */\nexport interface Header {\n  height: number                       /* Header visible height */\n  hidden: boolean                      /* Header is hidden */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Dependencies\n */\ninterface Dependencies {\n  viewport$: Observable<Viewport>      /* Viewport observable */\n  header$: Observable<Header>          /* Header observable */\n  main$: Observable<Main>              /* Main area observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Compute whether the header is hidden\n *\n * If the user scrolls past a certain threshold, the header can be hidden when\n * scrolling down, and shown when scrolling up.\n *\n * @param dependencies - Dependencies\n *\n * @returns Toggle observable\n */\nfunction isHidden(\n  { viewport$ }: Pick<Dependencies, \"viewport$\">\n): Observable<boolean> {\n  if (!feature(\"header.autohide\"))\n    return of(false)\n\n  /* Compute direction and turning point */\n  const direction$ = viewport$\n    .pipe(\n      map(({ offset: { y } }) => y),\n      bufferCount(2, 1),\n      map(([a, b]) => [a < b, b] as const),\n      distinctUntilKeyChanged(0)\n    )\n\n  /* Compute whether header should be hidden */\n  const hidden$ = combineLatest([viewport$, direction$])\n    .pipe(\n      filter(([{ offset }, [, y]]) => Math.abs(y - offset.y) > 100),\n      map(([, [direction]]) => direction),\n      distinctUntilChanged()\n    )\n\n  /* Compute threshold for hiding */\n  const search$ = watchToggle(\"search\")\n  return combineLatest([viewport$, search$])\n    .pipe(\n      map(([{ offset }, search]) => offset.y > 400 && !search),\n      distinctUntilChanged(),\n      switchMap(active => active ? hidden$ : of(false)),\n      startWith(false)\n    )\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch header\n *\n * @param el - Header element\n * @param dependencies - Dependencies\n *\n * @returns Header observable\n */\nexport function watchHeader(\n  el: HTMLElement, dependencies: Pick<Dependencies, \"viewport$\">\n): Observable<Header> {\n  return defer(() => combineLatest([\n    watchElementSize(el),\n    isHidden(dependencies)\n  ]))\n    .pipe(\n      map(([{ height }, hidden]) => ({\n        height,\n        hidden\n      })),\n      distinctUntilChanged((a, b) => (\n        a.height === b.height &&\n        a.hidden === b.hidden\n      )),\n      shareReplay(1)\n    )\n}\n\n/**\n * Mount header\n *\n * This function manages the different states of the header, i.e. whether it's\n * hidden or rendered with a shadow. This depends heavily on the main area.\n *\n * @param el - Header element\n * @param dependencies - Dependencies\n *\n * @returns Header component observable\n */\nexport function mountHeader(\n  el: HTMLElement, { header$, main$ }: Dependencies\n): Observable<Component<Header | Tooltip>> {\n  return defer(() => {\n    const push$ = new Subject<Main>()\n    const done$ = push$.pipe(ignoreElements(), endWith(true))\n    push$\n      .pipe(\n        distinctUntilKeyChanged(\"active\"),\n        combineLatestWith(header$)\n      )\n        .subscribe(([{ active }, { hidden }]) => {\n          el.classList.toggle(\"md-header--shadow\", active && !hidden)\n          el.hidden = hidden\n        })\n\n    /* Mount tooltips, if enabled */\n    const tooltips = from(getElements(\"[title]\", el))\n      .pipe(\n        filter(() => feature(\"content.tooltips\")),\n        mergeMap(child => mountTooltip(child))\n      )\n\n    /* Link to main area */\n    main$.subscribe(push$)\n\n    /* Create and return component */\n    return header$\n      .pipe(\n        takeUntil(done$),\n        map(state => ({ ref: el, ...state })),\n        mergeWith(tooltips.pipe(takeUntil(done$)))\n      )\n  })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  EMPTY,\n  Observable,\n  Subject,\n  defer,\n  distinctUntilKeyChanged,\n  finalize,\n  map,\n  tap\n} from \"rxjs\"\n\nimport {\n  Viewport,\n  getElementSize,\n  getOptionalElement,\n  watchViewportAt\n} from \"~/browser\"\n\nimport { Component } from \"../../_\"\nimport { Header } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Header\n */\nexport interface HeaderTitle {\n  active: boolean                      /* Header title is active */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n  viewport$: Observable<Viewport>      /* Viewport observable */\n  header$: Observable<Header>          /* Header observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  viewport$: Observable<Viewport>      /* Viewport observable */\n  header$: Observable<Header>          /* Header observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch header title\n *\n * @param el - Heading element\n * @param options - Options\n *\n * @returns Header title observable\n */\nexport function watchHeaderTitle(\n  el: HTMLElement, { viewport$, header$ }: WatchOptions\n): Observable<HeaderTitle> {\n  return watchViewportAt(el, { viewport$, header$ })\n    .pipe(\n      map(({ offset: { y } }) => {\n        const { height } = getElementSize(el)\n        return {\n          active: height > 0 && y >= height\n        }\n      }),\n      distinctUntilKeyChanged(\"active\")\n    )\n}\n\n/**\n * Mount header title\n *\n * This function swaps the header title from the site title to the title of the\n * current page when the user scrolls past the first headline.\n *\n * @param el - Header title element\n * @param options - Options\n *\n * @returns Header title component observable\n */\nexport function mountHeaderTitle(\n  el: HTMLElement, options: MountOptions\n): Observable<Component<HeaderTitle>> {\n  return defer(() => {\n    const push$ = new Subject<HeaderTitle>()\n    push$.subscribe({\n\n      /* Handle emission */\n      next({ active }) {\n        el.classList.toggle(\"md-header__title--active\", active)\n      },\n\n      /* Handle complete */\n      complete() {\n        el.classList.remove(\"md-header__title--active\")\n      }\n    })\n\n    /* Obtain headline, if any */\n    const heading = getOptionalElement(\".md-content h1\")\n    if (typeof heading === \"undefined\")\n      return EMPTY\n\n    /* Create and return component */\n    return watchHeaderTitle(heading, options)\n      .pipe(\n        tap(state => push$.next(state)),\n        finalize(() => push$.complete()),\n        map(state => ({ ref: el, ...state }))\n      )\n  })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  combineLatest,\n  distinctUntilChanged,\n  distinctUntilKeyChanged,\n  map,\n  switchMap\n} from \"rxjs\"\n\nimport {\n  Viewport,\n  watchElementSize\n} from \"~/browser\"\n\nimport { Header } from \"../header\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Main area\n */\nexport interface Main {\n  offset: number                       /* Main area top offset */\n  height: number                       /* Main area visible height */\n  active: boolean                      /* Main area is active */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n  viewport$: Observable<Viewport>      /* Viewport observable */\n  header$: Observable<Header>          /* Header observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch main area\n *\n * This function returns an observable that computes the visual parameters of\n * the main area which depends on the viewport vertical offset and height, as\n * well as the height of the header element, if the header is fixed.\n *\n * @param el - Main area element\n * @param options - Options\n *\n * @returns Main area observable\n */\nexport function watchMain(\n  el: HTMLElement, { viewport$, header$ }: WatchOptions\n): Observable<Main> {\n\n  /* Compute necessary adjustment for header */\n  const adjust$ = header$\n    .pipe(\n      map(({ height }) => height),\n      distinctUntilChanged()\n    )\n\n  /* Compute the main area's top and bottom borders */\n  const border$ = adjust$\n    .pipe(\n      switchMap(() => watchElementSize(el)\n        .pipe(\n          map(({ height }) => ({\n            top:    el.offsetTop,\n            bottom: el.offsetTop + height\n          })),\n          distinctUntilKeyChanged(\"bottom\")\n        )\n      )\n    )\n\n  /* Compute the main area's offset, visible height and if we scrolled past */\n  return combineLatest([adjust$, border$, viewport$])\n    .pipe(\n      map(([header, { top, bottom }, { offset: { y }, size: { height } }]) => {\n        height = Math.max(0, height\n          - Math.max(0, top    - y,  header)\n          - Math.max(0, height + y - bottom)\n        )\n        return {\n          offset: top - header,\n          height,\n          active: top - header <= y\n        }\n      }),\n      distinctUntilChanged((a, b) => (\n        a.offset === b.offset &&\n        a.height === b.height &&\n        a.active === b.active\n      ))\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  Subject,\n  asyncScheduler,\n  defer,\n  filter,\n  finalize,\n  fromEvent,\n  map,\n  mergeMap,\n  observeOn,\n  of,\n  repeat,\n  shareReplay,\n  skip,\n  startWith,\n  takeUntil,\n  tap,\n  withLatestFrom\n} from \"rxjs\"\n\nimport { getElements, watchMedia } from \"~/browser\"\nimport { h } from \"~/utilities\"\n\nimport {\n  Component,\n  getComponentElement\n} from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Palette colors\n */\nexport interface PaletteColor {\n  media?: string                       /* Media query */\n  scheme?: string                      /* Color scheme */\n  primary?: string                     /* Primary color */\n  accent?: string                      /* Accent color */\n}\n\n/**\n * Palette\n */\nexport interface Palette {\n  index: number                        /* Palette index */\n  color: PaletteColor                  /* Palette colors */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch color palette\n *\n * @param inputs - Color palette element\n *\n * @returns Color palette observable\n */\nexport function watchPalette(\n  inputs: HTMLInputElement[]\n): Observable<Palette> {\n  const current = __md_get<Palette>(\"__palette\") || {\n    index: inputs.findIndex(input => matchMedia(\n      input.getAttribute(\"data-md-color-media\")!\n    ).matches)\n  }\n\n  /* Emit changes in color palette */\n  const index = Math.max(0, Math.min(current.index, inputs.length - 1))\n  return of(...inputs)\n    .pipe(\n      mergeMap(input => fromEvent(input, \"change\").pipe(map(() => input))),\n      startWith(inputs[index]),\n      map(input => ({\n        index: inputs.indexOf(input),\n        color: {\n          media:   input.getAttribute(\"data-md-color-media\"),\n          scheme:  input.getAttribute(\"data-md-color-scheme\"),\n          primary: input.getAttribute(\"data-md-color-primary\"),\n          accent:  input.getAttribute(\"data-md-color-accent\")\n        }\n      } as Palette)),\n      shareReplay(1)\n    )\n}\n\n/**\n * Mount color palette\n *\n * @param el - Color palette element\n *\n * @returns Color palette component observable\n */\nexport function mountPalette(\n  el: HTMLElement\n): Observable<Component<Palette>> {\n  const inputs = getElements<HTMLInputElement>(\"input\", el)\n  const meta = h(\"meta\", { name: \"theme-color\" })\n  document.head.appendChild(meta)\n\n  // Add color scheme meta tag\n  const scheme = h(\"meta\", { name: \"color-scheme\" })\n  document.head.appendChild(scheme)\n\n  /* Mount component on subscription */\n  const media$ = watchMedia(\"(prefers-color-scheme: light)\")\n  return defer(() => {\n    const push$ = new Subject<Palette>()\n    push$.subscribe(palette => {\n      document.body.setAttribute(\"data-md-color-switching\", \"\")\n\n      /* Retrieve color palette for system preference */\n      if (palette.color.media === \"(prefers-color-scheme)\") {\n        const media = matchMedia(\"(prefers-color-scheme: light)\")\n        const input = document.querySelector(media.matches\n          ? \"[data-md-color-media='(prefers-color-scheme: light)']\"\n          : \"[data-md-color-media='(prefers-color-scheme: dark)']\"\n        )!\n\n        /* Retrieve colors for system preference */\n        palette.color.scheme  = input.getAttribute(\"data-md-color-scheme\")!\n        palette.color.primary = input.getAttribute(\"data-md-color-primary\")!\n        palette.color.accent  = input.getAttribute(\"data-md-color-accent\")!\n      }\n\n      /* Set color palette */\n      for (const [key, value] of Object.entries(palette.color))\n        document.body.setAttribute(`data-md-color-${key}`, value)\n\n      /* Set toggle visibility */\n      for (let index = 0; index < inputs.length; index++) {\n        const label = inputs[index].nextElementSibling\n        if (label instanceof HTMLElement)\n          label.hidden = palette.index !== index\n      }\n\n      /* Persist preference in local storage */\n      __md_set(\"__palette\", palette)\n    })\n\n    // Handle color switch on Enter or Space - see https://t.ly/YIhVj\n    fromEvent<KeyboardEvent>(el, \"keydown\").pipe(\n      filter(ev => ev.key === \"Enter\"),\n      withLatestFrom(push$, (_, palette) => palette)\n    )\n      .subscribe(({ index }) => {\n        index = (index + 1) % inputs.length\n        inputs[index].click()\n        inputs[index].focus()\n      })\n\n    /* Update theme-color meta tag */\n    push$\n      .pipe(\n        map(() => {\n          const header = getComponentElement(\"header\")\n          const style  = window.getComputedStyle(header)\n\n          // Set color scheme\n          scheme.content = style.colorScheme\n\n          /* Return color in hexadecimal format */\n          return style.backgroundColor.match(/\\d+/g)!\n            .map(value => (+value).toString(16).padStart(2, \"0\"))\n            .join(\"\")\n        })\n      )\n        .subscribe(color => meta.content = `#${color}`)\n\n    /* Revert transition durations after color switch */\n    push$.pipe(observeOn(asyncScheduler))\n      .subscribe(() => {\n        document.body.removeAttribute(\"data-md-color-switching\")\n      })\n\n    /* Create and return component */\n    return watchPalette(inputs)\n      .pipe(\n        takeUntil(media$.pipe(skip(1))),\n        repeat(),\n        tap(state => push$.next(state)),\n        finalize(() => push$.complete()),\n        map(state => ({ ref: el, ...state }))\n      )\n  })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  Subject,\n  defer,\n  finalize,\n  map,\n  tap\n} from \"rxjs\"\n\nimport { Component } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Progress indicator\n */\nexport interface Progress {\n  value: number                        // Progress value\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  progress$: Subject<number>           // Progress subject\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount progress indicator\n *\n * @param el - Progress indicator element\n * @param options - Options\n *\n * @returns Progress indicator component observable\n */\nexport function mountProgress(\n  el: HTMLElement, { progress$ }: MountOptions\n): Observable<Component<Progress>> {\n\n  // Mount component on subscription\n  return defer(() => {\n    const push$ = new Subject<Progress>()\n    push$.subscribe(({ value }) => {\n      el.style.setProperty(\"--md-progress-value\", `${value}`)\n    })\n\n    // Create and return component\n    return progress$\n      .pipe(\n        tap(value => push$.next({ value })),\n        finalize(() => push$.complete()),\n        map(value => ({ ref: el, value }))\n      )\n  })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  catchError,\n  map,\n  of,\n  share\n} from \"rxjs\"\n\nimport {\n  getElement,\n  getElements,\n  requestXML\n} from \"~/browser\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Sitemap, i.e. a list of URLs\n */\nexport type Sitemap = Map<string, URL[]>\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Resolve URL to the given base URL\n *\n * When serving the site with instant navigation, MkDocs will set the hostname\n * to the value as specified in `dev_addr`, but the browser allows for several\n * hostnames to be used: `localhost`, `127.0.0.1` or even `0.0.0.0`, depending\n * on configuration. This function resolves the URL to the given hostname.\n *\n * @param url - URL\n * @param base - Base URL\n *\n * @returns Resolved URL\n */\nfunction resolve(url: URL, base: URL) {\n  url.protocol = base.protocol\n  url.hostname = base.hostname\n  return url\n}\n\n/**\n * Extract sitemap from document\n *\n * This function extracts the URLs and alternate links from the document, and\n * associates alternate links to the original URL as found in `loc`, allowing\n * the browser to navigate to the correct page when switching languages. The\n * format of the sitemap is expected to adhere to:\n *\n * ``` xml\n * <urlset>\n *   <url>\n *     <loc>...</loc>\n *     <xhtml:link rel=\"alternate\" hreflang=\"en\" href=\"...\"/>\n *     <xhtml:link rel=\"alternate\" hreflang=\"de\" href=\"...\"/>\n *     ...\n *   </url>\n *   ...\n * </urlset>\n * ```\n *\n * @param document - Document\n * @param base - Base URL\n *\n * @returns Sitemap\n */\nfunction extract(document: Document, base: URL): Sitemap {\n  const sitemap: Sitemap = new Map()\n  for (const el of getElements(\"url\", document)) {\n    const url = getElement(\"loc\", el)\n\n    // Create entry for location and add it to the list of links\n    const links = [resolve(new URL(url.textContent!), base)]\n    sitemap.set(`${links[0]}`, links)\n\n    // Attach alternate links to current entry\n    for (const link of getElements(\"[rel=alternate]\", el)) {\n      const href = link.getAttribute(\"href\")\n      if (href != null)\n        links.push(resolve(new URL(href), base))\n    }\n  }\n\n  // Return sitemap\n  return sitemap\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch the sitemap for the given base URL\n *\n * If a network or parsing error occurs, we just default to an empty sitemap,\n * which means the caller should fall back to regular navigation.\n *\n * @param base - Base URL\n *\n * @returns Sitemap observable\n */\nexport function fetchSitemap(base: URL | string): Observable<Sitemap> {\n  return requestXML(new URL(\"sitemap.xml\", base))\n    .pipe(\n      map(document => extract(document, new URL(base))),\n      catchError(() => of(new Map())),\n      share()\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  EMPTY,\n  Observable,\n  catchError,\n  filter,\n  fromEvent,\n  map,\n  mergeMap,\n  of,\n  switchMap\n} from \"rxjs\"\n\nimport { configuration } from \"~/_\"\nimport {\n  getElements,\n  getLocation,\n  setLocation\n} from \"~/browser\"\n\nimport { Sitemap, fetchSitemap } from \"../sitemap\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Setup options\n */\ninterface SetupOptions {\n  document$: Observable<Document>      /* Document subject */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Set up alternate version navigation\n *\n * @param options - Options\n */\nexport function setupAlternate(\n  { document$ }: SetupOptions\n): void {\n  const alternate = new Map<string, Sitemap>()\n\n  // Fetch sitemaps for all discovered alternate versions\n  document$\n    .pipe(\n      switchMap(() => getElements<HTMLLinkElement>(\"link[rel=alternate]\")),\n      map(el => new URL(el.href)),\n      filter(url => !alternate.has(url.toString())),\n      mergeMap(url => fetchSitemap(url)\n        .pipe(\n          map(sitemap => [url, sitemap] as const),\n          catchError(() => EMPTY)\n        )\n      )\n    )\n\n      // Persist fully qualified URL, because alternate versions may be on\n      // entirely different domains, but as long a proper cross-origin policy\n      // is set, we can still navigate to them. Also, remove the trailing slash\n      // to normalize the URL\n      .subscribe(([url, sitemap]) => {\n        alternate.set(url.toString().replace(/\\/$/, \"\"), sitemap)\n      })\n\n  // Intercept alternate navigation - when refactoring instant navigation later,\n  // we should provide a single stream of events that we all subscribe to, and\n  // from which we implement version and alternate language navigation\n  fromEvent<MouseEvent>(document.body, \"click\")\n    .pipe(\n      filter(ev => !ev.metaKey && !ev.ctrlKey),\n      switchMap(ev => {\n        if (ev.target instanceof Element) {\n          const el = ev.target.closest(\"a\")\n\n          // Now, we need to check whether the navigation target is an alternate\n          // version. If so, we need to prevent the default navigation behavior\n          // and instead navigate to the correct page, if we can resolve it.\n          if (el && !el.target) {\n            const result = [...alternate].find(([url]) => (\n              el.href.startsWith(`${url}/`)\n            ))\n\n            // Check, that we got a sitemap at least, so we know that we either\n            // navigate on the current site, or to an alternate site\n            if (typeof result === \"undefined\")\n              return EMPTY\n\n            // Check that we go to and alternate site\n            const [url, sitemap] = result\n            const location = getLocation()\n            if (location.href.startsWith(url))\n              return EMPTY\n\n            // Isolate the part to which we navigate and check if it's in the\n            // sitemap that we resolved earlier @todo: refactor this, as the\n            // semantics slightly changed due to the new sitemap resolution\n            // implementation, which normalizes all URLs.\n            const config = configuration()\n            let path = location.href.replace(config.base, \"\")\n            path = `${url}/${path}`\n            const target = sitemap.has(path.split(\"#\")[0])\n              ? new URL(path, config.base)\n              : new URL(url)\n\n            // Steal navigation and navigate to the correct page\n            ev.preventDefault()\n            return of(target)\n          }\n        }\n        return EMPTY\n      })\n    )\n    .subscribe(url => setLocation(url, true))\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport ClipboardJS from \"clipboard\"\nimport {\n  Observable,\n  Subject,\n  map,\n  tap\n} from \"rxjs\"\n\nimport { translation } from \"~/_\"\nimport { getElement } from \"~/browser\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Setup options\n */\ninterface SetupOptions {\n  alert$: Subject<string>              /* Alert subject */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Extract text to copy\n *\n * @param el - HTML element\n *\n * @returns Extracted text\n */\nfunction extract(el: HTMLElement): string {\n  el.setAttribute(\"data-md-copying\", \"\")\n  const copy = el.closest(\"[data-copy]\")\n  const text = copy\n    ? copy.getAttribute(\"data-copy\")!\n    : el.innerText\n  el.removeAttribute(\"data-md-copying\")\n  return text.trimEnd()\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Set up Clipboard.js integration\n *\n * @param options - Options\n */\nexport function setupClipboardJS(\n  { alert$ }: SetupOptions\n): void {\n  if (ClipboardJS.isSupported()) {\n    new Observable<ClipboardJS.Event>(subscriber => {\n      new ClipboardJS(\"[data-clipboard-target], [data-clipboard-text]\", {\n        text: el => (\n          el.getAttribute(\"data-clipboard-text\")! ||\n          extract(getElement(\n            el.getAttribute(\"data-clipboard-target\")!\n          ))\n        )\n      })\n        .on(\"success\", ev => subscriber.next(ev))\n    })\n      .pipe(\n        tap(ev => {\n          const trigger = ev.trigger as HTMLElement\n          trigger.focus()\n        }),\n        map(() => translation(\"clipboard.copied\"))\n      )\n        .subscribe(alert$)\n  }\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  EMPTY,\n  Observable,\n  Subject,\n  catchError,\n  combineLatestWith,\n  concat,\n  debounceTime,\n  distinct,\n  distinctUntilChanged,\n  distinctUntilKeyChanged,\n  endWith,\n  exhaustMap,\n  fromEvent,\n  ignoreElements,\n  map,\n  merge,\n  of,\n  share,\n  switchMap,\n  take,\n  tap,\n  withLatestFrom\n} from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport {\n  Viewport,\n  getElements,\n  getLocation,\n  getOptionalElement,\n  requestHTML,\n  setLocation,\n  setLocationHash\n} from \"~/browser\"\nimport { getComponentElement } from \"~/components\"\n\nimport { Sitemap } from \"../sitemap\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Setup options\n */\ninterface SetupOptions {\n  sitemap$: Observable<Sitemap>        // Sitemap observable\n  location$: Subject<URL>              // Location subject\n  viewport$: Observable<Viewport>      // Viewport observable\n  progress$: Subject<number>           // Progress subject\n}\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Handle clicks on internal URLs while skipping external URLs\n *\n * @param ev - Mouse event\n * @param sitemap - Sitemap\n *\n * @returns Anchor observable\n */\nfunction handle(\n  ev: MouseEvent, sitemap: Sitemap\n): Observable<HTMLAnchorElement> {\n  if (!(ev.target instanceof Element))\n    return EMPTY\n\n  // Skip, as target is not within a link - clicks on non-link elements are\n  // also captured, which we need to exclude from processing\n  const el = ev.target.closest(\"a\")\n  if (el === null)\n    return EMPTY\n\n  // Skip, as link opens in new window - we now know we have captured a click\n  // on a link, but the link either has a `target` property defined, or the\n  // user pressed the `meta` or `ctrl` key to open it in a new window. Thus,\n  // we need to filter this event as well.\n  if (el.target || ev.metaKey || ev.ctrlKey)\n    return EMPTY\n\n  // Next, we must check if the URL is relevant for us, i.e., if it's an\n  // internal link to a page that is managed by MkDocs. Only then we can be\n  // sure that the structure of the page to be loaded adheres to the current\n  // document structure and can subsequently be injected into it without doing\n  // a full reload. For this reason, we must canonicalize the URL by removing\n  // all search parameters and hash fragments.\n  const url = new URL(el.href)\n  url.search = url.hash = \"\"\n\n  // Skip, if URL is not included in the sitemap - this could be the case when\n  // linking between versions or languages, or to another page that the author\n  // included as part of the build, but that is not managed by MkDocs. In that\n  // case we must not continue with instant navigation.\n  if (!sitemap.has(`${url}`))\n    return EMPTY\n\n  // We now know that we have a link to an internal page, so we prevent the\n  // browser from navigation and emit the URL for instant navigation. Note that\n  // this also includes anchor links, which means we need to implement anchor\n  // positioning ourselves. The reason for this is that if we wouldn't manage\n  // anchor links as well, scroll restoration will not work correctly (e.g.\n  // following an anchor link and scrolling).\n  ev.preventDefault()\n  return of(el)\n}\n\n/**\n * Create a map of head elements for lookup and replacement\n *\n * @param document - Document\n *\n * @returns Tag map\n */\nfunction head(document: Document): Map<string, HTMLElement> {\n  const tags = new Map<string, HTMLElement>()\n  for (const el of getElements(\":scope > *\", document.head))\n    tags.set(el.outerHTML, el)\n\n  // Return tag map\n  return tags\n}\n\n/**\n * Resolve relative URLs in the given document\n *\n * This function resolves relative `href` and `src` attributes, which can belong\n * to all sorts of tags, like meta tags, links, images, scripts and more.\n *\n * @param document - Document\n *\n * @returns Document observable\n */\nfunction resolve(document: Document): Observable<Document> {\n  for (const el of getElements(\"[href], [src]\", document))\n    for (const key of [\"href\", \"src\"]) {\n      const value = el.getAttribute(key)\n      if (value && !/^(?:[a-z]+:)?\\/\\//i.test(value)) {\n        // @ts-expect-error - trick: self-assign to resolve URL\n        el[key] = el[key]\n        break\n      }\n    }\n\n  // Return document observable\n  return of(document)\n}\n\n/**\n * Inject the contents of a document into the current one\n *\n * @param next - Next document\n *\n * @returns Document observable\n */\nfunction inject(next: Document): Observable<Document> {\n  for (const selector of [\n    \"[data-md-component=announce]\",\n    \"[data-md-component=container]\",\n    \"[data-md-component=header-topic]\",\n    \"[data-md-component=outdated]\",\n    \"[data-md-component=logo]\",\n    \"[data-md-component=skip]\",\n    ...feature(\"navigation.tabs.sticky\")\n      ? [\"[data-md-component=tabs]\"]\n      : []\n  ]) {\n    const source = getOptionalElement(selector)\n    const target = getOptionalElement(selector, next)\n    if (\n      typeof source !== \"undefined\" &&\n      typeof target !== \"undefined\"\n    ) {\n      source.replaceWith(target)\n    }\n  }\n\n  // Update meta tags\n  const tags = head(document)\n  for (const [html, el] of head(next))\n    if (tags.has(html))\n      tags.delete(html)\n    else\n      document.head.appendChild(el)\n\n  // Remove meta tags that are not present in the new document\n  for (const el of tags.values()) {\n    const name = el.getAttribute(\"name\")\n    // @todo - find a better way to handle attributes we add dynamically in\n    // other components without mounting components on every navigation, as\n    // this might impact overall performance - see https://t.ly/ehp_O\n    if (name !== \"theme-color\" && name !== \"color-scheme\")\n      el.remove()\n  }\n\n  // After components and meta tags were replaced, re-evaluate scripts\n  // that were provided by the author as part of Markdown files\n  const container = getComponentElement(\"container\")\n  return concat(getElements(\"script\", container))\n    .pipe(\n      switchMap(el => {\n        const script = next.createElement(\"script\")\n        if (el.src) {\n          for (const name of el.getAttributeNames())\n            script.setAttribute(name, el.getAttribute(name)!)\n          el.replaceWith(script)\n\n          // Complete when script is loaded\n          return new Observable(observer => {\n            script.onload = () => observer.complete()\n          })\n\n        // Complete immediately\n        } else {\n          script.textContent = el.textContent\n          el.replaceWith(script)\n          return EMPTY\n        }\n      }),\n      ignoreElements(),\n      endWith(document)\n    )\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Set up instant navigation\n *\n * This is a heavily orchestrated operation - see inline comments to learn how\n * this works with Material for MkDocs, and how you can hook into it.\n *\n * @param options - Options\n *\n * @returns Document observable\n */\nexport function setupInstantNavigation(\n  { sitemap$, location$, viewport$, progress$ }: SetupOptions\n): Observable<Document> {\n  if (location.protocol === \"file:\")\n    return EMPTY\n\n  // Since we might be on a slow connection, the user might trigger multiple\n  // instant navigation events that overlap. MkDocs produces relative URLs for\n  // all internal links, which becomes a problem in this case, because we need\n  // to change the base URL the moment the user clicks a link that should be\n  // intercepted in order to be consistent with popstate, which means that the\n  // base URL would now be incorrect when resolving another relative link from\n  // the same site. For this reason we always resolve all relative links to\n  // absolute links, so we can be sure this never happens.\n  of(document)\n    .subscribe(resolve)\n\n  // --------------------------------------------------------------------------\n  // Navigation interception\n  // --------------------------------------------------------------------------\n\n  // Intercept navigation - to keep the number of event listeners down we use\n  // the fact that uncaptured events bubble up to the body. This has the nice\n  // property that we don't need to detach and then re-attach event listeners\n  // when the document is replaced after a navigation event.\n  const instant$ =\n    fromEvent<MouseEvent>(document.body, \"click\")\n      .pipe(\n        combineLatestWith(sitemap$),\n        switchMap(([ev, sitemap]) => handle(ev, sitemap)),\n        map(({ href }) => new URL(href)),\n        share()\n      )\n\n  // Intercept history change events, e.g. when the user uses the browser's\n  // back or forward buttons, and emit new location for fetching and parsing\n  const history$ =\n    fromEvent<PopStateEvent>(window, \"popstate\")\n      .pipe(\n        map(getLocation),\n        share()\n      )\n\n  // While it would be better UX to defer navigation events until the document\n  // is fully fetched and parsed, we must schedule it here to synchronize with\n  // popstate events, as they are emitted immediately. Moreover we need to\n  // store the current viewport offset for scroll restoration later on.\n  instant$.pipe(withLatestFrom(viewport$))\n    .subscribe(([url, { offset }]) => {\n      history.replaceState(offset, \"\")\n      history.pushState(null, \"\", url)\n    })\n\n  // Emit URLs that should be fetched via instant navigation on location subject\n  // which was passed into this function. The state of instant navigation can be\n  // intercepted by other parts of the application, which can synchronously back\n  // up or restore state before or after instant navigation happens.\n  merge(instant$, history$)\n    .subscribe(location$)\n\n  // --------------------------------------------------------------------------\n  // Fetching and parsing\n  // --------------------------------------------------------------------------\n\n  // Fetch document - we deduplicate requests to the same location, so we don't\n  // end up with multiple requests for the same page. We use `switchMap`, since\n  // we want to cancel the previous request when a new one is triggered, which\n  // is automatically handled by the observable returned by `request`. This is\n  // essential to ensure a good user experience, as we don't want to load pages\n  // that are not needed anymore, e.g., when the user clicks multiple links in\n  // quick succession or on slow connections. If the request fails for some\n  // reason, we fall back and use regular navigation, forcing a reload.\n  const document$ =\n    location$.pipe(\n      distinctUntilKeyChanged(\"pathname\"),\n      switchMap(url => requestHTML(url, { progress$ })\n        .pipe(\n          catchError(() => {\n            setLocation(url, true)\n            return EMPTY\n          })\n        )\n      ),\n\n      // The document was successfully fetched and parsed, so we can inject its\n      // contents into the currently active document\n      switchMap(resolve),\n      switchMap(inject),\n      share()\n    )\n\n  // --------------------------------------------------------------------------\n  // Scroll restoration\n  // --------------------------------------------------------------------------\n\n  // Handle scroll restoration - we must restore the viewport offset after the\n  // document has been fetched and injected, and every time the user clicks an\n  // anchor that leads to an element on the same page, which might also happen\n  // when the user uses the back or forward button.\n  merge(\n    document$.pipe(withLatestFrom(location$, (_, url) => url)),\n\n    // Handle instant navigation events that are triggered by the user clicking\n    // on an anchor link with a hash fragment different from the current one, as\n    // well as from popstate events, which are emitted when the user navigates\n    // back and forth between pages.\n    document$.pipe(\n      switchMap(() => location$),\n      distinctUntilKeyChanged(\"hash\"),\n    ),\n\n    // Handle instant navigation events that are triggered by the user clicking\n    // on an anchor link with the same hash fragment as the current one in the\n    // URL. It is essential that we only intercept those from instant navigation\n    // events and not from history change events, or we'll end up in and endless\n    // loop. The top-level history entry must be removed, as it will be replaced\n    // with a new one, which would otherwise lead to a duplicate entry.\n    location$.pipe(\n      distinctUntilChanged((a, b) => (\n        a.pathname === b.pathname &&\n        a.hash     === b.hash\n      )),\n      switchMap(() => instant$),\n      tap(() => history.back())\n    )\n  )\n    .subscribe(url => {\n\n      // Check if the current history entry has a state, which happens when the\n      // user presses the back or forward button to visit a page we've already\n      // seen. If there's no state, it means a new page was visited and we must\n      // scroll to the top, unless an anchor is given.\n      if (history.state !== null || !url.hash) {\n        window.scrollTo(0, history.state?.y ?? 0)\n      } else {\n        history.scrollRestoration = \"auto\"\n        setLocationHash(url.hash)\n        history.scrollRestoration = \"manual\"\n      }\n    })\n\n  // Disable scroll restoration when an instant navigation event occurs, so the\n  // browser does not immediately set the viewport offset to the prior history\n  // entry, scrolling to the position on the same page, which would look odd.\n  // Instead, we manually restore the position once the page has loaded.\n  location$.subscribe(() => {\n    history.scrollRestoration = \"manual\"\n  })\n\n  // Enable scroll restoration before window unloads - this is essential to\n  // ensure that full reloads (F5) restore the viewport offset correctly. If\n  // only popstate events wouldn't reset the viewport offset prior to their\n  // emission, we could just reset this in popstate. Meh.\n  fromEvent(window, \"beforeunload\")\n    .subscribe(() => {\n      history.scrollRestoration = \"auto\"\n    })\n\n  // Track viewport offset, so we can restore it when the user navigates back\n  // and forth between pages. Note that this must be debounced and cannot be\n  // done in popstate, as popstate has already removed the entry from the\n  // history, which means it is too late.\n  viewport$.pipe(\n    distinctUntilKeyChanged(\"offset\"),\n    debounceTime(100)\n  )\n    .subscribe(({ offset }) => {\n      history.replaceState(offset, \"\")\n    })\n\n  // --------------------------------------------------------------------------\n  // Navigation prefetching\n  // --------------------------------------------------------------------------\n\n  // If prefetching is enabled, prefetch pages for links that would trigger\n  // inter-site navigation on mouse events - this should improve performance,\n  // since pages will be cached. Note that we exhaust map URLs, so we ensure\n  // that loading is properly debounced and we don't fill caches up to quickly.\n  if (feature(\"navigation.instant.prefetch\"))\n    merge(\n      fromEvent<MouseEvent>(document.body, \"mousemove\"),\n      fromEvent<MouseEvent>(document.body, \"focusin\")\n    )\n      .pipe(\n        combineLatestWith(sitemap$),\n        switchMap(([ev, sitemap]) => handle(ev, sitemap)),\n        debounceTime(25),\n        distinct(({ href }) => href),\n        exhaustMap(href => {\n          const link = document.createElement(\"link\")\n          link.rel = \"prefetch\"\n          link.href = href.toString()\n\n          // Instruct browser to prefetch link by adding a link tag of type\n          // prefetch to the head, and remove it again once the page was loaded\n          document.head.appendChild(link)\n          return fromEvent(link, \"load\")\n            .pipe(\n              map(() => link),\n              take(1)\n            )\n        })\n      )\n        .subscribe(link => link.remove())\n\n  // Return document observable\n  return document$\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport escapeHTML from \"escape-html\"\n\nimport { SearchConfig } from \"../config\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search highlight function\n *\n * @param value - Value\n *\n * @returns Highlighted value\n */\nexport type SearchHighlightFn = (value: string) => string\n\n/**\n * Search highlight factory function\n *\n * @param query - Query value\n *\n * @returns Search highlight function\n */\nexport type SearchHighlightFactoryFn = (query: string) => SearchHighlightFn\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Create a search highlighter\n *\n * @param config - Search configuration\n *\n * @returns Search highlight factory function\n */\nexport function setupSearchHighlighter(\n  config: SearchConfig\n): SearchHighlightFactoryFn {\n  // Hack: temporarily remove pure lookaheads and lookbehinds\n  const regex = config.separator.split(\"|\").map(term => {\n    const temp = term.replace(/(\\(\\?[!=<][^)]+\\))/g, \"\")\n    return temp.length === 0 ? \"\uFFFD\" : term\n  })\n    .join(\"|\")\n\n  const separator = new RegExp(regex, \"img\")\n  const highlight = (_: unknown, data: string, term: string) => {\n    return `${data}<mark data-md-highlight>${term}</mark>`\n  }\n\n  /* Return factory function */\n  return (query: string) => {\n    query = query\n      .replace(/[\\s*+\\-:~^]+/g, \" \")\n      .replace(/&/g, \"&amp;\")\n      .trim()\n\n    /* Create search term match expression */\n    const match = new RegExp(`(^|${config.separator}|)(${\n      query\n        .replace(/[|\\\\{}()[\\]^$+*?.-]/g, \"\\\\$&\")\n        .replace(separator, \"|\")\n    })`, \"img\")\n\n    /* Highlight string value */\n    return value => escapeHTML(value)\n      .replace(match, highlight)\n      .replace(/<\\/mark>(\\s+)<mark[^>]*>/img, \"$1\")\n  }\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A RTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { SearchResult } from \"../../_\"\nimport { SearchIndex } from \"../../config\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search message type\n */\nexport const enum SearchMessageType {\n  SETUP,                               /* Search index setup */\n  READY,                               /* Search index ready */\n  QUERY,                               /* Search query */\n  RESULT                               /* Search results */\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Message containing the data necessary to setup the search index\n */\nexport interface SearchSetupMessage {\n  type: SearchMessageType.SETUP        /* Message type */\n  data: SearchIndex                    /* Message data */\n}\n\n/**\n * Message indicating the search index is ready\n */\nexport interface SearchReadyMessage {\n  type: SearchMessageType.READY        /* Message type */\n}\n\n/**\n * Message containing a search query\n */\nexport interface SearchQueryMessage {\n  type: SearchMessageType.QUERY        /* Message type */\n  data: string                         /* Message data */\n}\n\n/**\n * Message containing results for a search query\n */\nexport interface SearchResultMessage {\n  type: SearchMessageType.RESULT       /* Message type */\n  data: SearchResult                   /* Message data */\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Message exchanged with the search worker\n */\nexport type SearchMessage =\n  | SearchSetupMessage\n  | SearchReadyMessage\n  | SearchQueryMessage\n  | SearchResultMessage\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Type guard for search ready messages\n *\n * @param message - Search worker message\n *\n * @returns Test result\n */\nexport function isSearchReadyMessage(\n  message: SearchMessage\n): message is SearchReadyMessage {\n  return message.type === SearchMessageType.READY\n}\n\n/**\n * Type guard for search result messages\n *\n * @param message - Search worker message\n *\n * @returns Test result\n */\nexport function isSearchResultMessage(\n  message: SearchMessage\n): message is SearchResultMessage {\n  return message.type === SearchMessageType.RESULT\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A RTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  ObservableInput,\n  Subject,\n  first,\n  merge,\n  of,\n  switchMap\n} from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport { watchToggle, watchWorker } from \"~/browser\"\n\nimport { SearchIndex } from \"../../config\"\nimport {\n  SearchMessage,\n  SearchMessageType\n} from \"../message\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Set up search worker\n *\n * This function creates and initializes a web worker that is used for search,\n * so that the user interface doesn't freeze. In general, the application does\n * not care how search is implemented, as long as the web worker conforms to\n * the format expected by the application as defined in `SearchMessage`. This\n * allows the author to implement custom search functionality, by providing a\n * custom web worker via configuration.\n *\n * Material for MkDocs' built-in search implementation makes use of Lunr.js, an\n * efficient and fast implementation for client-side search. Leveraging a tiny\n * iframe-based web worker shim, search is even supported for the `file://`\n * protocol, enabling search for local non-hosted builds.\n *\n * If the protocol is `file://`, search initialization is deferred to mitigate\n * freezing, as it's now synchronous by design - see https://bit.ly/3C521EO\n *\n * @see https://bit.ly/3igvtQv - How to implement custom search\n *\n * @param url - Worker URL\n * @param index$ - Search index observable input\n *\n * @returns Search worker\n */\nexport function setupSearchWorker(\n  url: string, index$: ObservableInput<SearchIndex>\n): Subject<SearchMessage> {\n  const worker$ = watchWorker<SearchMessage>(url)\n  merge(\n    of(location.protocol !== \"file:\"),\n    watchToggle(\"search\")\n  )\n    .pipe(\n      first(active => active),\n      switchMap(() => index$)\n    )\n      .subscribe(({ config, docs }) => worker$.next({\n        type: SearchMessageType.SETUP,\n        data: {\n          config,\n          docs,\n          options: {\n            suggest: feature(\"search.suggest\")\n          }\n        }\n      }))\n\n  /* Return search worker */\n  return worker$\n}\n", "import { Sitemap } from \"../../sitemap\"\n\n/** See docstring for `selectedVersionCorrespondingURL` for the meaning of these fields. */\ntype CorrespondingURLParams = {\n  selectedVersionSitemap: Sitemap\n  selectedVersionBaseURL: URL\n  currentLocation: URL\n  currentBaseURL: string\n}\n\n/**\n * Choose a URL to navigate to when the user chooses a version in the version\n * selector.\n *\n * The parameters in `params` are named as follows, in order to make it clearer\n * which parameter means what when invoking the function:\n *\n *  - selectedVersionSitemap: Sitemap - as obtained by fetchSitemap from `${selectedVersionBaseURL}/sitemap.xml`\n *\n *  - selectedVersionBaseURL: URL - usually `${currentBaseURL}/../selectedVersion`\n *\n *  - currentLocation: URL - current web browser location\n *\n *  - currentBaseURL: string - as obtained from `config.base`\n *\n * @param params - arguments with the meanings explained above.\n * @returns the URL to navigate to or null if we can't be sure that the\n * corresponding page to the current page exists in the selected version\n */\nexport function selectedVersionCorrespondingURL(\n  params: CorrespondingURLParams\n): URL | undefined {\n  const {selectedVersionSitemap,\n    selectedVersionBaseURL,\n    currentLocation,\n    currentBaseURL} = params\n  const current_path = safeURLParse(currentBaseURL)?.pathname\n  if (current_path === undefined) {\n    return\n  }\n  const currentRelativePath = stripPrefix(currentLocation.pathname, current_path)\n  if (currentRelativePath === undefined) {\n    return\n  }\n  const sitemapCommonPrefix = shortestCommonPrefix(selectedVersionSitemap.keys())\n  if (!selectedVersionSitemap.has(sitemapCommonPrefix)) {\n    // We could also check that `commonSitemapPrefix` ends in the canonical version,\n    // similarly to https://github.com/squidfunk/mkdocs-material/pull/7227. However,\n    // I don't believe that Mike/MkDocs ever generate sitemaps where it would matter\n    return\n  }\n\n  const potentialSitemapURL = safeURLParse(currentRelativePath, sitemapCommonPrefix)\n  if (!potentialSitemapURL || !selectedVersionSitemap.has(potentialSitemapURL.href)) {\n    return\n  }\n\n  const result = safeURLParse(currentRelativePath, selectedVersionBaseURL)\n  if (!result) {\n    return\n  }\n  result.hash = currentLocation.hash\n  result.search = currentLocation.search\n  return result\n}\n\n/**\n * A version of `new URL` that never throws. A polyfill for URL.parse() which is\n * not yet ubuquitous.\n *\n * @param url - passed to `new URL` constructor\n * @param base - passed to `new URL` constructor\n *\n * @returns `new URL(url, base)` or undefined if the URL is invalid.\n */\nfunction safeURLParse(url: string|URL, base?: string|URL): URL | undefined {\n  try {\n    return new URL(url, base)\n  } catch {\n    return\n  }\n}\n\n// Basic string manipulation\n\n/** Strip a given prefix from a function\n *\n * @param s - string\n * @param prefix - prefix to strip\n *\n * @returns either the string with the prefix stripped or undefined if the\n * string did not begin with the prefix.\n */\nexport function stripPrefix(s: string, prefix: string): string | undefined {\n  if (s.startsWith(prefix)) {\n    return s.slice(prefix.length)\n  }\n  return undefined\n}\n\n/** Find the length of the longest common prefix of two strings\n *\n * @param s1 - first string\n * @param s2 - second string\n *\n * @returns - the length of the longest common prefix of the two strings.\n */\nfunction commonPrefixLen(s1: string, s2: string): number {\n  const max = Math.min(s1.length, s2.length)\n  let result\n  for (result = 0; result < max; ++result) {\n    if (s1[result] !== s2[result]) {\n      break\n    }\n  }\n  return result\n}\n\n/** Find the longest common prefix of any number of strings\n *\n * @param strs - an iterable of strings\n *\n * @returns the longest common prefix of all the strings\n */\nexport function shortestCommonPrefix(strs: Iterable<string>): string {\n  let result  // Undefined if no iterations happened\n  for (const s of strs) {\n    if (result === undefined) {\n      result = s\n    } else {\n      result = result.slice(0, commonPrefixLen(result, s))\n    }\n  }\n  return result ?? \"\"\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  EMPTY,\n  Subject,\n  catchError,\n  combineLatest,\n  filter,\n  fromEvent,\n  map,\n  of,\n  switchMap,\n  withLatestFrom\n} from \"rxjs\"\n\nimport { configuration } from \"~/_\"\nimport {\n  getElement,\n  getLocation,\n  requestJSON,\n  setLocation\n} from \"~/browser\"\nimport { getComponentElements } from \"~/components\"\nimport {\n  Version,\n  renderVersionSelector\n} from \"~/templates\"\n\nimport { fetchSitemap } from \"../sitemap\"\n\nimport { selectedVersionCorrespondingURL } from \"./findurl\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Setup options\n */\ninterface SetupOptions {\n  document$: Subject<Document>         /* Document subject */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Set up version selector\n *\n * @param options - Options\n */\nexport function setupVersionSelector(\n  { document$ }: SetupOptions\n): void {\n  const config = configuration()\n  const versions$ = requestJSON<Version[]>(\n    new URL(\"../versions.json\", config.base)\n  )\n    .pipe(\n      catchError(() => EMPTY) // @todo refactor instant loading\n    )\n\n  /* Determine current version */\n  const current$ = versions$\n    .pipe(\n      map(versions => {\n        const [, current] = config.base.match(/([^/]+)\\/?$/)!\n        return versions.find(({ version, aliases }) => (\n          version === current || aliases.includes(current)\n        )) || versions[0]\n      })\n    )\n\n  /* Intercept inter-version navigation */\n  versions$\n    .pipe(\n      map(versions => new Map(versions.map(version => [\n        `${new URL(`../${version.version}/`, config.base)}`,\n        version\n      ]))),\n      switchMap(urls => fromEvent<MouseEvent>(document.body, \"click\")\n        .pipe(\n          filter(ev => !ev.metaKey && !ev.ctrlKey),\n          withLatestFrom(current$),\n          switchMap(([ev, current]) => {\n            if (ev.target instanceof Element) {\n              const el = ev.target.closest(\"a\")\n              if (el && !el.target && urls.has(el.href)) {\n                const url = el.href\n                // This is a temporary hack to detect if a version inside the\n                // version selector or on another part of the site was clicked.\n                // If we're inside the version selector, we definitely want to\n                // find the same page, as we might have different deployments\n                // due to aliases. However, if we're outside the version\n                // selector, we must abort here, because we might otherwise\n                // interfere with instant navigation. We need to refactor this\n                // at some point together with instant navigation.\n                //\n                // See https://github.com/squidfunk/mkdocs-material/issues/4012\n                if (!ev.target.closest(\".md-version\")) {\n                  const version = urls.get(url)!\n                  if (version === current)\n                    return EMPTY\n                }\n                ev.preventDefault()\n                return of(new URL(url))\n              }\n            }\n            return EMPTY\n          }),\n          switchMap(selectedVersionBaseURL => {\n            return fetchSitemap(selectedVersionBaseURL).pipe(\n              map(\n                sitemap =>\n                  selectedVersionCorrespondingURL({\n                    selectedVersionSitemap: sitemap,\n                    selectedVersionBaseURL,\n                    currentLocation: getLocation(),\n                    currentBaseURL: config.base\n                  }) ?? selectedVersionBaseURL,\n              ),\n            )\n          })\n        )\n      )\n    )\n      .subscribe(url => setLocation(url, true))\n\n  /* Render version selector and warning */\n  combineLatest([versions$, current$])\n    .subscribe(([versions, current]) => {\n      const topic = getElement(\".md-header__topic\")\n      topic.appendChild(renderVersionSelector(versions, current))\n    })\n\n  /* Integrate outdated version banner with instant navigation */\n  document$.pipe(switchMap(() => current$))\n    .subscribe(current => {\n\n      // Always scope outdate version banner to the base URL of the site\n      const base = new URL(config.base)\n\n      /* Check if version state was already determined */\n      let outdated = __md_get(\"__outdated\", sessionStorage, base)\n      if (outdated === null) {\n        outdated = true\n\n        /* Obtain and normalize default versions */\n        let ignored = config.version?.default || \"latest\"\n        if (!Array.isArray(ignored))\n          ignored = [ignored]\n\n        /* Check if version is considered a default */\n        main: for (const ignore of ignored)\n          for (const version of current.aliases.concat(current.version))\n            if (new RegExp(ignore, \"i\").test(version)) {\n              outdated = false\n              break main\n            }\n\n        /* Persist version state in session storage */\n        __md_set(\"__outdated\", outdated, sessionStorage, base)\n      }\n\n      /* Unhide outdated version banner */\n      if (outdated)\n        for (const warning of getComponentElements(\"outdated\"))\n          warning.hidden = false\n    })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  Subject,\n  combineLatest,\n  distinctUntilChanged,\n  distinctUntilKeyChanged,\n  endWith,\n  finalize,\n  first,\n  fromEvent,\n  ignoreElements,\n  map,\n  merge,\n  shareReplay,\n  takeUntil,\n  tap\n} from \"rxjs\"\n\nimport {\n  getElement,\n  getLocation,\n  setToggle,\n  watchElementFocus,\n  watchToggle\n} from \"~/browser\"\nimport {\n  SearchMessage,\n  SearchMessageType,\n  isSearchReadyMessage\n} from \"~/integrations\"\n\nimport { Component } from \"../../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search query\n */\nexport interface SearchQuery {\n  value: string                        /* Query value */\n  focus: boolean                       /* Query focus */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n  worker$: Subject<SearchMessage>      /* Search worker */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  worker$: Subject<SearchMessage>      /* Search worker */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch search query\n *\n * Note that the focus event which triggers re-reading the current query value\n * is delayed by `1ms` so the input's empty state is allowed to propagate.\n *\n * @param el - Search query element\n * @param options - Options\n *\n * @returns Search query observable\n */\nexport function watchSearchQuery(\n  el: HTMLInputElement, { worker$ }: WatchOptions\n): Observable<SearchQuery> {\n\n  /* Support search deep linking */\n  const { searchParams } = getLocation()\n  if (searchParams.has(\"q\")) {\n    setToggle(\"search\", true)\n\n    /* Set query from parameter */\n    el.value = searchParams.get(\"q\")!\n    el.focus()\n\n    /* Remove query parameter on close */\n    watchToggle(\"search\")\n      .pipe(\n        first(active => !active)\n      )\n        .subscribe(() => {\n          const url = getLocation()\n          url.searchParams.delete(\"q\")\n          history.replaceState({}, \"\", `${url}`)\n        })\n  }\n\n  /* Intercept focus and input events */\n  const focus$ = watchElementFocus(el)\n  const value$ = merge(\n    worker$.pipe(first(isSearchReadyMessage)),\n    fromEvent(el, \"keyup\"),\n    focus$\n  )\n    .pipe(\n      map(() => el.value),\n      distinctUntilChanged()\n    )\n\n  /* Combine into single observable */\n  return combineLatest([value$, focus$])\n    .pipe(\n      map(([value, focus]) => ({ value, focus })),\n      shareReplay(1)\n    )\n}\n\n/**\n * Mount search query\n *\n * @param el - Search query element\n * @param options - Options\n *\n * @returns Search query component observable\n */\nexport function mountSearchQuery(\n  el: HTMLInputElement, { worker$ }: MountOptions\n): Observable<Component<SearchQuery, HTMLInputElement>> {\n  const push$ = new Subject<SearchQuery>()\n  const done$ = push$.pipe(ignoreElements(), endWith(true))\n\n  /* Handle value change */\n  combineLatest([\n    worker$.pipe(first(isSearchReadyMessage)),\n    push$\n  ], (_, query) => query)\n    .pipe(\n      distinctUntilKeyChanged(\"value\")\n    )\n      .subscribe(({ value }) => worker$.next({\n        type: SearchMessageType.QUERY,\n        data: value\n      }))\n\n  /* Handle focus change */\n  push$\n    .pipe(\n      distinctUntilKeyChanged(\"focus\")\n    )\n      .subscribe(({ focus }) => {\n        if (focus)\n          setToggle(\"search\", focus)\n      })\n\n  /* Handle reset */\n  fromEvent(el.form!, \"reset\")\n    .pipe(\n      takeUntil(done$)\n    )\n      .subscribe(() => el.focus())\n\n  // Focus search query on label click - note that this is necessary to bring\n  // up the keyboard on iOS and other mobile platforms, as the search dialog is\n  // not visible at first, and programatically focusing an input element must\n  // be triggered by a user interaction - see https://t.ly/Cb30n\n  const label = getElement(\"header [for=__search]\")\n  fromEvent(label, \"click\")\n    .subscribe(() => el.focus())\n\n  /* Create and return component */\n  return watchSearchQuery(el, { worker$ })\n    .pipe(\n      tap(state => push$.next(state)),\n      finalize(() => push$.complete()),\n      map(state => ({ ref: el, ...state })),\n      shareReplay(1)\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  EMPTY,\n  Observable,\n  Subject,\n  bufferCount,\n  filter,\n  finalize,\n  first,\n  fromEvent,\n  map,\n  merge,\n  mergeMap,\n  of,\n  share,\n  skipUntil,\n  switchMap,\n  takeUntil,\n  tap,\n  withLatestFrom,\n  zipWith\n} from \"rxjs\"\n\nimport { translation } from \"~/_\"\nimport {\n  getElement,\n  getOptionalElement,\n  watchElementBoundary,\n  watchToggle\n} from \"~/browser\"\nimport {\n  SearchMessage,\n  SearchResult,\n  isSearchReadyMessage,\n  isSearchResultMessage\n} from \"~/integrations\"\nimport { renderSearchResultItem } from \"~/templates\"\nimport { round } from \"~/utilities\"\n\nimport { Component } from \"../../_\"\nimport { SearchQuery } from \"../query\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  query$: Observable<SearchQuery>      /* Search query observable */\n  worker$: Subject<SearchMessage>      /* Search worker */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount search result list\n *\n * This function performs a lazy rendering of the search results, depending on\n * the vertical offset of the search result container.\n *\n * @param el - Search result list element\n * @param options - Options\n *\n * @returns Search result list component observable\n */\nexport function mountSearchResult(\n  el: HTMLElement, { worker$, query$ }: MountOptions\n): Observable<Component<SearchResult>> {\n  const push$ = new Subject<SearchResult>()\n  const boundary$ = watchElementBoundary(el.parentElement!)\n    .pipe(\n      filter(Boolean)\n    )\n\n  /* Retrieve container */\n  const container = el.parentElement!\n\n  /* Retrieve nested components */\n  const meta = getElement(\":scope > :first-child\", el)\n  const list = getElement(\":scope > :last-child\", el)\n\n  /* Reveal to accessibility tree \u2013 see https://bit.ly/3iAA7t8 */\n  watchToggle(\"search\")\n    .subscribe(active => {\n      list.setAttribute(\"role\", active ? \"list\" : \"presentation\")\n      list.hidden = !active\n    })\n\n  /* Update search result metadata */\n  push$\n    .pipe(\n      withLatestFrom(query$),\n      skipUntil(worker$.pipe(first(isSearchReadyMessage)))\n    )\n      .subscribe(([{ items }, { value }]) => {\n        switch (items.length) {\n\n          /* No results */\n          case 0:\n            meta.textContent = value.length\n              ? translation(\"search.result.none\")\n              : translation(\"search.result.placeholder\")\n            break\n\n          /* One result */\n          case 1:\n            meta.textContent = translation(\"search.result.one\")\n            break\n\n          /* Multiple result */\n          default:\n            const count = round(items.length)\n            meta.textContent = translation(\"search.result.other\", count)\n        }\n      })\n\n  /* Render search result item */\n  const render$ = push$\n    .pipe(\n      tap(() => list.innerHTML = \"\"),\n      switchMap(({ items }) => merge(\n        of(...items.slice(0, 10)),\n        of(...items.slice(10))\n          .pipe(\n            bufferCount(4),\n            zipWith(boundary$),\n            switchMap(([chunk]) => chunk)\n          )\n      )),\n      map(renderSearchResultItem),\n      share()\n    )\n\n  /* Update search result list */\n  render$.subscribe(item => list.appendChild(item))\n  render$\n    .pipe(\n      mergeMap(item => {\n        const details = getOptionalElement(\"details\", item)\n        if (typeof details === \"undefined\")\n          return EMPTY\n\n        /* Keep position of details element stable */\n        return fromEvent(details, \"toggle\")\n          .pipe(\n            takeUntil(push$),\n            map(() => details)\n          )\n      })\n    )\n      .subscribe(details => {\n        if (\n          details.open === false &&\n          details.offsetTop <= container.scrollTop\n        )\n          container.scrollTo({ top: details.offsetTop })\n      })\n\n  /* Filter search result message */\n  const result$ = worker$\n    .pipe(\n      filter(isSearchResultMessage),\n      map(({ data }) => data)\n    )\n\n  /* Create and return component */\n  return result$\n    .pipe(\n      tap(state => push$.next(state)),\n      finalize(() => push$.complete()),\n      map(state => ({ ref: el, ...state }))\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  Subject,\n  endWith,\n  finalize,\n  fromEvent,\n  ignoreElements,\n  map,\n  takeUntil,\n  tap\n} from \"rxjs\"\n\nimport { getLocation } from \"~/browser\"\n\nimport { Component } from \"../../_\"\nimport { SearchQuery } from \"../query\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search sharing\n */\nexport interface SearchShare {\n  url: URL                             /* Deep link for sharing */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n  query$: Observable<SearchQuery>      /* Search query observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  query$: Observable<SearchQuery>      /* Search query observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount search sharing\n *\n * @param _el - Search sharing element\n * @param options - Options\n *\n * @returns Search sharing observable\n */\nexport function watchSearchShare(\n  _el: HTMLElement, { query$ }: WatchOptions\n): Observable<SearchShare> {\n  return query$\n    .pipe(\n      map(({ value }) => {\n        const url = getLocation()\n        url.hash = \"\"\n\n        /* Compute readable query strings */\n        value = value\n          .replace(/\\s+/g, \"+\")        /* Collapse whitespace */\n          .replace(/&/g, \"%26\")        /* Escape '&' character */\n          .replace(/=/g, \"%3D\")        /* Escape '=' character */\n\n        /* Replace query string */\n        url.search = `q=${value}`\n        return { url }\n      })\n    )\n}\n\n/**\n * Mount search sharing\n *\n * @param el - Search sharing element\n * @param options - Options\n *\n * @returns Search sharing component observable\n */\nexport function mountSearchShare(\n  el: HTMLAnchorElement, options: MountOptions\n): Observable<Component<SearchShare>> {\n  const push$ = new Subject<SearchShare>()\n  const done$ = push$.pipe(ignoreElements(), endWith(true))\n  push$.subscribe(({ url }) => {\n    el.setAttribute(\"data-clipboard-text\", el.href)\n    el.href = `${url}`\n  })\n\n  /* Prevent following of link */\n  fromEvent(el, \"click\")\n    .pipe(\n      takeUntil(done$)\n    )\n      .subscribe(ev => ev.preventDefault())\n\n  /* Create and return component */\n  return watchSearchShare(el, options)\n    .pipe(\n      tap(state => push$.next(state)),\n      finalize(() => push$.complete()),\n      map(state => ({ ref: el, ...state }))\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  Subject,\n  asyncScheduler,\n  combineLatestWith,\n  distinctUntilChanged,\n  filter,\n  finalize,\n  fromEvent,\n  map,\n  merge,\n  observeOn,\n  tap\n} from \"rxjs\"\n\nimport { Keyboard } from \"~/browser\"\nimport {\n  SearchMessage,\n  SearchResult,\n  isSearchResultMessage\n} from \"~/integrations\"\n\nimport { Component, getComponentElement } from \"../../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search suggestions\n */\nexport interface SearchSuggest {}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  keyboard$: Observable<Keyboard>      /* Keyboard observable */\n  worker$: Subject<SearchMessage>      /* Search worker */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount search suggestions\n *\n * This function will perform a lazy rendering of the search results, depending\n * on the vertical offset of the search result container.\n *\n * @param el - Search result list element\n * @param options - Options\n *\n * @returns Search result list component observable\n */\nexport function mountSearchSuggest(\n  el: HTMLElement, { worker$, keyboard$ }: MountOptions\n): Observable<Component<SearchSuggest>> {\n  const push$ = new Subject<SearchResult>()\n\n  /* Retrieve query component and track all changes */\n  const query  = getComponentElement(\"search-query\")\n  const query$ = merge(\n    fromEvent(query, \"keydown\"),\n    fromEvent(query, \"focus\")\n  )\n    .pipe(\n      observeOn(asyncScheduler),\n      map(() => query.value),\n      distinctUntilChanged(),\n    )\n\n  /* Update search suggestions */\n  push$\n    .pipe(\n      combineLatestWith(query$),\n      map(([{ suggest }, value]) => {\n        const words = value.split(/([\\s-]+)/)\n        if (suggest?.length && words[words.length - 1]) {\n          const last = suggest[suggest.length - 1]\n          if (last.startsWith(words[words.length - 1]))\n            words[words.length - 1] = last\n        } else {\n          words.length = 0\n        }\n        return words\n      })\n    )\n      .subscribe(words => el.innerHTML = words\n        .join(\"\")\n        .replace(/\\s/g, \"&nbsp;\")\n      )\n\n  /* Set up search keyboard handlers */\n  keyboard$\n    .pipe(\n      filter(({ mode }) => mode === \"search\")\n    )\n      .subscribe(key => {\n        switch (key.type) {\n\n          /* Right arrow: accept current suggestion */\n          case \"ArrowRight\":\n            if (\n              el.innerText.length &&\n              query.selectionStart === query.value.length\n            )\n              query.value = el.innerText\n            break\n        }\n      })\n\n  /* Filter search result message */\n  const result$ = worker$\n    .pipe(\n      filter(isSearchResultMessage),\n      map(({ data }) => data)\n    )\n\n  /* Create and return component */\n  return result$\n    .pipe(\n      tap(state => push$.next(state)),\n      finalize(() => push$.complete()),\n      map(() => ({ ref: el }))\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  NEVER,\n  Observable,\n  ObservableInput,\n  filter,\n  fromEvent,\n  merge,\n  mergeWith\n} from \"rxjs\"\n\nimport { configuration } from \"~/_\"\nimport {\n  Keyboard,\n  getActiveElement,\n  getElements,\n  setToggle\n} from \"~/browser\"\nimport {\n  SearchIndex,\n  SearchResult,\n  setupSearchWorker\n} from \"~/integrations\"\n\nimport {\n  Component,\n  getComponentElement,\n  getComponentElements\n} from \"../../_\"\nimport {\n  SearchQuery,\n  mountSearchQuery\n} from \"../query\"\nimport { mountSearchResult } from \"../result\"\nimport {\n  SearchShare,\n  mountSearchShare\n} from \"../share\"\nimport {\n  SearchSuggest,\n  mountSearchSuggest\n} from \"../suggest\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search\n */\nexport type Search =\n  | SearchQuery\n  | SearchResult\n  | SearchShare\n  | SearchSuggest\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  index$: ObservableInput<SearchIndex> /* Search index observable */\n  keyboard$: Observable<Keyboard>      /* Keyboard observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount search\n *\n * This function sets up the search functionality, including the underlying\n * web worker and all keyboard bindings.\n *\n * @param el - Search element\n * @param options - Options\n *\n * @returns Search component observable\n */\nexport function mountSearch(\n  el: HTMLElement, { index$, keyboard$ }: MountOptions\n): Observable<Component<Search>> {\n  const config = configuration()\n  try {\n    const worker$ = setupSearchWorker(config.search, index$)\n\n    /* Retrieve query and result components */\n    const query  = getComponentElement(\"search-query\", el)\n    const result = getComponentElement(\"search-result\", el)\n\n    /* Always close search on result selection */\n    fromEvent<PointerEvent>(el, \"click\")\n      .pipe(\n        filter(({ target }) => (\n          target instanceof Element && !!target.closest(\"a\")\n        ))\n      )\n        .subscribe(() => setToggle(\"search\", false))\n\n    /* Set up search keyboard handlers */\n    keyboard$\n      .pipe(\n        filter(({ mode }) => mode === \"search\")\n      )\n        .subscribe(key => {\n          const active = getActiveElement()\n          switch (key.type) {\n\n            /* Enter: go to first (best) result */\n            case \"Enter\":\n              if (active === query) {\n                const anchors = new Map<HTMLAnchorElement, number>()\n                for (const anchor of getElements<HTMLAnchorElement>(\n                  \":first-child [href]\", result\n                )) {\n                  const article = anchor.firstElementChild!\n                  anchors.set(anchor, parseFloat(\n                    article.getAttribute(\"data-md-score\")!\n                  ))\n                }\n\n                /* Go to result with highest score, if any */\n                if (anchors.size) {\n                  const [[best]] = [...anchors].sort(([, a], [, b]) => b - a)\n                  best.click()\n                }\n\n                /* Otherwise omit form submission */\n                key.claim()\n              }\n              break\n\n            /* Escape or Tab: close search */\n            case \"Escape\":\n            case \"Tab\":\n              setToggle(\"search\", false)\n              query.blur()\n              break\n\n            /* Vertical arrows: select previous or next search result */\n            case \"ArrowUp\":\n            case \"ArrowDown\":\n              if (typeof active === \"undefined\") {\n                query.focus()\n              } else {\n                const els = [query, ...getElements(\n                  \":not(details) > [href], summary, details[open] [href]\",\n                  result\n                )]\n                const i = Math.max(0, (\n                  Math.max(0, els.indexOf(active)) + els.length + (\n                    key.type === \"ArrowUp\" ? -1 : +1\n                  )\n                ) % els.length)\n                els[i].focus()\n              }\n\n              /* Prevent scrolling of page */\n              key.claim()\n              break\n\n            /* All other keys: hand to search query */\n            default:\n              if (query !== getActiveElement())\n                query.focus()\n          }\n        })\n\n    /* Set up global keyboard handlers */\n    keyboard$\n      .pipe(\n        filter(({ mode }) => mode === \"global\")\n      )\n        .subscribe(key => {\n          switch (key.type) {\n\n            /* Open search and select query */\n            case \"f\":\n            case \"s\":\n            case \"/\":\n              query.focus()\n              query.select()\n\n              /* Prevent scrolling of page */\n              key.claim()\n              break\n          }\n        })\n\n    /* Create and return component */\n    const query$ = mountSearchQuery(query, { worker$ })\n    return merge(\n      query$,\n      mountSearchResult(result, { worker$, query$ })\n    )\n      .pipe(\n        mergeWith(\n\n          /* Search sharing */\n          ...getComponentElements(\"search-share\", el)\n            .map(child => mountSearchShare(child, { query$ })),\n\n          /* Search suggestions */\n          ...getComponentElements(\"search-suggest\", el)\n            .map(child => mountSearchSuggest(child, { worker$, keyboard$ }))\n        )\n      )\n\n  /* Gracefully handle broken search */\n  } catch (err) {\n    el.hidden = true\n    return NEVER\n  }\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  ObservableInput,\n  combineLatest,\n  filter,\n  map,\n  startWith\n} from \"rxjs\"\n\nimport { getLocation } from \"~/browser\"\nimport {\n  SearchIndex,\n  setupSearchHighlighter\n} from \"~/integrations\"\nimport { h } from \"~/utilities\"\n\nimport { Component } from \"../../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search highlighting\n */\nexport interface SearchHighlight {\n  nodes: Map<ChildNode, string>        /* Map of replacements */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  index$: ObservableInput<SearchIndex> /* Search index observable */\n  location$: Observable<URL>           /* Location observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount search highlighting\n *\n * @param el - Content element\n * @param options - Options\n *\n * @returns Search highlighting component observable\n */\nexport function mountSearchHiglight(\n  el: HTMLElement, { index$, location$ }: MountOptions\n): Observable<Component<SearchHighlight>> {\n  return combineLatest([\n    index$,\n    location$\n      .pipe(\n        startWith(getLocation()),\n        filter(url => !!url.searchParams.get(\"h\"))\n      )\n  ])\n    .pipe(\n      map(([index, url]) => setupSearchHighlighter(index.config)(\n        url.searchParams.get(\"h\")!\n      )),\n      map(fn => {\n        const nodes = new Map<ChildNode, string>()\n\n        /* Traverse text nodes and collect matches */\n        const it = document.createNodeIterator(el, NodeFilter.SHOW_TEXT)\n        for (let node = it.nextNode(); node; node = it.nextNode()) {\n          if (node.parentElement?.offsetHeight) {\n            const original = node.textContent!\n            const replaced = fn(original)\n            if (replaced.length > original.length)\n              nodes.set(node as ChildNode, replaced)\n          }\n        }\n\n        /* Replace original nodes with matches */\n        for (const [node, text] of nodes) {\n          const { childNodes } = h(\"span\", null, text)\n          node.replaceWith(...Array.from(childNodes))\n        }\n\n        /* Return component */\n        return { ref: el, nodes }\n      })\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  Subject,\n  animationFrameScheduler,\n  asyncScheduler,\n  auditTime,\n  combineLatest,\n  defer,\n  distinctUntilChanged,\n  endWith,\n  finalize,\n  first,\n  from,\n  fromEvent,\n  ignoreElements,\n  map,\n  mergeMap,\n  observeOn,\n  takeUntil,\n  tap,\n  withLatestFrom\n} from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport {\n  Viewport,\n  getElement,\n  getElementOffset,\n  getElementSize,\n  getElements\n} from \"~/browser\"\n\nimport { Component } from \"../_\"\nimport { Header } from \"../header\"\nimport { Main } from \"../main\"\nimport { mountInlineTooltip2 } from \"../tooltip2\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Sidebar\n */\nexport interface Sidebar {\n  height: number                       /* Sidebar height */\n  locked: boolean                      /* Sidebar is locked */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n  viewport$: Observable<Viewport>      /* Viewport observable */\n  main$: Observable<Main>              /* Main area observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  viewport$: Observable<Viewport>      /* Viewport observable */\n  header$: Observable<Header>          /* Header observable */\n  main$: Observable<Main>              /* Main area observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch sidebar\n *\n * This function returns an observable that computes the visual parameters of\n * the sidebar which depends on the vertical viewport offset, as well as the\n * height of the main area. When the page is scrolled beyond the header, the\n * sidebar is locked and fills the remaining space.\n *\n * @param el - Sidebar element\n * @param options - Options\n *\n * @returns Sidebar observable\n */\nexport function watchSidebar(\n  el: HTMLElement, { viewport$, main$ }: WatchOptions\n): Observable<Sidebar> {\n  const parent = el.closest<HTMLElement>(\".md-grid\")!\n  const adjust =\n    parent.offsetTop -\n    parent.parentElement!.offsetTop\n\n  /* Compute the sidebar's available height and if it should be locked */\n  return combineLatest([main$, viewport$])\n    .pipe(\n      map(([{ offset, height }, { offset: { y } }]) => {\n        height = height\n          + Math.min(adjust, Math.max(0, y - offset))\n          - adjust\n        return {\n          height,\n          locked: y >= offset + adjust\n        }\n      }),\n      distinctUntilChanged((a, b) => (\n        a.height === b.height &&\n        a.locked === b.locked\n      ))\n    )\n}\n\n/**\n * Mount sidebar\n *\n * This function doesn't set the height of the actual sidebar, but of its first\n * child \u2013 the `.md-sidebar__scrollwrap` element in order to mitigiate jittery\n * sidebars when the footer is scrolled into view. At some point we switched\n * from `absolute` / `fixed` positioning to `sticky` positioning, significantly\n * reducing jitter in some browsers (respectively Firefox and Safari) when\n * scrolling from the top. However, top-aligned sticky positioning means that\n * the sidebar snaps to the bottom when the end of the container is reached.\n * This is what leads to the mentioned jitter, as the sidebar's height may be\n * updated too slowly.\n *\n * This behaviour can be mitigiated by setting the height of the sidebar to `0`\n * while preserving the padding, and the height on its first element.\n *\n * @param el - Sidebar element\n * @param options - Options\n *\n * @returns Sidebar component observable\n */\nexport function mountSidebar(\n  el: HTMLElement, { header$, ...options }: MountOptions\n): Observable<Component<Sidebar>> {\n  const inner = getElement(\".md-sidebar__scrollwrap\", el)\n  const { y } = getElementOffset(inner)\n  return defer(() => {\n    const push$ = new Subject<Sidebar>()\n    const done$ = push$.pipe(ignoreElements(), endWith(true))\n    const next$ = push$\n      .pipe(\n        auditTime(0, animationFrameScheduler)\n      )\n\n    /* Update sidebar height and offset */\n    next$.pipe(withLatestFrom(header$))\n      .subscribe({\n\n        /* Handle emission */\n        next([{ height }, { height: offset }]) {\n          inner.style.height = `${height - 2 * y}px`\n          el.style.top       = `${offset}px`\n        },\n\n        /* Handle complete */\n        complete() {\n          inner.style.height = \"\"\n          el.style.top       = \"\"\n        }\n      })\n\n    /* Bring active item into view on initial load */\n    next$.pipe(first())\n      .subscribe(() => {\n        for (const item of getElements(\".md-nav__link--active[href]\", el)) {\n          if (!item.clientHeight) // skip invisible toc in left sidebar\n            continue\n          const container = item.closest<HTMLElement>(\".md-sidebar__scrollwrap\")!\n          if (typeof container !== \"undefined\") {\n            const offset = item.offsetTop - container.offsetTop\n            const { height } = getElementSize(container)\n            container.scrollTo({\n              top: offset - height / 2\n            })\n          }\n        }\n      })\n\n    /* Handle accessibility for expandable items, see https://bit.ly/3jaod9p */\n    from(getElements<HTMLLabelElement>(\"label[tabindex]\", el))\n      .pipe(\n        mergeMap(label => fromEvent(label, \"click\")\n          .pipe(\n            observeOn(asyncScheduler),\n            map(() => label),\n            takeUntil(done$)\n          )\n        )\n      )\n        .subscribe(label => {\n          const input = getElement<HTMLInputElement>(`[id=\"${label.htmlFor}\"]`)\n          const nav = getElement(`[aria-labelledby=\"${label.id}\"]`)\n          nav.setAttribute(\"aria-expanded\", `${input.checked}`)\n        })\n\n    // Mount abbreviation tooltips\n    if (feature(\"content.tooltips\"))\n      from(getElements(\"abbr[title]\", el))\n        .pipe(\n          mergeMap(child => mountInlineTooltip2(child, { viewport$ })),\n          takeUntil(done$)\n        )\n          .subscribe()\n\n    /* Create and return component */\n    return watchSidebar(el, options)\n      .pipe(\n        tap(state => push$.next(state)),\n        finalize(() => push$.complete()),\n        map(state => ({ ref: el, ...state }))\n      )\n  })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { Repo, User } from \"github-types\"\nimport {\n  EMPTY,\n  Observable,\n  catchError,\n  defaultIfEmpty,\n  map,\n  zip\n} from \"rxjs\"\n\nimport { requestJSON } from \"~/browser\"\n\nimport { SourceFacts } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * GitHub release (partial)\n */\ninterface Release {\n  tag_name: string                     /* Tag name */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch GitHub repository facts\n *\n * @param user - GitHub user or organization\n * @param repo - GitHub repository\n *\n * @returns Repository facts observable\n */\nexport function fetchSourceFactsFromGitHub(\n  user: string, repo?: string\n): Observable<SourceFacts> {\n  if (typeof repo !== \"undefined\") {\n    const url = `https://api.github.com/repos/${user}/${repo}`\n    return zip(\n\n      /* Fetch version */\n      requestJSON<Release>(`${url}/releases/latest`)\n        .pipe(\n          catchError(() => EMPTY), // @todo refactor instant loading\n          map(release => ({\n            version: release.tag_name\n          })),\n          defaultIfEmpty({})\n        ),\n\n      /* Fetch stars and forks */\n      requestJSON<Repo>(url)\n        .pipe(\n          catchError(() => EMPTY), // @todo refactor instant loading\n          map(info => ({\n            stars: info.stargazers_count,\n            forks: info.forks_count\n          })),\n          defaultIfEmpty({})\n        )\n    )\n      .pipe(\n        map(([release, info]) => ({ ...release, ...info }))\n      )\n\n  /* User or organization */\n  } else {\n    const url = `https://api.github.com/users/${user}`\n    return requestJSON<User>(url)\n      .pipe(\n        map(info => ({\n          repositories: info.public_repos\n        })),\n        defaultIfEmpty({})\n      )\n  }\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { ProjectSchema } from \"gitlab\"\nimport {\n  EMPTY,\n  Observable,\n  catchError,\n  defaultIfEmpty,\n  map,\n  zip\n} from \"rxjs\"\n\nimport { requestJSON } from \"~/browser\"\n\nimport { SourceFacts } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * GitLab release (partial)\n */\ninterface Release { // @todo remove and use the ReleaseSchema type instead after switching from gitlab to @gitbeaker/rest\n  tag_name: string                     /* Tag name */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch GitLab repository facts\n *\n * @param base - GitLab base\n * @param project - GitLab project\n *\n * @returns Repository facts observable\n */\nexport function fetchSourceFactsFromGitLab(\n  base: string, project: string\n): Observable<SourceFacts> {\n  const url = `https://${base}/api/v4/projects/${encodeURIComponent(project)}`\n  return zip(\n\n    /* Fetch version */\n    requestJSON<Release>(`${url}/releases/permalink/latest`)\n      .pipe(\n        catchError(() => EMPTY), // @todo refactor instant loading\n        map(({ tag_name }) => ({\n          version: tag_name\n        })),\n        defaultIfEmpty({})\n      ),\n\n    /* Fetch stars and forks */\n    requestJSON<ProjectSchema>(url)\n      .pipe(\n        catchError(() => EMPTY), // @todo refactor instant loading\n        map(({ star_count, forks_count }) => ({\n          stars: star_count,\n          forks: forks_count\n        })),\n        defaultIfEmpty({})\n      )\n  )\n    .pipe(\n      map(([release, info]) => ({ ...release, ...info }))\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { EMPTY, Observable } from \"rxjs\"\n\nimport { fetchSourceFactsFromGitHub } from \"../github\"\nimport { fetchSourceFactsFromGitLab } from \"../gitlab\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Repository facts for repositories\n */\nexport interface RepositoryFacts {\n  stars?: number                       /* Number of stars */\n  forks?: number                       /* Number of forks */\n  version?: string                     /* Latest version */\n}\n\n/**\n * Repository facts for organizations\n */\nexport interface OrganizationFacts {\n  repositories?: number                /* Number of repositories */\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Repository facts\n */\nexport type SourceFacts =\n  | RepositoryFacts\n  | OrganizationFacts\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch repository facts\n *\n * @param url - Repository URL\n *\n * @returns Repository facts observable\n */\nexport function fetchSourceFacts(\n  url: string\n): Observable<SourceFacts> {\n\n  /* Try to match GitHub repository */\n  let match = url.match(/^.+github\\.com\\/([^/]+)\\/?([^/]+)?/i)\n  if (match) {\n    const [, user, repo] = match\n    return fetchSourceFactsFromGitHub(user, repo)\n  }\n\n  /* Try to match GitLab repository */\n  match = url.match(/^.+?([^/]*gitlab[^/]+)\\/(.+?)\\/?$/i)\n  if (match) {\n    const [, base, slug] = match\n    return fetchSourceFactsFromGitLab(base, slug)\n  }\n\n  /* Fallback */\n  return EMPTY\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  EMPTY,\n  Observable,\n  Subject,\n  catchError,\n  defer,\n  filter,\n  finalize,\n  map,\n  of,\n  shareReplay,\n  tap\n} from \"rxjs\"\n\nimport { getElement } from \"~/browser\"\nimport { ConsentDefaults } from \"~/components/consent\"\nimport { renderSourceFacts } from \"~/templates\"\n\nimport {\n  Component,\n  getComponentElements\n} from \"../../_\"\nimport {\n  SourceFacts,\n  fetchSourceFacts\n} from \"../facts\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Repository information\n */\nexport interface Source {\n  facts: SourceFacts                   /* Repository facts */\n}\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Repository information observable\n */\nlet fetch$: Observable<Source>\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch repository information\n *\n * This function tries to read the repository facts from session storage, and\n * if unsuccessful, fetches them from the underlying provider.\n *\n * @param el - Repository information element\n *\n * @returns Repository information observable\n */\nexport function watchSource(\n  el: HTMLAnchorElement\n): Observable<Source> {\n  return fetch$ ||= defer(() => {\n    const cached = __md_get<SourceFacts>(\"__source\", sessionStorage)\n    if (cached) {\n      return of(cached)\n    } else {\n\n      /* Check if consent is configured and was given */\n      const els = getComponentElements(\"consent\")\n      if (els.length) {\n        const consent = __md_get<ConsentDefaults>(\"__consent\")\n        if (!(consent && consent.github))\n          return EMPTY\n      }\n\n      /* Fetch repository facts */\n      return fetchSourceFacts(el.href)\n        .pipe(\n          tap(facts => __md_set(\"__source\", facts, sessionStorage))\n        )\n    }\n  })\n    .pipe(\n      catchError(() => EMPTY),\n      filter(facts => Object.keys(facts).length > 0),\n      map(facts => ({ facts })),\n      shareReplay(1)\n    )\n}\n\n/**\n * Mount repository information\n *\n * @param el - Repository information element\n *\n * @returns Repository information component observable\n */\nexport function mountSource(\n  el: HTMLAnchorElement\n): Observable<Component<Source>> {\n  const inner = getElement(\":scope > :last-child\", el)\n  return defer(() => {\n    const push$ = new Subject<Source>()\n    push$.subscribe(({ facts }) => {\n      inner.appendChild(renderSourceFacts(facts))\n      inner.classList.add(\"md-source__repository--active\")\n    })\n\n    /* Create and return component */\n    return watchSource(el)\n      .pipe(\n        tap(state => push$.next(state)),\n        finalize(() => push$.complete()),\n        map(state => ({ ref: el, ...state }))\n      )\n  })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  Subject,\n  defer,\n  distinctUntilKeyChanged,\n  finalize,\n  map,\n  of,\n  switchMap,\n  tap\n} from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport {\n  Viewport,\n  watchElementSize,\n  watchViewportAt\n} from \"~/browser\"\n\nimport { Component } from \"../_\"\nimport { Header } from \"../header\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Navigation tabs\n */\nexport interface Tabs {\n  hidden: boolean                      /* Navigation tabs are hidden */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n  viewport$: Observable<Viewport>      /* Viewport observable */\n  header$: Observable<Header>          /* Header observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  viewport$: Observable<Viewport>      /* Viewport observable */\n  header$: Observable<Header>          /* Header observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch navigation tabs\n *\n * @param el - Navigation tabs element\n * @param options - Options\n *\n * @returns Navigation tabs observable\n */\nexport function watchTabs(\n  el: HTMLElement, { viewport$, header$ }: WatchOptions\n): Observable<Tabs> {\n  return watchElementSize(document.body)\n    .pipe(\n      switchMap(() => watchViewportAt(el, { header$, viewport$ })),\n      map(({ offset: { y } }) => {\n        return {\n          hidden: y >= 10\n        }\n      }),\n      distinctUntilKeyChanged(\"hidden\")\n    )\n}\n\n/**\n * Mount navigation tabs\n *\n * This function hides the navigation tabs when scrolling past the threshold\n * and makes them reappear in a nice CSS animation when scrolling back up.\n *\n * @param el - Navigation tabs element\n * @param options - Options\n *\n * @returns Navigation tabs component observable\n */\nexport function mountTabs(\n  el: HTMLElement, options: MountOptions\n): Observable<Component<Tabs>> {\n  return defer(() => {\n    const push$ = new Subject<Tabs>()\n    push$.subscribe({\n\n      /* Handle emission */\n      next({ hidden }) {\n        el.hidden = hidden\n      },\n\n      /* Handle complete */\n      complete() {\n        el.hidden = false\n      }\n    })\n\n    /* Create and return component */\n    return (\n      feature(\"navigation.tabs.sticky\")\n        ? of({ hidden: false })\n        : watchTabs(el, options)\n    )\n      .pipe(\n        tap(state => push$.next(state)),\n        finalize(() => push$.complete()),\n        map(state => ({ ref: el, ...state }))\n      )\n  })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  Subject,\n  asyncScheduler,\n  bufferCount,\n  combineLatestWith,\n  debounceTime,\n  defer,\n  distinctUntilChanged,\n  distinctUntilKeyChanged,\n  endWith,\n  filter,\n  finalize,\n  ignoreElements,\n  map,\n  merge,\n  observeOn,\n  of,\n  repeat,\n  scan,\n  share,\n  skip,\n  startWith,\n  switchMap,\n  takeUntil,\n  tap,\n  withLatestFrom\n} from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport {\n  Viewport,\n  getElement,\n  getElementContainer,\n  getElementSize,\n  getElements,\n  getLocation,\n  getOptionalElement,\n  watchElementSize\n} from \"~/browser\"\n\nimport {\n  Component,\n  getComponentElement\n} from \"../_\"\nimport { Header } from \"../header\"\nimport { Main } from \"../main\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Table of contents\n */\nexport interface TableOfContents {\n  prev: HTMLAnchorElement[][]          /* Anchors (previous) */\n  next: HTMLAnchorElement[][]          /* Anchors (next) */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n  viewport$: Observable<Viewport>      /* Viewport observable */\n  header$: Observable<Header>          /* Header observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  viewport$: Observable<Viewport>      /* Viewport observable */\n  header$: Observable<Header>          /* Header observable */\n  main$: Observable<Main>              /* Main area observable */\n  target$: Observable<HTMLElement>     /* Location target observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch table of contents\n *\n * This is effectively a scroll spy implementation which will account for the\n * fixed header and automatically re-calculate anchor offsets when the viewport\n * is resized. The returned observable will only emit if the table of contents\n * needs to be repainted.\n *\n * This implementation tracks an anchor element's entire path starting from its\n * level up to the top-most anchor element, e.g. `[h3, h2, h1]`. Although the\n * Material theme currently doesn't make use of this information, it enables\n * the styling of the entire hierarchy through customization.\n *\n * Note that the current anchor is the last item of the `prev` anchor list.\n *\n * @param el - Table of contents element\n * @param options - Options\n *\n * @returns Table of contents observable\n */\nexport function watchTableOfContents(\n  el: HTMLElement, { viewport$, header$ }: WatchOptions\n): Observable<TableOfContents> {\n  const table = new Map<HTMLAnchorElement, HTMLElement>()\n\n  /* Compute anchor-to-target mapping */\n  const anchors = getElements<HTMLAnchorElement>(\".md-nav__link\", el)\n  for (const anchor of anchors) {\n    const id = decodeURIComponent(anchor.hash.substring(1))\n    const target = getOptionalElement(`[id=\"${id}\"]`)\n    if (typeof target !== \"undefined\")\n      table.set(anchor, target)\n  }\n\n  /* Compute necessary adjustment for header */\n  const adjust$ = header$\n    .pipe(\n      distinctUntilKeyChanged(\"height\"),\n      map(({ height }) => {\n        const main = getComponentElement(\"main\")\n        const grid = getElement(\":scope > :first-child\", main)\n        return height + 0.8 * (\n          grid.offsetTop -\n          main.offsetTop\n        )\n      }),\n      share()\n    )\n\n  /* Compute partition of previous and next anchors */\n  const partition$ = watchElementSize(document.body)\n    .pipe(\n      distinctUntilKeyChanged(\"height\"),\n\n      /* Build index to map anchor paths to vertical offsets */\n      switchMap(body => defer(() => {\n        let path: HTMLAnchorElement[] = []\n        return of([...table].reduce((index, [anchor, target]) => {\n          while (path.length) {\n            const last = table.get(path[path.length - 1])!\n            if (last.tagName >= target.tagName) {\n              path.pop()\n            } else {\n              break\n            }\n          }\n\n          /* If the current anchor is hidden, continue with its parent */\n          let offset = target.offsetTop\n          while (!offset && target.parentElement) {\n            target = target.parentElement\n            offset = target.offsetTop\n          }\n\n          /* Fix anchor offsets in tables - see https://bit.ly/3CUFOcn */\n          let parent = target.offsetParent as HTMLElement\n          for (; parent; parent = parent.offsetParent as HTMLElement)\n            offset += parent.offsetTop\n\n          /* Map reversed anchor path to vertical offset */\n          return index.set(\n            [...path = [...path, anchor]].reverse(),\n            offset\n          )\n        }, new Map<HTMLAnchorElement[], number>()))\n      })\n        .pipe(\n\n          /* Sort index by vertical offset (see https://bit.ly/30z6QSO) */\n          map(index => new Map([...index].sort(([, a], [, b]) => a - b))),\n          combineLatestWith(adjust$),\n\n          /* Re-compute partition when viewport offset changes */\n          switchMap(([index, adjust]) => viewport$\n            .pipe(\n              scan(([prev, next], { offset: { y }, size }) => {\n                const last = y + size.height >= Math.floor(body.height)\n\n                /* Look forward */\n                while (next.length) {\n                  const [, offset] = next[0]\n                  if (offset - adjust < y || last) {\n                    prev = [...prev, next.shift()!]\n                  } else {\n                    break\n                  }\n                }\n\n                /* Look backward */\n                while (prev.length) {\n                  const [, offset] = prev[prev.length - 1]\n                  if (offset - adjust >= y && !last) {\n                    next = [prev.pop()!, ...next]\n                  } else {\n                    break\n                  }\n                }\n\n                /* Return partition */\n                return [prev, next]\n              }, [[], [...index]]),\n              distinctUntilChanged((a, b) => (\n                a[0] === b[0] &&\n                a[1] === b[1]\n              ))\n            )\n          )\n        )\n      )\n    )\n\n  /* Compute and return anchor list migrations */\n  return partition$\n    .pipe(\n      map(([prev, next]) => ({\n        prev: prev.map(([path]) => path),\n        next: next.map(([path]) => path)\n      })),\n\n      /* Extract anchor list migrations */\n      startWith({ prev: [], next: [] }),\n      bufferCount(2, 1),\n      map(([a, b]) => {\n\n        /* Moving down */\n        if (a.prev.length < b.prev.length) {\n          return {\n            prev: b.prev.slice(Math.max(0, a.prev.length - 1), b.prev.length),\n            next: []\n          }\n\n        /* Moving up */\n        } else {\n          return {\n            prev: b.prev.slice(-1),\n            next: b.next.slice(0, b.next.length - a.next.length)\n          }\n        }\n      })\n    )\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Mount table of contents\n *\n * @param el - Table of contents element\n * @param options - Options\n *\n * @returns Table of contents component observable\n */\nexport function mountTableOfContents(\n  el: HTMLElement, { viewport$, header$, main$, target$ }: MountOptions\n): Observable<Component<TableOfContents>> {\n  return defer(() => {\n    const push$ = new Subject<TableOfContents>()\n    const done$ = push$.pipe(ignoreElements(), endWith(true))\n    push$.subscribe(({ prev, next }) => {\n\n      /* Look forward */\n      for (const [anchor] of next) {\n        anchor.classList.remove(\"md-nav__link--passed\")\n        anchor.classList.remove(\"md-nav__link--active\")\n      }\n\n      /* Look backward */\n      for (const [index, [anchor]] of prev.entries()) {\n        anchor.classList.add(\"md-nav__link--passed\")\n        anchor.classList.toggle(\n          \"md-nav__link--active\",\n          index === prev.length - 1\n        )\n      }\n    })\n\n    /* Set up following, if enabled */\n    if (feature(\"toc.follow\")) {\n\n      /* Toggle smooth scrolling only for anchor clicks */\n      const smooth$ = merge(\n        viewport$.pipe(debounceTime(1), map(() => undefined)),\n        viewport$.pipe(debounceTime(250), map(() => \"smooth\" as const))\n      )\n\n      /* Bring active anchor into view */ // @todo: refactor\n      push$\n        .pipe(\n          filter(({ prev }) => prev.length > 0),\n          combineLatestWith(main$.pipe(observeOn(asyncScheduler))),\n          withLatestFrom(smooth$)\n        )\n          .subscribe(([[{ prev }], behavior]) => {\n            const [anchor] = prev[prev.length - 1]\n            if (anchor.offsetHeight) {\n\n              /* Retrieve overflowing container and scroll */\n              const container = getElementContainer(anchor)\n              if (typeof container !== \"undefined\") {\n                const offset = anchor.offsetTop - container.offsetTop\n                const { height } = getElementSize(container)\n                container.scrollTo({\n                  top: offset - height / 2,\n                  behavior\n                })\n              }\n            }\n          })\n    }\n\n    /* Set up anchor tracking, if enabled */\n    if (feature(\"navigation.tracking\"))\n      viewport$\n        .pipe(\n          takeUntil(done$),\n          distinctUntilKeyChanged(\"offset\"),\n          debounceTime(250),\n          skip(1),\n          takeUntil(target$.pipe(skip(1))),\n          repeat({ delay: 250 }),\n          withLatestFrom(push$)\n        )\n          .subscribe(([, { prev }]) => {\n            const url = getLocation()\n\n            /* Set hash fragment to active anchor */\n            const anchor = prev[prev.length - 1]\n            if (anchor && anchor.length) {\n              const [active] = anchor\n              const { hash } = new URL(active.href)\n              if (url.hash !== hash) {\n                url.hash = hash\n                history.replaceState({}, \"\", `${url}`)\n              }\n\n            /* Reset anchor when at the top */\n            } else {\n              url.hash = \"\"\n              history.replaceState({}, \"\", `${url}`)\n            }\n          })\n\n    /* Create and return component */\n    return watchTableOfContents(el, { viewport$, header$ })\n      .pipe(\n        tap(state => push$.next(state)),\n        finalize(() => push$.complete()),\n        map(state => ({ ref: el, ...state }))\n      )\n  })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  Subject,\n  bufferCount,\n  combineLatest,\n  distinctUntilChanged,\n  distinctUntilKeyChanged,\n  endWith,\n  finalize,\n  fromEvent,\n  ignoreElements,\n  map,\n  repeat,\n  skip,\n  takeUntil,\n  tap\n} from \"rxjs\"\n\nimport { Viewport } from \"~/browser\"\n\nimport { Component } from \"../_\"\nimport { Header } from \"../header\"\nimport { Main } from \"../main\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Back-to-top button\n */\nexport interface BackToTop {\n  hidden: boolean                      /* Back-to-top button is hidden */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n  viewport$: Observable<Viewport>      /* Viewport observable */\n  main$: Observable<Main>              /* Main area observable */\n  target$: Observable<HTMLElement>     /* Location target observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  viewport$: Observable<Viewport>      /* Viewport observable */\n  header$: Observable<Header>          /* Header observable */\n  main$: Observable<Main>              /* Main area observable */\n  target$: Observable<HTMLElement>     /* Location target observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch back-to-top\n *\n * @param _el - Back-to-top element\n * @param options - Options\n *\n * @returns Back-to-top observable\n */\nexport function watchBackToTop(\n  _el: HTMLElement, { viewport$, main$, target$ }: WatchOptions\n): Observable<BackToTop> {\n\n  /* Compute direction */\n  const direction$ = viewport$\n    .pipe(\n      map(({ offset: { y } }) => y),\n      bufferCount(2, 1),\n      map(([a, b]) => a > b && b > 0),\n      distinctUntilChanged()\n    )\n\n  /* Compute whether main area is active */\n  const active$ = main$\n    .pipe(\n      map(({ active }) => active)\n    )\n\n  /* Compute threshold for hiding */\n  return combineLatest([active$, direction$])\n    .pipe(\n      map(([active, direction]) => !(active && direction)),\n      distinctUntilChanged(),\n      takeUntil(target$.pipe(skip(1))),\n      endWith(true),\n      repeat({ delay: 250 }),\n      map(hidden => ({ hidden }))\n    )\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Mount back-to-top\n *\n * @param el - Back-to-top element\n * @param options - Options\n *\n * @returns Back-to-top component observable\n */\nexport function mountBackToTop(\n  el: HTMLElement, { viewport$, header$, main$, target$ }: MountOptions\n): Observable<Component<BackToTop>> {\n  const push$ = new Subject<BackToTop>()\n  const done$ = push$.pipe(ignoreElements(), endWith(true))\n  push$.subscribe({\n\n    /* Handle emission */\n    next({ hidden }) {\n      el.hidden = hidden\n      if (hidden) {\n        el.setAttribute(\"tabindex\", \"-1\")\n        el.blur()\n      } else {\n        el.removeAttribute(\"tabindex\")\n      }\n    },\n\n    /* Handle complete */\n    complete() {\n      el.style.top = \"\"\n      el.hidden = true\n      el.removeAttribute(\"tabindex\")\n    }\n  })\n\n  /* Watch header height */\n  header$\n    .pipe(\n      takeUntil(done$),\n      distinctUntilKeyChanged(\"height\")\n    )\n      .subscribe(({ height }) => {\n        el.style.top = `${height + 16}px`\n      })\n\n  /* Go back to top */\n  fromEvent(el, \"click\")\n    .subscribe(ev => {\n      ev.preventDefault()\n      window.scrollTo({ top: 0 })\n    })\n\n  /* Create and return component */\n  return watchBackToTop(el, { viewport$, main$, target$ })\n    .pipe(\n      tap(state => push$.next(state)),\n      finalize(() => push$.complete()),\n      map(state => ({ ref: el, ...state }))\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  EMPTY,\n  Observable,\n  filter,\n  finalize,\n  map,\n  mergeMap,\n  skip,\n  switchMap,\n  take,\n  takeUntil\n} from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport {\n  Viewport,\n  getElements,\n  watchElementVisibility\n} from \"~/browser\"\nimport { mountInlineTooltip2 } from \"~/components/tooltip2\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Patch options\n */\ninterface PatchOptions {\n  document$: Observable<Document>      /* Document observable */\n  viewport$: Observable<Viewport>      /* Viewport observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Patch ellipsis\n *\n * This function will fetch all elements that are shortened with ellipsis, and\n * filter those which are visible. Once they become visible, they stay in that\n * state, even though they may be hidden again. This optimization is necessary\n * to reduce pressure on the browser, with elements fading in and out of view.\n *\n * @param options - Options\n */\nexport function patchEllipsis(\n  { document$, viewport$ }: PatchOptions\n): void {\n  document$\n    .pipe(\n      switchMap(() => getElements(\".md-ellipsis\")),\n      mergeMap(el => watchElementVisibility(el)\n        .pipe(\n          takeUntil(document$.pipe(skip(1))),\n          filter(visible => visible),\n          map(() => el),\n          take(1)\n        )\n      ),\n      filter(el => el.offsetWidth < el.scrollWidth),\n      mergeMap(el => {\n        const text = el.innerText\n        const host = el.closest(\"a\") || el\n        host.title = text\n\n        // Do not mount improved tooltip if feature is disabled\n        if (!feature(\"content.tooltips\"))\n          return EMPTY\n\n        /* Mount tooltip */\n        return mountInlineTooltip2(host, { viewport$ })\n          .pipe(\n            takeUntil(document$.pipe(skip(1))),\n            finalize(() => host.removeAttribute(\"title\"))\n          )\n      })\n    )\n      .subscribe()\n\n  // @todo move this outside of here and fix memleaks\n  if (feature(\"content.tooltips\"))\n    document$\n      .pipe(\n        switchMap(() => getElements(\".md-status\")),\n        mergeMap(el => mountInlineTooltip2(el, { viewport$ }))\n      )\n        .subscribe()\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  fromEvent,\n  map,\n  mergeMap,\n  switchMap,\n  takeWhile,\n  tap,\n  withLatestFrom\n} from \"rxjs\"\n\nimport { getElements } from \"~/browser\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Patch options\n */\ninterface PatchOptions {\n  document$: Observable<Document>      /* Document observable */\n  tablet$: Observable<boolean>         /* Media tablet observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Patch indeterminate checkboxes\n *\n * This function replaces the indeterminate \"pseudo state\" with the actual\n * indeterminate state, which is used to keep navigation always expanded.\n *\n * @param options - Options\n */\nexport function patchIndeterminate(\n  { document$, tablet$ }: PatchOptions\n): void {\n  document$\n    .pipe(\n      switchMap(() => getElements<HTMLInputElement>(\n        \".md-toggle--indeterminate\"\n      )),\n      tap(el => {\n        el.indeterminate = true\n        el.checked = false\n      }),\n      mergeMap(el => fromEvent(el, \"change\")\n        .pipe(\n          takeWhile(() => el.classList.contains(\"md-toggle--indeterminate\")),\n          map(() => el)\n        )\n      ),\n      withLatestFrom(tablet$)\n    )\n      .subscribe(([el, tablet]) => {\n        el.classList.remove(\"md-toggle--indeterminate\")\n        if (tablet)\n          el.checked = false\n      })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  filter,\n  fromEvent,\n  map,\n  mergeMap,\n  switchMap,\n  tap\n} from \"rxjs\"\n\nimport { getElements } from \"~/browser\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Patch options\n */\ninterface PatchOptions {\n  document$: Observable<Document>      /* Document observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Check whether the given device is an Apple device\n *\n * @returns Test result\n */\nfunction isAppleDevice(): boolean {\n  return /(iPad|iPhone|iPod)/.test(navigator.userAgent)\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Patch all elements with `data-md-scrollfix` attributes\n *\n * This is a year-old patch which ensures that overflow scrolling works at the\n * top and bottom of containers on iOS by ensuring a `1px` scroll offset upon\n * the start of a touch event.\n *\n * @see https://bit.ly/2SCtAOO - Original source\n *\n * @param options - Options\n */\nexport function patchScrollfix(\n  { document$ }: PatchOptions\n): void {\n  document$\n    .pipe(\n      switchMap(() => getElements(\"[data-md-scrollfix]\")),\n      tap(el => el.removeAttribute(\"data-md-scrollfix\")),\n      filter(isAppleDevice),\n      mergeMap(el => fromEvent(el, \"touchstart\")\n        .pipe(\n          map(() => el)\n        )\n      )\n    )\n      .subscribe(el => {\n        const top = el.scrollTop\n\n        /* We're at the top of the container */\n        if (top === 0) {\n          el.scrollTop = 1\n\n        /* We're at the bottom of the container */\n        } else if (top + el.offsetHeight === el.scrollHeight) {\n          el.scrollTop = top - 1\n        }\n      })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  combineLatest,\n  delay,\n  map,\n  of,\n  switchMap,\n  withLatestFrom\n} from \"rxjs\"\n\nimport {\n  Viewport,\n  watchToggle\n} from \"~/browser\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Patch options\n */\ninterface PatchOptions {\n  viewport$: Observable<Viewport>      /* Viewport observable */\n  tablet$: Observable<boolean>         /* Media tablet observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Patch the document body to lock when search is open\n *\n * For mobile and tablet viewports, the search is rendered full screen, which\n * leads to scroll leaking when at the top or bottom of the search result. This\n * function locks the body when the search is in full screen mode, and restores\n * the scroll position when leaving.\n *\n * @param options - Options\n */\nexport function patchScrolllock(\n  { viewport$, tablet$ }: PatchOptions\n): void {\n  combineLatest([watchToggle(\"search\"), tablet$])\n    .pipe(\n      map(([active, tablet]) => active && !tablet),\n      switchMap(active => of(active)\n        .pipe(\n          delay(active ? 400 : 100)\n        )\n      ),\n      withLatestFrom(viewport$)\n    )\n      .subscribe(([active, { offset: { y }}]) => {\n        if (active) {\n          document.body.setAttribute(\"data-md-scrolllock\", \"\")\n          document.body.style.top = `-${y}px`\n        } else {\n          const value = -1 * parseInt(document.body.style.top, 10)\n          document.body.removeAttribute(\"data-md-scrolllock\")\n          document.body.style.top = \"\"\n          if (value)\n            window.scrollTo(0, value)\n        }\n      })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Polyfills\n * ------------------------------------------------------------------------- */\n\n/* Polyfill `Object.entries` */\nif (!Object.entries)\n  Object.entries = function (obj: object) {\n    const data: [string, string][] = []\n    for (const key of Object.keys(obj))\n      // @ts-expect-error - ignore property access warning\n      data.push([key, obj[key]])\n\n    /* Return entries */\n    return data\n  }\n\n/* Polyfill `Object.values` */\nif (!Object.values)\n  Object.values = function (obj: object) {\n    const data: string[] = []\n    for (const key of Object.keys(obj))\n      // @ts-expect-error - ignore property access warning\n      data.push(obj[key])\n\n    /* Return values */\n    return data\n  }\n\n/* ------------------------------------------------------------------------- */\n\n/* Polyfills for `Element` */\nif (typeof Element !== \"undefined\") {\n\n  /* Polyfill `Element.scrollTo` */\n  if (!Element.prototype.scrollTo)\n    Element.prototype.scrollTo = function (\n      x?: ScrollToOptions | number, y?: number\n    ): void {\n      if (typeof x === \"object\") {\n        this.scrollLeft = x.left!\n        this.scrollTop = x.top!\n      } else {\n        this.scrollLeft = x!\n        this.scrollTop = y!\n      }\n    }\n\n  /* Polyfill `Element.replaceWith` */\n  if (!Element.prototype.replaceWith)\n    Element.prototype.replaceWith = function (\n      ...nodes: Array<string | Node>\n    ): void {\n      const parent = this.parentNode\n      if (parent) {\n        if (nodes.length === 0)\n          parent.removeChild(this)\n\n        /* Replace children and create text nodes */\n        for (let i = nodes.length - 1; i >= 0; i--) {\n          let node = nodes[i]\n          if (typeof node === \"string\")\n            node = document.createTextNode(node)\n          else if (node.parentNode)\n            node.parentNode.removeChild(node)\n\n          /* Replace child or insert before previous sibling */\n          if (!i)\n            parent.replaceChild(node, this)\n          else\n            parent.insertBefore(this.previousSibling!, node)\n        }\n      }\n    }\n}\n"],
+  "mappings": 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+}
diff --git a/DevDoc/assets/javascripts/lunr/min/lunr.ar.min.js b/DevDoc/assets/javascripts/lunr/min/lunr.ar.min.js
new file mode 100644
index 00000000..9b06c26c
--- /dev/null
+++ b/DevDoc/assets/javascripts/lunr/min/lunr.ar.min.js
@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. 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\ No newline at end of file
diff --git a/DevDoc/assets/javascripts/lunr/min/lunr.da.min.js b/DevDoc/assets/javascripts/lunr/min/lunr.da.min.js
new file mode 100644
index 00000000..b9d85098
--- /dev/null
+++ b/DevDoc/assets/javascripts/lunr/min/lunr.da.min.js
@@ -0,0 +1,18 @@
+/*!
+ * Lunr languages, `Danish` language
+ * https://github.com/MihaiValentin/lunr-languages
+ *
+ * Copyright 2014, Mihai Valentin
+ * http://www.mozilla.org/MPL/
+ */
+/*!
+ * based on
+ * Snowball JavaScript Library v0.3
+ * http://code.google.com/p/urim/
+ * http://snowball.tartarus.org/
+ *
+ * Copyright 2010, Oleg Mazko
+ * http://www.mozilla.org/MPL/
+ */
+
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.da=function(){this.pipeline.reset(),this.pipeline.add(e.da.trimmer,e.da.stopWordFilter,e.da.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.da.stemmer))},e.da.wordCharacters="A-Za-zªºÀ-ÖØ-öø-ʸˠ-ˤᴀ-ᴥᴬ-ᵜᵢ-ᵥᵫ-ᵷᵹ-ᶾḀ-ỿⁱⁿₐ-ₜKÅℲⅎⅠ-ↈⱠ-ⱿꜢ-ꞇꞋ-ꞭꞰ-ꞷꟷ-ꟿꬰ-ꭚꭜ-ꭤff-stＡ-Ｚａ-ｚ",e.da.trimmer=e.trimmerSupport.generateTrimmer(e.da.wordCharacters),e.Pipeline.registerFunction(e.da.trimmer,"trimmer-da"),e.da.stemmer=function(){var r=e.stemmerSupport.Among,i=e.stemmerSupport.SnowballProgram,n=new function(){function e(){var e,r=f.cursor+3;if(d=f.limit,0<=r&&r<=f.limit){for(a=r;;){if(e=f.cursor,f.in_grouping(w,97,248)){f.cursor=e;break}if(f.cursor=e,e>=f.limit)return;f.cursor++}for(;!f.out_grouping(w,97,248);){if(f.cursor>=f.limit)return;f.cursor++}d=f.cursor,d<a&&(d=a)}}function n(){var e,r;if(f.cursor>=d&&(r=f.limit_backward,f.limit_backward=d,f.ket=f.cursor,e=f.find_among_b(c,32),f.limit_backward=r,e))switch(f.bra=f.cursor,e){case 1:f.slice_del();break;case 2:f.in_grouping_b(p,97,229)&&f.slice_del()}}function t(){var e,r=f.limit-f.cursor;f.cursor>=d&&(e=f.limit_backward,f.limit_backward=d,f.ket=f.cursor,f.find_among_b(l,4)?(f.bra=f.cursor,f.limit_backward=e,f.cursor=f.limit-r,f.cursor>f.limit_backward&&(f.cursor--,f.bra=f.cursor,f.slice_del())):f.limit_backward=e)}function s(){var e,r,i,n=f.limit-f.cursor;if(f.ket=f.cursor,f.eq_s_b(2,"st")&&(f.bra=f.cursor,f.eq_s_b(2,"ig")&&f.slice_del()),f.cursor=f.limit-n,f.cursor>=d&&(r=f.limit_backward,f.limit_backward=d,f.ket=f.cursor,e=f.find_among_b(m,5),f.limit_backward=r,e))switch(f.bra=f.cursor,e){case 1:f.slice_del(),i=f.limit-f.cursor,t(),f.cursor=f.limit-i;break;case 2:f.slice_from("løs")}}function o(){var e;f.cursor>=d&&(e=f.limit_backward,f.limit_backward=d,f.ket=f.cursor,f.out_grouping_b(w,97,248)?(f.bra=f.cursor,u=f.slice_to(u),f.limit_backward=e,f.eq_v_b(u)&&f.slice_del()):f.limit_backward=e)}var a,d,u,c=[new r("hed",-1,1),new r("ethed",0,1),new r("ered",-1,1),new r("e",-1,1),new r("erede",3,1),new r("ende",3,1),new r("erende",5,1),new r("ene",3,1),new r("erne",3,1),new r("ere",3,1),new r("en",-1,1),new r("heden",10,1),new r("eren",10,1),new r("er",-1,1),new r("heder",13,1),new r("erer",13,1),new r("s",-1,2),new r("heds",16,1),new r("es",16,1),new r("endes",18,1),new r("erendes",19,1),new r("enes",18,1),new r("ernes",18,1),new r("eres",18,1),new r("ens",16,1),new r("hedens",24,1),new r("erens",24,1),new r("ers",16,1),new r("ets",16,1),new r("erets",28,1),new r("et",-1,1),new r("eret",30,1)],l=[new r("gd",-1,-1),new r("dt",-1,-1),new r("gt",-1,-1),new r("kt",-1,-1)],m=[new r("ig",-1,1),new r("lig",0,1),new r("elig",1,1),new r("els",-1,1),new r("løst",-1,2)],w=[17,65,16,1,0,0,0,0,0,0,0,0,0,0,0,0,48,0,128],p=[239,254,42,3,0,0,0,0,0,0,0,0,0,0,0,0,16],f=new i;this.setCurrent=function(e){f.setCurrent(e)},this.getCurrent=function(){return f.getCurrent()},this.stem=function(){var r=f.cursor;return e(),f.limit_backward=r,f.cursor=f.limit,n(),f.cursor=f.limit,t(),f.cursor=f.limit,s(),f.cursor=f.limit,o(),!0}};return function(e){return"function"==typeof e.update?e.update(function(e){return n.setCurrent(e),n.stem(),n.getCurrent()}):(n.setCurrent(e),n.stem(),n.getCurrent())}}(),e.Pipeline.registerFunction(e.da.stemmer,"stemmer-da"),e.da.stopWordFilter=e.generateStopWordFilter("ad af alle alt anden at blev blive bliver da de dem den denne der deres det dette dig din disse dog du efter eller en end er et for fra ham han hans har havde have hende hendes her hos hun hvad hvis hvor i ikke ind jeg jer jo kunne man mange med meget men mig min mine mit mod ned noget nogle nu når og også om op os over på selv sig sin sine sit skal skulle som sådan thi til ud under var vi vil ville vor være været".split(" ")),e.Pipeline.registerFunction(e.da.stopWordFilter,"stopWordFilter-da")}});
\ No newline at end of file
diff --git a/DevDoc/assets/javascripts/lunr/min/lunr.de.min.js b/DevDoc/assets/javascripts/lunr/min/lunr.de.min.js
new file mode 100644
index 00000000..f3b5c108
--- /dev/null
+++ b/DevDoc/assets/javascripts/lunr/min/lunr.de.min.js
@@ -0,0 +1,18 @@
+/*!
+ * Lunr languages, `German` language
+ * https://github.com/MihaiValentin/lunr-languages
+ *
+ * Copyright 2014, Mihai Valentin
+ * http://www.mozilla.org/MPL/
+ */
+/*!
+ * based on
+ * Snowball JavaScript Library v0.3
+ * http://code.google.com/p/urim/
+ * http://snowball.tartarus.org/
+ *
+ * Copyright 2010, Oleg Mazko
+ * http://www.mozilla.org/MPL/
+ */
+
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.de=function(){this.pipeline.reset(),this.pipeline.add(e.de.trimmer,e.de.stopWordFilter,e.de.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.de.stemmer))},e.de.wordCharacters="A-Za-zªºÀ-ÖØ-öø-ʸˠ-ˤᴀ-ᴥᴬ-ᵜᵢ-ᵥᵫ-ᵷᵹ-ᶾḀ-ỿⁱⁿₐ-ₜKÅℲⅎⅠ-ↈⱠ-ⱿꜢ-ꞇꞋ-ꞭꞰ-ꞷꟷ-ꟿꬰ-ꭚꭜ-ꭤff-stＡ-Ｚａ-ｚ",e.de.trimmer=e.trimmerSupport.generateTrimmer(e.de.wordCharacters),e.Pipeline.registerFunction(e.de.trimmer,"trimmer-de"),e.de.stemmer=function(){var r=e.stemmerSupport.Among,n=e.stemmerSupport.SnowballProgram,i=new function(){function e(e,r,n){return!(!v.eq_s(1,e)||(v.ket=v.cursor,!v.in_grouping(p,97,252)))&&(v.slice_from(r),v.cursor=n,!0)}function i(){for(var r,n,i,s,t=v.cursor;;)if(r=v.cursor,v.bra=r,v.eq_s(1,"ß"))v.ket=v.cursor,v.slice_from("ss");else{if(r>=v.limit)break;v.cursor=r+1}for(v.cursor=t;;)for(n=v.cursor;;){if(i=v.cursor,v.in_grouping(p,97,252)){if(s=v.cursor,v.bra=s,e("u","U",i))break;if(v.cursor=s,e("y","Y",i))break}if(i>=v.limit)return void(v.cursor=n);v.cursor=i+1}}function s(){for(;!v.in_grouping(p,97,252);){if(v.cursor>=v.limit)return!0;v.cursor++}for(;!v.out_grouping(p,97,252);){if(v.cursor>=v.limit)return!0;v.cursor++}return!1}function t(){m=v.limit,l=m;var e=v.cursor+3;0<=e&&e<=v.limit&&(d=e,s()||(m=v.cursor,m<d&&(m=d),s()||(l=v.cursor)))}function o(){for(var e,r;;){if(r=v.cursor,v.bra=r,!(e=v.find_among(h,6)))return;switch(v.ket=v.cursor,e){case 1:v.slice_from("y");break;case 2:case 5:v.slice_from("u");break;case 3:v.slice_from("a");break;case 4:v.slice_from("o");break;case 6:if(v.cursor>=v.limit)return;v.cursor++}}}function c(){return m<=v.cursor}function u(){return l<=v.cursor}function a(){var e,r,n,i,s=v.limit-v.cursor;if(v.ket=v.cursor,(e=v.find_among_b(w,7))&&(v.bra=v.cursor,c()))switch(e){case 1:v.slice_del();break;case 2:v.slice_del(),v.ket=v.cursor,v.eq_s_b(1,"s")&&(v.bra=v.cursor,v.eq_s_b(3,"nis")&&v.slice_del());break;case 3:v.in_grouping_b(g,98,116)&&v.slice_del()}if(v.cursor=v.limit-s,v.ket=v.cursor,(e=v.find_among_b(f,4))&&(v.bra=v.cursor,c()))switch(e){case 1:v.slice_del();break;case 2:if(v.in_grouping_b(k,98,116)){var t=v.cursor-3;v.limit_backward<=t&&t<=v.limit&&(v.cursor=t,v.slice_del())}}if(v.cursor=v.limit-s,v.ket=v.cursor,(e=v.find_among_b(_,8))&&(v.bra=v.cursor,u()))switch(e){case 1:v.slice_del(),v.ket=v.cursor,v.eq_s_b(2,"ig")&&(v.bra=v.cursor,r=v.limit-v.cursor,v.eq_s_b(1,"e")||(v.cursor=v.limit-r,u()&&v.slice_del()));break;case 2:n=v.limit-v.cursor,v.eq_s_b(1,"e")||(v.cursor=v.limit-n,v.slice_del());break;case 3:if(v.slice_del(),v.ket=v.cursor,i=v.limit-v.cursor,!v.eq_s_b(2,"er")&&(v.cursor=v.limit-i,!v.eq_s_b(2,"en")))break;v.bra=v.cursor,c()&&v.slice_del();break;case 4:v.slice_del(),v.ket=v.cursor,e=v.find_among_b(b,2),e&&(v.bra=v.cursor,u()&&1==e&&v.slice_del())}}var d,l,m,h=[new r("",-1,6),new r("U",0,2),new r("Y",0,1),new r("ä",0,3),new r("ö",0,4),new r("ü",0,5)],w=[new r("e",-1,2),new r("em",-1,1),new r("en",-1,2),new r("ern",-1,1),new r("er",-1,1),new r("s",-1,3),new r("es",5,2)],f=[new r("en",-1,1),new r("er",-1,1),new r("st",-1,2),new r("est",2,1)],b=[new r("ig",-1,1),new r("lich",-1,1)],_=[new r("end",-1,1),new r("ig",-1,2),new r("ung",-1,1),new r("lich",-1,3),new r("isch",-1,2),new r("ik",-1,2),new r("heit",-1,3),new r("keit",-1,4)],p=[17,65,16,1,0,0,0,0,0,0,0,0,0,0,0,0,8,0,32,8],g=[117,30,5],k=[117,30,4],v=new n;this.setCurrent=function(e){v.setCurrent(e)},this.getCurrent=function(){return v.getCurrent()},this.stem=function(){var e=v.cursor;return i(),v.cursor=e,t(),v.limit_backward=e,v.cursor=v.limit,a(),v.cursor=v.limit_backward,o(),!0}};return function(e){return"function"==typeof e.update?e.update(function(e){return i.setCurrent(e),i.stem(),i.getCurrent()}):(i.setCurrent(e),i.stem(),i.getCurrent())}}(),e.Pipeline.registerFunction(e.de.stemmer,"stemmer-de"),e.de.stopWordFilter=e.generateStopWordFilter("aber alle allem allen aller alles als also am an ander andere anderem anderen anderer anderes anderm andern anderr anders auch auf aus bei bin bis bist da damit dann das dasselbe dazu daß dein deine deinem deinen deiner deines dem demselben den denn denselben der derer derselbe derselben des desselben dessen dich die dies diese dieselbe dieselben diesem diesen dieser dieses dir doch dort du durch ein eine einem einen einer eines einig einige einigem einigen einiger einiges einmal er es etwas euch euer eure eurem euren eurer eures für gegen gewesen hab habe haben hat hatte hatten hier hin hinter ich ihm ihn ihnen ihr ihre ihrem ihren ihrer ihres im in indem ins ist jede jedem jeden jeder jedes jene jenem jenen jener jenes jetzt kann kein keine keinem keinen keiner keines können könnte machen man manche manchem manchen mancher manches mein meine meinem meinen meiner meines mich mir mit muss musste nach nicht nichts noch nun nur ob oder ohne sehr sein seine seinem seinen seiner seines selbst sich sie sind so solche solchem solchen solcher solches soll sollte sondern sonst um und uns unse unsem unsen unser unses unter viel vom von vor war waren warst was weg weil weiter welche welchem welchen welcher welches wenn werde werden wie wieder will wir wird wirst wo wollen wollte während würde würden zu zum zur zwar zwischen über".split(" ")),e.Pipeline.registerFunction(e.de.stopWordFilter,"stopWordFilter-de")}});
\ No newline at end of file
diff --git a/DevDoc/assets/javascripts/lunr/min/lunr.du.min.js b/DevDoc/assets/javascripts/lunr/min/lunr.du.min.js
new file mode 100644
index 00000000..49a0f3f0
--- /dev/null
+++ b/DevDoc/assets/javascripts/lunr/min/lunr.du.min.js
@@ -0,0 +1,18 @@
+/*!
+ * Lunr languages, `Dutch` language
+ * https://github.com/MihaiValentin/lunr-languages
+ *
+ * Copyright 2014, Mihai Valentin
+ * http://www.mozilla.org/MPL/
+ */
+/*!
+ * based on
+ * Snowball JavaScript Library v0.3
+ * http://code.google.com/p/urim/
+ * http://snowball.tartarus.org/
+ *
+ * Copyright 2010, Oleg Mazko
+ * http://www.mozilla.org/MPL/
+ */
+
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");console.warn('[Lunr Languages] Please use the "nl" instead of the "du". The "nl" code is the standard code for Dutch language, and "du" will be removed in the next major versions.'),e.du=function(){this.pipeline.reset(),this.pipeline.add(e.du.trimmer,e.du.stopWordFilter,e.du.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.du.stemmer))},e.du.wordCharacters="A-Za-zªºÀ-ÖØ-öø-ʸˠ-ˤᴀ-ᴥᴬ-ᵜᵢ-ᵥᵫ-ᵷᵹ-ᶾḀ-ỿⁱⁿₐ-ₜKÅℲⅎⅠ-ↈⱠ-ⱿꜢ-ꞇꞋ-ꞭꞰ-ꞷꟷ-ꟿꬰ-ꭚꭜ-ꭤff-stＡ-Ｚａ-ｚ",e.du.trimmer=e.trimmerSupport.generateTrimmer(e.du.wordCharacters),e.Pipeline.registerFunction(e.du.trimmer,"trimmer-du"),e.du.stemmer=function(){var r=e.stemmerSupport.Among,i=e.stemmerSupport.SnowballProgram,n=new function(){function e(){for(var e,r,i,o=C.cursor;;){if(C.bra=C.cursor,e=C.find_among(b,11))switch(C.ket=C.cursor,e){case 1:C.slice_from("a");continue;case 2:C.slice_from("e");continue;case 3:C.slice_from("i");continue;case 4:C.slice_from("o");continue;case 5:C.slice_from("u");continue;case 6:if(C.cursor>=C.limit)break;C.cursor++;continue}break}for(C.cursor=o,C.bra=o,C.eq_s(1,"y")?(C.ket=C.cursor,C.slice_from("Y")):C.cursor=o;;)if(r=C.cursor,C.in_grouping(q,97,232)){if(i=C.cursor,C.bra=i,C.eq_s(1,"i"))C.ket=C.cursor,C.in_grouping(q,97,232)&&(C.slice_from("I"),C.cursor=r);else if(C.cursor=i,C.eq_s(1,"y"))C.ket=C.cursor,C.slice_from("Y"),C.cursor=r;else if(n(r))break}else if(n(r))break}function n(e){return C.cursor=e,e>=C.limit||(C.cursor++,!1)}function o(){_=C.limit,f=_,t()||(_=C.cursor,_<3&&(_=3),t()||(f=C.cursor))}function t(){for(;!C.in_grouping(q,97,232);){if(C.cursor>=C.limit)return!0;C.cursor++}for(;!C.out_grouping(q,97,232);){if(C.cursor>=C.limit)return!0;C.cursor++}return!1}function s(){for(var e;;)if(C.bra=C.cursor,e=C.find_among(p,3))switch(C.ket=C.cursor,e){case 1:C.slice_from("y");break;case 2:C.slice_from("i");break;case 3:if(C.cursor>=C.limit)return;C.cursor++}}function u(){return _<=C.cursor}function c(){return f<=C.cursor}function a(){var e=C.limit-C.cursor;C.find_among_b(g,3)&&(C.cursor=C.limit-e,C.ket=C.cursor,C.cursor>C.limit_backward&&(C.cursor--,C.bra=C.cursor,C.slice_del()))}function l(){var e;w=!1,C.ket=C.cursor,C.eq_s_b(1,"e")&&(C.bra=C.cursor,u()&&(e=C.limit-C.cursor,C.out_grouping_b(q,97,232)&&(C.cursor=C.limit-e,C.slice_del(),w=!0,a())))}function m(){var e;u()&&(e=C.limit-C.cursor,C.out_grouping_b(q,97,232)&&(C.cursor=C.limit-e,C.eq_s_b(3,"gem")||(C.cursor=C.limit-e,C.slice_del(),a())))}function d(){var e,r,i,n,o,t,s=C.limit-C.cursor;if(C.ket=C.cursor,e=C.find_among_b(h,5))switch(C.bra=C.cursor,e){case 1:u()&&C.slice_from("heid");break;case 2:m();break;case 3:u()&&C.out_grouping_b(z,97,232)&&C.slice_del()}if(C.cursor=C.limit-s,l(),C.cursor=C.limit-s,C.ket=C.cursor,C.eq_s_b(4,"heid")&&(C.bra=C.cursor,c()&&(r=C.limit-C.cursor,C.eq_s_b(1,"c")||(C.cursor=C.limit-r,C.slice_del(),C.ket=C.cursor,C.eq_s_b(2,"en")&&(C.bra=C.cursor,m())))),C.cursor=C.limit-s,C.ket=C.cursor,e=C.find_among_b(k,6))switch(C.bra=C.cursor,e){case 1:if(c()){if(C.slice_del(),i=C.limit-C.cursor,C.ket=C.cursor,C.eq_s_b(2,"ig")&&(C.bra=C.cursor,c()&&(n=C.limit-C.cursor,!C.eq_s_b(1,"e")))){C.cursor=C.limit-n,C.slice_del();break}C.cursor=C.limit-i,a()}break;case 2:c()&&(o=C.limit-C.cursor,C.eq_s_b(1,"e")||(C.cursor=C.limit-o,C.slice_del()));break;case 3:c()&&(C.slice_del(),l());break;case 4:c()&&C.slice_del();break;case 5:c()&&w&&C.slice_del()}C.cursor=C.limit-s,C.out_grouping_b(j,73,232)&&(t=C.limit-C.cursor,C.find_among_b(v,4)&&C.out_grouping_b(q,97,232)&&(C.cursor=C.limit-t,C.ket=C.cursor,C.cursor>C.limit_backward&&(C.cursor--,C.bra=C.cursor,C.slice_del())))}var f,_,w,b=[new r("",-1,6),new r("á",0,1),new r("ä",0,1),new r("é",0,2),new r("ë",0,2),new r("í",0,3),new r("ï",0,3),new r("ó",0,4),new r("ö",0,4),new r("ú",0,5),new r("ü",0,5)],p=[new r("",-1,3),new r("I",0,2),new r("Y",0,1)],g=[new r("dd",-1,-1),new r("kk",-1,-1),new r("tt",-1,-1)],h=[new r("ene",-1,2),new r("se",-1,3),new r("en",-1,2),new r("heden",2,1),new r("s",-1,3)],k=[new r("end",-1,1),new r("ig",-1,2),new r("ing",-1,1),new r("lijk",-1,3),new r("baar",-1,4),new r("bar",-1,5)],v=[new r("aa",-1,-1),new r("ee",-1,-1),new r("oo",-1,-1),new r("uu",-1,-1)],q=[17,65,16,1,0,0,0,0,0,0,0,0,0,0,0,0,128],j=[1,0,0,17,65,16,1,0,0,0,0,0,0,0,0,0,0,0,0,128],z=[17,67,16,1,0,0,0,0,0,0,0,0,0,0,0,0,128],C=new i;this.setCurrent=function(e){C.setCurrent(e)},this.getCurrent=function(){return C.getCurrent()},this.stem=function(){var r=C.cursor;return e(),C.cursor=r,o(),C.limit_backward=r,C.cursor=C.limit,d(),C.cursor=C.limit_backward,s(),!0}};return function(e){return"function"==typeof e.update?e.update(function(e){return n.setCurrent(e),n.stem(),n.getCurrent()}):(n.setCurrent(e),n.stem(),n.getCurrent())}}(),e.Pipeline.registerFunction(e.du.stemmer,"stemmer-du"),e.du.stopWordFilter=e.generateStopWordFilter(" aan al alles als altijd andere ben bij daar dan dat de der deze die dit doch doen door dus een eens en er ge geen geweest haar had heb hebben heeft hem het hier hij hoe hun iemand iets ik in is ja je kan kon kunnen maar me meer men met mij mijn moet na naar niet niets nog nu of om omdat onder ons ook op over reeds te tegen toch toen tot u uit uw van veel voor want waren was wat werd wezen wie wil worden wordt zal ze zelf zich zij zijn zo zonder zou".split(" ")),e.Pipeline.registerFunction(e.du.stopWordFilter,"stopWordFilter-du")}});
\ No newline at end of file
diff --git a/DevDoc/assets/javascripts/lunr/min/lunr.el.min.js b/DevDoc/assets/javascripts/lunr/min/lunr.el.min.js
new file mode 100644
index 00000000..ace017bd
--- /dev/null
+++ b/DevDoc/assets/javascripts/lunr/min/lunr.el.min.js
@@ -0,0 +1 @@
+!function(e,t){"function"==typeof define&&define.amd?define(t):"object"==typeof exports?module.exports=t():t()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. 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null!==o&&(s=o[1]+l[o[2]]),null!==(o=/^(.+?)(ΑΔΕΣ|ΑΔΩΝ)$/.exec(s))&&(s=o[1],/(ΟΚ|ΜΑΜ|ΜΑΝ|ΜΠΑΜΠ|ΠΑΤΕΡ|ΓΙΑΓΙ|ΝΤΑΝΤ|ΚΥΡ|ΘΕΙ|ΠΕΘΕΡ|ΜΟΥΣΑΜ|ΚΑΠΛΑΜ|ΠΑΡ|ΨΑΡ|ΤΖΟΥΡ|ΤΑΜΠΟΥΡ|ΓΑΛΑΤ|ΦΑΦΛΑΤ)$/.test(o[1])||(s+="ΑΔ")),null!==(o=/^(.+?)(ΕΔΕΣ|ΕΔΩΝ)$/.exec(s))&&(s=o[1],/(ΟΠ|ΙΠ|ΕΜΠ|ΥΠ|ΓΗΠ|ΔΑΠ|ΚΡΑΣΠ|ΜΙΛ)$/.test(o[1])&&(s+="ΕΔ")),null!==(o=/^(.+?)(ΟΥΔΕΣ|ΟΥΔΩΝ)$/.exec(s))&&(s=o[1],/(ΑΡΚ|ΚΑΛΙΑΚ|ΠΕΤΑΛ|ΛΙΧ|ΠΛΕΞ|ΣΚ|Σ|ΦΛ|ΦΡ|ΒΕΛ|ΛΟΥΛ|ΧΝ|ΣΠ|ΤΡΑΓ|ΦΕ)$/.test(o[1])&&(s+="ΟΥΔ")),null!==(o=/^(.+?)(ΕΩΣ|ΕΩΝ|ΕΑΣ|ΕΑ)$/.exec(s))&&(s=o[1],/^(Θ|Δ|ΕΛ|ΓΑΛ|Ν|Π|ΙΔ|ΠΑΡ|ΣΤΕΡ|ΟΡΦ|ΑΝΔΡ|ΑΝΤΡ)$/.test(o[1])&&(s+="Ε")),null!==(o=/^(.+?)(ΕΙΟ|ΕΙΟΣ|ΕΙΟΙ|ΕΙΑ|ΕΙΑΣ|ΕΙΕΣ|ΕΙΟΥ|ΕΙΟΥΣ|ΕΙΩΝ)$/.exec(s))&&o[1].length>4&&(s=o[1]),null!==(o=/^(.+?)(ΙΟΥΣ|ΙΑΣ|ΙΕΣ|ΙΟΣ|ΙΟΥ|ΙΟΙ|ΙΩΝ|ΙΟΝ|ΙΑ|ΙΟ)$/.exec(s))&&(s=o[1],(t(s)||s.length<2||/^(ΑΓ|ΑΓΓΕΛ|ΑΓΡ|ΑΕΡ|ΑΘΛ|ΑΚΟΥΣ|ΑΞ|ΑΣ|Β|ΒΙΒΛ|ΒΥΤ|Γ|ΓΙΑΓ|ΓΩΝ|Δ|ΔΑΝ|ΔΗΛ|ΔΗΜ|ΔΟΚΙΜ|ΕΛ|ΖΑΧΑΡ|ΗΛ|ΗΠ|ΙΔ|ΙΣΚ|ΙΣΤ|ΙΟΝ|ΙΩΝ|ΚΙΜΩΛ|ΚΟΛΟΝ|ΚΟΡ|ΚΤΗΡ|ΚΥΡ|ΛΑΓ|ΛΟΓ|ΜΑΓ|ΜΠΑΝ|ΜΠΡ|ΝΑΥΤ|ΝΟΤ|ΟΠΑΛ|ΟΞ|ΟΡ|ΟΣ|ΠΑΝΑΓ|ΠΑΤΡ|ΠΗΛ|ΠΗΝ|ΠΛΑΙΣ|ΠΟΝΤ|ΡΑΔ|ΡΟΔ|ΣΚ|ΣΚΟΡΠ|ΣΟΥΝ|ΣΠΑΝ|ΣΤΑΔ|ΣΥΡ|ΤΗΛ|ΤΙΜ|ΤΟΚ|ΤΟΠ|ΤΡΟΧ|ΦΙΛ|ΦΩΤ|Χ|ΧΙΛ|ΧΡΩΜ|ΧΩΡ)$/.test(o[1]))&&(s+="Ι"),/^(ΠΑΛ)$/.test(o[1])&&(s+="ΑΙ")),null!==(o=/^(.+?)(ΙΚΟΣ|ΙΚΟΝ|ΙΚΕΙΣ|ΙΚΟΙ|ΙΚΕΣ|ΙΚΟΥΣ|ΙΚΗ|ΙΚΗΣ|ΙΚΟ|ΙΚΑ|ΙΚΟΥ|ΙΚΩΝ|ΙΚΩΣ)$/.exec(s))&&(s=o[1],(t(s)||/^(ΑΔ|ΑΛ|ΑΜΑΝ|ΑΜΕΡ|ΑΜΜΟΧΑΛ|ΑΝΗΘ|ΑΝΤΙΔ|ΑΠΛ|ΑΤΤ|ΑΦΡ|ΒΑΣ|ΒΡΩΜ|ΓΕΝ|ΓΕΡ|Δ|ΔΙΚΑΝ|ΔΥΤ|ΕΙΔ|ΕΝΔ|ΕΞΩΔ|ΗΘ|ΘΕΤ|ΚΑΛΛΙΝ|ΚΑΛΠ|ΚΑΤΑΔ|ΚΟΥΖΙΝ|ΚΡ|ΚΩΔ|ΛΟΓ|Μ|ΜΕΡ|ΜΟΝΑΔ|ΜΟΥΛ|ΜΟΥΣ|ΜΠΑΓΙΑΤ|ΜΠΑΝ|ΜΠΟΛ|ΜΠΟΣ|ΜΥΣΤ|Ν|ΝΙΤ|ΞΙΚ|ΟΠΤ|ΠΑΝ|ΠΕΤΣ|ΠΙΚΑΝΤ|ΠΙΤΣ|ΠΛΑΣΤ|ΠΛΙΑΤΣ|ΠΟΝΤ|ΠΟΣΤΕΛΝ|ΠΡΩΤΟΔ|ΣΕΡΤ|ΣΗΜΑΝΤ|ΣΤΑΤ|ΣΥΝΑΔ|ΣΥΝΟΜΗΛ|ΤΕΛ|ΤΕΧΝ|ΤΡΟΠ|ΤΣΑΜ|ΥΠΟΔ|Φ|ΦΙΛΟΝ|ΦΥΛΟΔ|ΦΥΣ|ΧΑΣ)$/.test(o[1])||/(ΦΟΙΝ)$/.test(o[1]))&&(s+="ΙΚ")),"ΑΓΑΜΕ"===s&&(s="ΑΓΑΜ"),null!==(o=/^(.+?)(ΑΓΑΜΕ|ΗΣΑΜΕ|ΟΥΣΑΜΕ|ΗΚΑΜΕ|ΗΘΗΚΑΜΕ)$/.exec(s))&&(s=o[1]),null!==(o=/^(.+?)(ΑΜΕ)$/.exec(s))&&(s=o[1],/^(ΑΝΑΠ|ΑΠΟΘ|ΑΠΟΚ|ΑΠΟΣΤ|ΒΟΥΒ|ΞΕΘ|ΟΥΛ|ΠΕΘ|ΠΙΚΡ|ΠΟΤ|ΣΙΧ|Χ)$/.test(o[1])&&(s+="ΑΜ")),null!==(o=/^(.+?)(ΑΓΑΝΕ|ΗΣΑΝΕ|ΟΥΣΑΝΕ|ΙΟΝΤΑΝΕ|ΙΟΤΑΝΕ|ΙΟΥΝΤΑΝΕ|ΟΝΤΑΝΕ|ΟΤΑΝΕ|ΟΥΝΤΑΝΕ|ΗΚΑΝΕ|ΗΘΗΚΑΝΕ)$/.exec(s))&&(s=o[1],/^(ΤΡ|ΤΣ)$/.test(o[1])&&(s+="ΑΓΑΝ")),null!==(o=/^(.+?)(ΑΝΕ)$/.exec(s))&&(s=o[1],(r(s)||/^(ΒΕΤΕΡ|ΒΟΥΛΚ|ΒΡΑΧΜ|Γ|ΔΡΑΔΟΥΜ|Θ|ΚΑΛΠΟΥΖ|ΚΑΣΤΕΛ|ΚΟΡΜΟΡ|ΛΑΟΠΛ|ΜΩΑΜΕΘ|Μ|ΜΟΥΣΟΥΛΜΑΝ|ΟΥΛ|Π|ΠΕΛΕΚ|ΠΛ|ΠΟΛΙΣ|ΠΟΡΤΟΛ|ΣΑΡΑΚΑΤΣ|ΣΟΥΛΤ|ΤΣΑΡΛΑΤ|ΟΡΦ|ΤΣΙΓΓ|ΤΣΟΠ|ΦΩΤΟΣΤΕΦ|Χ|ΨΥΧΟΠΛ|ΑΓ|ΟΡΦ|ΓΑΛ|ΓΕΡ|ΔΕΚ|ΔΙΠΛ|ΑΜΕΡΙΚΑΝ|ΟΥΡ|ΠΙΘ|ΠΟΥΡΙΤ|Σ|ΖΩΝΤ|ΙΚ|ΚΑΣΤ|ΚΟΠ|ΛΙΧ|ΛΟΥΘΗΡ|ΜΑΙΝΤ|ΜΕΛ|ΣΙΓ|ΣΠ|ΣΤΕΓ|ΤΡΑΓ|ΤΣΑΓ|Φ|ΕΡ|ΑΔΑΠ|ΑΘΙΓΓ|ΑΜΗΧ|ΑΝΙΚ|ΑΝΟΡΓ|ΑΠΗΓ|ΑΠΙΘ|ΑΤΣΙΓΓ|ΒΑΣ|ΒΑΣΚ|ΒΑΘΥΓΑΛ|ΒΙΟΜΗΧ|ΒΡΑΧΥΚ|ΔΙΑΤ|ΔΙΑΦ|ΕΝΟΡΓ|ΘΥΣ|ΚΑΠΝΟΒΙΟΜΗΧ|ΚΑΤΑΓΑΛ|ΚΛΙΒ|ΚΟΙΛΑΡΦ|ΛΙΒ|ΜΕΓΛΟΒΙΟΜΗΧ|ΜΙΚΡΟΒΙΟΜΗΧ|ΝΤΑΒ|ΞΗΡΟΚΛΙΒ|ΟΛΙΓΟΔΑΜ|ΟΛΟΓΑΛ|ΠΕΝΤΑΡΦ|ΠΕΡΗΦ|ΠΕΡΙΤΡ|ΠΛΑΤ|ΠΟΛΥΔΑΠ|ΠΟΛΥΜΗΧ|ΣΤΕΦ|ΤΑΒ|ΤΕΤ|ΥΠΕΡΗΦ|ΥΠΟΚΟΠ|ΧΑΜΗΛΟΔΑΠ|ΨΗΛΟΤΑΒ)$/.test(o[1]))&&(s+="ΑΝ")),null!==(o=/^(.+?)(ΗΣΕΤΕ)$/.exec(s))&&(s=o[1]),null!==(o=/^(.+?)(ΕΤΕ)$/.exec(s))&&(s=o[1],(r(s)||/(ΟΔ|ΑΙΡ|ΦΟΡ|ΤΑΘ|ΔΙΑΘ|ΣΧ|ΕΝΔ|ΕΥΡ|ΤΙΘ|ΥΠΕΡΘ|ΡΑΘ|ΕΝΘ|ΡΟΘ|ΣΘ|ΠΥΡ|ΑΙΝ|ΣΥΝΔ|ΣΥΝ|ΣΥΝΘ|ΧΩΡ|ΠΟΝ|ΒΡ|ΚΑΘ|ΕΥΘ|ΕΚΘ|ΝΕΤ|ΡΟΝ|ΑΡΚ|ΒΑΡ|ΒΟΛ|ΩΦΕΛ)$/.test(o[1])||/^(ΑΒΑΡ|ΒΕΝ|ΕΝΑΡ|ΑΒΡ|ΑΔ|ΑΘ|ΑΝ|ΑΠΛ|ΒΑΡΟΝ|ΝΤΡ|ΣΚ|ΚΟΠ|ΜΠΟΡ|ΝΙΦ|ΠΑΓ|ΠΑΡΑΚΑΛ|ΣΕΡΠ|ΣΚΕΛ|ΣΥΡΦ|ΤΟΚ|Υ|Δ|ΕΜ|ΘΑΡΡ|Θ)$/.test(o[1]))&&(s+="ΕΤ")),null!==(o=/^(.+?)(ΟΝΤΑΣ|ΩΝΤΑΣ)$/.exec(s))&&(s=o[1],/^ΑΡΧ$/.test(o[1])&&(s+="ΟΝΤ"),/ΚΡΕ$/.test(o[1])&&(s+="ΩΝΤ")),null!==(o=/^(.+?)(ΟΜΑΣΤΕ|ΙΟΜΑΣΤΕ)$/.exec(s))&&(s=o[1],/^ΟΝ$/.test(o[1])&&(s+="ΟΜΑΣΤ")),null!==(o=/^(.+?)(ΙΕΣΤΕ)$/.exec(s))&&(s=o[1],/^(Π|ΑΠ|ΣΥΜΠ|ΑΣΥΜΠ|ΑΚΑΤΑΠ|ΑΜΕΤΑΜΦ)$/.test(o[1])&&(s+="ΙΕΣΤ")),null!==(o=/^(.+?)(ΕΣΤΕ)$/.exec(s))&&(s=o[1],/^(ΑΛ|ΑΡ|ΕΚΤΕΛ|Ζ|Μ|Ξ|ΠΑΡΑΚΑΛ|ΠΡΟ|ΝΙΣ)$/.test(o[1])&&(s+="ΕΣΤ")),null!==(o=/^(.+?)(ΗΘΗΚΑ|ΗΘΗΚΕΣ|ΗΘΗΚΕ)$/.exec(s))&&(s=o[1]),null!==(o=/^(.+?)(ΗΚΑ|ΗΚΕΣ|ΗΚΕ)$/.exec(s))&&(s=o[1],(/(ΣΚΩΛ|ΣΚΟΥΛ|ΝΑΡΘ|ΣΦ|ΟΘ|ΠΙΘ)$/.test(o[1])||/^(ΔΙΑΘ|Θ|ΠΑΡΑΚΑΤΑΘ|ΠΡΟΣΘ|ΣΥΝΘ)$/.test(o[1]))&&(s+="ΗΚ")),null!==(o=/^(.+?)(ΟΥΣΑ|ΟΥΣΕΣ|ΟΥΣΕ)$/.exec(s))&&(s=o[1],(t(s)||/^(ΦΑΡΜΑΚ|ΧΑΔ|ΑΓΚ|ΑΝΑΡΡ|ΒΡΟΜ|ΕΚΛΙΠ|ΛΑΜΠΙΔ|ΛΕΧ|Μ|ΠΑΤ|Ρ|Λ|ΜΕΔ|ΜΕΣΑΖ|ΥΠΟΤΕΙΝ|ΑΜ|ΑΙΘ|ΑΝΗΚ|ΔΕΣΠΟΖ|ΕΝΔΙΑΦΕΡ)$/.test(o[1])||/(ΠΟΔΑΡ|ΒΛΕΠ|ΠΑΝΤΑΧ|ΦΡΥΔ|ΜΑΝΤΙΛ|ΜΑΛΛ|ΚΥΜΑΤ|ΛΑΧ|ΛΗΓ|ΦΑΓ|ΟΜ|ΠΡΩΤ)$/.test(o[1]))&&(s+="ΟΥΣ")),null!==(o=/^(.+?)(ΑΓΑ|ΑΓΕΣ|ΑΓΕ)$/.exec(s))&&(s=o[1],(/^(ΑΒΑΣΤ|ΠΟΛΥΦ|ΑΔΗΦ|ΠΑΜΦ|Ρ|ΑΣΠ|ΑΦ|ΑΜΑΛ|ΑΜΑΛΛΙ|ΑΝΥΣΤ|ΑΠΕΡ|ΑΣΠΑΡ|ΑΧΑΡ|ΔΕΡΒΕΝ|ΔΡΟΣΟΠ|ΞΕΦ|ΝΕΟΠ|ΝΟΜΟΤ|ΟΛΟΠ|ΟΜΟΤ|ΠΡΟΣΤ|ΠΡΟΣΩΠΟΠ|ΣΥΜΠ|ΣΥΝΤ|Τ|ΥΠΟΤ|ΧΑΡ|ΑΕΙΠ|ΑΙΜΟΣΤ|ΑΝΥΠ|ΑΠΟΤ|ΑΡΤΙΠ|ΔΙΑΤ|ΕΝ|ΕΠΙΤ|ΚΡΟΚΑΛΟΠ|ΣΙΔΗΡΟΠ|Λ|ΝΑΥ|ΟΥΛΑΜ|ΟΥΡ|Π|ΤΡ|Μ)$/.test(o[1])||/(ΟΦ|ΠΕΛ|ΧΟΡΤ|ΛΛ|ΣΦ|ΡΠ|ΦΡ|ΠΡ|ΛΟΧ|ΣΜΗΝ)$/.test(o[1])&&!/^(ΨΟΦ|ΝΑΥΛΟΧ)$/.test(o[1])||/(ΚΟΛΛ)$/.test(o[1]))&&(s+="ΑΓ")),null!==(o=/^(.+?)(ΗΣΕ|ΗΣΟΥ|ΗΣΑ)$/.exec(s))&&(s=o[1],/^(Ν|ΧΕΡΣΟΝ|ΔΩΔΕΚΑΝ|ΕΡΗΜΟΝ|ΜΕΓΑΛΟΝ|ΕΠΤΑΝ|Ι)$/.test(o[1])&&(s+="ΗΣ")),null!==(o=/^(.+?)(ΗΣΤΕ)$/.exec(s))&&(s=o[1],/^(ΑΣΒ|ΣΒ|ΑΧΡ|ΧΡ|ΑΠΛ|ΑΕΙΜΝ|ΔΥΣΧΡ|ΕΥΧΡ|ΚΟΙΝΟΧΡ|ΠΑΛΙΜΨ)$/.test(o[1])&&(s+="ΗΣΤ")),null!==(o=/^(.+?)(ΟΥΝΕ|ΗΣΟΥΝΕ|ΗΘΟΥΝΕ)$/.exec(s))&&(s=o[1],/^(Ν|Ρ|ΣΠΙ|ΣΤΡΑΒΟΜΟΥΤΣ|ΚΑΚΟΜΟΥΤΣ|ΕΞΩΝ)$/.test(o[1])&&(s+="ΟΥΝ")),null!==(o=/^(.+?)(ΟΥΜΕ|ΗΣΟΥΜΕ|ΗΘΟΥΜΕ)$/.exec(s))&&(s=o[1],/^(ΠΑΡΑΣΟΥΣ|Φ|Χ|ΩΡΙΟΠΛ|ΑΖ|ΑΛΛΟΣΟΥΣ|ΑΣΟΥΣ)$/.test(o[1])&&(s+="ΟΥΜ")),null!=(o=/^(.+?)(ΜΑΤΟΙ|ΜΑΤΟΥΣ|ΜΑΤΟ|ΜΑΤΑ|ΜΑΤΩΣ|ΜΑΤΩΝ|ΜΑΤΟΣ|ΜΑΤΕΣ|ΜΑΤΗ|ΜΑΤΗΣ|ΜΑΤΟΥ)$/.exec(s))&&(s=o[1]+"Μ",/^(ΓΡΑΜ)$/.test(o[1])?s+="Α":/^(ΓΕ|ΣΤΑ)$/.test(o[1])&&(s+="ΑΤ")),null!==(o=/^(.+?)(ΟΥΑ)$/.exec(s))&&(s=o[1]+"ΟΥ"),n.length===s.length&&null!==(o=/^(.+?)(Α|ΑΓΑΤΕ|ΑΓΑΝ|ΑΕΙ|ΑΜΑΙ|ΑΝ|ΑΣ|ΑΣΑΙ|ΑΤΑΙ|ΑΩ|Ε|ΕΙ|ΕΙΣ|ΕΙΤΕ|ΕΣΑΙ|ΕΣ|ΕΤΑΙ|Ι|ΙΕΜΑΙ|ΙΕΜΑΣΤΕ|ΙΕΤΑΙ|ΙΕΣΑΙ|ΙΕΣΑΣΤΕ|ΙΟΜΑΣΤΑΝ|ΙΟΜΟΥΝ|ΙΟΜΟΥΝΑ|ΙΟΝΤΑΝ|ΙΟΝΤΟΥΣΑΝ|ΙΟΣΑΣΤΑΝ|ΙΟΣΑΣΤΕ|ΙΟΣΟΥΝ|ΙΟΣΟΥΝΑ|ΙΟΤΑΝ|ΙΟΥΜΑ|ΙΟΥΜΑΣΤΕ|ΙΟΥΝΤΑΙ|ΙΟΥΝΤΑΝ|Η|ΗΔΕΣ|ΗΔΩΝ|ΗΘΕΙ|ΗΘΕΙΣ|ΗΘΕΙΤΕ|ΗΘΗΚΑΤΕ|ΗΘΗΚΑΝ|ΗΘΟΥΝ|ΗΘΩ|ΗΚΑΤΕ|ΗΚΑΝ|ΗΣ|ΗΣΑΝ|ΗΣΑΤΕ|ΗΣΕΙ|ΗΣΕΣ|ΗΣΟΥΝ|ΗΣΩ|Ο|ΟΙ|ΟΜΑΙ|ΟΜΑΣΤΑΝ|ΟΜΟΥΝ|ΟΜΟΥΝΑ|ΟΝΤΑΙ|ΟΝΤΑΝ|ΟΝΤΟΥΣΑΝ|ΟΣ|ΟΣΑΣΤΑΝ|ΟΣΑΣΤΕ|ΟΣΟΥΝ|ΟΣΟΥΝΑ|ΟΤΑΝ|ΟΥ|ΟΥΜΑΙ|ΟΥΜΑΣΤΕ|ΟΥΝ|ΟΥΝΤΑΙ|ΟΥΝΤΑΝ|ΟΥΣ|ΟΥΣΑΝ|ΟΥΣΑΤΕ|Υ||ΥΑ|ΥΣ|Ω|ΩΝ|ΟΙΣ)$/.exec(s))&&(s=o[1]),null!=(o=/^(.+?)(ΕΣΤΕΡ|ΕΣΤΑΤ|ΟΤΕΡ|ΟΤΑΤ|ΥΤΕΡ|ΥΤΑΤ|ΩΤΕΡ|ΩΤΑΤ)$/.exec(s))&&(/^(ΕΞ|ΕΣ|ΑΝ|ΚΑΤ|Κ|ΠΡ)$/.test(o[1])||(s=o[1]),/^(ΚΑ|Μ|ΕΛΕ|ΛΕ|ΔΕ)$/.test(o[1])&&(s+="ΥΤ")),s}var 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t.update(function(t){for(var r="",n=0;n<t.length;n++)r+=e[t.charAt(n)]||t.charAt(n);return r});for(var r="",n=0;n<t.length;n++)r+=e[t.charAt(n)]||t.charAt(n);return r}}(),e.Pipeline.registerFunction(e.el.normilizer,"normilizer-el")}});
\ No newline at end of file
diff --git a/DevDoc/assets/javascripts/lunr/min/lunr.es.min.js b/DevDoc/assets/javascripts/lunr/min/lunr.es.min.js
new file mode 100644
index 00000000..2989d342
--- /dev/null
+++ b/DevDoc/assets/javascripts/lunr/min/lunr.es.min.js
@@ -0,0 +1,18 @@
+/*!
+ * Lunr languages, `Spanish` language
+ * https://github.com/MihaiValentin/lunr-languages
+ *
+ * Copyright 2014, Mihai Valentin
+ * http://www.mozilla.org/MPL/
+ */
+/*!
+ * based on
+ * Snowball JavaScript Library v0.3
+ * http://code.google.com/p/urim/
+ * http://snowball.tartarus.org/
+ *
+ * Copyright 2010, Oleg Mazko
+ * http://www.mozilla.org/MPL/
+ */
+
+!function(e,s){"function"==typeof define&&define.amd?define(s):"object"==typeof exports?module.exports=s():s()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. 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\ No newline at end of file
diff --git a/DevDoc/assets/javascripts/lunr/min/lunr.fi.min.js b/DevDoc/assets/javascripts/lunr/min/lunr.fi.min.js
new file mode 100644
index 00000000..29f5dfce
--- /dev/null
+++ b/DevDoc/assets/javascripts/lunr/min/lunr.fi.min.js
@@ -0,0 +1,18 @@
+/*!
+ * Lunr languages, `Finnish` language
+ * https://github.com/MihaiValentin/lunr-languages
+ *
+ * Copyright 2014, Mihai Valentin
+ * http://www.mozilla.org/MPL/
+ */
+/*!
+ * based on
+ * Snowball JavaScript Library v0.3
+ * http://code.google.com/p/urim/
+ * http://snowball.tartarus.org/
+ *
+ * Copyright 2010, Oleg Mazko
+ * http://www.mozilla.org/MPL/
+ */
+
+!function(i,e){"function"==typeof define&&define.amd?define(e):"object"==typeof exports?module.exports=e():e()(i.lunr)}(this,function(){return function(i){if(void 0===i)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===i.stemmerSupport)throw new Error("Lunr stemmer support is not present. 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i(),k=!1,A.limit_backward=e,A.cursor=A.limit,s(),A.cursor=A.limit,o(),A.cursor=A.limit,u(),A.cursor=A.limit,c(),A.cursor=A.limit,k?(m(),A.cursor=A.limit):(A.cursor=A.limit,w(),A.cursor=A.limit),_(),!0}};return function(i){return"function"==typeof i.update?i.update(function(i){return n.setCurrent(i),n.stem(),n.getCurrent()}):(n.setCurrent(i),n.stem(),n.getCurrent())}}(),i.Pipeline.registerFunction(i.fi.stemmer,"stemmer-fi"),i.fi.stopWordFilter=i.generateStopWordFilter("ei eivät emme en et ette että he heidän heidät heihin heille heillä heiltä heissä heistä heitä hän häneen hänelle hänellä häneltä hänen hänessä hänestä hänet häntä itse ja johon joiden joihin joiksi joilla joille joilta joina joissa joista joita joka joksi jolla jolle jolta jona jonka jos jossa josta jota jotka kanssa keiden keihin keiksi keille keillä keiltä keinä keissä keistä keitä keneen keneksi kenelle kenellä keneltä kenen kenenä kenessä kenestä kenet ketkä ketkä ketä koska kuin kuka kun me meidän meidät meihin meille meillä meiltä meissä meistä meitä mihin miksi mikä mille millä miltä minkä minkä minua minulla minulle minulta minun minussa minusta minut minuun minä minä missä mistä mitkä mitä mukaan mutta ne niiden niihin niiksi niille niillä niiltä niin niin niinä niissä niistä niitä noiden noihin noiksi noilla noille noilta noin noina noissa noista noita nuo nyt näiden näihin näiksi näille näillä näiltä näinä näissä näistä näitä nämä ole olemme olen olet olette oli olimme olin olisi olisimme olisin olisit olisitte olisivat olit olitte olivat olla olleet ollut on ovat poikki se sekä sen siihen siinä siitä siksi sille sillä sillä siltä sinua sinulla sinulle sinulta sinun sinussa sinusta sinut sinuun sinä sinä sitä tai te teidän teidät teihin teille teillä teiltä teissä teistä teitä tuo tuohon tuoksi tuolla tuolle tuolta tuon tuona tuossa tuosta tuota tähän täksi tälle tällä tältä tämä tämän tänä tässä tästä tätä vaan vai vaikka yli".split(" 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\ No newline at end of file
diff --git a/DevDoc/assets/javascripts/lunr/min/lunr.fr.min.js b/DevDoc/assets/javascripts/lunr/min/lunr.fr.min.js
new file mode 100644
index 00000000..68cd0094
--- /dev/null
+++ b/DevDoc/assets/javascripts/lunr/min/lunr.fr.min.js
@@ -0,0 +1,18 @@
+/*!
+ * Lunr languages, `French` language
+ * https://github.com/MihaiValentin/lunr-languages
+ *
+ * Copyright 2014, Mihai Valentin
+ * http://www.mozilla.org/MPL/
+ */
+/*!
+ * based on
+ * Snowball JavaScript Library v0.3
+ * http://code.google.com/p/urim/
+ * http://snowball.tartarus.org/
+ *
+ * Copyright 2010, Oleg Mazko
+ * http://www.mozilla.org/MPL/
+ */
+
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. 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\ No newline at end of file
diff --git a/DevDoc/assets/javascripts/lunr/min/lunr.he.min.js b/DevDoc/assets/javascripts/lunr/min/lunr.he.min.js
new file mode 100644
index 00000000..b863d3ea
--- /dev/null
+++ b/DevDoc/assets/javascripts/lunr/min/lunr.he.min.js
@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.he=function(){this.pipeline.reset(),this.pipeline.add(e.he.trimmer,e.he.stopWordFilter,e.he.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.he.stemmer))},e.he.wordCharacters="֑-״א-תa-zA-Zａ-ｚＡ-Ｚ0-9０-９",e.he.trimmer=e.trimmerSupport.generateTrimmer(e.he.wordCharacters),e.Pipeline.registerFunction(e.he.trimmer,"trimmer-he"),e.he.stemmer=function(){var e=this;return e.result=!1,e.preRemoved=!1,e.sufRemoved=!1,e.pre={pre1:"ה ו י ת",pre2:"ב כ ל מ ש כש",pre3:"הב הכ הל המ הש בש לכ",pre4:"וב וכ ול ומ וש",pre5:"מה שה כל",pre6:"מב מכ מל ממ מש",pre7:"בה בו בי בת כה כו כי כת לה לו לי לת",pre8:"ובה ובו ובי ובת וכה וכו וכי וכת ולה ולו ולי ולת"},e.suf={suf1:"ך כ ם ן נ",suf2:"ים ות וך וכ ום ון ונ הם הן יכ יך ינ ים",suf3:"תי תך תכ תם תן תנ",suf4:"ותי ותך ותכ ותם ותן ותנ",suf5:"נו כם כן הם הן",suf6:"ונו וכם וכן והם והן",suf7:"תכם תכן תנו תהם תהן",suf8:"הוא היא הם הן אני אתה את אנו אתם אתן",suf9:"ני נו כי כו כם כן תי תך תכ תם תן",suf10:"י ך כ ם ן נ ת"},e.patterns=JSON.parse('{"hebrewPatterns": [{"pt1": [{"c": "ה", "l": 0}]}, {"pt2": [{"c": "ו", "l": 0}]}, {"pt3": [{"c": "י", "l": 0}]}, {"pt4": [{"c": "ת", "l": 0}]}, {"pt5": [{"c": "מ", "l": 0}]}, {"pt6": [{"c": "ל", "l": 0}]}, {"pt7": [{"c": "ב", "l": 0}]}, {"pt8": [{"c": "כ", "l": 0}]}, {"pt9": [{"c": "ש", "l": 0}]}, {"pt10": [{"c": "כש", "l": 0}]}, {"pt11": [{"c": "בה", "l": 0}]}, {"pt12": [{"c": "וב", "l": 0}]}, {"pt13": [{"c": "וכ", "l": 0}]}, {"pt14": [{"c": "ול", "l": 0}]}, {"pt15": [{"c": "ומ", "l": 0}]}, {"pt16": [{"c": "וש", "l": 0}]}, {"pt17": [{"c": "הב", "l": 0}]}, {"pt18": [{"c": "הכ", "l": 0}]}, {"pt19": [{"c": "הל", "l": 0}]}, {"pt20": [{"c": "המ", "l": 0}]}, {"pt21": [{"c": "הש", "l": 0}]}, {"pt22": [{"c": "מה", "l": 0}]}, {"pt23": [{"c": "שה", "l": 0}]}, {"pt24": [{"c": "כל", "l": 0}]}]}'),e.execArray=["cleanWord","removeDiacritics","removeStopWords","normalizeHebrewCharacters"],e.stem=function(){var r=0;for(e.result=!1,e.preRemoved=!1,e.sufRemoved=!1;r<e.execArray.length&&1!=e.result;)e.result=e[e.execArray[r]](),r++},e.setCurrent=function(r){e.word=r},e.getCurrent=function(){return e.word},e.cleanWord=function(){return!!new RegExp("[^֑-״א-ת]").test("")},e.removeDiacritics=function(){var r=new RegExp("[ְ-ֿ]","g");return e.word=e.word.replace(r,""),!1},e.removeStopWords=function(){if("אבל או אולי אותו אותי אותך אותם אותן אותנו אז אחר אחרות אחרי אחריכן אחרים אחרת אי איזה איך אין איפה אל אלה אלו אם אנחנו אני אף אפשר את אתה אתכם אתכן אתם אתן באיזה באיזו בגלל בין בלבד בעבור בעזרת בכל בכן בלי במידה במקום שבו ברוב בשביל בשעה ש בתוך גם דרך הוא היא היה היי היכן היתה היתי הם הן הנה הסיבה שבגללה הרי ואילו ואת זאת זה זות יהיה יוכל יוכלו יותר מדי יכול יכולה יכולות יכולים יכל יכלה יכלו יש כאן כאשר כולם כולן כזה כי כיצד כך כל כלל כמו כן כפי כש לא לאו לאיזותך לאן לבין לה להיות להם להן לו לזה לזות לי לך לכם לכן למה למעלה למעלה מ למטה למטה מ למעט למקום שבו למרות לנו לעבר לעיכן לפיכך לפני מאד מאחורי מאיזו סיבה מאין מאיפה מבלי מבעד מדוע מה מהיכן מול מחוץ מי מידע מכאן מכל מכן מלבד מן מנין מסוגל מעט מעטים מעל מצד מקום בו מתחת מתי נגד נגר נו עד עז על עלי עליו עליה עליהם עליך עלינו עם עצמה עצמהם עצמהן עצמו עצמי עצמם עצמן עצמנו פה רק שוב של שלה שלהם שלהן שלו שלי שלך שלכה שלכם שלכן שלנו שם תהיה תחת".split(" ").indexOf(e.word)>=0)return!0},e.normalizeHebrewCharacters=function(){return e.word=e.word.replace("ך","כ"),e.word=e.word.replace("ם","מ"),e.word=e.word.replace("ן","נ"),e.word=e.word.replace("ף","פ"),e.word=e.word.replace("ץ","צ"),!1},function(r){return"function"==typeof r.update?r.update(function(r){return e.setCurrent(r),e.stem(),e.getCurrent()}):(e.setCurrent(r),e.stem(),e.getCurrent())}}(),e.Pipeline.registerFunction(e.he.stemmer,"stemmer-he"),e.he.stopWordFilter=e.generateStopWordFilter("אבל או אולי אותו אותי אותך אותם אותן אותנו אז אחר אחרות אחרי אחריכן אחרים אחרת אי איזה איך אין איפה אל אלה אלו אם אנחנו אני אף אפשר את אתה אתכם אתכן אתם אתן באיזה באיזו בגלל בין בלבד בעבור בעזרת בכל בכן בלי במידה במקום שבו ברוב בשביל בשעה ש בתוך גם דרך הוא היא היה היי היכן היתה היתי הם הן הנה הסיבה שבגללה הרי ואילו ואת זאת זה זות יהיה יוכל יוכלו יותר מדי יכול יכולה יכולות יכולים יכל יכלה יכלו יש כאן כאשר כולם כולן כזה כי כיצד כך כל כלל כמו כן כפי כש לא לאו לאיזותך לאן לבין לה להיות להם להן לו לזה לזות לי לך לכם לכן למה למעלה למעלה מ למטה למטה מ למעט למקום שבו למרות לנו לעבר לעיכן לפיכך לפני מאד מאחורי מאיזו סיבה מאין מאיפה מבלי מבעד מדוע מה מהיכן מול מחוץ מי מידע מכאן מכל מכן מלבד מן מנין מסוגל מעט מעטים מעל מצד מקום בו מתחת מתי נגד נגר נו עד עז על עלי עליו עליה עליהם עליך עלינו עם עצמה עצמהם עצמהן עצמו עצמי עצמם עצמן עצמנו פה רק שוב של שלה שלהם שלהן שלו שלי שלך שלכה שלכם שלכן שלנו שם תהיה תחת".split(" ")),e.Pipeline.registerFunction(e.he.stopWordFilter,"stopWordFilter-he")}});
\ No newline at end of file
diff --git a/DevDoc/assets/javascripts/lunr/min/lunr.hi.min.js b/DevDoc/assets/javascripts/lunr/min/lunr.hi.min.js
new file mode 100644
index 00000000..7dbc4140
--- /dev/null
+++ b/DevDoc/assets/javascripts/lunr/min/lunr.hi.min.js
@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.hi=function(){this.pipeline.reset(),this.pipeline.add(e.hi.trimmer,e.hi.stopWordFilter,e.hi.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.hi.stemmer))},e.hi.wordCharacters="ऀ-ःऄ-एऐ-टठ-यर-िी-ॏॐ-य़ॠ-९॰-ॿa-zA-Zａ-ｚＡ-Ｚ0-9０-９",e.hi.trimmer=e.trimmerSupport.generateTrimmer(e.hi.wordCharacters),e.Pipeline.registerFunction(e.hi.trimmer,"trimmer-hi"),e.hi.stopWordFilter=e.generateStopWordFilter("अत अपना अपनी अपने अभी अंदर आदि आप इत्यादि इन इनका इन्हीं इन्हें इन्हों इस इसका इसकी इसके इसमें इसी इसे उन उनका उनकी उनके उनको उन्हीं उन्हें उन्हों उस उसके उसी उसे एक एवं एस ऐसे और कई कर करता करते करना करने करें कहते कहा का काफ़ी कि कितना किन्हें किन्हों किया किर किस किसी किसे की कुछ कुल के को कोई कौन कौनसा गया घर जब जहाँ जा जितना जिन जिन्हें जिन्हों जिस जिसे जीधर जैसा जैसे जो तक तब तरह तिन तिन्हें तिन्हों तिस तिसे तो था थी थे दबारा दिया दुसरा दूसरे दो द्वारा न नके नहीं ना निहायत नीचे ने पर पहले पूरा पे फिर बनी बही बहुत बाद बाला बिलकुल भी भीतर मगर मानो मे में यदि यह यहाँ यही या यिह ये रखें रहा रहे ऱ्वासा लिए लिये लेकिन व वग़ैरह वर्ग वह वहाँ वहीं वाले वुह वे वो सकता सकते सबसे सभी साथ साबुत साभ सारा से सो संग ही हुआ हुई हुए है हैं हो होता होती होते होना होने".split(" ")),e.hi.stemmer=function(){return function(e){return"function"==typeof e.update?e.update(function(e){return e}):e}}();var r=e.wordcut;r.init(),e.hi.tokenizer=function(i){if(!arguments.length||null==i||void 0==i)return[];if(Array.isArray(i))return i.map(function(r){return isLunr2?new e.Token(r.toLowerCase()):r.toLowerCase()});var t=i.toString().toLowerCase().replace(/^\s+/,"");return r.cut(t).split("|")},e.Pipeline.registerFunction(e.hi.stemmer,"stemmer-hi"),e.Pipeline.registerFunction(e.hi.stopWordFilter,"stopWordFilter-hi")}});
\ No newline at end of file
diff --git a/DevDoc/assets/javascripts/lunr/min/lunr.hu.min.js b/DevDoc/assets/javascripts/lunr/min/lunr.hu.min.js
new file mode 100644
index 00000000..ed9d909f
--- /dev/null
+++ b/DevDoc/assets/javascripts/lunr/min/lunr.hu.min.js
@@ -0,0 +1,18 @@
+/*!
+ * Lunr languages, `Hungarian` language
+ * https://github.com/MihaiValentin/lunr-languages
+ *
+ * Copyright 2014, Mihai Valentin
+ * http://www.mozilla.org/MPL/
+ */
+/*!
+ * based on
+ * Snowball JavaScript Library v0.3
+ * http://code.google.com/p/urim/
+ * http://snowball.tartarus.org/
+ *
+ * Copyright 2010, Oleg Mazko
+ * http://www.mozilla.org/MPL/
+ */
+
+!function(e,n){"function"==typeof define&&define.amd?define(n):"object"==typeof exports?module.exports=n():n()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.hu=function(){this.pipeline.reset(),this.pipeline.add(e.hu.trimmer,e.hu.stopWordFilter,e.hu.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.hu.stemmer))},e.hu.wordCharacters="A-Za-zªºÀ-ÖØ-öø-ʸˠ-ˤᴀ-ᴥᴬ-ᵜᵢ-ᵥᵫ-ᵷᵹ-ᶾḀ-ỿⁱⁿₐ-ₜKÅℲⅎⅠ-ↈⱠ-ⱿꜢ-ꞇꞋ-ꞭꞰ-ꞷꟷ-ꟿꬰ-ꭚꭜ-ꭤff-stＡ-Ｚａ-ｚ",e.hu.trimmer=e.trimmerSupport.generateTrimmer(e.hu.wordCharacters),e.Pipeline.registerFunction(e.hu.trimmer,"trimmer-hu"),e.hu.stemmer=function(){var n=e.stemmerSupport.Among,r=e.stemmerSupport.SnowballProgram,i=new function(){function e(){var e,n=L.cursor;if(d=L.limit,L.in_grouping(W,97,252))for(;;){if(e=L.cursor,L.out_grouping(W,97,252))return L.cursor=e,L.find_among(g,8)||(L.cursor=e,e<L.limit&&L.cursor++),void(d=L.cursor);if(L.cursor=e,e>=L.limit)return void(d=e);L.cursor++}if(L.cursor=n,L.out_grouping(W,97,252)){for(;!L.in_grouping(W,97,252);){if(L.cursor>=L.limit)return;L.cursor++}d=L.cursor}}function i(){return d<=L.cursor}function a(){var e;if(L.ket=L.cursor,(e=L.find_among_b(h,2))&&(L.bra=L.cursor,i()))switch(e){case 1:L.slice_from("a");break;case 2:L.slice_from("e")}}function t(){var e=L.limit-L.cursor;return!!L.find_among_b(p,23)&&(L.cursor=L.limit-e,!0)}function s(){if(L.cursor>L.limit_backward){L.cursor--,L.ket=L.cursor;var e=L.cursor-1;L.limit_backward<=e&&e<=L.limit&&(L.cursor=e,L.bra=e,L.slice_del())}}function c(){var e;if(L.ket=L.cursor,(e=L.find_among_b(_,2))&&(L.bra=L.cursor,i())){if((1==e||2==e)&&!t())return;L.slice_del(),s()}}function o(){L.ket=L.cursor,L.find_among_b(v,44)&&(L.bra=L.cursor,i()&&(L.slice_del(),a()))}function w(){var e;if(L.ket=L.cursor,(e=L.find_among_b(z,3))&&(L.bra=L.cursor,i()))switch(e){case 1:L.slice_from("e");break;case 2:case 3:L.slice_from("a")}}function l(){var e;if(L.ket=L.cursor,(e=L.find_among_b(y,6))&&(L.bra=L.cursor,i()))switch(e){case 1:case 2:L.slice_del();break;case 3:L.slice_from("a");break;case 4:L.slice_from("e")}}function u(){var e;if(L.ket=L.cursor,(e=L.find_among_b(j,2))&&(L.bra=L.cursor,i())){if((1==e||2==e)&&!t())return;L.slice_del(),s()}}function m(){var e;if(L.ket=L.cursor,(e=L.find_among_b(C,7))&&(L.bra=L.cursor,i()))switch(e){case 1:L.slice_from("a");break;case 2:L.slice_from("e");break;case 3:case 4:case 5:case 6:case 7:L.slice_del()}}function k(){var e;if(L.ket=L.cursor,(e=L.find_among_b(P,12))&&(L.bra=L.cursor,i()))switch(e){case 1:case 4:case 7:case 9:L.slice_del();break;case 2:case 5:case 8:L.slice_from("e");break;case 3:case 6:L.slice_from("a")}}function f(){var e;if(L.ket=L.cursor,(e=L.find_among_b(F,31))&&(L.bra=L.cursor,i()))switch(e){case 1:case 4:case 7:case 8:case 9:case 12:case 13:case 16:case 17:case 18:L.slice_del();break;case 2:case 5:case 10:case 14:case 19:L.slice_from("a");break;case 3:case 6:case 11:case 15:case 20:L.slice_from("e")}}function b(){var e;if(L.ket=L.cursor,(e=L.find_among_b(S,42))&&(L.bra=L.cursor,i()))switch(e){case 1:case 4:case 5:case 6:case 9:case 10:case 11:case 14:case 15:case 16:case 17:case 20:case 21:case 24:case 25:case 26:case 29:L.slice_del();break;case 2:case 7:case 12:case 18:case 22:case 27:L.slice_from("a");break;case 3:case 8:case 13:case 19:case 23:case 28:L.slice_from("e")}}var d,g=[new n("cs",-1,-1),new n("dzs",-1,-1),new n("gy",-1,-1),new n("ly",-1,-1),new n("ny",-1,-1),new n("sz",-1,-1),new n("ty",-1,-1),new n("zs",-1,-1)],h=[new n("á",-1,1),new n("é",-1,2)],p=[new n("bb",-1,-1),new n("cc",-1,-1),new n("dd",-1,-1),new n("ff",-1,-1),new n("gg",-1,-1),new n("jj",-1,-1),new n("kk",-1,-1),new n("ll",-1,-1),new n("mm",-1,-1),new n("nn",-1,-1),new n("pp",-1,-1),new n("rr",-1,-1),new n("ccs",-1,-1),new n("ss",-1,-1),new n("zzs",-1,-1),new n("tt",-1,-1),new n("vv",-1,-1),new n("ggy",-1,-1),new n("lly",-1,-1),new n("nny",-1,-1),new n("tty",-1,-1),new n("ssz",-1,-1),new n("zz",-1,-1)],_=[new n("al",-1,1),new n("el",-1,2)],v=[new n("ba",-1,-1),new n("ra",-1,-1),new n("be",-1,-1),new n("re",-1,-1),new n("ig",-1,-1),new n("nak",-1,-1),new 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keressünk keresztül ki kívül között közül legalább legyen lehet lehetett lenne lenni lesz lett maga magát majd majd meg mellett mely melyek mert mi mikor milyen minden mindenki mindent mindig mint mintha mit mivel miért most már más másik még míg nagy nagyobb nagyon ne nekem neki nem nincs néha néhány nélkül olyan ott pedig persze rá s saját sem semmi sok sokat sokkal szemben szerint szinte számára talán tehát teljes tovább továbbá több ugyanis utolsó után utána vagy vagyis vagyok valaki valami valamint való van vannak vele vissza viszont volna volt voltak voltam voltunk által általában át én éppen és így õ õk õket össze úgy új újabb újra".split(" ")),e.Pipeline.registerFunction(e.hu.stopWordFilter,"stopWordFilter-hu")}});
\ No newline at end of file
diff --git a/DevDoc/assets/javascripts/lunr/min/lunr.hy.min.js b/DevDoc/assets/javascripts/lunr/min/lunr.hy.min.js
new file mode 100644
index 00000000..b37f7929
--- /dev/null
+++ b/DevDoc/assets/javascripts/lunr/min/lunr.hy.min.js
@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.hy=function(){this.pipeline.reset(),this.pipeline.add(e.hy.trimmer,e.hy.stopWordFilter)},e.hy.wordCharacters="[A-Za-z԰-֏ff-ﭏ]",e.hy.trimmer=e.trimmerSupport.generateTrimmer(e.hy.wordCharacters),e.Pipeline.registerFunction(e.hy.trimmer,"trimmer-hy"),e.hy.stopWordFilter=e.generateStopWordFilter("դու և եք էիր էիք հետո նաև նրանք որը վրա է որ պիտի են այս մեջ ն իր ու ի այդ որոնք այն կամ էր մի ես համար այլ իսկ էին ենք հետ ին թ էինք մենք նրա նա դուք եմ էի ըստ որպես ում".split(" ")),e.Pipeline.registerFunction(e.hy.stopWordFilter,"stopWordFilter-hy"),e.hy.stemmer=function(){return function(e){return"function"==typeof e.update?e.update(function(e){return e}):e}}(),e.Pipeline.registerFunction(e.hy.stemmer,"stemmer-hy")}});
\ No newline at end of file
diff --git a/DevDoc/assets/javascripts/lunr/min/lunr.it.min.js b/DevDoc/assets/javascripts/lunr/min/lunr.it.min.js
new file mode 100644
index 00000000..344b6a3c
--- /dev/null
+++ b/DevDoc/assets/javascripts/lunr/min/lunr.it.min.js
@@ -0,0 +1,18 @@
+/*!
+ * Lunr languages, `Italian` language
+ * https://github.com/MihaiValentin/lunr-languages
+ *
+ * Copyright 2014, Mihai Valentin
+ * http://www.mozilla.org/MPL/
+ */
+/*!
+ * based on
+ * Snowball JavaScript Library v0.3
+ * http://code.google.com/p/urim/
+ * http://snowball.tartarus.org/
+ *
+ * Copyright 2010, Oleg Mazko
+ * http://www.mozilla.org/MPL/
+ */
+
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r("evo",-1,1),new r("ivo",-1,1),new r("ar",-1,1),new r("ir",-1,1),new r("erà",-1,1),new r("irà",-1,1),new r("erò",-1,1),new r("irò",-1,1)],L=[17,65,16,0,0,0,0,0,0,0,0,0,0,0,0,128,128,8,2,1],y=[17,65,0,0,0,0,0,0,0,0,0,0,0,0,0,128,128,8,2],U=[17],x=new n;this.setCurrent=function(e){x.setCurrent(e)},this.getCurrent=function(){return x.getCurrent()},this.stem=function(){var e=x.cursor;return i(),x.cursor=e,u(),x.limit_backward=e,x.cursor=x.limit,f(),x.cursor=x.limit,v()||(x.cursor=x.limit,b()),x.cursor=x.limit,_(),x.cursor=x.limit_backward,c(),!0}};return function(e){return"function"==typeof e.update?e.update(function(e){return i.setCurrent(e),i.stem(),i.getCurrent()}):(i.setCurrent(e),i.stem(),i.getCurrent())}}(),e.Pipeline.registerFunction(e.it.stemmer,"stemmer-it"),e.it.stopWordFilter=e.generateStopWordFilter("a abbia abbiamo abbiano abbiate ad agl agli ai al all alla alle allo anche avemmo avendo avesse avessero avessi avessimo aveste avesti avete aveva avevamo avevano avevate avevi avevo avrai avranno avrebbe avrebbero avrei avremmo avremo avreste avresti avrete avrà avrò avuta avute avuti avuto c che chi ci coi col come con contro cui da dagl dagli dai dal dall dalla dalle dallo degl degli dei del dell della delle dello di dov dove e ebbe ebbero ebbi ed era erano eravamo eravate eri ero essendo faccia facciamo facciano facciate faccio facemmo facendo facesse facessero facessi facessimo faceste facesti faceva facevamo facevano facevate facevi facevo fai fanno farai faranno farebbe farebbero farei faremmo faremo fareste faresti farete farà farò fece fecero feci fosse fossero fossi fossimo foste fosti fu fui fummo furono gli ha hai hanno ho i il in io l la le lei li lo loro lui ma mi mia mie miei mio ne negl negli nei nel nell nella nelle nello noi non nostra nostre nostri nostro o per perché più quale quanta quante quanti quanto quella quelle quelli quello questa queste questi questo sarai saranno sarebbe sarebbero sarei saremmo saremo sareste saresti sarete sarà sarò se sei si sia siamo siano siate siete sono sta stai stando stanno starai staranno starebbe starebbero starei staremmo staremo stareste staresti starete starà starò stava stavamo stavano stavate stavi stavo stemmo stesse stessero stessi stessimo steste stesti stette stettero stetti stia stiamo stiano stiate sto su sua sue sugl sugli sui sul sull sulla sulle sullo suo suoi ti tra tu tua tue tuo tuoi tutti tutto un una uno vi voi vostra vostre vostri vostro è".split(" ")),e.Pipeline.registerFunction(e.it.stopWordFilter,"stopWordFilter-it")}});
\ No newline at end of file
diff --git a/DevDoc/assets/javascripts/lunr/min/lunr.ja.min.js b/DevDoc/assets/javascripts/lunr/min/lunr.ja.min.js
new file mode 100644
index 00000000..5f254ebe
--- /dev/null
+++ b/DevDoc/assets/javascripts/lunr/min/lunr.ja.min.js
@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");var r="2"==e.version[0];e.ja=function(){this.pipeline.reset(),this.pipeline.add(e.ja.trimmer,e.ja.stopWordFilter,e.ja.stemmer),r?this.tokenizer=e.ja.tokenizer:(e.tokenizer&&(e.tokenizer=e.ja.tokenizer),this.tokenizerFn&&(this.tokenizerFn=e.ja.tokenizer))};var t=new e.TinySegmenter;e.ja.tokenizer=function(i){var n,o,s,p,a,u,m,l,c,f;if(!arguments.length||null==i||void 0==i)return[];if(Array.isArray(i))return i.map(function(t){return r?new e.Token(t.toLowerCase()):t.toLowerCase()});for(o=i.toString().toLowerCase().replace(/^\s+/,""),n=o.length-1;n>=0;n--)if(/\S/.test(o.charAt(n))){o=o.substring(0,n+1);break}for(a=[],s=o.length,c=0,l=0;c<=s;c++)if(u=o.charAt(c),m=c-l,u.match(/\s/)||c==s){if(m>0)for(p=t.segment(o.slice(l,c)).filter(function(e){return!!e}),f=l,n=0;n<p.length;n++)r?a.push(new e.Token(p[n],{position:[f,p[n].length],index:a.length})):a.push(p[n]),f+=p[n].length;l=c+1}return a},e.ja.stemmer=function(){return function(e){return e}}(),e.Pipeline.registerFunction(e.ja.stemmer,"stemmer-ja"),e.ja.wordCharacters="一二三四五六七八九十百千万億兆一-龠々〆ヵヶぁ-んァ-ヴーｱ-ﾝﾞa-zA-Zａ-ｚＡ-Ｚ0-9０-９",e.ja.trimmer=e.trimmerSupport.generateTrimmer(e.ja.wordCharacters),e.Pipeline.registerFunction(e.ja.trimmer,"trimmer-ja"),e.ja.stopWordFilter=e.generateStopWordFilter("これ それ あれ この その あの ここ そこ あそこ こちら どこ だれ なに なん 何 私 貴方 貴方方 我々 私達 あの人 あのかた 彼女 彼 です あります おります います は が の に を で え から まで より も どの と し それで しかし".split(" ")),e.Pipeline.registerFunction(e.ja.stopWordFilter,"stopWordFilter-ja"),e.jp=e.ja,e.Pipeline.registerFunction(e.jp.stemmer,"stemmer-jp"),e.Pipeline.registerFunction(e.jp.trimmer,"trimmer-jp"),e.Pipeline.registerFunction(e.jp.stopWordFilter,"stopWordFilter-jp")}});
\ No newline at end of file
diff --git a/DevDoc/assets/javascripts/lunr/min/lunr.jp.min.js b/DevDoc/assets/javascripts/lunr/min/lunr.jp.min.js
new file mode 100644
index 00000000..c055ebaf
--- /dev/null
+++ b/DevDoc/assets/javascripts/lunr/min/lunr.jp.min.js
@@ -0,0 +1 @@
+module.exports=require("./lunr.ja");
\ No newline at end of file
diff --git a/DevDoc/assets/javascripts/lunr/min/lunr.kn.min.js b/DevDoc/assets/javascripts/lunr/min/lunr.kn.min.js
new file mode 100644
index 00000000..1cef9bef
--- /dev/null
+++ b/DevDoc/assets/javascripts/lunr/min/lunr.kn.min.js
@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.kn=function(){this.pipeline.reset(),this.pipeline.add(e.kn.trimmer,e.kn.stopWordFilter,e.kn.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.kn.stemmer))},e.kn.wordCharacters="ಀ-಄ಅ-ಔಕ-ಹಾ-ೌ಼-ಽೕ-ೖೝ-ೞೠ-ೡೢ-ೣ೤೥೦-೯ೱ-ೳ",e.kn.trimmer=e.trimmerSupport.generateTrimmer(e.kn.wordCharacters),e.Pipeline.registerFunction(e.kn.trimmer,"trimmer-kn"),e.kn.stopWordFilter=e.generateStopWordFilter("ಮತ್ತು ಈ ಒಂದು ರಲ್ಲಿ ಹಾಗೂ ಎಂದು ಅಥವಾ ಇದು ರ ಅವರು ಎಂಬ ಮೇಲೆ ಅವರ ತನ್ನ ಆದರೆ ತಮ್ಮ ನಂತರ ಮೂಲಕ ಹೆಚ್ಚು ನ ಆ ಕೆಲವು ಅನೇಕ ಎರಡು ಹಾಗು ಪ್ರಮುಖ ಇದನ್ನು ಇದರ ಸುಮಾರು ಅದರ ಅದು ಮೊದಲ ಬಗ್ಗೆ ನಲ್ಲಿ ರಂದು ಇತರ ಅತ್ಯಂತ ಹೆಚ್ಚಿನ ಸಹ ಸಾಮಾನ್ಯವಾಗಿ ನೇ ಹಲವಾರು ಹೊಸ ದಿ ಕಡಿಮೆ ಯಾವುದೇ ಹೊಂದಿದೆ ದೊಡ್ಡ ಅನ್ನು ಇವರು ಪ್ರಕಾರ ಇದೆ ಮಾತ್ರ ಕೂಡ ಇಲ್ಲಿ ಎಲ್ಲಾ ವಿವಿಧ ಅದನ್ನು ಹಲವು ರಿಂದ ಕೇವಲ ದ ದಕ್ಷಿಣ ಗೆ ಅವನ ಅತಿ ನೆಯ ಬಹಳ ಕೆಲಸ ಎಲ್ಲ ಪ್ರತಿ ಇತ್ಯಾದಿ ಇವು ಬೇರೆ ಹೀಗೆ ನಡುವೆ ಇದಕ್ಕೆ ಎಸ್ ಇವರ ಮೊದಲು ಶ್ರೀ ಮಾಡುವ ಇದರಲ್ಲಿ ರೀತಿಯ ಮಾಡಿದ ಕಾಲ ಅಲ್ಲಿ ಮಾಡಲು ಅದೇ ಈಗ ಅವು ಗಳು ಎ ಎಂಬುದು ಅವನು ಅಂದರೆ ಅವರಿಗೆ ಇರುವ ವಿಶೇಷ ಮುಂದೆ ಅವುಗಳ ಮುಂತಾದ ಮೂಲ ಬಿ ಮೀ ಒಂದೇ ಇನ್ನೂ ಹೆಚ್ಚಾಗಿ ಮಾಡಿ ಅವರನ್ನು ಇದೇ ಯ ರೀತಿಯಲ್ಲಿ ಜೊತೆ ಅದರಲ್ಲಿ ಮಾಡಿದರು ನಡೆದ ಆಗ ಮತ್ತೆ ಪೂರ್ವ ಆತ ಬಂದ ಯಾವ ಒಟ್ಟು ಇತರೆ ಹಿಂದೆ ಪ್ರಮಾಣದ ಗಳನ್ನು ಕುರಿತು ಯು ಆದ್ದರಿಂದ ಅಲ್ಲದೆ ನಗರದ ಮೇಲಿನ ಏಕೆಂದರೆ ರಷ್ಟು ಎಂಬುದನ್ನು ಬಾರಿ ಎಂದರೆ ಹಿಂದಿನ ಆದರೂ ಆದ ಸಂಬಂಧಿಸಿದ ಮತ್ತೊಂದು ಸಿ ಆತನ ".split(" ")),e.kn.stemmer=function(){return function(e){return"function"==typeof e.update?e.update(function(e){return e}):e}}();var r=e.wordcut;r.init(),e.kn.tokenizer=function(t){if(!arguments.length||null==t||void 0==t)return[];if(Array.isArray(t))return t.map(function(r){return isLunr2?new e.Token(r.toLowerCase()):r.toLowerCase()});var n=t.toString().toLowerCase().replace(/^\s+/,"");return r.cut(n).split("|")},e.Pipeline.registerFunction(e.kn.stemmer,"stemmer-kn"),e.Pipeline.registerFunction(e.kn.stopWordFilter,"stopWordFilter-kn")}});
\ No newline at end of file
diff --git a/DevDoc/assets/javascripts/lunr/min/lunr.ko.min.js b/DevDoc/assets/javascripts/lunr/min/lunr.ko.min.js
new file mode 100644
index 00000000..eaf9dabf
--- /dev/null
+++ b/DevDoc/assets/javascripts/lunr/min/lunr.ko.min.js
@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.ko=function(){this.pipeline.reset(),this.pipeline.add(e.ko.trimmer,e.ko.stopWordFilter)},e.ko.wordCharacters="[A-Za-z가-힣]",e.ko.trimmer=e.trimmerSupport.generateTrimmer(e.ko.wordCharacters),e.Pipeline.registerFunction(e.ko.trimmer,"trimmer-ko"),e.ko.stopWordFilter=e.generateStopWordFilter("아 휴 아이구 아이쿠 아이고 어 나 우리 저희 따라 의해 을 를 에 의 가 으로 로 에게 뿐이다 의거하여 근거하여 입각하여 기준으로 예하면 예를 들면 예를 들자면 저 소인 소생 저희 지말고 하지마 하지마라 다른 물론 또한 그리고 비길수 없다 해서는 안된다 뿐만 아니라 만이 아니다 만은 아니다 막론하고 관계없이 그치지 않다 그러나 그런데 하지만 든간에 논하지 않다 따지지 않다 설사 비록 더라도 아니면 만 못하다 하는 편이 낫다 불문하고 향하여 향해서 향하다 쪽으로 틈타 이용하여 타다 오르다 제외하고 이 외에 이 밖에 하여야 비로소 한다면 몰라도 외에도 이곳 여기 부터 기점으로 따라서 할 생각이다 하려고하다 이리하여 그리하여 그렇게 함으로써 하지만 일때 할때 앞에서 중에서 보는데서 으로써 로써 까지 해야한다 일것이다 반드시 할줄알다 할수있다 할수있어 임에 틀림없다 한다면 등 등등 제 겨우 단지 다만 할뿐 딩동 댕그 대해서 대하여 대하면 훨씬 얼마나 얼마만큼 얼마큼 남짓 여 얼마간 약간 다소 좀 조금 다수 몇 얼마 지만 하물며 또한 그러나 그렇지만 하지만 이외에도 대해 말하자면 뿐이다 다음에 반대로 반대로 말하자면 이와 반대로 바꾸어서 말하면 바꾸어서 한다면 만약 그렇지않으면 까악 툭 딱 삐걱거리다 보드득 비걱거리다 꽈당 응당 해야한다 에 가서 각 각각 여러분 각종 각자 제각기 하도록하다 와 과 그러므로 그래서 고로 한 까닭에 하기 때문에 거니와 이지만 대하여 관하여 관한 과연 실로 아니나다를가 생각한대로 진짜로 한적이있다 하곤하였다 하 하하 허허 아하 거바 와 오 왜 어째서 무엇때문에 어찌 하겠는가 무슨 어디 어느곳 더군다나 하물며 더욱이는 어느때 언제 야 이봐 어이 여보시오 흐흐 흥 휴 헉헉 헐떡헐떡 영차 여차 어기여차 끙끙 아야 앗 아야 콸콸 졸졸 좍좍 뚝뚝 주룩주룩 솨 우르르 그래도 또 그리고 바꾸어말하면 바꾸어말하자면 혹은 혹시 답다 및 그에 따르는 때가 되어 즉 지든지 설령 가령 하더라도 할지라도 일지라도 지든지 몇 거의 하마터면 인젠 이젠 된바에야 된이상 만큼\t어찌됏든 그위에 게다가 점에서 보아 비추어 보아 고려하면 하게될것이다 일것이다 비교적 좀 보다더 비하면 시키다 하게하다 할만하다 의해서 연이서 이어서 잇따라 뒤따라 뒤이어 결국 의지하여 기대여 통하여 자마자 더욱더 불구하고 얼마든지 마음대로 주저하지 않고 곧 즉시 바로 당장 하자마자 밖에 안된다 하면된다 그래 그렇지 요컨대 다시 말하자면 바꿔 말하면 즉 구체적으로 말하자면 시작하여 시초에 이상 허 헉 허걱 바와같이 해도좋다 해도된다 게다가 더구나 하물며 와르르 팍 퍽 펄렁 동안 이래 하고있었다 이었다 에서 로부터 까지 예하면 했어요 해요 함께 같이 더불어 마저 마저도 양자 모두 습니다 가까스로 하려고하다 즈음하여 다른 다른 방면으로 해봐요 습니까 했어요 말할것도 없고 무릎쓰고 개의치않고 하는것만 못하다 하는것이 낫다 매 매번 들 모 어느것 어느 로써 갖고말하자면 어디 어느쪽 어느것 어느해 어느 년도 라 해도 언젠가 어떤것 어느것 저기 저쪽 저것 그때 그럼 그러면 요만한걸 그래 그때 저것만큼 그저 이르기까지 할 줄 안다 할 힘이 있다 너 너희 당신 어찌 설마 차라리 할지언정 할지라도 할망정 할지언정 구토하다 게우다 토하다 메쓰겁다 옆사람 퉤 쳇 의거하여 근거하여 의해 따라 힘입어 그 다음 버금 두번째로 기타 첫번째로 나머지는 그중에서 견지에서 형식으로 쓰여 입장에서 위해서 단지 의해되다 하도록시키다 뿐만아니라 반대로 전후 전자 앞의것 잠시 잠깐 하면서 그렇지만 다음에 그러한즉 그런즉 남들 아무거나 어찌하든지 같다 비슷하다 예컨대 이럴정도로 어떻게 만약 만일 위에서 서술한바와같이 인 듯하다 하지 않는다면 만약에 무엇 무슨 어느 어떤 아래윗 조차 한데 그럼에도 불구하고 여전히 심지어 까지도 조차도 하지 않도록 않기 위하여 때 시각 무렵 시간 동안 어때 어떠한 하여금 네 예 우선 누구 누가 알겠는가 아무도 줄은모른다 줄은 몰랏다 하는 김에 겸사겸사 하는바 그런 까닭에 한 이유는 그러니 그러니까 때문에 그 너희 그들 너희들 타인 것 것들 너 위하여 공동으로 동시에 하기 위하여 어찌하여 무엇때문에 붕붕 윙윙 나 우리 엉엉 휘익 윙윙 오호 아하 어쨋든 만 못하다\t하기보다는 차라리 하는 편이 낫다 흐흐 놀라다 상대적으로 말하자면 마치 아니라면 쉿 그렇지 않으면 그렇지 않다면 안 그러면 아니었다면 하든지 아니면 이라면 좋아 알았어 하는것도 그만이다 어쩔수 없다 하나 일 일반적으로 일단 한켠으로는 오자마자 이렇게되면 이와같다면 전부 한마디 한항목 근거로 하기에 아울러 하지 않도록 않기 위해서 이르기까지 이 되다 로 인하여 까닭으로 이유만으로 이로 인하여 그래서 이 때문에 그러므로 그런 까닭에 알 수 있다 결론을 낼 수 있다 으로 인하여 있다 어떤것 관계가 있다 관련이 있다 연관되다 어떤것들 에 대해 이리하여 그리하여 여부 하기보다는 하느니 하면 할수록 운운 이러이러하다 하구나 하도다 다시말하면 다음으로 에 있다 에 달려 있다 우리 우리들 오히려 하기는한데 어떻게 어떻해 어찌됏어 어때 어째서 본대로 자 이 이쪽 여기 이것 이번 이렇게말하자면 이런 이러한 이와 같은 요만큼 요만한 것 얼마 안 되는 것 이만큼 이 정도의 이렇게 많은 것 이와 같다 이때 이렇구나 것과 같이 끼익 삐걱 따위 와 같은 사람들 부류의 사람들 왜냐하면 중의하나 오직 오로지 에 한하다 하기만 하면 도착하다 까지 미치다 도달하다 정도에 이르다 할 지경이다 결과에 이르다 관해서는 여러분 하고 있다 한 후 혼자 자기 자기집 자신 우에 종합한것과같이 총적으로 보면 총적으로 말하면 총적으로 대로 하다 으로서 참 그만이다 할 따름이다 쿵 탕탕 쾅쾅 둥둥 봐 봐라 아이야 아니 와아 응 아이 참나 년 월 일 령 영 일 이 삼 사 오 육 륙 칠 팔 구 이천육 이천칠 이천팔 이천구 하나 둘 셋 넷 다섯 여섯 일곱 여덟 아홉 령 영".split(" ")),e.Pipeline.registerFunction(e.ko.stopWordFilter,"stopWordFilter-ko"),e.ko.stemmer=function(){return function(e){return"function"==typeof e.update?e.update(function(e){return e}):e}}(),e.Pipeline.registerFunction(e.ko.stemmer,"stemmer-ko")}});
\ No newline at end of file
diff --git a/DevDoc/assets/javascripts/lunr/min/lunr.multi.min.js b/DevDoc/assets/javascripts/lunr/min/lunr.multi.min.js
new file mode 100644
index 00000000..7debad09
--- /dev/null
+++ b/DevDoc/assets/javascripts/lunr/min/lunr.multi.min.js
@@ -0,0 +1 @@
+!function(e,t){"function"==typeof define&&define.amd?define(t):"object"==typeof exports?module.exports=t():t()(e.lunr)}(this,function(){return function(e){e.multiLanguage=function(){for(var t=Array.prototype.slice.call(arguments),i=t.join("-"),r="",n=[],s=[],p=0;p<t.length;++p)"en"==t[p]?(r+="\\w",n.unshift(e.stopWordFilter),n.push(e.stemmer),s.push(e.stemmer)):(r+=e[t[p]].wordCharacters,e[t[p]].stopWordFilter&&n.unshift(e[t[p]].stopWordFilter),e[t[p]].stemmer&&(n.push(e[t[p]].stemmer),s.push(e[t[p]].stemmer)));var o=e.trimmerSupport.generateTrimmer(r);return e.Pipeline.registerFunction(o,"lunr-multi-trimmer-"+i),n.unshift(o),function(){this.pipeline.reset(),this.pipeline.add.apply(this.pipeline,n),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add.apply(this.searchPipeline,s))}}}});
\ No newline at end of file
diff --git a/DevDoc/assets/javascripts/lunr/min/lunr.nl.min.js b/DevDoc/assets/javascripts/lunr/min/lunr.nl.min.js
new file mode 100644
index 00000000..c4a25359
--- /dev/null
+++ b/DevDoc/assets/javascripts/lunr/min/lunr.nl.min.js
@@ -0,0 +1,18 @@
+/*!
+ * Lunr languages, `Dutch` language
+ * https://github.com/MihaiValentin/lunr-languages
+ *
+ * Copyright 2014, Mihai Valentin
+ * http://www.mozilla.org/MPL/
+ */
+/*!
+ * based on
+ * Snowball JavaScript Library v0.3
+ * http://code.google.com/p/urim/
+ * http://snowball.tartarus.org/
+ *
+ * Copyright 2010, Oleg Mazko
+ * http://www.mozilla.org/MPL/
+ */
+
+!function(r,e){"function"==typeof define&&define.amd?define(e):"object"==typeof exports?module.exports=e():e()(r.lunr)}(this,function(){return function(r){if(void 0===r)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===r.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");r.nl=function(){this.pipeline.reset(),this.pipeline.add(r.nl.trimmer,r.nl.stopWordFilter,r.nl.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(r.nl.stemmer))},r.nl.wordCharacters="A-Za-zªºÀ-ÖØ-öø-ʸˠ-ˤᴀ-ᴥᴬ-ᵜᵢ-ᵥᵫ-ᵷᵹ-ᶾḀ-ỿⁱⁿₐ-ₜKÅℲⅎⅠ-ↈⱠ-ⱿꜢ-ꞇꞋ-ꞭꞰ-ꞷꟷ-ꟿꬰ-ꭚꭜ-ꭤff-stＡ-Ｚａ-ｚ",r.nl.trimmer=r.trimmerSupport.generateTrimmer(r.nl.wordCharacters),r.Pipeline.registerFunction(r.nl.trimmer,"trimmer-nl"),r.nl.stemmer=function(){var e=r.stemmerSupport.Among,i=r.stemmerSupport.SnowballProgram,n=new function(){function r(){for(var r,e,i,o=C.cursor;;){if(C.bra=C.cursor,r=C.find_among(b,11))switch(C.ket=C.cursor,r){case 1:C.slice_from("a");continue;case 2:C.slice_from("e");continue;case 3:C.slice_from("i");continue;case 4:C.slice_from("o");continue;case 5:C.slice_from("u");continue;case 6:if(C.cursor>=C.limit)break;C.cursor++;continue}break}for(C.cursor=o,C.bra=o,C.eq_s(1,"y")?(C.ket=C.cursor,C.slice_from("Y")):C.cursor=o;;)if(e=C.cursor,C.in_grouping(q,97,232)){if(i=C.cursor,C.bra=i,C.eq_s(1,"i"))C.ket=C.cursor,C.in_grouping(q,97,232)&&(C.slice_from("I"),C.cursor=e);else if(C.cursor=i,C.eq_s(1,"y"))C.ket=C.cursor,C.slice_from("Y"),C.cursor=e;else if(n(e))break}else if(n(e))break}function n(r){return C.cursor=r,r>=C.limit||(C.cursor++,!1)}function o(){_=C.limit,d=_,t()||(_=C.cursor,_<3&&(_=3),t()||(d=C.cursor))}function t(){for(;!C.in_grouping(q,97,232);){if(C.cursor>=C.limit)return!0;C.cursor++}for(;!C.out_grouping(q,97,232);){if(C.cursor>=C.limit)return!0;C.cursor++}return!1}function s(){for(var r;;)if(C.bra=C.cursor,r=C.find_among(p,3))switch(C.ket=C.cursor,r){case 1:C.slice_from("y");break;case 2:C.slice_from("i");break;case 3:if(C.cursor>=C.limit)return;C.cursor++}}function u(){return _<=C.cursor}function c(){return d<=C.cursor}function a(){var r=C.limit-C.cursor;C.find_among_b(g,3)&&(C.cursor=C.limit-r,C.ket=C.cursor,C.cursor>C.limit_backward&&(C.cursor--,C.bra=C.cursor,C.slice_del()))}function l(){var r;w=!1,C.ket=C.cursor,C.eq_s_b(1,"e")&&(C.bra=C.cursor,u()&&(r=C.limit-C.cursor,C.out_grouping_b(q,97,232)&&(C.cursor=C.limit-r,C.slice_del(),w=!0,a())))}function m(){var r;u()&&(r=C.limit-C.cursor,C.out_grouping_b(q,97,232)&&(C.cursor=C.limit-r,C.eq_s_b(3,"gem")||(C.cursor=C.limit-r,C.slice_del(),a())))}function f(){var r,e,i,n,o,t,s=C.limit-C.cursor;if(C.ket=C.cursor,r=C.find_among_b(h,5))switch(C.bra=C.cursor,r){case 1:u()&&C.slice_from("heid");break;case 2:m();break;case 3:u()&&C.out_grouping_b(j,97,232)&&C.slice_del()}if(C.cursor=C.limit-s,l(),C.cursor=C.limit-s,C.ket=C.cursor,C.eq_s_b(4,"heid")&&(C.bra=C.cursor,c()&&(e=C.limit-C.cursor,C.eq_s_b(1,"c")||(C.cursor=C.limit-e,C.slice_del(),C.ket=C.cursor,C.eq_s_b(2,"en")&&(C.bra=C.cursor,m())))),C.cursor=C.limit-s,C.ket=C.cursor,r=C.find_among_b(k,6))switch(C.bra=C.cursor,r){case 1:if(c()){if(C.slice_del(),i=C.limit-C.cursor,C.ket=C.cursor,C.eq_s_b(2,"ig")&&(C.bra=C.cursor,c()&&(n=C.limit-C.cursor,!C.eq_s_b(1,"e")))){C.cursor=C.limit-n,C.slice_del();break}C.cursor=C.limit-i,a()}break;case 2:c()&&(o=C.limit-C.cursor,C.eq_s_b(1,"e")||(C.cursor=C.limit-o,C.slice_del()));break;case 3:c()&&(C.slice_del(),l());break;case 4:c()&&C.slice_del();break;case 5:c()&&w&&C.slice_del()}C.cursor=C.limit-s,C.out_grouping_b(z,73,232)&&(t=C.limit-C.cursor,C.find_among_b(v,4)&&C.out_grouping_b(q,97,232)&&(C.cursor=C.limit-t,C.ket=C.cursor,C.cursor>C.limit_backward&&(C.cursor--,C.bra=C.cursor,C.slice_del())))}var d,_,w,b=[new e("",-1,6),new e("á",0,1),new e("ä",0,1),new e("é",0,2),new e("ë",0,2),new e("í",0,3),new e("ï",0,3),new e("ó",0,4),new e("ö",0,4),new e("ú",0,5),new e("ü",0,5)],p=[new e("",-1,3),new e("I",0,2),new e("Y",0,1)],g=[new e("dd",-1,-1),new e("kk",-1,-1),new e("tt",-1,-1)],h=[new e("ene",-1,2),new e("se",-1,3),new e("en",-1,2),new e("heden",2,1),new e("s",-1,3)],k=[new e("end",-1,1),new e("ig",-1,2),new e("ing",-1,1),new e("lijk",-1,3),new e("baar",-1,4),new e("bar",-1,5)],v=[new e("aa",-1,-1),new e("ee",-1,-1),new e("oo",-1,-1),new e("uu",-1,-1)],q=[17,65,16,1,0,0,0,0,0,0,0,0,0,0,0,0,128],z=[1,0,0,17,65,16,1,0,0,0,0,0,0,0,0,0,0,0,0,128],j=[17,67,16,1,0,0,0,0,0,0,0,0,0,0,0,0,128],C=new i;this.setCurrent=function(r){C.setCurrent(r)},this.getCurrent=function(){return C.getCurrent()},this.stem=function(){var e=C.cursor;return r(),C.cursor=e,o(),C.limit_backward=e,C.cursor=C.limit,f(),C.cursor=C.limit_backward,s(),!0}};return function(r){return"function"==typeof r.update?r.update(function(r){return n.setCurrent(r),n.stem(),n.getCurrent()}):(n.setCurrent(r),n.stem(),n.getCurrent())}}(),r.Pipeline.registerFunction(r.nl.stemmer,"stemmer-nl"),r.nl.stopWordFilter=r.generateStopWordFilter(" aan al alles als altijd andere ben bij daar dan dat de der deze die dit doch doen door dus een eens en er ge geen geweest haar had heb hebben heeft hem het hier hij hoe hun iemand iets ik in is ja je kan kon kunnen maar me meer men met mij mijn moet na naar niet niets nog nu of om omdat onder ons ook op over reeds te tegen toch toen tot u uit uw van veel voor want waren was wat werd wezen wie wil worden wordt zal ze zelf zich zij zijn zo zonder zou".split(" ")),r.Pipeline.registerFunction(r.nl.stopWordFilter,"stopWordFilter-nl")}});
\ No newline at end of file
diff --git a/DevDoc/assets/javascripts/lunr/min/lunr.no.min.js b/DevDoc/assets/javascripts/lunr/min/lunr.no.min.js
new file mode 100644
index 00000000..92bc7e4e
--- /dev/null
+++ b/DevDoc/assets/javascripts/lunr/min/lunr.no.min.js
@@ -0,0 +1,18 @@
+/*!
+ * Lunr languages, `Norwegian` language
+ * https://github.com/MihaiValentin/lunr-languages
+ *
+ * Copyright 2014, Mihai Valentin
+ * http://www.mozilla.org/MPL/
+ */
+/*!
+ * based on
+ * Snowball JavaScript Library v0.3
+ * http://code.google.com/p/urim/
+ * http://snowball.tartarus.org/
+ *
+ * Copyright 2010, Oleg Mazko
+ * http://www.mozilla.org/MPL/
+ */
+
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.no=function(){this.pipeline.reset(),this.pipeline.add(e.no.trimmer,e.no.stopWordFilter,e.no.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.no.stemmer))},e.no.wordCharacters="A-Za-zªºÀ-ÖØ-öø-ʸˠ-ˤᴀ-ᴥᴬ-ᵜᵢ-ᵥᵫ-ᵷᵹ-ᶾḀ-ỿⁱⁿₐ-ₜKÅℲⅎⅠ-ↈⱠ-ⱿꜢ-ꞇꞋ-ꞭꞰ-ꞷꟷ-ꟿꬰ-ꭚꭜ-ꭤff-stＡ-Ｚａ-ｚ",e.no.trimmer=e.trimmerSupport.generateTrimmer(e.no.wordCharacters),e.Pipeline.registerFunction(e.no.trimmer,"trimmer-no"),e.no.stemmer=function(){var r=e.stemmerSupport.Among,n=e.stemmerSupport.SnowballProgram,i=new function(){function e(){var e,r=w.cursor+3;if(a=w.limit,0<=r||r<=w.limit){for(s=r;;){if(e=w.cursor,w.in_grouping(d,97,248)){w.cursor=e;break}if(e>=w.limit)return;w.cursor=e+1}for(;!w.out_grouping(d,97,248);){if(w.cursor>=w.limit)return;w.cursor++}a=w.cursor,a<s&&(a=s)}}function i(){var e,r,n;if(w.cursor>=a&&(r=w.limit_backward,w.limit_backward=a,w.ket=w.cursor,e=w.find_among_b(m,29),w.limit_backward=r,e))switch(w.bra=w.cursor,e){case 1:w.slice_del();break;case 2:n=w.limit-w.cursor,w.in_grouping_b(c,98,122)?w.slice_del():(w.cursor=w.limit-n,w.eq_s_b(1,"k")&&w.out_grouping_b(d,97,248)&&w.slice_del());break;case 3:w.slice_from("er")}}function t(){var e,r=w.limit-w.cursor;w.cursor>=a&&(e=w.limit_backward,w.limit_backward=a,w.ket=w.cursor,w.find_among_b(u,2)?(w.bra=w.cursor,w.limit_backward=e,w.cursor=w.limit-r,w.cursor>w.limit_backward&&(w.cursor--,w.bra=w.cursor,w.slice_del())):w.limit_backward=e)}function o(){var e,r;w.cursor>=a&&(r=w.limit_backward,w.limit_backward=a,w.ket=w.cursor,e=w.find_among_b(l,11),e?(w.bra=w.cursor,w.limit_backward=r,1==e&&w.slice_del()):w.limit_backward=r)}var s,a,m=[new r("a",-1,1),new r("e",-1,1),new r("ede",1,1),new r("ande",1,1),new r("ende",1,1),new r("ane",1,1),new r("ene",1,1),new r("hetene",6,1),new r("erte",1,3),new r("en",-1,1),new r("heten",9,1),new r("ar",-1,1),new r("er",-1,1),new r("heter",12,1),new r("s",-1,2),new r("as",14,1),new r("es",14,1),new r("edes",16,1),new r("endes",16,1),new r("enes",16,1),new r("hetenes",19,1),new r("ens",14,1),new r("hetens",21,1),new r("ers",14,1),new r("ets",14,1),new r("et",-1,1),new r("het",25,1),new r("ert",-1,3),new r("ast",-1,1)],u=[new r("dt",-1,-1),new r("vt",-1,-1)],l=[new r("leg",-1,1),new r("eleg",0,1),new r("ig",-1,1),new r("eig",2,1),new r("lig",2,1),new r("elig",4,1),new r("els",-1,1),new r("lov",-1,1),new r("elov",7,1),new r("slov",7,1),new r("hetslov",9,1)],d=[17,65,16,1,0,0,0,0,0,0,0,0,0,0,0,0,48,0,128],c=[119,125,149,1],w=new n;this.setCurrent=function(e){w.setCurrent(e)},this.getCurrent=function(){return w.getCurrent()},this.stem=function(){var r=w.cursor;return e(),w.limit_backward=r,w.cursor=w.limit,i(),w.cursor=w.limit,t(),w.cursor=w.limit,o(),!0}};return function(e){return"function"==typeof e.update?e.update(function(e){return i.setCurrent(e),i.stem(),i.getCurrent()}):(i.setCurrent(e),i.stem(),i.getCurrent())}}(),e.Pipeline.registerFunction(e.no.stemmer,"stemmer-no"),e.no.stopWordFilter=e.generateStopWordFilter("alle at av bare begge ble blei bli blir blitt både båe da de deg dei deim deira deires dem den denne der dere deres det dette di din disse ditt du dykk dykkar då eg ein eit eitt eller elles en enn er et ett etter for fordi fra før ha hadde han hans har hennar henne hennes her hjå ho hoe honom hoss hossen hun hva hvem hver hvilke hvilken hvis hvor hvordan hvorfor i ikke ikkje ikkje ingen ingi inkje inn inni ja jeg kan kom korleis korso kun kunne kva kvar kvarhelst kven kvi kvifor man mange me med medan meg meget mellom men mi min mine mitt mot mykje ned no noe noen noka noko nokon nokor nokre nå når og også om opp oss over på samme seg selv si si sia sidan siden sin sine sitt sjøl skal skulle slik so som som somme somt så sånn til um upp ut uten var vart varte ved vere verte vi vil ville vore vors vort vår være være vært å".split(" ")),e.Pipeline.registerFunction(e.no.stopWordFilter,"stopWordFilter-no")}});
\ No newline at end of file
diff --git a/DevDoc/assets/javascripts/lunr/min/lunr.pt.min.js b/DevDoc/assets/javascripts/lunr/min/lunr.pt.min.js
new file mode 100644
index 00000000..6c16996d
--- /dev/null
+++ b/DevDoc/assets/javascripts/lunr/min/lunr.pt.min.js
@@ -0,0 +1,18 @@
+/*!
+ * Lunr languages, `Portuguese` language
+ * https://github.com/MihaiValentin/lunr-languages
+ *
+ * Copyright 2014, Mihai Valentin
+ * http://www.mozilla.org/MPL/
+ */
+/*!
+ * based on
+ * Snowball JavaScript Library v0.3
+ * http://code.google.com/p/urim/
+ * http://snowball.tartarus.org/
+ *
+ * Copyright 2010, Oleg Mazko
+ * http://www.mozilla.org/MPL/
+ */
+
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. 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diff --git a/DevDoc/assets/javascripts/lunr/min/lunr.ro.min.js b/DevDoc/assets/javascripts/lunr/min/lunr.ro.min.js
new file mode 100644
index 00000000..72771401
--- /dev/null
+++ b/DevDoc/assets/javascripts/lunr/min/lunr.ro.min.js
@@ -0,0 +1,18 @@
+/*!
+ * Lunr languages, `Romanian` language
+ * https://github.com/MihaiValentin/lunr-languages
+ *
+ * Copyright 2014, Mihai Valentin
+ * http://www.mozilla.org/MPL/
+ */
+/*!
+ * based on
+ * Snowball JavaScript Library v0.3
+ * http://code.google.com/p/urim/
+ * http://snowball.tartarus.org/
+ *
+ * Copyright 2010, Oleg Mazko
+ * http://www.mozilla.org/MPL/
+ */
+
+!function(e,i){"function"==typeof define&&define.amd?define(i):"object"==typeof exports?module.exports=i():i()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. 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dă ea ei el ele eram este eu eşti face fata fi fie fiecare fii fim fiu fiţi frumos fără graţie halbă iar ieri la le li lor lui lângă lîngă mai mea mei mele mereu meu mi mie mine mult multă mulţi mulţumesc mâine mîine mă ne nevoie nici nicăieri nimeni nimeri nimic nişte noastre noastră noi noroc nostru nouă noştri nu opt ori oricare orice oricine oricum oricând oricât oricînd oricît oriunde patra patru patrulea pe pentru peste pic poate pot prea prima primul prin puţin puţina puţină până pînă rog sa sale sau se spate spre sub sunt suntem sunteţi sută sînt sîntem sînteţi să săi său ta tale te timp tine toate toată tot totuşi toţi trei treia treilea tu tăi tău un una unde undeva unei uneia unele uneori unii unor unora unu unui unuia unul vi voastre voastră voi vostru vouă voştri vreme vreo vreun vă zece zero zi zice îi îl îmi împotriva în  înainte înaintea încotro încât încît între întrucât întrucît îţi ăla ălea ăsta ăstea ăştia şapte şase şi ştiu ţi ţie".split(" 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\ No newline at end of file
diff --git a/DevDoc/assets/javascripts/lunr/min/lunr.ru.min.js b/DevDoc/assets/javascripts/lunr/min/lunr.ru.min.js
new file mode 100644
index 00000000..186cc485
--- /dev/null
+++ b/DevDoc/assets/javascripts/lunr/min/lunr.ru.min.js
@@ -0,0 +1,18 @@
+/*!
+ * Lunr languages, `Russian` language
+ * https://github.com/MihaiValentin/lunr-languages
+ *
+ * Copyright 2014, Mihai Valentin
+ * http://www.mozilla.org/MPL/
+ */
+/*!
+ * based on
+ * Snowball JavaScript Library v0.3
+ * http://code.google.com/p/urim/
+ * http://snowball.tartarus.org/
+ *
+ * Copyright 2010, Oleg Mazko
+ * http://www.mozilla.org/MPL/
+ */
+
+!function(e,n){"function"==typeof define&&define.amd?define(n):"object"==typeof exports?module.exports=n():n()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. 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вниз внизу во вокруг вон восемнадцатый восемнадцать восемь восьмой вот впрочем времени время все всегда всего всем всеми всему всех всею всю всюду вся всё второй вы г где говорил говорит год года году да давно даже далеко дальше даром два двадцатый двадцать две двенадцатый двенадцать двух девятнадцатый девятнадцать девятый девять действительно дел день десятый десять для до довольно долго должно другая другие других друго другое другой е его ее ей ему если есть еще ещё ею её ж же жизнь за занят занята занято заняты затем зато зачем здесь значит и из или им именно иметь ими имя иногда их к каждая каждое каждые каждый кажется как какая какой кем когда кого ком кому конечно которая которого которой которые который которых кроме кругом кто куда лет ли лишь лучше люди м мало между меля менее меньше меня миллионов мимо мира мне много многочисленная многочисленное многочисленные многочисленный мной мною мог могут мож может можно можхо мои мой мор мочь моя моё мы на наверху над надо назад наиболее наконец нам нами нас начала наш наша наше наши не него недавно недалеко нее ней нельзя нем немного нему непрерывно нередко несколько нет нею неё ни нибудь ниже низко никогда никуда ними них ничего но ну нужно нх о об оба обычно один одиннадцатый одиннадцать однажды однако одного одной около он она они оно опять особенно от отовсюду отсюда очень первый перед по под пожалуйста позже пока пор пора после посреди потом потому почему почти прекрасно при про просто против процентов пятнадцатый пятнадцать пятый пять раз разве рано раньше рядом с сам сама сами самим самими самих само самого самой самом самому саму свое своего своей свои своих свою сеаой себе себя сегодня седьмой сейчас семнадцатый семнадцать семь сих сказал сказала сказать сколько слишком сначала снова со собой собою совсем спасибо стал суть т та так такая также такие такое такой там твой твоя твоё те тебе тебя тем теми теперь тех то тобой тобою тогда того тоже только том тому тот тою третий три тринадцатый тринадцать ту туда тут ты тысяч у уж уже уметь хорошо хотеть хоть хотя хочешь часто чаще чего человек чем чему через четвертый четыре четырнадцатый четырнадцать что чтоб чтобы чуть шестнадцатый шестнадцать шестой шесть эта эти этим этими этих это этого этой этом этому этот эту я \ufeffа".split(" ")),e.Pipeline.registerFunction(e.ru.stopWordFilter,"stopWordFilter-ru")}});
\ No newline at end of file
diff --git a/DevDoc/assets/javascripts/lunr/min/lunr.sa.min.js b/DevDoc/assets/javascripts/lunr/min/lunr.sa.min.js
new file mode 100644
index 00000000..50ee5642
--- /dev/null
+++ b/DevDoc/assets/javascripts/lunr/min/lunr.sa.min.js
@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.sa=function(){this.pipeline.reset(),this.pipeline.add(e.sa.trimmer,e.sa.stopWordFilter,e.sa.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.sa.stemmer))},e.sa.wordCharacters="ऀ-ःऄ-एऐ-टठ-यर-िी-ॏॐ-य़ॠ-९॰-ॿ꣠-꣱ꣲ-ꣷ꣸-ꣻ꣼-ꣽꣾ-ꣿᆰ0-ᆰ9",e.sa.trimmer=e.trimmerSupport.generateTrimmer(e.sa.wordCharacters),e.Pipeline.registerFunction(e.sa.trimmer,"trimmer-sa"),e.sa.stopWordFilter=e.generateStopWordFilter('तथा अयम्‌ एकम्‌ इत्यस्मिन्‌ तथा तत्‌ वा अयम्‌ इत्यस्य ते आहूत उपरि तेषाम्‌  किन्तु तेषाम्‌ तदा इत्यनेन अधिकः इत्यस्य तत्‌ केचन बहवः द्वि तथा महत्वपूर्णः अयम्‌ अस्य  विषये अयं अस्ति तत्‌ प्रथमः विषये इत्युपरि इत्युपरि इतर अधिकतमः अधिकः अपि सामान्यतया ठ इतरेतर नूतनम्‌ द  न्यूनम्‌ कश्चित्‌ वा विशालः द  सः अस्ति तदनुसारम् तत्र अस्ति केवलम्‌ अपि अत्र सर्वे विविधाः तत्‌ बहवः यतः इदानीम्‌ द  दक्षिण इत्यस्मै तस्य उपरि नथ अतीव कार्यम्‌ सर्वे एकैकम्‌ इत्यादि। एते सन्ति  उत इत्थम्‌ मध्ये एतदर्थं . स कस्य प्रथमः श्री. करोति अस्मिन् प्रकारः निर्मिता कालः तत्र कर्तुं  समान अधुना ते सन्ति स एकः अस्ति सः अर्थात् तेषां कृते . स्थितम्  विशेषः अग्रिम तेषाम्‌ समान स्रोतः ख म समान इदानीमपि अधिकतया करोतु ते समान इत्यस्य वीथी सह यस्मिन्  कृतवान्‌ धृतः तदा पुनः पूर्वं सः आगतः किम्‌ कुल इतर पुरा  मात्रा स विषये उ अतएव अपि नगरस्य  उपरि यतः प्रतिशतं  कतरः कालः साधनानि भूत तथापि जात सम्बन्धि अन्यत्‌ ग अतः अस्माकं स्वकीयाः अस्माकं इदानीं अन्तः इत्यादयः भवन्तः इत्यादयः एते एताः तस्य अस्य इदम् एते तेषां तेषां तेषां तान् तेषां तेषां तेषां समानः सः एकः च तादृशाः बहवः अन्ये च वदन्ति यत् कियत् कस्मै  कस्मै  यस्मै  यस्मै  यस्मै  यस्मै न अतिनीचः किन्तु प्रथमं सम्पूर्णतया  ततः चिरकालानन्तरं पुस्तकं सम्पूर्णतया अन्तः  किन्तु अत्र वा इह इव श्रद्धाय अवशिष्यते  परन्तु अन्ये वर्गाः सन्ति ते सन्ति शक्नुवन्ति सर्वे मिलित्वा सर्वे एकत्र"'.split(" ")),e.sa.stemmer=function(){return function(e){return"function"==typeof e.update?e.update(function(e){return e}):e}}();var r=e.wordcut;r.init(),e.sa.tokenizer=function(t){if(!arguments.length||null==t||void 0==t)return[];if(Array.isArray(t))return t.map(function(r){return isLunr2?new e.Token(r.toLowerCase()):r.toLowerCase()});var i=t.toString().toLowerCase().replace(/^\s+/,"");return r.cut(i).split("|")},e.Pipeline.registerFunction(e.sa.stemmer,"stemmer-sa"),e.Pipeline.registerFunction(e.sa.stopWordFilter,"stopWordFilter-sa")}});
\ No newline at end of file
diff --git a/DevDoc/assets/javascripts/lunr/min/lunr.stemmer.support.min.js b/DevDoc/assets/javascripts/lunr/min/lunr.stemmer.support.min.js
new file mode 100644
index 00000000..abd4475b
--- /dev/null
+++ b/DevDoc/assets/javascripts/lunr/min/lunr.stemmer.support.min.js
@@ -0,0 +1 @@
+!function(r,t){"function"==typeof define&&define.amd?define(t):"object"==typeof exports?module.exports=t():t()(r.lunr)}(this,function(){return function(r){r.stemmerSupport={Among:function(r,t,i,s){if(this.toCharArray=function(r){for(var t=r.length,i=new Array(t),s=0;s<t;s++)i[s]=r.charCodeAt(s);return i},!r&&""!=r||!t&&0!=t||!i)throw"Bad Among initialisation: s:"+r+", substring_i: "+t+", result: "+i;this.s_size=r.length,this.s=this.toCharArray(r),this.substring_i=t,this.result=i,this.method=s},SnowballProgram:function(){var r;return{bra:0,ket:0,limit:0,cursor:0,limit_backward:0,setCurrent:function(t){r=t,this.cursor=0,this.limit=t.length,this.limit_backward=0,this.bra=this.cursor,this.ket=this.limit},getCurrent:function(){var t=r;return r=null,t},in_grouping:function(t,i,s){if(this.cursor<this.limit){var e=r.charCodeAt(this.cursor);if(e<=s&&e>=i&&(e-=i,t[e>>3]&1<<(7&e)))return this.cursor++,!0}return!1},in_grouping_b:function(t,i,s){if(this.cursor>this.limit_backward){var e=r.charCodeAt(this.cursor-1);if(e<=s&&e>=i&&(e-=i,t[e>>3]&1<<(7&e)))return this.cursor--,!0}return!1},out_grouping:function(t,i,s){if(this.cursor<this.limit){var e=r.charCodeAt(this.cursor);if(e>s||e<i)return this.cursor++,!0;if(e-=i,!(t[e>>3]&1<<(7&e)))return this.cursor++,!0}return!1},out_grouping_b:function(t,i,s){if(this.cursor>this.limit_backward){var e=r.charCodeAt(this.cursor-1);if(e>s||e<i)return this.cursor--,!0;if(e-=i,!(t[e>>3]&1<<(7&e)))return this.cursor--,!0}return!1},eq_s:function(t,i){if(this.limit-this.cursor<t)return!1;for(var s=0;s<t;s++)if(r.charCodeAt(this.cursor+s)!=i.charCodeAt(s))return!1;return this.cursor+=t,!0},eq_s_b:function(t,i){if(this.cursor-this.limit_backward<t)return!1;for(var s=0;s<t;s++)if(r.charCodeAt(this.cursor-t+s)!=i.charCodeAt(s))return!1;return this.cursor-=t,!0},find_among:function(t,i){for(var s=0,e=i,n=this.cursor,u=this.limit,o=0,h=0,c=!1;;){for(var a=s+(e-s>>1),f=0,l=o<h?o:h,_=t[a],m=l;m<_.s_size;m++){if(n+l==u){f=-1;break}if(f=r.charCodeAt(n+l)-_.s[m])break;l++}if(f<0?(e=a,h=l):(s=a,o=l),e-s<=1){if(s>0||e==s||c)break;c=!0}}for(;;){var _=t[s];if(o>=_.s_size){if(this.cursor=n+_.s_size,!_.method)return _.result;var b=_.method();if(this.cursor=n+_.s_size,b)return _.result}if((s=_.substring_i)<0)return 0}},find_among_b:function(t,i){for(var s=0,e=i,n=this.cursor,u=this.limit_backward,o=0,h=0,c=!1;;){for(var a=s+(e-s>>1),f=0,l=o<h?o:h,_=t[a],m=_.s_size-1-l;m>=0;m--){if(n-l==u){f=-1;break}if(f=r.charCodeAt(n-1-l)-_.s[m])break;l++}if(f<0?(e=a,h=l):(s=a,o=l),e-s<=1){if(s>0||e==s||c)break;c=!0}}for(;;){var _=t[s];if(o>=_.s_size){if(this.cursor=n-_.s_size,!_.method)return _.result;var b=_.method();if(this.cursor=n-_.s_size,b)return _.result}if((s=_.substring_i)<0)return 0}},replace_s:function(t,i,s){var e=s.length-(i-t),n=r.substring(0,t),u=r.substring(i);return r=n+s+u,this.limit+=e,this.cursor>=i?this.cursor+=e:this.cursor>t&&(this.cursor=t),e},slice_check:function(){if(this.bra<0||this.bra>this.ket||this.ket>this.limit||this.limit>r.length)throw"faulty slice operation"},slice_from:function(r){this.slice_check(),this.replace_s(this.bra,this.ket,r)},slice_del:function(){this.slice_from("")},insert:function(r,t,i){var s=this.replace_s(r,t,i);r<=this.bra&&(this.bra+=s),r<=this.ket&&(this.ket+=s)},slice_to:function(){return this.slice_check(),r.substring(this.bra,this.ket)},eq_v_b:function(r){return this.eq_s_b(r.length,r)}}}},r.trimmerSupport={generateTrimmer:function(r){var t=new RegExp("^[^"+r+"]+"),i=new RegExp("[^"+r+"]+$");return function(r){return"function"==typeof r.update?r.update(function(r){return r.replace(t,"").replace(i,"")}):r.replace(t,"").replace(i,"")}}}}});
\ No newline at end of file
diff --git a/DevDoc/assets/javascripts/lunr/min/lunr.sv.min.js b/DevDoc/assets/javascripts/lunr/min/lunr.sv.min.js
new file mode 100644
index 00000000..3e5eb640
--- /dev/null
+++ b/DevDoc/assets/javascripts/lunr/min/lunr.sv.min.js
@@ -0,0 +1,18 @@
+/*!
+ * Lunr languages, `Swedish` language
+ * https://github.com/MihaiValentin/lunr-languages
+ *
+ * Copyright 2014, Mihai Valentin
+ * http://www.mozilla.org/MPL/
+ */
+/*!
+ * based on
+ * Snowball JavaScript Library v0.3
+ * http://code.google.com/p/urim/
+ * http://snowball.tartarus.org/
+ *
+ * Copyright 2010, Oleg Mazko
+ * http://www.mozilla.org/MPL/
+ */
+
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.sv=function(){this.pipeline.reset(),this.pipeline.add(e.sv.trimmer,e.sv.stopWordFilter,e.sv.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.sv.stemmer))},e.sv.wordCharacters="A-Za-zªºÀ-ÖØ-öø-ʸˠ-ˤᴀ-ᴥᴬ-ᵜᵢ-ᵥᵫ-ᵷᵹ-ᶾḀ-ỿⁱⁿₐ-ₜKÅℲⅎⅠ-ↈⱠ-ⱿꜢ-ꞇꞋ-ꞭꞰ-ꞷꟷ-ꟿꬰ-ꭚꭜ-ꭤff-stＡ-Ｚａ-ｚ",e.sv.trimmer=e.trimmerSupport.generateTrimmer(e.sv.wordCharacters),e.Pipeline.registerFunction(e.sv.trimmer,"trimmer-sv"),e.sv.stemmer=function(){var r=e.stemmerSupport.Among,n=e.stemmerSupport.SnowballProgram,t=new function(){function e(){var e,r=w.cursor+3;if(o=w.limit,0<=r||r<=w.limit){for(a=r;;){if(e=w.cursor,w.in_grouping(l,97,246)){w.cursor=e;break}if(w.cursor=e,w.cursor>=w.limit)return;w.cursor++}for(;!w.out_grouping(l,97,246);){if(w.cursor>=w.limit)return;w.cursor++}o=w.cursor,o<a&&(o=a)}}function t(){var e,r=w.limit_backward;if(w.cursor>=o&&(w.limit_backward=o,w.cursor=w.limit,w.ket=w.cursor,e=w.find_among_b(u,37),w.limit_backward=r,e))switch(w.bra=w.cursor,e){case 1:w.slice_del();break;case 2:w.in_grouping_b(d,98,121)&&w.slice_del()}}function i(){var e=w.limit_backward;w.cursor>=o&&(w.limit_backward=o,w.cursor=w.limit,w.find_among_b(c,7)&&(w.cursor=w.limit,w.ket=w.cursor,w.cursor>w.limit_backward&&(w.bra=--w.cursor,w.slice_del())),w.limit_backward=e)}function s(){var e,r;if(w.cursor>=o){if(r=w.limit_backward,w.limit_backward=o,w.cursor=w.limit,w.ket=w.cursor,e=w.find_among_b(m,5))switch(w.bra=w.cursor,e){case 1:w.slice_del();break;case 2:w.slice_from("lös");break;case 3:w.slice_from("full")}w.limit_backward=r}}var a,o,u=[new r("a",-1,1),new r("arna",0,1),new r("erna",0,1),new r("heterna",2,1),new r("orna",0,1),new r("ad",-1,1),new r("e",-1,1),new r("ade",6,1),new r("ande",6,1),new r("arne",6,1),new r("are",6,1),new r("aste",6,1),new r("en",-1,1),new r("anden",12,1),new r("aren",12,1),new r("heten",12,1),new r("ern",-1,1),new r("ar",-1,1),new r("er",-1,1),new r("heter",18,1),new r("or",-1,1),new r("s",-1,2),new r("as",21,1),new r("arnas",22,1),new r("ernas",22,1),new r("ornas",22,1),new r("es",21,1),new r("ades",26,1),new r("andes",26,1),new r("ens",21,1),new r("arens",29,1),new r("hetens",29,1),new r("erns",21,1),new r("at",-1,1),new r("andet",-1,1),new r("het",-1,1),new r("ast",-1,1)],c=[new r("dd",-1,-1),new r("gd",-1,-1),new r("nn",-1,-1),new r("dt",-1,-1),new r("gt",-1,-1),new r("kt",-1,-1),new r("tt",-1,-1)],m=[new r("ig",-1,1),new r("lig",0,1),new r("els",-1,1),new r("fullt",-1,3),new r("löst",-1,2)],l=[17,65,16,1,0,0,0,0,0,0,0,0,0,0,0,0,24,0,32],d=[119,127,149],w=new n;this.setCurrent=function(e){w.setCurrent(e)},this.getCurrent=function(){return w.getCurrent()},this.stem=function(){var r=w.cursor;return e(),w.limit_backward=r,w.cursor=w.limit,t(),w.cursor=w.limit,i(),w.cursor=w.limit,s(),!0}};return function(e){return"function"==typeof e.update?e.update(function(e){return t.setCurrent(e),t.stem(),t.getCurrent()}):(t.setCurrent(e),t.stem(),t.getCurrent())}}(),e.Pipeline.registerFunction(e.sv.stemmer,"stemmer-sv"),e.sv.stopWordFilter=e.generateStopWordFilter("alla allt att av blev bli blir blivit de dem den denna deras dess dessa det detta dig din dina ditt du där då efter ej eller en er era ert ett från för ha hade han hans har henne hennes hon honom hur här i icke ingen inom inte jag ju kan kunde man med mellan men mig min mina mitt mot mycket ni nu när någon något några och om oss på samma sedan sig sin sina sitta själv skulle som så sådan sådana sådant till under upp ut utan vad var vara varför varit varje vars vart vem vi vid vilka vilkas vilken vilket vår våra vårt än är åt över".split(" ")),e.Pipeline.registerFunction(e.sv.stopWordFilter,"stopWordFilter-sv")}});
\ No newline at end of file
diff --git a/DevDoc/assets/javascripts/lunr/min/lunr.ta.min.js b/DevDoc/assets/javascripts/lunr/min/lunr.ta.min.js
new file mode 100644
index 00000000..a644bed2
--- /dev/null
+++ b/DevDoc/assets/javascripts/lunr/min/lunr.ta.min.js
@@ -0,0 +1 @@
+!function(e,t){"function"==typeof define&&define.amd?define(t):"object"==typeof exports?module.exports=t():t()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.ta=function(){this.pipeline.reset(),this.pipeline.add(e.ta.trimmer,e.ta.stopWordFilter,e.ta.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.ta.stemmer))},e.ta.wordCharacters="஀-உஊ-ஏஐ-ஙச-ட஠-னப-யர-ஹ஺-ிீ-௉ொ-௏ௐ-௙௚-௟௠-௩௪-௯௰-௹௺-௿a-zA-Zａ-ｚＡ-Ｚ0-9０-９",e.ta.trimmer=e.trimmerSupport.generateTrimmer(e.ta.wordCharacters),e.Pipeline.registerFunction(e.ta.trimmer,"trimmer-ta"),e.ta.stopWordFilter=e.generateStopWordFilter("அங்கு அங்கே அது அதை அந்த அவர் அவர்கள் அவள் அவன் அவை ஆக ஆகவே ஆகையால் ஆதலால் ஆதலினால் ஆனாலும் ஆனால் இங்கு இங்கே இது இதை இந்த இப்படி இவர் இவர்கள் இவள் இவன் இவை இவ்வளவு உனக்கு உனது உன் உன்னால் எங்கு எங்கே எது எதை எந்த எப்படி எவர் எவர்கள் எவள் எவன் எவை எவ்வளவு எனக்கு எனது எனவே என் என்ன என்னால் ஏது ஏன் தனது தன்னால் தானே தான் நாங்கள் நாம் நான் நீ நீங்கள்".split(" ")),e.ta.stemmer=function(){return function(e){return"function"==typeof e.update?e.update(function(e){return e}):e}}();var t=e.wordcut;t.init(),e.ta.tokenizer=function(r){if(!arguments.length||null==r||void 0==r)return[];if(Array.isArray(r))return r.map(function(t){return isLunr2?new e.Token(t.toLowerCase()):t.toLowerCase()});var i=r.toString().toLowerCase().replace(/^\s+/,"");return t.cut(i).split("|")},e.Pipeline.registerFunction(e.ta.stemmer,"stemmer-ta"),e.Pipeline.registerFunction(e.ta.stopWordFilter,"stopWordFilter-ta")}});
\ No newline at end of file
diff --git a/DevDoc/assets/javascripts/lunr/min/lunr.te.min.js b/DevDoc/assets/javascripts/lunr/min/lunr.te.min.js
new file mode 100644
index 00000000..9fa7a93b
--- /dev/null
+++ b/DevDoc/assets/javascripts/lunr/min/lunr.te.min.js
@@ -0,0 +1 @@
+!function(e,t){"function"==typeof define&&define.amd?define(t):"object"==typeof exports?module.exports=t():t()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.te=function(){this.pipeline.reset(),this.pipeline.add(e.te.trimmer,e.te.stopWordFilter,e.te.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.te.stemmer))},e.te.wordCharacters="ఀ-ఄఅ-ఔక-హా-ౌౕ-ౖౘ-ౚౠ-ౡౢ-ౣ౦-౯౸-౿఼ఽ్ౝ౷౤౥",e.te.trimmer=e.trimmerSupport.generateTrimmer(e.te.wordCharacters),e.Pipeline.registerFunction(e.te.trimmer,"trimmer-te"),e.te.stopWordFilter=e.generateStopWordFilter("అందరూ అందుబాటులో అడగండి అడగడం అడ్డంగా అనుగుణంగా అనుమతించు అనుమతిస్తుంది అయితే ఇప్పటికే ఉన్నారు ఎక్కడైనా ఎప్పుడు ఎవరైనా ఎవరో ఏ ఏదైనా ఏమైనప్పటికి ఒక ఒకరు కనిపిస్తాయి కాదు కూడా గా గురించి చుట్టూ చేయగలిగింది తగిన తర్వాత దాదాపు దూరంగా నిజంగా పై ప్రకారం ప్రక్కన మధ్య మరియు మరొక మళ్ళీ మాత్రమే మెచ్చుకో వద్ద వెంట వేరుగా వ్యతిరేకంగా సంబంధం".split(" ")),e.te.stemmer=function(){return function(e){return"function"==typeof e.update?e.update(function(e){return e}):e}}();var t=e.wordcut;t.init(),e.te.tokenizer=function(r){if(!arguments.length||null==r||void 0==r)return[];if(Array.isArray(r))return r.map(function(t){return isLunr2?new e.Token(t.toLowerCase()):t.toLowerCase()});var i=r.toString().toLowerCase().replace(/^\s+/,"");return t.cut(i).split("|")},e.Pipeline.registerFunction(e.te.stemmer,"stemmer-te"),e.Pipeline.registerFunction(e.te.stopWordFilter,"stopWordFilter-te")}});
\ No newline at end of file
diff --git a/DevDoc/assets/javascripts/lunr/min/lunr.th.min.js b/DevDoc/assets/javascripts/lunr/min/lunr.th.min.js
new file mode 100644
index 00000000..dee3aac6
--- /dev/null
+++ b/DevDoc/assets/javascripts/lunr/min/lunr.th.min.js
@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");var r="2"==e.version[0];e.th=function(){this.pipeline.reset(),this.pipeline.add(e.th.trimmer),r?this.tokenizer=e.th.tokenizer:(e.tokenizer&&(e.tokenizer=e.th.tokenizer),this.tokenizerFn&&(this.tokenizerFn=e.th.tokenizer))},e.th.wordCharacters="[฀-๿]",e.th.trimmer=e.trimmerSupport.generateTrimmer(e.th.wordCharacters),e.Pipeline.registerFunction(e.th.trimmer,"trimmer-th");var t=e.wordcut;t.init(),e.th.tokenizer=function(i){if(!arguments.length||null==i||void 0==i)return[];if(Array.isArray(i))return i.map(function(t){return r?new e.Token(t):t});var n=i.toString().replace(/^\s+/,"");return t.cut(n).split("|")}}});
\ No newline at end of file
diff --git a/DevDoc/assets/javascripts/lunr/min/lunr.tr.min.js b/DevDoc/assets/javascripts/lunr/min/lunr.tr.min.js
new file mode 100644
index 00000000..563f6ec1
--- /dev/null
+++ b/DevDoc/assets/javascripts/lunr/min/lunr.tr.min.js
@@ -0,0 +1,18 @@
+/*!
+ * Lunr languages, `Turkish` language
+ * https://github.com/MihaiValentin/lunr-languages
+ *
+ * Copyright 2014, Mihai Valentin
+ * http://www.mozilla.org/MPL/
+ */
+/*!
+ * based on
+ * Snowball JavaScript Library v0.3
+ * http://code.google.com/p/urim/
+ * http://snowball.tartarus.org/
+ *
+ * Copyright 2010, Oleg Mazko
+ * http://www.mozilla.org/MPL/
+ */
+
+!function(r,i){"function"==typeof define&&define.amd?define(i):"object"==typeof exports?module.exports=i():i()(r.lunr)}(this,function(){return function(r){if(void 0===r)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===r.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");r.tr=function(){this.pipeline.reset(),this.pipeline.add(r.tr.trimmer,r.tr.stopWordFilter,r.tr.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(r.tr.stemmer))},r.tr.wordCharacters="A-Za-zªºÀ-ÖØ-öø-ʸˠ-ˤᴀ-ᴥᴬ-ᵜᵢ-ᵥᵫ-ᵷᵹ-ᶾḀ-ỿⁱⁿₐ-ₜKÅℲⅎⅠ-ↈⱠ-ⱿꜢ-ꞇꞋ-ꞭꞰ-ꞷꟷ-ꟿꬰ-ꭚꭜ-ꭤff-stＡ-Ｚａ-ｚ",r.tr.trimmer=r.trimmerSupport.generateTrimmer(r.tr.wordCharacters),r.Pipeline.registerFunction(r.tr.trimmer,"trimmer-tr"),r.tr.stemmer=function(){var i=r.stemmerSupport.Among,e=r.stemmerSupport.SnowballProgram,n=new function(){function r(r,i,e){for(;;){var n=Dr.limit-Dr.cursor;if(Dr.in_grouping_b(r,i,e)){Dr.cursor=Dr.limit-n;break}if(Dr.cursor=Dr.limit-n,Dr.cursor<=Dr.limit_backward)return!1;Dr.cursor--}return!0}function n(){var i,e;i=Dr.limit-Dr.cursor,r(Wr,97,305);for(var n=0;n<Br.length;n++){e=Dr.limit-Dr.cursor;var t=Br[n];if(Dr.eq_s_b(1,t[0])&&r(t[1],t[2],t[3]))return Dr.cursor=Dr.limit-i,!0;Dr.cursor=Dr.limit-e}return Dr.cursor=Dr.limit-e,!(!Dr.eq_s_b(1,"ü")||!r(Zr,246,252))&&(Dr.cursor=Dr.limit-i,!0)}function t(r,i){var e,n=Dr.limit-Dr.cursor;return r()&&(Dr.cursor=Dr.limit-n,Dr.cursor>Dr.limit_backward&&(Dr.cursor--,e=Dr.limit-Dr.cursor,i()))?(Dr.cursor=Dr.limit-e,!0):(Dr.cursor=Dr.limit-n,r()?(Dr.cursor=Dr.limit-n,!1):(Dr.cursor=Dr.limit-n,!(Dr.cursor<=Dr.limit_backward)&&(Dr.cursor--,!!i()&&(Dr.cursor=Dr.limit-n,!0))))}function u(r){return t(r,function(){return Dr.in_grouping_b(Wr,97,305)})}function o(){return u(function(){return Dr.eq_s_b(1,"n")})}function s(){return u(function(){return Dr.eq_s_b(1,"s")})}function c(){return u(function(){return Dr.eq_s_b(1,"y")})}function l(){return t(function(){return Dr.in_grouping_b(Lr,105,305)},function(){return Dr.out_grouping_b(Wr,97,305)})}function a(){return Dr.find_among_b(ur,10)&&l()}function m(){return n()&&Dr.in_grouping_b(Lr,105,305)&&s()}function d(){return Dr.find_among_b(or,2)}function f(){return n()&&Dr.in_grouping_b(Lr,105,305)&&c()}function b(){return n()&&Dr.find_among_b(sr,4)}function w(){return n()&&Dr.find_among_b(cr,4)&&o()}function _(){return n()&&Dr.find_among_b(lr,2)&&c()}function k(){return n()&&Dr.find_among_b(ar,2)}function p(){return n()&&Dr.find_among_b(mr,4)}function g(){return n()&&Dr.find_among_b(dr,2)}function y(){return n()&&Dr.find_among_b(fr,4)}function z(){return n()&&Dr.find_among_b(br,2)}function v(){return n()&&Dr.find_among_b(wr,2)&&c()}function h(){return Dr.eq_s_b(2,"ki")}function q(){return n()&&Dr.find_among_b(_r,2)&&o()}function C(){return n()&&Dr.find_among_b(kr,4)&&c()}function P(){return n()&&Dr.find_among_b(pr,4)}function F(){return n()&&Dr.find_among_b(gr,4)&&c()}function S(){return Dr.find_among_b(yr,4)}function W(){return n()&&Dr.find_among_b(zr,2)}function L(){return n()&&Dr.find_among_b(vr,4)}function x(){return n()&&Dr.find_among_b(hr,8)}function A(){return Dr.find_among_b(qr,2)}function E(){return n()&&Dr.find_among_b(Cr,32)&&c()}function j(){return Dr.find_among_b(Pr,8)&&c()}function T(){return n()&&Dr.find_among_b(Fr,4)&&c()}function Z(){return Dr.eq_s_b(3,"ken")&&c()}function B(){var r=Dr.limit-Dr.cursor;return!(T()||(Dr.cursor=Dr.limit-r,E()||(Dr.cursor=Dr.limit-r,j()||(Dr.cursor=Dr.limit-r,Z()))))}function D(){if(A()){var r=Dr.limit-Dr.cursor;if(S()||(Dr.cursor=Dr.limit-r,W()||(Dr.cursor=Dr.limit-r,C()||(Dr.cursor=Dr.limit-r,P()||(Dr.cursor=Dr.limit-r,F()||(Dr.cursor=Dr.limit-r))))),T())return!1}return!0}function G(){if(W()){Dr.bra=Dr.cursor,Dr.slice_del();var r=Dr.limit-Dr.cursor;return Dr.ket=Dr.cursor,x()||(Dr.cursor=Dr.limit-r,E()||(Dr.cursor=Dr.limit-r,j()||(Dr.cursor=Dr.limit-r,T()||(Dr.cursor=Dr.limit-r)))),nr=!1,!1}return!0}function H(){if(!L())return!0;var r=Dr.limit-Dr.cursor;return!E()&&(Dr.cursor=Dr.limit-r,!j())}function I(){var r,i=Dr.limit-Dr.cursor;return!(S()||(Dr.cursor=Dr.limit-i,F()||(Dr.cursor=Dr.limit-i,P()||(Dr.cursor=Dr.limit-i,C()))))||(Dr.bra=Dr.cursor,Dr.slice_del(),r=Dr.limit-Dr.cursor,Dr.ket=Dr.cursor,T()||(Dr.cursor=Dr.limit-r),!1)}function J(){var r,i=Dr.limit-Dr.cursor;if(Dr.ket=Dr.cursor,nr=!0,B()&&(Dr.cursor=Dr.limit-i,D()&&(Dr.cursor=Dr.limit-i,G()&&(Dr.cursor=Dr.limit-i,H()&&(Dr.cursor=Dr.limit-i,I()))))){if(Dr.cursor=Dr.limit-i,!x())return;Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,r=Dr.limit-Dr.cursor,S()||(Dr.cursor=Dr.limit-r,W()||(Dr.cursor=Dr.limit-r,C()||(Dr.cursor=Dr.limit-r,P()||(Dr.cursor=Dr.limit-r,F()||(Dr.cursor=Dr.limit-r))))),T()||(Dr.cursor=Dr.limit-r)}Dr.bra=Dr.cursor,Dr.slice_del()}function K(){var r,i,e,n;if(Dr.ket=Dr.cursor,h()){if(r=Dr.limit-Dr.cursor,p())return Dr.bra=Dr.cursor,Dr.slice_del(),i=Dr.limit-Dr.cursor,Dr.ket=Dr.cursor,W()?(Dr.bra=Dr.cursor,Dr.slice_del(),K()):(Dr.cursor=Dr.limit-i,a()&&(Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,W()&&(Dr.bra=Dr.cursor,Dr.slice_del(),K()))),!0;if(Dr.cursor=Dr.limit-r,w()){if(Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,e=Dr.limit-Dr.cursor,d())Dr.bra=Dr.cursor,Dr.slice_del();else{if(Dr.cursor=Dr.limit-e,Dr.ket=Dr.cursor,!a()&&(Dr.cursor=Dr.limit-e,!m()&&(Dr.cursor=Dr.limit-e,!K())))return!0;Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,W()&&(Dr.bra=Dr.cursor,Dr.slice_del(),K())}return!0}if(Dr.cursor=Dr.limit-r,g()){if(n=Dr.limit-Dr.cursor,d())Dr.bra=Dr.cursor,Dr.slice_del();else if(Dr.cursor=Dr.limit-n,m())Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,W()&&(Dr.bra=Dr.cursor,Dr.slice_del(),K());else if(Dr.cursor=Dr.limit-n,!K())return!1;return!0}}return!1}function M(r){if(Dr.ket=Dr.cursor,!g()&&(Dr.cursor=Dr.limit-r,!k()))return!1;var i=Dr.limit-Dr.cursor;if(d())Dr.bra=Dr.cursor,Dr.slice_del();else if(Dr.cursor=Dr.limit-i,m())Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,W()&&(Dr.bra=Dr.cursor,Dr.slice_del(),K());else if(Dr.cursor=Dr.limit-i,!K())return!1;return!0}function N(r){if(Dr.ket=Dr.cursor,!z()&&(Dr.cursor=Dr.limit-r,!b()))return!1;var i=Dr.limit-Dr.cursor;return!(!m()&&(Dr.cursor=Dr.limit-i,!d()))&&(Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,W()&&(Dr.bra=Dr.cursor,Dr.slice_del(),K()),!0)}function O(){var r,i=Dr.limit-Dr.cursor;return Dr.ket=Dr.cursor,!(!w()&&(Dr.cursor=Dr.limit-i,!v()))&&(Dr.bra=Dr.cursor,Dr.slice_del(),r=Dr.limit-Dr.cursor,Dr.ket=Dr.cursor,!(!W()||(Dr.bra=Dr.cursor,Dr.slice_del(),!K()))||(Dr.cursor=Dr.limit-r,Dr.ket=Dr.cursor,!(a()||(Dr.cursor=Dr.limit-r,m()||(Dr.cursor=Dr.limit-r,K())))||(Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,W()&&(Dr.bra=Dr.cursor,Dr.slice_del(),K()),!0)))}function Q(){var r,i,e=Dr.limit-Dr.cursor;if(Dr.ket=Dr.cursor,!p()&&(Dr.cursor=Dr.limit-e,!f()&&(Dr.cursor=Dr.limit-e,!_())))return!1;if(Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,r=Dr.limit-Dr.cursor,a())Dr.bra=Dr.cursor,Dr.slice_del(),i=Dr.limit-Dr.cursor,Dr.ket=Dr.cursor,W()||(Dr.cursor=Dr.limit-i);else if(Dr.cursor=Dr.limit-r,!W())return!0;return Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,K(),!0}function R(){var r,i,e=Dr.limit-Dr.cursor;if(Dr.ket=Dr.cursor,W())return Dr.bra=Dr.cursor,Dr.slice_del(),void K();if(Dr.cursor=Dr.limit-e,Dr.ket=Dr.cursor,q())if(Dr.bra=Dr.cursor,Dr.slice_del(),r=Dr.limit-Dr.cursor,Dr.ket=Dr.cursor,d())Dr.bra=Dr.cursor,Dr.slice_del();else{if(Dr.cursor=Dr.limit-r,Dr.ket=Dr.cursor,!a()&&(Dr.cursor=Dr.limit-r,!m())){if(Dr.cursor=Dr.limit-r,Dr.ket=Dr.cursor,!W())return;if(Dr.bra=Dr.cursor,Dr.slice_del(),!K())return}Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,W()&&(Dr.bra=Dr.cursor,Dr.slice_del(),K())}else if(Dr.cursor=Dr.limit-e,!M(e)&&(Dr.cursor=Dr.limit-e,!N(e))){if(Dr.cursor=Dr.limit-e,Dr.ket=Dr.cursor,y())return Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,i=Dr.limit-Dr.cursor,void(a()?(Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,W()&&(Dr.bra=Dr.cursor,Dr.slice_del(),K())):(Dr.cursor=Dr.limit-i,W()?(Dr.bra=Dr.cursor,Dr.slice_del(),K()):(Dr.cursor=Dr.limit-i,K())));if(Dr.cursor=Dr.limit-e,!O()){if(Dr.cursor=Dr.limit-e,d())return Dr.bra=Dr.cursor,void Dr.slice_del();Dr.cursor=Dr.limit-e,K()||(Dr.cursor=Dr.limit-e,Q()||(Dr.cursor=Dr.limit-e,Dr.ket=Dr.cursor,(a()||(Dr.cursor=Dr.limit-e,m()))&&(Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,W()&&(Dr.bra=Dr.cursor,Dr.slice_del(),K()))))}}}function U(){var r;if(Dr.ket=Dr.cursor,r=Dr.find_among_b(Sr,4))switch(Dr.bra=Dr.cursor,r){case 1:Dr.slice_from("p");break;case 2:Dr.slice_from("ç");break;case 3:Dr.slice_from("t");break;case 4:Dr.slice_from("k")}}function V(){for(;;){var r=Dr.limit-Dr.cursor;if(Dr.in_grouping_b(Wr,97,305)){Dr.cursor=Dr.limit-r;break}if(Dr.cursor=Dr.limit-r,Dr.cursor<=Dr.limit_backward)return!1;Dr.cursor--}return!0}function X(r,i,e){if(Dr.cursor=Dr.limit-r,V()){var n=Dr.limit-Dr.cursor;if(!Dr.eq_s_b(1,i)&&(Dr.cursor=Dr.limit-n,!Dr.eq_s_b(1,e)))return!0;Dr.cursor=Dr.limit-r;var t=Dr.cursor;return Dr.insert(Dr.cursor,Dr.cursor,e),Dr.cursor=t,!1}return!0}function Y(){var r=Dr.limit-Dr.cursor;(Dr.eq_s_b(1,"d")||(Dr.cursor=Dr.limit-r,Dr.eq_s_b(1,"g")))&&X(r,"a","ı")&&X(r,"e","i")&&X(r,"o","u")&&X(r,"ö","ü")}function $(){for(var r,i=Dr.cursor,e=2;;){for(r=Dr.cursor;!Dr.in_grouping(Wr,97,305);){if(Dr.cursor>=Dr.limit)return Dr.cursor=r,!(e>0)&&(Dr.cursor=i,!0);Dr.cursor++}e--}}function rr(r,i,e){for(;!Dr.eq_s(i,e);){if(Dr.cursor>=Dr.limit)return!0;Dr.cursor++}return(tr=i)!=Dr.limit||(Dr.cursor=r,!1)}function ir(){var r=Dr.cursor;return!rr(r,2,"ad")||(Dr.cursor=r,!rr(r,5,"soyad"))}function er(){var r=Dr.cursor;return!ir()&&(Dr.limit_backward=r,Dr.cursor=Dr.limit,Y(),Dr.cursor=Dr.limit,U(),!0)}var nr,tr,ur=[new i("m",-1,-1),new i("n",-1,-1),new i("miz",-1,-1),new i("niz",-1,-1),new i("muz",-1,-1),new i("nuz",-1,-1),new i("müz",-1,-1),new i("nüz",-1,-1),new i("mız",-1,-1),new i("nız",-1,-1)],or=[new i("leri",-1,-1),new i("ları",-1,-1)],sr=[new i("ni",-1,-1),new i("nu",-1,-1),new i("nü",-1,-1),new i("nı",-1,-1)],cr=[new i("in",-1,-1),new i("un",-1,-1),new i("ün",-1,-1),new i("ın",-1,-1)],lr=[new i("a",-1,-1),new i("e",-1,-1)],ar=[new i("na",-1,-1),new i("ne",-1,-1)],mr=[new i("da",-1,-1),new i("ta",-1,-1),new i("de",-1,-1),new i("te",-1,-1)],dr=[new i("nda",-1,-1),new i("nde",-1,-1)],fr=[new i("dan",-1,-1),new i("tan",-1,-1),new i("den",-1,-1),new i("ten",-1,-1)],br=[new i("ndan",-1,-1),new i("nden",-1,-1)],wr=[new i("la",-1,-1),new i("le",-1,-1)],_r=[new i("ca",-1,-1),new i("ce",-1,-1)],kr=[new i("im",-1,-1),new i("um",-1,-1),new i("üm",-1,-1),new i("ım",-1,-1)],pr=[new i("sin",-1,-1),new i("sun",-1,-1),new i("sün",-1,-1),new i("sın",-1,-1)],gr=[new i("iz",-1,-1),new i("uz",-1,-1),new i("üz",-1,-1),new i("ız",-1,-1)],yr=[new i("siniz",-1,-1),new i("sunuz",-1,-1),new i("sünüz",-1,-1),new i("sınız",-1,-1)],zr=[new i("lar",-1,-1),new i("ler",-1,-1)],vr=[new i("niz",-1,-1),new i("nuz",-1,-1),new i("nüz",-1,-1),new i("nız",-1,-1)],hr=[new i("dir",-1,-1),new i("tir",-1,-1),new i("dur",-1,-1),new i("tur",-1,-1),new i("dür",-1,-1),new i("tür",-1,-1),new i("dır",-1,-1),new i("tır",-1,-1)],qr=[new i("casına",-1,-1),new i("cesine",-1,-1)],Cr=[new i("di",-1,-1),new i("ti",-1,-1),new i("dik",-1,-1),new i("tik",-1,-1),new i("duk",-1,-1),new i("tuk",-1,-1),new i("dük",-1,-1),new i("tük",-1,-1),new i("dık",-1,-1),new i("tık",-1,-1),new i("dim",-1,-1),new i("tim",-1,-1),new i("dum",-1,-1),new i("tum",-1,-1),new i("düm",-1,-1),new i("tüm",-1,-1),new i("dım",-1,-1),new i("tım",-1,-1),new i("din",-1,-1),new i("tin",-1,-1),new i("dun",-1,-1),new i("tun",-1,-1),new i("dün",-1,-1),new i("tün",-1,-1),new i("dın",-1,-1),new i("tın",-1,-1),new i("du",-1,-1),new i("tu",-1,-1),new i("dü",-1,-1),new i("tü",-1,-1),new i("dı",-1,-1),new i("tı",-1,-1)],Pr=[new i("sa",-1,-1),new i("se",-1,-1),new i("sak",-1,-1),new i("sek",-1,-1),new i("sam",-1,-1),new i("sem",-1,-1),new i("san",-1,-1),new i("sen",-1,-1)],Fr=[new i("miş",-1,-1),new i("muş",-1,-1),new i("müş",-1,-1),new i("mış",-1,-1)],Sr=[new i("b",-1,1),new i("c",-1,2),new i("d",-1,3),new i("ğ",-1,4)],Wr=[17,65,16,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,32,8,0,0,0,0,0,0,1],Lr=[1,16,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,8,0,0,0,0,0,0,1],xr=[1,64,16,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1],Ar=[17,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,130],Er=[1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1],jr=[17],Tr=[65],Zr=[65],Br=[["a",xr,97,305],["e",Ar,101,252],["ı",Er,97,305],["i",jr,101,105],["o",Tr,111,117],["ö",Zr,246,252],["u",Tr,111,117]],Dr=new e;this.setCurrent=function(r){Dr.setCurrent(r)},this.getCurrent=function(){return Dr.getCurrent()},this.stem=function(){return!!($()&&(Dr.limit_backward=Dr.cursor,Dr.cursor=Dr.limit,J(),Dr.cursor=Dr.limit,nr&&(R(),Dr.cursor=Dr.limit_backward,er())))}};return function(r){return"function"==typeof r.update?r.update(function(r){return n.setCurrent(r),n.stem(),n.getCurrent()}):(n.setCurrent(r),n.stem(),n.getCurrent())}}(),r.Pipeline.registerFunction(r.tr.stemmer,"stemmer-tr"),r.tr.stopWordFilter=r.generateStopWordFilter("acaba altmış altı ama ancak arada aslında ayrıca bana bazı belki ben benden beni benim beri beş bile bin bir biri birkaç birkez birçok birşey birşeyi biz bizden bize bizi bizim bu buna bunda bundan bunlar bunları bunların bunu bunun burada böyle böylece da daha dahi de defa değil diye diğer doksan dokuz dolayı dolayısıyla dört edecek eden ederek edilecek ediliyor edilmesi ediyor elli en etmesi etti ettiği ettiğini eğer gibi göre halen hangi hatta hem henüz hep hepsi her herhangi herkesin hiç hiçbir iki ile ilgili ise itibaren itibariyle için işte kadar karşın katrilyon kendi kendilerine kendini kendisi kendisine kendisini kez ki kim kimden kime kimi kimse kırk milyar milyon mu mü mı nasıl ne neden nedenle nerde nerede nereye niye niçin o olan olarak oldu olduklarını olduğu olduğunu olmadı olmadığı olmak olması olmayan olmaz olsa olsun olup olur olursa oluyor on ona ondan onlar onlardan onları onların onu onun otuz oysa pek rağmen sadece sanki sekiz seksen sen senden seni senin siz sizden sizi sizin tarafından trilyon tüm var vardı ve veya ya yani yapacak yapmak yaptı yaptıkları yaptığı yaptığını yapılan yapılması yapıyor yedi yerine yetmiş yine yirmi yoksa yüz zaten çok çünkü öyle üzere üç şey şeyden şeyi şeyler şu şuna şunda şundan şunları şunu şöyle".split(" ")),r.Pipeline.registerFunction(r.tr.stopWordFilter,"stopWordFilter-tr")}});
\ No newline at end of file
diff --git a/DevDoc/assets/javascripts/lunr/min/lunr.vi.min.js b/DevDoc/assets/javascripts/lunr/min/lunr.vi.min.js
new file mode 100644
index 00000000..22aed28c
--- /dev/null
+++ b/DevDoc/assets/javascripts/lunr/min/lunr.vi.min.js
@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.vi=function(){this.pipeline.reset(),this.pipeline.add(e.vi.stopWordFilter,e.vi.trimmer)},e.vi.wordCharacters="[A-Za-ẓ̀͐́͑̉̃̓ÂâÊêÔôĂ-ăĐ-đƠ-ơƯ-ư]",e.vi.trimmer=e.trimmerSupport.generateTrimmer(e.vi.wordCharacters),e.Pipeline.registerFunction(e.vi.trimmer,"trimmer-vi"),e.vi.stopWordFilter=e.generateStopWordFilter("là cái nhưng mà".split(" "))}});
\ No newline at end of file
diff --git a/DevDoc/assets/javascripts/lunr/min/lunr.zh.min.js b/DevDoc/assets/javascripts/lunr/min/lunr.zh.min.js
new file mode 100644
index 00000000..fda66e9c
--- /dev/null
+++ b/DevDoc/assets/javascripts/lunr/min/lunr.zh.min.js
@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r(require("@node-rs/jieba")):r()(e.lunr)}(this,function(e){return function(r,t){if(void 0===r)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===r.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");var i="2"==r.version[0];r.zh=function(){this.pipeline.reset(),this.pipeline.add(r.zh.trimmer,r.zh.stopWordFilter,r.zh.stemmer),i?this.tokenizer=r.zh.tokenizer:(r.tokenizer&&(r.tokenizer=r.zh.tokenizer),this.tokenizerFn&&(this.tokenizerFn=r.zh.tokenizer))},r.zh.tokenizer=function(n){if(!arguments.length||null==n||void 0==n)return[];if(Array.isArray(n))return n.map(function(e){return i?new r.Token(e.toLowerCase()):e.toLowerCase()});t&&e.load(t);var o=n.toString().trim().toLowerCase(),s=[];e.cut(o,!0).forEach(function(e){s=s.concat(e.split(" "))}),s=s.filter(function(e){return!!e});var u=0;return s.map(function(e,t){if(i){var n=o.indexOf(e,u),s={};return s.position=[n,e.length],s.index=t,u=n,new r.Token(e,s)}return e})},r.zh.wordCharacters="\\w一-龥",r.zh.trimmer=r.trimmerSupport.generateTrimmer(r.zh.wordCharacters),r.Pipeline.registerFunction(r.zh.trimmer,"trimmer-zh"),r.zh.stemmer=function(){return function(e){return e}}(),r.Pipeline.registerFunction(r.zh.stemmer,"stemmer-zh"),r.zh.stopWordFilter=r.generateStopWordFilter("的 一 不 在 人 有 是 为 為 以 于 於 上 他 而 后 後 之 来 來 及 了 因 下 可 到 由 这 這 与 與 也 此 但 并 並 个 個 其 已 无 無 小 我 们 們 起 最 再 今 去 好 只 又 或 很 亦 某 把 那 你 乃 它 吧 被 比 别 趁 当 當 从 從 得 打 凡 儿 兒 尔 爾 该 該 各 给 給 跟 和 何 还 還 即 几 幾 既 看 据 據 距 靠 啦 另 么 麽 每 嘛 拿 哪 您 凭 憑 且 却 卻 让 讓 仍 啥 如 若 使 谁 誰 虽 雖 随 隨 同 所 她 哇 嗡 往 些 向 沿 哟 喲 用 咱 则 則 怎 曾 至 致 着 著 诸 諸 自".split(" ")),r.Pipeline.registerFunction(r.zh.stopWordFilter,"stopWordFilter-zh")}});
\ No newline at end of file
diff --git a/DevDoc/assets/javascripts/lunr/tinyseg.js b/DevDoc/assets/javascripts/lunr/tinyseg.js
new file mode 100644
index 00000000..167fa6dd
--- /dev/null
+++ b/DevDoc/assets/javascripts/lunr/tinyseg.js
@@ -0,0 +1,206 @@
+/**
+ * export the module via AMD, CommonJS or as a browser global
+ * Export code from https://github.com/umdjs/umd/blob/master/returnExports.js
+ */
+;(function (root, factory) {
+    if (typeof define === 'function' && define.amd) {
+        // AMD. Register as an anonymous module.
+        define(factory)
+    } else if (typeof exports === 'object') {
+        /**
+         * Node. Does not work with strict CommonJS, but
+         * only CommonJS-like environments that support module.exports,
+         * like Node.
+         */
+        module.exports = factory()
+    } else {
+        // Browser globals (root is window)
+        factory()(root.lunr);
+    }
+}(this, function () {
+    /**
+     * Just return a value to define the module export.
+     * This example returns an object, but the module
+     * can return a function as the exported value.
+     */
+
+    return function(lunr) {
+        // TinySegmenter 0.1 -- Super compact Japanese tokenizer in Javascript
+        // (c) 2008 Taku Kudo <taku@chasen.org>
+        // TinySegmenter is freely distributable under the terms of a new BSD licence.
+        // For details, see http://chasen.org/~taku/software/TinySegmenter/LICENCE.txt
+
+        function TinySegmenter() {
+          var patterns = {
+            "[一二三四五六七八九十百千万億兆]":"M",
+            "[一-龠々〆ヵヶ]":"H",
+            "[ぁ-ん]":"I",
+            "[ァ-ヴーｱ-ﾝﾞｰ]":"K",
+            "[a-zA-Zａ-ｚＡ-Ｚ]":"A",
+            "[0-9０-９]":"N"
+          }
+          this.chartype_ = [];
+          for (var i in patterns) {
+            var regexp = new RegExp(i);
+            this.chartype_.push([regexp, patterns[i]]);
+          }
+
+          this.BIAS__ = -332
+          this.BC1__ = {"HH":6,"II":2461,"KH":406,"OH":-1378};
+          this.BC2__ = {"AA":-3267,"AI":2744,"AN":-878,"HH":-4070,"HM":-1711,"HN":4012,"HO":3761,"IA":1327,"IH":-1184,"II":-1332,"IK":1721,"IO":5492,"KI":3831,"KK":-8741,"MH":-3132,"MK":3334,"OO":-2920};
+          this.BC3__ = {"HH":996,"HI":626,"HK":-721,"HN":-1307,"HO":-836,"IH":-301,"KK":2762,"MK":1079,"MM":4034,"OA":-1652,"OH":266};
+          this.BP1__ = {"BB":295,"OB":304,"OO":-125,"UB":352};
+          this.BP2__ = {"BO":60,"OO":-1762};
+          this.BQ1__ = {"BHH":1150,"BHM":1521,"BII":-1158,"BIM":886,"BMH":1208,"BNH":449,"BOH":-91,"BOO":-2597,"OHI":451,"OIH":-296,"OKA":1851,"OKH":-1020,"OKK":904,"OOO":2965};
+          this.BQ2__ = {"BHH":118,"BHI":-1159,"BHM":466,"BIH":-919,"BKK":-1720,"BKO":864,"OHH":-1139,"OHM":-181,"OIH":153,"UHI":-1146};
+          this.BQ3__ = {"BHH":-792,"BHI":2664,"BII":-299,"BKI":419,"BMH":937,"BMM":8335,"BNN":998,"BOH":775,"OHH":2174,"OHM":439,"OII":280,"OKH":1798,"OKI":-793,"OKO":-2242,"OMH":-2402,"OOO":11699};
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+            if (str.match(this.chartype_[i][0])) {
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+        TinySegmenter.prototype.ts_ = function(v) {
+          if (v) { return v; }
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+        TinySegmenter.prototype.segment = function(input) {
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+          for (var i = 4; i < seg.length - 3; ++i) {
+            var score = this.BIAS__;
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+            var c5 = ctype[i+1];
+            var c6 = ctype[i+2];
+            score += this.ts_(this.UP1__[p1]);
+            score += this.ts_(this.UP2__[p2]);
+            score += this.ts_(this.UP3__[p3]);
+            score += this.ts_(this.BP1__[p1 + p2]);
+            score += this.ts_(this.BP2__[p2 + p3]);
+            score += this.ts_(this.UW1__[w1]);
+            score += this.ts_(this.UW2__[w2]);
+            score += this.ts_(this.UW3__[w3]);
+            score += this.ts_(this.UW4__[w4]);
+            score += this.ts_(this.UW5__[w5]);
+            score += this.ts_(this.UW6__[w6]);
+            score += this.ts_(this.BW1__[w2 + w3]);
+            score += this.ts_(this.BW2__[w3 + w4]);
+            score += this.ts_(this.BW3__[w4 + w5]);
+            score += this.ts_(this.TW1__[w1 + w2 + w3]);
+            score += this.ts_(this.TW2__[w2 + w3 + w4]);
+            score += this.ts_(this.TW3__[w3 + w4 + w5]);
+            score += this.ts_(this.TW4__[w4 + w5 + w6]);
+            score += this.ts_(this.UC1__[c1]);
+            score += this.ts_(this.UC2__[c2]);
+            score += this.ts_(this.UC3__[c3]);
+            score += this.ts_(this.UC4__[c4]);
+            score += this.ts_(this.UC5__[c5]);
+            score += this.ts_(this.UC6__[c6]);
+            score += this.ts_(this.BC1__[c2 + c3]);
+            score += this.ts_(this.BC2__[c3 + c4]);
+            score += this.ts_(this.BC3__[c4 + c5]);
+            score += this.ts_(this.TC1__[c1 + c2 + c3]);
+            score += this.ts_(this.TC2__[c2 + c3 + c4]);
+            score += this.ts_(this.TC3__[c3 + c4 + c5]);
+            score += this.ts_(this.TC4__[c4 + c5 + c6]);
+        //  score += this.ts_(this.TC5__[c4 + c5 + c6]);    
+            score += this.ts_(this.UQ1__[p1 + c1]);
+            score += this.ts_(this.UQ2__[p2 + c2]);
+            score += this.ts_(this.UQ3__[p3 + c3]);
+            score += this.ts_(this.BQ1__[p2 + c2 + c3]);
+            score += this.ts_(this.BQ2__[p2 + c3 + c4]);
+            score += this.ts_(this.BQ3__[p3 + c2 + c3]);
+            score += this.ts_(this.BQ4__[p3 + c3 + c4]);
+            score += this.ts_(this.TQ1__[p2 + c1 + c2 + c3]);
+            score += this.ts_(this.TQ2__[p2 + c2 + c3 + c4]);
+            score += this.ts_(this.TQ3__[p3 + c1 + c2 + c3]);
+            score += this.ts_(this.TQ4__[p3 + c2 + c3 + c4]);
+            var p = "O";
+            if (score > 0) {
+              result.push(word);
+              word = "";
+              p = "B";
+            }
+            p1 = p2;
+            p2 = p3;
+            p3 = p;
+            word += seg[i];
+          }
+          result.push(word);
+
+          return result;
+        }
+
+        lunr.TinySegmenter = TinySegmenter;
+    };
+
+}));
\ No newline at end of file
diff --git a/DevDoc/assets/javascripts/lunr/wordcut.js b/DevDoc/assets/javascripts/lunr/wordcut.js
new file mode 100644
index 00000000..0d898c9e
--- /dev/null
+++ b/DevDoc/assets/javascripts/lunr/wordcut.js
@@ -0,0 +1,6708 @@
+(function(f){if(typeof exports==="object"&&typeof module!=="undefined"){module.exports=f()}else if(typeof define==="function"&&define.amd){define([],f)}else{var g;if(typeof window!=="undefined"){g=window}else if(typeof global!=="undefined"){g=global}else if(typeof self!=="undefined"){g=self}else{g=this}(g.lunr || (g.lunr = {})).wordcut = f()}})(function(){var define,module,exports;return (function e(t,n,r){function s(o,u){if(!n[o]){if(!t[o]){var a=typeof require=="function"&&require;if(!u&&a)return a(o,!0);if(i)return i(o,!0);var f=new Error("Cannot find module '"+o+"'");throw f.code="MODULE_NOT_FOUND",f}var l=n[o]={exports:{}};t[o][0].call(l.exports,function(e){var n=t[o][1][e];return s(n?n:e)},l,l.exports,e,t,n,r)}return n[o].exports}var i=typeof require=="function"&&require;for(var o=0;o<r.length;o++)s(r[o]);return s})({1:[function(require,module,exports){
+var _ = require("underscore");
+
+var Acceptors = {
+  creators: null,
+  current: null,
+  tag: null,
+
+  init: function() {
+    this.creators = [];
+    this.current = [];
+    this.tag = {};
+  },
+
+  reset: function() {
+    this.current = [];
+    this.tag = {}
+  },
+
+  transit: function(ch) {
+    var self = this;
+
+    self.creators.forEach(function(creator) {
+      var acceptor = creator.createAcceptor(self.tag);
+      if (acceptor) 
+        self.current.push(acceptor);
+    });
+    
+    var _current = [];
+    self.tag = {};
+
+    for (var i = 0; i < self.current.length; i++) {
+      var _acceptor = self.current[i]
+        , acceptor = _acceptor.transit(ch);
+      
+      if (!acceptor.isError) {
+        _current.push(acceptor);
+        self.tag[acceptor.tag] = acceptor;
+      }
+    }
+    self.current = _current;
+
+  },
+
+  getFinalAcceptors: function() {    
+    return this.current.filter(function(acceptor) {
+      return acceptor.isFinal;
+    });
+  }
+};
+
+module.exports = function() {
+  var acceptors = _.clone(Acceptors);
+  acceptors.init();
+  return acceptors;
+};
+
+},{"underscore":25}],2:[function(require,module,exports){
+(function (__dirname){
+
+var LEFT = 0;
+var RIGHT = 1;
+var path = require("path");
+var glob = require("glob");
+
+var WordcutDict = {
+
+
+  init: function (dictPathFile, withDefault, words) {
+    withDefault = withDefault || false
+    var defaultDict = path.normalize(__dirname + "/..") + "/data/tdict-*.txt";
+    this.dict=[]
+    var dictPathIsDefined = dictPathFile !== undefined
+    var dictPath = (withDefault || !dictPathIsDefined) ? [defaultDict]: [];
+    var dictPathFile = dictPathFile || defaultDict
+
+    if(dictPathIsDefined){
+      if (Array.isArray(dictPathFile)) {
+        dictPath.concat.apply(dictPath, dictPathFile);
+      } else {
+        dictPath.push(dictPathFile)
+      }
+    }
+
+    this.addFiles(dictPath, false)
+
+    if(words!==undefined){
+      this.addWords(words, false)
+    }
+    this.finalizeDict();
+  },
+
+  addWords: function(words, finalize){
+    finalize = finalize===undefined || finalize;
+    this.dict.push.apply(this.dict, words)
+    if(finalize){
+      this.finalizeDict();
+    }
+  },
+
+  finalizeDict: function(){
+    this.dict = this.sortuniq(this.dict);
+  },
+
+  addFiles: function(files, finalize){
+    finalize = finalize===undefined || finalize;
+    
+    for (var i = 0; i < 1; i++) {
+      var words = "ก.ก.\nก.ก.น.\nก.ข.ค.\nก.ค.\nก.จ.\nก.ช.น.\nก.ฌ.\nก.ต.\nก.ต.ง.\nก.ต.ช.\nก.ตร.\nก.ท.\nก.น.ช.\nก.บช.\nก.บถ.\nก.ป.ส.\nก.พ.\nก.ม.\nก.ย.\nก.ร.\nก.ล.ต.\nก.ว.\nก.ศ.ว.\nก.ส.ท.\nก.ส.ธ.\nก.ส.อ.\nก.อ.\nกก.ตชด.\nกก.ตร.น.\nกก.ภ.จว.\nกก.รสช.\nกกบ.ขส.ทบ.\nกกล.รพน.\nกง.กห.\nกง.ทบ.\nกง.ทร.\nกซข.ป.\nกซม.ป.\nกทม.กรุงเทพมหานคร\nกบ.ทบ.\nกป.สป.\nกพ.ทบ.\nกพ.ทร.\nกพ.ทหาร\nกร.ทบ.\nกรป.กลาง\nกรอ.พอ.\nกศ.ด.\nกศ.บ.\nกศ.บป.\nกศ.ม.\nกษ.ด.\nกษ.บ.\nกษ.ม.\nกส.ด.\nกส.ทบ.\nกส.บ.\nกส.ม.\nกอ.ปค.\nกอ.รพน.\nกอ.รมน.\nกอ.รสต.\nข.ต.ว.\nขว.ทบ.\nขว.ทร.\nขว.ทหาร\nขส.ทบ.\nขส.ทร.\nขส.ทอ.\nค.ด.\nค.บ.\nค.พ.ศ.\nค.ม.\nค.ร.น.\nค.ร.ฟ.\nค.ร.ม.\nค.ศ.\nค.อ.ด.\nค.อ.บ.\nค.อ.ม.\nคศ.ด.\nคศ.บ.\nคศ.ม.\nง.ด.\nจ.จ.\nจ.จ.จ.\nจ.ช.\nจ.ต.\nจ.ท.\nจ.ป.ร.\nจ.ม.\nจ.ศ.\nจ.ส.ต.\nจ.ส.ท.\nจ.ส.อ.\nจ.อ.\nจ.อ.ร.\nจ.๑๘\nจก.ธน.\nจก.สน.\nช.ค.\nช.ค.บ.\nช.พ.ค.\nช.ส.\nช.ส.ค.\nฌ.ป.ค.\nฌ.ศ.ร.\nฌ.ส.อ.\nฐท.สห.\nด.ช.\nด.ญ.\nด.ต.\nด.ศ.ค.\nด.ศ.ร.\nดย.ทร.\nต.ก.\nต.ค.\nต.จ.\nต.จ.ว.\nต.ช.\nต.ต.\nต.บ.\nต.ม.\nต.ร.\nต.ศ.ร.\nต.ห.\nต.อ.\nต.อ.จ.\nตร.กม.\nตร.ซม.\nตร.ต.\nตร.ทล.\nตร.น.\nตร.ปม.\nตร.ภ.\nตร.ม.\nตร.รฟ.\nตร.ว.\nตร.ส.\nตร.สข.\nท.จ.\nท.จ.ว.\nท.ช.\nท.ญ.\nท.ด.\nท.ท.ท.\nท.ทบ.\nท.บ.\nท.พ.\nท.ม.\nท.ศ.\nทก.ด.\nทก.บ.\nทก.ม.\nทส.ปช.\nทส.รมว.กห.\nทุ.ส.นิ.ม.\nธ.ก.ส.\nธ.ค.\nธ.ญ\nธ.บ.\nน.ช.\nน.ญ.\nน.ด.\nน.ต.\nน.ท.\nน.น.\nน.บ.\nน.บ.ท.\nน.ป.ท.\nน.พ.\nน.ม.\nน.ร.\nน.ว.\nน.ศ.\nน.ส.\nน.ส.พ.\nน.ส.๓\nน.สพ.\nน.อ.\nนปพ.ภ.\nนศ.ด.\nนศ.บ.\nนศ.ม.\nบ.ก.\nบ.ข.ส.\nบ.ช.\nบ.ด.ท.\nบ.ตร.\nบ.ภ.\nบ.ม.\nบก.จร.\nบก.ตชด.\nบก.ตม.\nบก.ทล.\nบก.น.\nบก.ป.\nบก.ปค.\nบก.ปม.\nบก.ภ.เขต\nบก.รน.\nบก.รฟ.\nบก.ร้อย.ตชด.\nบก.ส.\nบกข.ป.\nบจพ.ป.\nบช.ก.\nบช.ด.\nบช.ตชด.\nบช.น.\nบช.บ.\nบช.ปส.\nบช.ภ.\nบช.ม.\nบชท.ป.\nบชน.ป.\nบชส.ป.\nบธ.ด.\nบธ.บ.\nบธ.ม.\nบนท.ป.\nบนอ.ป.\nบปช.ป.\nป.กท.\nป.กศ.\nป.กศ.สูง\nป.จ.\nป.จ.ว.\nป.ช.\nป.ธ.\nป.ป.\nป.ป.ก.\nป.ป.ช.\nป.ป.ป.\nป.ป.ร.\nป.ป.ส.\nป.พ.\nป.พ.พ.\nป.พย.\nป.ม.\nป.ม.ก.\nป.ม.ช.\nป.ม.ธ.\nป.ม.ศ.\nป.ม.อ.\nป.ร.ร.๔\nป.ร.ร.๕\nป.ร.ร.๖\nป.ล.\nป.ว.พ.\nป.วิ.อ.\nป.ส.ส.\nป.อ.\nป.อ.ร.ส.\nป.๑\nปม.วส.\nปอ.พ.\nผกก.ภ.\nผช.ผอ.\nผต.มท.\nผบ.ตร.\nผบ.ทบ.\nผบ.ทร.\nผบ.ทสส.\nผบ.ทอ.\nผบก.น.\nผบก.ป.\nผบก.ปค.\nผบก.ปม.\nผบก.ภ.\nผบช.ก.\nผบช.ตชด.\nผบช.น.\nผบช.ภ.\nผว.กทม.\nผอ.ปจ.\nพ.ก.ง.\nพ.กศ.\nพ.ข.ต.\nพ.ค.\nพ.ค.ช.\nพ.ค.ว.\nพ.ค.ศ.\nพ.จ.ต.\nพ.จ.ท.\nพ.จ.อ.\nพ.ช.\nพ.ช.ค.\nพ.ด.\nพ.ต.\nพ.ต.ต.\nพ.ต.ท.\nพ.ต.อ.\nพ.ต.อ.พิเศษ\nพ.ท.\nพ.บ.\nพ.ป.\nพ.ภ.ม.\nพ.ม.\nพ.ม.ช.\nพ.ย.\nพ.ร.ก.\nพ.ร.ฎ.\nพ.ร.ต.\nพ.ร.ธ.\nพ.ร.บ.\nพ.ศ.\nพ.ศ.บ.\nพ.ส.ร.\nพ.ส.ล.\nพ.อ.\nพ.อ.ต.\nพ.อ.ท.\nพ.อ.พิเศษ\nพ.อ.อ.\nพณ.ด.\nพณ.บ.\nพณ.ม.\nพธ.ด.\nพธ.บ.\nพธ.ม.\nพบ.ด.\nพบ.บ.\nพบ.ม.\nพย.ด.\nพย.บ.\nพย.ม.\nพล.จ.\nพล.ต.\nพล.ต.จ.\nพล.ต.ต.\nพล.ต.ท.\nพล.ต.อ.\nพล.ท.\nพล.ปตอ.\nพล.ม.\nพล.ม.๒\nพล.ร.จ.\nพล.ร.ต.\nพล.ร.ท.\nพล.ร.อ.\nพล.อ.\nพล.อ.จ.\nพล.อ.ต.\nพล.อ.ท.\nพล.อ.อ.\nพลา.ทร.\nพศ.ด.\nพศ.บ.\nพศ.ม.\nพอ.สว.\nภ.ง.ด.\nภ.ง.ด.๙\nภ.ด.\nภ.บ.\nภ.บ.ท.๕\nภ.ป.ร.\nภ.พ.\nภ.ม.\nภ.สถ.บ.\nม.ค.\nม.จ.\nม.ป.ท.\nม.ป.ป.\nม.ป.พ.\nม.ร.ว.\nม.ศ.\nม.อ.\nม.อ.ปัตตานี\nมิ.ย.\nมี.ค.\nยศ.ทบ.\nยศ.ทร.\nยศ.ทอ.\nร.ง.\nร.ด.\nร.ต.\nร.ต.ต.\nร.ต.ท.\nร.ต.อ.\nร.ท.\nร.น.\nร.บ.\nร.พ.\nร.ฟ.ล.\nร.ย.ล.\nร.ย.ส.ท.\nร.ล.\nร.ศ.\nร.ส.พ.\nร.อ.\nรป.ม.\nรร.จปร.\nรร.จอ.\nรร.ชท.\nรร.ตท.\nรร.นร.\nรร.นรต.\nรร.นอ.\nล.ญ.\nล.ว.\nลส.ชบ.\nว.ค.\nว.ฉ.\nว.ช.\nว.ด.ป.\nว.ป.ถ.\nวท.บ.\nศ.บ.\nศ.ป.ก.\nศ.ศ.ป.\nศฝร.ภ.\nศศ.บ.\nศษ.บ.\nศส.บ.\nส.ก.\nส.ก.ศ.ท.\nส.ค.\nส.ค.1\nส.ค.ร.\nส.ค.ส.\nส.ต.\nส.ต.ต.\nส.ต.ท.\nส.ต.อ.\nส.ท.\nส.ทร.\nส.ป.ช.\nส.ป.ส.ท.\nส.ป.อ.\nส.ร.\nส.ล.น.\nส.ว.\nส.ว.ท.\nส.ว.ส.ท.\nส.ส.\nส.ส.ท.\nส.ส.ร.\nส.ห.\nส.อ.\nสถ.บ.\nสนง.สสอ.\nสพ.ญ.\nสพ.บ.\nสว.จร.\nสว.ธร.\nสว.ส.\nสว.สป.\nสว.สส.\nสว.อก.\nสส.บ.\nสุ.จิ.ปุ.ลิ.\nห.ร.ม.\nอ.ก.ค.\nอ.ก.จ.\nอ.จ.\nอ.ช.พ.\nอ.ตร.\nอ.บ.\nอ.ส.ท.\nอ.ส.ม.ท.\nอ.ส.ย.\nอ.อ.ป.\nอส.รด.\nอุ.อา.ก.ส.\nฮ.จ.\nฮ.ท.\nฮ.ฝ.\nฮ.ล.\nฮ.ศ.\nเม.ย.\n\nกรีนิช\nกลันตัน\nกัลกัตตา\nกัวลาลัมเปอร์\nกัศมีร์\nกาฐมาณฑุ\nโกลกาตา\nควิเบก\nคอนเนตทิคัต\nคาบูล\nคุชราต\nคุนหมิง\nเคนตักกี\nเคนทักกี\nเคมบริดจ์\nแคชเมียร์\nแคนซัส\nแคนเบอร์รา\nแคโรไลนา\nแคลิฟอร์เนีย\nโคเปนเฮเกน\nโคลัมโบ\nโคโลราโด\nไครสต์เชิร์ช\nไคโร\nจาการ์ตา\nจำปาศักดิ์\nเจนไน\nเจนีวา\nเจ้อเจียง\nฉงชิ่ง\nเฉิงตู\nชานตง\nชิคาโก\nเชนไน\nเชอร์โนบิล\nซัปโปโร\nซานมารีโน\nซาบาห์\nซาราเยโว\nซาราวัก\nซิดนีย์\nซีอาน\nซีแอตเทิล\nซูริก\nซูริค\nเซเชลส์\nเซนได\nเซี่ยงไฮ้\nโซเฟีย\nโซล\nโซโลมอน\nไซ่ง่อน\nไซบีเรีย\nดัลลัส\nดาโคตา\nดานัง\nดีทรอยต์\nดูไบ\nเดนเวอร์\nเดลาแวร์\nเดียนเบียนฟู\nโดเวอร์\nโดฮา\nไดฟุกุ\nไดฟูกุ\nตรังกานู\nตริโปลี\nตูวาลู\nเตหะราน\nโตเกียว\nโตรอนโต\nทมิฬนาฑู\nทริโปลี\nทิเบต\nเทกซัส\nเท็กซัส\nเทนเนสซี\nเทลอาวีฟ\nแทสเมเนีย\nโทรอนโต\nไทเป\nธากา\nนางาซากิ\nนาริตะ\nนิวเจอร์ซีย์\nนิวเดลี\nนิวยอร์ก\nนิวยอร์ค\nนิวแฮมป์เชียร์\nเนบราสกา\nเนแบรสกา\nเนวาดา\nบรัสเซลส์\nบราซิเลีย\nบอมเบย์\nบอสตัน\nบังกาลอร์\nบังคาลอร์\nบูคาเรสต์\nบูดาเปสต์\nเบงกาซี\nเบนกาซี\nเบรุต\nเบลเกรด\nเบอร์ลิน\nแบกแดด\nปอยเปต\nปะลิส\nปะหัง\nปักกิ่ง\nปัญจาบ\nปัฏนา\nปารีส\nปีนัง\nเประ\nเปียงยาง\nพนมเปญ\nพระตะบอง\nพะโค\nพะสิม\nพาราณสี\nพิหารี\nเพนซิลวาเนีย\nเพนซิลเวเนีย\nฟรานซ์\nฟลอริดา\nฟิลาเดลเฟีย\nฟุกุชิมะ\nฟุกุชิมา\nฟุกุโอกะ\nฟูกูโอกะ\nแฟรงก์เฟิร์ต\nมอสโก\nมะนิลา\nมะละแหม่ง\nมัณฑะเลย์\nมัทราส\nมาดริด\nมิชิแกน\nมินนิโซตา\nมิยางิ\nมิลาน\nมิวนิก\nมิสซูรี\nมุมไบ\nเมน\nเมลเบิร์น\nเมาะตะมะ\nเมาะลำเลิง\nแมนจูเรีย\nแมนเชสเตอร์\nแมนฮัตตัน\nแมริแลนด์\nแมรีแลนด์\nแมสซาชูเซตส์\nยะไข่\nย่างกุ้ง\nยูทาห์\nยูนนาน\nเยรูซาเล็ม\nโยโกฮามา\nริยาด\nรีโอเดจาเนโร\nโรดไอแลนด์\nลอนดอน\nลอสแองเจลิส\nลาปาซ\nลาสเวกัส\nลิสบอน\nลุยเซียนา\nโลซาน\nโลซานน์\nวอชิงตัน\nวอร์ซอ\nวิสคอนซิน\nเวนิส\nเวลส์\nเวอร์จิเนีย\nเวอร์มอนต์\nเวียงจันทน์\nเวียนนา\nแวนคูเวอร์\nไวโอมิง\nสกอตแลนด์\nสก็อตแลนด์\nสตอกโฮล์ม\nสลังงอร์\nเสฉวน\nเสียมราฐ\nเสียมเรียบ\nหงสา\nหงสาวดี\nหนานไห่\nหลวงพระบาง\nหูเป่ย\nหูเป่ย์\nหูหนาน\nเหอเป่ย\nเหอเป่ย์\nเหอหนาน\nอชันตา\nอลาสกา\nอวันตี\nออริกอน\nออสโล\nอะแลสกา\nอัตตะปือ\nอัมมาน\nอัมสเตอร์ดัม\nอัสสัม\nอาบูดาบี\nอาร์คันซอ\nอินเดียนา\nอิบารากิ\nอิลลินอยส์\nอิสตันบูล\nอิสลามาบัด\nอุรุมชี\nอูลานบาตอร์\nเอดินบะระ\nเอเธนส์\nแอตแลนตา\nแอริโซนา\nแอลเจียร์\nโอคลาโฮมา\nโอค็อตสค์\nโอกินาวา\nโอซากา\nโอริสสา\nโอเรกอน\nโอไฮโอ\nไอดาโฮ\nไอโอวา\nฮอนโนลูลู\nฮานอย\nฮาเนดะ\nฮาราเร\nฮาวาย\nฮิโรชิมา\nฮุสตัน\nเฮลซิงกิ\n\nมกรา\nกุมภา\nมีนา\nเมษา\nพฤษภา\nมิถุนา\nกรกฎา\nสิงหา\nกันยา\nตุลา\nพฤศจิกา\nธันวา\nเอ\nบี\nซี\nดี\nอี\nเอฟ\nจี\nเอช\nไอ\nเจ\nเค\nแอล\nเอ็ม\nเอ็น\nโอ\nพี\nคิว\nอาร์\nเอส\nที\nยู\nวี\nดับเบิล\nดับบลิว\nเอ็กซ์\nเอ๊กซ์\nวาย\nแซด\nแอลฟา\nแอลฟ่า\nเบตา\nเบต้า\nแกมมา\nแกมม่า\nเดลตา\nเดลต้า\nโอเมกา\nโอเมก้า\nเมกะ\nกิกะ\nนาโน\nไมโคร\n\nกรรมาชน\nกรอบรูป\nกระดี๊กระด๊า\nกระบับ\nกราวนด์\nกรีน\nกรุ๊ป\nกฤษณ์\nกลาส\nก๊วน\nกษัตริยา\nกษัตริยาธิราช\nก่อนหน้า\nกะบับ\nกับดัก\nกัมมันตะ\nก๊าก\nก๋ากั่น\nกาญจน์\nกาญจนาภิเษก\nกามิกาเซ่\nการันตี\nกาหลิบ\nกิฟท์\nกิมจิ\nกีวี\nกึ๊ก\nกึ๋ย\nกุนซือ\nกุมภาพันธ์\nกู๋\nเกจิ\nเกมส์\nเกย์\nเกรด\nเกรย์\nเกสต์เฮาส์\nเก๊ะ\nเก๋ากี้\nเกิร์ล\nแกงค์\nแกรนด์\nแกสโซฮอล์\nแก๊สโซฮอล์\nโกเต็กซ์\nโกลด์\nโกะ\nโก๊ะ\nไกด์\nขั้นตอน\nเขวี้ยง\nคณาญาติ\nครัวซอง\nครัวซองต์\nคร่ำครวญ\nครีเอทีฟ\nครูเสด\nคลับ\nคลาสสิก\nคลิตอริส\nคลิป\nความหมาย\nควิก\nควีน\nคองเกรส\nคอนซูเมอร์\nคอนเซปต์\nคอนเซ็ปต์\nคอนโด\nคอนโดมิเนียม\nคอนเทนเนอร์\nคอนแทค\nคอนแท็ค\nคอนโทรล\nคอนเฟิร์ม\nคอปเตอร์\nคอมพ์\nคอมเพล็กซ์\nคอมมอนส์\nคอมเมนท์\nคอมเมนต์\nคอร์ป\nคอร์ปอเรชั่น\nคอร์รัปชัน\nคอร์รัปชั่น\nคอรัปชัน\nคอรัปชั่น\nคอร์ส\nคอลเล็กชั่น\nคอลัมน์\nคอลัมนิสต์\nคัตเอาต์\nคันคาก\nคันถธุระ\nคันธาระ\nคันยิ\nคัสตาร์ด\nคาราโอเกะ\nคีตกวี\nคีตปฏิภาณ\nคีตราชัน\nคาปูชิโน\nคามิคาเซ่\nคาเฟ่\nคาร์\nคาร์โก้\nคาราเมล\nคาแรกเตอร์\nคาแร็กเตอร์\nคาแรคเตอร์\nคาแร็คเตอร์\nคาวบอย\nคาสิโน\nคิกขุ\nคิวบิก\nคูลเลอร์\nเคบับ\nเครป\nเคลม\nเคลียร์\nเคลื่อนย้าย\nเคส\nเคอร์ฟิว\nแคชเชียร์\nแคทวอล์ค\nแคนดิเดต\nแคนตาลูป\nแคนยอน\nแคนู\nแคป\nแคมป์\nแคมปัส\nแคมเปญ\nแคร์\nแครกเกอร์\nแคร็กเกอร์\nแครอท\nแคสต์\nแคสติง\nแคสติ้ง\nโค้ก\nโค้ช\nโคโยตี\nโคโยตี้\nโครนา\nโคอะล่า\nโคอาลา\nโคอาล่า\nไคลแมกซ์\nไคลแม็กซ์\nงั้น\nง่าว\nงี้\nเง็ง\nโง่เขลา\nไง\nจตุคาม\nจ๊อกกี้\nจอหงวน\nจังโก้\nจัมโบ้\nจ๊าบ\nจารกรรม\nจารชน\nจิ๊ก\nจิ๊กโก๋\nจิ๊กซอว์\nจิตพิสัย\nจิตเภท\nจีดีพี\nจึ๊ก\nจุ๊ย\nจูน\nจูเนียร์\nเจ๊\nเจได\nเจ็ต\nเจล\nเจ๊าะแจ๊ะ\nเจี๊ยว\nแจ็กเก็ต\nแจ๊กเก็ต\nแจ็กพอต\nแจ็กพ็อต\nแจ๊กพอต\nแจ๊กพ็อต\nแจม\nแจ๊ส\nโจ๋\nฉลุย\nเฉิ่ม\nชนะเลิศ\nช็อค\nช็อต\nช็อป\nช็อปปิ้ง\nช็อปเปอร์\nชะโนด\nชัตเตอร์\nชัวร์\nชาร์จ\nชาร์ต\nชาร์ป\nชินบัญชร\nชิฟฟอน\nชีส\nชีอะห์\nเช็ก\nเช็งเม้ง\nเชฟ\nเชลียร์\nเชอร์รี่\nแชเชือน\nแช่แข็ง\nแชมป์\nแชมปิยอง\nแชมเปญ\nแชมเปี้ยน\nแชมพู\nโชว์รูม\nโชห่วย\nใช้งาน\nไชน่า\nซ้อ\nซอมบี้\nซะ\nซังเต\nซันตาคลอส\nซัพพลาย\nซัพพลายเออร์\nซัมเมอร์\nซากุระ\nซาดิสต์\nซาดิสม์\nซาตาน\nซานตาคลอส\nซาฟารี\nซาบะ\nซามูไร\nซาร์\nซาร์ดีน\nซาเล้ง\nซิง\nซิ่ง\nซิงเกิล\nซิตี\nซิตี้\nซินโดรม\nซิม\nซิ้ม\nซิมโฟนี\nซิมโฟนี่\nซิลเวอร์\nซี้\nซี้ซั้ว\nซีดาน\nซีน\nซีนีเพล็กซ์\nซีเนียร์\nซีร็อกซ์\nซีรีส์\nซีเรียส\nซีอีโอ\nซื่อบื้อ\nซุนหนี่\nซุปเปอร์\nซูชิ\nซูเปอร์\nซูม\nซูโม่\nซูเอี๋ย\nซูฮก\nเซ็กซ์\nเซ็กซี่\nเซ็กส์\nเซนเซอร์\nเซ็นเซอร์\nเซนเตอร์\nเซ็นเตอร์\nเซ็นทรัล\nเซนส์\nเซ่นไหว้\nเซฟตี้\nเซรามิก\nเซลส์\nเซลส์แมน\nเซอร์\nเซอร์ไพรส์\nเซอร์วิส\nเซาท์\nเซี้ยว\nแซ็ก\nแซกโซโฟน\nแซ็กโซโฟน\nแซนด์วิช\nแซมบ้า\nแซลมอน\nแซว\nโซเชียล\nโซน\nโซนี่\nโซลาร์\nโซโล\nโซโล่\nญาณทัสสนะ\nดยุก\nดยุค\nดร็อป\nดรัมเมเยอร์\nดรามา\nดราม่า\nดอกเตอร์\nด็อกเตอร์\nดัมพ์\nดั๊มพ์\nดาวน์\nดิกชันนารี\nดิสเครดิต\nดีกรี\nดีเจ\nดีไซน์\nดีไซน์เนอร์\nดีไซเนอร์\nดีเบต\nดีพาร์ตเมนต์\nดีพาร์ตเมนท์\nดีพาร์ทเมนต์\nดีพาร์ทเมนท์\nดีมานด์\nดีล\nดีลเลอร์\nดีเลย์\nเดชานุภาพ\nเดบิต\nเดโม\nเดย์\nเด้อ\nเดอะ\nเด๊ะ\nเดี้ยง\nเดี๊ยะ\nแดนซ์\nแดนเซอร์\nแดรี่\nโดนัท\nโดมิโน\nโดรายากิ\nไดเอ็ต\nตถตา\nตนเอง\nตรวจทาน\nตรวจสอบ\nตอกย้ำ\nต๊อง\nต่อยอด\nต่อรอง\nตะหงิด\nตังค์\nตันเถียน\nตัวตน\nตัวเอง\nตาปรือ\nต้าอ่วย\nติงต๊อง\nติ๋ม\nติ่มซำ\nติว\nติวเตอร์\nตี๋\nตื้บ\nตุ๊ก\nตุ๊กตุ๊ก\nตุ๊ด\nตุ๋ย\nตู้เซฟ\nเต๊ะ\nเตี๊ยม\nแตงกวา\nแตงโม\nแต๋ว\nโต๋เต๋\nโต๊ะจีน\nไตรมาส\nถ่ายทำ\nถูกต้อง\nทงคัตสึ\nทริป\nทรู\nทอม\nท็อป\nทอร์นาโด\nทอล์ค\nทักซิโด\nทันตกรรม\nทันตแพทยศาสตร์\nทับซ้อน\nทัวร์\nทัวร์นาเมนต์\nทัวร์นาเมนท์\nทัวริสต์\nทาเลนต์\nทาวน์\nทาวน์เฮาส์\nทำงาน\nทิป\nทิพยสมบัติ\nทิวลิป\nทีรามิสุ\nทีวี\nทูน่า\nเท็กซ์\nเทค\nเทคโน\nเทคโนแครต\nเทควันโด\nเทป\nเทรด\nเทรนด์\nเทรนเนอร์\nเทรลเลอร์\nเทรลเล่อร์\nเทเลกราฟ\nเทวบัญชา\nเทวบุตร\nเทวา\nเทวาธิราช\nเทโวโรหนะ\nเทอร์โบ\nเที่ยงคืน\nเที่ยงวัน\nเทียมทาน\nแทกติค\nแทคติค\nแทงกั๊ก\nแทงโก้\nโทมาฮอก\nโทมาฮอว์ก\nโทมาฮอว์ค\nโทร\nโทรโข่ง\nไทม์\nไทยแลนด์\nไทเฮา\nธรรมา\nธรรมาภิบาล\nธัมโม\nธีม\nธุรกรรม\nธุหร่ำ\nเธค\nนพมาศ\nนรีแพทย์\nน็อก\nน็อค\nน้องใหม่\nนอมินี\nนอร์ท\nน่ะ\nนางแบบ\nนาฏยศาลา\nนายแบบ\nนายพราน\nนินจา\nนิรันดร์\nนิว\nนิวส์\nนู้ด\nเนอะ\nเนิร์สเซอรี\nเนิร์สเซอรี่\nเนี้ยบ\nโนติส\nไนท์\nไนน์\nบรรพชน\nบร็อกโคลี\nบร็อคโคลี\nบรา\nบริกร\nบริวเวอรี่ส์\nบลอนด์\nบลูเบอร์รี\nบลูเบอร์รี่\nบ๊วย\nบอกซ์\nบ็อกซ์\nบ๊อกซ์\nบอดี้\nบอนด์\nบ๊อบ\nบอมบ์\nบ๋อย\nบอยคอต\nบอยคอตต์\nบอร์ด\nบังเกอร์\nบัตเตอร์\nบัลลาสต์\nบัส\nบาบูน\nบาร์บีคิว\nบาร์บี้\nบาลานซ์\nบิ๊ก\nบิล\nบึม\nบึ้ม\nบุญคุณ\nบุ๋น\nบุปผา\nบู๊\nบูชิโด\nบูติก\nบูติค\nบูม\nเบเกอรี่\nเบญจมบพิตร\nเบตาดีน\nเบนโตะ\nเบนโล\nเบบี้\nเบลอ\nเบอร์เกอร์\nเบอร์รี\nเบิร์ด\nเบิร์น\nแบ็กโฮ\nแบคโฮ\nแบด\nแบต\nแบนเนอร์\nแบรนด์\nแบล็ก\nแบล็ค\nไบโอ\nโบกี้\nโบตั๋น\nโบ้ย\nโบรกเกอร์\nโบรชัวร์\nโบว์\nโบว์ลิ่ง\nไบเบิล\nปฏิสัมพันธ์\nป๊อก\nปอดแหก\nป๊อป\nป๋อหลอ\nปักขคณนา\nปัจเจกชน\nปัจฉิมนิเทศ\nป๊า\nป๋า\nป่าไม้\nปาร์ตี้\nปาสกาล\nปาสคาล\nปาสเตอร์\nปิกอัพ\nปิ๊ง\nปิโตรเคมี\nปิยมิตร\nปึ้ก\nปูอัด\nเปโซ\nเป็นไง\nเปปเปอร์มินต์\nเปเปอร์\nเปราะบาง\nเป๊ะ\nเป่ายิงฉุบ\nเป่ายิ้งฉุบ\nเปียโน\nแป้ก\nแป๋ว\nแป๊ะเจี๊ยะ\nโปร\nโปรเจกต์\nโปรเจ็กต์\nโปรเจกเตอร์\nโปรเจ็กเตอร์\nโปรเจคท์\nโปรเจ็คท์\nโปรดักชั่น\nโปรดิวเซอร์\nโปรโมชั่น\nโปรโมต\nโปรโมเตอร์\nโปรโมท\nโปลิศ\nโปสเตอร์\nผลไม้\nผลักดัน\nผ้าห่ม\nผิดพลาด\nผู้นำ\nแผดเผา\nเฝอ\nพงษ์\nพริตตี้\nพรีเซนต์\nพรีเซ็นเตอร์\nพรีเมียม\nพรีเมียร์\nพฤหัส\nพล็อต\nพลาซ่า\nพลานุภาพ\nพ่อค้า\nพอเพียง\nพะเรอ\nพันธกิจ\nพันธุวิศวกรรม\nพาร์\nพาร์ตเนอร์\nพาร์ทเนอร์\nพาวเวอร์\nพาสเจอร์ไรส์\nพาสตา\nพาสต้า\nพาสปอร์ต\nพาเหรด\nพิซซ่า\nพีเรียด\nพุดดิ้ง\nพุทธภูมิ\nพุทธศตวรรษ\nพุทโธ\nพูล\nเพทนาการ\nเพนกวิน\nเพนตากอน\nเพรส\nเพรียวบาง\nเพลซ\nเพลท\nเพลย์บอย\nเพียบแปร้\nเพียว\nเพาเวอร์\nแพกเกจ\nแพ็ค\nแพตเทิร์น\nแพทเทิร์น\nแพทยสภา\nแพนงเชิญ\nแพนดา\nแพนด้า\nแพลน\nโพลล์\nโพลารอยด์\nโพสต์\nไพลิน\nฟยอร์ด\nฟรังก์\nฟรุต\nฟลอร์\nฟลุก\nฟลุค\nฟลุต\nฟลุท\nฟอยล์\nฟอร์ม\nฟันด์\nฟาวล์\nฟาสต์ฟู้ด\nฟินิกซ์\nฟิวเจอร์\nฟีด\nฟีเวอร์\nฟุตบาท\nเฟรช\nเฟรชชี่\nเฟรม\nเฟมินิสต์\nเฟส\nเฟอร์นิเจอร์\nเฟอร์รี่\nเฟิร์ม\nเฟี้ยวฟ้าว\nแฟกซ์\nแฟ็กซ์\nแฟนซี\nแฟนตาซี\nแฟ้บ\nแฟร์\nแฟรนไชส์\nแฟรี\nแฟรี่\nแฟลช\nแฟล็ต\nโฟน\nโฟม\nโฟล์ค\nไฟต์\nไฟแนนซ์\nไฟลต์\nไฟลท์\nภควัทคีตา\nภควัมบดี\nภควัมปติ\nภคันทลาพาธ\nภววิสัย\nภารตะ\nภูมิทัศน์\nม้ง\nมวลชน\nมยุราภิรมย์\nมลภาวะ\nมหภาค\nมหาอุปราชา\nมอคคา\nมอคค่า\nมอนสเตอร์\nม็อบ\nมอบตัว\nมอยส์เจอไรเซอร์\nมอลล์\nมะกัน\nมั้ง\nมัฟฟิน\nมั้ย\nม้านั่ง\nมาเฟีย\nมาม่า\nมายองเนส\nมายาคติ\nมาร์ก\nมาร์เก็ต\nมาร์เก็ตติ้ง\nมาร์ค\nมาร์จิน\nมาร์ช\nมาร์ต\nมาร์ท\nมาราธอน\nม้าหินอ่อน\nมินต์\nมินท์\nมินิ\nมิลค์\nมิวสิค\nมิสซัง\nมิสไซล์\nมิสเตอร์\nมือถือ\nมุมมอง\nเมคอัพ\nเมจิก\nเมจิค\nเมทัล\nเมเปิล\nเมาท์\nเมี่ยงคำ\nแมกกาซีน\nแม็กกาซีน\nแมคเคอเรล\nแม่ค้า\nแมชชีน\nแมชีน\nแมนชั่น\nแมมบ้า\nแมมโบ้\nโมจิ\nโมเดล\nโมเดิร์น\nโมเต็ล\nโมโนเรล\nโมหจริต\nไมค์\nไมเกรน\nยนตรกรรม\nยอมรับ\nยะเยือก\nยังไง\nยากูซ่า\nยาวี\nยิม\nยิว\nยุวทูต\nยูโทเปีย\nยูโร\nยูวี\nเยน\nเยลลี่\nเย้ว\nเยอบีรา\nเยอบีร่า\nเยอร์บีรา\nเยอร์บีร่า\nแยมโรล\nโยเกิร์ต\nโยโย่\nรวมมิตร\nร็อค\nร็อคเก็ต\nรองรับ\nรอมฎอน\nรอยัลตี้\nระโงก\nรันเวย์\nรัม\nรากหญ้า\nราชบัณฑิตยสถาน\nราชานุญาต\nราชานุสาวรีย์\nรามเทพ\nรามาธิบดี\nรามายณะ\nราเม็ง\nราเมน\nรายชื่อ\nราสเบอร์รี\nริกเตอร์\nริคเตอร์\nรีไซเคิล\nรีดไถ\nรีทัช\nรีเทิร์น\nรีไทร์\nรีแบรนด์\nรีพอร์ท\nรีโมต\nรีโมท\nรีวิว\nรีสอร์ต\nรีสอร์ท\nรีเสิร์ช\nรุมบ้า\nรุสโซ\nรูบิก\nรูบิค\nเรซิน\nเรซิ่น\nเรดิโอ\nเรต\nเรตติ้ง\nแรงใจ\nแรงดูด\nแรงผลัก\nแรลลี\nแรลลี่\nโรดแมป\nโรเนียว\nโรแมนติก\nโรแมนติค\nโรล\nโรลออน\nไรเฟิล\nล็อกเกอร์\nลอจิสติกส์\nล็อต\nล็อบบี้\nลอร์ด\nล้มเหลว\nละติน\nละอ่อน\nลาซานญ่า\nลาติน\nลาเต้\nลานีญา\nลามะ\nลิมิต\nลิมูซีน\nลิสต์\nลีก\nลีด\nลีดเดอร์\nลีเมอร์\nลีลาวดี\nลุค\nลูกชาย\nลูกสาว\nเลกเชอร์\nเลคเชอร์\nเลดี้\nเลสเบี้ยน\nเลิฟ\nแลนด์\nแล็บ\nโลโก้\nโลชั่น\nไลท์\nไลน์\nไลฟ์\nวนาราม\nวราราม\nวโรกาส\nว้อดก้า\nวอเตอร์\nวอฟเฟิล\nว้อย\nวอร์ม\nวอร์มอัพ\nวอร์รูม\nวอล์ก\nวอล์ค\nวอลซ์\nวอลนัต\nวอลนัท\nวอลล์\nว่ะ\nวันเวย์\nวัสสา\nวาซาบิ\nวาทกรรม\nวาทะ\nวานิลลา\nวานิลา\nวาฟเฟิล\nวาริชศาสตร์\nว้าว\nวัคค์\nวัจนะ\nวาไรตี้\nวิก\nวิดีโอ\nวิทย์\nวิน\nวิป\nวิปปิ้ง\nวิภัชภาค\nวิว\nวิลล์\nวิลเลจ\nวีเจ\nวีซ่า\nวีดิทัศน์\nวีน\nวีไอพี\nวืด\nเวณิกา\nเวเฟอร์\nเวสต์\nเวอร์\nเวิร์ก\nเวิร์กช็อป\nเวิร์ค\nเวิร์ลด์\nเวิลด์\nแวมไพร์\nไวกิ้ง\nไวเบรเตอร์\nไวอะกร้า\nไวอากร้า\nศากยบุตร\nศิรินทร์\nศิลปวัฒนธรรม\nศิลปากร\nศิวิไลซ์\nศึกษาศาสตร์\nสกรัม\nสกาย\nสกู๊ป\nสเกตช์\nสเก็ตช์\nสคริปต์\nสแควร์\nสงบสุข\nสจ๊วต\nสตรอเบอร์รี\nสตรอเบอรี\nสตรอว์เบอร์รี\nสตริง\nสต็อก\nสต๊อก\nสต็อค\nสต๊อค\nสตอรี\nสตาร์\nสตาร์ท\nสติกเกอร์\nสติ๊กเกอร์\nสตีล\nสตูดิโอ\nสเตชัน\nสเตชั่น\nสเตเดียม\nสเตนเลส\nสเต็ป\nสเตย์\nสเตริโอ\nสเตอริโอ\nสแตนดาร์ด\nสแตนเลส\nสโตน\nสโตร์\nสไตรค์\nสไตล์\nสถาปัตย์\nสไนเปอร์\nสปอต\nสป็อต\nสปอนเซอร์\nสปอร์ต\nสปา\nสปาย\nสปิริต\nสเปก\nสเปค\nสไปเดอร์\nสมณพราหมณ์\nสมาพันธ์\nสมิติเวช\nสโรชา\nสลัม\nสแล็ก\nสโลแกน\nสโลว์\nสไลด์\nสวีท\nสหรัฐ\nสหัชญาณ\nสหัสวรรษ\nสะกอม\nสะเด่า\nสะบึม\nสะบึมส์\nสะออน\nสังโฆ\nสะโหลสะเหล\nสันทนาการ\nสัมนา\nสามช่า\nสามแยก\nสารขัณฑ์\nสี่แยก\nสึนามิ\nสุนทรีย์\nสุริยยาตร\nสุริยยาตร์\nสุหนี่\nเสกสรรค์\nเสพติด\nเสือโคร่ง\nหงวน\nหน่อมแน้ม\nหมวย\nหมั่นโถว\nหม่านโถว\nหมายปอง\nหมิง\nหยวน\nหลวงตา\nหลวงปู่\nหลวงพี่\nหล่อฮังก้วย\nหลินจือ\nห่วย\nเห็นด้วย\nเหมย\nเห่ย\nเหี่ยวย่น\nแหม็บ\nแหวว\nโหงว\nโหงวเฮ้ง\nโหลน\nโหลยโท่ย\nไหง\nไหร่\nอพาร์ตเมนต์\nอพาร์ตเมนท์\nอพาร์ทเมนต์\nอพาร์ทเมนท์\nอมาตยาธิปไตย\nอยุติธรรม\nอริยสงฆ์\nอ่วม\nอวอร์ด\nออกแบบ\nออดิชั่น\nออดิทอเรียม\nออเดอร์\nออโต้\nออทิสติก\nอ่อนด้อย\nออฟ\nออยล์\nออร์แกน\nออร์แกนิก\nออร์แกนิค\nออร์เดอร์\nออรัล\nออสซี่\nอะ\nอัตลักษณ์\nอัตวิสัย\nอันเดอร์\nอันตรกิริยา\nอัลตรา\nอัลไซเมอร์\nอัลบัม\nอัลบั้ม\nอัลมอนด์\nอาข่า\nอาโนเนะ\nอาฟเตอร์\nอาร์ติสต์\nอาร์พีจี\nอาว์\nอาสวะ\nอิกัวนา\nอินดอร์\nอินดัสตรีส์\nอินเตอร์\nอิ่มแปร้\nอิมพีเรียล\nอิเล็กทริก\nอิเล็กทริค\nอิเลียด\nอิสรชน\nอิเหนา\nอิออน\nอีแต๋น\nอีโรติก\nอีเวนท์\nอีสต์\nอีสเตอร์\nอึ๊บ\nอึ้ม\nอึ๋ม\nอึมครึม\nอุด้ง\nอุตสาหการ\nอุเทน\nอุปการคุณ\nอุปทาน\nอุปนายก\nอุปนายิกา\nอุปสงค์\nอุปัทวเหตุ\nอุรังคธาตุ\nอูคูเลเล่\nอู้ฟู่\nเอ๋\nเอ็กซ์โป\nเอ็กซ์เพรส\nเอ็กโซเซต์\nเอ็กโซเซ่ต์\nเอเซีย\nเอ็นจีโอ\nเอ็นเตอร์เทน\nเอนทรานซ์\nเอ็นทรานซ์\nเอฟเฟ็กต์\nเอเยนต์\nเอลนีโญ\nเอสเปรสโซ\nเอสเพรสโซ\nเอ๋อ\nเอาต์\nเอาท์\nเอาท์ดอร์\nเอ๊าะ\nแอ็กชั่น\nแอ็คชั่น\nแอคทีฟ\nแอดมิชชั่น\nแอดมิสชัน\nแอนด์\nแอ๊บแบ๊ว\nแอปเปิล\nแอปเปิ้ล\nแอปพริคอท\nแอพพริคอท\nแอพริคอต\nแอร์\nแอโรบิก\nแอโรบิค\nแอลมอนด์\nแอสเตอร์\nโอเค\nโอเปอเรเตอร์\nโอเปร่า\nโอเพ่น\nโอ้ย\nโอยัวะ\nโอรสาธิราช\nโอเลี้ยง\nโอวัลติน\nโอเวอร์\nไอซ์\nไอซียู\nไอดอล\nไอเดีย\nไอติม\nฮวงจุ้ย\nฮ่องเต้\nฮองเฮา\nฮอต\nฮ็อต\nฮอตดอก\nฮ็อตด็อก\nฮันนีมูน\nฮัม\nฮัลโลวีน\nฮัลโหล\nฮากกา\nฮาร์ด\nฮาราคีรี\nฮาลาล\nฮาโลวีน\nฮิ\nฮิต\nฮิบรู\nฮิปโป\nฮิปฮอป\nฮีโร่\nฮูลาฮูป\nฮูล่าฮูป\nเฮฟวี\nเฮฟวี่\nเฮอร์ริเคน\nเฮีย\nแฮนด์\nแฮปปี้\nแฮมเบอร์เกอร์\nโฮป\nโฮม\nโฮลดิงส์\nโฮลวีต\nโฮสเตส\nไฮกุ\nไฮแจ็ค\nไฮโซ\nไฮเทค\nไฮบริด\nไฮเปอร์\nไฮไลต์\nไฮไลท์\nไฮเวย์\nไฮสคูล\nไฮเอนด์\n\nกรีซ\nกัมพูชา\nกัวเตมาลา\nกาตาร์\nกานา\nกาบอง\nกายอานา\nกินี\nเกรนาดีนส์\nเกรเนดา\nเกาหลี\nแกมเบีย\nโกตดิวัวร์\nคองโก\nคอโมโรส\nคอสตาริกา\nคาซัคสถาน\nคิตส์\nคิริบาตี\nคิริบาส\nคิวบา\nคีร์กีซสถาน\nคูเวต\nเคนยา\nเคปเวิร์ด\nเคย์แมน\nแคนาดา\nแคเมอรูน\nโครเอเชีย\nโคลอมเบีย\nจอร์เจีย\nจอร์แดน\nจาเมกา\nจิบูตี\nจีน\nชาด\nชิลี\nเช็ก\nซามัว\nซาอุ\nซิมบับเว\nซีเรีย\nซูดาน\nซูรินาเม\nเซนต์\nเซเนกัล\nเซอร์เบีย\nเซาตูเม\nเซียร์รา\nแซมเบีย\nโซมาเลีย\nโซเวียต\nไซปรัส\nญี่ปุ่น\nดารุสซาลาม\nเดนมาร์ก\nโดมินิกัน\nโดมินิกา\nตรินิแดด\nตองกา\nติมอร์\nตุรกี\nตูนิเซีย\nเติร์กเมนิสถาน\nโตโก\nโตเบโก\nไต้หวัน\nทาจิกิสถาน\nแทนซาเนีย\nนอร์เวย์\nนามิเบีย\nนาอูรู\nนิการากัว\nนิวซีแลนด์\nเนเธอร์แลนด์\nเนปาล\nเนวิส\nไนจีเรีย\nไนเจอร์\nบราซิล\nบริติช\nบริเตน\nบรูไน\nบอตสวานา\nบอสเนีย\nบังกลาเทศ\nบังคลาเทศ\nบัลแกเรีย\nบาร์บูดา\nบาร์เบโดส\nบาห์เรน\nบาฮามาส\nบิสเซา\nบุรุนดี\nบูร์กินาฟาโซ\nเบนิน\nเบลเยียม\nเบลารุส\nเบลีซ\nเบอร์มิวดา\nโบลิเวีย\nปรินซิปี\nปากีสถาน\nปานามา\nปาปัวนิวกินี\nปารากวัย\nปาเลสไตน์\nปาเลา\nเปรู\nเปอร์เซีย\nเปอร์โตริโก\nโปรตุเกส\nโปแลนด์\nฝรั่งเศส\nพม่า\nฟิจิ\nฟินแลนด์\nฟิลิปปินส์\nเฟรนช์\nภูฏาน\nภูฐาน\nมองโกเลีย\nมอนเตเนโกร\nมอนแทนา\nมอริเชียส\nมอริเตเนีย\nมอลโดวา\nมอลตา\nมัลดีฟส์\nมาเก๊า\nมาซิโดเนีย\nมาดากัสการ์\nมาร์แชลล์\nมาลาวี\nมาลี\nมาเลเซีย\nเม็กซิโก\nเมียนมาร์\nโมซัมบิก\nโมนาโก\nโมนาโค\nโมร็อกโก\nไมโครนีเซีย\nยูกันดา\nยูโกสลาเวีย\nยูเครน\nเยเมน\nเยอรมนี\nรวันดา\nรัสเซีย\nโรมาเนีย\nลักเซมเบิร์ก\nลัตเวีย\nลาว\nลิกเตนสไตน์\nลิทัวเนีย\nลิเบีย\nลีโอน\nลูเซีย\nเลโซโท\nเลบานอน\nเลสเต\nไลบีเรีย\nวาติกัน\nวานูอาตู\nวินเซนต์\nเวเนซุเอลา\nเวียดนาม\nศรีลังกา\nสเปน\nสโลวะเกีย\nสโลวัก\nสโลวีเนีย\nสวาซิแลนด์\nสวิตเซอร์แลนด์\nสวีเดน\nสหรัฐ\nสหราชอาณาจักร\nสิกขิม\nสิงคโปร์\nอเมริกา\nออสเตรเลีย\nออสเตรีย\nอันดอร์รา\nอัฟกานิสถาน\nอาเซอร์ไบจาน\nอาร์เจนตินา\nอาร์เมเนีย\nอาระเบีย\nอิเควทอเรียล\nอิตาลี\nอินเดีย\nอินโดนีเซีย\nอิรัก\nอิสราเอล\nอิหร่าน\nอียิปต์\nอุซเบกิสถาน\nอุรุกวัย\nเอกวาดอร์\nเอธิโอเปีย\nเอมิเรตส์\nเอริเทรีย\nเอลซัลวาดอร์\nเอสโตเนีย\nแองโกลา\nแอนติกา\nแอลจีเรีย\nแอลเบเนีย\nโอมาน\nไอซ์แลนด์\nไอร์แลนด์\nฮ่องกง\nฮอนดูรัส\nฮังการี\nเฮติ\nเฮอร์เซโกวีนา\n\nกระบี่\nกรุงเทพ\nกาญจนบุรี\nกาฬสินธุ์\nกำแพงเพชร\nขอนแก่น\nจันทบุรี\nฉะเชิงเทรา\nชลบุรี\nชัยนาท\nชัยภูมิ\nชุมพร\nเชียงราย\nเชียงใหม่\nตรัง\nตราด\nตาก\nนครนายก\nนครปฐม\nนครพนม\nนครราชสีมา\nนครศรีธรรมราช\nนครสวรรค์\nนนทบุรี\nนราธิวาส\nน่าน\nบึงกาฬ\nบุรีรัมย์\nปทุมธานี\nประจวบคีรีขันธ์\nปราจีนบุรี\nปัตตานี\nพะเยา\nพังงา\nพัทลุง\nพิจิตร\nพิษณุโลก\nเพชรบุรี\nเพชรบูรณ์\nแพร่\nภูเก็ต\nมหาสารคาม\nมุกดาหาร\nแม่ฮ่องสอน\nยโสธร\nยะลา\nร้อยเอ็ด\nระนอง\nระยอง\nราชบุรี\nลพบุรี\nลำปาง\nลำพูน\nเลย\nศรีสะเกษ\nสกลนคร\nสงขลา\nสตูล\nสมุทรปราการ\nสมุทรสงคราม\nสมุทรสาคร\nสระแก้ว\nสระบุรี\nสิงห์บุรี\nสุโขทัย\nสุพรรณบุรี\nสุราษฎร์\nสุราษฎร์ธานี\nสุรินทร์\nหนองคาย\nหนองบัวลำภู\nอยุธยา\nอ่างทอง\nอำนาจเจริญ\nอุดรธานี\nอุตรดิตถ์\nอุทัยธานี\nอุบลราชธานี\nกันทรลักษ์\nจตุจักร\nไชยา\nซีคอน\nดอนเมือง\nถลาง\nไทรโยค\nธนบุรี\nธัญบุรี\nบางกอก\nบางปะกง\nบางระจัน\nปะทิว\nปาย\nพญาไท\nพัฒน์พงษ์\nพัทยา\nพารากอน\nภูมิซรอล\nรัตนาธิเบศร์\nรังสิต\nลันตา\nลาดพร้าว\nวโรรส\nวิภาวดี\nสตึก\nสมุย\nสัตหีบ\nสิมิลัน\nสุขุมวิท\nสุไหง\nเสลภูมิ\nอังรีดูนังต์\nอ่างขาง\nอินทนนท์\nเอ็มโพเรียม\n\nคิวชู\nแคริบเบียน\nแคสเปียน\nดานูบ\nตะนาวศรี\nนอร์วีเจียน\nนิโคบาร์\nเนรัญชรา\nไนล์\nบอร์เนียว\nบอลติก\nเบงกอล\nปิง\nแปซิฟิก\nมะละกา\nมินดาเนา\nมิสซิสซิปปี\nเมดิเตอร์เรเนียน\nเมโสโปเตเมีย\nยมุนา\nยุโรป\nยูเรเชีย\nยูเรเซีย\nแยงซี\nแยงซีเกียง\nสแกนดิเนเวีย\nสะโตง\nสาละวิน\nสุมาตรา\nสุเอซ\nอะเมซอน\nอันดามัน\nอัลไต\nอาร์กติก\nอาหรับ\nอินโดจีน\nอิรวดี\nอิระวดี\nอีเจียน\nอุษาคเณย์\nอูราล\nเอเชีย\nเอเดรียติก\nเอเวอเรสต์\nแอตแลนติก\nแอนตาร์กติก\nแอนตาร์กติกา\nแอฟริกา\nโอลิมปัส\nไอโอเนียน\nฮวงโห\nฮอกไกโด\nฮอนชู\n\nกบิลพัสดุ์\nกุสินารา\nโกลิยะ\nโกสัมพี\nโคตรบอง\nโคตรบูรณ์\nตองอู\nทรอย\nทวารวดี\nทวาราวดี\nเทวทหะ\nไทรบุรี\nนาลันทา\nไบแซนไทน์\nปรัสเซีย\nปัลลวะ\nปาฏลีบุตร\nพุทธคยา\nมถุรา\nมายัน\nมิถิลา\nราชคฤห์\nล้านช้าง\nล้านนา\nลุมพินี\nวัชชี\nเวสาลี\nสารนาถ\nสาวัตถี\nหริภุญชัย\nอโยธยา\nออตโตมัน\nอังวะ\nอินทปัตถ์\nอุชเชนี\n\nกราฟิก\nกราฟิกส์\nกราฟิค\nกริด\nกิกะไบต์\nกูเกิล\nกูเกิ้ล\nเกตเวย์\nโกลบอล\nคลัสเตอร์\nคลาส\nคลิก\nคลิปอาร์ต\nคอนโซล\nคอนเทนต์\nคอมพิวติ้ง\nคอมไพล์\nคอมไพเลอร์\nคอมมูนิเคชั่น\nคอร์\nคีย์\nคีย์บอร์ด\nเครือข่าย\nเคอร์เซอร์\nเคอร์เนล\nแคช\nแคมฟรอก\nแคมฟร็อก\nแคร็ก\nโค้ด\nจาวา\nจีพีเอส\nชิป\nชิพ\nเชลล์\nแช็ต\nแชนเนล\nแชนแนล\nซ็อกเก็ต\nซอฟต์แวร์\nซอฟท์แวร์\nซอร์ส\nซัพพอร์ต\nซัพพอร์ท\nซีดี\nซีดีรอม\nซีเนอร์\nเซิร์ฟเวอร์\nโซลูชัน\nโซลูชั่น\nไซต์\nไซเบอร์\nทรานแซกชัน\nทรานแซกชั่น\nทรานแซ็กชัน\nทรานแซ็กชั่น\nทรานแซคชัน\nทรานแซคชั่น\nทรานแซ็คชัน\nทรานแซ็คชั่น\nทวิตเตอร์\nทวีต\nทัชแพด\nเทมเพลต\nเทอร์มินัล\nแท็ก\nแท็บ\nแทบเล็ต\nโทรจัน\nเน็ต\nเน็ตบุ๊ก\nเน็ตบุค\nเน็ตบุ๊ค\nเน็ตเวิร์ก\nเน็ตเวิร์ค\nโน้ตบุ๊ก\nโน้ตบุค\nโน้ตบุ๊ค\nดอส\nดาวน์เกรด\nดาวน์โหลด\nดิจิตอล\nดิจิทัล\nดีบั๊ก\nดีวีดี\nดีไวซ์\nเดเบียน\nเดลไฟ\nเดสก์ท็อป\nโดเมน\nไดรว์\nไดรเวอร์\nไดเรกทอรี\nไดโอด\nเทเลคอม\nบล็อกเกอร์\nบรอดแบนด์\nบราวเซอร์\nบลูทูท\nบลูทูธ\nบลูเรย์\nบั๊ก\nบัฟเฟอร์\nบิต\nบิท\nบูต\nเบราว์เซอร์\nแบนด์วิดท์\nไบต์\nไบนารี\nโปรแกรมเมอร์\nโปรเซส\nโปรเซสเซอร์\nโปรโตคอล\nพร็อกซี\nพอร์ต\nพอร์ท\nพาเนล\nพาร์ทิชัน\nพารามิเตอร์\nพาสเวิร์ด\nพิกเซล\nเพจ\nเพจเจอร์\nแพกเก็ต\nแพตช์\nแพลตฟอร์ม\nโพรเซส\nโพรเซสเซอร์\nโพรโทคอล\nไพธอน\nฟล็อปส์\nฟอนต์\nฟอร์แมต\nฟอร์เวิร์ด\nฟอรัม\nฟีเจอร์\nเฟซบุ๊ก\nเฟิร์มแวร์\nแฟล็ก\nโฟลเดอร์\nไฟร์ฟอกซ์\nไฟร์วอลล์\nไฟล์\nมอดูล\nมอนิเตอร์\nมัลติ\nมัลติทัช\nมัลติเพล็กซ์\nมัลแวร์\nมาสเตอร์\nมีเดีย\nเมนู\nเมมโมรี\nเมล\nเมาส์\nแมค\nโมดูล\nโมเด็ม\nโมบาย\nโมบายล์\nโมไบล์\nไมโครซอฟท์\nยูนิกซ์\nยูนิโคด\nยูนิโค้ด\nริงโทน\nรีเฟรช\nรีเลย์\nเราเตอร์\nเรียลไทม์\nลิงก์\nลินุกซ์\nลีนุกซ์\nลูป\nเลเยอร์\nแล็ปท็อป\nไลเซนส์\nไลบรารี\nวิกิ\nวิกิพีเดีย\nวินโดวส์\nวินโดว์ส\nเว็บ\nเวอร์ชวล\nเวอร์ชัน\nเวอร์ชั่น\nเวิร์กสเตชัน\nเวิร์กสเตชั่น\nเวิร์คสเตชัน\nเวิร์คสเตชั่น\nเวิร์ด\nเวิร์ม\nไวแมกซ์\nสกรีน\nสแกน\nสแกนเนอร์\nสแต็ก\nสนิฟเฟอร์\nสปายแวร์\nสเปซ\nสแปม\nสมาร์ท\nสล็อต\nเสิร์ช\nโหลด\nออนไลน์\nออปติก\nออปติคอล\nออปติคัล\nออฟไลน์\nออราเคิล\nอัพเกรด\nอัพเดต\nอัพโหลด\nอัปเกรด\nอัปเดต\nอัปโหลด\nอัลกอริทึม\nอาร์กิวเมนต์\nอินเตอร์เน็ต\nอินทิเกรเตอร์\nอินเทอร์เน็ต\nอินเทอร์เฟซ\nอินเทล\nอินพุต\nอินพุท\nอีเมล\nอีเมล์\nอูบุนตู\nอูบันตู\nเอนจิน\nเอ็นจิน\nเอาต์พุต\nเอาต์พุท\nเอาท์พุต\nเอาท์พุท\nแอนะล็อก\nแอนิเมชัน\nแอนิเมชั่น\nแอปพลิเคชัน\nแอปพลิเคชั่น\nแอพพลิเคชัน\nแอพพลิเคชั่น\nแอสเซมบลี\nแอสเซมเบลอร์\nโอเพน\nไอคอน\nไอซี\nไอพอด\nไอพ็อด\nไอแพด\nไอโฟน\nฮับ\nฮาร์ดดิสก์\nฮาร์ดแวร์\nแฮกเกอร์\nแฮ็กเกอร์\nแฮนด์เฮลด์\nโฮสต์\n\nกรีก\nกัณณาฑ\nกัศมีรี\nคันจิ\nคาตาคานะ\nคุชราตี\nคุรุมุขี\nซีริลลิก\nซูลู\nเซลติก\nเซิร์บ\nตากาล็อก\nเตลุคู\nเติร์ก\nทราวิฑ\nเบงกาลี\nปัญจาบี\nพินอิน\nมลยาฬัม\nมองโกล\nมาราฐี\nมาเลย์\nเม็กซิกัน\nแมนจู\nแมนดาริน\nไมถิลี\nเยอรมัน\nรัสเซียน\nสวาฮิลี\nสวิส\nสินธี\nอูรดู\nอัสสมี\nอารบิก\nอิตาเลียน\nอุยกูร์\nแอฟริกัน\nโอริยา\nไอริช\nฮันกึล\nฮินดี\nฮิรางานะ\nฮีบรู\n\nกรีนพีซ\nกรือเซะ\nกวนอิม\nกวนอู\nกัดดาฟี\nกัลยาณวัตร\nกัสสปะ\nกาลิเลโอ\nกินเนส\nกุมภกรรณ\nกูเตนเบิร์ก\nเกตส์\nเกษมณี\nโกณฑัญญะ\nขงเบ้ง\nคริสโตเฟอร์\nคองคอร์ด\nคอลเกต\nคานธี\nคาเบรียล\nคาร์ฟูร์\nคาร์สัน\nคาราบาว\nคาสิโอ\nคิริน\nคุนลุ้น\nคูโบต้า\nเครมลิน\nแคทรีนา\nโคตมะ\nโคตมี\nโคลัมบัส\nไคฟง\nไครสเลอร์\nง้อไบ๊\nจตุพร\nจ็อบส์\nจอห์น\nจิ้น\nจิม\nจิ๋ม\nจิว\nจุฬาภรณ์\nจุฬาลงกรณ์\nเจมส์\nแจ็กสัน\nโจเซฟ\nโจว\nชมัยมรุเชฐ\nชมัยมรุเชษฐ์\nชเวดากอง\nชาร์ลส์\nชินราช\nชินวัตร\nชุนชิว\nเช็ง\nเชตวัน\nเชฟรอน\nเชฟโรเลต\nเชลซี\nไชยานุชิต\nซ่ง\nซังฮี้\nซัดดัม\nซันซิล\nซัมซุง\nซัวเจ๋ง\nซินหัว\nซีซาร์\nซีแพค\nซูซาน\nซูซูกิ\nซูบารุ\nเซ็นทารา\nเซเวน\nเซเว่น\nโซฟิเทล\nโซยุซ\nโซยูซ\nณัฐวุฒิ\nดาร์ลี่\nดาวโจนส์\nดิสนีย์\nดีแทค\nดูปองท์\nเดโมแครต\nเดลล์\nเดลินิวส์\nเดวิด\nแดวู\nโดนัลด์\nโดราเอมอน\nโดเรมอน\nต๋อง\nตั๊กม้อ\nตากสิน\nตาเมือน\nตาลีบัน\nตูน\nเตมีย์\nโต๋\nโตชิบา\nโตโยต้า\nถังซัมจั๋ง\nถังซำจั๋ง\nทรพา\nทราเวล\nทรูมูฟ\nทีปังกร\nเทปโก\nเทพรัตน\nเทวทัต\nเทสโก้\nโทมัส\nไททานิก\nไททานิค\nไทยรัฐ\nธีออส\nนครินทรา\nนโปเลียน\nนพดล\nนราดูร\nนเรนทร\nนอสตราดามุส\nนาซา\nนาซ่า\nนาซี\nนาโต\nนาโต้\nนาลแก\nนิคอน\nนิโคลัส\nนิด้า\nนินเทนโด\nนิปปอน\nนิวตัน\nนิสสัน\nเนคเทค\nเนชั่น\nเนชันแนล\nเนชั่นแนล\nเนวิน\nเนสเล่\nเนสาด\nแนท\nแนสแดค\nโนเกีย\nโนเบล\nโนเวลล์\nโนโวเทล\nไนเม็กซ์\nบรอดเวย์\nบรัดเลย์\nบรู๊ซ\nบัลเมอร์\nบารัก\nบารัค\nบู๊ตึ๊ง\nเบญกาย\nเบนซ์\nเบ็นซ์\nเบนจามิน\nโบตัน\nไบโอเทค\nประชาธิปัตย์\nปวีณา\nปอเต็กตึ๊ง\nปอเต๊กตึ๊ง\nป่อเต็กตึ๊ง\nปัตตะโชติ\nปารุสก์\nปีเตอร์\nปูติน\nเป๊ปซี่\nเป้ย\nเปอร์โยต์\nเปาบุ้นจิ้น\nโปเกมอน\nโป๊ยก่าย\nพรหมทัต\nพลาโต\nพอลล่า\nพานาโซนิค\nพานาโซนิก\nพิทยานุกูล\nพิมพิสาร\nเพนแทกซ์\nเพลโต\nไพโอเนียร์\nฟรอยด์\nฟรังซิส\nฟรานซิส\nฟลอเรนซ์\nฟอร์ด\nฟิลิปส์\nฟูจิ\nแฟซ่า\nโฟร์โมสต์\nภูมิพล\nภูริทัต\nมงฟอร์ต\nมณโฑ\nมติชน\nมหิตลาธิเบศร\nมโหสถ\nมัจฉานุ\nมาร์กาเร็ต\nมาร์ติน\nมาสด้า\nมิตซูบิชิ\nมิราเคิล\nมุสโสลินี\nเม้ง\nเมจิ\nเมอร์ซีเดส\nเมอร์เซเดส\nแมกซ์เวลล์\nแมกไซไซ\nแมคอินทอช\nแมชีนเนอรี่\nโมคคัลลานะ\nโมโตโรลา\nโมโตโรล่า\nโมเนีย\nไมเคิล\nไมยราพณ์\nยโสธรา\nยะโฮวา\nยะโฮวาห์\nยามาฮ่า\nยาเวห์\nยาฮู\nยูนิเซฟ\nยูเนสโก\nยูไล\nเยโฮวาห์\nรอยเตอร์\nรอยัล\nรัชดา\nรัสปูติน\nราฟาเอล\nรามาวตาร\nราเมศวร\nราหุล\nริชาร์ด\nรีพับลิกัน\nรูนีย์\nเรนโบว์\nแรมโบ้\nโรตารี\nโรนัลโด\nโรนัลโด้\nโรบินสัน\nโรเบิร์ต\nล็อกซเล่ย์\nลิงคอล์น\nลิจฉวี\nลิไท\nลิไทย\nลินคอล์น\nลิเวอร์พูล\nเลโนโว\nเลียดก๊ก\nโลตัส\nวชิราลงกรณ์\nวลาดิเมียร์\nวอลล์สตรีท\nวาเลนไทน์\nวิกตอเรีย\nวิทยานุสรณ์\nวิทยายน\nวิมเบิลดัน\nวิลเลียม\nวีระ\nวุฒิชัย\nเวียดกง\nไวตามิลค์\nศกุนตลา\nศรีวิชัย\nศิริพงษ์\nศิริราช\nศุภชลาศัย\nสดกก๊อกธม\nสดายุ\nสตาลิน\nสตีฟ\nสแตนฟอร์ด\nสวรินทิรา\nสังกัจจายน์\nสาทิตย์\nสารีบุตร\nสิริกิติ์\nสิรินธร\nสิหิงค์\nสีวลี\nสีหนุ\nสีหมุนี\nสีหโมนี\nสุครีพ\nสุทโธทนะ\nสุเทพ\nสุนทราภรณ์\nสุนีย์\nสุรนารี\nสุรยุทธ์\nสุริยาสน์\nเส้าหลิน\nโสกราตีส\nโสภิต\nหนุมาน\nหลินฮุ่ย\nหลุยส์\nเห้งเจีย\nไหหม่า\nองคต\nองคุลิมาล\nอชาตศัตรู\nอดุลยเดช\nอพอลโล\nอริสโตเติล\nอริสมันต์\nอลิซาเบธ\nอ๋อม\nออร์คิด\nออสการ์\nอะพอลโล\nอับราฮัม\nอั้ม\nอัลกออิดะห์\nอัลคาเทล\nอัลจาซีราห์\nอัลเฟรด\nอัลเลาะห์\nอัสซุส\nอัสสชิ\nอัสสัมชัญ\nอาเซม\nอาเซ็ม\nอาเซียน\nอาฟต้า\nอาร์เซนอล\nอินทรชิต\nอินทราทิตย์\nอีซูซุ\nอีเลฟเวน\nอีเลฟเว่น\nอุณรุท\nอุบลรัตน์\nอุบาลี\nอุ๋ย\nเอกทัศน์\nเอเซอร์\nเอ็ดเวิร์ด\nเอดิสัน\nเอแบค\nเอลิซาเบธ\nเอสพลานาด\nเอสพลานาร์ด\nแอคคอร์\nแอคคอร์ด\nแองเจลิน่า\nแอตแลนติส\nแอน\nแอ๋ม\nแอมบาสซาเดอร์\nแอมบาสเดอร์\nแอมเวย์\nแอ๋ว\nโอดีสซีย์\nโอเดียน\nโอบามา\nโอรสาราม\nโอลิมเปีย\nโออิชิ\nไอน์สไตน์\nฮอนด้า\nฮอปกินส์\nฮอลลีวูด\nฮอลลีวู้ด\nฮานามิ\nฮามาส\nฮิตเลอร์\nฮิตาชิ\nฮุนเซน\nฮุนเซ็น\nฮุนได\nฮุสเซ็น\nเฮนรี\nเฮนรี่\nเฮเลน\nโฮจิมินห์\nโฮปเวลล์\nโฮเมอร์\n\nกลีเซอรีน\nกำทอน\nแกนีมีด\nครอส\nคริสตัล\nคลอโรพลาสต์\nคลอไรด์\nควอนตัม\nคอนดักเตอร์\nคอปเปอร์\nคอลลาเจน\nคอเลสเตอรอล\nคอสมิก\nคูลอมบ์\nเคอราติน\nแคโรทีน\nแคสสินี\nโครมาโทกราฟี\nไคโตซาน\nจีโนม\nจุลชีววิทยา\nชิคุนกุนยา\nซัลฟิวริก\nซัลเฟต\nซัลไฟด์\nซิงค์\nซิริอุส\nซิลิกา\nซิลิเกต\nซิลิโคน\nซีเทน\nซีเวิร์ต\nเซ็กเตอร์\nเซ็กเมนต์\nเซมิ\nโซนาร์\nไซบอร์ก\nดอปเปลอร์\nดอปเพลอร์\nไดนามิก\nไดนามิกส์\nไดนามิค\nไดนามิคส์\nไดออกไซด์\nทรานส์\nทามิฟลู\nเทฟลอน\nเทสโทสเตอโรน\nเทอร์โม\nแทนนิน\nไททัน\nไทฟอยด์\nไทรอยด์\nธาลัสซีเมีย\nเนกาตีฟ\nโนวา\nบอแรกซ์\nโบทอกซ์\nโบท็อกซ์\nไบโอติน\nปฏิยานุพันธ์\nโปรเจสเตอโรน\nพอลิเมอร์\nพันธุศาสตร์\nพัลซาร์\nพาร์กินสัน\nพาราเซตามอล\nพาราโบลา\nเพอร์ออกไซด์\nโพรเจสเทอโรน\nโพลาไรซ์\nโพลิเมอร์\nโพลีเอทิลีน\nไพรเมต\nฟลาโวนอยด์\nฟลูออเรสเซนซ์\nฟลูออไรด์\nฟอสซิล\nฟิชชัน\nฟิวชัน\nฟีโรโมน\nไฟเบอร์\nมอนอกไซด์\nมิราจ\nเมตริกซ์\nเมทริกซ์\nเมลานิน\nเมลามีน\nโมเมนตัม\nไมโตคอนเดรีย\nไมโทคอนเดรีย\nยีสต์\nยูริก\nยูเรีย\nรูมาตอยด์\nวีก้า\nเวกเตอร์\nเวก้า\nเวสิเคิล\nโวลต์\nสเกล\nสเกลาร์\nสเต็ม\nสเตียรอยด์\nสปีชีส์\nสเปิร์ม\nสัมพัทธภาพ\nสุริยจักรวาล\nออกเทน\nออโรรา\nออโรร่า\nอะคริลิก\nอะครีลิก\nอะซีติก\nอะซีโตน\nอะมิโน\nอะลูมินา\nอันโดรเมดา\nอัลคาไลน์\nอัลตราซาวด์\nอัลตราซาวนด์\nอัลลอยด์\nอินทิกรัล\nอินทิเกรต\nอีโบลา\nอีโบล่า\nเอ็กซ์โพเนนเชียล\nเอทานอล\nเอทิลีน\nเอนโทรปี\nเอสเตอร์\nเอสโตรเจน\nเอสโทรเจน\nแอนดรอยด์\nแอนแทร็กซ์\nแอมพลิจูด\nแอมโมเนียม\nแอลกอฮอลิซึม\nแอสพาร์แตม\nโอเซลทามิเวียร์\nฮับเบิล\nฮิวมัส\nไฮดรอกไซด์\nไฮดรอลิก\nไฮโดรลิก\nไฮเพอร์โบลา\n\nกงเต็ก\nกฎุมพี\nกฏ\nกฏหมาย\nกบฎ\nกราไฟต์\nก๊อปปี้\nกะทะ\nกังวาล\nกุฎฐัง\nกุฏุมพี\nฃวด\nคฑา\nคลินิค\nคลีนิก\nคลีนิค\nคาทอลิค\nคึ่นฉ่าย\nแคตตาล็อก\nโควต้า\nฅน\nจุมพฎ\nช็อคโกแลต\nแซ่ด\nดัทช์\nทนง\nทรมาณ\nทราก\nทะแยง\nทิฏฐิ\nบล็อค\nบ๊องแบ๊ว\nบัลเล่ต์\nเบรค\nแบงค์\nปรากฎ\nปัคคหะ\nปาฏิโมกข์\nปิติ\nปิรามิด\nโปรเตสแตนท์\nพนิช\nพยักเพยิด\nพริ้ว\nพลูโตเนียม\nพากษ์\nเฟิร์น\nยากี้\nเยภุยยสิกา\nรุสเซีย\nฤาษี\nล็อค\nล็อคเกอร์\nวันทยาหัตถ์\nวานิช\nวิญญาน\nวิศิษฐ์\nศรีษะ\nสเปกโทรสโคป\nสฤษฎ์\nสลิ่ม\nสัตตสดก\nสาราณียากร\nสุกี้\nสุกี้ยากี้\nสูญญากาศ\nหยอมแหยม\nหยอย\nหล่ะ\nอะดรีนาลีน\nอะหลั่ย\nอัตคัต\nอัฟริกา\nอานิสงค์\nอาฟริกา\nอิริยาบท\nอิเลคโทรนิคส์\nอีรุงตุงนัง\nอุตรายัน\nอุลตรา\nอุลตร้า\nโอกาศ\n\nกกหู\nกงการ\nกงจักร\nกฎเกณฑ์\nกฎบัตร\nกฎหมาย\nกฎหมู่\nกดขี่\nกดดัน\nก้นกบ\nก้นบึ้ง\nก้นปล่อง\nกนิษฐภคินี\nกนิษฐภาดา\nกรงเล็บ\nกรมการ\nกรมท่า\nกรมธรรม์\nกรมนา\nกรมวัง\nกรรมกร\nกรรมการ\nกรรมฐาน\nกรรมบถ\nกรรมพันธุ์\nกรรมวิธี\nกรรมสิทธิ์\nกระจกเงา\nกระจกตา\nกระจกนูน\nกระจกเว้า\nกระจอกชวา\nกระจอกเทศ\nกระจ้อยร่อย\nกระจับบก\nกระจับปิ้ง\nกระจับปี่\nกระโชกโฮกฮาก\nกระดานดำ\nกระดานหก\nกระดาษแก้ว\nกระดาษไข\nกระดาษทราย\nกระดาษสา\nกระดูกงู\nกระทาชาย\nกระเท่เร่\nกระบวนการ\nกระบองเพชร\nกระผีกริ้น\nกระยาทิพย์\nกระยาสารท\nกระยาหาร\nกระสอบทราย\nกระสุนปืน\nกระแสจิต\nกระแสน้ำ\nกระแสลม\nกรับคู่\nกรับพวง\nกรับเสภา\nกราดเกรี้ยว\nกราวรูด\nกริ่งเกรง\nกรีฑาสถาน\nกรีดกราย\nกรี๊ดกร๊าด\nกลไก\nกลบท\nกลเม็ด\nกลยุทธ์\nกลวิธี\nกลศาสตร์\nกลอักษร\nกลบเกลื่อน\nกลมกล่อม\nกลมกลืน\nกลมเกลียว\nกล้วยแขก\nกล้วยไม้\nกล่องเสียง\nกล่อมเกลา\nกล่อมเกลี้ยง\nกลัดกลุ้ม\nกลัดมัน\nกลั่นกรอง\nกลั่นแกล้ง\nกลับกลอก\nกลางคน\nกลางคัน\nกลางค่ำ\nกลางคืน\nกลางแจ้ง\nกลางแปลง\nกลางวัน\nกลาดเกลื่อน\nกล่าวขวัญ\nกล่าวโทษ\nกล่าวหา\nกล้ำกราย\nกล้ำกลืน\nกลิ้งกลอก\nกลิ้งเกลือก\nกลิ่นอาย\nกลียุค\nกวดขัน\nกวัดแกว่ง\nกวัดไกว\nกวีนิพนธ์\nก่อกวน\nก่อการ\nก่อตั้ง\nก่อสร้าง\nก่อหวอด\nก้อร่อก้อติก\nกองกลาง\nกองเกิน\nกองโจร\nกองทัพ\nกองทุน\nกองพล\nกองพัน\nกองฟอน\nกองร้อย\nกองหนุน\nกอบโกย\nกะเกณฑ์\nกะบังลม\nกักกัน\nกักขัง\nกักตัว\nกักตุน\nกัณฑ์เทศน์\nกัดฟัน\nกันชน\nกันท่า\nกันสาด\nกันเอง\nกับแกล้ม\nกับข้าว\nกับระเบิด\nกากเพชร\nกากหมู\nกาชาด\nกาญจนาภิเษก\nก้านคอ\nกาฝาก\nก้ามกราม\nกามกิจ\nกามคุณ\nกามเทพ\nกามโรค\nก้ามปู\nกายกรรม\nกายบริหาร\nกายภาพ\nกายวิภาค\nกายสิทธิ์\nก่ายกอง\nการคลัง\nการเงิน\nการบ้าน\nการเปรียญ\nการเมือง\nการเรือน\nการละเล่น\nกาลกิริยา\nกาลเทศะ\nก้าวก่าย\nก้าวร้าว\nก้าวหน้า\nกาสาวพัสตร์\nกาฬพฤกษ์\nกาฬโรค\nกำปั้น\nกำมือ\nกำแพงขาว\nกำลังใจ\nกำลังม้า\nกี่งอำเภอ\nกิจกรรม\nกิจการ\nกิจวัตร\nกิจจะลักษณะ\nกิตติคุณ\nกิตติศัพท์\nกินขาด\nกินใจ\nกินดอง\nกินโต๊ะ\nกินแบ่ง\nกินเปล่า\nกินเลี้ยง\nกินเส้น\nกินแหนง\nกิโลกรัม\nกิโลเมตร\nกิโลลิตร\nกิโลเฮิรตซ์\nกีดกัน\nกีดกั้น\nกีดขวาง\nกึกก้อง\nกึกกัก\nกึกกือ\nกึ่งกลาง\nกุกกัก\nกุ๊กกิ๊ก\nกุ้งฝอย\nกุ้งมังกร\nกุ้งแห้ง\nกุ้งเต้น\nกุ้งยิง\nกุญแจผี\nกุญแจมือ\nกุญแจเลื่อน\nกุญแจเสียง\nกุลธิดา\nกุลบุตร\nกุลสตรี\nกู้ยืม\nเก้งก้าง\nเก็บกวาด\nเก็บเกี่ยว\nเก็บงำ\nเก็บตก\nเกรงกลัว\nเกรงใจ\nเกรงขาม\nเกรียงไกร\nเกรียมกรม\nเกรี้ยวกราด\nเกล็ดเลือด\nเกลี้ยกล่อม\nเกลี้ยงเกลา\nเกลือกกลั้ว\nเกลือกกลิ้ง\nเกลื่อนกล่น\nเกลื่อนกลาด\nเกศธาตุ\nเกษตรกร\nเกษตรกรรม\nเกษตรศาสตร์\nเกษมสันต์\nเกษียรสมุทร\nเก้อเขิน\nเกาะแกะ\nเกี่ยงงอน\nเกียจคร้าน\nเกียรติคุณ\nเกียรตินิยม\nเกียรติประวัติ\nเกียรติภูมิ\nเกียรติยศ\nเกียรติศักดิ์\nเกียรติมุข\nเกี่ยวข้อง\nเกี่ยวดอง\nเกี่ยวพัน\nเกี่ยวโยง\nเกี้ยวพาน\nเกี้ยวพาราสี\nแก่แดด\nแก้ขัด\nแก้ไข\nแก้ตัว\nแก้เผ็ด\nแก้ลำ\nแกงคั่ว\nแกงจืด\nแกงบวด\nแกงป่า\nแกงเผ็ด\nแกงส้ม\nแก่งแย่ง\nแก่นแก้ว\nแก่นสาร\nแก้วตา\nแก้วหู\nแกว่งกวัด\nแกว่งไกว\nแกะรอย\nโก้เก๋\nโกรธเกรี้ยว\nโกรธขึ้ง\nไก่เขี่ย\nไก่ชน\nไก่บ้าน\nไก่ป่า\nไก่ฟ้า\nไกล่เกลี่ย\nขจัดขจาย\nขนเพชร\nขนสัตว์\nขนหนู\nขนส่ง\nขนมจีน\nขบขัน\nขบวนการ\nข่มขี่\nข่มขู่\nข่มขืน\nข่มเหง\nขมหิน\nขมิ้นชัน\nขมุบขมิบ\nขยะแขยง\nขยักขย่อน\nขยักขย้อน\nขยับขยาย\nขยับเขยื้อน\nขวดโหล\nขวยเขิน\nขวัญใจ\nขวัญตา\nขวัญอ่อน\nขวากหนาม\nขวางโลก\nของ้าว\nขอสับ\nขอขมา\nขอทาน\nขอโทษ\nขอร้อง\nขออภัย\nข้อเขียน\nข้อความ\nข้อเท็จจริง\nของกลาง\nของขวัญ\nของแข็ง\nของชำ\nของลับ\nของเล่น\nของว่าง\nของเหลว\nของไหล\nของไหว้\nข้องใจ\nข้องแวะ\nขอบข่าย\nขอบเขต\nขอบคุณ\nขอบใจ\nขอบพระคุณ\nข้อมูล\nข้อแม้\nข้อหา\nข้อสังเกต\nขัดข้อง\nขัดขืน\nขัดเขิน\nขัดจังหวะ\nขัดดอก\nขัดแตะ\nขัดยอก\nขัดแย้ง\nขัดสมาธิ\nขันหมาก\nขันอาสา\nขับขี่\nขับเคี่ยว\nขั้วโลก\nขาจร\nขาประจำ\nข้าราชการ\nข้าศึก\nข้าหลวง\nขาดแคลน\nขาดใจ\nขาดตอน\nขาดตัว\nขาดทุน\nขาดเหลือ\nขายหน้า\nข่าวกรอง\nข่าวคราว\nข่าวล่า\nข่าวลือ\nข่าวสาร\nข้าวเกรียบ\nข้าวแกง\nข้าวของ\nข้าวจี่\nข้าวเจ้า\nข้าวซอย\nข้าวต้ม\nข้าวตอก\nข้าวตัง\nข้าวแตน\nข้าวทิพย์\nข้าวบิณฑ์\nข้าวเปลือก\nข้าวโพด\nข้าวฟ่าง\nข้าวเม่า\nข้าวสวย\nข้าวสาร\nข้าวเหนียว\nข้าวหมาก\nข้าวหลาม\nขี้เกียจ\nขี้ข้า\nขี้ครอก\nขี้คร้าน\nขี้คุก\nขี้ไคล\nขี้เซา\nขีดขั้น\nขีดคร่อม\nขีดคั่น\nขีดฆ่า\nขี้ตา\nขี้ตืด\nขี้เถ้า\nขี้ทูด\nขี้ปะติ๋ว\nขี้ผึ้ง\nขี้มูก\nขี้ยา\nขี้แย\nขี้ริ้ว\nขี้เรื้อน\nขี้เล็บ\nขี้หู\nขี้หน้า\nขี้เหนียว\nขี้เหล็ก\nขี้เหร่\nขึงขัง\nขึงพืด\nขึ้งโกรธ\nขึ้นใจ\nขึ้นชื่อ\nขึ้นมือ\nขืนใจ\nขื่นขม\nขุดคุ้ย\nขุนทอง\nขุนนาง\nขุนพล\nขุนศึก\nขุนหลวง\nขูดรีด\nเข็มกลัด\nเข็มขัด\nเข้มข้น\nเข้มแข็ง\nเข้มงวด\nเข็มทิศ\nเข็มหมุด\nเข้าขา\nเข้าเค้า\nเข้าใจ\nเข้าชื่อ\nเข้าตัว\nเข้าถึง\nเข้าทรง\nเข้าท่า\nเข้าที\nเข้าเนื้อ\nเข้าเล่ม\nเขียวเสวย\nเขียวหวาน\nแขกเต้า\nแข็งกร้าว\nแข็งกล้า\nแข็งแกร่ง\nแข็งข้อ\nแข็งขัน\nแข่งขัน\nแข็งใจ\nแข็งตัว\nแข็งเมือง\nแข็งแรง\nแขวนลอย\nโขกสับ\nโขยกเขยก\nไขข้อ\nไขควง\nไขมัน\nไข่มุก\nไขว่ห้าง\nไขสันหลัง\nไขสือ\nไข่เค็ม\nไข่เยี่ยวม้า\nไข่หงส์\nไข่เหี้ย\nคงกระพัน\nคงตัว\nคงทน\nคงที่\nคชลักษณ์\nคชสาร\nคชสีห์\nคชราช\nคณิตศาสตร์\nคดเคี้ยว\nคติธรรม\nคติพจน์\nคนกลาง\nคนไข้\nคนใช้\nคนทรง\nคบไฟ\nคบเพลิง\nคบค้า\nคบคิด\nคบหา\nคมคาย\nครบครัน\nครบถ้วน\nครอบครอง\nครอบคลุม\nครอบครัว\nครอบงำ\nครอบจักรวาล\nคริสตกาล\nคริสตจักร\nคริสต์มาส\nคริสต์ศตวรรษ\nคริสต์ศักราช\nคริสตัง\nคริสเตียน\nครุกรรม\nครุภัณฑ์\nครุศาสตร์\nครุฑพ่าห์\nครุ่นคิด\nคลอเคลีย\nคล่องแคล่ว\nคล่องตัว\nคล่องมือ\nคลั่งไคล้\nคลาคล่ำ\nคลาไคล\nคลาดเคลื่อน\nคลาดแคล้ว\nคลี่คลาย\nคลึงเคล้น\nคลึงเคล้า\nคลื่นไส้\nคลื่นเหียน\nคลุกคลี\nคลุกคลาน\nคลุมเครือ\nคลุมโปง\nคลุ้มคลั่ง\nควงสว่าน\nควบคุม\nควบคู่\nควบแน่น\nควันหลง\nความคิด\nความหลัง\nความเห็น\nคอหอย\nคอห่าน\nคอแห้ง\nค่อนขอด\nค่อนแคะ\nค้อนควัก\nคั่งค้าง\nคั่งแค้น\nคัดค้าน\nคัดง้าง\nคัดท้าย\nคัดเลือก\nคันจาม\nคันฉ่อง\nคันฉาย\nคันชัก\nคันชั่ง\nคันไถ\nคันนา\nคันเร่ง\nคับขัน\nคับคั่ง\nคับแค้น\nคับแคบ\nคางทูม\nคางหมู\nค้างคืน\nค้างปี\nคาดคั้น\nคาดเชือก\nคาดโทษ\nคาดหมาย\nคานหาม\nคาบเกี่ยว\nคาบศิลา\nคาบสมุทร\nคำขาด\nคำนำ\nคิดค้น\nคืนดี\nคืนตัว\nคุกเข่า\nคุณค่า\nคุณชาย\nคุณธรรม\nคุณนาย\nคุณภาพ\nคุณลักษณะ\nคุณวุฒิ\nคุณศัพท์\nคุณสมบัติ\nคุณหญิง\nคุณากร\nคุณูปการ\nคุโณปการ\nคุมเชิง\nคุ้มกัน\nคุยเขื่อง\nคุยโต\nคุ้ยเขี่ย\nคุ้มครอง\nคู่กรณี\nคู่กัด\nคู่ขา\nคู่แข่ง\nคู่ครอง\nคู่ควร\nคู่คิด\nคู่คี่\nคู่ใจ\nคู่ชีพ\nคู่ชีวิต\nคู่บารมี\nคู่บุญ\nคู่ปรปักษ์\nคู่ปรับ\nคู่ผสม\nคู่มือ\nคู่รัก\nคู่ลำดับ\nคู่สาย\nคู่หมั้น\nคู่หู\nคู่อริ\nคู่อาฆาต\nเคมีภัณฑ์\nเคยตัว\nเคร่งขรึม\nเคร่งครัด\nเคร่งเครียด\nเครดิตฟองซิเอร์\nเครื่องกล\nเครื่องกัณฑ์\nเครื่องแกง\nเครื่องเขิน\nเครื่องครัว\nเครื่องเคียง\nเครื่องเงิน\nเครื่องจักร\nเครื่องเซ่น\nเครื่องดนตรี\nเครื่องต้น\nเครื่องทุ่นแรง\nเครื่องเทศ\nเครื่องใน\nเครื่องบิน\nเครื่องบูชา\nเครื่องแบบ\nเครื่องประดับ\nเครื่องปรุง\nเครื่องปรุงรส\nเครื่องมือ\nเครื่องยนต์\nเครื่องร่อน\nเครื่องราง\nเครื่องเรือน\nเครื่องล่าง\nเครื่องเล่น\nเครื่องสาย\nเครื่องสำอาง\nเครื่องสุกำศพ\nเครื่องหมาย\nเครือรัฐ\nเคลียคลอ\nเคลื่อนที่\nเคลื่อนไหว\nเคลือบแคลง\nเคลือบแฝง\nเคลือบฟัน\nเคว้งคว้าง\nเคหสถาน\nเค้าโครง\nเคียดแค้น\nเคี่ยวเข็ญ\nเคี้ยวเอื้อง\nเคืองขุ่น\nโคนม\nโคบาล\nโคมูตร\nโคมลอย\nโครงการ\nโครงเรื่อง\nโครงงาน\nโครงสร้าง\nโครมคราม\nโคลงเคลง\nฆ้องกระแต\nฆ้องชัย\nฆ้องวง\nฆ้องหุ่ย\nฆ้องเหม่ง\nฆ้องโหม่ง\nฆาตกร\nฆาตกรรม\nฆานประสาท\nงงงวย\nงงงัน\nงดเว้น\nงบดุล\nงบประมาณ\nงมโข่ง\nงมงาย\nง่วงงุน\nง่วงเหงา\nงอหาย\nง้องอน\nงอนง้อ\nงอมแงม\nงาช้าง\nง่าเงย\nงานการ\nง่ายดาย\nงึมงำ\nเงินเดือน\nเงินตรา\nเงินยวง\nเงียบกริบ\nเงียบเชียบ\nเงียบเหงา\nเงื่องหงอย\nเงื่อนไข\nเงื่อนงำ\nเงื่อนเวลา\nเงื้อมมือ\nแง่งอน\nจงใจ\nจงรัก\nจดจ่อ\nจดจำ\nจดหมาย\nจดหมายเหตุ\nจรจัด\nจรรยาบรรณ\nจริงจัง\nจริงใจ\nจอมขวัญ\nจอมใจ\nจอมทัพ\nจอมปลวก\nจอมพล\nจ๊ะเอ๋\nจักสาน\nจักรพรรดิ\nจักรภพ\nจักรยาน\nจักรยานยนต์\nจักรราศี\nจักรวรรดิ\nจักรวรรดินิยม\nจักรวาล\nจังหนับ\nจัดการ\nจัดจ้าน\nจัดเจน\nจัดแจง\nจัดตั้ง\nจัดสรร\nจับกุม\nจับจด\nจับเจ่า\nจ่าหน้า\nจาตุทสี\nจาตุมหาราช\nจาตุมหาราชิก\nจาตุมหาราชิกา\nจาตุรงคสันนิบาต\nจาตุรราชการ\nจานเชิง\nจานบิน\nจานผี\nจานเสียง\nจาบจ้วง\nจำเป็น\nจำพรรษา\nจำวัด\nจ้ำจี้จ้ำไช\nจำเลาะตา\nจิงโจ้น้ำ\nจิตใจ\nจิตตภาวนา\nจิตตัง\nจิตตานุปัสสนา\nจิตนิยม\nจิตบำบัด\nจิตแพทย์\nจิตวิสัย\nจิตรกร\nจิตรกรรม\nจิตรลดา\nจิตวิทยา\nจิตเวช\nจิตเวชศาสตร์\nจินตกวี\nจินตนา\nจินตนาการ\nจินตภาพ\nจุฑามณี\nจุฑามาศ\nจุฑารัตน์\nจุนเจือ\nจุ้นจ้าน\nจุลชีพ\nจุลชีวัน\nจุลชีวิน\nจุลทรรศน์\nจุลภาค\nจุลวรรค\nจุลศักราช\nจุลสาร\nจุลินทรีย์\nจุฬามณี\nจุฬาลักษณ์\nเจตคติ\nเจตจำนง\nเจตนารมณ์\nเจตภูต\nเจริญพร\nเจ้ากรม\nเจ้ากรรม\nเจ้าของ\nเจ้าขา\nเจ้าข้า\nเจ้าคณะ\nเจ้าค่ะ\nเจ้าจอม\nเจ้าชู้\nเจ้าตัว\nเจ้าถิ่น\nเจ้าท่า\nเจ้าที่\nเจ้าทุกข์\nเจ้านาย\nเจ้าเนื้อ\nเจ้าบ้าน\nเจ้าบ่าว\nเจ้าประคุณ\nเจ้าประคู้น\nเจ้าพนักงาน\nเจ้าพระคุณ\nเจ้าพระยา\nเจ้าพ่อ\nเจ้าพายุ\nเจ้าฟ้า\nเจ้าภาพ\nเจ้ามือ\nเจ้าแม่\nเจ้าเรือน\nเจ้าสังกัด\nเจ้าสัว\nเจ้าสาว\nเจ้าหน้าที่\nเจ้าหนี้\nเจ้าอาวาส\nเจาะจง\nเจือจาง\nเจือจาน\nเจือปน\nเจื้อยแจ้ว\nแจกจ่าย\nแจ่มแจ้ง\nแจ่มใส\nโจงกระเบน\nโจมตี\nโจรกรรม\nโจรสลัด\nใจความ\nใจคอ\nฉกฉวย\nฉกชิง\nฉลองได\nฉ้อฉล\nฉัตรมงคล\nฉันทลักษณ์\nฉายาลักษณ์\nฉิบหาย\nฉุกเฉิน\nฉุกละหุก\nฉุนเฉียว\nฉุปศาสตร์\nเฉไฉ\nเฉยเมย\nเฉาโฉด\nเฉิดฉัน\nเฉิดฉาย\nเฉิดฉิน\nเฉียบขาด\nเฉียบพลัน\nเฉียบแหลม\nเฉื่อยชา\nแฉะแบะ\nโฉดเฉา\nโฉมงาม\nโฉมฉาย\nโฉมเฉลา\nโฉมตรู\nโฉมยง\nโฉมศรี\nโฉมหน้า\nชดช้อย\nชดเชย\nชดใช้\nชนบท\nชนินทร์\nชนกกรรม\nชนมพรรษา\nชนมายุ\nชมเชย\nชมพูทวีป\nชมพูนท\nชมพูนุท\nชราธรรม\nชราภาพ\nชลจร\nชลธาร\nชลธี\nชลนัยน์\nชลนา\nชลเนตร\nชลประทาน\nชลมารค\nชลาธาร\nชลาลัย\nชลาศัย\nชลาสินธุ์\nชโลทร\nช่วงชิง\nช่วงใช้\nชวนชม\nชวนหัว\nช่วยเหลือ\nช่อฟ้า\nช่อม่วง\nชอกช้ำ\nช่องเขา\nช่องแคบ\nช่องไฟ\nช่องว่าง\nช้องนาง\nชอบกล\nชอบใจ\nชอบธรรม\nชอบพอ\nชักโครก\nชักเงา\nชักจูง\nชักชวน\nชักนำ\nชักเนื้อ\nชักพระ\nชักเย่อ\nชักใย\nชั่งใจ\nชังฆวิหาร\nชัดเจน\nชั้นเชิง\nชั่วคน\nชั่วคราว\nชั่วช้า\nชั่วโมง\nชั่วแล่น\nชาเย็น\nช้านาน\nช่างเครื่อง\nช่างฝีมือ\nช่างฟิต\nช่างไฟ\nช้างน้ำ\nช้างเผือก\nช้างพลาย\nช้างพัง\nช้างสาร\nช้างสีดอ\nชาติธรรม\nชาตินิยม\nชาติพันธุ์\nชาติพันธุ์วิทยา\nชาติภูมิ\nชานชาลา\nชายชาตรี\nชายคา\nชายฝั่ง\nชายทะเล\nชาวเล\nชาววัง\nช้ำใจ\nช้ำชอก\nชิงชัง\nชิงพลบ\nชินชา\nชินบุตร\nชิ้นเอก\nชิมลาง\nชีเปลือย\nชี้ขาด\nชี้แจง\nชี้นำ\nชี้แนะ\nชี้ฟ้า\nชีพจร\nชีพิตักษัย\nชื่นชม\nชื่นบาน\nชื่นมื่น\nชื่อย่อ\nชื่อรอง\nชื่อเล่น\nชื่อเสียง\nชุกชุม\nชุติมา\nชุบตัว\nชุบเลี้ยง\nชุมชน\nชุมทาง\nชุมสาย\nชุ่มใจ\nชุ่มชื่น\nชุ่มชื้น\nชุมนุมชน\nชูชีพ\nชูโรง\nชู้สาว\nเชยชม\nเชลยศักดิ์\nเชลยศึก\nเช่าซื้อ\nเช้าตรู่\nเช้ามืด\nเชิงกราน\nเชิงกล\nเชิงชั้น\nเชิงชาย\nเชิงซ้อน\nเชิงเดียว\nเชิงเดี่ยว\nเชิงตะกอน\nเชิงเทิน\nเชิงมุม\nเชิดชู\nเชิงอรรถ\nเชี่ยนหมาก\nเชี่ยวชาญ\nเชื่องช้า\nเชื่อใจ\nเชื่อถือ\nเชื่อฟัง\nเชื่อมือ\nเชื้อชาติ\nเชื้อเพลิง\nเชื้อไฟ\nเชื้อโรค\nเชื้อสาย\nเชื้อเชิญ\nเชื่องช้า\nเชือนแช\nเชื่อวัน\nแช่เย็น\nแช่อิ่ม\nแช่มช้อย\nแช่มชื่น\nโชกโชน\nโชติช่วง\nโชติรส\nใช้สอย\nซบเซา\nซมซาน\nซวนเซ\nซอกซอน\nซอกแซก\nซ่องสุม\nซ่องเสพ\nซ่องแซ่ง\nซ่อนรูป\nซ่อนเร้น\nซ่อนหา\nซ่อนกลิ่น\nซ่อนทราย\nซ่อมแซม\nซักค้าน\nซักซ้อม\nซักไซ้\nซักฟอก\nซักแห้ง\nซังกะตาย\nซังตาย\nซัดเซ\nซัดทอด\nซับซ้อน\nซับใน\nซับพระพักตร์\nซากศพ\nซ่านเซ็น\nซ้ำซ้อน\nซ้ำซาก\nซ้ำเติม\nซ้ำร้าย\nซี่โครง\nซีดเซียว\nซึมกะทือ\nซึมซาบ\nซึมเซา\nซึมทราบ\nซึมเศร้า\nซื่อตรง\nซื่อสัตย์\nซื้อขาย\nซุกซน\nซุกซ่อน\nซุบซิบ\nซู่ซ่า\nเซซัง\nเซ่อซ่า\nแซ่ซ้อง\nโซดาไฟ\nญาณทัสนะ\nญาณวิทยา\nญาณศาสตร์\nญาติกา\nฐานราก\nดกดื่น\nดงดิบ\nดลใจ\nดลบันดาล\nดวงแก้ว\nดวงใจ\nดวงเดือน\nดวงตรา\nดวงตา\nดวงสมร\nดอกจัน\nดอกจิก\nดอกบัว\nดอกเบี้ย\nดอกฟ้า\nดอกไม้\nดอกยาง\nดอกเล็บ\nดอกทอง\nดอกสร้อย\nดองยา\nดักคอ\nดักฟัง\nดังนั้น\nดังนี้\nดังหนึ่ง\nดั้งเดิม\nดัดจริต\nดัดแปลง\nดันทุรัง\nดับขันธ์\nดับจิต\nดับชีพ\nด่าทอ\nด่างทับทิม\nด่างพร้อย\nดาดฟ้า\nดาราศาสตร์\nดาลเดือด\nดาวกระจาย\nดาวเคราะห์\nดาวตก\nดาวเทียม\nดาวรุ่ง\nดาวเรือง\nดาวฤกษ์\nดาวหาง\nดาวเหนือ\nดาษดื่น\nดินขาว\nดินดาน\nดินดำ\nดินประสิว\nดินปืน\nดินระเบิด\nดินสอ\nดินสอพอง\nดิ้นรน\nดิบดี\nดีเกลือ\nดีใจ\nดีซ่าน\nดีดัก\nดีเดือด\nดีฝ่อ\nดีดดิ้น\nดึกดำบรรพ์\nดึกดื่น\nดึงดัน\nดึงดูด\nดื่มด่ำ\nดื้อด้าน\nดื้อดึง\nดื้อแพ่ง\nดื้อยา\nดื้อรั้น\nดุดัน\nดุเดือด\nดุร้าย\nดุลการค้า\nดุลพินิจ\nดุลภาค\nดุลยพินิจ\nดุลยภาพ\nดุษฎีนิพนธ์\nดุษฎีบัณฑิต\nดุษณีภาพ\nดูแคลน\nดูถูก\nดูดาย\nดูเบา\nดูแล\nดูหมิ่น\nดูเหมือน\nดูดดื่ม\nเด็ดขาด\nเด็ดดวง\nเด็ดเดี่ยว\nเดนตาย\nเดาสวด\nเดาสุ่ม\nเดินทาง\nเดินสะพัด\nเดินสาย\nเดินเหิน\nเดิมพัน\nเดียงสา\nเดียดฉันท์\nเดียวกัน\nเดียวดาย\nเดี๋ยวเดียว\nเดี๋ยวนี้\nเดือดดาล\nเดือดร้อน\nเดือนมืด\nเดือนหงาย\nแดดาล\nแดดิ้น\nแดกดัน\nโด่เด่\nโด่งดัง\nโดดเดี่ยว\nโดยสาร\nได้การ\nได้แก่\nได้ใจ\nได้ที\nได้ยิน\nได้เสีย\nตกเขียว\nตกค้าง\nตกใจ\nตกต่ำ\nตกแต่ง\nตกทอด\nตกฟาก\nตกมัน\nตกยาก\nตกลง\nตกหล่น\nต้นขั้ว\nต้นคิด\nต้นฉบับ\nต้นตอ\nต้นตำรับ\nต้นทุน\nต้นแบบ\nต้นเพลิง\nต้นมือ\nต้นไม้\nต้นร่าง\nต้นเรื่อง\nต้นสังกัด\nต้นหน\nต้นเหตุ\nตบตา\nตบแต่ง\nตบแผละ\nตบมือ\nต้มข่า\nต้มโคล้ง\nต้มยำ\nต้มส้ม\nตรมตรอม\nตรรกวิทยา\nตรรกศาสตร์\nตรวจการ\nตรวจการณ์\nตรวจตรา\nตระบัดสัตย์\nตรัสรู้\nตราตั้ง\nตราบาป\nตรายาง\nตราสาร\nตริตรอง\nตรีกฏุก\nตรีกาย\nตรีโกณ\nตรีโกณมิติ\nตรีคูณ\nตรีทูต\nตรีปิฎก\nตรีภพ\nตรีมูรติ\nตรึกตรอง\nตรึงตรา\nตรุษจีน\nตฤณชาติ\nตฤณมัย\nตลกบาตร\nตลบตะแลง\nตลบหลัง\nตลาดนัด\nตลาดน้ำ\nตลาดมืด\nตลาดสด\nต่อตี\nต่อเติม\nต่อว่า\nต่อสู้\nต่อกร\nต่อต้าน\nต่อแย้ง\nต้องการ\nต้องโทษ\nต้องหา\nต้อนรับ\nตอบโต้\nตอบแทน\nต่อยหอย\nตะพาบน้ำ\nตักตวง\nตักบาตร\nตั้งเข็ม\nตั้งไข่\nตั้งเค้า\nตั้งแง่\nตั้งใจ\nตั้งต้น\nตั้งแต่\nตั้งท้อง\nตัดขาด\nตัดใจ\nตัดเชือก\nตัดตอน\nตัดทอน\nตัดบท\nตัดพ้อ\nตัดรอน\nตัดสิน\nตับเต่า\nตับแลบ\nตับอ่อน\nตัวกลาง\nตัวการ\nตัวเก็ง\nตัวดี\nตัวตั้ง\nตัวเต็ง\nตัวถัง\nตัวแทน\nตัวประกอบ\nตัวประกัน\nตัวแปร\nตัวผู้\nตัวพิมพ์\nตัวเมีย\nตัวยืน\nตัวเลข\nตัวอย่าง\nตั๋วเงิน\nตั๋วแลกเงิน\nตากล้อง\nตาไก่\nตาข่าย\nตาชั่ง\nตาตุ่ม\nตาทวด\nตาปลา\nตาราง\nต่างหาก\nต้านทาน\nตามใจ\nตายใจ\nตายซาก\nตายด้าน\nตายตัว\nตายทั้งกลม\nตายห่า\nตายโหง\nตาลปัตร\nต่ำช้า\nต่ำต้อย\nตำส้ม\nติเตียน\nติณชาติ\nติดขัด\nติดใจ\nติดต่อ\nติดตั้ง\nติดตาม\nติดตื้น\nติดพัน\nติดลม\nติดอ่าง\nตีเกลียว\nตีขลุม\nตีความ\nตีคู่\nตีจาก\nตีตื้น\nตีแผ่\nตีรวน\nตีลังกา\nตีวง\nตีเสมอ\nตีนกา\nตีนคู้\nตีนจก\nตีนตะขาบ\nตีนผี\nตีนเหยียด\nตึกแถว\nตึกระฟ้า\nตึงเครียด\nตึงตัง\nตื้นตัน\nตื่นตัว\nตื่นตูม\nตื่นเต้น\nตุ๊ต๊ะ\nตุ้บตั้บ\nตุ้มหู\nตุลาการ\nตุลาคม\nตู้นิรภัย\nตูมตาม\nตู้เสบียง\nเตโชธาตุ\nเตร็ดเตร่\nเต้นรำ\nเตาแก๊ส\nเตาผิง\nเตาฟู่\nเตาไฟ\nเตารีด\nเตาสูบ\nเต่าทอง\nเต้ารับ\nเต้าส่วน\nเต้าเสียบ\nเต้าหู้ยี้\nแต่ละ\nแตกคอ\nแตกคอก\nแตกฉาน\nแตกดับ\nแตกตื่น\nแตกพาน\nแตกแยก\nแตกร้าว\nแตกหัก\nแต่งงาน\nแต่งตั้ง\nแต้มคู\nแต้มต่อ\nแตรงอน\nแตรเดี่ยว\nแตรฝรั่ง\nแตรฟันฟาร์\nแตรวง\nโต้ตอบ\nโต้เถียง\nโต้แย้ง\nโต๊ะหมู่\nโต๊ะอิหม่าม\nใต้ถุน\nไต้ก๋ง\nไต่คู้\nไต่เต้า\nไต่ถาม\nไต้ฝุ่น\nไตรจักร\nไตรจีวร\nไตรตรึงษ์\nไตรทวาร\nไตรปิฎก\nไตรเพท\nไตรภพ\nไตรภูมิ\nไตรภาคี\nไตรยางศ์\nไตรรงค์\nไตรรัตน์\nไตรลักษณ์\nไตรโลก\nไตรสรณคมน์\nไตรสิกขา\nไต่สวน\nถกเถียง\nถดถอย\nถนัดถนี่\nถนิมสร้อย\nถมถืด\nถมเถ\nถมไป\nถลากไถล\nถ้วนถี่\nถ้วยฟู\nถ่องแท้\nถอดถอน\nถ้อยคำ\nถ้อยแถลง\nถากถาง\nถ่านไฟฉาย\nถ่านหิน\nถามไถ่\nถ่ายทอด\nถ่ายทุกข์\nถ่ายเท\nถาวรวัตถุ\nถ้ำมอง\nถี่ถ้วน\nถึงใจ\nถูกใจ\nถูกชะตา\nเถรวาท\nเถ้าแก่\nเถ้าแก่เนี้ย\nแถมพก\nแถลงการณ์\nไถ่ถอน\nไถ่ถาม\nทดแทน\nทดรอง\nทดลอง\nทดสอบ\nทนทาน\nทนายความ\nทบทวน\nทแยงมุม\nทรงกลด\nทรงเครื่อง\nทรงเจ้า\nทรัพย์สิน\nทรามชม\nทรามเชย\nทรามวัย\nทรามสงวน\nทรามสวาท\nทรุดโทรม\nทฤษฎีบท\nท้วงติง\nท่วมท้น\nทวาทศ\nทวาทศมาส\nทวาบรยุค\nทวารบาล\nทวิบถ\nทวิบท\nทวิบาท\nทวิภาค\nทวิภาคี\nทวีคูณ\nทศกัณฐ์\nทศชาติ\nทศทิศ\nทศนิยม\nทศพร\nทศพล\nทศพิธราชธรรม\nทศมาส\nทศวรรษ\nท่อไอเสีย\nท้อถอย\nท้อแท้\nทองขาว\nทองคำ\nทองคำขาว\nทองคำเปลว\nทองเค\nทองแดง\nทองบรอนซ์\nทองม้วน\nทองย้อย\nทองสัมฤทธิ์\nทองหยอด\nทองหยิบ\nทองเหลือง\nทองเอก\nท่องเที่ยว\nท้องตรา\nท้องถิ่น\nท้องที่\nท้องน้อย\nท้องร่อง\nท้องเรื่อง\nทอดมัน\nทอดทิ้ง\nทอดน่อง\nทอดยอด\nทอดหุ่ย\nทอยกอง\nทะเบียนบ้าน\nทะเลทราย\nทะเลสาบ\nทะเลหลวง\nทักขิณาวัฏ\nทักท้วง\nทักทาย\nทักษิณาวรรต\nทักษิณาทาน\nทักษิณานุประทาน\nทั้งกลม\nทั้งคน\nทั้งดุ้น\nทั้งที\nทั้งนั้น\nทั้งนี้\nทั้งปวง\nทั้งผอง\nทั้งเพ\nทั้งมวล\nทั้งสิ้น\nทั้งหมด\nทั้งหลาย\nทัณฑ์บน\nทัดทาน\nทัดเทียม\nทันควัน\nทันใจ\nทันใด\nทันตา\nทันสมัย\nทันที\nทับถม\nทับทรวง\nทับศัพท์\nทั่วถึง\nทั่วไป\nท่าทาง\nท่าที\nท้าทาย\nทางการ\nทางข้าม\nทางด่วน\nทางเท้า\nทางโท\nทางใน\nทางผ่าน\nทางม้าลาย\nทางหลวง\nทางออก\nทางเอก\nทานกัณฑ์\nทานตะวัน\nท่านชาย\nทานบารมี\nท่านผู้หญิง\nท่านหญิง\nทาบทาม\nท้ายทอย\nทารุณกรรม\nทำคลอด\nทำใจ\nทำซ้ำ\nทำท่า\nทำที\nทำแท้ง\nทำโทษ\nทำบาป\nทำบุญ\nทำพิษ\nทำฟัน\nทำร้าย\nทำวัตร\nทำสาว\nทำเสน่ห์\nทำหมัน\nทำให้\nทิ้งขว้าง\nทิ้งทวน\nทิ้งท้าย\nทินกร\nทิพจักขุ\nทิพโสต\nทิพยจักษุ\nทิพยญาณ\nทิพยเนตร\nทิพยรส\nทิพากร\nทิ่มตำ\nทิ่มแทง\nทิวากร\nทิวากาล\nทิศทาง\nทีเด็ด\nทีท่า\nทีนี้\nทีหลัง\nทีฆนิกาย\nทีฆสระ\nที่ดิน\nที่นอน\nที่นั่ง\nที่ปรึกษา\nที่พึ่ง\nที่มั่น\nที่ราบ\nที่ว่าการ\nที่สุด\nที่หมาย\nที่ไหน\nทุกที\nทุกเมื่อ\nทุกข์สุข\nทุนทรัพย์\nทุนนิยม\nทุนรอน\nทุนสำรอง\nทุ่มเถียง\nทุ่มเท\nทูนหัว\nทูลกระหม่อม\nเทกระจาด\nเทครัว\nเทพเจ้า\nเทพดา\nเทพธิดา\nเทพนม\nเทพนิยม\nเทพนิยาย\nเทพบุตร\nเทพสังหรณ์\nเทศกาล\nเทศนาโวหาร\nเทศบัญญัติ\nเทศบาล\nเทศมนตรี\nเทห์ฟากฟ้า\nเท่ากับ\nเท่าใด\nเท่าตัว\nเท่าทัน\nเท่าทุน\nเท่าเทียม\nเท่านั้น\nเท่าไร\nเท้าช้าง\nเทิดทูน\nเที่ยงตรง\nเที่ยงแท้\nเที่ยงธรรม\nเทียนชนวน\nเทียนพรรษา\nเทียบเคียง\nเทียบเท่า\nเทือกเขา\nเทือกเถา\nแท็งก์น้ำ\nแท่นพิมพ์\nแท่นมณฑล\nแท่นหมึก\nแทรกซอน\nแทรกซ้อน\nแทรกซึม\nแทรกแซง\nแทะโลม\nไทยดำ\nไทยทาน\nไทยธรรม\nไทยน้อย\nไทยใหญ่\nธงชัย\nธงชาติ\nธงทิว\nธรณีวิทยา\nธรณีสงฆ์\nธรรมกาย\nธรรมการ\nธรรมเกษตร\nธรรมขันธ์\nธรรมคุณ\nธรรมจรรยา\nธรรมจริยา\nธรรมจักร\nธรรมจักษุ\nธรรมจาคะ\nธรรมจารี\nธรรมชาติ\nธรรมดา\nธรรมเนียม\nธรรมราชา\nธรรมศาสตร์\nธรรมสภา\nธรรมสังเวช\nธัญพืช\nธารพระกร\nธีรภาพ\nธีรราช\nนกเขา\nนกต่อ\nนกยูง\nนกรู้\nนกหวีด\nนครบาล\nนครรัฐ\nนงคราญ\nนงนุช\nนงพะงา\nนงเยาว์\nนงราม\nนงลักษณ์\nนบนอบ\nนพเก้า\nนพคุณ\nนพเคราะห์\nนพปฎล\nนพพล\nนพรัตน์\nนพศก\nนพศูล\nนมข้น\nนมผง\nนมไม้\nนมนาน\nนมหนู\nนมแมว\nนรีเวช\nนรีเวชวิทยา\nนวดฟั้น\nนวยนาด\nนวลระหง\nนวลลออ\nนวลละออง\nนวลจันทร์\nนอกครู\nนอกคอก\nนอกจาก\nนอกใจ\nนอกชาน\nนอกรีต\nนอกเหนือ\nนองเนือง\nนองเลือด\nนอนก้น\nนอนใจ\nนอบนบ\nนอนเล่น\nนอบน้อม\nน้อมนำ\nน้อยใจ\nน้อยหน้า\nนักการ\nนักการเมือง\nนักกีฬา\nนักข่าว\nนักท่องเที่ยว\nนักเทศน์\nนักโทษ\nนักธรรม\nนักบวช\nนักบิน\nนักบุญ\nนักปราชญ์\nนักพรต\nนักรบ\nนักเรียน\nนักเลง\nนักวิชาการ\nนักศึกษา\nนักสิทธิ์\nนักสืบ\nนักหนา\nนั่งเทียน\nนั่งร้าน\nนัดแนะ\nนัดหมาย\nนั่นแหละ\nนั่นเอง\nนับถือ\nนับประสา\nนัยน์ตา\nนาดำ\nนาปรัง\nนาปี\nนาสวน\nนาหว่าน\nนาคบาศ\nนาคปรก\nนาคราช\nนางกวัก\nนางกำนัล\nนางงาม\nนางใน\nนางบำเรอ\nนางแบบ\nนางพญา\nนางฟ้า\nนางไม้\nนางโลม\nนางสาว\nนางห้าม\nนางเอก\nนาฏกรรม\nนาฏดนตรี\nนาฏศิลป์\nนานนม\nน่านน้ำ\nน่านฟ้า\nนามกร\nนามธรรม\nนามไธย\nนามบัตร\nนามปากกา\nนามแฝง\nนามสกุล\nนามสงเคราะห์\nนามสมญา\nนายทะเบียน\nนายท่า\nนายท้าย\nนายทุน\nนายประกัน\nนายหน้า\nนายอำเภอ\nนารายณ์หัตถ์\nนารีผล\nนาวิกโยธิน\nนำจับ\nนำพา\nนำทาง\nนำร่อง\nนำสืบ\nนำแสดง\nน้ำกรด\nน้ำกาม\nน้ำเกลือ\nน้ำข้าว\nน้ำแข็ง\nน้ำแข็งไส\nน้ำแข็งแห้ง\nน้ำครำ\nน้ำคร่ำ\nน้ำค้าง\nน้ำค้างแข็ง\nน้ำคาวปลา\nน้ำคำ\nน้ำเค็ม\nน้ำเคย\nน้ำเงิน\nน้ำเงี้ยว\nน้ำจัณฑ์\nน้ำจิ้ม\nน้ำใจ\nน้ำเชื้อ\nน้ำเชื่อม\nน้ำซาวข้าว\nน้ำดอกไม้\nน้ำดี\nน้ำตก\nน้ำตา\nน้ำตาล\nน้ำท่า\nน้ำนม\nน้ำนวล\nน้ำบาดาล\nน้ำประสานทอง\nน้ำประปา\nน้ำปลา\nน้ำป่า\nน้ำผึ้ง\nน้ำพริก\nน้ำพริกเผา\nน้ำพี้\nน้ำพุ\nน้ำมนต์\nน้ำมนตร์\nน้ำมัน\nน้ำมือ\nน้ำมูก\nน้ำเมา\nน้ำย่อย\nน้ำยา\nน้ำรัก\nน้ำแร่\nน้ำลาย\nน้ำเลี้ยง\nน้ำสต๊อก\nน้ำส้ม\nน้ำส้มสายชู\nน้ำสังข์\nน้ำสาบาน\nน้ำเสียง\nน้ำหนวก\nน้ำหนอง\nน้ำหนัก\nน้ำหน้า\nน้ำหนึ่ง\nน้ำหมึก\nน้ำหอม\nน้ำเหลือง\nน้ำอบ\nน้ำอ้อย\nน้ำอัดลม\nนิ่งเฉย\nนิจศีล\nนิดเดียว\nนิดหน่อย\nนิติกร\nนิติกรรม\nนิติธรรม\nนิตินัย\nนิติบัญญัติ\nนิติบุคคล\nนิติภาวะ\nนิติวิทยาศาสตร์\nนิติเวช\nนิติเวชศาสตร์\nนิติศาสตร์\nนิเทศศาสตร์\nนิ่มนวล\nนิรุกติศาสตร์\nนิเวศวิทยา\nนิศากร\nนิศากาล\nนิศาชล\nนิศารัตน์\nนี่แน่ะ\nนี่แหละ\nนี่เอง\nนึกคิด\nนุงถุง\nนุ่งห่ม\nนุ่มนวล\nนุ่มนิ่ม\nเนตรนารี\nเนติบัณฑิต\nเนยเทียม\nเนยใส\nเนิ่นนาน\nเนิบนาบ\nเนื้อความ\nเนื้อคู่\nเนื้อเค็ม\nเนื้องอก\nเนื้อตัว\nเนื้อตาย\nเนื้อที่\nเนื้อแท้\nเนื้อเปื่อย\nเนื้อผ้า\nเนื้อเพลง\nเนื้อไม้\nเนื้อเยื่อ\nเนื้อร้อง\nเนื้อร้าย\nเนื้อเรื่อง\nเนื้อหา\nเนืองนอง\nเนืองนิตย์\nเนืองแน่น\nแน่ใจ\nแน่ชัด\nแน่แท้\nแน่นอน\nแน่นิ่ง\nแน่แน่ว\nแน่นแฟ้น\nแน่นหนา\nแนบเนียน\nแนบแน่น\nแนวคิด\nแนวทาง\nแนวโน้ม\nแนวป่า\nแนวรบ\nแนวร่วม\nแนวหน้า\nแนวหลัง\nแน่วแน่\nแนะนำ\nแนะแนว\nโน้มน้าว\nในหลวง\nบกพร่อง\nบงกช\nบงการ\nบดบัง\nบทกลอน\nบทกวี\nบทความ\nบทคัดย่อ\nบทเฉพาะกาล\nบทนำ\nบทบัญญัติ\nบทบาท\nบทประพันธ์\nบทเพลง\nบทร้อง\nบทเรียน\nบทลงโทษ\nบทสนทนา\nบทอัศจรรย์\nบทจร\nบทบงสุ์\nบทมาลย์\nบทรัช\nบทเรศ\nบทวลัญช์\nบนบาน\nบรมครู\nบรมธาตุ\nบรมบพิตร\nบรมวงศานุวงศ์\nบรมอัฐิ\nบรรณพิภพ\nบรรณศาลา\nบรรณาการ\nบรรณาธิการ\nบรรณานุกรม\nบรรณารักษ์\nบรรณารักษศาสตร์\nบรรดามี\nบรรดาศักดิ์\nบรรทัดฐาน\nบรรพบุรุษ\nบรรลัยกัลป์\nบรรลัยจักร\nบริคณห์สนธิ\nบวงสรวง\nบ่วงบาศ\nบ้วนพระโอษฐ์\nบ่อเกิด\nบอกกล่าว\nบอกบท\nบอกบุญ\nบอกใบ้\nบอกปัด\nบ้องกัญชา\nบ้องตื้น\nบ้องไฟ\nบ้องหู\nบอดสี\nบ่อนทำลาย\nบอบช้ำ\nบอบบาง\nบอบแบบ\nบังโกลน\nบังโคลน\nบังใบ\nบั้งไฟ\nบังคับการ\nบังคับบัญชา\nบัญชาการ\nบัณฑุกัมพล\nบัดดล\nบัดเดี๋ยว\nบัดนั้น\nบัดนี้\nบัดสีบัดเถลิง\nบัตรเครดิต\nบัตรพลี\nบัตรสนเท่ห์\nบัตรสินเชื่อ\nบั่นทอน\nบั้นท้าย\nบั้นปลาย\nบั้นพระองค์\nบั้นเอว\nบันไดลิง\nบันไดเลื่อน\nบันเทิงคดี\nบัวลอย\nบัวบก\nบ้าจี้\nบ้าดีเดือด\nบ้าน้ำลาย\nบ้าบิ่น\nบ้าระห่ำ\nบ้าเลือด\nบ้าหอบฟาง\nบากบั่น\nบากหน้า\nบางตา\nบางเบา\nบางที\nบาดเจ็บ\nบาดแผล\nบาดหมาง\nบาตรใหญ่\nบาทบงกช\nบาทบงสุ์\nบาทบริจาริกา\nบาทวิถี\nบานเกล็ด\nบานตะเกียง\nบานตะไท\nบานเบอะ\nบานปลาย\nบานแผละ\nบานพับ\nบ้านจัดสรร\nบ้านช่อง\nบ้านนอก\nบ้านพัก\nบ้านเมือง\nบ้านรับรอง\nบ้านเรือน\nบาปกรรม\nบายศรี\nบ่ายเบี่ยง\nบ่ายหน้า\nบ่าวไพร่\nบิดเบี้ยว\nบิดเบือน\nบิดพลิ้ว\nบี้แบน\nบีบคั้น\nบีบรัด\nบึ้งตึง\nบึ้งบูด\nบุกบั่น\nบุกเบิก\nบุกรุก\nบุคลิกภาพ\nบุคลิกลักษณะ\nบุญธรรม\nบุญนิธิ\nบุญฤทธิ์\nบุบสลาย\nบุ้ยใบ้\nบุรุษเพศ\nบุหงารำไป\nบู้บี้\nบูชายัญ\nบูดบึ้ง\nบูดเบี้ยว\nเบาความ\nเบาใจ\nเบาบาง\nเบาปัญญา\nเบามือ\nเบาแรง\nเบาสมอง\nเบาหวาน\nเบาโหวง\nเบ้าตา\nเบาะแส\nเบิกความ\nเบิกบาน\nเบี้ยล่าง\nเบี้ยเลี้ยง\nเบี้ยหวัด\nเบี่ยงบ่าย\nเบียดบัง\nเบียดเบียน\nเบียดเสียด\nเบื้องต้น\nเบื้องบน\nเบื้องหน้า\nเบื้องหลัง\nแบกะดิน\nแบเบาะ\nแบ่งเบา\nแบ่งปัน\nแบ่งแยก\nแบบฉบับ\nแบบแปลน\nแบบแผน\nแบบฝึกหัด\nแบบพิมพ์\nแบบสอบถาม\nแบบอย่าง\nแบะแฉะ\nแบะท่า\nโบแดง\nโบราณคดี\nโบราณวัตถุ\nโบราณสถาน\nใบขับขี่\nใบจอง\nใบตอง\nใบแทรก\nใบบอก\nใบบุญ\nใบเบิกทาง\nใบปลิว\nใบพัด\nใบโพ\nใบไม้\nใบระกา\nใบรับรอง\nใบลา\nใบเลี้ยง\nใบสั่ง\nใบสำคัญ\nใบสุทธิ\nใบเสร็จ\nใบหน้า\nใบอนุญาต\nใบระกา\nปกครอง\nปกคลุม\nปกป้อง\nปกปิด\nปฏิบัติการ\nปฏิบัติบูชา\nปฐพีวิทยา\nปฐมฌาน\nปฐมทัศน์\nปฐมเทศนา\nปฐมนิเทศ\nปฐมพยาบาล\nปฐมยาม\nปฐมฤกษ์\nปฐมวัย\nปฐมสมโพธิ\nปนเป\nป่นปี้\nปมเขื่อง\nปมเด่น\nปมด้อย\nปรนเปรอ\nปรบไก่\nปรบมือ\nปรสิตวิทยา\nประโปรย\nประพรม\nประกันชีวิต\nประกันภัย\nประจักษ์พยาน\nประจัญบาน\nประจันหน้า\nประจำการ\nประจำเดือน\nประจำเมือง\nประจำยาม\nประชดประชัน\nประชากร\nประชากรศาสตร์\nประชาคม\nประชาชน\nประชาราษฎร์\nประชาชาติ\nประชาชี\nประชาทัณฑ์\nประชาบาล\nประชาพิจารณ์\nประชาภิบาล\nประชามติ\nประชาสงเคราะห์\nประชาสัมพันธ์\nประดับประดา\nประดามี\nประดาน้ำ\nประเดี๋ยวเดียว\nประเดี๋ยวนี้\nประทับใจ\nประทุษร้าย\nประเทศราช\nประพาสต้น\nประเพณีนิยม\nประลัยกัลป์\nประวัติการณ์\nประวัติศาสตร์\nประสบการณ์\nประสบการณ์นิยม\nประสาทการ\nประสูติการ\nประสูติกาล\nประเส\nปรับทุกข์\nปรับโทษ\nปรับปรุง\nปรากฏการณ์\nปราดเปรียว\nปราดเปรื่อง\nปราบปราม\nปริญญาบัตร\nปรัยัติธรรม\nปรุโปร่ง\nปลงใจ\nปลงตก\nปลดทุกข์\nปลดปลง\nปลดปล่อย\nปลดเปลื้อง\nปลดระวาง\nปลดแอก\nปล้นสะดม\nปลอกกระสุน\nปลอกคอ\nปลอดโปร่ง\nปลอดภัย\nปลอมปน\nปลอมแปลง\nปลอบโยน\nปล่อยใจ\nปล่อยตัว\nปล่อยปละ\nปลั๊กไฟ\nปลากริม\nปลาเค็ม\nปลาจ่อม\nปลาเจ่า\nปลาแดก\nปลาตู้\nปลาทอง\nปลาร้า\nปลาส้ม\nปลาดาว\nปลาบิน\nปลาฝา\nปลาวาฬ\nปลาหมึก\nปลาบปลื้ม\nปลายข้าว\nปลายแถว\nปลายทาง\nปลิ้นปลอก\nปลิ้นปล้อน\nปลีกตัว\nปลีกย่อย\nปลุกใจ\nปลุกปล้ำ\nปลุกปั่น\nปลุกระดม\nปลุกเสก\nปลูกฝัง\nปลูกสร้าง\nปวดถ่วง\nปวดมวน\nปวดร้าว\nป่วนปั่น\nป่วยการ\nปอกลอก\nป้องกัน\nปักใจ\nปักดำ\nปักหลัก\nปัจเจกบุคคล\nปัจเจกพุทธะ\nปัจเจกโพธิ\nปัจฉิมชน\nปัจฉิมทิศ\nปัจฉิมภาค\nปัจฉิมยาม\nปัจฉิมลิขิต\nปัจฉิมวัย\nปัจฉิมวาจา\nปัญญาชน\nปัญญาวิมุติ\nปัญญาอ่อน\nปัดเป่า\nปันส่วน\nปั่นป่วน\nปั่นแปะ\nปั่นหัว\nปั้นจิ้ม\nปั้นเจ๋อ\nปั้นปึ่ง\nปั้นสิบ\nปั๊มน้ำมัน\nป่าช้า\nป่าชายเลน\nป่าดง\nป่าดงดิบ\nป่าดิบ\nป่าเถื่อน\nป่าเบญจพรรณ\nป่าละเมาะ\nปากกา\nปากขอ\nปากแข็ง\nปากคอ\nปากคำ\nปากคีบ\nปากจัด\nปากน้ำ\nปากเปล่า\nปากเสียง\nปานกลาง\nป่านนี้\nป้านลม\nป้ายสี\nป่าวร้อง\nปิดฉาก\nปิดบัง\nปิตุฆาต\nปิตุภูมิ\nปีมะโว้\nปีแสง\nปี่กลาง\nปี่ไฉน\nปี่ชวา\nปี่นอก\nปี่ใน\nปี่พาทย์\nปี่อ้อ\nปีกกา\nปีนเกลียว\nปีนป่าย\nปึกแผ่น\nปึงปัง\nปืนกล\nปืนครก\nปืนพก\nปืนยา\nปืนยาว\nปืนลม\nปืนเล็ก\nปืนเล็กยาว\nปืนสั้น\nปืนใหญ่\nปุบปับ\nปุ๊บปั๊บ\nปุ่มเปือก\nปุยฝ้าย\nปุ๋ยคอก\nปุ๋ยเคมี\nปุ๋ยวิทยาศาสตร์\nปุ๋ยหมัก\nปุ๋ยอินทรีย์\nปูจ๋า\nปูเสฉวน\nปู่เจ้า\nปู่ทวด\nปูนขาว\nปูนซีเมนต์\nปูนดิบ\nปูนแดง\nปูนปลาสเตอร์\nปูนปั้น\nเป็ดเทศ\nเป็ดน้ำ\nเป็นกลาง\nเป็นใจ\nเป็นต้น\nเป็นต่อ\nเป็นรอง\nเป็นไร\nเป็นลม\nเป็นห่วง\nเป็นอยู่\nเปรมปรีดิ์\nเปรอะเปื้อน\nเปรียบเทียบ\nเปรียบเปรย\nเปรี้ยวปาก\nเปรี้ยวหวาน\nเปรื่องปราด\nเปลญวน\nเปล่งปลั่ง\nเปล่าดาย\nเปล่าเปลี่ยว\nเปลี่ยนใจ\nเปลี่ยนตัว\nเปลี่ยนแปลง\nเปลี่ยนมือ\nเปลี่ยนหน้า\nเป๋อเหลอ\nเปะปะ\nเป่ากบ\nเป้านิ่ง\nเป้าหมาย\nเปิดฉาก\nเปิดเปิง\nเปิดโปง\nเปิดผนึก\nเปิดเผย\nเปียกปูน\nแป้งสาลี\nแป้งนวล\nแป้งเปียก\nแป้งมัน\nแป้งฝุ่น\nแป้งร่ำ\nแป้งสิงคโปร์\nแป้งหมี่\nแปดปน\nแปดเปื้อน\nแปรปรวน\nแปรผัน\nแปรพักตร์\nแปรรูป\nแปรอักษร\nแปลกปลอม\nแปะโป้ง\nโป้ปด\nโปร่งแสง\nโปร่งใส\nโปรดปราน\nโปรยทาน\nโปรยปราย\nโปโลน้ำ\nผกผัน\nผกากรอง\nผงขาว\nผงชูรส\nผงซักฟอก\nผงฟู\nผดุงครรภ์\nผมไฟ\nผลพลอยได้\nผลลัพธ์\nผลัดเปลี่ยน\nผลิตผล\nผลิตภัณฑ์\nผลุบโผล่\nผสมเทียม\nผสมผสาน\nผสมผเส\nผสมพันธุ์\nผสมโรง\nผสมเสร็จ\nผ่องแผ้ว\nผ่องใส\nผ่อนคลาย\nผ่อนชำระ\nผ่อนปรน\nผ่อนผัน\nผ่อนส่ง\nผอมโซ\nผอมแห้ง\nผักชี\nผักตบชวา\nผักบุ้ง\nผังเมือง\nผัดผ่อน\nผันแปร\nผันผวน\nผ่าตัด\nผ่าเผย\nผ่าหมาก\nผ่าเหล่า\nผ้าขนหนู\nผ้าขาวม้า\nผ้าขี้ริ้ว\nผ้าเช็ดตัว\nผ้าเช็ดปาก\nผ้าเช็ดมือ\nผ้าเช็ดหน้า\nผ้าดิบ\nผ้าต่วน\nผ้าไตร\nผ้าถุง\nผ้าแถบ\nผ้านวม\nผ้านุ่ง\nผ้าใบ\nผ้าป่า\nผ้าป่าน\nผ้าผ่อน\nผ้าพันคอ\nผ้าพันแผล\nผ้าแพร\nผ้าโพกหัว\nผ้ามัดหมี่\nผ้ายาง\nผ้าลูกไม้\nผ้าเหลือง\nผ้าอนามัย\nผ้าอ้อม\nผาดโผน\nผาติกรรม\nผิดหวัง\nผิวเผิน\nผิวพรรณ\nผิวหนัง\nผีกระสือ\nผีกระหัง\nผีกองกอย\nผีโขมด\nผีดิบ\nผีตองเหลือง\nผีถ้วยแก้ว\nผีแถน\nผีทะเล\nผีบุญ\nผีปอบ\nผีพุ่งไต้\nผีฟ้า\nผีเรือน\nผีสาง\nผีเสื้อ\nผีห่า\nผึ่งผาย\nผุดผ่อง\nผุดผาด\nผู้คน\nผู้คุม\nผู้จัดการ\nผู้ชาย\nผู้เชี่ยวชาญ\nผู้ดี\nผู้โดยสาร\nผู้ต้องขัง\nผู้ต้องหา\nผู้แทน\nผู้น้อย\nผู้บริโภค\nผู้บังคับบัญชา\nผู้ปกครอง\nผู้ประกอบการ\nผู้ป่วย\nผู้พิพากษา\nผู้เยาว์\nผู้ร้าย\nผู้วิเศษ\nผู้สื่อข่าว\nผู้เสียหาย\nผู้หญิง\nผู้ใหญ่\nผู้ใหญ่บ้าน\nผูกขวัญ\nผูกขาด\nผูกพัน\nผูกมัด\nเผชิญหน้า\nเผด็จการ\nเผด็จศึก\nเผยแผ่\nเผยแพร่\nเผละผละ\nเผ่าพันธุ์\nเผื่อแผ่\nแผงลอย\nแผนการ\nแผนงาน\nแผนที่\nแผนผัง\nแผนภาพ\nแผนภูมิ\nแผ่นดิน\nแผ่นเสียง\nแผ้วพาน\nโผงผาง\nฝนทอง\nฝอยทอง\nฝักแค\nฝักบัว\nฝักฝ่าย\nฝักใฝ่\nฝังใจ\nฝังหัว\nฝาชี\nฝาแฝด\nฝาละมี\nฝ่าพระบาท\nฝ่าฝืน\nฝ่าฟัน\nฝ้าฟาง\nฝากตัว\nฝากฝัง\nฝีดาษ\nฝีมะม่วง\nฝีจักร\nฝีเท้า\nฝีปาก\nฝีพาย\nฝีมือ\nฝีเย็บ\nฝึกงาน\nฝึกปรือ\nฝึกฝน\nฝึกสอน\nฝึกหัด\nฝืดเคือง\nใฝ่ฝัน\nพงพี\nพงศ์พันธุ์\nพญาโศก\nพญาไฟ\nพบปะ\nพบพาน\nพรสวรรค์\nพรมคด\nพรมแดน\nพรมมิ\nพรรคพวก\nพรรณราย\nพรวดพราด\nพรหมชาติ\nพรหมลิขิต\nพรหมโลก\nพรหมวิหาร\nพร้อมใจ\nพร้อมพรั่ง\nพร้อมเพรียง\nพร้อมมูล\nพร้อมสรรพ\nพร้อมหน้า\nพระครู\nพระคุณ\nพระเคราะห์\nพระเครื่อง\nพระเจ้า\nพระเจ้าอยู่หัว\nพระชายา\nพระทัย\nพระนาง\nพระนางเจ้า\nพระเป็นเจ้า\nพระผู้เป็นเจ้า\nพระพิมพ์\nพระพุทธเจ้า\nพระพุทธองค์\nพระภูมิ\nพระยา\nพระรอง\nพระสนม\nพระสนมเอก\nพระองค์\nพระองค์เจ้า\nพระเอก\nพรั่งพร้อม\nพรั่งพรู\nพรั่นพรึง\nพร่างพราว\nพรายน้ำ\nพรายแพรว\nพราวแพรว\nพร่ำพลอด\nพร่ำเพรื่อ\nพร่ำเพ้อ\nพริกไทย\nพริ้งพราย\nพริ้งเพรา\nพริ้งเพริศ\nพริบตา\nพริ้มพราย\nพริ้มเพรา\nพรุ่งนี้\nพฤติกรรม\nพฤติการณ์\nพฤตินัย\nพลการ\nพลขับ\nพลความ\nพลเมือง\nพลรบ\nพลร่ม\nพลเรือน\nพลโลก\nพลศึกษา\nพลบค่ำ\nพลอดรัก\nพลังงาน\nพลังเงียบ\nพลังจิต\nพลั้งปาก\nพลั้งเผลอ\nพลั้งพลาด\nพลัดถิ่น\nพลัดพราก\nพลาดท่า\nพลาดพลั้ง\nพลิกแพลง\nพลีกรรม\nพลุ่งพล่าน\nพวกพ้อง\nพวงมาลัย\nพวงมาลา\nพวงหรีด\nพวงคราม\nพวงชมพู\nพวงแสด\nพ่วงพี\nพวยน้ำ\nพวยพุ่ง\nพสกนิกร\nพหุคูณ\nพหุภาคี\nพหูพจน์\nพหูสูต\nพอควร\nพอใจ\nพอใช้\nพอใช้ได้\nพอดี\nพอตัว\nพอทำเนา\nพอประมาณ\nพอเพียง\nพอแรง\nพอสมควร\nพอเหมาะ\nพ่อขุน\nพ่อครัว\nพ่อตา\nพ่อบ้าน\nพ่อพันธุ์\nพ่อม่าย\nพ่อเมือง\nพ่อเลี้ยง\nพ่อสื่อ\nพอกพูน\nพ้องพาน\nพักผ่อน\nพักพิง\nพักฟื้น\nพักร้อน\nพักแรม\nพัดยศ\nพัดลม\nพันพัว\nพับฐาน\nพับเพียบ\nพัวพัน\nพาซื่อ\nพาดพิง\nพิณพาทย์\nพิธีกร\nพิธีกรรม\nพิธีการ\nพิธีรีตอง\nพิธีสาร\nพินัยกรรม\nพิมพ์เขียว\nพิมพ์ใจ\nพิมพ์ดีด\nพิษสง\nพี่น้อง\nพี่เบิ้ม\nพี่เลี้ยง\nพึงใจ\nพึงพอใจ\nพึ่งพา\nพึ่งพิง\nพืชพันธุ์\nพืชมงคล\nพื้นฐาน\nพื้นที่\nพื้นบ้าน\nพื้นเพ\nพื้นเมือง\nพื้นเสีย\nพุพอง\nพุทธกาล\nพุทธคุณ\nพุทธจักร\nพุทธเจดีย์\nพุทธฎีกา\nพุทธปฏิมา\nพุทธปฏิมากร\nพุทธมามกะ\nพุทธศักราช\nพุทธศาสนิกชน\nพุทธองค์\nพุทธชาด\nพุทธรักษา\nพุ่มพวง\nพุ่มไม้\nพู่กัน\nพูดจา\nเพ่งเล็ง\nเพดานบิน\nเพดานปาก\nเพริศพราย\nเพริศพริ้ง\nเพริศแพร้ว\nเพรียกพร้อง\nเพรียวลม\nเพลงเชิด\nเพลงยาว\nเพลิงกัลป์\nเพลินใจ\nเพลินตา\nเพลี่ยงพล้ำ\nเพ้อฝัน\nเพาะกาย\nเพาะชำ\nเพาะปลูก\nเพิกถอน\nเพิกเฉย\nเพิ่มเติม\nเพิ่มพูน\nเพียงตา\nเพียงพอ\nเพียบแประ\nเพียบพร้อม\nเพื่อนเกลอ\nเพื่อนตาย\nเพื่อนบ้าน\nเพื่อนฝูง\nเพื่อนยาก\nแพ้ท้อง\nแพร่หลาย\nแพร่งพราย\nแพรวพราว\nโพธิญาณ\nโพธิบัลลังก์\nโพธิสมภาร\nโพธิสัตว์\nโพ้นทะเล\nโพยภัย\nไพ่ตาย\nไพ่ป๊อก\nไพรวัน\nไพรสณฑ์\nไพรสัณฑ์\nไพร่พล\nไพร่ฟ้า\nไพร่สม\nไพร่ส่วย\nไพร่หลวง\nฟกช้ำ\nฟองเต้าหู้\nฟองน้ำ\nฟองมัน\nฟ้องกลับ\nฟ้องร้อง\nฟอนเฟะ\nฟักทอง\nฟัดเฟียด\nฟันดาบ\nฟันฝ่า\nฟันแท้\nฟันน้ำนม\nฟันปลา\nฟันฟาง\nฟันเฟือง\nฟันม้า\nฟันเลื่อย\nฟันหนู\nฟั่นเฝือ\nฟั่นเฟือน\nฟื้นตัว\nฟื้นฝอย\nฟื้นฟู\nฟุ้งซ่าน\nฟุ้งเฟ้อ\nฟุ้งเฟื่อง\nฟุตบอล\nฟูฟ่อง\nฟูเฟื่อง\nฟูมฟัก\nฟูมฟาย\nเฟะฟะ\nเฟื่องฟ้า\nเฟื่องฟุ้ง\nเฟื่องฟู\nไฟฉาย\nไฟแช็ก\nไฟธาตุ\nไฟฟ้า\nภัตกิจ\nภาคทัณฑ์\nภาคพื้น\nภาคเรียน\nภาคภูมิ\nภาพถ่าย\nภาพนิ่ง\nภาพประกอบ\nภาพพจน์\nภาพยนตร์\nภาพลวงตา\nภาพลักษณ์\nภายนอก\nภายใน\nภายหน้า\nภายหลัง\nภารกิจ\nภารธุระ\nภารโรง\nภารตวิทยา\nภาษาศาสตร์\nภาสกร\nภิญโญภาพ\nภินชาติ\nภูธร\nภูธเรศ\nภูบาล\nภูเบศ\nภูเบศวร์\nภูเขา\nภูเขาไฟ\nภูผา\nภูตคาม\nภูตบดี\nภูตรูป\nภูเตศวร\nภูมินทร์\nภูมิบาล\nภูมิประเทศ\nภูมิภาค\nภูมิรัฐศาสตร์\nภูมิลำเนา\nภูมิศาสตร์\nภูมิอากาศ\nภูมิธรรม\nภูมิปัญญา\nภูมิรู้\nภูมิใจ\nภูมิฐาน\nภูมิคุ้มกัน\nภูมิแพ้\nภูษาโยง\nเภทภัย\nเภสัชกร\nเภสัชกรรม\nเภสัชวิทยา\nเภสัชศาสตร์\nโภคทรัพย์\nโภคภัณฑ์\nโภชนากร\nโภชนาการ\nมกุฎราชกุมาร\nมงคลแฝด\nมงคลสูตร\nมงคลหัตถี\nมณเฑียรบาล\nมดดำ\nมดแดง\nมดเท็จ\nมดยอบ\nมดลูก\nมธุปายาส\nมธุรส\nมนเทียรบาล\nมนุษย์กบ\nมโนกรรม\nมโนคติ\nมโนทุจริต\nมโนธรรม\nมโนภาพ\nมโนมัย\nมโนรถ\nมโนรมย์\nมโนสุจริต\nมรรคนายก\nมรรคผล\nมฤคชาติ\nมฤคทายวัน\nมฤคราช\nมลทิน\nมลพิษ\nมลสาร\nมวกเหล็ก\nม้วนหน้า\nมวยไทย\nมวยปล้ำ\nมวยล้ม\nมวยวัด\nมวยสากล\nมวยหมู่\nมวลสาร\nมอคราม\nมอซอ\nมอหมึก\nมองเมียง\nมอบตัว\nมอบหมาย\nมอมเมา\nมะขามเทศ\nมะขามป้อม\nมะขามเปียก\nมะเขือเทศ\nมะเขือพวง\nมะพร้าวแก้ว\nมักคุ้น\nมักจี่\nมักง่าย\nมักน้อย\nมักมาก\nมักใหญ่\nมั่งคั่ง\nมั่งมี\nมัจจุราช\nมัชฌิมนิกาย\nมัชฌิมประเทศ\nมัชฌิมยาม\nมัชฌิมวัย\nมัดจำ\nมัดหมี่\nมัธยมกาล\nมัธยมศึกษา\nมันแกว\nมันเทศ\nมันฝรั่ง\nมันเปลว\nมันสมอง\nมั่นคง\nมั่นใจ\nมั่นหมาย\nมั่นเหมาะ\nมัวเมา\nมัวหมอง\nมั่วสุม\nม้าเทศ\nม้าน้ำ\nม้ามืด\nม้าเร็ว\nม้าล่อ\nม้าลาย\nมากมาย\nมาตรการ\nมาตรฐาน\nมาตราส่วน\nมาตุคาม\nมาตุฆาต\nมาตุภูมิ\nม่านตา\nม่านบังตา\nมายากร\nมายากล\nมายาการ\nมายาวี\nมารผจญ\nมารวิชัย\nมารสังคม\nมารหัวขน\nมาลาการ\nมิ่งขวัญ\nมิ่งมิตร\nมิจฉาจาร\nมิจฉาชีพ\nมิดชิด\nมิดเมี้ยน\nมิดหมี\nมิตรจิต\nมิตรภาพ\nมิตรสหาย\nมิน่า\nมีหน้า\nมีดโกน\nมีดดาบ\nมีดโต้\nมีดพก\nมีดพับ\nมีดสั้น\nมึนงง\nมึนชา\nมึนตึง\nมึนเมา\nมืดครึ้ม\nมืดมน\nมืดมัว\nมือจับ\nมือดี\nมือเติบ\nมือปืน\nมือเปล่า\nมือมืด\nมือสอง\nมือเสือ\nมือหนึ่ง\nมือใหม่\nมุกตลก\nมุขปาฐะ\nมุขมนตรี\nมุ่งมั่น\nมุ่งมาด\nมุ่งหน้า\nมุ่งหมาย\nมุ่งหวัง\nมุ้งลวด\nมุ้งสายบัว\nมุมก้ม\nมุมกลับ\nมุมเงย\nมุมฉาก\nมุมตรง\nมุมป้าน\nมุมมืด\nมุมแย้ง\nมุมสะท้อน\nมุมหักเห\nมุมแหลม\nมุสาวาท\nมูกเลือด\nมูกมัน\nมูกหลวง\nมูนดิน\nมูลฐาน\nมูลนาย\nมูลนิธิ\nมูลเหตุ\nมูลค่า\nมูลฝอย\nเม็ดเงิน\nเม็ดเลือด\nเม็ดโลหิต\nเม่นทะเล\nเมรุมาศ\nเมรุราช\nเมล์อากาศ\nเมาดิบ\nเมามัน\nเมามัว\nเมามาย\nเมินเฉย\nเมียน้อย\nเมียหลวง\nเมียงมอง\nเมี่ยงลาว\nเมี่ยงส้ม\nเมื่อกี้\nเมื่อตะกี้\nเมื่อใด\nเมื่อไร\nเมื่อไหร่\nเมื่อนั้น\nเมืองขึ้น\nเมืองท่า\nเมืองนอก\nเมืองหลวง\nเมื่อยขบ\nเมื่อยล้า\nแม่กอง\nแม่กุญแจ\nแม่คุณ\nแม่งาน\nแม่เจ้า\nแม่ชี\nแม่ทัพ\nแม่นม\nแม่น้ำ\nแม่บท\nแม่บ้าน\nแม่เบี้ย\nแม่พระ\nแม่พิมพ์\nแม่เพลง\nแม่มด\nแม่ม่าย\nแม่ไม้\nแม่ยก\nแม่ยาย\nแม่ร้าง\nแม่เรือน\nแม่แรง\nแม่เล้า\nแม่เลี้ยง\nแม่สี\nแม่สื่อ\nแม่เหล็ก\nแมงมุม\nแม่นยำ\nแมลงช้าง\nแมลงวัน\nแมลงปอ\nแมลงภู่\nแมลงเม่า\nแมวเซา\nแมวน้ำ\nแมวป่า\nแมวมอง\nไม้กลัด\nไม้กวาด\nไม้กางเขน\nไม้เกาหลัง\nไม้ขีดไฟ\nไม้จิ้มฟัน\nไม้เด็ด\nไม้ตาย\nไม้ตีพริก\nไม้ที\nไม้เท้า\nไม้บรรทัด\nไม้เมตร\nไม้ระแนง\nไม้เรียว\nไม้หมอน\nไม้อัด\nไม้จัตวา\nไม้ตรี\nไม้ไต่คู้\nไม้โท\nไม้ผัด\nไม้มลาย\nไม้ม้วน\nไม้ยมก\nไม้หน้า\nไม้หันอากาศ\nไม้เอก\nยกกลีบ\nยกครู\nยกเครื่อง\nยกเค้า\nยกทรง\nยกฟ้อง\nยกเมฆ\nยกยอ\nยกย่อง\nยกเลิก\nยกเว้น\nย่นย่อ\nยมทูต\nยมบาล\nยมราช\nยมโลก\nยวดยิ่ง\nยวดยาน\nยวนยี\nยวบยาบ\nย่อท้อ\nย่อส่วน\nย่อหน้า\nย่อหย่อน\nยอกย้อน\nยองใย\nย่องเบา\nย่องแย่ง\nยอดเยี่ยม\nยอดอก\nย้อนยอก\nย้อนรอย\nย้อนศร\nย้อนแสง\nย้อนหลัง\nยอบแยบ\nยอมความ\nย่อมเยา\nย่อยยับ\nยักยอก\nยักย้าย\nยักเยื้อง\nยัญกรรม\nยัญพิธี\nยัดเยียด\nยับเยิน\nยับยั้ง\nยั่วยวน\nยั่วยุ\nยั่วเย้า\nยากวาด\nยากันยุง\nยาเขียว\nยาใจ\nยาฉุน\nยาชา\nยาซัด\nยาดอง\nยาแดง\nยาถ่าย\nยาธาตุ\nยานัตถุ์\nยาเบื่อ\nยาโป๊\nยาแฝด\nยาพิษ\nยาระบาย\nยาสลบ\nยาสั่ง\nยาสีฟัน\nยาสูบ\nยาเส้น\nยาเสพติด\nยาหม่อง\nยาเหลือง\nย่าทวด\nย่านาง\nยากแค้น\nยากจน\nยากเย็น\nยากไร้\nยางนอก\nยางใน\nยางมะตอย\nยางมะตูม\nยางลบ\nยางสน\nยางอาย\nย่างกราย\nย่างเยื้อง\nย่างสด\nย่างสามขุม\nย่างเหยียบ\nยานเกราะ\nยานพาหนะ\nยานอวกาศ\nยานคาง\nยายทวด\nยาวเฟื้อย\nยาวยืด\nยาวเหยียด\nยำทวาย\nยำใหญ่\nยำเกรง\nยำเยง\nย่ำต๊อก\nย่ำยี\nย่ำแย่\nยิงเป้า\nยิ่งนัก\nยิ่งยวด\nยิ่งใหญ่\nยินดี\nยินยอม\nยินร้าย\nยิ้มกริ่ม\nยิ้มแฉ่ง\nยิ้มแต้\nยิ้มแป้น\nยิ้มเผล่\nยิ้มเยาะ\nยิ้มแย้ม\nยียวน\nยึดครอง\nยึดถือ\nยึดมั่น\nยึดเหนี่ยว\nยืดยาด\nยืดยาว\nยืดเยื้อ\nยืดหยุ่น\nยืดอก\nยืนกราน\nยืนต้น\nยืนพื้น\nยืนยง\nยืนยัน\nยืนหยัด\nยื้อยุด\nยุยง\nยุแยง\nยุแหย่\nยุคลบาท\nยุคเข็ญ\nยุคทอง\nยุคมืด\nยุ่งขิง\nยุ่งยาก\nยุ่งเหยิง\nยุติธรรม\nยุทธการ\nยุทธนาวี\nยุทธปัจจัย\nยุทธภัณฑ์\nยุทธภูมิ\nยุทธวิธี\nยุทธศาสตร์\nยุทธหัตถี\nยุทธนาการ\nยุทธนาธิการ\nยุบยับ\nยุบยิบ\nยุพราช\nยู่ยี่\nเย็นเจี๊ยบ\nเย็นใจ\nเย็นฉ่ำ\nเย็นเฉียบ\nเย็นชา\nเย็นชืด\nเย็นตา\nเย็นเยียบ\nเย็นเยือก\nเย็นวาบ\nเย็นวูบ\nเย็บกี่\nเย็บจักร\nเย็บด้าย\nเย้ยหยัน\nเย้าหยอก\nเยาะเย้ย\nเยี่ยมกราย\nเยี่ยมเยียน\nเยี่ยมเยือน\nเยี่ยมยอด\nเยื่อเคย\nเยื่อใย\nเยือกเย็น\nเยื้องกราย\nเยื้องยัก\nเยื้องย่าง\nแยกย้าย\nแยกแยะ\nแย่งชิง\nแยบคาย\nแยบยล\nแย้มพราย\nแย้มยิ้ม\nแย้มสรวล\nโยเย\nโย้เย้\nโยกโคลง\nโยกย้าย\nโยกโย้\nโยนกลอง\nใยหิน\nรกชัฏ\nรกร้าง\nรกเรี้ยว\nรกเรื้อ\nรกราก\nรงควัตถุ\nรชนีกร\nรถกระบะ\nรถเก๋ง\nรถเข็น\nรถแข่ง\nรถจักร\nรถจี๊ป\nรถตู้\nรถทัวร์\nรถบรรทุก\nรถพ่วง\nรถพยาบาล\nรถไฟ\nรถไฟฟ้า\nรถม้า\nรถเมล์\nรถยนต์\nรถราง\nรถลาก\nรถสปอร์ต\nรถสิบล้อ\nรบกวน\nรบรา\nรบเร้า\nรมดำ\nร่มเกล้า\nร่มชูชีพ\nร่มเย็น\nร่มรื่น\nร่วงโรย\nรวงผึ้ง\nรวงรัง\nรวดเร็ว\nรวนเร\nรวบยอด\nรวบรวม\nรวบรัด\nรวมพล\nรวมหัว\nร่วมใจ\nร่วมเพศ\nร่วมมือ\nร่วมรัก\nร่วมสมัย\nรวยริน\nรวยรื่น\nรสชาติ\nรสนิยม\nรองท้อง\nรองเท้า\nรองพื้น\nร่องน้ำ\nร่องรอย\nร้องขอ\nร้องทุกข์\nร้องเรียน\nร้องห่ม\nร้องไห้\nรองช้ำ\nรองทรง\nรอดชีวิต\nรอดตัว\nรอดตาย\nรอนแรม\nร่อนเร่\nร้อนใจ\nร้อนตัว\nร้อนรน\nร้อนรุ่ม\nร้อนวิชา\nร้อนอาสน์\nรอบจัด\nรอบเดือน\nรอบรู้\nรอยร้าว\nร่อยหรอ\nร้อยละ\nร้อยกรอง\nร้อยแก้ว\nร้อยหวาย\nระนาดทุ้ม\nระนาดเอก\nระเบิดขวด\nระเบิดมือ\nระเบียบการ\nรักใคร่\nรักษาการ\nรักษาการณ์\nรังไข่\nรังแตน\nรังนก\nรังผึ้ง\nรังเพลิง\nรังมด\nรังสรรค์\nรังสฤษฏ์\nรั้งรอ\nรังสีแพทย์\nรังสีวิทยา\nรัชกาล\nรัชทายาท\nรัชนีกร\nรัฐธรรมนูญ\nรัฐบาล\nรัฐบุรุษ\nรัฐประศาสน์\nรัฐประหาร\nรัฐพิธี\nรัฐมนตรี\nรัฐวิสาหกิจ\nรัฐศาสตร์\nรัฐสภา\nรัดกุม\nรัดเกล้า\nรัดตัว\nรัดประคด\nรัดรึง\nรัดรูป\nรัตติกาล\nรับขวัญ\nรับจ้าง\nรับช่วง\nรับใช้\nรับซื้อ\nรับทราบ\nรับประกัน\nรับประทาน\nรับปาก\nรับผิด\nรับผิดชอบ\nรับฟ้อง\nรับฟัง\nรับมือ\nรับรอง\nรับรู้\nรับสมัคร\nรับสั่ง\nรับหน้า\nรับเหมา\nรั่วไหล\nรามือ\nร่าเริง\nรากแก้ว\nรากขวัญ\nรากฐาน\nรากฟัน\nรากศัพท์\nรากเหง้า\nร่างกาย\nร่างแห\nร้างรา\nราชกรณียกิจ\nราชการ\nราชกิจ\nราชครู\nราชฐาน\nราชทัณฑ์\nราชทินนาม\nราชทูต\nราชธานี\nราชนาวี\nราชบัณฑิต\nราชบัลลังก์\nราชบาตร\nราชบุตร\nราชปะแตน\nราชภัฏ\nราชมัล\nราชยาน\nราชรถ\nราชลัญจกร\nราชเลขาธิการ\nราชเลขานุการ\nราชวงศ์\nราชวัติ\nราชสกุล\nราชสมบัติ\nราชสาส์น\nราชหัตถเลขา\nราชองครักษ์\nราชโองการ\nราชาคณะ\nราชาศัพท์\nราชินีนาถ\nร้านชำ\nร้านรวง\nราบคาบ\nราบรื่น\nราบเรียบ\nรายการ\nรายงาน\nรายจ่าย\nรายได้\nรายทาง\nรายรับ\nรายล้อม\nรายละเอียด\nรายวิชา\nร่ายยาว\nร่ายรำ\nร้ายกาจ\nร้ายแรง\nราวนม\nราวป่า\nร้าวฉาน\nร้าวราน\nรำพัด\nรำแพน\nรำวง\nร่ำไป\nร่ำร้อง\nร่ำเรียน\nร่ำไร\nร่ำลา\nร่ำไห้\nริเริ่ม\nริอ่าน\nริมฝีปาก\nริ้วรอย\nรีบร้อน\nรีบรุด\nรีบเร่ง\nรื่นรมย์\nรื่นเริง\nรื้อถอน\nรื้อฟื้น\nรุกฆาต\nรุกราน\nรุกล้ำ\nรุกไล่\nรุ่งขึ้น\nรุ่งแจ้ง\nรุ่งเช้า\nรุ่งเรือง\nรุ่งโรจน์\nรุ่งสว่าง\nรุ่งสาง\nรุ่งอรุณ\nรุจิเรข\nรุดหน้า\nรุนแรง\nรุมเร้า\nรุมล้อม\nรุ่มรวย\nรุ่มร้อน\nรุ่ยร่าย\nรู้แกว\nรู้ความ\nรู้คุณ\nรู้งาน\nรู้จัก\nรู้แจ้ง\nรู้ใจ\nรู้เชิง\nรู้ตัว\nรู้ทัน\nรู้เท่า\nรู้เรื่อง\nรู้สำนึก\nรู้สึก\nรู้เห็น\nรูปการณ์\nรูปโฉม\nรูปฌาน\nรูปถ่าย\nรูปทรง\nรูปธรรม\nรูปแบบ\nรูปพรรณ\nรูปพรหม\nรูปภพ\nรูปภาพ\nรูปร่าง\nรูปสมบัติ\nเร่ร่อน\nเร่งด่วน\nเร่งมือ\nเร่งรัด\nเร่งรีบ\nเร่งเร้า\nเร้นลับ\nเร่อร่า\nเร่าร้อน\nเราะราย\nเราะร้าย\nเริงใจ\nเริงรมย์\nเริดร้าง\nเริ่มต้น\nเริ่มแรก\nเรี่ยราด\nเรี่ยไร\nเรียกคืน\nเรียกตัว\nเรียกร้อง\nเรียกหา\nเรียบร้อย\nเรียงความ\nเรียงตัว\nเรียงเบอร์\nเรียงพิมพ์\nเรียงเม็ด\nเรียงราย\nเรียนรู้\nเรียบร้อย\nเรียบเรียง\nเรียบวุธ\nเรี่ยมเร้\nเรี่ยวแรง\nเรือกลไฟ\nเรือกอและ\nเรือกำปั่น\nเรือจ้าง\nเรือดำน้ำ\nเรือโดยสาร\nเรือตรวจการณ์\nเรือตังเก\nเรือธง\nเรือนำร่อง\nเรือบด\nเรือบิน\nเรือใบ\nเรือประมง\nเรือพ่วง\nเรือพิฆาต\nเรือยนต์\nเรือยาว\nเรือโยง\nเรือรบ\nเรือลากจูง\nเรือสำปั้น\nเรือสำเภา\nเรือหลวง\nเรือหางยาว\nเรืออีโปง\nเรือเอี้ยมจุ๊น\nเรื้อรัง\nเรือกสวน\nเรืองนาม\nเรืองรอง\nเรืองแสง\nเรื่องราว\nเรื่องสั้น\nเรือนแก้ว\nเรือนจำ\nเรือนเบี้ย\nเรือนแพ\nเรือนหอ\nเรื่อยเจื้อย\nเรื่อยเฉื่อย\nเรื่อยเปื่อย\nแรเงา\nแรกนา\nแรกนาขวัญ\nแรงงาน\nแรงดึงดูด\nแรงเทียน\nแรงม้า\nแรงเหวี่ยง\nแรมรอน\nแรมรา\nแรมโรย\nโรคจิต\nโรงครัว\nโรงงาน\nโรงเจ\nโรงเตี๊ยม\nโรงทาน\nโรงนา\nโรงพยาบาล\nโรงพัก\nโรงพิมพ์\nโรงเรียน\nโรงเรือน\nโรงแรม\nโรงเลี้ยง\nโรงเลื่อย\nโรงสี\nโรงสีข้าว\nโรงอาหาร\nโรมรัน\nโรยรา\nฤชากร\nฤดูกาล\nลงขัน\nลงแขก\nลงคอ\nลงตัว\nลงท้าย\nลงทุน\nลงโทษ\nลงพุง\nลงมือ\nลงรัก\nลงรอย\nลงแรง\nลงโรง\nลงเอย\nลดตัว\nลดละ\nลดเลี้ยว\nลดหย่อน\nลดหลั่น\nลนลาน\nล้นพ้น\nล้นหลาม\nล้นเหลือ\nลบล้าง\nลบเลือน\nลบหลู่\nลมกรด\nลมค้า\nลมงวง\nลมแดด\nลมทะเล\nลมบก\nลมบน\nลมบ้าหมู\nลมปราณ\nลมปาก\nลมพิษ\nลมว่าว\nลมเสีย\nลมหนาว\nลมหายใจ\nล่มจม\nล่มสลาย\nล้มละลาย\nล้มลุก\nล้มเลิก\nล่วงเกิน\nล่วงรู้\nล่วงละเมิด\nล่วงลับ\nล่วงล้ำ\nล่วงเลย\nล่วงหน้า\nลวดลาย\nลวดสปริง\nลวดหนาม\nล้วนแล้ว\nลหุโทษ\nล่อลวง\nล่อหลอก\nล่อแหลม\nล้อต๊อก\nล้อเลื่อน\nล้อเล่น\nล้อเลียน\nล้อหลอก\nลองเชิง\nลองดี\nลองภูมิ\nล่องหน\nลอดช่อง\nล่อนจ้อน\nลอบกัด\nล้อมวง\nลอยแก้ว\nลอยชาย\nลอยตัว\nลอยนวล\nลอยแพ\nลอยลำ\nละทิ้ง\nละเลย\nละเว้น\nละครนอก\nละครใน\nละครเพลง\nละครร้อง\nละครรำ\nละครลิง\nละครสัตว์\nละเอียดอ่อน\nลักไก่\nลักพา\nลักเพศ\nลักยิ้ม\nลักลอบ\nลักลั่น\nลักหลับ\nลัดเลาะ\nลับตา\nลับแล\nลับหลัง\nลาออก\nล่าช้า\nล่าทัพ\nล้าสมัย\nล้าหลัง\nลากข้าง\nล้างบาง\nล้างผลาญ\nลาดเขา\nลาดตระเวน\nลาดเท\nลาดยาง\nลานบิน\nลาภปาก\nลาภลอย\nลามปาม\nลามเลีย\nลายคราม\nลายเซ็น\nลายแทง\nลายน้ำ\nลายพร้อย\nลายมือ\nลายลักษณ์\nลายเส้น\nลำกล้อง\nลำแข้ง\nลำธาร\nลำแสง\nลำไส้\nลำตัด\nลำนำ\nล่ำสัน\nล้ำยุค\nล้ำสมัย\nล้ำลึก\nล้ำเลิศ\nล้ำเส้น\nล้ำหน้า\nลิงจุ่น\nลิงลม\nลิงโลด\nลิดรอน\nลิ้นไก่\nลิ้นชัก\nลิ้นปี่\nลิ้นควาย\nลิ้นงูเห่า\nลิ้นหมา\nลิบลับ\nลิบลิ่ว\nลิ่มเลือด\nลี้ภัย\nลี้ลับ\nลึกซึ้ง\nลึกลับ\nลึกล้ำ\nลืมตน\nลืมต้น\nลืมตัว\nลืมตา\nลืมเลือน\nลือชา\nลือชื่อ\nลือลั่น\nลุล่วง\nลุกลน\nลุกลาม\nลุกลี้ลุกลน\nลุกฮือ\nลุ่มน้ำ\nลุ่มลึก\nลุ่มหลง\nลุ่ทาง\nลูกกรง\nลูกกรอก\nลูกกรุง\nลูกกลอน\nลูกกลิ้ง\nลูกกวาด\nลูกกะจ๊อก\nลูกกุญแจ\nลูกเกด\nลูกแก้ว\nลูกขนไก่\nลูกข่าง\nลูกขุน\nลูกเขย\nลูกครึ่ง\nลูกคลื่น\nลูกความ\nลูกคอ\nลูกค้า\nลูกคิด\nลูกคู่\nลูกจ้าง\nลูกช้าง\nลูกชิด\nลูกชิ้น\nลูกชุบ\nลูกซอง\nลูกโซ่\nลูกดอก\nลูกดิ่ง\nลูกตะกั่ว\nลูกตุ้ม\nลูกเต้า\nลูกเต๋า\nลูกถ้วย\nลูกทุ่ง\nลูกเธอ\nลูกน้อง\nลูกน้ำ\nลูกนิมิต\nลูกบอล\nลูกบ้าน\nลูกบาศก์\nลูกบิด\nลูกเบี้ยว\nลูกประคบ\nลูกประคำ\nลูกปัด\nลูกปืน\nลูกโป่ง\nลูกผสม\nลูกผู้ชาย\nลูกผู้หญิง\nลูกพรรค\nลูกพี่\nลูกฟูก\nลูกไฟ\nลูกมือ\nลูกโม่\nลูกไม้\nลูกยาเธอ\nลูกรอก\nลูกรัง\nลูกเรือ\nลูกล้อ\nลูกลอย\nลูกเล่น\nลูกเลี้ยง\nลูกโลก\nลูกวัด\nลูกศร\nลูกศิษย์\nลูกสมุน\nลูกสะใภ้\nลูกสูบ\nลูกเสือ\nลูกหนัง\nลูกหนี้\nลูกหนู\nลูกหมาก\nลูกหลง\nลูกหลาน\nลูกหาบ\nลูกหิน\nลูกเห็บ\nลูกเหม็น\nลูกแหง่\nลูกอม\nลูกหม้อ\nลูบคม\nลูบคลำ\nลูบไล้\nเล็กน้อย\nเลขคณิต\nเลขผา\nเลขหมาย\nเล็ดลอด\nเล่นงาน\nเล่นแง่\nเล่นชู้\nเล่นตัว\nเล่นลิ้น\nเล่นหัว\nเลนส์นูน\nเลนส์เว้า\nเล็บครุฑ\nเลยเถิด\nเลศนัย\nเล่ห์กล\nเล่ห์เหลี่ยม\nเลอโฉม\nเลอมาน\nเลอเลิศ\nเลอสรวง\nเล่อล่า\nเลอะเลือน\nเล่าเรียน\nเล่าลือ\nเลาะลัด\nเลิกรา\nเลิกร้าง\nเลิกล้ม\nเลิศเลอ\nเลี้ยงชีพ\nเลี้ยงดู\nเลี้ยงต้อย\nเลียบเคียง\nเลี้ยวลด\nเลือกตั้ง\nเลือกเฟ้น\nเลือกสรร\nเลื่องลือ\nเลือดกำเดา\nเลือดเนื้อ\nเลือดฝาด\nเลือดเย็น\nเลือดร้อน\nเลือดหมู\nเลือดอุ่น\nเลือนราง\nเลื่อนเปื้อน\nเลื่อนลอย\nเลื่อมพราย\nเลื่อมใส\nเลื่อยฉลุ\nเลื่อยลันดา\nเลื่อยวงเดือน\nเลื้อยคลาน\nแลเหลียว\nแลกเปลี่ยน\nแล้วกัน\nและเล็ม\nโล่งใจ\nโล่งโถง\nโล่งอก\nโลดเต้น\nโลดโผน\nโลดลิ่ว\nโลดแล่น\nไล่ที่\nไล่เบี้ย\nไล่เลี่ย\nไล่เลียง\nไล่หลัง\nไล่ออก\nวกวน\nวงกบ\nวงกลม\nวงการ\nวงแขน\nวงเงิน\nวงจร\nวงนอก\nวงใน\nวงรี\nวงเล็บ\nวงเวียน\nวงแหวน\nวงศ์วาน\nวจีกรรม\nวจีเภท\nวจีภาค\nวนเวียน\nวอดวาย\nว็อบแว็บ\nวังวน\nวังหน้า\nวังหลวง\nวังหลัง\nวัดราษฎร์\nวัดวา\nวัดหลวง\nวัดผล\nวัดพื้น\nวัตถุนิยม\nวัตถุประสงค์\nวัตรปฏิบัติ\nวันโกน\nวันพระ\nวันเพ็ญ\nวัยรุ่น\nวัยวุฒิ\nว่ากล่าว\nว่าจ้าง\nว่าด้วย\nว่าที่\nวางก้าม\nวางใจ\nวางตัว\nวางตา\nวางโต\nวางท่า\nวางมวย\nวางมาด\nวางมือ\nวางวาย\nว่างเปล่า\nว่างเว้น\nวาดเขียน\nว่านเครือ\nวาบหวาม\nวายชนม์\nวายปราณ\nวายวาง\nวายวอด\nวายร้าย\nวายุภักษ์\nวาววับ\nวาววาม\nวาวแวว\nวาวแสง\nวิกฤตการณ์\nวิกฤติการณ์\nวิกฤตกาล\nวิกฤติกาล\nวิกลจริต\nวิงเวียน\nวิ่งเต้น\nวิ่งผลัด\nวิ่งรอก\nวิ่งราว\nวิจิตรศิลป์\nวิชาการ\nวิชาชีพ\nวิชาธร\nวิญญูชน\nวิดพื้น\nวิตกจริต\nวิถีทาง\nวิทยากร\nวิทยากล\nวิทยาการ\nวิทยาเขต\nวิทยาทาน\nวิทยาธร\nวิทยานิพนธ์\nวิทยาศาสตร์\nวิเทศสัมพันธ์\nวิธีการ\nวินัยธร\nวินัยปิฎก\nวินาศกรรม\nวินาศภัย\nวินาศสันตะโร\nวิภัชพยากรณ์\nวิภัชวาที\nวิไลวรรณ\nวิสัญญีแพทย์\nวิสัญญีภาพ\nวิสัญญีวิทยา\nวุฒิบัตร\nวุฒิสภา\nวุฒิสมาชิก\nวุ่นวาย\nวุ้นเส้น\nวูบวาบ\nเวจกุฎี\nเวจมรรค\nเวชกรรม\nเวชภัณฑ์\nเวชศาสตร์\nเวทมนตร์\nเวนคืน\nเวรกรรม\nเวฬุการ\nเวฬุวัน\nเว้าวอน\nเวิ้งว้าง\nเวียงวัง\nเวียนเทียน\nแว้งกัด\nแวดล้อม\nแวดวง\nแว่นขยาย\nแว่นแคว้น\nแว่นตา\nแวบวับ\nแววตา\nแวววาม\nแวววาว\nแวะเวียน\nโวยวาย\nไวไฟ\nไว้ใจ\nไว้ชื่อ\nไว้ตัว\nไว้ทุกข์\nไว้ลาย\nไว้หน้า\nไว้อาลัย\nศนิวาร\nศอกกลับ\nศอกกำ\nศอกกำมา\nศักดิ์ศรี\nศักดิ์สิทธิ์\nศารทวิษุวัติ\nศาลแขวง\nศาลจังหวัด\nศาลชั้นต้น\nศาลฎีกา\nศาลเตี้ย\nศาลทหาร\nศาลปกครอง\nศาลพระภูมิ\nศาลเพียงตา\nศาลแพ่ง\nศาลรัฐธรรมนูญ\nศาลแรงงาน\nศาลล้มละลาย\nศาลโลก\nศาลสูง\nศาลสูงสุด\nศาลอาญา\nศาลอุทธรณ์\nศาลากลาง\nศาลาดิน\nศาลาราย\nศาลาวัด\nศิลาฤกษ์\nศิลาแลง\nศิษย์เก่า\nศิษย์เอก\nศีลจุ่ม\nศีลธรรม\nศีลวัต\nศีลอด\nศูนย์กลาง\nศูนย์การค้า\nศูนย์ถ่วง\nศูนย์สูตร\nศูนย์หน้า\nเศร้าใจ\nเศร้าโศก\nเศร้าสร้อย\nเศร้าสลด\nเศร้าหมอง\nเศวตฉัตร\nเศษเกิน\nเศษซ้อน\nเศษวรรค\nเศษส่วน\nเศษเหล็ก\nโศกนาฏกรรม\nโศกศัลย์\nโศกเศร้า\nโศกสลด\nสกลโลก\nส่งเดช\nส่งท้าย\nส่งเสริม\nส่งเสีย\nส่งเสียง\nสงบเงียบ\nสงบเสงี่ยม\nสง่างาม\nสง่าราศี\nสดชื่น\nสดใส\nสตรีเพศ\nสติปัญญา\nสถลมารค\nสถานกงสุล\nสถานที่\nสถานทูต\nสถานการณ์\nสถานภาพ\nสถิติศาสตร์\nสนตะพาย\nสนใจ\nส้นตีน\nสนธิสัญญา\nสนนราคา\nสนับแข้ง\nสนับเพลา\nสนับมือ\nสนามบิน\nสนามเพลาะ\nสนิทสนม\nสนิมขุม\nสนิมสร้อย\nสนุกสนาน\nสบประมาท\nสบายใจ\nสภาพธรรม\nสมควร\nสมจริง\nสมใจ\nสมนัย\nสมน้ำหน้า\nสมประกอบ\nสมส่วน\nสมหวัง\nสมคบ\nสมทบ\nสมยอม\nสมรัก\nสมรู้\nสมสู่\nส้มฉุน\nส้มตำ\nส้มลิ้ม\nส้มกุ้ง\nส้มเช้า\nสมญานาม\nสมมติฐาน\nสมมุติฐาน\nสมมติเทพ\nสมรภูมิ\nสมัครใจ\nสมัยนิยม\nสมุทรศาสตร์\nสมุทรเสนา\nสยดสยอง\nสยองขวัญ\nสยามรัฐ\nสรรหา\nสรวมชีพ\nสรวลเส\nสร้อยเศร้า\nสร้างสรรค์\nสร้างเสริม\nสลดใจ\nสลบไสล\nสละสลวย\nสลาเหิน\nสลากภัต\nสวนครัว\nสวนป่า\nสวนสนุก\nสวนหย่อม\nส่วนกลาง\nส่วนเกิน\nส่วนตัว\nส่วนบุญ\nส่วนแบ่ง\nส่วนประกอบ\nส่วนพระองค์\nส่วนผสม\nส่วนรวม\nส่วนร่วม\nส่วนลด\nส่วนสัด\nสวมกอด\nสวมเขา\nสวมรอย\nสวยมภู\nสว่างไสว\nสวามิภักดิ์\nสวิงสวาย\nสสารนิยม\nส่อเสียด\nสอดคล้อง\nสอดแทรก\nสอดแนม\nสอบถาม\nสอบทาน\nสอบไล่\nสอบสวน\nส้อมเสียง\nสะสวย\nสะแกวัลย์\nสะแกแสง\nสะใจ\nสะเด็ดยาด\nสะเทือนใจ\nสะบัดช่อ\nสั่งสม\nสั่งสอน\nสั่งเสีย\nสังเกตการณ์\nสังคมนิยม\nสังคมวิทยา\nสังคมศาสตร์\nสังคมศึกษา\nสังคมสงเคราะห์\nสัญญาบัตร\nสัดส่วน\nสัตการ\nสัตบุรุษ\nสัตบริภัณฑ์\nสัตภัณฑ์\nสัตมหาสถาน\nสัตโลหะ\nสันเขา\nสันดอน\nสันหลัง\nสั่นเทา\nสั่นเทิ้ม\nสันติบาล\nสันติภาพ\nสันติวิธี\nสันติสุข\nสับเปลี่ยน\nสับสน\nสับหลีก\nสับหว่าง\nสัมมาคารวะ\nสัมมาชีพ\nส่าเหล้า\nสากกะเบือ\nสาทิสลักษณ์\nสาธุการ\nสาธุชน\nสาบเสือ\nสาปสรร\nสาปแช่ง\nสาปส่ง\nสามง่าม\nสามล้อ\nสามเหลี่ยม\nสามเวท\nสามัญชน\nสามัญสำนึก\nสายดิ่ง\nสายดิน\nสายตรวจ\nสายน้ำ\nสายบัว\nสายพาน\nสายฟ้า\nสายยาง\nสายยู\nสายใย\nสายรก\nสายรุ้ง\nสายล่อฟ้า\nสายลับ\nสายเลือด\nสายโลหิต\nสายวัด\nสายส่ง\nสายสวาท\nสายสะดือ\nสายสะพาย\nสายสัมพันธ์\nสายสิญจน์\nสายสืบ\nสายไหม\nสายอากาศ\nสายตา\nสายหยุด\nสารตรา\nสารประกอบ\nสารละลาย\nสารส้ม\nสารหนู\nสารทฤดู\nสาวใช้\nสาวน้อย\nสาวใหญ่\nสำนักงาน\nสำนักพิมพ์\nสำนักสงฆ์\nสำมะโนครัว\nสำเร็จรูป\nสิกขาบท\nสิงสถิต\nสิงสู่\nสิ่งก่อสร้าง\nสิ่งของ\nสิ่งปฏิกูล\nสิ่งพิมพ์\nสิ่งแวดล้อม\nสิ่งศักดิ์สิทธิ์\nสิทธิกร\nสิทธิ์ขาด\nสิทธิชัย\nสิทธิโชค\nสิทธิบัตร\nสินค้า\nสินจ้าง\nสินเชื่อ\nสินไถ่\nสินทรัพย์\nสินน้ำใจ\nสินบน\nสินแร่\nสินสมรส\nสินสอด\nสินไหม\nสิ้นเชิง\nสิ้นสุด\nสีผึ้ง\nสีลม\nสีชอล์ก\nสีถ่าน\nสีเทียน\nสีน้ำ\nสีน้ำมัน\nสีโปสเตอร์\nสีฝุ่น\nสี่เหลี่ยม\nสีหน้า\nสึกหรอ\nสืบทอด\nสืบค้น\nสืบสวน\nสืบสาว\nสืบเสาะ\nสื่อผสม\nสื่อมวลชน\nสื่อสาร\nสุกงอม\nสุกดิบ\nสุกปลั่ง\nสุกใส\nสุขนาฏกรรม\nสุขภัณฑ์\nสุขภาพ\nสุขลักษณะ\nสุขวิทยา\nสุขศาลา\nสุขศึกษา\nสุดท้าย\nสุตกวี\nสุนทรพจน์\nสุภาพชน\nสู่ขอ\nสู่รู้\nสู่สม\nสูงส่ง\nสูญเปล่า\nสูญสิ้น\nสูญเสีย\nสูญหาย\nเสสรวล\nเสแสร้ง\nเสกสรร\nเสถียรภาพ\nเส้นชัย\nเส้นตรง\nเส้นตาย\nเส้นทาง\nเส้นใย\nเส้นรุ้ง\nเส้นเลือด\nเส้นแวง\nเส้นสาย\nเส้นเสียง\nเส้นหมี่\nเส้นเอ็น\nเสบียงกรัง\nเสมอภาค\nเสมอหน้า\nเสมอเหมือน\nเสมียนตรา\nเสร็จสรรพ\nเสร็จสิ้น\nเสริมส่ง\nเสริมสร้าง\nเสริมสวย\nเสรีไทย\nเสรีธรรม\nเสรีนิยม\nเสรีภาพ\nเสาเข็ม\nเสาธง\nเสียใจ\nเสียเชิง\nเสียดาย\nเสียที\nเสียเที่ยว\nเสียเปรียบ\nเสียเปล่า\nเสียรู้\nเสียแรง\nเสียสละ\nเสียหลัก\nเสียหาย\nเสี่ยงทาย\nเสียดแทง\nเสียดแทรก\nเสียดสี\nเสี้ยนศึก\nเสี้ยนหนาม\nเสี้ยมสอน\nเสียวซ่าน\nเสียวไส้\nเสือดาว\nเสือดำ\nเสือปลา\nเสือป่า\nเสือไฟ\nเสื่อกก\nเสื่อกระจูด\nเสื่อน้ำมัน\nเสื่อลำแพน\nเสื้อกล้าม\nเสื้อกั๊ก\nเสื้อเกราะ\nเสื้อครุย\nเสื้อแสง\nเสื้อเมือง\nเสือกคลาน\nเสือกสน\nเสือกไส\nเสื่อมคลาย\nเสื่อมถอย\nเสื่อมทราม\nเสื่อมโทรม\nเสื่อมสลาย\nเสื่อมสูญ\nเสื่อมเสีย\nเสือหมอบ\nแสกหน้า\nแสดงออก\nแสเถา\nแสนกล\nแสนรู้\nแสร้งว่า\nใส่ความ\nใส่ไคล้\nใส่ใจ\nใส่ไฟ\nไส้กรอก\nไส้ไก่\nไส้ติ่ง\nไส้ศึก\nไส้อั่ว\nไส้เดือน\nไส้ตัน\nไสยเวท\nไสยศาสตร์\nหกล้ม\nหงส์หยก\nหงอนไก่\nหงอยก๋อย\nหงอยเหงา\nหงายท้อง\nหงายหลัง\nหงำเหงอะ\nหงำเหงือก\nหดหาย\nหดหู่\nหนทาง\nหนวกหู\nหน่วงเหนี่ยว\nหน่วยก้าน\nหน่อไม้\nหนองใน\nหนองแซง\nหนักข้อ\nหนักใจ\nหนักแน่น\nหนักหน่วง\nหนักหนา\nหนังกลับ\nหนังตะลุง\nหนังเรียด\nหนังสด\nหนังใหญ่\nหนังสือพิมพ์\nหนาแน่น\nหน้ากระดาน\nหน้ากาก\nหน้ากาฬ\nหน้าแข้ง\nหน้าจั่ว\nหน้าฉาน\nหน้าตัก\nหน้าตา\nหน้าต่าง\nหน้าท้อง\nหน้าทับ\nหน้าที่\nหน้าที่นั่ง\nหน้าบัน\nหน้าปัด\nหน้าผา\nหน้าผาก\nหน้าม้า\nหน้ามุข\nหน้าไม้\nหน้าเลือด\nหน้าอก\nหนามเตย\nหน่ายหนี\nหน่ายแหนง\nหนาวเหน็บ\nหนำใจ\nหนี้สิน\nหนี้ส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น\nกณิกนันต์\nกณิการ์\nกด\nกตเวทิตา\nกตเวที\nกตัญชลี\nกตัญญุตา\nกตัญญู\nกตาธิการ\nกตาภินิหาร\nกติกา\nกถา\nกถิกาจารย์\nกทลี\nกน\nก่น\nก้น\nกนก\nกนิษฐ์\nกนิษฐา\nกบ\nกบฏ\nกบดาน\nกบทู\nกบาล\nกบินทร์\nกบิล\nกบี่\nกบูร\nกเบนทร์\nกม\nก้ม\nกมณฑลาภิเษก\nกมณฑโลทก\nกมล\nกมลา\nกมลาศ\nกมลาสน์\nกมเลศ\nกมัณฑลุ\nกมุท\nกร\nกรกฎ\nกรกฎาคม\nกรกฏ\nกรง\nกรชกาย\nกรณฑ์\nกรณิการ์\nกรณี\nกรณีย์\nกรณียกิจ\nกรณียะ\nกรด\nกรน\nกรบ\nกรบูร\nกรพินธุ์\nกรม\nกรรกฎ\nกรรกศ\nกรรเกด\nกรรไกร\nกรรเจียก\nกรรชิง\nกรรเชียง\nกรรโชก\nกรรฐ์\nกรรฐา\nกรรณ\nกรรณา\nกรรณิกา\nกรรณิการ์\nกรรดิ\nกรรดิก\nกรรดึก\nกรรตุ\nกรรไตร\nกรรทบ\nกรรแทก\nกรรบิด\nกรรบูร\nกรรภิรมย์\nกรรม\nกรรม์\nกรรม์ภิรมย์\nกรรมชวาต\nกรรมัชวาต\nกรรมาชีพ\nกรรมาธิการ\nกรรมาร\nกรรษก\nกรรสะ\nกรรแสง\nกรวด\nกรวบ\nกรวม\nกร้วม\nกรวย\nกรวิก\nกรสาปน์\nกรสุทธิ์\nกรอ\nกร้อ\nกรอก\nกร็อกกร๋อย\nกรอกแกรก\nกรอง\nกรองกรอย\nกรอด\nกร่อน\nกรอบ\nกรอม\nกร่อย\nกระ\nกระกร\nกระกรุ่น\nกระกลับกลอก\nกระกี้\nกระเกรอก\nกระเกริก\nกระเกริ่น\nกระคน\nกระคาย\nกระงกกระเงิ่น\nกระง่องกระแง่ง\nกระง่อนกระแง่น\nกระเง้ากระงอด\nกระโงก\nกระจก\nกระจง\nกระจร\nกระจอก\nกระจองหง่อง\nกระจ๋องหง่อง\nกระจองอแง\nกระจ้อน\nกระจอนหู\nกระจ้อย\nกระจ๋อหวอ\nกระจะ\nกระจัก\nกระจัง\nกระจัด\nกระจับ\nกระจ่า\nกระจ่าง\nกระจาด\nกระจาน\nกระจาบ\nกระจาม\nกระจาย\nกระจาว\nกระจิก\nกระจิ๋ง\nกระจิด\nกระจิบ\nกระจิ๋ม\nกระจิริด\nกระจิ๋ว\nกระจี้\nกระจี๋\nกระจุก\nกระจุ๋งกระจิ๋ง\nกระจุบ\nกระจุ๊บ\nกระจุ๋มกระจิ๋ม\nกระจุย\nกระจู้\nกระจู๋กระจี๋\nกระจูด\nกระเจอะกระเจิง\nกระเจา\nกระเจ่า\nกระเจ้า\nกระเจาะ\nกระเจิง\nกระเจิดกระเจิง\nกระเจี้ยง\nกระเจี๊ยบ\nกระเจียว\nกระเจี๊ยว\nกระแจะ\nกระโจน\nกระโจม\nกระฉอก\nกระฉ่อน\nกระฉับกระเฉง\nกระฉิ่ง\nกระฉีก\nกระฉูด\nกระเฉก\nกระเฉด\nกระแฉก\nกระโฉกกระเฉก\nกระโฉม\nกระชดกระช้อย\nกระชอน\nกระชอมดอก\nกระช้อย\nกระชัง\nกระชั้น\nกระชับ\nกระชาก\nกระชาย\nกระชิง\nกระชิด\nกระชุ\nกระชุก\nกระชุ่มกระชวย\nกระเชอ\nกระเชา\nกระเช้า\nกระเชียง\nกระแชง\nกระแชะ\nกระโชก\nกระซ่องกระแซ่ง\nกระซับ\nกระซาบ\nกระซิก\nกระซิบ\nกระซี้\nกระซุง\nกระซุบกระซิบ\nกระซุ้ม\nกระซู่\nกระเซ็น\nกระเซอ\nกระเซอะกระเซอ\nกระเซอะกระเซิง\nกระเซ้า\nกระเซิง\nกระแซ\nกระแซะ\nกระโซกระเซ\nกระฎี\nกระฎุมพี\nกระดก\nกระด้ง\nกระดนโด่\nกระดวง\nกระดวน\nกระด้วมกระเดี้ยม\nกระดอ\nกระดอง\nกระดองหาย\nกระดอน\nกระดอม\nกระดักกระเดี้ย\nกระดังงัว\nกระดังงา\nกระดาก\nกระด้าง\nกระดางลาง\nกระดาด\nกระดาดขาว\nกระดาน\nกระดานพน\nกระดาษ\nกระดำกระด่าง\nกระดิก\nกระดิ่ง\nกระดิ้ง\nกระดิบ\nกระดี่\nกระดี้กระเดียม\nกระดึง\nกระดืบ\nกระดุ\nกระดุกกระดิก\nกระดุ้งกระดิ้ง\nกระดุบ\nกระดุบกระดิบ\nกระดุม\nกระดูก\nกระเดก\nกระเด้ง\nกระเด็น\nกระเด้า\nกระเดาะ\nกระเดิด\nกระเดี้ย\nกระเดียด\nกระเดือก\nกระเดื่อง\nกระแด็ก\nกระแด้ง\nกระแด้แร่\nกระแด่ว\nกระแดะ\nกระโดก\nกระโดง\nกระโดด\nกระโดน\nกระได\nกระตรับ\nกระตราก\nกระตรุด\nกระตรุม\nกระต้วมกระเตี้ยม\nกระต้อ\nกระต่องกระแต่ง\nกระต๊อบ\nกระต้อยตีวิด\nกระตัก\nกระตั้ว\nกระต่าย\nกระติก\nกระติ๊ด\nกระติบ\nกระตือรือร้น\nกระตุก\nกระตุ้งกระติ้ง\nกระตุ่น\nกระตุ้น\nกระตูบ\nกระเตง\nกระเต็น\nกระเตอะ\nกระเตาะ\nกระเตาะกระแตะ\nกระเตื้อง\nกระแต\nกระแตแต้แว้ด\nกระโตกกระตาก\nกระโตน\nกระถด\nกระถอบ\nกระถั่ว\nกระถาง\nกระถิก\nกระถิน\nกระเถิบ\nกระโถน\nกระทก\nกระทง\nกระทบ\nกระทรวง\nกระทอก\nกระท้อน\nกระท่อนกระแท่น\nกระท่อม\nกระท้อมกระแท้ม\nกระทะ\nกระทั่ง\nกระทั้น\nกระทา\nกระทาย\nกระทาสี\nกระทาหอง\nกระทำ\nกระทิกกระทวย\nกระทิง\nกระทึง\nกระทืบ\nกระทุ\nกระทุง\nกระทุ้ง\nกระทุ่ม\nกระทู้\nกระเท่\nกระเทียบ\nกระเทียม\nกระเทือน\nกระเทื้อม\nกระแทก\nกระแท่น\nกระแทะ\nกระไทชาย\nกระน่อง\nกระนั้น\nกระนี้\nกระแนะกระแหน\nกระโน้น\nกระไน\nกระบก\nกระบม\nกระบวน\nกระบวย\nกระบวร\nกระบอก\nกระบอง\nกระบะ\nกระบัด\nกระบั้วกระเบี้ย\nกระบ่า\nกระบ้า\nกระบาก\nกระบาย\nกระบาล\nกระบิ\nกระบิ้ง\nกระบิด\nกระบิล\nกระบี่\nกระบือ\nกระบุง\nกระบุ่มกระบ่าม\nกระบู้กระบี้\nกระบูน\nกระบูร\nกระเบง\nกระเบญ\nกระเบ็ดกระบวน\nกระเบน\nกระเบา\nกระเบิก\nกระเบียด\nกระเบียน\nกระเบื้อง\nกระแบก\nกระแบะ\nกระโบม\nกระปมกระปำ\nกระปมกระเปา\nกระปรอก\nกระปรอกว่าว\nกระปรี้กระเปร่า\nกระปอก\nกระป้อกระแป้\nกระป่อง\nกระป๋อง\nกระปอดกระแปด\nกระป๋อหลอ\nกระปั้วกระเปี้ย\nกระป่ำ\nกระปุก\nกระปุ๊กลุก\nกระปุ่ม\nกระปุ่มกระป่ำ\nกระปุ่มกระปิ่ม\nกระเป๋า\nกระเปาะ\nกระโปก\nกระโปรง\nกระผม\nกระผลีกระผลาม\nกระผาน\nกระผีก\nกระพรวน\nกระพริ้ม\nกระพอก\nกระพอง\nกระพ้อม\nกระพัก\nกระพัง\nกระพังเหิร\nกระพังโหม\nกระพัด\nกระพัตร\nกระพัน\nกระพั่น\nกระพา\nกระพาก\nกระพี้\nกระพือ\nกระพุ้ง\nกระพุ่ม\nกระเพาะ\nกระเพิง\nกระเพื่อม\nกระแพ้ง\nกระฟัดกระเฟียด\nกระฟูมกระฟาย\nกระมล\nกระมอบ\nกระมอมกระแมม\nกระมัง\nกระมัน\nกระมิดกระเมี้ยน\nกระมุท\nกระเมาะ\nกระย่อง\nกระย่องกระแย่ง\nกระย่อน\nกระย่อม\nกระยา\nกระยาง\nกระยาจก\nกระยาหงัน\nกระยิก\nกระยิ้มกระย่อง\nกระยึกกระยือ\nกระยืดกระยาด\nกระเย้อกระแหย่ง\nกระรอก\nกระเรียน\nกระโรกน้ำข้าว\nกระโรกใหญ่\nกระไร\nกระลด\nกระลบ\nกระลอก\nกระลอม\nกระละหล่ำ\nกระลัด\nกระลับ\nกระลัมพร\nกระลา\nกระลำ\nกระลำพัก\nกระลำพุก\nกระลิง\nกระลี\nกระลุมพาง\nกระลุมพุก\nกระลุมพู\nกระลูน\nกระลู่น์\nกระเล็น\nกระเลียด\nกระเลือก\nกระโลง\nกระวน\nกระวัด\nกระวาด\nกระวาน\nกระวาย\nกระวิน\nกระวี\nกระวีกระวาด\nกระวูดกระวาด\nกระเวน\nกระเวยกระวาย\nกระแวน\nกระโวยกระวาย\nกระษัย\nกระษาปณ์\nกระสง\nกระสบ\nกระสม\nกระสรวล\nกระสร้อย\nกระสวน\nกระสวย\nกระสอบ\nกระสะ\nกระสัง\nกระสัน\nกระสับกระส่าย\nกระสา\nกระสานติ์\nกระสาบ\nกระสาย\nกระสือ\nกระสุงกระสิง\nกระส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ทิง\nกากะเยีย\nกากี\nกาง\nก้าง\nกางเกง\nกางเขน\nก๊าซ\nกาซะลอง\nกาญจนา\nกาฐ\nกาด\nก๊าด\nกาน\nก่าน\nก้าน\nก๊าน\nกานดา\nกานต์\nกานน\nก้านพร้าว\nกานพลู\nกาน้า\nกาบ\nก้าบ\nกาบู\nกาพย์\nกาเฟอีน\nกาแฟ\nกาม\nก้าม\nกามารมณ์\nกามินี\nกาเมสุมิจฉาจาร\nกาย\nก่าย\nกาเยน\nการ\nการณ์\nการ์ด\nการ์ตูน\nการบูร\nการย์\nการวิก\nการเวก\nการะเกด\nการะบุหนิง\nการัณย์\nการันต์\nการางหัวขวาน\nการิตการก\nการิตวาจก\nการุญ\nการุณย์\nกาเรการ่อน\nกาล\nกาลกรรณี\nกาลกิณี\nกาลจักร\nกาลัญญุตา\nกาลัญญู\nกาลัด\nกาลานุกาล\nกาลิก\nกาลี\nกาแล\nกาแล็กซี\nกาแล็กโทส\nกาว\nก้าว\nกาววาว\nกาวาง\nกาแวน\nกาศิก\nกาษฐะ\nกาษา\nกาสร\nกาสะ\nกาสา\nกาสาร\nกาสาวะ\nกาสิโน\nกาหล\nกาหลง\nกาหลา\nกาเหว่า\nกาไหล่\nกาฬ\nกาฬาวก\nกาฮัง\nกำ\nก่ำ\nกำกวม\nกำกัด\nกำกับ\nก้ำกึ่ง\nกำกูน\nก้ำเกิน\nกำเกียง\nกำคูน\nกำจร\nกำจัด\nกำจาย\nกำชับ\nกำชำ\nกำซาบ\nกำซำ\nกำด้น\nกำดัด\nกำดาล\nกำเดา\nกำธร\nกำนล\nกำนัน\nกำนัล\nกำเนิด\nกำบัง\nก่ำบึ้ง\nกำเบ้อ\nกำปอ\nกำปั่น\nกำผลา\nกำพง\nกำพด\nกำพต\nกำพร้า\nกำพราก\nกำพวด\nกำพอง\nกำพืด\nกำพุด\nกำพู\nกำเพลิง\nกำแพง\nกำภู\nกำมลาศน์\nกำมเลศ\nกำมะถัน\nกำมะลอ\nกำมะหยี่\nกำมะหริด\nกำมังละการ\nกำมังวิลิต\nกำมัชพล\nกำยาน\nกำยำ\nกำรอ\nกำราบ\nกำราล\nกำเริบ\nกำไร\nกำลัง\nกำลุง\nกำเลา\nกำไล\nกำสรด\nกำสรวล\nกำหนด\nกำหนัด\nกำเหน็จ\nกำแหง\nกิก\nกิ๊ก\nกิ่ง\nกิ้งก่า\nกิ้งกือ\nกิ้งโครง\nกิจ\nกิจจะ\nกิจจา\nกิดาการ\nกิดาหยัน\nกิตติ\nกิตติมศักดิ์\nกิน\nกินนร\nกินปลี\nกินเปี้ยว\nกินริน\nกินรี\nกิ๊บ\nกิมตึ๋ง\nกิมิชาติ\nกิมิวิทยา\nกิโมโน\nกิโยตีน\nกิระ\nกิริณี\nกิรินท\nกิริเนศวร\nกิริยา\nกิเลน\nกิเลส\nกิโล\nกิโลมกะ\nกิ่ว\nกิ๋ว\nกี\nกี่\nกี้\nกี๊\nกี๋\nกีฏวิทยา\nกีด\nกีตาร์\nกีบ\nกีรติ\nกีฬา\nกึก\nกึง\nกึ่ง\nกึ๋น\nกุ\nกุก\nกุ๊ก\nกุกกุฏ\nกุกกุร\nกุกรรม\nกุ้ง\nกุงอน\nกุงาน\nกุโงก\nกุจี\nกุญแจ\nกุญชร\nกุฎ\nกุฎา\nกุฎี\nกุฎุมพี\nกุฏฐัง\nกุฏิ\nกุณฑ์\nกุณฑล\nกุณฑี\nกุณโฑ\nกุณาล\nกุณี\nกุด\nกุดัง\nกุดั่น\nกุดา\nกุทัณฑ์\nกุน\nกุ๊น\nกุนเชียง\nกุนที\nกุโนกามอ\nกุบ\nกุบกับ\nกุม\nกุ่ม\nกุมฝอย\nกุมภ์\nกุมภนิยา\nกุมภัณฑ์\nกุมภา\nกุมภิล\nกุมภีล์\nกุมเหง\nกุมาร\nกุมารา\nกุมารี\nกุมุท\nกุย\nกุ๊ย\nกุ๋ย\nกุยช่าย\nกุยเฮง\nกุรระ\nกุรุพินท์\nกุเรา\nกุล\nกุลา\nกุลาหล\nกุลี\nกุลีกุจอ\nกุเลา\nกุแล\nกุเวร\nกุศราช\nกุศล\nกุศโลบาย\nกุสุม\nกุสุมภ์\nกุสุมา\nกุสุมาลย์\nกุสุมิตลดาเวลลิตา\nกุหนี\nกุหนุง\nกุหร่า\nกุหล่า\nกุหลาบ\nกุแหละ\nกู\nกู่\nกู้\nกู๊ก\nกูฏ\nกูฏา\nกูณฑ์\nกูด\nกูบ\nกูปรี\nกูรมะ\nกูรมาวตาร\nเก\nเก้\nเก๊\nเก๋\nเกก\nเก๊ก\nเกกมะเหรก\nเก๊กฮวย\nเก้กัง\nเก็ง\nเก่ง\nเก้ง\nเก๋ง\nเกงกอย\nเก่งกาจ\nเกงเขง\nเก๋งเคง\nเก็จ\nเกจิอาจารย์\nเกชา\nเกณฑ์\nเกด\nเก็ด\nเกตุ\nเกน\nเก็บ\nเกม\nเกย\nเกยูร\nเกรง\nเกร็ง\nเกร็ด\nเกรน\nเกร่อ\nเกรอะ\nเกราะ\nเกริก\nเกริน\nเกริ่น\nเกรียก\nเกรียง\nเกรียด\nเกรียน\nเกรียบ\nเกรียม\nเกรียว\nเกรี้ยว\nเกเร\nเกล็ด\nเกลศ\nเกลอ\nเกลา\nเกล้า\nเกลาะ\nเกลี่ย\nเกลี้ย\nเกลียง\nเกลี้ยง\nเกลียด\nเกลียว\nเกลือ\nเกลื้อ\nเกลือก\nเกลื่อน\nเกลื้อน\nเกวัฏ\nเกวียน\nเกศ\nเกศว\nเกศวะ\nเกศา\nเกศินี\nเกศี\nเกษตร\nเกษม\nเกษียณ\nเกษียน\nเกษียร\nเกส\nเกสร\nเกสรี\nเกสา\nเกสี\nเก้อ\nเกอิชา\nเกะ\nเกะกะ\nเกา\nเก่า\nเก้า\nเก๋า\nเกาต์\nเกาทัณฑ์\nเกาบิล\nเกาลัด\nเกาลิน\nเกาไศย\nเกาหลี\nเกาเหลา\nเกาเหลียง\nเก้าอี้\nเกาะ\nเกิ้ง\nเกิด\nเกิน\nเกิบ\nเกีย\nเกียกกาย\nเกียง\nเกี่ยง\nเกี๋ยง\nเกียจ\nเกียด\nเกียน\nเกี้ยมไฉ่\nเกี้ยมอี๋\nเกียร์\nเกียรติ\nเกียรติ์\nเกี่ยว\nเกี้ยว\nเกี๊ยว\nเกี๊ยะ\nเกื้อ\nเกือก\nเกื้อกูล\nเกือบ\nแก\nแก่\nแก้\nแกง\nแก่ง\nแก้ง\nแก๊ง\nแกงได\nแกงแนง\nแกโดลิเนียม\nแกน\nแก่น\nแก๊ป\nแกม\nแก้ม\nแกมมา\nแกรก\nแกร่ง\nแกร็น\nแกรนิต\nแกรไฟต์\nแกร่ว\nแกระ\nแกล\nแกล้ง\nแกลน\nแกลบ\nแกล้ม\nแกลลอน\nแกลเลียม\nแกล้ว\nแกละ\nแกแล\nแกว\nแก้ว\nแกว่ง\nแก๊ส\nแกะ\nโก\nโก่\nโก้\nโก๋\nโกก\nโกกนุท\nโกกิลา\nโกโก้\nโกง\nโก่ง\nโกงกาง\nโก้งเก้ง\nโกงโก้\nโก้งโค้ง\nโกเชาว์\nโกญจนาท\nโกญจา\nโกฏิ\nโกฐ\nโกฐาส\nโกณะ\nโกดัง\nโกทัณฑ์\nโกน\nโก่น\nโก๋น\nโกมล\nโกมุท\nโกเมน\nโกเมศ\nโกย\nโกรก\nโกรกกราก\nโกรง\nโกร่ง\nโกร่งกร่าง\nโกรงเกรง\nโกร๋งเกร๋ง\nโกรญจ\nโกรต๋น\nโกรธ\nโกรธา\nโกร๋น\nโกรม\nโกรย\nโกรศ\nโกโรโกเต\nโกโรโกโรก\nโกโรโกโส\nโกลน\nโกลาหล\nโกไล\nโกวิท\nโกศ\nโกศล\nโกษม\nโกสน\nโกสัช\nโกสินทร์\nโกสีย์\nโกสุม\nโกไสย\nโกหก\nใกล้\nไก\nไก่\nไก๊\nไก๋\nไก่กอม\nไกพัล\nไกร\nไกรพ\nไกรลาส\nไกรศร\nไกรศรี\nไกรสร\nไกรสรี\nไกรสิทธิ\nไกล\nไกล่\nไกลาส\nไกว\nไกวัล\nขงจื๊อ\nขจร\nขจรจบ\nขจัด\nขจ่าง\nขจาย\nขจาว\nขจิต\nขจี\nขจุย\nขเจา\nขณะ\nขด\nขน\nข้น\nขนง\nขนด\nขนบ\nขนม\nขนอง\nขนอน\nขนอบ\nขนัด\nขนัน\nขนาก\nขนาง\nขนาด\nขนาน\nขนาบ\nขนาย\nขนำ\nขนิษฐ\nขนิษฐา\nขนุน\nขนุนนก\nขบ\nขบถ\nขบวน\nขบวร\nขม\nข่ม\nขมงโกรย\nขมวด\nขมวน\nขมอง\nขม่อม\nขมัง\nขมับ\nขมา\nขม้ำ\nขมิ้น\nขมิบ\nขมีขมัน\nขมึง\nขมึงทึง\nขมุ\nขมุกขมัว\nขมุบ\nขโมย\nขยด\nขยม\nขย่ม\nขยอก\nขยอง\nขย่อน\nขย้อน\nขยะ\nขยัก\nขยัน\nขยั้น\nขยับ\nขยาด\nขยาย\nขยำ\nขย้ำ\nขยิก\nขยิบ\nขยิ่ม\nขยี้\nขยุกขยิก\nขยุกขยุย\nขยุบ\nขยุบขยิบ\nขยุม\nขยุ้ม\nขยุย\nขรม\nขรรค์\nขรัว\nขริบ\nขรี\nขรึม\nขรุขระ\nขลบ\nขล้อ\nขลัง\nขลับ\nขลาด\nขลาย\nขลิบ\nขลุก\nขลุกขลัก\nขลุกขลิก\nขลุบ\nขลุม\nขลุ่ย\nขลู\nขลู่\nขวง\nข่วง\nขวด\nข่วน\nขวนขวาย\nขวบ\nขวย\nขวักไขว่\nขวัญ\nขวั้น\nขวับ\nขวับเขวียว\nขวา\nขวาก\nขวาง\nขว้าง\nขวาด\nขวาน\nขวายขวน\nขวาว\nขว้าว\nขวิด\nขอ\nข่อ\nข้อ\nของ\nข้อง\nขอด\nขอน\nข้อน\nขอบ\nขอม\nข่อย\nข้อย\nข่อยหยอง\nขะแจะ\nขะเน็ด\nขะมอมขะแมม\nขะมักเขม้น\nขะมุกขะมอม\nขะยิก\nขะยุก\nขะเย้อแขย่ง\nขัค\nขัง\nขังขอก\nขัช\nขัณฑสกร\nขัณฑสีมา\nขัด\nขัดมอน\nขัตติยมานะ\nขัน\nขั้น\nขันติ\nขันตี\nขันโตก\nขันที\nขันธ์\nขันธาวาร\nขับ\nขัว\nขั้ว\nขา\nข่า\nข้า\nขาก\nขาก๊วย\nขาง\nข่าง\nข้าง\nขาณุ\nขาด\nขาทนียะ\nขาน\nขาบ\nข้าพเจ้า\nขาม\nข่าม\nข้าม\nขาย\nข่าย\nขาล\nขาว\nข่าว\nข้าว\nข้าวอังกุลี\nขำ\nขิก\nขิง\nขิงแกลง\nขิงแครง\nขิด\nขิปสัทโท\nขิม\nขี่\nขี้\nขี้เข็บ\nขีณาสพ\nขีด\nขี้ตังนี\nขีปนาวุธ\nขี้ยอก\nขีระ\nขึง\nขึ้ง\nขึ้น\nขึ้นฉ่าย\nขืน\nขื่น\nขื่อ\nขุก\nขุด\nขุน\nขุ่น\nขุนเพ็ด\nขุม\nขุย\nขู่\nขูด\nเข\nเข้\nเขก\nเข็ง\nเข่ง\nเขจร\nเข็ญ\nเข็ด\nเขดา\nเขต\nเขน\nเข็น\nเข่น\nเขนง\nเขน็ด\nเขนย\nเขบ็จขบวน\nเขบ็ต\nเขม\nเข็ม\nเข้ม\nเข้มขาบ\nเขม็ง\nเขม็ดแขม่\nเขม่น\nเขม้น\nเขม้นขะมัก\nเขมร\nเขมา\nเขม่า\nเขมือบ\nเขย\nเขยก\nเขย่ง\nเขย้อแขย่ง\nเขย่า\nเขยิน\nเขยิบ\nเขยื้อน\nเขรอะ\nเขลง\nเขลอะ\nเขละ\nเขลา\nเขลาะ\nเขว\nเขษม\nเขฬะ\nเขะขะ\nเขา\nเข่า\nเข้า\nเขิง\nเขิน\nเขิบ\nเขี่ย\nเขียง\nเขียด\nเขียดตะปาด\nเขียน\nเขี่ยน\nเขียม\nเขียว\nเขี้ยว\nเขียะ\nเขือ\nเขือง\nเขื่อง\nเขื่อน\nเขือม\nแข\nแข้\nแขก\nแข็ง\nแข่ง\nแข้ง\nแขน\nแข่น\nแข้น\nแขนง\nแขม\nแขม็บ\nแขม่ว\nแขยง\nแขย่ง\nแขวก\nแขวง\nแขวน\nแขวะ\nโข\nโขก\nโขง\nโข่ง\nโขด\nโขดง\nโขน\nโขนง\nโขม\nโขมง\nโขมด\nโขยก\nโขยง\nโขย่ง\nโขยด\nโขลก\nโขลง\nโขลน\nโขษม\nไข\nไข่\nไข้\nไขว่\nไขว้\nคคนะ\nคคนัมพร\nคคนางค์\nคคนานต์\nคง\nคงคา\nคงไคย\nคช\nคชาชาติ\nคชาชีพ\nคชาธาร\nคชาภรณ์\nคณนา\nคณบดี\nคณะ\nคณาจารย์\nคณาธิการ\nคณาธิปไตย\nคณานับ\nคณิกา\nคณิต\nคเณศ\nคด\nคดี\nคติ\nคทา\nคน\nค้น\nคนทา\nคนทิสอ\nคนที\nคนโท\nคนธ์\nคันธ์\nคนธรรพ์\nคเนจร\nคบ\nคม\nคมน์\nคมนาการ\nคมนาคม\nคมิกภัต\nครก\nครบ\nครรชิต\nครรภ\nครรภ์\nครรลอง\nครรโลง\nครรไล\nครวญ\nครวี\nครหา\nครอก\nครอง\nครองแครง\nคร่อเงาะ\nคร่อเทียน\nครอบ\nคร่อม\nคระเมิม\nคระแลง\nคระไล\nคระแวง\nคระหน\nคระหวน\nคระหาย\nคระโหย\nครั่ง\nครั้ง\nครัดเคร่ง\nครัน\nครั่น\nครั้น\nครับ\nครัว\nครา\nคร่า\nคราก\nคราง\nคราญ\nคราด\nคร้าน\nคราบ\nคราม\nคร้าม\nครามครัน\nคราว\nคร่าว\nคราส\nครำ\nคร่ำ\nคร่ำเคร่ง\nคริปทอน\nคริสต์\nครีบ\nครีม\nครีษมายัน\nครึ\nครึกครื้น\nครึกโครม\nครึ่ง\nครึ่ด\nครึน\nครึ้ม\nครืด\nครืน\nครื้น\nครืนครั่น\nครื้นครั่น\nครื้นครึก\nครื้นเครง\nครือ\nครุ\nครุคระ\nครุฑ\nครุ่น\nครุมเครือ\nครุย\nครุวนา\nครู\nครู่\nครูด\nคฤโฆษ\nคฤนถ์\nคฤหบดี\nคฤหัสถ์\nคฤหาสน์\nคลวง\nคลอ\nคล้อ\nคลอก\nคลอง\nคล่อง\nคล้อง\nคลอด\nคลอน\nคล้อย\nคลอรีน\nคลอโรฟอร์ม\nคลอโรฟีลล์\nคละ\nคละคลุ้ง\nคลัก\nคลั่ก\nคลัง\nคลั่ง\nคลัตช์\nคลับคล้าย\nคลับคลา\nคลา\nคล้า\nคลางแคลง\nคลาด\nคลาน\nคลาย\nคล้าย\nคล้ายคลึง\nคล่าว\nคลำ\nคล่ำ\nคล้ำ\nคลิ้งโคลง\nคลิด\nคลินิก\nคลี\nคลี่\nคลึง\nคลื่น\nคลุก\nคลุ้ง\nคลุบ\nคลุม\nคลุ่ม\nคลุ้ม\nควง\nควณ\nควน\nควบ\nควย\nควร\nควัก\nควั่ก\nควั่งคว้าง\nควัน\nควั่น\nคว้า\nควาก\nคว้าง\nควาญ\nควาน\nคว้าน\nความ\nควาย\nคว่าว\nคว่ำ\nควินิน\nควิวคว่าง\nคหกรรม\nคหกรรมศาสตร์\nคหบดี\nคหัฐ\nคอ\nค้อ\nคอก\nค็อกคัส\nค็อกเทล\nคอเคซอยด์\nค่องอ้อย\nคอด\nคอแดง\nคอน\nค่อน\nค้อน\nคอนกรีต\nคอนเดนเซอร์\nคอนแวนต์\nคอนเสิร์ต\nคอม\nค่อม\nค้อม\nคอมพิวเตอร์\nคอมมานโด\nคอมมิวนิสต์\nคอย\nค่อย\nค้อย\nคอยล์\nคอร์ด\nคอแลน\nคอสติกโซดา\nคะ\nค่ะ\nคะไขว่\nคะค้อย\nคะคาน\nคะนน\nคะนอง\nคะน้า\nคะนึง\nคะเน\nคะเนงร้าย\nคะเน็ด\nคะแนน\nคะมำ\nคะยั้นคะยอ\nคะเยอ\nคัก\nคั่ก\nคัคนะ\nคัคนัมพร\nคัคนางค์\nคัคนานต์\nคั่ง\nคังไคย\nคัจฉ\nคัณฑมาลา\nคัณฑสูตร\nคัด\nคัดเค้า\nคัดมอน\nคัดเม็ง\nคัทลียา\nคัน\nคั่น\nคั้น\nคันถรจนาจารย์\nคันธกุฎี\nคันธมาทน์\nคันธารราษฎร์\nคับ\nคับค้อน\nคับคา\nคับแค\nคัพภ์\nคัมภีร์\nคัมภีรภาพ\nคัล\nคั่ว\nคา\nค่า\nค้า\nค่าคบ\nคาง\nค่าง\nค้าง\nคางคก\nค้างคาว\nคาด\nคาถา\nคาทอลิก\nคาน\nค้าน\nคาบ\nคาพยุต\nคาม\nคามวาสี\nคามณีย์\nคามภีร์\nคาย\nค่าย\nคาร์บอน\nคาร์บอเนต\nคาร์บอลิก\nคาร์บูเรเตอร์\nคาร์โบรันดัม\nคาร์โบไฮเดรต\nคารม\nคารวะ\nคาราเต้\nคาราวาน\nคาว\nค่าว\nค้าว\nคาวตอง\nคาวี\nคาวุต\nคาส\nคำ\nค่ำ\nค้ำ\nคำนวณ\nคำนวร\nคำนับ\nคำนัล\nคำนึง\nคำนูณ\nคำฝอย\nคำเพลิง\nคำรน\nคำรบ\nคำราม\nคำแสด\nคำแหง\nคำโอง\nคิก\nคิง\nคิด\nคิมหันต์\nคิรี\nคิลาน\nคิลานะ\nคิว\nคิ้ว\nคี่\nคีต\nคีบ\nคีม\nคีรี\nคีรีบูน\nคึก\nคึ่ก\nคึกคัก\nคืน\nคืบ\nคือ\nคุ\nคุก\nคุกกี้\nคุกคาม\nคุกพาทย์\nคุ้ง\nคุณ\nคุด\nคุดทะราด\nคุต\nคุตติ\nคุ่น\nคุ้น\nคุป\nคุปต์\nคุปติ\nคุม\nคุ่ม\nคุ้ม\nคุย\nคุ้ย\nคุยหฐาน\nคุยหประเทศ\nคุรุ\nคุลา\nคุลิก่า\nคุลีการ\nคุหา\nคู\nคู่\nคู้\nคูณ\nคูถ\nคูน\nคูปอง\nคูเรียม\nคูหา\nเค้ก\nเค้เก้\nเค้ง\nเคณฑะ\nเคด\nเค็ด\nเคน\nเค้น\nเคเบิล\nเค็ม\nเคมี\nเคย\nเครง\nเคร่ง\nเครงครา\nเครงครำ\nเครดิต\nเครน\nเครา\nเคร่า\nเคราหณี\nเคราะห์\nเครียด\nเครียว\nเครือ\nเครื่อง\nเคล้ง\nเคล็ด\nเคล้น\nเคล้า\nเคล่าคล่อง\nเคลิบเคลิ้ม\nเคลิ้ม\nเคลีย\nเคลื่อน\nเคลือบ\nเคว้ง\nเคหะ\nเคหา\nเคอะ\nเค้า\nเคาน์เตอร์\nเคารพ\nเคาะ\nเคาะแคะ\nเคียง\nเคียด\nเคียน\nเคียม\nเคี่ยม\nเคียร\nเคียว\nเคี่ยว\nเคี้ยว\nเคือง\nแค\nแค่\nแค้\nแคแล\nแคดเมียม\nแค็ตตาล็อก\nแคแตร\nแคโทด\nแคน\nแค่น\nแค้น\nแคบ\nแคบหมู\nแคปซูล\nแคม\nแคร่\nแครก\nแครง\nแคระ\nแคลคูลัส\nแคลง\nแคลเซียม\nแคลน\nแคล้ว\nแคล่วคล่อง\nแคลอรี\nแคลิฟอร์เนียม\nแคว\nแควก\nแคว้น\nแคแสด\nแคะ\nโค\nโคก\nโคเคน\nโค่ง\nโค้ง\nโคจร\nโคเซแคนต์\nโคไซน์\nโคตร\nโคแทนเจนต์\nโคธา\nโคน\nโค่น\nโคบอลต์\nโคปผกะ\nโคม\nโคม่า\nโครก\nโครกคราก\nโครง\nโคร่ง\nโคร่งคร่าง\nโครม\nโครเมียม\nโครโมโซม\nโคราช\nโครำ\nโคล\nโคลง\nโคลน\nโควตา\nโคออร์ดิเนต\nใคร\nใคร่\nใคร่ครวญ\nไค\nไค้\nไคร้\nไคร้เครือ\nไคล\nไคล้\nฆนะ\nฆราวาส\nฆ้อง\nฆ่า\nฆาต\nฆาน\nฆานินทรีย์\nเฆี่ยน\nโฆรวิส\nโฆษก\nโฆษณา\nโฆษะ\nโฆษ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nเฉ่ง\nเฉด\nเฉท\nเฉนียน\nเฉพาะ\nเฉย\nเฉลย\nเฉลว\nเฉลา\nเฉลิม\nเฉลี่ย\nเฉลียง\nเฉลี่ยง\nเฉลียบ\nเฉลียว\nเฉวียง\nเฉวียน\nเฉอะแฉะ\nเฉา\nเฉาก๊วย\nเฉาฮื้อ\nเฉาะ\nเฉิด\nเฉิบ\nเฉียง\nเฉียงพร้านางแอ\nเฉียด\nเฉียบ\nเฉียว\nเฉี่ยว\nเฉือน\nเฉื่อย\nแฉ\nแฉ่\nแฉก\nแฉง\nแฉ่ง\nแฉลบ\nแฉล้ม\nแฉะ\nโฉ\nโฉ่\nโฉเก\nโฉ่งฉ่าง\nโฉงเฉง\nโฉด\nโฉนด\nโฉบ\nโฉเบ๊\nโฉม\nโฉลก\nไฉน\nไฉไล\nชก\nชคัตตรัย\nชง\nชงโค\nชงฆ์\nชงฆา\nชงโลง\nชฎา\nชฎามังษี\nชฎามังสี\nชฎิล\nชด\nชน\nชนก\nชนนี\nชนม์\nชนวน\nชนะ\nชนัก\nชนา\nชนาง\nชนิด\nชเนตตี\nชบา\nชม\nชมดชม้อย\nชมนาด\nชมพู\nชมพู่\nชมรม\nชม้อย\nชม้าย\nชไม\nชยา\nชโย\nชรทึง\nชรริน\nชรอุ่ม\nชระล้ำ\nชระลุ\nชระอาบ\nชระเอม\nชรัด\nชรา\nชล\nชโลง\nชโลม\nช่วง\nชวด\nชวน\nชวย\nช่วย\nชวร\nชวลิต\nชวา\nชวาล\nชวาลา\nช่อ\nชอก\nช็อก\nช็อกโกเลต\nช็อกโกแลต\nชอง\nช่อง\nช้อง\nชองระอา\nชอน\nช่อน\nช้อน\nชอบ\nชอม\nช้อย\nชอล์ก\nชอ่ำ\nชอุ่ม\nชะ\nชะคราม\nชะงอก\nชะง่อน\nชะงัก\nชะงัด\nชะง้ำ\nชะงุ้ม\nชะเง้อ\nชะเงื้อม\nชะแง้\nชะโงก\nชะฉ่า\nชะช่อง\nชะชะ\nชะช้า\nชะโด\nชะตา\nชะต้า\nชะนี\nชะเนาะ\nชะเนียง\nชะพลู\nชะเพลิง\nชะมด\nชะมบ\nชะมวง\nชะมัง\nชะมัด\nชะแม่\nชะรอย\nชะลอ\nชะลอม\nชะล่า\nชะลาน\nชะลิน\nชะลูด\nชะเลง\nชะเลย\nชะแล็ก\nชะแลง\nชะวาก\nชะวาด\nชะเวิกชะวาก\nชะแวง\nชะอม\nชะอ้อน\nชะเอม\nชะโอน\nชัก\nชักคราม\nชักช้า\nชัง\nชั่ง\nชังคา\nชังฆ\nชัชวาล\nชัฏ\nชัด\nชัดช้า\nชัน\nชั้น\nชันกาด\nชันชี\nชันตุ\nชันนะตุ\nชันนุ\nชันโรง\nชันษา\nชันสูตร\nชัปนะ\nชัพ\nชัมพูนท\nชัย\nชัยพฤกษ์\nชัยภูมิ\nชัลลุกา\nชั่ว\nชั้ว\nชัวชม\nชา\nช้า\nชาคระ\nชาคริต\nชาคริยานุโยค\nช่าง\nช้าง\nช้าช่อน\nชาญ\nชาด\nชาดก\nชาต\nชาตบุษย์\nชาตรี\nชาตะ\nชาตา\nชาติ\nชาน\nชานุ\nช้าปี่\nชาปีไหน\nช้าแป้น\nช้าพลู\nชาม\nชามพูนท\nชามาดร\nชามาดา\nชามาตุ\nชาย\nชายา\nชาล\nชาลา\nชาลินี\nช้าเลือด\nชาว\nชาวี\nชำ\nช่ำ\nช้ำ\nชำงัด\nชำงาย\nช่ำชอง\nชำนะ\nชำนัญ\nชำนัน\nชำนาญ\nชำนิ\nชำเนียร\nชำมะนาด\nชำมะเลียง\nชำร่วย\nชำระ\nช้ำรั่ว\nชำรุด\nชำเรา\nชำเราะ\nชำแรก\nชำแระ\nชำเลือง\nชำแหละ\nชิ\nชิง\nชิ่ง\nชิงชัน\nชิงช้า\nชิงช้าชาลี\nชิงชี่\nชิงฮื้อ\nชิชะ\nชิชิ\nชิณณะ\nชิด\nชิเดนทรีย์\nชิต\nชิตินทรีย์\nชิน\nชิ้น\nชินโต\nชิโนรส\nชิม\nชิมแปนซี\nชิยา\nชิรณะ\nชิระ\nชิวหา\nชิสา\nชี\nชี่\nชี้\nชีปะขาว\nชีผะขาว\nชีผ้าขาว\nชีพ\nชีฟอง\nชีรณ\nชีระ\nชีวเคมี\nชีวประวัติ\nชีวภาพ\nชีววิทยา\nชีวะ\nชีวัน\nชีวา\nชีวาตม์\nชีวาลัย\nชีวิต\nชีวิตักษัย\nชีวิน\nชีวี\nชืด\nชื่น\nชื้น\nชื่อ\nชุก\nชุกชี\nชุ้ง\nชุณห\nชุด\nชุติ\nชุน\nชุบ\nชุม\nชุ่ม\nชุมนุม\nชุมพร\nชุมพา\nชุมแพรก\nชุมรุม\nชุมแสง\nชุมเห็ด\nชุ่ย\nชุลมุน\nชุลี\nชุษณะ\nชู\nชู้\nเช็ค\nเช้ง\nเช้งวับ\nเชงเลง\nเช็ด\nเชน\nเช่น\nเชย\nเชลง\nเชลย\nเชลแล็ก\nเชลียง\nเชวง\nเชษฐะ\nเชษฐา\nเชอ\nเช่า\nเช้า\nเชาว์\nเชาวน์\nเชิง\nเชิญ\nเชิด\nเชิ้ต\nเชียง\nเชี่ยน\nเชียบ\nเชี่ยม\nเชียร\nเชียร์\nเชียว\nเชี่ยว\nเชื่อ\nเชื้อ\nเชือก\nเชื่อง\nเชือด\nเชือน\nเชื่อม\nแช\nแช่\nแช่ง\nแชงมา\nแชบ๊วย\nแช่ม\nแชร์\nแชล่ม\nแชสซี\nแชะ\nโชก\nโชค\nโชงโลง\nโชดก\nโชดึก\nโชต\nโชตก\nโชติ\nโชติก\nโชน\nโชมโรม\nโชย\nโชยงการ\nโชยชาย\nโชยติส\nโชว์\nใช่\nใช้\nไช\nไชนะ\nไชย\nไชโย\nซก\nซ่ก\nซงดำ\nซ่งฮื้อ\nซด\nซน\nซ้น\nซบ\nซม\nซวดเซ\nซวน\nซวย\nซอ\nซอก\nซอง\nซ่อง\nซ้อง\nซองแมว\nซ้องแมว\nซอน\nซ่อน\nซ้อน\nซอม\nซ่อม\nซ้อม\nซอมซ่อ\nซอย\nซอส\nซัก\nซักส้าว\nซัง\nซั้ง\nซัด\nซับ\nซัลฟา\nซั้ว\nซา\nซ่า\nซาก\nซาง\nซ่าง\nซาด\nซาน\nซ่าน\nซาบซ่าน\nซาบซึ้ง\nซ่าโบะ\nซาแมเรียม\nซ้าย\nซาลาเปา\nซาว\nซ่าหริ่ม\nซำ\nซ้ำ\nซิ\nซี\nซิก\nซิกข์\nซิกซี้\nซิกแซ็ก\nซิการ์\nซิงโคนา\nซิ่น\nซินนามิก\nซินแส\nซิบ\nซิป\nซิฟิลิส\nซิลิคอน\nซิว\nซี่\nซีก\nซีเซียม\nซีด\nซี้ด\nซีนอน\nซีป่าย\nซีเมนต์\nซีเรียม\nซีลีเนียม\nซีอิ๊ว\nซึก\nซึง\nซึ่ง\nซึ้ง\nซึม\nซื่อ\nซื้อ\nซุก\nซุง\nซุน\nซุบ\nซุป\nซุ่ม\nซุ้ม\nซุ่มซ่าม\nซุย\nซู่\nซูโครส\nซูด\nซู้ด\nซูดซาด\nซูบ\nเซ\nเซ็ก\nเซแคนต์\nเซ็ง\nเซ่ง\nเซ้ง\nเซ็งแซ่\nเซต\nเซน\nเซ็น\nเซ่น\nเซนติกรัม\nเซนติเกรด\nเซนติเมตร\nเซนติลิตร\nเซปักตะกร้อ\nเซราะ\nเซรุ่ม\nเซลเซียส\nเซลล์\nเซลลูลอยด์\nเซลลูโลส\nเซ่อ\nเซอร์โคเนียม\nเซอะ\nเซา\nเซ้าซี้\nเซาะ\nเซิง\nเซิ้ง\nเซียน\nเซียบ\nเซียมซี\nเซียว\nเซี่ยว\nเซี่ยวกาง\nเซื่อง\nแซ\nแซ่\nแซ็กคาริน\nแซง\nแซงแซว\nแซด\nแซบ\nแซม\nแซยิด\nแซ่ว\nแซะ\nโซ\nโซ่\nโซก\nโซ่ง\nโซงโขดง\nโซเซ\nโซดา\nโซเดียม\nโซม\nโซรม\nโซลา\nไซ\nไซ้\nไซเกิล\nไซโคลน\nไซน์\nไซยาไนด์\nไซร้\nไซเรน\nไซโล\nฌาน\nฌาปน\nฌาปนกิจ\nฌาปนสถาน\nเฌอ\nเฌอเอม\nญวน\nญัตติ\nญาณ\nญาติ\nญานาซะฮ์\nญิบ\nญี่ปุ่น\nเญยธรรม\nไญยธรรม\nฎีกา\nฐกัด\nฐากูร\nฐาน\nฐานะ\nฐานันดร\nฐานานุกรม\nฐานานุรูป\nฐานานุศักดิ์\nฐานียะ\nฐาปน\nฐาปนา\nฐายี\nฐิต\nฐิติ\nฑาหก\nฑาหะ\nเฒ่า\nณรงค์\nเณร\nดก\nดง\nด้ง\nด้น\nดนโด่\nดนตรี\nดนัย\nดนุ\nดนู\nดบัสวิน\nดบัสวี\nดม\nดรงค์\nดรณี\nดรรชนี\nดราฟต์\nดรุณ\nดรุณี\nดล\nดวง\nด้วง\nดวด\nด่วน\nด้วน\nด้วย\nดอก\nดอง\nด่อง\nด้อง\nดองฉาย\nดองดึง\nดอด\nดอน\nด่อน\nดอม\nด้อม\nดอย\nด้อย\nดอลลาร์\nดะ\nดะโต๊ะ\nดะหมัง\nดัก\nดักดาน\nดักแด้\nดัง\nดั่ง\nดั้ง\nดัชนี\nดัด\nดัตช์\nดัน\nดั้น\nดับ\nดัมพ์\nดั้วเดี้ย\nดัสกร\nดา\nด่า\nดาก\nด่าง\nด้าง\nดาด\nดาน\nด่าน\nด้าน\nดาบ\nดาบส\nดาม\nด้าม\nด้ามจิ้ว\nดามพ์\nดาย\nด้าย\nดารกะ\nดารณี\nดารดาษ\nดาระ\nดารา\nดาล\nดาลัด\nดาว\nด่าว\nด้าว\nดาวดึงส์\nดาวบส\nดาษ\nดาษดา\nดำ\nด่ำ\nด้ำ\nดำกล\nดำเกิง\nดำแคง\nดำดง\nดำนาณ\nดำเนิน\nดำบล\nดำรง\nดำรวจ\nดำรัส\nดำริ\nดำรี\nดำรู\nดำฤษณา\nดำเลิง\nดิก\nดิ่ง\nดิฉัน\nดิฐ\nดิตถ์\nดิถี\nดิน\nดิ้น\nดิบ\nดิรัจฉาน\nดิลก\nดิ่ว\nดิ้ว\nดิ้วเดี้ยว\nดิษฐ์\nดิสโพรเซียม\nดี\nดีเซล\nดีด\nดีดีที\nดีบุก\nดีปลี\nดีเปรสชัน\nดีหมี\nดีหลี\nดึก\nดึง\nดึ่ง\nดึ่ม\nดื่น\nดื่ม\nดือ\nดื้อ\nดุ\nดุก\nดุกดิก\nดุกทะเล\nดุ้ง\nดุ้งดิ้ง\nดุจ\nดุด\nดุน\nดุ้น\nดุบ\nดุม\nดุ่ม\nดุ่ย\nดุรงค์\nดุริยะ\nดุริยางค์\nดุริยางคศาสตร์\nดุริยางคศิลป์\nดุล\nดุษฎี\nดุษณี\nดุษณีภาพ\nดุษิต\nดุสิต\nดุเหว่า\nดู\nดูกค่าง\nดูกร\nดูด\nดูรา\nดูแล\nเด\nเด่\nเดก\nเด็ก\nเดกซ์โทรส\nเดคากรัม\nเดคาเมตร\nเดคาลิตร\nเด้ง\nเด็จ\nเดช\nเดชน์\nเดชนะ\nเดชะ\nเดโช\nเดซิกรัม\nเดซิเมตร\nเดซิลิตร\nเด็ด\nเดน\nเด่น\nเดนมาร์ก\nเดรัจฉาน\nเด๋อ\nเด๋อด๋า\nเดา\nเด้า\nเดาะ\nเดิน\nเดิ่น\nเดิม\nเดียง\nเดียด\nเดียรดาษ\nเดียรถีย์\nเดียรัจฉาน\nเดียว\nเดี่ยว\nเดี๋ยว\nเดียะ\nเดื่อ\nเดือก\nเดื่อง\nเดือด\nเดือน\nเดือย\nแด\nแด่\nแดก\nแด็ก\nแดกงา\nแดกแด้\nแดง\nแดด\nแดน\nแด่น\nแด่ว\nแดะ\nแดะแด๋\nโด\nโด่\nโดกเดก\nโด่ง\nโดด\nโดน\nโดม\nโดมร\nโดย\nโดรณ\nใด\nได\nได้\nไดแซ็กคาไรด์\nไดนาโม\nไดนาไมต์\nไดโนเสาร์\nไดเรกตริกซ์\nตก\nต๊กโต\nตง\nต๋ง\nตงฉิน\nตงิด\nตงุ่น\nตด\nตติย\nตถาคต\nตน\nต้น\nตนัย\nตนุ\nตบ\nตบะ\nตปนียะ\nตม\nต้ม\nตมูก\nตยาคี\nตรง\nตรณี\nตรม\nตรรก\nตรรกะ\nตรลบ\nตรลอด\nตรลาด\nตรวจ\nตรวน\nตรอก\nตรอง\nตรอมใจ\nตรอมตรม\nตระ\nตระกล\nตระกวน\nตระกอง\nตระการ\nตระกูล\nตระคัร\nตระเตรียม\nตระนาว\nตระบก\nตระบอก\nตระบอง\nตระบัด\nตระบัน\nตระเบ็ง\nตระแบก\nตระแบง\nตระโบม\nตระพอง\nตระพัง\nตระลาการ\nตระวัน\nตระเว็ด\nตระเวน\nตระสัก\nตระหง่าน\nตระหนก\nตระหนัก\nตระหน่ำ\nตระหนี่\nตรัง\nตรังค์\nตรับ\nตรับฟัง\nตรัย\nตรัยตรึงศ์\nตรัส\nตรัสสา\nตรา\nตรากตรำ\nตราชู\nตราบ\nตราสัง\nตรำ\nตริ\nตริว\nตรี\nตรีปวาย\nตรีพิธพรรณ\nตรียัมปวาย\nตรึก\nตรึง\nตรุ\nตรุณ\nตรุณะ\nตรุษ\nตรู\nตรู่\nตฤณ\nตฤตีย\nตฤษณา\nตลก\nตลบ\nตลอด\nตลับ\nตลาด\nตลิ่ง\nตลึง\nตวง\nต่วน\nต้วมเตี้ยม\nตวัก\nตวัด\nตวาด\nตอ\nตอม่อ\nต่อ\nต้อ\nตอก\nต๊อก\nต๊อกต๋อย\nตอง\nต้อง\nตองกราย\nต้องเต\nตองแตก\nต่องแต่ง\nตองเหลือง\nตอด\nตอน\nต้อน\nตอบ\nตอเบา\nตอม\nต่อม\nต๋อม\nต่อย\nต้อย\nต้อยตริ่ง\nต้อยติ่ง\nต้อยตีวิด\nตอแย\nตอร์ปิโด\nต่อไส้\nตอแหล\nตะ\nตะกรน\nตะกร้อ\nตะกรัน\nตะกรับ\nตะกร้า\nตะกราม\nตะกรุด\nตะกรุม\nตะกรุมตะกราม\nตะกละ\nตะกลาม\nตะกวด\nตะกอ\nตะกอน\nตะกัง\nตะกั่ว\nตะกาง\nตะกาด\nตะกาย\nตะกาว\nตะกุกตะกัก\nตะกุย\nตะกู\nตะกูด\nตะเกียกตะกาย\nตะเกียง\nตะเกียบ\nตะแก\nตะแก่\nตะแกรง\nตะโก\nตะโก้\nตะโกก\nตะโกน\nตะโกรง\nตะโกรม\nตะไกร\nตะขบ\nตะขอ\nตะขาบ\nตะขิดตะขวง\nตะเข้\nตะเข็บ\nตะโขง\nตะคร้อ\nตะครอง\nตะครั่นตะครอ\nตะคร้ำ\nตะคริว\nตะคิว\nตะครุบ\nตะคอก\nตะคัน\nตะค้า\nตะคาก\nตะค้าน\nตะคุ่ม\nตะเครียว\nตะเคียว\nตะเคียน\nตะแคง\nตะไคร่\nตะไคร้\nตะเฆ่\nตะนอย\nตะนาว\nตะบม\nตะบอง\nตะบอย\nตะบัน\nตะบิ้ง\nตะบิด\nตะบิดตะบอย\nตะบี้ตะบัน\nตะบึง\nตะบูน\nตะเบ็ง\nตะเบ็งมาน\nตะเบ๊ะ\nตะแบก\nตะแบง\nตะโบม\nตะไบ\nตะปบ\nตะปลิง\nตะปิ้ง\nตะปุ่มตะป่ำ\nตะปู\nตะพง\nตะพด\nตะพอง\nตะพัก\nตะพัง\nตะพัด\nตะพั้น\nตะพาก\nตะพาน\nตะพาบ\nตะพาย\nตะพึด\nตะพึดตะพือ\nตะพุ่น\nตะเพรา\nตะเพิง\nตะเพิด\nตะเพียน\nตะโพก\nตะโพง\nตะโพน\nตะเภา\nตะใภ้\nตะม่อ\nตะมอย\nตะรังกะนู\nตะรังตังกวาง\nตะรังตังช้าง\nตะราง\nตะลอง\nตะลอน\nตะล่อม\nตะละ\nตะลาน\nตะลิงปลิง\nตะลิบ\nตะลีตะลาน\nตะลึง\nตะลึงพรึงเพริด\nตะลุง\nตะลุ่ม\nตะลุ่มนก\nตะลุมบอน\nตะลุ่มโปง\nตะลุมพอ\nตะลุมพุก\nตะลุย\nตะเลง\nตะแลงแกง\nตะไล\nตะวัน\nตะเวน\nตะหลิว\nตะหลุก\nตะหลุง\nตะแหง่ว\nตะแหมะแขะ\nตะโหงก\nตัก\nตักกะ\nตักเตือน\nตั๊กแตน\nตักษัย\nตัง\nตั่ง\nตั้ง\nตังเก\nตังฉ่าย\nตังเม\nตังวาย\nตังโอ๋\nตัจฉก\nตัจฉนี\nตัณฑุล\nตัณหา\nตัด\nตัน\nตันตระ\nตันติ\nตันหยง\nตับ\nตับปิ้ง\nตัว\nตั๋ว\nตัวจี๊ด\nตัวตืด\nตั้วโผ\nตั้วเหี่ย\nตา\nตาก\nตากวาง\nต่าง\nตาด\nตาน\nต่าน\nต้าน\nตานนกกด\nตานี\nตาบ\nตาม\nตามะแน\nตามิน\nตาย\nตาราไต\nตาล\nตาลุ\nต๋าว\nตาเสือ\nตาหนู\nตาฬ\nตำ\nต่ำ\nตำนาน\nตำบล\nตำแบ\nตำแย\nตำรวจ\nตำรับ\nตำรา\nตำรุ\nตำลึง\nตำเสา\nตำหนัก\nตำหนิ\nตำแหน่ง\nติ\nติก\nติ๊ก\nติกะ\nติกาหรัง\nติง\nติ่ง\nติ๋ง\nติ่งตั่ง\nติ๋งต่าง\nติงส\nติงสติ\nติณ\nติด\nติตติกะ\nติตติร\nติตถ\nติตถะ\nติถี\nติมิงคละ\nติรัจฉาน\nติลก\nติละ\nติ้ว\nตี\nตี่\nตีน\nตีบ\nตีรถะ\nตีระ\nตึ\nตึก\nตึ้ก\nตึ้กตั้ก\nตึง\nตึดตื๋อ\nตึ๊ดตื๋อ\nตืด\nตื่น\nตื้น\nตื้อ\nตื๊อ\nตื๋อ\nตุ\nตุ๊\nตุ๊กแก\nตุ๊กตา\nตุ๊กต่ำ\nตุกติก\nตุ๊กติ๊ก\nตุ๊กตุ่น\nตุ๊กตุ๋ย\nตุง\nตุ้งก่า\nตุ้งติ้ง\nตุ๊ดตู่\nตุน\nตุ่น\nตุ๋น\nตุนาหงัน\nตุบ\nตุ้บ\nตุ๊บป่อง\nตุปัดตุป่อง\nตุปัดตุเป๋\nตุ่ม\nตุ้ม\nตุ๋ม\nตุ้มกว้าว\nตุมกา\nตุ้มแซะ\nตุมตัง\nตุ้มเต๋น\nตุ้มปี่\nตุมพะ\nตุ่ย\nตุ้ย\nตุ๊ย\nตุ๋ยตุ่ย\nตุรคะ\nตุรงค์\nตุล\nตุลา\nตุหรัดตุเหร่\nตู\nตู่\nตู้\nตูก\nตูด\nตูบ\nตูม\nเต๊ก\nเต็ง\nเต่ง\nเตช\nเตโช\nเต้น\nเต็นท์\nเต็ม\nเตย\nเตร่\nเตร็ด\nเตรตา\nเตรียม\nเตรียมตรม\nเตละ\nเตลิด\nเตว็ด\nเต่อ\nเตอะ\nเตะ\nเตา\nเต่า\nเต้า\nเต๋า\nเต่าเกียด\nเต้าเจี้ยว\nเต้าทึง\nเต้าหู้\nเต้าฮวย\nเต๊าะ\nเตาะแตะ\nเติ่ง\nเติบ\nเติม\nเตี้ย\nเตียง\nเตียน\nเตียบ\nเตี๋ยม\nเตียรถ์\nเตียว\nเตี่ยว\nเตือน\nแต่\nแต้\nแตก\nแตง\nแต่ง\nแตงเม\nแต้จิ๋ว\nแตด\nแต๊ดแต๋\nแตน\nแต้ม\nแตร\nแตระ\nแต้ว\nแต้วแร้ว\nแต้วแล้ว\nแต่ว่า\nแต้แว้ด\nแตะ\nโต\nโต้\nโตก\nโต่ง\nโต้ง\nโตงเตง\nโตฎก\nโต๊ด\nโตน\nโตนด\nโต้โผ\nโตมร\nโตย\nโตรก\nโต๊ะ\nใต้\nไต\nไต่\nไต้\nไต๋\nไตร\nไตรกิศยา\nไตรดายุค\nไตร่ตรอง\nไตรย\nไต้หวัน\nถก\nถกล\nถงาด\nถด\nถนน\nถนอม\nถนัด\nถนัน\nถนำ\nถนิม\nถม\nถ่ม\nถมอ\nถมึงทึง\nถลก\nถลกบาตร\nถลน\nถล่ม\nถลอก\nถลัน\nถลา\nถลาก\nถลาย\nถลำ\nถลึงตา\nถลุง\nถ่วง\nถ้วน\nถ้วย\nถวัล\nถวัลย์\nถวาย\nถวิน\nถวิล\nถ่อ\nถ้อ\nถอก\nถอง\nถ่อง\nถ้อง\nถอด\nถอน\nถอบ\nถอบแถบ\nถ่อม\nถอย\nถ่อย\nถ้อย\nถะ\nถะถั่น\nถะมัดถะแมง\nถัก\nถัง\nถั่ง\nถัด\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นยา\nบิลเลียด\nบิวเรตต์\nบิสมัท\nบี้\nบีฑา\nบีตา\nบีบ\nบีเยศ\nบึก\nบึกบึน\nบึง\nบึ่ง\nบึ้ง\nบุ\nบุก\nบุคคล\nบุคลากร\nบุคลาธิษฐาน\nบุคลิก\nบุง\nบุ่ง\nบุ้ง\nบุ้งกี๋\nบุญ\nบุญญาธิการ\nบุญญานุภาพ\nบุญญาภินิหาร\nบุญญาภิสังขาร\nบุณฑริก\nบุณมี\nบุณย์\nบุตร\nบุตรี\nบุถุชน\nบุทคล\nบุนนาค\nบุบ\nบุบบิบ\nบุปผชาติ\nบุพกรรม\nบุพการี\nบุพกิจ\nบุพชาติ\nบุพทักษิณ\nบุพนิมิต\nบุพบท\nบุพพาจารย์\nบุพเพสันนิวาส\nบุพโพ\nบุ๋ม\nบุ่มบ่าม\nบุ้ย\nบุรณะ\nบุรพทิศ\nบุรพบท\nบุรพาจารย์\nบูรพาจารย์\nบุระ\nบุราณ\nบุรินทร์\nบุริมทิศ\nบุริมพรรษา\nบุริมสิทธิ\nบุรี\nบุรุษ\nบุโรทั่ง\nบุษกร\nบุษบก\nบุษบง\nบุษบัน\nบุษบา\nบุษบามินตรา\nบุษปราค\nบุษปะ\nบุษย์\nบุษย์น้ำทอง\nบุษยมาส\nบุษยะ\nบุษราคัม\nบุหงัน\nบุหงา\nบุหรง\nบุหรี่\nบุหลัน\nบู่\nบู้\nบูชนียสถาน\nบูชา\nบูชิต\nบูด\nบูดู\nบูร\nบูรณ์\nบูรณภาพ\nบูรณมี\nบูรณะ\nบูรณาการ\nบูรพ์\nบูรพะ\nบูรพา\nเบ้\nเบ่ง\nเบ๊จี๋\nเบญกานี\nเบญจกัลยาณี\nเบญจกามคุณ\nเบญจขันธ์\nเบญจดุริยางค์\nเบญจธรรม\nเบญจบรรพต\nเบญจพรรณ\nเบญจเพส\nเบญจมาศ\nเบญจรงค์\nเบญจศก\nเบญจศีล\nเบญจะ\nเบญจา\nเบญจางค์\nเบญจางคประดิษฐ์\nเบญญา\nเบญพาด\nเบ็ด\nเบ็ดเตล็ด\nเบ็ดเสร็จ\nเบน\nเบนซิน\nเบรก\nเบริลเลียม\nเบส\nเบ้อ\nเบอร์\nเบอร์คีเลียม\nเบ้อเร่อ\nเบ้อเร่อเท่อ\nเบ้อเริ่ม\nเบ้อเริ่มเทิ่ม\nเบอะ\nเบอะบะ\nเบะ\nเบา\nเบ้า\nเบาราณ\nเบาะ\nเบิก\nเบิ่ง\nเบี้ย\nเบี่ยง\nเบียด\nเบียน\nเบียร์\nเบี้ยว\nเบือ\nเบื่อ\nเบื้อ\nเบื้อง\nเบือน\nแบ\nแบ้\nแบก\nแบคทีเรีย\nแบ่ง\nแบงก์\nแบดมินตัน\nแบตเตอรี่\nแบน\nแบนโจ\nแบบ\nแบ็บ\nแบเรียม\nแบหลา\nแบะ\nโบ\nโบ้\nโบ๋\nโบก\nโบกขรณี\nโบกขรพรรษ\nโบชุก\nโบต\nโบนัส\nโบ๊เบ๊\nโบย\nโบรมีน\nโบรอน\nโบราณ\nโบสถ์\nใบ\nใบ้\nไบ่\nปก\nปกติ\nปกรณ์\nปกรณัม\nปกิณกะ\nปกีรณัม\nปโกฏิ\nปง\nป่ง\nปงช้าง\nปฎล\nปฏัก\nปฏิกรณ์\nปฏิกรรม\nปฏิการะ\nปฏิกิริยา\nปฏิกูล\nปฏิคม\nปฏิคหิต\nปฏิคาหก\nปฏิฆะ\nปฏิชีวนะ\nปฏิญญา\nปฏิญาณ\nปฏิทิน\nปฏิบถ\nปฏิบัติ\nปฏิปทา\nปฏิปักษ์\nปฏิปัน\nปฏิปุจฉาพยากรณ์\nปฏิปุจฉาวาที\nปฏิพัทธ์\nปฏิพากย์\nปฏิภาค\nปฏิภาณ\nปฏิมา\nปฏิมากร\nปฏิยุทธ์\nปฏิรพ\nปฏิรูป\nปฏิโลม\nปฏิวัติ\nปฏิวาต\nปฏิวาท\nปฏิเวธ\nปฏิสนธิ\nปฏิสวะ\nปฏิสังขรณ์\nปฏิสันถาร\nปฏิสัมภิทา\nปฏิเสธ\nปฐพี\nปฐม\nปฐวี\nปณต\nปณาม\nปณิธาน\nปณิธิ\nปณีต\nปด\nปดิวรัดา\nปติ\nปถพี\nปถมัง\nปถวี\nปทัฏฐาน\nปทัสถาน\nปทานุกรม\nปทีป\nปทุม\nปน\nป่น\nปนัดดา\nปปัญจะ\nปม\nปรนัย\nปรปักษ์\nปรโลก\nปรวาที\nปรก\nปรกติ\nปรง\nปรตยักษ์\nปรน\nปรนนิบัติ\nปรนิมมิตวสวัตดี\nปรบ\nปรปักษ์\nปรมัตถ์\nปรมาจารย์\nปรมาณู\nปรมาภิไธย\nปรมาภิเษก\nปรมินทร์\nบรเมนทร์\nปรเมศวร์\nปรเมษฐ์\nปรวด\nปรวนแปร\nปรศุ\nปรสิต\nปร๋อ\nปรองดอง\nปรอด\nปรอท\nปรอย\nประ\nประกบ\nประกฤต\nประกฤติ\nประกล\nประกวด\nประกวดประขัน\nประกอบ\nประกัน\nประกับ\nประกาย\nประกายพรึก\nประการ\nประกาศ\nประกาศนียบัตร\nประกาศิต\nประกำ\nประกิด\nประกิต\nประคด\nประคนธรรพ\nประคนธรรพ์\nประคบ\nประคบประหงม\nประคอง\nประคับประคอง\nประคัลภ์\nประคำ\nประคิ่น\nประคุณ\nประเคน\nประเคราะห์\nประโคน\nประโคนธรรพ\nประโคนธรรพ์\nประโคม\nประจง\nประจญ\nประจบ\nประจบประแจง\nประจวบ\nประจ๋อประแจ๋\nประจักษ์\nประจักษนิยม\nประจัญ\nประจัน\nประจาก\nประจาค\nประจาน\nประจำ\nประจิม\nประจิ้มประเจ๋อ\nประจุ\nประจุคมน์\nประจุบัน\nประเจก\nประเจิด\nประเจิดประเจ้อ\nประเจียด\nประแจ\nประชด\nประชน\nประชวม\nประชวร\nประชัน\nประชา\nประชาธิปไตย\nประชิด\nประชี\nประชุม\nประเชิญ\nประณต\nประณม\nประณาม\nประณิธาน\nประณิธิ\nประณีต\nประณุท\nประดง\nประดน\nประดวน\nประดอน\nประดอย\nประดัก\nประดักประเดิด\nประดัง\nประดับ\nประดา\nประดาก\nประดาป\nประดาษ\nประดิชญา\nประดิดประดอย\nประดิทิน\nประดิษฐ์\nประดิษฐกรรม\nประดิษฐาน\nประดุง\nประดุจ\nประดู่\nประเด\nประเด็น\nประเดิม\nประเดียง\nประเดี๋ยว\nประเดี๋ยวประด๋าว\nประแดง\nประแดะ\nประโดง\nประโดย\nประตง\nประตัก\nประตาป\nประติชญา\nประติญาณ\nประติทิน\nประติมากร\nประติมากรรม\nประติรพ\nประตู\nประถม\nประถมจินดา\nประทม\nประท้วง\nประทวน\nประทักษ์\nประทักษิณ\nประทัง\nประทัด\nประทับ\nประทาน\nประทาย\nประทาศี\nประทิน\nประทิ่น\nประทีป\nประทุฐ\nประทุน\nประทุษ\nประทุษฐ์\nประเทศ\nประเทา\nประเทียด\nประเทียบ\nประเทือง\nประธาน\nประธานาธิบดี\nประนม\nประนอ\nประนอม\nประนัง\nประนัปดา\nประนีประนอม\nประปราน\nประปราย\nประปา\nประเปรี้ยง\nประเปรียว\nประพจน์\nประพนธ์\nประพรม\nประพฤติ\nประพฤทธิ์\nประพัด\nประพัทธ์\nประพันธ์\nประพาต\nประพาส\nประพาสมหรณพ\nประพาฬ\nประพิณ\nประพิมพ์ประพาย\nประพุทธ์\nประเพณี\nประโพธ\nประไพ\nประไพร\nประภพ\nประภัสสร\nประภา\nประภาคาร\nประภาพ\nประภาษ\nประภาส\nประเภท\nประมง\nประมวล\nประมาณ\nประมาท\nประมุข\nประมุท\nประมูล\nประเมิน\nประโมง\nประโมทย์\nประยงค์\nประยุกต์\nประยุทธ์\nประยุร\nประยูร\nประโยค\nประโยชน์\nประโรหิต\nประลมพ์\nประลอง\nประลัย\nประลาต\nประลาย\nประลุ\nประเล่ห์\nประเล้าประโลม\nประโลม\nประวรรต\nประวรรตน์\nประวัติ\nประวาล\nประวาลปัทม์\nประวาส\nประวิง\nประวิช\nประวิตร\nประวิน\nประวีณ\nประเวณี\nประเวศ\nประเวศน์\nประศม\nประศาสน์\nประศุ\nประสก\nประสงค์\nประสบ\nประสพ\nประสม\nประสะ\nประสัก\nประสันนาการ\nประสัยห์\nประสา\nประสาท\nประสาธน์\nประสาน\nประสาร\nประสิทธิ์\nประสิทธิผล\nประสิทธิภาพ\nประสีประสา\nประสูต\nประสูติ\nประเสบัน\nประเสบันอากง\nประเสริฐ\nประหนึ่ง\nประหม่า\nประหยัด\nประหลาด\nประหล่ำ\nประหวัด\nประหวั่น\nประหัตประหาร\nประหาณ\nประหาร\nประเหล\nประเหส\nประไหมสุหรี\nประอบ\nประอร\nปรัก\nปรักปรำ\nปรักมะ\nปรัง\nปรัชญา\nปรัตถจริยา\nปรัตยุบัน\nปรัน\nปรับ\nปรัมปรา\nปรัศจิม\nปรัศนา\nปรัศนี\nปรัศว์\nปรัสสบท\nปร่า\nปรากฏ\nปรากรม\nปรากฤต\nปราการ\nปราง\nปรางค์\nปราจีน\nปราชญ์\nปราชญา\nปราชัย\nปราณ\nปราณี\nปราด\nปราน\nปรานี\nปราบ\nปราบดาภิเษก\nปราปต์\nปราม\nปรามาส\nปราโมช\nปราโมทย์\nปราย\nปรารถนา\nปรารภ\nปรารมภ์\nปราศ\nปราศจาก\nปราศรัย\nปราษณี\nปราษาณ\nปราสัย\nปราสาท\nปรำ\nปริ\nปริก\nปริกขาร\nปริกรรม\nปริกัป\nปริคณห์\nปริจาค\nปริจาริกา\nปริเฉท\nปริชน\nปริซึม\nปริญญา\nปริณาม\nปริณายก\nปริต\nปริตตะ\nปริตโตทก\nปริตร\nปริทรรศน์\nปริทัยหัคคี\nปริทัศน์\nปริเทพ\nปริเทวะ\nปรินิพพาน\nปริบ\nปริบท\nปริปันถ์\nปริพนธ์\nปริพัตร\nปริพันธ์\nปริพาชก\nปริภัณฑ์\nปริภาษ\nปริภูมิ\nปริโภค\nปริ่ม\nปริมณฑล\nปริมาณ\nปริมาตร\nปริยัติ\nปริยานุช\nปริยาย\nปริเยศ\nปริโยสาน\nปริวรรต\nปริวัตร\nปริวาร\nปริวาส\nปริวิตก\nปริเวณ\nปริศนา\nปริษัท\nปริสัญญู\nปริสุทธิ\nปริหาน\nปริหาร\nปรี่\nปรีชญา\nปรีชา\nปรี๊ด\nปรีดา\nปรีดิ\nปรีดิ์\nปรีดี\nปรีติ\nปรียะ\nปรียา\nปรึก\nปรึกษา\nปรึง\nปรือ\nปรื๋อ\nปรุ\nปรุง\nปรู\nปรู๋\nปรูด\nปรู๊ด\nปรู๊ดปร๊าด\nปรู๊ฟ\nปฤงคพ\nปฤจฉา\nปฤษฎางค์\nปฤษฐ\nปลก\nปลกเปลี้ย\nปลง\nปล่ง\nปลด\nปล้น\nปลวก\nปลอก\nปล่อง\nปล้อง\nปลอด\nปล้อน\nปลอบ\nปลอม\nปล่อย\nปละ\nปลัก\nปลั๊ก\nปลัง\nปลั่ง\nปลัด\nปลัดขิก\nปลา\nปลาต\nปลาบ\nปลาย\nปลาสเตอร์\nปลาสนาการ\nปล้ำ\nปลิง\nปลิด\nปลิ้น\nปลิโพธ\nปลิม\nปลิ่ม\nปลิว\nปลี\nปลีก\nปลื้ม\nปลุก\nปลูก\nปวกเปียก\nปวง\nป่วง\nปวด\nป่วน\nป้วน\nป้วนเปี้ยน\nป่วย\nปวัตน์\nปวารณา\nปวาล\nปวาส\nปวาฬ\nปวิช\nปวิตร\nปวิธ\nปวิเวก\nปวีณ\nปวุติ\nปเวณี\nปเวส\nปเวสน์\nปศุ\nปสันนะ\nปสันนาการ\nปสาท\nปสาน\nปสาสน์\nปสุ\nปสุต\nปสูติ\nปหังสนะ\nปหาน\nปหาร\nปหาส\nปอ\nป้อ\nป๋อ\nปอก\nปอง\nป่อง\nป้อง\nปอด\nปอน\nป้อน\nปอนด์\nปอเนาะ\nปอบ\nป้อแป้\nปอม\nป้อม\nป๋อม\nปอย\nป้อย\nป้อยอ\nปะ\nปะกน\nปะกัง\nปะการัง\nปะกำ\nปะขาว\nปะงาบ\nปะตาปา\nปะตาระกาหลา\nปะติดปะต่อ\nปะติยาน\nปะทะ\nปะทะปะทัง\nปะทุ\nปะทุน\nปะปน\nปะมง\nปะราลี\nปะรำ\nปะไร\nปะลอม\nปะเลง\nปะแล่ม\nปะโลง\nปะวะหล่ำ\nปะหงับ\nปะหนัน\nปะหัง\nปะเหลาะ\nปัก\nปักข์\nปักเป้า\nปักษ์\nปักษา\nปักษิน\nปักษี\nปัง\nปั๋ง\nปังสุ์\nปังสุกุล\nปัจจัตตะ\nปัจจันต์\nปัจจันตคาม\nปัจจันตชนบท\nปัจจันตประเทศ\nปัจจัย\nปัจจามิตร\nปัจจุคมน์\nปัจจุทธรณ์\nปัจจุบัน\nปัจจุสมัย\nปัจเจก\nปัจโจปการกิจ\nปัจฉา\nปัจฉิม\nปัจถรณ์\nปัจนึก\nปัจยาการ\nปัจเวกขณ์\nปัชชุน\nปัญจนที\nปัญจวัคคีย์\nปัญจก\nปัญจกะ\nปัญจมี\nปัญจวีสติ\nปัญญัติ\nปัญญา\nปัญหา\nปัฏ\nปัฏนะ\nปัฐยาวัต\nปัณฑรหัตถี\nปัณณะ\nปัณณาส\nปัณณาสก์\nปัณรสี\nปัณหิ\nปัด\nปัตคาด\nปัตตะ\nปัตตานึก\nปัตตานุโมทนา\nปัตตาเวีย\nปัตติ\nปัตติก\nปัตถร\nปัตถะ\nปัตนิ\nปัตนี\nปัตหล่า\nปัถพี\nปัถวี\nปัทม์\nปัทมะ\nปัทมาสน์\nปัน\nปั่น\nปั้น\nปั้นจั่น\nปันจุเหร็จ\nปั้นลม\nปั้นหยา\nปั้นเหน่ง\nปับ\nปั๊บ\nปัปผาสะ\nปัพพาชนียกรรม\nปัพภาระ\nปั๊ม\nปัยกา\nปัยยิกา\nปัวเปีย\nปัศจิม\nปัศตัน\nปัสสาวะ\nปัสสาสะ\nปา\nป่า\nป้า\nปาก\nปาง\nป้าง\nปาจรีย์\nปาจิตตีย์\nปาจีน\nปาฏลิ\nปาฏิบท\nปาฏิบุคลิก\nปาฏิโภค\nปาฏิหาริย์\nปาฐก\nปาฐกถา\nปาฐะ\nปาณกชาติ\nปาณะ\nปาณาติบาต\nปาณิ\nปาณี\nปาด\nปาติโมกข์\nปาตี\nปาเต๊ะ\nปาท่องโก๋\nปาทังกา\nปาทาน\nปาทุกา\nปาน\nป่าน\nป้าน\nปานะ\nปานียะ\nป้าบ\nป๊าบ\nปาพจน์\nปาม\nปาโมกข์\nป่าย\nป้าย\nปายาส\nปาร์เกต์\nปารมี\nปารเมศ\nปาราชิก\nปาริฉัตร\nปาริชาต\nปารุสกวัน\nปาล\nปาล์ม\nปาลิไลยก์\nปาลี\nปาว\nป่าว\nป๊าว\nปาวาร\nปาษาณ\nปาส\nปาสาณ\nปาสาทิกะ\nปาหนัน\nปาหี่\nปำ\nป้ำ\nป้ำเป๋อ\nปิกนิก\nปิ้ง\nปิงคละ\nปิงปอง\nปิฎก\nปิฏฐะ\nปิฐิ\nปิณฑะ\nปิด\nปิตตะ\nปิตา\nปิตามหัยกา\nปิตามหัยยิกา\nปิตุ\nปิตุจฉา\nปิตุภูมิ\nปิตุลา\nปิโตรเลียม\nปิ่น\nปิ่นแก้ว\nปิ่นโต\nปิปผลี\nปิ่ม\nปิ้ม\nปิยะ\nปิยังคุ\nปิโยรส\nปิลันธน์\nปิ๋ว\nปิศาจ\nปิหกะ\nปี\nปี่\nปี้\nปี๋\nปีก\nปีฐะ\nปี๊ด\nปีติ\nปีน\nปีบ\nปี๊บ\nปีศาจ\nปีฬกะ\nปึก\nปึง\nปึ่ง\nปึ๋ง\nปึ้ด\nปึมปื้อ\nปืน\nปื้น\nปือ\nปื้อ\nปื๋อ\nปุ\nปุ๊\nปุก\nปุกปุย\nปุคละ\nปุ้งกี๋\nปุงควะ\nปุงลิงค์\nปุงลึงค์\nปุจฉา\nปุฏะ\nปุณฑริก\nปุด\nปุตตะ\nปุถุชน\nปุนนาค\nปุนภพ\nปุนัพสุ\nปุบ\nปุ๊บ\nปุปผะ\nปุปะ\nปุพพะ\nปุ่ม\nปุ่มป่ำ\nปุ้ม\nปุ๋ม\nปุย\nปุ้ย\nปุ๋ย\nปุรณะ\nปุระ\nปุราณ\nปุราณะ\nปุริมพรรษา\nปุเรจาริก\nปุโรหิต\nปุลลิงค์\nปุลลึงค์\nปุลินท์\nปุโลปุเล\nปุษยะ\nปุสสะ\nปู\nปู่\nปูชกะ\nปูชนียบุคคล\nปูชนียวัตถุ\nปูชนียะ\nปูชา\nปูชิต\nปูด\nปูน\nปูม\nปู้ยี่ปู้ยำ\nปูระ\nปูลู\nเป้\nเป๋\nเปก\nเป๊ก\nเป่ง\nเป้ง\nเป๋ง\nเป็ด\nเปตพลี\nเปตอง\nเป็น\nเปยยาล\nเปร็ง\nเปรต\nเปรม\nเปรย\nเปรอ\nเปรอะ\nเปราะ\nเปรียง\nเปรี้ยง\nเปรี้ยงปร้าง\nเปรียญ\nเปรียบ\nเปรี่ยม\nเปรียว\nเปรี้ยว\nเปรียะ\nเปรี๊ยะ\nเปรื่อง\nเปรื้อย\nเปล\nเปล่ง\nเปลว\nเปลา\nเปล่า\nเปล้า\nเปลาะ\nเปลี้ย\nเปลี่ยน\nเปลี่ยม\nเปลี่ยว\nเปลือก\nเปลือง\nเปลื้อง\nเปลือย\nเปศะ\nเปศัส\nเปสการ\nเปสละ\nเปสุญวาท\nเป๋อ\nเป้อเย้อ\nเปอร์\nเปอร์เซ็นต์\nเปะ\nเปา\nเป่า\nเป้า\nเป๊า\nเป๋า\nเป๋าฮื้อ\nเปาะ\nเป๊าะ\nเปาะเปี๊ยะ\nเปาะแปะ\nเปิก\nเปิง\nเปิงมาง\nเปิด\nเปิ่น\nเปิบ\nเปิ๊บ\nเปีย\nเปียก\nเปี๊ยก\nเปี๊ยบ\nเปี่ยม\nเปี้ยว\nเปี๊ยว\nเปียะ\nเปี๊ยะ\nเปือก\nเปื้อน\nเปื่อย\nแป\nแป้ง\nแป๋ง\nแปด\nแป๊ด\nแปทู\nแป้น\nแป๊น\nแปบ\nแป๊บ\nแปม\nแปร\nแปร๋\nแปรก\nแปรง\nแปร่ง\nแปร๊ด\nแปร้น\nแปร๋น\nแปรปรวน\nแประ\nแปล\nแปล้\nแปลก\nแปลง\nแปลน\nแปลบ\nแปล๊บ\nแป้ว\nแป๊ว\nแปะ\nแป๊ะ\nแป๊ะซะ\nโป\nโป่\nโป้\nโป๊\nโปก\nโป๊ก\nโป๊กเกอร์\nโปกขรณี\nโปกขรพรรษ\nโปเก\nโปง\nโป่ง\nโป้ง\nโป่งข่าม\nโปงลาง\nโป่งวิด\nโปฐบท\nโปฐปทมาส\nโปดก\nโปตถกะ\nโปน\nโป๊ป\nโป๊ยเซียน\nโปรแกรม\nโปรง\nโปร่ง\nโปรด\nโปรตอน\nโปรตีน\nโปรเตสแตนต์\nโปรแทรกเตอร์\nโปรย\nโปล่ง\nโปลิโอ\nโปโล\nโปสก\nโปสต์การ์ด\nโปะ\nโป๊ะ\nโป๊ะจ้าย\nไป\nไป่\nไป๋\nไปยาล\nไปรษณีย์\nไปรษณียบัตร\nไปรษณียภัณฑ์\nไปรษณียากร\nไปล่\nไปศาจ\nผก\nผกา\nผกาย\nผคม\nผง\nผงก\nผงม\nผงะ\nผงาด\nผง่าน\nผจง\nผจญ\nผจัญ\nผจาน\nผชุม\nผณิน\nผณินทร\nผณิศวร\nผด\nผดุง\nผเดิน\nผทม\nผนวก\nผนวช\nผนัง\nผนิด\nผนึก\nผม\nผยอง\nผรณาปีติ\nผรสุ\nผริต\nผรุสวาท\nผล\nผลคุน\nผลคุนี\nผล็อย\nผละ\nผลัก\nผลัด\nผลับ\nผลัวะ\nผลา\nผลาญ\nผลานิสงส์\nผลาผล\nผลาหาร\nผลิ\nผลิกะ\nผลิต\nผลิน\nผลี\nผลีผลาม\nผลึก\nผลึ่ง\nผลือ\nผลุ\nผลุง\nผลุด\nผลุน\nผลุนผลัน\nผลุบ\nผลุบผลับ\nผลุย\nผลู\nผวน\nผวย\nผวา\nผสม\nผสาน\nผอง\nผ่อง\nผ่อน\nผอบ\nผอม\nผ็อย\nผอูน\nผะ\nผะดา\nผะสา\nผัก\nผัคคุณ\nผัคคุณี\nผัง\nผัด\nผัน\nผับ\nผัว\nผัวะ\nผัสสะ\nผัสสาหาร\nผา\nผ่า\nผ้า\nผาก\nผาง\nผ่าง\nผาณิต\nผาด\nผาติ\nผ่าน\nผาม\nผาย\nผ่ายผอม\nผาล\nผาลคุน\nผาลา\nผ่าว\nผาสุก\nผ้าฮาด\nผำ\nผ้ำ\nผิ\nผิง\nผิด\nผิตะ\nผิน\nผิว\nผี\nผี้ว์\nผึง\nผึ่ง\nผึ้ง\nผึ้งรวง\nผืน\nผื่น\nผุ\nผุด\nผุยผง\nผุสราคา\nผู้\nผูก\nเผ\nเผง\nเผชิญ\nเผ็ด\nเผด็จ\nเผดิม\nเผดียง\nเผ่น\nเผนิก\nเผย\nเผยอ\nเผยิบ\nเผยิบผยาบ\nเผล\nเผล่\nเผล็ด\nเผลอ\nเผลอไผล\nเผละ\nเผลาะ\nเผลาะแผละ\nเผลียง\nเผอเรอ\nเผอิญ\nเผอิล\nเผะ\nเผา\nเผ่า\nเผ้า\nเผาะ\nเผิ้ง\nเผิน\nเผียน\nเผือ\nเผื่อ\nเผือก\nเผือด\nเผือน\nเผื่อน\nแผ่\nแผก\nแผง\nแผด\nแผน\nแผ่น\nแผนก\nแผล\nแผลง\nแผล็บ\nแผล็ว\nแผละ\nแผ่ว\nแผ้ว\nโผ\nโผง\nโผฏฐัพพะ\nโผน\nโผเผ\nโผย\nโผล่\nโผลกเผลก\nโผละ\nโผอน\nโผะ\nไผ\nไผ่\nไผท\nฝน\nฝรั่ง\nฝรั่งเศส\nฝ่อ\nฝอย\nฝัก\nฝัง\nฝั่ง\nฝัด\nฝัน\nฝา\nฝ่า\nฝ้า\nฝาก\nฝาง\nฝาด\nฝาน\nฝาย\nฝ่าย\nฝ้าย\nฝิ่น\nฝี\nฝี่\nฝีก\nฝึก\nฝืด\nฝืน\nฝุ่น\nฝูง\nเฝ้า\nเฝือ\nเฝือก\nเฝือง\nเฝื่อน\nแฝก\nแฝง\nแฝด\nใฝ่\nไฝ\nพก\nพกุล\nพง\nพงศ์\nพงศกร\nพงศธร\nพงศา\nพงศาวดาร\nพจน์\nพจนา\nพจนานุกรม\nพจนารถ\nพจนีย์\nพจมาน\nพจี\nพชระ\nพญา\nพญาลอ\nพณิช\nพณิชย์\nพดด้วง\nพธู\nพนันดร\nพนาดร\nพนาดอน\nพนาราม\nพนาลัย\nพนาลี\nพนาวาส\nพนาเวศ\nพนาศรม\nพนาสณฑ์\nพนาสัณฑ์\nพเนจร\nพ่น\nพ้น\nพนม\nพนอง\nพนอม\nพนัก\nพนักงาน\nพนัง\nพนัน\nพนัส\nพนา\nพนาย\nพนิดา\nพนิต\nพบ\nพม่า\nพยนต์\nพยศ\nพยัก\nพยักพเยิด\nพยัคฆ์\nพยัคฆา\nพยัคฆิน\nพยัคฆี\nพยัชน์\nพยัญชนะ\nพยัต\nพยับ\nพยากรณ์\nพยาฆร์\nพยางค์\nพยาธิ\nพยาน\nพยาบาท\nพยาบาล\nพยาม\nพยามะ\nพยายาม\nพยุ\nพยุง\nพยุหยาตรา\nพยุหโยธา\nพยุหเสนา\nพยุหะ\nพยู่ห์\nพเยีย\nพร\nพรต\nพรม\nพรรค\nพรรค์\nพรรคานต์\nพรรณ\nพรรณนา\nพรรดึก\nพรรลาย\nพรรษ\nพรรษา\nพรรเอิญ\nพรวด\nพรวน\nพรหม\nพรหมจรรย์\nพรหมจาริณี\nพรหมจารี\nพรหมา\nพรหมาสตร์\nพรหมินทร์\nพรอก\nพร่อง\nพร้อง\nพรอด\nพร้อม\nพร้อมพรัก\nพร่อย\nพร้อย\nพระ\nพระนอม\nพระนาด\nพระฮาม\nพรักพร้อม\nพรั่ง\nพรัด\nพรั่น\nพรับ\nพร่า\nพร้า\nพราก\nพราง\nพร่าง\nพราด\nพราน\nพราย\nพราว\nพราหมณ์\nพราหมณะ\nพราหมณี\nพราหมี\nพรำ\nพร่ำ\nพริก\nพริ้ง\nพริบ\nพริ้ม\nพรึง\nพรึน\nพรึบ\nพรึ่บ\nพรืด\nพรุ\nพรุ่ง\nพรุน\nพรู\nพรูด\nพฤกษ์\nพฤกษชาติ\nพฤกษเทวดา\nพฤกษราช\nพฤกษศาสตร์\nพฤกษา\nพฤฒ\nพฤฒา\nพฤฒาจารย์\nพฤฒิ\nพฤต\nพฤติ\nพฤทธ์\nพฤทธิ์\nพฤนต์\nพฤนท์\nพฤศจิก\nพฤศจิกายน\nพฤษภ\nพฤษภาคม\nพฤหัสบดี\nพล\nพละ\nพลากร\nพลาดิศัย\nพลาธิการ\nพลานามัย\nพลบ\nพลวก\nพลวง\nพลวัต\nพลศาสตร์\nพลอ\nพล้อ\nพลอง\nพลอด\nพลอน\nพลอมแพลม\nพลอย\nพล่อย\nพลั่ก\nพลัง\nพลั่ง\nพลั้ง\nพลัด\nพลัน\nพลับ\nพลับพลา\nพลับพลึง\nพลั่ว\nพล่า\nพลาง\nพลาญ\nพลาด\nพล่าน\nพลาม\nพล่าม\nพลาย\nพลาสติก\nพลาสมา\nพลาหก\nพลำ\nพล้ำ\nพลำภัง\nพลิก\nพลิพัท\nพลิ้ว\nพลี\nพลุ\nพลุก\nพลุ่ก\nพลุกพล่าน\nพลุ่ง\nพลุ้ย\nพลู\nพลูโต\nพลูโทเนียม\nพวก\nพวง\nพ่วง\nพวน\nพวย\nพสก\nพสุ\nพสุธา\nพสุสงกรานต์\nพหล\nพหุ\nพหุล\nพหู\nพอ\nพ่อ\nพ้อ\nพอก\nพอง\nพ้อง\nพอน\nพ้อม\nพอโลเนียม\nพะ\nพะงา\nพะงาบ\nพะจง\nพะทำมะรง\nพะนอ\nพะเน้าพะนอ\nพะเนิน\nพะเนียง\nพะแนง\nพะพาน\nพะพิง\nพะเพิง\nพะยอม\nพ่ะย่ะค่ะ\nพะยูง\nพะยูน\nพะเยิบ\nพะเยิบพะยาบ\nพะรุงพะรัง\nพะโล้\nพะไล\nพะวง\nพะวักพะวน\nพะวา\nพะว้าพะวัง\nพะอง\nพะอากพะอำ\nพะอืดพะอม\nพัก\nพักตร์\nพักตรา\nพักร\nพัง\nพังกา\nพังงา\nพังผืด\nพังพวย\nพังพอน\nพังพาน\nพังพาบ\nพังเพย\nพัช\nพัชนี\nพัชระ\nพัญจน์\nพัฒนะ\nพัฒนา\nพัฒนากร\nพัฒนาการ\nพัด\nพัดชา\nพัดดึงส์\nพัตร\nพัทธ์\nพัทธยา\nพัทธสีมา\nพัทร\nพัน\nพันตู\nพันทาง\nพันธ์\nพันธะ\nพันธกรณี\nพันธบัตร\nพันธมิตร\nพันธนะ\nพันธนาคาร\nพันธนาการ\nพันธุ์\nพันธุกรรม\nพันลึก\nพันลือ\nพันเลิศ\nพันเอิญ\nพับ\nพัลลภ\nพัลวัน\nพัว\nพัวะ\nพัศดี\nพัสดุ\nพัสตร์\nพัสถาน\nพา\nพาก\nพากเพียร\nพากย์\nพาง\nพ่าง\nพาชี\nพาณิช\nพาณิชย์\nพาณิชยกรรม\nพาณิชยการ\nพาณิชยศาสตร์\nพาณิชยศิลป์\nพาณินี\nพาณี\nพาณีนี\nพาด\nพาท\nพาทย์\nพาธ\nพาธา\nพาน\nพ่าน\nพานร\nพานรินทร์\nพาม\nพาย\nพ่าย\nพายม้า\nพายัพ\nพายุ\nพาร์เซก\nพารณ\nพารา\nพาราฟิน\nพาล\nพาลา\nพาลี\nพาลุก\nพาโล\nพาไล\nพาส\nพาสน์\nพาสนา\nพาสุกรี\nพ่าห์\nพาหนะ\nพาหะ\nพาหา\nพาหิรกะ\nพาหิระ\nพาหุ\nพาหุรัด\nพาหุสัจจะ\nพาเหียร\nพาฬ\nพำ\nพำนัก\nพำพึม\nพำลา\nพิกล\nพิกสิต\nพิกัด\nพิกัติ\nพิกัน\nพิการ\nพิกุล\nพิเคราะห์\nพิฆน์\nพิฆเนศ\nพิฆเนศวร\nพิฆาต\nพิง\nพิจัย\nพิจาร\nพิจารณ์\nพิจารณา\nพิจิก\nพิจิต\nพิจิตร\nพิชญ์\nพิชัย\nพิชาน\nพิชิต\nพิเชฐ\nพิเชียร\nพิฑูรย์\nพิณ\nพิดทูล\nพิดาน\nพิโดร\nพิตร\nพิถี\nพิถีพิถัน\nพิทย\nพิทย์\nพิทยา\nพิทยาคม\nพิทยาคาร\nพิทยาธร\nพิทยาลัย\nพิทักษ์\nพิทูร\nพิเทศ\nพิธาน\nพิธี\nพิธุ\nพินทุ\nพินอบพิเทา\nพินัย\nพินาศ\nพินิจ\nพินิต\nพินิศ\nพินิศจัย\nพิเนต\nพิบัติ\nพิบุล\nพิบูล\nพิปริต\nพิปลาส\nพิพรรธ\nพิพรรธน์\nพิพักพิพ่วน\nพิพัฒ\nพิพัฒน์\nพิพากษ์\nพิพากษา\nพิพาท\nพิพิธ\nพิพิธภัณฑ์\nพิพิธภัณฑสถาน\nพิภพ\nพิภัช\nพิภาค\nพิภูษณะ\nพิเภก\nพิมปะการัง\nพิมพ์\nพิมพการัง\nพิมพา\nพิมพาภรณ์\nพิมล\nพิมเสน\nพิมาน\nพิมุข\nพิโมกข์\nพิโมกษ์\nพิโยกพิเกน\nพิโยค\nพิรอด\nพิระ\nพิรากล\nพิราบ\nพิราม\nพิราลัย\nพิริยะ\nพิรี้พิไร\nพิรุณ\nพิรุธ\nพิรุฬห์\nพิเรนทร์\nพิเราะ\nพิโรธ\nพิไร\nพิลังกาสา\nพิลาป\nพิลาส\nพิลิปดา\nพิลึก\nพิลึกกึกกือ\nพิลึกพิลั่น\nพิโลน\nพิไล\nพิศ\nพิศวง\nพิศวาส\nพิศาล\nพิศุทธ์\nพิศุทธิ์\nพิเศษ\nพิษ\nพิษฐาน\nพิษนาศน์\nพิสดาร\nพิสมร\nพิสมัย\nพิสัง\nพิสัช\nพิสัย\nพิสิฐ\nพิสุทธิ์\nพิสูจน์\nพิหค\nพิหาร\nพิฬาร\nพี\nพี่\nพี้\nพีชคณิต\nพีระมิด\nพึง\nพึ่ง\nพึ่บ\nพึ่บพั่บ\nพึม\nพึมพำ\nพืช\nพืด\nพื้น\nพุ\nพุก\nพุกาม\nพุง\nพุ่ง\nพุงดอ\nพุฒ\nพุฒิ\nพุด\nพุดตาน\nพุทธ\nพุทธะ\nพุทธังกูร\nพุทธางกูร\nพุทธันดร\nพุทธาภิเษก\nพุทธาวาส\nพุทธิ\nพุทโธ่\nพุทรา\nพุธ\nพุ่ม\nพุมเรียง\nพุ้ย\nพู\nพูพอน\nพู่\nพูด\nพูน\nพู้น\nพู่ระหง\nเพ\nเพ็ก\nเพกา\nเพคะ\nเพ็ง\nเพ่ง\nเพ็จ\nเพชฉลูกรรม\nเพชฌฆาต\nเพชร\nเพชรดา\nเพชรปาณี\nเพชรฤกษ์\nเพชรายุธ\nเพชรกลับ\nเพชรสังฆาต\nเพชรหลีก\nเพชรหึง\nเพ็ญ\nเพฑูริย์\nเพณี\nเพ็ดทูล\nเพดาน\nเพท\nเพทนา\nเพทาย\nเพทุบาย\nเพโทบาย\nเพ่นพ่าน\nเพนียด\nเพไนย\nเพ้ย\nเพรง\nเพรซีโอดิเมียม\nเพรา\nเพราะ\nเพริด\nเพริศ\nเพรียก\nเพรียง\nเพรียบ\nเพรี้ยม\nเพรียว\nเพรื่อ\nเพรือง\nเพล\nเพลง\nเพล็ด\nเพล้โพล้\nเพลา\nเพลาะ\nเพลิง\nเพลิดเพลิน\nเพลิน\nเพลีย\nเพลี้ย\nเพลี่ยง\nเพศ\nเพส\nเพสลาด\nเพ่อ\nเพ้อ\nเพ้อเจ้อ\nเพอิญ\nเพะ\nเพา\nเพาะ\nเพิก\nเพิง\nเพิ่ง\nเพิดเพ้ย\nเพิ่ม\nเพี้ย\nเพียง\nเพี้ยง\nเพียงออ\nเพี้ยน\nเพียบ\nเพียร\nเพื่อ\nเพื่อน\nแพ\nแพ้\nแพง\nแพ่ง\nแพงพวย\nแพทย์\nแพทยศาสตร์\nแพน\nแพ่น\nแพนก\nแพนงเชิง\nแพร\nแพร่\nแพรก\nแพร่ง\nแพรว\nแพร้ว\nแพลง\nแพลทินัม\nแพล็บ\nแพลม\nแพลเลเดียม\nแพละ\nแพละโลม\nแพว\nแพ้ว\nแพศย์\nแพศยา\nแพะ\nโพ\nโพก\nโพกพาย\nโพง\nโพงพาง\nโพชฌงค์\nโพซิตรอน\nโพด\nโพทะเล\nโพแทสเซียม\nโพธ\nโพธิ\nโพธิ์\nโพน\nโพ้น\nโพนทะนา\nโพบาย\nโพย\nโพยก๊วน\nโพยม\nโพรก\nโพรง\nโพรโทแอกทิเนียม\nโพรมีเทียม\nโพระดก\nโพล่\nโพลง\nโพล่ง\nโพล้ง\nโพลน\nโพล้เพล้\nโพละ\nโพสพ\nไพ\nไพ่\nไพจิตร\nไพชน\nไพชยนต์\nไพฑูรย์\nไพที\nไพบูลย์\nไพพรรณ\nไพร\nไพร่\nไพรจิตร\nไพรชน\nไพรชยนต์\nไพรฑูรย์\nไพรที\nไพรบูลย์\nไพรเราะ\nไพรัช\nไพรำ\nไพริน\nไพรินทร์\nไพรี\nไพเราะ\nไพโรจน์\nไพล\nไพล่\nไพศาขะ\nไพศาล\nไพเศษ\nไพสพ\nไพสิฐ\nไพหาร\nฟก\nฟ้ง\nฟรักโทส\nฟรี\nฟลูออรีน\nฟ่อ\nฟ้อ\nฟอก\nฟอง\nฟ่อง\nฟ้อง\nฟอด\nฟอน\nฟ่อน\nฟ้อน\nฟ้อแฟ้\nฟอร์มาลดีไฮด์\nฟอร์มาลิน\nฟอสฟอรัส\nฟอสเฟต\nฟัก\nฟักฟุ้น\nฟัง\nฟังก์ชัน\nฟัด\nฟัน\nฟั่น\nฟั้น\nฟ้า\nฟาก\nฟาง\nฟ่าง\nฟาด\nฟาทอม\nฟาน\nฟ่าม\nฟาย\nฟาร์ม\nฟาสซิสต์\nฟิด\nฟิต\nฟิบ\nฟิล์ม\nฟิวส์\nฟิสิกส์\nฟี่\nฟี้\nฟืดฟาด\nฟืน\nฟื้น\nฟืม\nฟุ\nฟุ้ง\nฟุต\nฟุน\nฟุบ\nฟุ่บ\nฟุ่มเฟือย\nฟุลสแก๊ป\nฟู\nฟู่\nฟูก\nฟูด\nฟูม\nเฟ็ด\nเฟ้น\nเฟลด์สปาร์\nเฟ้อ\nเฟอร์เมียม\nเฟอะ\nเฟอะฟะ\nเฟะ\nเฟะฟะ\nเฟิน\nเฟี้ยม\nเฟี้ยว\nเฟือ\nเฟื้อ\nเฟือง\nเฟื่อง\nเฟื้อง\nเฟือน\nเฟือย\nเฟื้อย\nแฟ่\nแฟง\nแฟชั่น\nแฟน\nแฟบ\nแฟ้ม\nแฟรนเซียม\nแฟลกซ์\nแฟลต\nแฟะ\nโฟกัส\nไฟ\nภควดี\nภควัต\nภควันต์\nภควัม\nภควา\nภควาน\nภคะ\nภคันทลา\nภคินี\nภณะ\nภณิดา\nภพ\nภมร\nภมริน\nภมรี\nภมุกา\nภยันตราย\nภยาคติ\nภระ\nภรณี\nภรต\nภรรดร\nภรรดา\nภรรยา\nภระมร\nภระมรี\nภราดร\nภราดรภาพ\nภราดา\nภริยา\nภฤศ\nภวะ\nภวตัณหา\nภวนะ\nภวังค์\nภวังคจิต\nภักดี\nภักตะ\nภักติ\nภักษ์\nภักษา\nภักษาหาร\nภัค\nภัคน์\nภังคะ\nภังคี\nภัจ\nภัณฑ์\nภัณฑาคาร\nภัณฑาคาริก\nภัณฑารักษ์\nภัณฑนะ\nภัณฑู\nภัต\nภัตตาคาร\nภัตตาหาร\nภัตร\nภัทระ\nภัทรกัป\nภัพ\nภัย\nภัสดา\nภัสตรา\nภัสมะ\nภัสสร\nภา\nภาค\nภาคย์\nภาคยานุวัติ\nภาคินี\nภาคิไนย\nภาคี\nภาคียะ\nภาชนะ\nภาชี\nภาณ\nภาณวาร\nภาณกะ\nภาณี\nภาณุ\nภาดร\nภาดา\nภาตระ\nภาตา\nภาตุ\nภาติกะ\nภาติยะ\nภาพ\nภาพย์\nภาม\nภาย\nภาร\nภาระ\nภารดี\nภารต\nภารตี\nภารยทรัพย์\nภารยา\nภารา\nภาวนา\nภาวะ\nภาษ\nภาษณ์\nภาษา\nภาษิต\nภาษี\nภาส\nภาสน์\nภาสวร\nภาสา\nภาสุระ\nภิกขา\nภิกขาจาร\nภิกขุ\nภิกขุนี\nภิกษา\nภิกษาจาร\nภิกษาหาร\nภิกษุ\nภิกษุณี\nภิงคาร\nภิญโญ\nภิตติ\nภินท์\nภินทนาการ\nภิยโย\nภิรมย์\nภิรมย์สุรางค์\nภิษัช\nภิสัก\nภีตะ\nภีมะ\nภีรุ\nภุกต์\nภุขัน\nภุช\nภุชงค์\nภุต\nภุมมะ\nภุมรัตน์\nภุมวาร\nภุมรา\nภุมริน\nภุมรี\nภุมเรศ\nภู\nภู่\nภูต\nภูติ\nภูม\nภูมิ\nภูมี\nภูริ\nภูรี\nภูวดล\nภูวนาถ\nภูวเนตร\nภูวไนย\nภูษา\nภูษิต\nเภกะ\nเภตรา\nเภท\nเภทุบาย\nเภรี\nเภสัช\nโภค\nโภคะ\nโภคิน\nโภคี\nโภไคย\nโภไคศวรรย์\nโภช\nโภชย์\nโภชก\nโภชนะ\nโภชนา\nโภชนาหาร\nโภชนียะ\nไภริน\nไภรี\nไภษัชคุรุ\nไภษัชย์\nมกร\nมกราคม\nมกุฎ\nมคธ\nมฆวัน\nมฆะ\nมฆา\nม่ง\nมงกุฎ\nมงโกรย\nมงคล\nมงคลวาร\nมณฑ์\nมณฑก\nมณฑนะ\nมณฑป\nมณฑล\nมณฑา\nมณฑารพ\nมณฑิระ\nมณเฑียร\nมณี\nมด\nมตะ\nมตกภัต\nมติ\nมทนะ\nมทะ\nมธุ\nมธุกร\nมธุการี\nมธุลีห์\nมธุระ\nมธุรพจน์\nมน\nมนินทรีย์\nม่น\nมนต์\nมนตร์\nมนตรี\nมนท์\nมนทิราลัย\nมนเทียร\nมนสิการ\nมนัส\nมนัสวี\nมนินทรีย์\nมนิมนา\nมนิลา\nมนุญ\nมนุษย์\nมนุษยชาติ\nมนุษยธรรม\nมนุษย์มนา\nมนุษยโลก\nมนุษยศาสตร์\nมนุษยสัมพันธ์\nมนุสาร\nมนู\nมนูสาร\nมโน\nมโนช\nมโนชญ์\nมโนราห์\nมโนสาเร่\nมโนห์รา\nมมังการ\nมยุรฉัตร\nมยุระ\nมยุรา\nมยุรี\nมยุเรศ\nมยูร\nมรกต\nมรคา\nมรฑป\nมรณ์\nมรณะ\nมรณกรรม\nมรณบัตร\nมรณภัย\nมรณภาพ\nมรดก\nมรรค\nมรรคา\nมรรตัย\nมรรยาท\nมรรษ\nมรสุม\nมริจ\nมริยาท\nมรีจิ\nมรุต\nมฤค\nมฤคย์\nมฤคศิระ\nมฤคศิรมาส\nมฤคเศียร\nมฤคินทร์\nมฤเคนทร์\nมฤดก\nมฤต\nมฤตยู\nมฤทุ\nมล\nมละ\nมลัก\nมลังเมลือง\nมล้าง\nมลาย\nมลายู\nมวก\nม่วง\nมวน\nม่วน\nม้วน\nม้วนต้วน\nมวย\nม้วย\nมวล\nมหกรรม\nมหรณพ\nมหรรณพ\nมหรสพ\nมหัจฉริยะ\nมหัต\nมหัทธนะ\nมหันต์\nมหันตโทษ\nมหัพภาค\nมหัศจรรย์\nมหา\nมหากฐิน\nมหากาฬ\nมหาขันธกะ\nมหาจักร\nมหาชน\nมหาชัย\nมหาชาติ\nมหาโชตรัต\nมหาดไทย\nมหาดเล็ก\nมหาตมะ\nมหาไถ่\nมหาเทพ\nมหาเทพี\nมหาเทวี\nมหาธาตุ\nมหานิกาย\nมหานิล\nมหาบพิตร\nมหาบัณฑิต\nมหาพน\nมหาพรหม\nมหาภารตะ\nมหาภิเนษกรมณ์\nมหาภูต\nมหาเมฆ\nมหายาน\nมหายุค\nมหาราช\nมหาฤกษ์\nมหาละลวย\nมหาละลาย\nมหาวงศ์\nมหาวรรค\nมหาวิทยาลัย\nมหาศักราช\nมหาศาล\nมหาสงกรานต์\nมหาสดมภ์\nมหาสดำ\nมหาสมุทร\nมหาสาวก\nมหาหงส์\nมหาหิงคุ์\nมหาอำนาจ\nมหาอุจ\nมหาอุด\nมหาอุปรากร\nมหาอุปราช\nมหิ\nมหิดล\nมหิธร\nมหิป\nมหิงส์\nมหิทธิ\nมหินท์\nมหิมา\nมหิศร\nมหิศวร\nมหิษ\nมหิษี\nมหึมา\nมเหยงค์\nมเหศ\nมเหศวร\nมเหศักดิ์\nมเหสักข์\nมเหสิ\nมเหสี\nมเหาฬาร\nมโหรสพ\nมโหระทึก\nมโหรี\nมโหฬาร\nมไหศวรรย์\nมอ\nมอง\nมองโกลอยด์\nมองโกเลีย\nมองคร่อ\nมอญ\nมอด\nม่อต้อ\nมอเตอร์\nมอเตอร์ไซค์\nมอน\nม่อน\nมอบ\nมอม\nมอมแมม\nม่อย\nมอร์ฟีน\nมอระกู่\nมอลโทส\nม่อลอกม่อแลก\nม่อห้อม\nม่อฮ่อม\nมะ\nมะกรูด\nมะกล่ำ\nมะกอก\nมะก่อง\nมะกะโรนี\nมะกา\nมะเกลือ\nมะเกี๋ยง\nมะข่วง\nมะขวิด\nมะขาม\nมะเขือ\nมะแข่น\nมะคังแดง\nมะค่า\nมะคำไก่\nมะคำดีควาย\nมะงั่ว\nมะงุมมะงาหรา\nมะซัก\nมะซาง\nมะดัน\nมะดีหวี\nมะดูก\nมะเดหวี\nมะเดื่อ\nมะต้อง\nมะตะบะ\nมะตาด\nมะตาหะรี\nมะตึ่ง\nมะตื๋น\nมะตูม\nมะแตก\nมะโต\nมะนาว\nมะปราง\nมะปริง\nมะฝ่อ\nมะพร้าว\nมะพลับ\nมะพูด\nมะแพน\nมะแพร้ว\nมะเฟือง\nมะแฟน\nมะไฟ\nมะม่วง\nมะม่าว\nมะมี่\nมะมื่น\nมะมุด\nมะเมอ\nมะเมีย\nมะเมื่อย\nมะแม\nมะยง\nมะยม\nมะระ\nมะริด\nมะรืน\nมะรุม\nมะรุมมะตุ้ม\nมะเร็ง\nมะเรื่อง\nมะโรง\nมะลอกมะแลก\nมะละกอ\nมะลิ\nมะลื่น\nมะลืมดำ\nมะลุลี\nมะแว้ง\nมะสัง\nมะเส็ง\nมะหวด\nมะหะหมัด\nมะหาด\nมะหิ่ง\nมะเหงก\nมะอึก\nมะฮอกกานี\nมัก\nมักกะโรนี\nมักกะลีผล\nมักกะสัน\nมักขะ\nมั่กขั้ก\nมักขิกา\nมัค\nมัคคะ\nมัคคุเทศก์\nมัคนายก\nมัฆวาน\nมั่ง\nมังกง\nมังกร\nมังกุ\nมังคละ\nมังค่า\nมังคุด\nมังตาน\nมังสวิรัติ\nมังสะ\nมังสี\nมัจจะ\nมัจจุ\nมัจฉริยะ\nมัจฉรี\nมัจฉะ\nมัจฉา\nมัชชะ\nมัชวิรัติ\nมัชชาระ\nมัชฌันติกสมัย\nมัชฌิม\nมัชฌิมา\nมัญจา\nมัญชิษฐา\nมัญชุ\nมัญชุสา\nมัญชูสา\nมัญเชฏฐะ\nมัฏฐะ\nมัณฑนศิลป์\nมัณฑนา\nมัด\nมัตตะ\nมัตตัญญู\nมัตตา\nมัตติกา\nมัตถกะ\nมัตถลุงค์\nมัตสยะ\nมัตสยา\nมัตสระ\nมัตสริน\nมัททวะ\nมัทนะ\nมัทยะ\nมัธยฐาน\nมัธยม\nมัธยันห์\nมัธยัสถ์\nมัน\nมั่น\nมันตา\nมันถะ\nมันทิระ\nมันทิราลัย\nมับ\nมั้ม\nมัมมี่\nมัย\nมัลละ\nมัลลิกา\nมัว\nมัวซัว\nมั่ว\nมัศยา\nมัสตุ\nมัสตาร์ด\nมัสมั่น\nมัสยิด\nมัสรู่\nมัสลิน\nมัสสุ\nมา\nม้า\nมาก\nมาคสิระ\nมาฆบูชา\nมาฆะ\nม้าง\nมางสะ\nมาณพ\nมาณวิกา\nมาด\nมาดา\nมาตงค์\nมาตร\nมาตรา\nมาตฤ\nมาตังคะ\nมาตา\nมาตามหัยกะ\nมาตามหัยกา\nมาตามหัยยิกา\nมาติกะ\nมาติกา\nมาตุ\nมาตุจฉา\nมาตุรงค์\nมาตุเรศ\nมาตุละ\nมาตุลา\nมาตุลานี\nมาทะ\nมาธยมิก\nมาธยมิกะ\nมาธุระ\nมาธุสร\nมาธูระ\nมาน\nม่าน\nม้าน\nมานพ\nมานะ\nมานัต\nมานัส\nมานิต\nมานี\nมานุษ\nมานุษยวิทยา\nมาโนชญ์\nมาบ\nมาภา\nม้าม\nม่าย\nมายา\nมาร\nมาราธิราช\nมารค\nมารดร\nมารดา\nมารยา\nมารยาท\nมารศรี\nมารษา\nมาริต\nมารุต\nมาลย์\nมาลัย\nมาลา\nมาลาตี\nมาลาเรีย\nมาลินี\nมาลี\nมาลุต\nมาศ\nมาส\nมาสก\nมาห์\nม่าห์\nมาหิส\nม่าเหมี่ยว\nมาฬก\nมิ\nมิค\nมิคสัญญี\nมิ่ง\nมิจฉา\nมิด\nมิตร\nมิติ\nมิเตอร์\nมิถยา\nมิถุน\nมิถุนายน\nมิทธะ\nมินตรา\nมินตา\nมินหม้อ\nมิ่ม\nมิ้ม\nมิไย\nมิรันตี\nมิลลิกรัม\nมิลลิบาร์\nมิลลิเมตร\nมิลลิลิตร\nมิลักขะ\nมิลักขู\nมิส\nมิสกรี\nมิสกวัน\nมิสซา\nมี\nมี่\nมีด\nมีเทน\nมีน\nมีนาคม\nมี่สั้ว\nมึง\nมึน\nมืด\nมืน\nมื่น\nมือ\nมื้อ\nมุ\nมุก\nมุกดา\nมุกดาหาร\nมุกุระ\nมุข\nมุขเด็จ\nมุขยประโยค\nมุโขโลกนะ\nมุคคะ\nมุง\nมุ่ง\nมุ้ง\nมุจฉา\nมุจนะ\nมุจลินท์\nมุญจนะ\nมุญชะ\nมุฐิ\nมุณฑกะ\nมุณฑะ\nมุด\nมุตกิด\nมุตฆาต\nมุตตะ\nมุตตา\nมุตติ\nมุตะ\nมุติ\nมุททา\nมุทธชะ\nมุทธา\nมุทธาภิเษก\nมุทรา\nมุทริกา\nมุทะลุ\nมุทา\nมุทิกา\nมุทิงค์\nมุทิตา\nมุทุ\nมุทุตา\nมุ่น\nมุนิ\nมุนินทร์\nมุนี\nมุบ\nมุบมิบ\nมุม\nมุ้ม\nมุ่ย\nมุรธา\nมุรธาภิเษก\nมุสละ\nมุสลิม\nมุสา\nมุสิก\nมุหงิด\nมุหน่าย\nมุหุต\nมุฮัมมัด\nมูก\nมูเซอ\nมูตร\nมู่ทู่\nมูน\nมูมมาม\nมูรติ\nมูรธา\nมูรธาภิเษก\nมูล\nมูละ\nมูลา\nมูลิกากร\nมู่ลี่\nมู่เล่\nมูสัง\nมูสิก\nมูสิกะ\nมูสิกทันต์\nเม\nเม็ก\nเมกะเฮิรตซ์\nเมขลา\nเมฆ\nเมฆา\nเมฆินทร์\nเมฆี\nเม็ง\nเม็ด\nเมตตา\nเมตไตรย\nเมตร\nเมตริก\nเมตริกตัน\nเมถุน\nเมท\nเมโท\nเมทนี\nเมทินี\nเมทนีดล\nเมทานอล\nเมทิลแอลกอฮอล์\nเมธ\nเมธา\nเมธาวี\nเมธี\nเมน\nเม่น\nเม้น\nเมนเดลีเวียม\nเมนทอล\nเม้ม\nเมรัย\nเมริเดียน\nเมรุ\nเมล์\nเมล็ด\nเมลือง\nเมษ\nเมษายน\nเมห์\nเมหนะ\nเมหะ\nเมะ\nเมา\nเม่า\nเม้า\nเมารี\nเมาลี\nเมาฬี\nเมาะ\nเมิง\nเมิน\nเมิล\nเมีย\nเมียง\nเมี่ยง\nเมี้ยน\nเมือ\nเมื้อ\nเมื่อ\nเมือก\nเมือง\nเมือบ\nเมื่อย\nแม่\nแม้\nแมก\nแมกนีเซียม\nแมง\nแมงกะพรุน\nแมงกานิน\nแมงกานีส\nแมงคา\nแมงคาเรือง\nแมงช้าง\nแมงดา\nแมงลัก\nแม่ตะงาว\nแมน\nแม่น\nแม้น\nแมลง\nแมลบ\nแมว\nแม้ว\nแมะ\nโม\nโม่\nโม้\nโมก\nโมกข์\nโมกษะ\nโมฆกรรม\nโมฆสัญญา\nโมฆะ\nโมฆียกรรม\nโมฆียะ\nโมง\nโม่ง\nโมงครุ่ม\nโมทนา\nโมโนแซ็กคาไรด์\nโมไนย\nโมเม\nโมเมนต์\nโมเย\nโมรา\nโมรี\nโมเรส\nโมลิบดีนัม\nโมลี\nโมเลกุล\nโมเสก\nโมเสส\nโม่ห์\nโมหะ\nโมหันธ์\nโมหาคติ\nโมโห\nไม่\nไม้\nไมกา\nไมครอน\nไมโครกรัม\nไมโครฟิล์ม\nไมโครโฟน\nไมโครมิเตอร์\nไมโครเมตร\nไมโครลิตร\nไมโครเวฟ\nไมตรี\nไมยราบ\nไมล์\nยก\nยกกระบัตร\nยกนะ\nยง\nยงโย่\nยชุรเวท\nยติ\nยติภังค์\nยถากรรม\nยถาภูตญาณ\nย่น\nยนต์\nยนตร์\nยม\nยมก\nยมโดย\nยมนา\nยมล\nยมะ\nยรรยง\nยล\nยวง\nยวด\nยวน\nยวบ\nย้วย\nยวรยาตร\nยศ\nยโส\nยอ\nย่อ\nยอก\nย็อกแย็ก\nยอง\nย่อง\nย้อง\nยอด\nยอน\nย้อน\nยอบ\nยอม\nย่อม\nย้อม\nย่อย\nย้อย\nย้อแย้\nยะ\nย่ะ\nยะยอบ\nยะยับ\nยัก\nยักข์\nยักขินี\nยักษ์\nยักษา\nยักษิณี\nยักษี\nยัง\nยั้ง\nยั่งยืน\nยัชโญปวีต\nยัญ\nยัญญะ\nยัด\nยัติภังค์\nยัน\nยั่น\nยันต์\nยันตร\nยันตร์\nยันตรกรรม\nยั่นตะนี\nยับ\nยั่ว\nยั้ว\nยั้วเยี้ย\nยัวรยาตร\nยัวะ\nยัษฏิ\nยา\nย่า\nยาก\nยาคุ\nยาคู\nยาง\nย่าง\nยางพารา\nยาจก\nยาจนา\nยาไฉน\nยาด\nยาดา\nยาตร\nยาตรา\nยาน\nย่าน\nย่านพาโหม\nยานมาศ\nยานุมาศ\nยานี\nยาม\nย่าม\nยามะ\nยามักการ\nยามา\nยาย\nย้าย\nยายี\nยาว\nย้าว\nยาวกาลิก\nยาวชีวิก\nยาสูบ\nย่าหยา\nยาหยี\nยำ\nย่ำ\nย้ำ\nยำเยีย\nยิก\nยิง\nยิ่ง\nยิฏฐะ\nยิน\nยิบ\nยิบหยี\nยิปซัม\nยิปซี\nยิ้ม\nยิมนาสติก\nยิหวา\nยี\nยี่\nยี้\nยี่ก่า\nยี่เก\nยี่เข่ง\nยี่โถ\nยีน\nยี่โป้\nยี่ภู่\nยีราฟ\nยี่สก\nยี่สง\nยี่สน\nยี่สาน\nยี่สุ่น\nยี่หระ\nยี่หร่า\nยี่ห้อ\nยี่หุบ\nยึกยัก\nยึกยือ\nยึด\nยืด\nยืน\nยื่น\nยืม\nยื้อ\nยุ\nยุกกระบัตร\nยุกดิ\nยุกติ\nยุกติธรรม\nยุกต์\nยุค\nยุคนธร\nยุคล\nยุคันต์\nยุคันธร\nยุคุนธร\nยุง\nยุ่ง\nยุ้ง\nยุด\nยุต\nยุติ\nยุทธ\nยุทธ์\nยุทธนา\nยุทโธปกรณ์\nยุบ\nยุ่บ\nยุ่บยั่บ\nยุบล\nยุพดี\nยุพเรศ\nยุพา\nยุพาน\nยุพาพาล\nยุพาพิน\nยุ่มย่าม\nยุ่ย\nยุ้ย\nยุรยาตร\nยูรยาตร\nยุวชน\nยุวดี\nยุวราช\nยุวา\nยุวาน\nยู\nยู่\nยูง\nยูโด\nยูถะ\nยูถิกา\nยูริก\nยูเรนัส\nยูเรเนียม\nยูโรเพียม\nเย\nเย้\nเยง\nเยซู\nเย็ด\nเย็น\nเย็นตาโฟ\nเย็นเตาโฟ\nเย็บ\nเย้ย\nเยอ\nเย่อ\nเยอรมัน\nเยอว\nเย่อหยิ่ง\nเยอะ\nเยอะแยะ\nเยา\nเย้า\nเยาว์\nเยาวชน\nเยาวมาลย์\nเยาวยอด\nเยาวราช\nเยาวเรศ\nเยาวลักษณ์\nเยาวพา\nเยาวพาณี\nเยาวพาน\nเยาะ\nเยิง\nเยิน\nเยิ่น\nเยิ่นเย้อ\nเยินยอ\nเยิบ\nเยิบยาบ\nเยิ้ม\nเยีย\nเยี่ยง\nเยี่ยงอย่าง\nเยียงผา\nเยียดยัด\nเยียน\nเยียบ\nเยี่ยม\nเยียรบับ\nเยียรยง\nเยียว\nเยี่ยว\nเยียวยา\nเยือ\nเยื่อ\nเยื้อ\nเยือก\nเยือง\nเยื่อง\nเยื้อง\nเยือน\nเยื้อน\nแย่\nแย้\nแยก\nแยง\nแย่ง\nแย้ง\nแยงแย่\nแยงแย้\nแยบ\nแย็บ\nแยม\nแย้ม\nแยแส\nแยะ\nโย\nโย้\nโยก\nโยกเยก\nโยคาพจร\nโยคาวจร\nโยคเกณฑ์\nโยคยะ\nโยคะ\nโยคิน\nโยคี\nโยง\nโย่ง\nโย่งเย่ง\nโยงโย่\nโยชน์\nโยชนา\nโยถิกะ\nโยทะกา\nโยธวาทิต\nโยธา\nโยธิน\nโยน\nโยนก\nโยนิโส\nโยนี\nโยม\nโยโส\nใย\nไย\nไย่\nไยดี\nไยไพ\nรก\nรง\nรงค์\nรงควัตถุ\nรงรอง\nรจนา\nรจเรข\nรจเลข\nรจิต\nรชตะ\nรชนิ\nรชนี\nรชะ\nรณรงค์\nรด\nรดี\nรตนะ\nรตะ\nรติ\nรถ\nรน\nร่น\nรบ\nรบาญ\nรพี\nรม\nร่ม\nรมณี\nรมณีย์\nรมณียสถาน\nรมย์\nรมเยศ\nรยางค์\nรวก\nรวง\nร่วง\nรวด\nรวน\nรวนเร\nร่วน\nรวบ\nรวม\nร่วม\nรวย\nรวิ\nรวิวาร\nรวี\nรศนา\nรส\nรสนา\nรสสุคนธ์\nรสายนเวท\nรสิก\nรหัท\nรหัส\nรโห\nรโหฐาน\nรอ\nร่อ\nรอก\nรอง\nร่อง\nร้อง\nรองเง็ง\nร่องแร่ง\nรอด\nรอน\nร่อน\nร้อน\nรอบ\nรอบคอบ\nรอม\nรอมชอม\nรอมร่อ\nรอย\nร่อย\nร้อย\nร่อแร่\nระ\nระกะ\nระกา\nระกำ\nระเกะระกะ\nระคน\nระคาง\nระคาย\nระแคะ\nระฆัง\nระงม\nระงับ\nระแง้\nระโงกหิน\nระชวย\nระดม\nระดะ\nระดับ\nระดา\nระด่าว\nระดู\nระเด่น\nระเดียง\nระแด\nระตู\nระทก\nระทด\nระทม\nระทวย\nระทา\nระทึก\nระแทะ\nระนาด\nระนาบ\nระนาม\nระนาว\nระเนน\nระเนระนาด\nระเนียด\nระแนง\nระแนะ\nระบบ\nระบม\nระบอบ\nระบัด\nระบับ\nระบาด\nระบาย\nระบำ\nระบิล\nระบือ\nระบุ\nระเบง\nระเบ็ง\nระเบิด\nระเบียง\nระเบียน\nระเบียบ\nระแบบ\nระมัดระวัง\nระมาด\nระเมียร\nระย่อ\nระย่อม\nระยะ\nระยั้ง\nระยับ\nระย้า\nระยาบ\nระยำ\nระยิบระยับ\nระโยง\nระโยงระยาง\nระรวย\nระรอง\nระร่อน\nระรัว\nระราน\nระร่าย\nระริก\nระรี่\nระรึง\nระรื่น\nระรื้น\nระเร้ง\nระเริง\nระเรียง\nระเรื่อย\nระแรง\nระลวง\nระลอก\nระลึก\nระวัง\nระวาง\nระวาย\nระวิง\nระแวง\nระแวดระวัง\nระไว\nระส่ำระสาย\nระหกระเหิน\nระหง\nระหวย\nระหว่าง\nระหองระแหง\nระหัด\nระหาย\nระเห็จ\nระเหย\nระเหระหน\nระเหหน\nระเหิด\nระเหินระหก\nระแหง\nระโหย\nระอา\nระอิดระอา\nระอุ\nรัก\nรักข์\nรักขิต\nรักตะ\nรักบี้\nรักเร่\nรักแร้\nรักษ์\nรักษา\nรัง\nรั้ง\nรังเกียจ\nรังแก\nรังค์\nรังควาน\nรังแค\nรังรอง\nรังวัด\nรังสิ\nรังสี\nรังสิมันตุ์\nรังสิมา\nรัจฉา\nรัช\nรัชชูปการ\nรัชมังคลาภิเษก\nรัชชุ\nรัชฎาภิเษก\nรัชดาภิเษก\nรัชนะ\nรัชนี\nรัญจวน\nรัฏฐาภิปาลโนบาย\nรัฐ\nรัฐประศาสโนบาย\nรัฐประศาสนศาสตร์\nรัด\nรัต\nรัตกัมพล\nรัตมณี\nรัตคน\nรัตจันทน์\nรัตตัญญู\nรัตติ\nรัตน์\nรัตนะ\nรัตนโกสินทร์\nรัตนโกสินทรศก\nรัตนชาติ\nรัตนตรัย\nรัตนบัลลังก์\nรัตนวราภรณ์\nรัตนสิงหาสน์\nรัตนา\nรัตนากร\nรัตนาภรณ์\nรัตนาวลี\nรัตมา\nรัถ\nรัถยา\nรัทเทอร์ฟอร์เดียม\nรัน\nรั้น\nรันทด\nรันทวย\nรับ\nรัมณียสถาน\nรัมภา\nรัมมี่\nรัมย์\nรัย\nรัว\nรั่ว\nรั้ว\nรัศมิมัต\nรัศมิมาน\nรัศมี\nรัษฎากร\nรัสเซีย\nรัสสะ\nรัสสระ\nรา\nร่า\nร้า\nราก\nรากษส\nรากสาด\nราคะ\nราคจริต\nราคา\nราคิน\nราคี\nราง\nร่าง\nร้าง\nรางจืด\nรางชาง\nรางวัล\nราช\nราชกิจจานุเบกษา\nราชนิกุล\nราชวโรงการ\nราชญี\nราชดัด\nราชพฤกษ์\nราชมาณพ\nราชมาษ\nราชมาส\nราชย์\nราชสีห์\nราชะ\nราชัน\nราชันย์\nราชัย\nราชา\nราชาธิปไตย\nราชาธิราช\nราชาภิเษก\nราชายตนะ\nราชาวดี\nราชี\nราชินิกุล\nราชินีกุล\nราชินี\nราชินูปถัมภ์\nราชูปถัมภ์\nราชูปโภค\nราเชน\nราเชนทร์\nราเชนทรยาน\nราโชวาท\nราไชศวรรย์\nราญ\nราญรอน\nราด\nราต\nราตร\nราตรี\nราน\nร่าน\nร้าน\nราบ\nราพณ์\nราพณาสูร\nราม\nรามเกียรติ์\nรามสูร\nรามัญ\nรามา\nราย\nร่าย\nร้าย\nราว\nร้าว\nราวี\nราศี\nราษฎร\nราษฎร์\nราษตรี\nราษราตรี\nราหุ\nราหู\nรำ\nร่ำ\nรำคาญ\nรำงับ\nรำจวน\nรำบาญ\nรำพัน\nรำพาย\nรำพึง\nรำเพย\nรำไพ\nรำมะนา\nรำมะนาด\nรำมะร่อ\nร่ำรวย\nร่ำร่ำ\nรำไร\nรำลึก\nรำหัด\nรำหัส\nริ\nริก\nริดสีดวง\nริน\nริ้น\nริบ\nริบบิ้น\nริบรี่\nริบหรี่\nริปุ\nริปู\nริม\nริ้ว\nริษยา\nรี\nรี่\nรี้พล\nรีด\nรีดักชัน\nรีต\nรีเนียม\nรีบ\nรีม\nรีรอ\nรี้ริก\nรึง\nรึ้ง\nรื่น\nรื้น\nรื้อ\nรุ\nรุก\nรุกข์\nรุกขชาติ\nรุกขเทวดา\nรุกขมูล\nรุกขา\nรุกรุย\nรุ่ง\nรุ้ง\nรุงรัง\nรุ่งริ่ง\nรุจ\nรุจา\nรุจนะ\nรุจิ\nรุจี\nรุจิระ\nรุจิรา\nรุด\nรุต\nรุทธ์\nรุทระ\nรุธิร\nรุธิระ\nรุเธียร\nรุน\nรุ่น\nรุบรู่\nรุม\nรุ่ม\nรุ่มร่าม\nรุย\nรุ่ย\nรุรุ\nรุหะ\nรู\nรู่\nรู้\nรูจี\nรูด\nรูทีเนียม\nรูบิเดียม\nรูป\nรูปิยะ\nรูปี\nรูเล็ตต์\nเร่\nเรข\nเรขา\nเรขาคณิต\nเร็ง\nเร่ง\nเร้ง\nเรณุ\nเรณู\nเรดอน\nเรดาร์\nเรเดียม\nเร้น\nเรรวน\nเรไร\nเร็ว\nเร่ว\nเรวดี\nเรอ\nเร่อ\nเรา\nเร่า\nเร้า\nเราะ\nเริง\nเริด\nเริม\nเริ่ม\nเริ้ม\nเริศร้าง\nเรี่ย\nเรี้ย\nเรียก\nเรียง\nเรียด\nเรียน\nเรียบ\nเรียม\nเรี่ยม\nเรียว\nเรี่ยว\nเรี้ยวรก\nเรือ\nเรื่อ\nเรื้อ\nเรือก\nเรือง\nเรื่อง\nเรื้อง\nเรืองรอง\nเรือด\nเรือน\nเรื้อน\nเรื่อย\nแร\nแร่\nแรก\nแร็กเกต\nแรง\nแร่ง\nแร้ง\nแรด\nแร้นแค้น\nแรม\nแร้ว\nแระ\nโร\nโร่\nโรค\nโรคา\nโรคาพาธ\nโรง\nโรจ\nโรจน์\nโรเดียม\nโรตี\nโรท\nโรธ\nโรม\nโรมัน\nโรเมอร์\nโรย\nโรเร\nโรหิณี\nโรหิต\nไร\nไร่\nไร้\nไรย์\nฤกษ์\nฤกษณะ\nฤคเวท\nฤชา\nฤชุ\nฤณ\nฤดี\nฤดียา\nฤดู\nฤต\nฤติยา\nฤตุ\nฤทธา\nฤทธิ์\nฤทัย\nฤษภ\nฤษยา\nฤษี\nฤๅ\nฤๅดี\nฤๅทัย\nฤๅษี\nฤๅสาย\nลก\nล่ก\nลฆุ\nลง\nล่ง\nลงกา\nล้งเล้ง\nลด\nลดา\nลดาวัลย์\nลน\nล้น\nลบ\nลบอง\nลพ\nลพุช\nลม\nล่ม\nล้ม\nลมาด\nลรรลุง\nลลนา\nลลิต\nลวก\nลวง\nล่วง\nล้วง\nลวณะ\nลวด\nล้วน\nลวนลาม\nลวนะ\nล่วม\nลวะ\nลวิตร\nลหุ\nลหุกาบัติ\nล่อ\nล้อ\nลอก\nล็อก\nล็อกเกต\nลอกแลก\nลอการิทึม\nลอง\nล่อง\nลองกอง\nลองจิจูด\nลองไน\nลอด\nลอตเตอรี่\nลอน\nล่อน\nลอบ\nลอม\nล้อม\nลอมชอม\nลอมพอก\nลอย\nล่อย\nล่อแล่\nลอว์เรนเซียม\nลออ\nละ\nล่ะ\nละคร\nละติจูด\nละบม\nละบอง\nละบือ\nละเบ็ง\nละโบม\nละม่อม\nละมั่ง\nละมาน\nละม้าย\nละมุ\nละมุด\nละมุน\nละเมอ\nละเมาะ\nละเมิด\nละเมียด\nละแมะ\nละโมก\nละโมบ\nละไม\nละลวย\nละลอก\nละล้า\nละล้าละลัง\nละลาน\nละลาบละล้วง\nละลาย\nละล้าว\nละล่ำละลัก\nละลิบ\nละลุม\nละเลง\nละเล้า\nละเลาะ\nละเลิง\nละเลียด\nละเลียบ\nละไล้\nละว้า\nละวาด\nละเวง\nละแวก\nละโว้\nละหมาด\nละห้อย\nละหาน\nละหาร\nละหุ่ง\nละเหย\nละเหี่ย\nละอง\nละออง\nละอาย\nละเอียด\nละแอน\nลัก\nลักขณะ\nลักขณา\nลักขะ\nลักขี\nลักจั่น\nลักปิดลักเปิด\nลักษณ์\nลักษณนาม\nลักษณะ\nลักษณาการ\nลักษมณ์\nลักษมาณา\nลักษมี\nลักษะ\nลัคคะ\nลัคน์\nลัคนา\nลัง\nลั่ง\nลังกา\nลังคี\nลังถึง\nลังลอง\nลังเล\nลังสาด\nลัชชา\nลัชชี\nลัญจ์\nลัญจกร\nลัญฉกร\nลัญฉน์\nลัฐิ\nลัฐิกา\nลัด\nลัดา\nลัทธ์\nลัทธิ\nลัน\nลั่น\nลันเต\nลันเตา\nลันไต\nลั่นทม\nลันโทม\nลับ\nลัพธ์\nลัพธิ\nลัภ\nลัภนะ\nลัภย์\nลัมพ์\nลัย\nลา\nล่า\nล้า\nลาก\nลาง\nล่าง\nล้าง\nลางลิง\nลางสาด\nลาช\nลาชะ\nลาชา\nลาญ\nลาด\nลาดเลา\nล้าต้า\nล่าเตียง\nลาน\nล่าน\nล้าน\nลาบ\nลาพอน\nลาภ\nลาม\nล่าม\nลามก\nลาย\nล้าย\nลายสือ\nลาลา\nลาว\nลาวัณย์\nลาวา\nลำ\nล่ำ\nล้ำ\nลำเข็ญ\nลำแข\nลำเค็ญ\nลำเจียก\nลำดวน\nลำดับ\nลำเนา\nลำบอง\nลำบาก\nลำปำ\nลำพวน\nลำพอง\nลำพัง\nลำพู\nลำเพ็ญ\nลำเพา\nลำแพน\nลำโพง\nลำไพ่\nลำภุขัน\nลำมะลอก\nลำยอง\nลำไย\nลำลอง\nล่ำลา\nลำลาบ\nลำลึก\nลำเลาะ\nลำเลิก\nลำเลียง\nลำเวียง\nลำเอียก\nลำเอียง\nลิ\nลิกขา\nลิกไนต์\nลิกู\nลิเก\nลิขนะ\nลิขสิทธิ์\nลิขิต\nลิง\nลิงค์\nลิด\nลิต\nลิตมัส\nลิตร\nลิเทียม\nลิ่น\nลิ้น\nลินจง\nลิ้นจี่\nลินลา\nลินสีด\nลิ่นฮื้อ\nลินิน\nลิบ\nลิปดา\nลิปสติก\nลิปิ\nลิฟต์\nลิเภา\nลิ่ม\nลิ้ม\nลิมป์\nลิมปนะ\nลิลิต\nลิว\nลิ่ว\nลิสง\nลี\nลี่\nลี้\nลีซอ\nลีบ\nลีลา\nลีลาศ\nลีฬหา\nลึก\nลึงค์\nลืด\nลื่น\nลื้น\nลืบ\nลืม\nลือ\nลื่อ\nลื้อ\nลุ\nลุก\nลุง\nลุ้ง\nลุ่น\nลุ้น\nลุพธ์\nลุ่ม\nลุมพี\nลุมพู\nลุย\nลุ่ย\nลุ้ย\nลู่\nลูก\nลูกระมาศ\nลูกเอ็น\nลูขะ\nลูทีเชียม\nลูบ\nเลก\nเล็ก\nเลข\nเลขา\nเลขาธิการ\nเลขานุการ\nเล็ง\nเล้ง\nเล่งฮื้อ\nเลเซอร์\nเลฑฑุ\nเลณฑุ\nเลณะ\nเล็ด\nเลน\nเล็น\nเล่น\nเลนส์\nเล็บ\nเลบง\nเลปกร\nเลปน์\nเลเป\nเลเพ\nเล็ม\nเล่ม\nเลย\nเลว\nเลวง\nเลวูโลส\nเลศ\nเลษฏุ\nเล่ห์\nเล่ห์กระเท่ห์\nเลหลัง\nเลหะ\nเลอ\nเล่อ\nเลอะ\nเลอะเทอะ\nเละ\nเละเทะ\nเลา\nเล่า\nเล้า\nเลากัย\nเล้าโลม\nเลาะ\nเลิก\nเลิ่กลั่ก\nเลิง\nเลิ้ง\nเลินเล่อ\nเลิศ\nเลีย\nเลียง\nเลี่ยง\nเลี้ยง\nเลียงผา\nเลียงฝ้าย\nเลียงมัน\nเลียน\nเลี่ยน\nเลียนไฟ\nเลียบ\nเลี่ยม\nเลียว\nเลี้ยว\nเลือก\nเลือง\nเลื่อง\nเลือด\nเลือน\nเลื่อน\nเลื่อม\nเลื่อย\nเลื้อย\nเลื่อยล้า\nแล\nแล่\nแล้\nแลก\nแล็กเกอร์\nแล็กโทส\nแลง\nแล่ง\nแล้ง\nแลน\nแล่น\nแลนทานัม\nแลบ\nแล้ว\nและ\nโล่\nโล้\nโลก\nโลกเชษฐ์\nโลกธรรม\nโลกธาตุ\nโลกนาถ\nโลกบาล\nโลกย์\nโลกัย\nโลกวัชชะ\nโลกวิทู\nโลกัตถจริยา\nโลกันตร์\nโลกา\nโลกาธิบดี\nโลกาธิปไตย\nโลกานุวัตร\nโลกาภิวัตน์\nโลกามิส\nโลกายัต\nโลกาวินาศ\nโลกิยะ\nโลกีย์\nโลกียวัตร\nโลกียวิสัย\nโลกียสุข\nโลกุตระ\nโลกุตรธรรม\nโลกุตรภูมิ\nโลง\nโล่ง\nโล้ง\nโล่งโจ้ง\nโล่งโต้ง\nโล้งโต้ง\nโลจนะ\nโลณะ\nโลด\nโล่ติ๊น\nโลโต\nโลท\nโลน\nโล้น\nโลภ\nโลม\nโลมเล้า\nโลมะ\nโลมา\nโลลุป\nโลเล\nโลโล\nโลโล้\nโลหะ\nโลหกุมภี\nโลหัช\nโลหิต\nไล่\nไล้\nไลย\nไลลา\nไล่เลี่ย\nฦๅ\nฦๅชา\nฦๅสาย\nวก\nวง\nวงก์\nวงกต\nวงศ์\nวงศกร\nวงศา\nวงษ์\nวจนะ\nวจี\nวชิระ\nวชิรปาณี\nวชิรหัตถ์\nวชิราวุธ\nวฏะ\nวฏาการ\nวณิช\nวณิชชา\nวณิชย์\nวณิชยา\nวณิพก\nวดี\nวทนะ\nวทัญญุตา\nวทัญญู\nวธุกา\nวธู\nวน\nวนศาสตร์\nวนสณฑ์\nวนสัณฑ์\nวนอุทยาน\nวนัส\nวนัสบดี\nวนา\nวนาดร\nวนาดอน\nวนานต์\nวนาลัย\nวนาลี\nวนาวาส\nวนาศรม\nวนาสณฑ์\nวนาสัณฑ์\nวนิดา\nวนิพก\nวเนจร\nวโนทยาน\nวยัคฆ์\nวยากรณ์\nวรดนู\nวรทาน\nวรมหาวิหาร\nวรงค์\nวรณะ\nวรรค\nวรรคย์\nวรรช\nวรรชย์\nวรรณะ\nวรรณกรรม\nวรรณคดี\nวรรณยุกต์\nวรรณยุต\nวรรณศิลป์\nวรรณนา\nวรรณพฤติ\nวรรณึก\nวรรธกะ\nวรรธนะ\nวรรษ\nวรรษา\nวรวิหาร\nวรัญญู\nวรางคณา\nวรางคนา\nวราห์\nวราหะ\nวรุณ\nวโรดม\nวฤก\nวลัช\nวลัญช์\nวลัญชน์\nวลัย\nวลาหก\nวลี\nวศค\nวศะ\nวศิน\nวสนะ\nวสภะ\nวสละ\nวสวัดดี\nวสวัตตี\nวสะ\nวสันต์\nวสันตดิลก\nวสันตฤดู\nวสันตวิษุวัต\nวสา\nวสี\nวสุ\nวสุธา\nวสุนธรา\nวสุมดี\nวหะ\nวอ\nวอก\nวอกแวก\nว่องไว\nวอด\nวอน\nว่อน\nว็อบ\nวอมแวม\nวอลเลย์บอล\nวอแว\nวะ\nวัก\nวักกะ\nวัคคีย์\nวัคคุ\nวัคซีน\nวัง\nวังก์\nวังชา\nวังเวง\nวังศะ\nวังสะ\nวัจจะ\nวัจกุฎี\nวัจฉละ\nวัจน์\nวัช\nวัชชะ\nวัชพืช\nวัชฌ์\nวัชระ\nวัชรปาณี\nวัชรยาน\nวัชรอาสน์\nวัชราสน์\nวัชรินทร์\nวัชรี\nวัชเรนทร์\nวัฏ\nวัฏฏะ\nวัฏจักร\nวัฏทุกข์\nวัฏสงสาร\nวัฏกะ\nวัฏฏิ\nวัฒกะ\nวัฒกี\nวัฒนธรรม\nวัฒนะ\nวัฒนา\nวัณ\nวัณโรค\nวัณฏ์\nวัณณะ\nวัณนา\nวัด\nวัต\nวัตต์\nวัตตา\nวัตถ์\nวัตถาภรณ์\nวัตถาลังการ\nวัตถุ\nวัตนะ\nวัตร\nวัตสดร\nวัตสะ\nวัติ\nวัทน์\nวัน\nวันต์\nวันทนา\nวันทนาการ\nวันทนีย์\nวันทยหัตถ์\nวันทยาวุธ\nวันทา\nวันทิ\nวับ\nวับวาบ\nวับวาม\nวับแวบ\nวับแวม\nวัปปะ\nวัมมิกะ\nวัย\nวัลก์\nวัลคุ\nวัลย์\nวัลลภ\nวัลลี\nวัว\nวัสสะ\nวัสโสทก\nวัสดุ\nวัสตร์\nวัสน์\nวัสนะ\nวัสสานะ\nวัสสานฤดู\nวา\nว่า\nว้า\nว้าเหว่\nวาก\nว้าก\nวากยสัมพันธ์\nวากยะ\nวาง\nว่าง\nว้าง\nวาจก\nวาจา\nวาจาไปยะ\nวาจาล\nวาชเปยะ\nวาณิช\nวาณิชกะ\nวาณิชย์\nวาณี\nวาด\nวาต\nวาตะ\nวาตภัย\nวาท\nวาทศาสตร์\nวาทศิลป์\nวาทกะ\nวาทนะ\nวาทย์\nวาทยกร\nวาทิต\nวาทิน\nวาที\nวาน\nวานซืน\nว่าน\nวานร\nวานรินทร์\nวาเนเดียม\nวาบ\nวาปี\nวาม\nวามน\nวามนาวตาร\nวามะ\nวาย\nว่าย\nว้าย\nวายะ\nวาโย\nวายามะ\nวายุ\nวายุกูล\nวาร\nวาระ\nวารสาร\nวารสารศาสตร์\nวาริ\nวารี\nวาริช\nวารีช\nวาริท\nวาริธร\nวารุณ\nวารุณี\nวาล\nวาลวีชนี\nวาล์ว\nวาลิกา\nวาลุกา\nวาว\nว่าว\nว้าว่อน\nว้าวุ่น\nวาสนะ\nวาสนา\nวาสพ\nวาสะ\nวาสิน\nวาสี\nวาสุกรี\nวาสุกี\nวาสุเทพ\nวาหนะ\nวาหะ\nวาหินี\nวาฬ\nวิกขัมภ์\nวิกขัมภนะ\nวิกเขป\nวิกรม\nวิกรัย\nวิกรานต์\nวิกฤต\nวิกฤติ\nวิกล\nวิกสิต\nวิกัต\nวิกัติ\nวิกัติการก\nวิกัป\nวิกัย\nวิการ\nวิกาล\nวิกาลโภชน์\nวิคหะ\nวิเคราะห์\nวิฆเนศ\nวิฆเนศวร\nวิฆาต\nวิง\nวิ่ง\nวิ่งเปี้ยว\nวิงวอน\nวิจฉิกะ\nวิจล\nวิจักขณ์\nวิจักษ์\nวิจักษณ์\nวิจัย\nวิจาร\nวิจารณ์\nวิจารณญาณ\nวิจิ\nวิจิกิจฉา\nวิจิต\nวิจิตร\nวิจิน\nวิจุณ\nวิจุรณ\nวิชชา\nวิชชุ\nวิชชุดา\nวิชชุตา\nวิชชุลดา\nวิชญะ\nวิชน\nวิชนี\nวิชย\nวิชัย\nวิชา\nวิชานนะ\nวิชิต\nวิเชียร\nวิญญัตติ\nวิญญาณ\nวิญญาณกทรัพย์\nวิญญู\nวิฑูรย์\nวิด\nวิตก\nวิตถาร\nวิตามิน\nวิถี\nวิทธะ\nวิทยฐานะ\nวิทยา\nวิทยาคม\nวิทยาคาร\nวิทยาลัย\nวิทยุ\nวิทยุต\nวิทวัส\nวิทัตถิ\nวิทัศน์\nวิทารณ์\nวิทิต\nวิทู\nวิทูร\nวิเทศ\nวิเทโศบาย\nวิธ\nวิธวา\nวิธาน\nวิธี\nวิธุระ\nวิธู\nวิธูปนะ\nวิ่น\nวินตกะ\nวินัย\nวินาที\nวินายก\nวินาศ\nวินิจ\nวินิจฉัย\nวินิต\nวินิบาต\nวินิปาติก\nวิเนต\nวิบัติ\nวิบาก\nวิบุล\nวิบุลย์\nวิบูล\nวิบูลย์\nวิปการ\nวิปฏิสาร\nวิปโยค\nวิประโยค\nวิปริต\nวิปลาส\nวิปวาส\nวิปักษ์\nวิปัสสก\nวิปัสสนา\nวิปัสสนายานิก\nวิพากษ์\nวิพิธทัศนา\nวิพุธ\nวิภว\nวิภวตัณหา\nวิภังค์\nวิภัช\nวิภัตติ\nวิภา\nวิภาค\nวิภาช\nวิภาดา\nวิภาวี\nวิภาษ\nวิภาส\nวิภู\nวิภูษณะ\nวิภูษา\nวิภูษิต\nวิมน\nวิมล\nวิมลัก\nวิมังสา\nวิมัติ\nวิมาน\nวิมุข\nวิมุต\nวิมุตติ\nวิเมลือง\nวิโมกข์\nวิโยค\nวิระ\nวิรงรอง\nวิรังรอง\nวิรัช\nวิรัต\nวิรัติ\nวิราคะ\nวิราม\nวิริยภาพ\nวิริยะ\nวิรุธ\nวิรุฬห์\nวิรุฬหก\nวิรูป\nวิรูปักษ์\nวิเรนทร์\nวิโรจ\nวิโรจน์\nวิโรฒ\nวิโรธ\nวิลันดา\nวิลัย\nวิลาด\nวิลาศ\nวิลาป\nวิลาวัณย์\nวิลาส\nวิลาสินี\nวิลิปดา\nวิลิศมาหรา\nวิเลป\nวิเลปนะ\nวิโลกนะ\nวิโลม\nวิไล\nวิไลวรรณ\nวิวรณ์\nวิวรรธน์\nวิวัฏ\nวิวัฒน์\nวิวัฒนาการ\nวิวัน\nวิวาท\nวิวาห์\nวิวาหมงคล\nวิวาหะ\nวิวิต\nวิวิธ\nวิเวก\nวิศรุต\nวิศว\nวิศวกร\nวิศวกรรม\nวิศวกรรมศาสตร์\nวิศัลย์\nวิศาขบูชา\nวิศาขา\nวิศาล\nวิศิษฏ์\nวิศุทธ์\nวิศุทธิ์\nวิเศษ\nวิเศษณ์\nวิษณุ\nวิษณุกรรม\nวิษธร\nวิษัย\nวิษาณ\nวิษุวัต\nวิสกี้\nวิสรรชนีย์\nวิสฤต\nวิสสุกรรม\nวิสัชนา\nวิสัญญี\nวิสัย\nวิสัยทัศน์\nวิสาขบูชา\nวิสาขะ\nวิสาขา\nวิสามัญ\nวิสามานยนาม\nวิสาร\nวิสารทะ\nวิสาล\nวิสาสะ\nวิสาหกิจ\nวิสิฐ\nวิสุงคามสีมา\nวิสุทธ์\nวิสุทธิ์\nวิสูตร\nวิเสท\nวิหค\nวิหลั่น\nวิหาร\nวิหิงสา\nวิเหสา\nวิฬาร\nวิฬาร์\nวี\nวีจิ\nวีชนี\nวีณา\nวี้ด\nวีรกรรม\nวีรชน\nวีรบุรุษ\nวีรสตรี\nวี่วัน\nวี่แวว\nวีสะ\nวุ้ง\nวุฐิ\nวุฒ\nวุฒิ\nวุด\nวุ่น\nวุ้น\nวุบ\nวุ้ย\nวุลแฟรม\nวู้\nวูดวาด\nวูบ\nวู่วาม\nเว้\nเวค\nเวคิน\nเวคี\nเวจ\nเวช\nเวชยันต์\nเวฐน์\nเวณิ\nเวณิก\nเวณุ\nเวตน์\nเวตร\nเวตาล\nเวท\nเวทคู\nเวทนา\nเวทย์\nเวทัลละ\nเวทางค์\nเวทางคศาสตร์\nเวทานต์\nเวทานตะ\nเวทิ\nเวที\nเวธะ\nเวน\nเว้น\nเวนไตย\nเวไนย\nเวมัต\nเว้ย\nเวยยากรณะ\nเวร\nเวรมณี\nเวรี\nเวโรจน์\nเวลา\nเวเลนซี\nเวศม์\nเวศย์\nเวศยา\nเวสน์\nเวสภู\nเวสม์\nเวสวัณ\nเวสสะ\nเวสสันดร\nเวสสุกรรม\nเวสสุวัณ\nเวสารัช\nเวสิยา\nเวหน\nเวหะ\nเวหา\nเวหาส\nเวฬุ\nเวฬุริยะ\nเว่อ\nเว้า\nเวิก\nเวิ้ง\nเวี่ย\nเวียง\nเวียด\nเวียดนาม\nเวียน\nเวียร\nเวี่ยว\nแว้\nแวง\nแว้ง\nแวด\nแว้ด\nแวน\nแว่น\nแวนดา\nแวบ\nแว็บ\nแวม\nแว็ม\nแวว\nแว่ว\nแวะ\nโว\nโว่\nโวการ\nโว่ง\nโวทาน\nโวย\nโว้ย\nโว้เว้\nโวหาร\nไว\nไว้\nไวกูณฐ์\nไวฑูรย์\nไวทย์\nไวน์\nไวพจน์\nไวยากรณ์\nไวยาวัจกร\nไวยาวัจมัย\nไวรัส\nไววรรณ\nไวษณพ\nไวโอลิน\nศก\nศกุน\nศกุนต์\nศกุนิ\nศกุนี\nศจี\nศตะ\nศตภิษัช\nศตวรรษ\nศตพรรษ\nศตกะ\nศนิ\nศพ\nศมนะ\nศมะ\nศยาม\nศยามล\nศร\nศรายุธ\nศราวรณ์\nศรรกรา\nศรวณะ\nศรวณีย์\nศรวิษฐา\nศรัณย์\nศรัณยู\nศรัท\nศรัทธา\nศรัย\nศราทธ์\nศราทธพรต\nศราพก\nศราวก\nศราวณะ\nศรี\nศรีตรัง\nศรุติ\nศฤคาล\nศฤงค์\nศฤงคาร\nศฤงคาริน\nศฤงคารี\nศลิษฏ์\nศลิษา\nศวะ\nศวัส\nศวา\nศวาน\nศศะ\nศศธร\nศศพินทุ์\nศศลักษณ์\nศศิ\nศศิน\nศศี\nศศิขัณฑ์\nศศิธร\nศศิมณฑล\nศศิวิมล\nศอ\nศอก\nศักดา\nศักดิ\nศักดิ์\nศักดินา\nศักติ\nศักย\nศักยภาพ\nศักย์\nศักยะ\nศักร\nศักรินทร์\nศักเรนทร์\nศักราช\nศังกร\nศัตรู\nศันสนะ\nศันสนีย์\nศัพท์\nศัยยา\nศัล\nศัลย์\nศัลยกรรม\nศัลยแพทย์\nศัลยศาสตร์\nศัสดร\nศัสตร\nศัสตรศาสตร์\nศัสตรา\nศัสตราวุธ\nศากตะ\nศากย\nศากยะ\nศากยพุทธ\nศากยมุนี\nศาฎก\nศาณ\nศานต์\nศานติ\nศาป\nศารท\nศารทูล\nศาริกา\nศาล\nศาลา\nศาศวัต\nศาสดา\nศาสตร์\nศาสตรา\nศาสตราจารย์\nศาสนา\nศาสนกิจ\nศาสนจักร\nศาสนธรรม\nศาสนบุคคล\nศาสนพิธี\nศาสนวัตถุ\nศาสนศาสตร์\nศาสนสถาน\nศาสนสมบัติ\nศาสนิกชน\nศาสนีย์\nศาสนูปถัมภก\nศาสน์\nศิกษก\nศิการ\nศิขร\nศิขริน\nศิขรี\nศิขัณฑ์\nศิคาล\nศิงขร\nศิงขริน\nศิตะ\nศิถี\nศิพิระ\nศิระ\nศิรประภา\nศิราภรณ์\nศิโรรัตน์\nศิโรเวฐน์\nศิรา\nศิรามพุช\nศิโรราบ\nศิลป\nศิลป์\nศิลปะ\nศิลปกร\nศิลปกรรม\nศิลปกิจ\nศิลปวัตถุ\nศิลปวิทยา\nศิลปศาสตร์\nศิลปศึกษา\nศิลปหัตถกรรม\nศิลปิน\nศิลปี\nศิลา\nศิวะ\nศิวโมกข์\nศิวลึงค์\nศิวเวท\nศิวาลัย\nศิศีระ\nศิษฎิ\nศิษฏ์\nศิษย์\nศิษยานุศิษย์\nศีขร\nศีต\nศีตกาล\nศีรษะ\nศีล\nศึก\nศึกษา\nศึกษาธิการ\nศึกษานิเทศก์\nศุกร์\nศุกรวรรณ\nศุกรวาร\nศุกระ\nศุกล\nศุกลปักษ์\nศุจิ\nศุทธะ\nศุทธิ\nศุนะ\nศุนิ\nศุภกร\nศุภเคราะห์\nศุภนิมิต\nศุภมัสดุ\nศุภมาตรา\nศุภมาส\nศุภอักษร\nศุภางค์\nศูกร\nศุลกากร\nศุลการักษ์\nศุลี\nศุษิร\nศูทร\nศูนย์\nศูนยวาท\nศูละ\nศูลิน\nเศรณี\nเศรษฐ\nเศรษฐ์\nเศรษฐกิจ\nเศรษฐศาสตร์\nเศรษฐี\nเศร้า\nเศลษ\nเศวต\nเศวตร\nเศวตัมพร\nเศษ\nเศาจ\nเศาร์\nเศารยะ\nเศิก\nเศียร\nโศก\nโศกา\nโศกาดูร\nโศกาลัย\nโศกี\nโศจิ\nโศธนะ\nโศภน\nโศภะ\nโศภา\nโศภิต\nโศภิน\nโศภิษฐ์\nโศภี\nโศรดา\nโศรตร\nโศลก\nไศล\nไศวะ\nษมา\nษัฏ\nษัฑ\nษัณ\nษัษ\nษัษฐะ\nษัษฐี\nโษฑศัน\nสก\nสกวาที\nสกฏะ\nสกทาคามิผล\nสกิทาคามิผล\nสกทาคามิมรรค\nสกิทาคามิมรรค\nสกทาคามี\nสกิทาคามี\nสกนธ์\nสกปรก\nสกรณีย์\nสกรรจ์\nสกรรมกริยา\nสกล\nสกลมหาสังฆปริณายก\nสกัด\nสกา\nสกาว\nสกี\nสกุณ\nสกุณา\nสกุณี\nสกุน\nสกุนต์\nสกุล\nสเกต\nสแกนเดียม\nสขะ\nสง\nส่ง\nสงกร\nสงกรานต์\nสงกา\nสงค์\nสงคร\nสงคราม\nสงเคราะห์\nสงฆ์\nสงบ\nสงวน\nส่งสการ\nสงสัย\nสงสาร\nสงสารวัฏ\nสงัด\nสง่า\nสฐะ\nสณฑ์\nสด\nสดมภ์\nสดับ\nสดับปกรณ์\nสดำ\nสดุดี\nสตะ\nสตน\nสตภิสชะ\nสตรอนเชียม\nสตริกนิน\nสตรี\nสตัฟฟ์\nสตัมภ์\nสตางค์\nสติ\nสติปัฏฐาน\nสตี\nสตู\nสตูป\nสเต๊ก\nสถบดี\nสถล\nสถวีระ\nสถาน\nสถานะ\nสถานี\nสถาบัน\nสถาปนา\nสถาปนิก\nสถาปัตยกรรม\nสถาปัตยกรรมศาสตร์\nสถาปัตยเรขา\nสถาปัตยเวท\nสถาพร\nสถาวร\nสถิต\nสถิตยศาสตร์\nสถิติ\nสถิร\nสถีรวาท\nสถุล\nสถูป\nสทิง\nสทึง\nสทุม\nสธนะ\nสาธุสะ\nสน\nส้น\nสนทนา\nสนทรรศ\nสนทรรศน์\nสนเทศ\nสนเท่ห์\nสนธยา\nสนธิ\nสนน\nสนม\nสนวน\nสนอง\nสนอบ\nสนอม\nสนะ\nสนัด\nสนั่น\nสนับ\nสนับทึบ\nสนับสนุน\nสนาน\nสนาม\nสนายุ\nสนิกะ\nสนิท\nสนิธ\nสนิม\nสนุก\nสนุกเกอร์\nสนุข\nสนุต\nสนุ่น\nสบ\nสบง\nสบถ\nสบัน\nสบาย\nสบู่\nสไบ\nสปริง\nสปอร์\nสปาเกตตี\nสเปกตรัม\nสเปกโทรสโกป\nสไปริลลัม\nสพาบ\nสภา\nสภาพ\nสภาวการณ์\nสภาวะ\nสม\nสมการ\nสมจารี\nสมดุล\nสมมูล\nส้ม\nสมญา\nสมณะ\nสมณบริขาร\nสมณศักดิ์\nสมณสารูป\nสมเด็จ\nสมถะ\nสมถยานิก\nสมถวิปัสสนา\nสมนาคุณ\nสมบัติ\nสมบุกสมบัน\nสมบูรณ์\nสมบูรณาญาสิทธิราชย์\nสมประดี\nสมปฤดี\nสมปฤๅดี\nส้มป่อย\nสมปัก\nสมผุส\nสมพง\nสมพงศ์\nสมพล\nสมพัตสร\nสมพาส\nสมเพช\nสมโพธน์\nสมโพธิ\nสมภพ\nสมภาร\nสมโภค\nสมโภช\nสมมต\nสมมติ\nสมมุติ\nสมมาตร\nส้มมือ\nสมโมท\nสมโยค\nสมร\nสมรด\nสมรรถ\nสมรรถนะ\nสมรรถภาพ\nสมรส\nสมฤดี\nสมฤติ\nสมวายะ\nสมเสร็จ\nสมอ\nสมอง\nสมะ\nสมัคร\nสมังคี\nสมัช\nสมัชชา\nสมัญญา\nสมัต\nสมัน\nสมันต์\nสมัย\nสมา\nสมาคม\nสมาจาร\nสมาชิก\nสมาทาน\nสมาธิ\nสมาน\nสมานฉันท์\nสมาบัติ\nสมาพันธรัฐ\nสมาส\nสม่ำเสมอ\nสมิง\nสมิต\nสมิติ\nสมิทธ์\nสมิทธิ\nสมี\nสมุก\nสมุจจัย\nสมุจเฉท\nสมุฏฐาน\nสมุด\nสมุทร\nสมุทรโคดม\nสมุทัย\nสมุน\nสมุนไพร\nสมุลแว้ง\nสมุห\nสมุห์\nสมุหกลาโหม\nสมุหเทศาภิบาล\nสมุหนาม\nสมุหนายก\nสโมธาน\nสโมสร\nสยด\nสยนะ\nสยบ\nสยมพร\nสยมภู\nสยอง\nสยอน\nสยัมวรา\nสยาม\nสยามานุสติ\nสยามินทร์\nสยาย\nสยิว\nสยิ้ว\nสยุมพร\nสยุมภู\nสร\nสรง\nสร่ง\nสรณะ\nสรณคมน์\nสรณาคมน์\nสรณตรัย\nสรตะ\nสรทะ\nสรนุก\nสรเนาะ\nสรไน\nสรเพชญ\nสรภะ\nสรภัญญะ\nสรภู\nสรม\nสรร\nสรรค์\nสรรพ\nสรรพคุณ\nสรรพนาม\nสรรพสามิต\nสรรพัชญ\nสรรพากร\nสรรพางค์\nสรรเพชญ\nสรรเพชุดา\nสรรเสริญ\nสรลอน\nสรเลข\nสรวง\nสรวม\nสรวล\nสรเสริญ\nสร้อย\nสระ\nสระกอ\nสระท้อน\nสระพรั่ง\nสระอาด\nสรั่ง\nสรัสวดี\nสร่าง\nสร้าง\nสราญ\nสรี้\nสรีระ\nสรีรกิจ\nสรีรธาตุ\nสรีรวิทยา\nสรีรศาสตร์\nสรีรังคาร\nสรีรางคาร\nสรุป\nสโรช\nสโรชะ\nสฤก\nสฤต\nสฤษฎิ\nสฤษฎี\nสฤษฏ์\nสฤษดิ์\nสลด\nสลบ\nสลวน\nสลวย\nสลอด\nสลอน\nสลอย\nสละ\nสลัก\nสลัด\nสลัดได\nสลับ\nสลัว\nสลา\nสลาก\nสลาง\nสล้าง\nสลาด\nสลาตัน\nสลาบ\nสลาย\nสลิด\nสลิล\nสลึก\nสลึง\nสลุต\nสลุบ\nสลุมพร\nสแลง\nสวการย์\nสวภาพ\nสวราชย์\nสวก\nส้วง\nสวด\nสวน\nสวนะ\nสวนาการ\nส่วน\nสวนิต\nสวบ\nสวม\nส้วม\nสวย\nส่วย\nส้วย\nสวยม\nสวรรค\nสวรรค์\nสวรรคต\nสวรรคาลัย\nสวรรยา\nสวระ\nสวะ\nสวัสดิ\nสวัสดิ์\nสวัสดิการ\nสวัสดิภาพ\nสวัสดิมงคล\nสวัสดี\nสวัสติ\nสวาตี\nสวัสติกะ\nสวา\nสวาปาม\nสวาคตะ\nสวาง\nสว่าง\nสวาด\nสวาดิ\nสวาท\nสว่าน\nสว้าน\nสวาบ\nสวามิ\nสวามี\nสวามินี\nสวาย\nสวาสดิ์\nสวาหะ\nสวิง\nสวิญญาณกทรัพย์\nสวิตช์\nสสาร\nสสุระ\nสสุรี\nสหกรณ์\nสหการ\nสหจร\nสหชาต\nสหชาติ\nสหธรรม\nสหธรรมิก\nสหประชาชาติ\nสหพันธ์\nสหพันธรัฐ\nสหภาพ\nสหศึกษา\nสหัช\nสหัมบดี\nสหัส\nสหัสสะ\nสหัสธารา\nสหัสนัยน์\nสหัสเนตร\nสหัสรังสี\nสหัสา\nสหาย\nสอ\nส่อ\nสอง\nส่อง\nส้อง\nสอด\nสอน\nส่อน\nสอบ\nสอพลอ\nส้อม\nสอย\nสะ\nสะกด\nสะกอ\nสะกาง\nสะการะ\nสะกิด\nสะกิดสะเกา\nสะเก็ด\nสะแก\nสะคร้อ\nสะคราญ\nสะค้าน\nสะเงาะสะแงะ\nสะดม\nสะดวก\nสะดิ้ง\nสะดึง\nสะดือ\nสะดุ้ง\nสะดุด\nสะเด็ด\nสะเดา\nสะเดาะ\nสะตอ\nสะตาหมัน\nสะตึ\nสะตือ\nสะตุ\nสะเต๊ะ\nสะโตก\nสะทก\nสะท้อน\nสะท้าน\nสะทึก\nสะเทิน\nสะเทิ้น\nสะเทือน\nสะเทื้อน\nสะบะ\nสะบัก\nสะบักสะบอม\nสะบัด\nสะบัดสะบิ้ง\nสะบั้น\nสะบันงา\nสะบ้า\nสะบู\nสะแบง\nสะเปะสะปะ\nสะพรั่ง\nสะพรึงกลัว\nสะพรึบ\nสะพรึ่บ\nสะพัก\nสะพัง\nสะพัด\nสะพั้น\nสะพาน\nสะพาย\nสะเพร่า\nสะโพก\nสะเภา\nสะใภ้\nสะโมง\nสะระตะ\nสะระแหน่\nสะลาง\nสะลาบ\nสะลึมสะลือ\nสะวี้ดสะว้าด\nสะสม\nสะสวย\nสะสาง\nสะเหล่อ\nสะอาง\nสะอาด\nสะอ้าน\nสะอิ้ง\nสะอิดสะเอียน\nสะอึก\nสะอื้น\nสะเอ้ง\nสะเอว\nสะเออะ\nสะโอดสะอง\nสะไอ\nสัก\nสักกะ\nสักยะ\nสักกัจจะ\nสักกายทิฐิ\nสักการ\nสักการะ\nสักขี\nสักวา\nสักหลาด\nสัค\nสัคคะ\nสั่ง\nสังกร\nสังกรณี\nสังกรประโยค\nสังกะตัง\nสังกะวัง\nสังกะวาด\nสังกะสี\nสังกัด\nสังกัปปะ\nสังกา\nสังการ\nสังกาศ\nสังกิเลส\nสังเกต\nสังข์\nสังขกร\nสังขตธรรม\nสังขตะ\nสังขยา\nสังขลิก\nสังขลิกา\nสังขาร\nสังขารา\nสังเขป\nสังค์\nสังคญาติ\nสังคม\nสังคหะ\nสังคัง\nสังคายนา\nสังคายนาย\nสังคีต\nสังคีติ\nสังเค็ด\nสังเคราะห์\nสังฆกรรม\nสังฆการี\nสังฆเถระ\nสังฆทาน\nสังฆนายก\nสังฆปาโมกข์\nสังฆภัต\nสังฆเภท\nสังฆมณฑล\nสังฆมนตรี\nสังฆราช\nสังฆสภา\nสังฆาณัติ\nสังฆาฏิ\nสังฆาทิเสส\nสังฆาธิการ\nสังฆานุสติ\nสังฆาวาส\nสังยุตนิกาย\nสังโยค\nสังโยชน์\nสังวร\nสังวัจฉระ\nสังวัธยาย\nสังวาล\nสังวาส\nสังเวคะ\nสังเวช\nสังเวชนียสถาน\nสังเวย\nสังเวียน\nสังสกฤต\nสังสการ\nสังสนทนา\nสั่งสนทนา\nสังสรรค์\nสังสารวัฏ\nสังสิทธิ\nสังสุทธ์\nสังสุทธิ\nสังหร\nสังหรณ์\nสังหาร\nสังหาริมทรัพย์\nสังหาริมะ\nสังหิต\nสัจ\nสัจกิริยา\nสัจจะ\nสัจญาณ\nสัจธรรม\nสัจนิยม\nสัจพจน์\nสัชฌะ\nสัชฌุ\nสัญจร\nสัญเจตนา\nสัญชาตญาณ\nสัญชาติ\nสัญฌา\nสัญญา\nสัญญาณ\nสัญญี\nสัญโญชน์\nสัญนิยม\nสัญประกาศ\nสัญลักษณ์\nสัฐิ\nสัณฐาน\nสัณฐิติ\nสัณฑ์\nสัณห์\nสัด\nสัดจอง\nสัต\nสัตตะ\nสัตตาหกรณียะ\nสัตตาหกาลิก\nสัตมวาร\nสัตสดก\nสัตตบงกช\nสัตตบรรณ\nสัตตบุษย์\nสัตตู\nสัตถันดร\nสัตถา\nสัตถิ\nสัตถุ\nสัตถุศาสนา\nสัตบรรณ\nสัตย์\nสัตยพรต\nสัตยวาที\nสัตยาเคราะห์\nสัตยาธิษฐาน\nสัตยาบัน\nสัตว์\nสัตวชาติ\nสัตวบาล\nสัตวแพทย์\nสัตววิทยา\nสัตวา\nสัทธรรม\nสัทธา\nสัทธาจริต\nสัทธาธิกะ\nสัทธินทรีย์\nสัทธิงวิหาริก\nสัทธิวิหาริก\nสัทวิทยา\nสัทศาสตร์\nสัทอักษร\nสัน\nสั่น\nสั้น\nสันดาน\nสันดาป\nสันโดษ\nสันต์\nสันตติ\nสันตะปาปา\nสันตะวา\nสันติ\nสันตุฏฐี\nสันถวไมตรี\nสันถวะ\nสันถัต\nสันถาร\nสันทนะ\nสันทะ\nสันทัด\nสันทัสนะ\nสันทาน\nสันทิฐิก\nสันทิส\nสันเทหะ\nสันธาน\nสันนิธิ\nสันนิบาต\nสันนิวาส\nสันนิษฐาน\nสันสกฤต\nสับ\nสับปลับ\nสับปลี้\nสับปะรด\nสัปคับ\nสัปดาห์\nสัปดาหะ\nสัปดน\nสัปตศก\nสัปทน\nสัปปะ\nสัปปิ\nสัปปุริส\nสัปปุรุษ\nสัประยุทธ์\nสัปหงก\nสัปเหร่อ\nสัพ\nสัพพะ\nสัพพัญญู\nสัพเพเหระ\nสัพยอก\nสัมบูรณ์\nสัมปชัญญะ\nสัมปทา\nสัมปทาน\nสัมปยุต\nสัมปโยค\nสัมประสิทธิ์\nสัมประหาร\nสัมปรายภพ\nสัมปรายิกภพ\nสัมปัตติ\nสัมผัปลาป\nสัมผัปลาปะ\nสัมผัส\nสัมพล\nสัมพหุลา\nสัมพัจฉรฉินท์\nสัมพัตสร\nสัมพัทธ์\nสัมพันธ์\nสัมพันธน์\nสัมพันธภาพ\nสัมพันธมิตร\nสัมพันธไมตรี\nสัมพาหะ\nสัมพุทธ\nสัมพุทธะ\nสัมโพธิ\nสัมภวะ\nสัมภเวสี\nสัมภัต\nสัมภัตตะ\nสัมภาระ\nสัมภาษณ์\nสัมโภคกาย\nสัมมนา\nสัมมัปธาน\nสัมมา\nสัมโมทนียกถา\nสัมฤทธิ\nสัมฤทธิ์\nสัมฤทธิศก\nสัยน์\nสัลเลข\nสัสดี\nสัสตทิฐิ\nสัสสะ\nสัสสุ\nสัสสู\nสา\nส่า\nสาก\nสากรรจ์\nสากล\nสากัจฉา\nสากัลย์\nสากิยะ\nสาเก\nสาขา\nสาคร\nสาคเรศ\nสาคู\nสาง\nส้าง\nสาชล\nสาฎก\nสาฏิก\nสาณี\nสาด\nสาไถย\nสาทร\nสาทิส\nสาทุ\nสาโท\nสาธก\nสาธยะ\nสาธยาย\nสาธารณะ\nสาธารณชน\nสาธารณประโยชน์\nสาธารณภัย\nสาธารณรัฐ\nสาธารณสถาน\nสาธารณสมบัติ\nสาธารณสุข\nสาธารณูปการ\nสาธารณูปโภค\nสาธารณ์\nสาธิต\nสาธุ\nสาน\nส่าน\nสานุ\nสานู\nสานุศิษย์\nสาบ\nสาบสูญ\nสาบาน\nสาป\nสาปไตย\nสาม\nสามชุก\nสามเณร\nสามเณรี\nสามนต์\nสามนตราช\nสามยทรัพย์\nสามล\nสามหาว\nสามะ\nสามัคคี\nสามัญ\nสามัตถิยะ\nสามานย์\nสามานยนาม\nสามารถ\nสามิต\nสามินี\nสามิภักดิ์\nสามี\nสามีจิกรรม\nสาย\nส่าย\nส้าย\nสายชู\nสายัณห์\nสายาห์\nสาร\nสารคดี\nสารธรรม\nสารนิเทศ\nสารบบ\nสารบรรณ\nสารบัญ\nสารบาญ\nสารบาญชี\nสารประโยชน์\nสารสนเทศ\nสารทุกข์\nสารถี\nสารท\nสารพัด\nสารพัน\nสารพางค์\nสารภาพ\nสารภี\nสารวัตร\nสาระ\nสาระแน\nสาระพา\nสาระยำ\nสาระวารี\nสาระสะมา\nสารัตถประโยชน์\nสารัตถศึกษา\nสารัตถะ\nสารัทธ์\nสารัมภ์\nสาราณียกร\nสาราณียธรรม\nสาราณียะ\nสารานุกรม\nสารีริกธาตุ\nสารูป\nสาโรช\nสาละ\nสาละวน\nสาลิ\nสาลิกา\nสาลินี\nสาลี\nสาลี่\nสาลู\nสาโลหิต\nสาว\nสาวก\nสาวิกา\nสาวิตร\nสาวิตรี\nสาสน\nสาสน์\nสาส์น\nสาสนา\nสาสม\nสาหร่าย\nสาหรี\nส่าหรี\nสาหัส\nสาเหตุ\nสาแหรก\nสำ\nสำส่อน\nส่ำ\nสำคัญ\nสำซ่าง\nสำแดง\nสำทับ\nสำนวน\nสำนอง\nสำนัก\nสำนาน\nสำนึก\nสำนึง\nสำเนา\nสำเนียง\nสำบัด\nสำปะลอ\nสำปะหลัง\nสำปั้น\nสำปันนี\nสำเภา\nสำมะงา\nสำมะโน\nสำมะลอ\nสำมะเลเทเมา\nสำมะหา\nสำรด\nสำรวจ\nสำรวม\nสำรวย\nสำรวล\nสำรอก\nสำรอง\nสำรับ\nสำราก\nสำราญ\nสำริด\nสำเร็จ\nสำเรา\nสำเริง\nสำโรง\nสำลัก\nสำลาน\nสำลี\nสำแลง\nสำหรวด\nสำหรับ\nสำหา\nสำเหนียก\nสำเหร่\nสำออย\nสำอาง\nสิ\nสิกข์\nสิข\nสิกขมานา\nสิกขา\nสิขร\nสิขรี\nสิขเรศ\nสิขา\nสิขานล\nสิขี\nสิคาล\nสิง\nสิ่ง\nสิงขร\nสิงค์\nสิงคลิ้ง\nสิงคลี\nสิงคาร\nสิงคาล\nสิงคี\nสิงโต\nสิงห์\nสิงหนาท\nสิงหบัญชร\nสิงหรา\nสิงหราช\nสิงหาคม\nสิงหาสน์\nสิงหล\nสิญจน์\nสิตะ\nสิตางศุ์\nสิถิล\nสิทธ์\nสิทธัตถะ\nสิทธา\nสิทธาจารย์\nสิทธารถ\nสิทธิ\nสิทธิ์\nสิทธิการิยะ\nสิธยะ\nสิน\nสิ้น\nสินเทา\nสินธพ\nสินธุ\nสินธุ์\nสินธุระ\nสินธู\nสินเธาว์\nสินาด\nสินิทธ์\nสินี\nสิเนรุ\nสิเนหก\nสิเนหะ\nสิเนหา\nสิเน่หา\nสิบ\nสิปปะ\nสิมพลี\nสิระ\nสิโรดม\nสิโรตม์\nสิริ\nสิรี\nสิลา\nสิว\nสิ่ว\nสิวะ\nสิวาลัย\nสิวิกา\nสี\nสี่\nสี้\nสีกา\nสีกุน\nสีข้าง\nสีด\nสีดอ\nสีดา\nสีตลรัศมี\nสีตโลทก\nสีโตทก\nสีทันดร\nสีมันต์\nสีมา\nสีละมัน\nสีวิกา\nสีสอ\nสีสะ\nสีสา\nสีสุก\nสีเสียด\nสีห์\nสีหนาท\nสีหบัญชร\nสีหราช\nสีหไสยา\nสีหไสยาสน์\nสีหะ\nสึก\nสึง\nสืบ\nสื่อ\nสุ\nสุก\nสุกข์\nสุกร\nสุกรม\nสุกำศพ\nสุกียากี้\nสุข\nสุขา\nสุขาภิบาล\nสุขารมณ์\nสุขาวดี\nสุขิน\nสุขี\nสุขุม\nสุขุมาล\nสุโข\nสุคต\nสุคติ\nสุคนธ\nสุคนธ์\nสุคนธชาติ\nสุคนธรส\nสุคันธ์\nสุคันธรส\nสุงกะ\nสุงกากร\nสุงสิง\nสุงสุมาร\nสุจริต\nสุจหนี่\nสุจิ\nสุจิต\nสุจิตร\nสุชน\nสุชัมบดี\nสุชา\nสุชาดา\nสุญ\nสุญญากาศ\nสุญตา\nสุญนิยม\nสุณ\nสุณิสา\nสุด\nสุดา\nสุต\nสุตตนิบาต\nสุตตะ\nสุตตันตปิฎก\nสุตตันตะ\nสุติ\nสุทธ\nสุทธ์\nสุทธาวาส\nสุทธิ\nสุทรรศน์\nสุทัศน์\nสุธา\nสุธาโภชน์\nสุธารส\nสุธาสินี\nสุธาสี\nสุธี\nสุนทร\nสุนทรี\nสุนทรียภาพ\nสุนทรียศาสตร์\nสุนทรียะ\nสุนัข\nสุนันท์\nสุโนก\nสุบดี\nสุบรรณ\nสุบิน\nสุปรีดิ์\nสุปรีย์\nสุปาณี\nสุพพัต\nสุพรรณ\nสุพรรณบัฏ\nสุพรรณภาชน์\nสุพรรณราช\nสุพรรณศรี\nสุพรรณถัน\nสุพรรณิการ์\nสุภร\nสุภัค\nสุภา\nสุภาพ\nสุภาษิต\nสุม\nสุ่ม\nสุมทุม\nสุมน\nสุมนะ\nสุมนัส\nสุมนา\nสุ้มเสียง\nสุมะ\nสุมาลี\nสุเมธ\nสุเมรุ\nสุรคต\nสุรเชษฐ์\nสุรบดี\nสุรภาพ\nสุรโลก\nสุรสีหนาท\nสุรเสียง\nสุรงค์\nสุรังค์\nสุรภี\nสุรัติ\nสุรัสวดี\nสุรา\nสุรางค์จำเรียง\nสุรางคนา\nสุรางคนางค์\nสุรารักษ์\nสุราลัย\nสุรินทร์\nสุรินทราหู\nสุริยะ\nสุริยกันต์\nสุริยกานต์\nสุริยการ\nสุริยกาล\nสุริยคติ\nสุริยคราส\nสุริยมณฑล\nสุริยวงศ์\nสุริยง\nสุริยา\nสุริเยนทร์\nสุริเยศ\nสุริโย\nสุริยน\nสุริยัน\nสุริยุปราคา\nสุรีย์\nสุรุ่ยสุร่าย\nสุลต่าน\nสุวคนธ์\nสุวภาพ\nสุวรรณ\nสุวรรณภูมิ\nสุวะ\nสุวาน\nสุวินัย\nสุวิมล\nสุษิระ\nสุสาน\nสุหนัต\nสุหร่ง\nสุหร่าย\nสุหฤท\nสุหัท\nสุเหร่า\nสู\nสู่\nสู้\nสูง\nสูจิ\nสูจิบัตร\nสูญ\nสูด\nสูต\nสูตร\nสูติ\nสูติกรรม\nสูตินรีเวช\nสูติบัตร\nสูติแพทย์\nสูติศาสตร์\nสูท\nสูทกรรม\nสูทศาสตร์\nสูบ\nสูปะ\nสูร\nสูรย์\nสูรยกานต์\nสูริ\nสูสี\nเส\nเสก\nเสกขบุคคล\nเสกขะ\nเสขบุคคล\nเสขะ\nเส็ง\nเส้ง\nเส็งเคร็ง\nเสงี่ยม\nเสฏฐี\nเสณี\nเสด\nเสด็จ\nเสตุ\nเสถียร\nเสทะ\nเสโท\nเสน\nเส้น\nเสนง\nเสน่ง\nเสน่ห์\nเสนหา\nเสน่หา\nเสนอ\nเสนะ\nเสนา\nเสนาธิการ\nเสนาบดี\nเสน่า\nเสนากุฎ\nเสนางค์\nเสนางคนิกร\nเสนานี\nเสนาสนะ\nเสนาะ\nเสนี\nเสนีย์\nเสนียะ\nเสนียด\nเสบย\nเสบียง\nเสพ\nเสพย์\nเสเพล\nเสภา\nเสม็ด\nเสมหะ\nเสมอ\nเสมา\nเสมียน\nเสมือน\nเสย\nเสร็จ\nเสริด\nเสริม\nเสรี\nเสลด\nเสลบรรพต\nเสลา\nเสลี่ยง\nเสลือกสลน\nเสโล\nเสวก\nเสวกามาตย์\nเสวนะ\nเสวนา\nเสวย\nเสวียน\nเสสรวง\nเสสรวล\nเสา\nเส้า\nเสาร์\nเสารภย์\nเสารี\nเสาวคนธ์\nเสาวธาร\nเสาวภา\nเสาวภาคย์\nเสาวภาพ\nเสาวรภย์\nเสาวรส\nเสาวลักษณ์\nเสาวณิต\nเสาวนะ\nเสาวนา\nเสาวนีย์\nเสาหฤท\nเสาะ\nเสาะแสะ\nเสิร์จ\nเสิร์ฟ\nเสีย\nเสียง\nเสี่ยง\nเสียด\nเสี้ยน\nเสียบ\nเสียม\nเสี่ยม\nเสี้ยม\nเสียว\nเสี่ยว\nเสี้ยว\nเสือ\nเสื่อ\nเสื้อ\nเสือก\nเสื่อม\nแส\nแส่\nแส้\nแสก\nแสง\nแสด\nแสดง\nแสตมป์\nแสน\nแสนย์\nแสนยากร\nแสนยานุภาพ\nแสบ\nแสม\nแสยก\nแสยง\nแสยะ\nแสรก\nแสร้ง\nแสลง\nแสล้ม\nแสวง\nแสะ\nโสก\nโสกโดก\nโสกันต์\nโสโครก\nโสณฑ์\nโสณิ\nโสณี\nโสด\nโสดก\nโสดม\nโสดา\nโสดาบัน\nโสดาปัตติผล\nโสดาปัตติมรรค\nโสต\nโสตทัศนวัสดุ\nโสตทัศนอุปกรณ์\nโสตทัศนูปกรณ์\nโสตินทรีย์\nโสตถิ\nโสทก\nโสทร\nโสธก\nโสธนะ\nโสน\nโสภณ\nโสภา\nโสภี\nโสภิณี\nโสเภณี\nโสม\nโสมนัส\nโสมม\nโสมย์\nโสร่ง\nโสรจ\nโสรวาร\nโสโร\nโสวรรณ\nโสหุ้ย\nโสฬส\nใส\nใส่\nไส\nไส้\nไสย\nไสยา\nไสยาสน์\nไสร้\nไสว\nหก\nหกคะเมน\nหง\nหงก\nหงส์\nหงสบาท\nหงสรถ\nหงอ\nหงอก\nหง่อง\nหงองแหงง\nหงอด\nหงอน\nหง่อม\nหงอย\nหง่อย\nหงัก\nหงับ\nหง่าง\nหงาย\nหง่าว\nหงำ\nหงิก\nหงิง\nหงิม\nหงึก\nหงุงหงิง\nหงุดหงิด\nหงุบ\nหงุ่ย\nหญ้า\nหญ้าฝรั่น\nหญ้ายายเภา\nหญิง\nหญิบ\nหด\nหตะ\nหทัย\nหน\nหนวก\nหน่วง\nหนวด\nหน่วย\nหน่วยกิต\nหนอ\nหน่อ\nหนอก\nหนอง\nหนอน\nหนอนตายหยาก\nหน่อย\nหน็อยแน่\nหนัก\nหนัง\nหนังสติ๊ก\nหนังสือ\nหนั่น\nหนับ\nหนา\nหน้า\nหน่าง\nหนาด\nหนาน\nหนาม\nหน่าย\nหนาว\nหนำ\nหนำเลี้ยบ\nหนี\nหนี้\nหนีบ\nหนึก\nหนึ่ง\nหนึบ\nหนืด\nหนุ\nหนุน\nหนุบ\nหนุ่ม\nหนุ่ย\nหนู\nห่ม\nหมก\nหมด\nหม่น\nหมวก\nหมวด\nหมวน\nหมอ\nหม่อ\nหม้อ\nหมอก\nหมอง\nหม่อง\nหมอน\nหม่อน\nหมอบ\nหม่อม\nหมอย\nหม้อห้อม\nหมัก\nหมักหมม\nหมัด\nหมัน\nหมั่น\nหมั้น\nหมับ\nหมา\nหม่า\nหมาก\nหมากฮอส\nหมาง\nหมาด\nหมามุ่ย\nหมามุ้ย\nหมาย\nหม้าย\nหมาร่า\nหม่ำ\nหม้ำ\nหมิ่น\nหมี\nหมี่\nหมึก\nหมืน\nหมื่น\nหมุด\nหมุน\nหมุบ\nหมุบหมับ\nหมุบหมิบ\nหมุ่ย\nหมุยขาว\nหมู\nหมู่\nหมูหริ่ง\nหยก\nหย่ง\nหยด\nหยวก\nหยวบ\nหยอก\nหยอกเอิน\nหย็อกหย็อย\nหยอง\nหย็อง\nหย่อง\nหย็องกรอด\nหย็องแหย็ง\nหยอด\nหยอน\nหย่อน\nหย่อม\nหย็อมแหย็ม\nหย็อย\nหย่อย\nหยัก\nหยักไย่\nหยักเหยา\nหยัง\nหยั่ง\nหยังหยัง\nหยัด\nหยัน\nหยับ\nหยั่วเมือง\nหย่า\nหยากเยื่อ\nหยากไย่\nหยาด\nหยาบ\nหยาม\nหยาว\nหย้าว\nหยำเป\nหยำเหยอะ\nหยำแหยะ\nหยิก\nหยิ่ง\nหยิบ\nหยิม\nหยี\nหยี่\nหยุกหยิก\nหยุด\nหยุ่น\nหยุบ\nหยุมหยิม\nหยูกยา\nหโยดม\nหรคุณ\nหรณะ\nหรดาล\nหรดี\nหรรษ์\nหรรษา\nหรอ\nหรอก\nหร็อมแหร็ม\nหรอย\nหระ\nหรับ\nหรา\nหริ\nหริ่ง\nหริณะ\nหริต\nหริตกี\nหรีตกี\nหรี่\nหรีด\nหรือ\nหรุบ\nหรุบรู่\nหรุบหรู่\nหรุ่ม\nหรู\nหรูหรา\nหฤทัย\nหฤทย์\nหฤษฎ์\nหฤษฎี\nหฤหรรษ์\nหฤโหด\nหลง\nหลงใหล\nหลงจู๊\nหลด\nหลน\nหล่น\nหลบ\nหล่ม\nหลวง\nหลวม\nหลอ\nหล่อ\nหลอก\nหลอด\nหลอน\nหล็อน\nหล่อน\nหลอม\nหละ\nหละหลวม\nหลัก\nหลัง\nหลั่ง\nหลัด\nหลั่น\nหลับ\nหลัว\nหลา\nหล้า\nหลาก\nหลาน\nหลาบ\nหลาม\nหลาย\nหลาว\nหลิ่ง\nหลิท\nหลิน\nหลิม\nหลิว\nหลิ่ว\nหลี\nหลีก\nหลีโก\nหลีบ\nหลีฮื้อ\nหลืบ\nหลุกหลิก\nหลุด\nหลุน\nหลุบ\nหลุม\nหลุมพอ\nหลุมพี\nหลู่\nหวง\nห่วง\nห้วง\nหวด\nหวน\nห้วน\nหวย\nห้วย\nหวอ\nหวอด\nหวะ\nหวัง\nหวัด\nหวั่น\nหวันยิหวา\nหวัว\nหวัวร่อ\nหวัวเราะ\nหวา\nหว่า\nหว้า\nหวาก\nหว่าง\nหวาด\nหวาน\nหว่าน\nหวาม\nหวาย\nหวำ\nหวิด\nหวิว\nหวี\nหวี่\nหวีด\nหวือ\nหวุดหวิด\nหวูด\nหอ\nห่อ\nห้อ\nหอก\nหอง\nห้อง\nหอน\nห่อน\nหอบ\nหอม\nห้อม\nหอย\nห้อย\nหะ\nหะยี\nหะหาย\nหัก\nหัจญ์\nหัจญี\nหัช\nหัฏฐะ\nหัด\nหัต\nหัตถ์\nหัตถกรรม\nหัตถการ\nหัตถกิจ\nหัตถบาส\nหัตถพันธ์\nหัตถาภรณ์\nหัตถศาสตร์\nหัตถศิลป์\nหัตถศึกษา\nหัตถาจารย์\nหัตถินี\nหัตถี\nหัน\nหั่น\nหั้น\nหันตรา\nหับ\nหัย\nหัว\nหัวร่อ\nหัวเราะ\nหัส\nหัสดิน\nหัสดี\nหัสต์\nหัสตะ\nหา\nห่า\nห้า\nหาก\nหาง\nห่าง\nห้าง\nหาญ\nหาด\nห่าน\nหาบ\nหาม\nห่าม\nห้าม\nหาย\nหายใจ\nหายนะ\nหาร\nหารือ\nหาว\nห้าว\nหาสะ\nหำ\nห้ำ\nหิ้ง\nหิงคุ\nหิงสา\nหิงห้อย\nหิ่งห้อย\nหิ่งหาย\nหิด\nหิต\nหิตานุหิตประโยชน์\nหิน\nหิมพาน\nหิมพานต์\nหิมวัต\nหิมวันต์\nหิมวา\nหิมะ\nหิมาลัย\nหิรัญ\nหิรัญญิการ์\nหิรัญบัฏ\nหิรัณย์\nหิรัณยรัศมี\nหิริ\nหิว\nหิ้ว\nหี\nหีด\nหีนยาน\nหีบ\nหึ\nหึง\nหึ่ง\nหึงสา\nหืด\nหืน\nหื่น\nหือ\nหื้อ\nหุง\nหุน\nหุ่น\nหุ้น\nหุนหัน\nหุบ\nหุ้ม\nหุยฮา\nหู\nหู่\nหูก\nหูด\nเห\nเห่\nเหง\nเหง่ง\nเหงา\nเหง้า\nเหงื่อ\nเหงือก\nเห็จ\nเห็ด\nเหติ\nเหตุ\nเห็น\nเหน่ง\nเหนงนายพราน\nเหน็ดเหนื่อย\nเหน็บ\nเหน่อ\nเห็นอ้ม\nเหนอะ\nเหนอะหนะ\nเหน้า\nเหนาะ\nเหนียง\nเหนี่ยง\nเหนี่ยน\nเหนียม\nเหนียว\nเหนี่ยว\nเหนือ\nเหนื่อย\nเห็บ\nเหม\nเหม่\nเหม็ง\nเหม่ง\nเหม็น\nเหมวดี\nเหม่อ\nเหมันต์\nเหมันตฤดู\nเหมา\nเหมายัน\nเหมาะ\nเหมียว\nเหมี่ยว\nเหมือง\nเหมือด\nเหมือน\nเหมื่อย\nเหย\nเหยง\nเหย่อย\nเหยา\nเหย่า\nเหย้า\nเหยาะ\nเหยาะแหยะ\nเหยิง\nเหยิบ\nเหยียด\nเหยียบ\nเหยี่ยว\nเหยื่อ\nเหยือก\nเหรอ\nเหรอะ\nเหรัญญิก\nเหรา\nเหราะ\nเหรียญ\nเหล่\nเหล็ก\nเหลน\nเหลว\nเหลอ\nเหลา\nเหล่า\nเหล้า\nเหลาะแหละ\nเหลิง\nเหลิงเจิ้ง\nเหลียน\nเหลี่ยม\nเหลียว\nเหลือ\nเหลือก\nเหลือง\nเหลือบ\nเหลือม\nเหลื่อม\nเหว\nเหว่\nเหวง\nเหวย\nเหวอะ\nเหวอะหวะ\nเหวี่ยง\nเห่อ\nเหอะ\nเหะ\nเหะหะ\nเหา\nเห่า\nเหาะ\nเหิน\nเหิม\nเหี้ย\nเหียง\nเหียน\nเหี้ยน\nเหี้ยม\nเหี่ยว\nเหื่อ\nเหือด\nแห\nแห่\nแห้\nแหก\nแหง\nแหง่\nแห่ง\nแห้ง\nแหงแก๋\nแหง่ง\nแหงน\nแหน\nแห้น\nแหนง\nแหนบ\nแหนม\nแหบ\nแหม\nแหม่\nแหม่ม\nแหมะ\nแหย\nแหย่\nแหยง\nแหย่ง\nแหยม\nแหย็ม\nแหยะ\nแหล่\nแหลก\nแหล่ง\nแหลน\nแหลม\nแหละ\nแหว\nแห้ว\nแหวก\nแหว่ง\nแหวด\nแหวน\nแหวะ\nแหะ\nโห่\nโหง\nโหด\nโหน\nโหนก\nโหน่ง\nโหม\nโหม่ง\nโหมด\nโหย\nโหยกเหยก\nโหยง\nโหย่ง\nโหร\nโหรง\nโหรงเหรง\nโหรดาจารย์\nโหระพา\nโหรา\nโหราจารย์\nโหราศาสตร์\nโหล\nโหล่\nโหลงโจ้ง\nโหว\nโหว่\nโหว้\nโหวกเหวก\nโหวง\nโหวด\nโหวต\nให้\nใหญ่\nใหม่\nไห\nไห่\nไห้\nไหน\nไหม\nไหม้\nไหรณย์\nไหล\nไหล่\nไหว\nไหว้\nไหหลำ\nอก\nอกตเวทิตา\nอกตเวที\nอกตัญญุตา\nอกตัญญู\nอกนิษฐ์\nอกรณีย์\nอกรรมกริยา\nอกัปปิยวัตถุ\nอกัปปิยะ\nอกุศล\nอคติ\nอคาธ\nอโฆษะ\nองก์\nองค์\nองคชาต\nองคมนตรี\nองครักษ์\nองคาพยพ\nองคุลี\nองศ์\nองศา\nองอาจ\nองุ่น\nอจลา\nอจินตา\nอจินไตย\nอจิระ\nอเจลก\nอเจละ\nอชะ\nอชิน\nอชินี\nอชิระ\nอฏวี\nอณิ\nอณู\nอโณทัย\nอด\nอดิถี\nอดิเทพ\nอดิเรก\nอดิศร\nอดิศวร\nอดิศัย\nอดีต\nอดุล\nอดุลย์\nอติ\nอติชาต\nอติมานะ\nอติราช\nอติเรก\nอติสาร\nอถรรพเวท\nอาถรรพเวท\nอทระ\nอทินนาทาน\nอธรรม\nอธิ\nอธิกมาส\nอธิกรณ์\nอธิกวาร\nอธิกสุรทิน\nอธิการ\nอธิคม\nอธิฏฐาน\nอธิบดี\nอธิบาย\nอธิป\nอธิปไตย\nอธิมาตร\nอธิมุตติ\nอธิโมกข์\nอธิราช\nอธิวาส\nอธิวาสนะ\nอธิศีล\nอธิษฐาน\nอธึก\nอ้น\nอนงค์\nอนงคณะ\nอนงคเลขา\nอนธการ\nอนนต์\nอนยะ\nอนรรฆ\nอนรรถ\nอนล\nอนวัช\nอนัญ\nอนัตตา\nอนันต์\nอนันตริยกรรม\nอนัม\nอนาคต\nอนาคามิผล\nอนาคามิมรรค\nอนาคามี\nอนาจาร\nอนาถ\nอนาถา\nอนาทร\nอนาธิปไตย\nอนามัย\nอนามิกา\nอนารยชน\nอนารยธรรม\nอนารยะ\nอนาลัย\nอนำ\nอนิจ\nอนิจจัง\nอนิจจา\nอนิฏฐารมณ์\nอนิยต\nอนิยม\nอนิล\nอนิวรรต\nอนิวรรตน์\nอนีกะ\nอนีจะ\nอนึก\nอนึ่ง\nอนุ\nอนุกร\nอนุกรม\nอนุกรรมการ\nอนุกระเบียด\nอนุกาชาด\nอนุการ\nอนุกูล\nอนุคามิก\nอนุเคราะห์\nอนุจร\nอนุช\nอนุชน\nอนุชา\nอนุชาต\nอนุชิต\nอนุญาต\nอนุญาโตตุลาการ\nอนุตร\nอนุเถระ\nอนุทิน\nอนุบท\nอนุบาล\nอนุประโยค\nอนุปริญญา\nอนุปสัมบัน\nอนุปัสนา\nอนุพงศ์\nอนุพัทธ์\nอนุพันธ์\nอนุโพธ\nอนุภรรยา\nอนุภริยา\nอนุภาค\nอนุภาษ\nอนุมัติ\nอนุมาตรา\nอนุมาน\nอนุมูล\nอนุโมทนา\nอนุโยค\nอนุรักษ์\nอนุรักษนิยม\nอนุราช\nอนุราธ\nอนุราธะ\nอนุราธา\nอนุรูป\nอนุโลม\nอนุวงศ์\nอนุวรรตน์\nอนุวัต\nอนุวัตน์\nอนุวัตร\nอนุวัติ\nอนุวาต\nอนุศาสก\nอนุศาสน์\nอนุศาสนาจารย์\nอนุศิษฏ์\nอนุสติ\nอนุสนธิ\nอนุสร\nอนุสรณ์\nอนุสัญญา\nอนุสัย\nอนุสาวรีย์\nอนุสาสนี\nอเนก\nอเนกคุณ\nอเนกรรถประโยค\nอเนจอนาถ\nอโนชา\nอโนดาต\nอบ\nอบเชย\nอบาย\nอปจายนธรรม\nอปจายนมัย\nอปมงคล\nอปยศ\nอประไมย\nอปรัณณชาติ\nอปรา\nอปราชัย\nอปราชิต\nอปริมาณ\nอปลักษณ์\nอปโลกน์\nอปวาท\nอเปหิ\nอพพะ\nอพยพ\nอภัพ\nอภัย\nอภิ\nอภิฆาต\nอภิชฌา\nอภิชน\nอภิชนาธิปไตย\nอภิชัย\nอภิชาต\nอภิชิต\nอภิญญา\nอภิญญาณ\nอภิธรรม\nอภิธาน\nอภิไธย\nอภินันท์\nอภินันทนาการ\nอภินัย\nอภินิหาร\nอภิเนษกรมณ์\nอภิบาล\nอภิปรัชญา\nอภิปราย\nอภิมหาอำนาจ\nอภิมานะ\nอภิมุข\nอภิรดี\nอภิรติ\nอภิรมย์\nอภิรักษ์\nอภิราม\nอภิรุต\nอภิรุม\nอภิรูป\nอภิลักขิต\nอภิลักขิตสมัย\nอภิเลปน์\nอภิวันท์\nอภิวาท\nอภิวาทน์\nอภิเษก\nอภิสมโพธิ\nอภิสมัย\nอภิสมาจาร\nอภิสัมโพธิ\nอภิสัมโพธิญาณ\nอภิสิต\nอภิสิทธิ์\nอภูตะ\nอม\nอมพะนำ\nอ้ม\nอมตธรรม\nอมตบท\nอมตะ\nอมนุษย์\nอมร\nอมรา\nอมราวดี\nอมรินทร์\nอมเรนทร์\nอมเรศ\nอมฤต\nอมัตร\nอมาตย์\nอมาวสี\nอมาวสุ\nอมาวาสี\nอมิตร\nอเมริกัน\nอย่า\nอยาก\nอย่าง\nอยุทธ์\nอยู่\nอร\nอรชร\nอรชุน\nอรดี\nอรติ\nอรทัย\nอรไท\nอรนุช\nอรพินท์\nอรพิม\nอรรค\nอรรฆ\nอรรฆย์\nอรรจน์\nอรรณพ\nอรรถ\nอรรถกถา\nอรรถกถาจารย์\nอรรถาธิบาย\nอรรธ\nอรสุม\nอรหะ\nอรหัง\nอรหัต\nอรหัตผล\nอรหัตมรรค\nอรหัน\nอรหันต์\nอรหันตฆาต\nอร่อย\nอรัญ\nอรัญญิก\nอรัญวาส\nอรัญวาสี\nอรัณย์\nอราดี\nอร่าม\nอริ\nอรินทร์\nอริน\nอริยกะ\nอริยทรัพย์\nอริยบุคคล\nอริยผล\nอริยมรรค\nอริยสั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nอำพล\nอำพะนำ\nอำพัน\nอำไพ\nอำเภอ\nอำมร\nอำมฤคโชค\nอำมฤต\nอำมหิต\nอำมาตย์\nอำมาตยาธิปไตย\nอำยวน\nอำรุง\nอำลา\nอำอวม\nอ้ำอึ้ง\nอิก\nอิง\nอิงค์\nอิงอร\nอิจฉา\nอิฉัน\nอิชยา\nอิฏฐารมณ์\nอิฐ\nอิฐผล\nอิด\nอิตถี\nอิตเทรียม\nอิตเทอร์เบียม\nอิติวุตตกะ\nอิทธิ\nอิน\nอินซูลิน\nอินเดีย\nอินเดียนแดง\nอินเดียม\nอินท์\nอินทขีล\nอินทนิล\nอินทผลัม\nอินทร์\nอินทรธนู\nอินทรวงศ์\nอินทรวิเชียร\nอินทรศักดิ์\nอินทราณี\nอินทราภิเษก\nอินทรายุธ\nอินทรี\nอินทรีย์\nอินทรียสังวร\nอินทีวร\nอินทุ\nอินฟราเรด\nอินัง\nอิ่ม\nอิมัลชัน\nอิริเดียม\nอิริยา\nอิริยาบถ\nอิรุพเพท\nอิเล็กตรอน\nอิเล็กทรอนิกส์\nอิเล็กโทน\nอิศร\nอิศวร\nอิษฏ์\nอิษฏี\nอิส\nอิสตรี\nอิสัตรี\nอิสรภาพ\nอิสระ\nอิสริยยศ\nอิสริยะ\nอิสริยาภรณ์\nอิสลาม\nอิสสา\nอิสิ\nอิสี\nอิหม่าม\nอิหลักอิเหลื่อ\nอี\nอี่\nอี้\nอี๊\nอี๋\nอี๋อ๋อ\nอีก\nอีก้อ\nอีก๋อย\nอีโก้ง\nอีจู้\nอี๊ด\nอีเต้อ\nอีโต้\nอีทุบ\nอีเทอร์\nอีนุงตุงนัง\nอีนูน\nอีโน\nอีแปะ\nอีโปง\nอีเพา\nอีมู\nอีรม\nอีลุ้ม\nอีลุ่ยฉุยแฉก\nอีเลิ้ง\nอีศ\nอีศวร\nอีส\nอีสาน\nอีสุกอีใส\nอีหรอบ\nอีหลักอีเหลื่อ\nอีหลี\nอีหลุกขลุกขลัก\nอีหลุกขลุกขลุ่ย\nอีเห็น\nอีเหน็บ\nอีเหนียว\nอีเหละเขละขละ\nอีเหละเขะขะ\nอีโหน่อีเหน่\nอีโหลกโขลกเขลก\nอีแอ่น\nอึ\nอึก\nอึ้ก\nอึ๊ก\nอึกทึก\nอึกอัก\nอึง\nอึ่ง\nอึ้ง\nอึด\nอึดตะปือ\nอึ้ดทึ่ด\nอึน\nอืด\nอื่น\nอื้น\nอือ\nอื้อ\nอื้อฮือ\nอุ\nอุก\nอุกกา\nอุกกาบาต\nอุกฤษฏ์\nอุกลาบาต\nอุค\nอุคระ\nอุคหนิมิต\nอุโฆษ\nอุ้ง\nอุจ\nอุจจาระ\nอุจฉุ\nอุจเฉท\nอุจเฉททิฐิ\nอุจาด\nอุชุ\nอุฏฐาการ\nอุณหภูมิ\nอุณหะ\nอุณหาหาร\nอุณหิส\nอุณา\nอุณาโลม\nอุด\nอุดเตา\nอุดม\nอุดมการณ์\nอุดมคติ\nอุดมศึกษา\nอุดร\nอุดหนุน\nอุตดม\nอุตตมะ\nอุตมภาพ\nอุตมางค์\nอุตดร\nอุตรกุรุทวีป\nอุตตรายัน\nอุตรนิกาย\nอุตรผลคุนี\nอุตตรผลคุนี\nอุตรภัทรบท\nอุตตรภัทรบท\nอุตตรภัททะ\nอุตราภิมุข\nอุตราวรรต\nอุตราวัฏ\nอุตราษาฒ\nอุตตราสาฬหะ\nอุตราสงค์\nอุตตานภาพ\nอุตพิด\nอุตรา\nอุตริ\nอุตริมนุสธรรม\nอุตลุด\nอุตส่าห์\nอุตสาหกรรม\nอุตสาหะ\nอุตุ\nอุตุนิยม\nอุตุนิยมวิทยา\nอุทก\nอุทกธาร\nอุทกธารา\nอุทกภัย\nอุทกวิทยา\nอุทกศาสตร์\nอุทธรณ์\nอุทธัจ\nอุทยาน\nอุทร\nอุทริยะ\nอุทลุม\nอุทัช\nอุทัย\nอุทาน\nอุทาร\nอุทาหรณ์\nอุทิศ\nอุทุมพร\nอุเทศ\nอุเทสิกเจดีย์\nอุธัจ\nอุ่น\nอุบ\nอุบล\nอุบะ\nอุบ๊ะ\nอุบัติ\nอุบาท\nอุบาทว์\nอุบาย\nอุบาสก\nอุบาสิกา\nอุเบกขา\nอุโบสถ\nอุปกรณ์\nอุปกรม\nอุปการ\nอุปการะ\nอุปการี\nอุปกิเลส\nอุปจาร\nอุปถัมภ์\nอุปถัมภก\nอุปทม\nอุปทูต\nอุปเทศ\nอุปเท่ห์\nอุปธิ\nอุปนัย\nอุปนิกขิต\nอุปนิษัท\nอุปนิสัย\nอุปบัติ\nอุปปาติกะ\nอุปพัทธ์\nอุปพันธ์\nอุปโภค\nอุปมา\nอุปมาน\nอุปไมย\nอุปยุวราช\nอุปรากร\nอุปราคา\nอุปราช\nอุปริ\nอุปริมปริยาย\nอุปโลกน์\nอุปเวท\nอุปสมบท\nอุปสมบัน\nอุปสัมบัน\nอุปสรรค\nอุปสัมปทา\nอุปฮาด\nอุปัชฌาย์\nอุปัชฌายวัตร\nอุปัชฌายะ\nอุปัฏฐาก\nอุปัฏฐานะ\nอุปัทวะ\nอุปัทวันตราย\nอุปาทาน\nอุปาหนา\nอุภัย\nอุ้ม\nอุมงค์\nอุโมงค์\nอุย\nอุ่ย\nอุ้ย\nอุ๊ย\nอุยยาน\nอุยยาม\nอุรณะ\nอุรพี\nอุระ\nอุรังอุตัง\nอุรัจฉัท\nอุรัจฉทะ\nอุรา\nอุรุ\nอุไร\nอุลกมณี\nอุลโลจ\nอุลามก\nอุลิด\nอุโลก\nอุแว้\nอุษณกร\nอุษณกาล\nอุษณรัศมี\nอุษณรุจี\nอุษณาการ\nอุษณีษ์\nอุษมะ\nอุษมัน\nอุษา\nอุษาโยค\nอุสภ\nอุสส่าห์\nอุสสาหะ\nอุสา\nอุสุ\nอุสุภ\nอุสุภราช\nอุสุม\nอุหรับ\nอุหลบ\nอุเหม่\nอุฬาร\nอู\nอู่\nอู้\nอูฐ\nอูด\nอูม\nอูย\nอูรุ\nอู๋อี๋\nเอ\nเอ้\nเอ๊\nเอก\nเอกเขนก\nเอกซเรย์\nเอกรรถประโยค\nเอกัคตา\nเอกังสพยากรณ์\nเอกังสวาที\nเอกา\nเอ้กา\nเอกาธิปไตย\nเอเคอร์\nเอง\nเอ็ง\nเอ๋ง\nเอ็ด\nเอ็ดตะโร\nเอดส์\nเอตทัคคะ\nเอ้เต\nเอทิล\nเอน\nเอ็น\nเอนไซม์\nเอ็นดู\nเอ็นอ่อน\nเอม\nเอ็มบริโอ\nเอย\nเอ่ย\nเอ๊ย\nเอ๋ย\nเอร็ดอร่อย\nเอราวัณ\nเอว\nเอ๊ว\nเอวัง\nเอฬกะ\nเอฬา\nเออ\nเอ่อ\nเออร์เบียม\nเอ้อระเหย\nเอ้อเร้อ\nเอ้อเฮอ\nเอ๊ะ\nเอะใจ\nเอะอะ\nเอะอะมะเทิ่ง\nเอา\nเอาทาร\nเอาทารย์\nเอารส\nเอาฬาร\nเอาะลาย\nเอิก\nเอิกเกริก\nเอิ้น\nเอิบ\nเอียง\nเอี้ยง\nเอียด\nเอี๊ยด\nเอียน\nเอี่ยน\nเอี่ยม\nเอี๊ยม\nเอี้ยมจุ๊น\nเอี้ยมเฟี้ยม\nเอี่ยว\nเอี้ยว\nเอื้อ\nเอื๊อก\nเอื้อง\nเอือด\nเอือน\nเอื้อน\nเอือม\nเอื้อม\nเอื่อย\nเอื้อย\nแอ\nแอ้\nแอ๋\nแอก\nแอกทิเนียม\nแอ่ง\nแอ้งแม้ง\nแอด\nแอ้ด\nแอ๊ด\nแอ่น\nแอนติเจน\nแอนติบอดี\nแอนติอิเล็กตรอน\nแอโนด\nแอบ\nแอม\nแอ้ม\nแอมแปร์\nแอมมิเตอร์\nแอมโมเนีย\nแอร่ม\nแอลกอฮอล์\nแอลฟา\nแอว\nแอ่ว\nแอ้วแซ่ว\nแอสทาทีน\nแอสไพริน\nแอสฟัลต์\nแอหนัง\nแออัด\nโอ\nโอ่\nโอ้\nโอ๋\nโอก\nโอ้ก\nโอ้กอ้าก\nโอ๊ก\nโอกาส\nโอฆชล\nโอฆสงสาร\nโอฆะ\nโอ่ง\nโองการ\nโองโขดง\nโอชะ\nโอชา\nโอโซน\nโอฐ\nโอด\nโอ๊ต\nโอตตัปปะ\nโอทนะ\nโอน\nโอบ\nโอปปาติกะ\nโอภา\nโอภาส\nโอม\nโอย\nโอ๊ย\nโอรส\nโอละพ่อ\nโอลิมปิก\nโอวาท\nโอษฐ์\nโอษฐชะ\nโอษฐภัย\nโอสถ\nโอห์ม\nโอหัง\nโอฬาร\nโอฬาริก\nโอฬารึก\nโอ้เอ้\nโอเอซิส\nโอ้โฮ\nไอ\nไอ้\nไอโซโทป\nไอน์สไตเนียม\nไอยรา\nไอยเรศ\nไอราพต\nไอราวัณ\nไอราวัต\nไอศกรีม\nไอศวรรย์\nไอศุริยสมบัติ\nไอศูรย์\nไอออน\nไอโอดีน\nฮกเกี้ยน\nฮด\nฮวงซุ้ย\nฮวน\nฮ้วนหมู\nฮวบ\nฮ่อ\nฮ้อ\nฮอกกี้\nฮอด\nฮ่อม\nฮ่อยจ๊อ\nฮอร์โมน\nฮอลแลนด์\nฮอลันดา\nฮะ\nฮะเบส\nฮะเรีย\nฮัก\nฮังเล\nฮัจญ์\nฮัจญะฮ์\nฮัจญี\nฮั่น\nฮั้ว\nฮา\nฮ้า\nฮ่างหลวง\nฮาจญ์\nฮาม\nฮาเร็ม\nฮาห์เนียม\nฮิจเราะห์\nฮินดู\nฮิปโปโปเตมัส\nฮิสทีเรีย\nฮีเลียม\nฮึ\nฮึก\nฮึด\nฮึดฮัด\nฮึ่ม\nฮึย\nฮึ่ย\nฮืดฮาด\nฮือ\nฮื่อ\nฮื้อ\nฮื้อฉี่\nฮุด\nฮุบ\nฮุยเลฮุย\nฮู้\nฮูก\nฮูม\nเฮ\nเฮฮา\nเฮกตาร์\nเฮกโตกรัม\nเฮกโตเมตร\nเฮกโตลิตร\nเฮง\nเฮ็ด\nเฮโมโกลบิน\nเฮย\nเฮ่ย\nเฮ้ย\nเฮโรอีน\nเฮลิคอปเตอร์\nเฮโล\nเฮละโล\nเฮ้ว\nเฮอ\nเฮ่อ\nเฮ้อ\nเฮอริเคน\nเฮิรตซ์\nเฮี้ยน\nเฮี้ยบ\nเฮี้ยว\nเฮือก\nเฮือน\nแฮ\nแฮ่\nแฮก\nแฮ่กึ๊น\nแฮนด์บอล\nแฮฟเนียม\nแฮม\nแฮะ\nโฮ\nโฮก\nโฮ่ง\nโฮ้ง\nโฮเต็ล\nโฮลเมียม\nโฮะ\nไฮ้\nไฮโกรมิเตอร์\nไฮดรา\nไฮโดร\nไฮโดรคาร์บอน\nไฮโดรเจน\nไฮโดรมิเตอร์\nไฮไฟ\nไฮโล\nไฮฮี\n"
+              .split(/[\r\n]+/)
+              .filter(function (w) {
+                return w.length > 1;
+              })
+      this.addWords(words, false)
+    }
+    if(finalize){
+      this.finalizeDict();
+    }
+  },
+
+  dictSeek: function (l, r, ch, strOffset, pos) {
+    var ans = null;
+    while (l <= r) {
+      var m = Math.floor((l + r) / 2),
+        dict_item = this.dict[m],
+        len = dict_item.length;
+      if (len <= strOffset) {
+        l = m + 1;
+      } else {
+        var ch_ = dict_item[strOffset];
+        if (ch_ < ch) {
+          l = m + 1;
+        } else if (ch_ > ch) {
+          r = m - 1;
+        } else {
+          ans = m;
+          if (pos == LEFT) {
+            r = m - 1;
+          } else {
+            l = m + 1;
+          }
+        }
+      }
+    }
+    return ans;
+  },
+
+  isFinal: function (acceptor) {
+    return this.dict[acceptor.l].length == acceptor.strOffset;
+  },
+
+  createAcceptor: function () {
+    return {
+      l: 0,
+      r: this.dict.length - 1,
+      strOffset: 0,
+      isFinal: false,
+      dict: this,
+      transit: function (ch) {
+        return this.dict.transit(this, ch);
+      },
+      isError: false,
+      tag: "DICT",
+      w: 1,
+      type: "DICT"
+    };
+  },
+
+  transit: function (acceptor, ch) {
+    var l = this.dictSeek(acceptor.l,
+      acceptor.r,
+      ch,
+      acceptor.strOffset,
+      LEFT);
+    if (l !== null) {
+      var r = this.dictSeek(l,
+        acceptor.r,
+        ch,
+        acceptor.strOffset,
+        RIGHT);
+      acceptor.l = l;
+      acceptor.r = r;
+      acceptor.strOffset++;
+      acceptor.isFinal = this.isFinal(acceptor);
+    } else {
+      acceptor.isError = true;
+    }
+    return acceptor;
+  },
+
+  sortuniq: function(a){
+    return a.sort().filter(function(item, pos, arr){
+      return !pos || item != arr[pos - 1];
+    })
+  },
+
+  flatten: function(a){
+    //[[1,2],[3]] -> [1,2,3]
+    return [].concat.apply([], a);
+  }
+};
+module.exports = WordcutDict;
+
+}).call(this,"/dist/tmp")
+},{"glob":16,"path":22}],3:[function(require,module,exports){
+var WordRule = {
+  createAcceptor: function(tag) {
+    if (tag["WORD_RULE"])
+      return null;
+
+    return {strOffset: 0,
+            isFinal: false,
+            transit: function(ch) {
+              var lch = ch.toLowerCase();
+              if (lch >= "a" && lch <= "z") {
+                this.isFinal = true;
+                this.strOffset++;
+              } else {
+                this.isError = true;
+              }
+              return this;
+            },
+            isError: false,
+            tag: "WORD_RULE",
+            type: "WORD_RULE",
+            w: 1};
+  }
+};
+
+var NumberRule = {
+  createAcceptor: function(tag) {
+    if (tag["NUMBER_RULE"])
+      return null;
+
+    return {strOffset: 0,
+            isFinal: false,
+            transit: function(ch) {
+              if (ch >= "0" && ch <= "9") {
+                this.isFinal = true;
+                this.strOffset++;
+              } else {
+                this.isError = true;
+              }
+              return this;
+            },
+            isError: false,
+            tag: "NUMBER_RULE",
+            type: "NUMBER_RULE",
+            w: 1};
+  }
+};
+
+var SpaceRule = {
+  tag: "SPACE_RULE",
+  createAcceptor: function(tag) {
+
+    if (tag["SPACE_RULE"])
+      return null;
+
+    return {strOffset: 0,
+            isFinal: false,
+            transit: function(ch) {
+              if (ch == " " || ch == "\t" || ch == "\r" || ch == "\n" ||
+                  ch == "\u00A0" || ch=="\u2003"//nbsp and emsp
+                 ) {
+                this.isFinal = true;
+                this.strOffset++;
+              } else {
+                this.isError = true;
+              }
+              return this;
+            },
+            isError: false,
+            tag: SpaceRule.tag,
+            w: 1,
+            type: "SPACE_RULE"};
+  }
+}
+
+var SingleSymbolRule = {
+  tag: "SINSYM",
+  createAcceptor: function(tag) {
+    return {strOffset: 0,
+            isFinal: false,
+            transit: function(ch) {
+              if (this.strOffset == 0 && ch.match(/^[\@\(\)\/\,\-\."`]$/)) {
+                this.isFinal = true;
+                this.strOffset++;
+              } else {
+                this.isError = true;
+              }
+              return this;
+            },
+            isError: false,
+            tag: "SINSYM",
+            w: 1,
+            type: "SINSYM"};
+  }
+}
+
+
+var LatinRules = [WordRule, SpaceRule, SingleSymbolRule, NumberRule];
+
+module.exports = LatinRules;
+
+},{}],4:[function(require,module,exports){
+var _ = require("underscore")
+  , WordcutCore = require("./wordcut_core");
+var PathInfoBuilder = {
+
+  /*
+    buildByPartAcceptors: function(path, acceptors, i) {
+    var 
+    var genInfos = partAcceptors.reduce(function(genInfos, acceptor) {
+      
+    }, []);
+    
+    return genInfos;
+  } 
+  */
+
+  buildByAcceptors: function(path, finalAcceptors, i) {
+    var self = this;
+    var infos = finalAcceptors.map(function(acceptor) {
+      var p = i - acceptor.strOffset + 1
+        , _info = path[p];            
+      
+      var info = {p: p, 
+                  mw: _info.mw + (acceptor.mw === undefined ? 0 : acceptor.mw),
+                  w: acceptor.w + _info.w,
+                  unk: (acceptor.unk ? acceptor.unk : 0) + _info.unk, 
+                  type: acceptor.type};
+
+      if (acceptor.type == "PART") {
+        for(var j = p + 1; j <= i; j++) {
+          path[j].merge = p;
+        }
+        info.merge = p;
+      }
+
+      return info;
+    });
+    return infos.filter(function(info) { return info; });
+  },
+  
+  fallback: function(path, leftBoundary, text, i) {
+    var _info = path[leftBoundary];
+    if (text[i].match(/[\u0E48-\u0E4E]/)) {
+      if (leftBoundary != 0) 
+        leftBoundary = path[leftBoundary].p;
+      return {p: leftBoundary,
+              mw: 0,
+              w: 1 + _info.w,
+              unk: 1 + _info.unk,
+              type: "UNK"};      
+/*    } else if(leftBoundary > 0 && path[leftBoundary].type !== "UNK") {
+      leftBoundary = path[leftBoundary].p;
+      return {p: leftBoundary,
+              w: 1 + _info.w,
+              unk: 1 + _info.unk,
+              type: "UNK"};            */
+    } else {      
+      return {p: leftBoundary,
+              mw: _info.mw,
+              w: 1 + _info.w,
+              unk: 1 + _info.unk,
+              type: "UNK"};
+    }
+  },
+  
+  build: function(path, finalAcceptors, i, leftBoundary, text) {
+    var basicPathInfos = this.buildByAcceptors(path, finalAcceptors, i);
+    if (basicPathInfos.length > 0) {
+      return basicPathInfos;
+    } else {
+      return [this.fallback(path, leftBoundary, text, i)];
+    }
+  }
+};
+
+module.exports = function() {
+  return _.clone(PathInfoBuilder);
+}
+
+},{"./wordcut_core":8,"underscore":25}],5:[function(require,module,exports){
+var _ = require("underscore");
+
+
+var PathSelector = {
+  selectPath: function(paths) {
+    var path = paths.reduce(function(selectedPath, path) {
+      if (selectedPath == null) {        
+        return path;
+      } else {
+        if (path.unk < selectedPath.unk) 
+          return path;        
+        if (path.unk == selectedPath.unk) {
+          if (path.mw < selectedPath.mw)
+            return path
+          if (path.mw == selectedPath.mw) {
+            if (path.w < selectedPath.w) 
+              return path;
+          }
+        }
+        return selectedPath;
+      }
+    }, null);
+    return path;
+  },
+  
+  createPath: function() {
+    return [{p:null, w:0, unk:0, type: "INIT", mw:0}];
+  }
+};
+
+module.exports = function() {
+  return _.clone(PathSelector);
+};
+
+},{"underscore":25}],6:[function(require,module,exports){
+function isMatch(pat, offset, ch) {
+  if (pat.length <= offset)
+    return false;
+  var _ch = pat[offset];
+  return _ch == ch ||
+         (_ch.match(/[กข]/) && ch.match(/[ก-ฮ]/)) ||
+         (_ch.match(/[มบ]/) && ch.match(/[ก-ฮ]/)) ||
+         (_ch.match(/\u0E49/) && ch.match(/[\u0E48-\u0E4B]/));
+}
+
+var Rule0 = {
+  pat: "เหก็ม",
+  createAcceptor: function(tag) {
+    return {strOffset: 0,
+            isFinal: false,
+            transit: function(ch) {
+              if (isMatch(Rule0.pat, this.strOffset,ch)) {                 
+                this.isFinal = (this.strOffset + 1 == Rule0.pat.length);                
+                this.strOffset++;
+              } else {              
+                this.isError = true;             
+              }
+              return this;
+            },
+            isError: false,
+            tag: "THAI_RULE",
+            type: "THAI_RULE", 
+            w: 1};                        
+  }
+};
+
+var PartRule = {
+  createAcceptor: function(tag) {
+    return {strOffset: 0,
+            patterns: [
+              "แก", "เก", "ก้", "กก์", "กา", "กี", "กิ", "กืก"  
+            ],
+            isFinal: false,
+            transit: function(ch) {
+              var offset = this.strOffset;
+              this.patterns = this.patterns.filter(function(pat) {
+                return isMatch(pat, offset, ch);
+              });
+              
+              if (this.patterns.length > 0) {
+                var len = 1 + offset;
+                this.isFinal = this.patterns.some(function(pat) {
+                  return pat.length == len; 
+                });
+                this.strOffset++;
+              } else {              
+                this.isError = true;             
+              }
+              return this;
+            },
+            isError: false,
+            tag: "PART",
+            type: "PART", 
+            unk: 1,
+            w: 1};                        
+  }
+};
+
+var ThaiRules = [Rule0, PartRule];
+
+module.exports = ThaiRules;
+
+},{}],7:[function(require,module,exports){
+var sys = require("sys")
+  , WordcutDict = require("./dict")
+  , WordcutCore = require("./wordcut_core")
+  , PathInfoBuilder = require("./path_info_builder")
+  , PathSelector = require("./path_selector")
+  , Acceptors = require("./acceptors")
+  , latinRules = require("./latin_rules")
+  , thaiRules = require("./thai_rules")
+  , _ = require("underscore");
+
+
+var Wordcut = Object.create(WordcutCore);
+Wordcut.defaultPathInfoBuilder = PathInfoBuilder;
+Wordcut.defaultPathSelector = PathSelector;
+Wordcut.defaultAcceptors = Acceptors;
+Wordcut.defaultLatinRules = latinRules;
+Wordcut.defaultThaiRules = thaiRules;
+Wordcut.defaultDict = WordcutDict;
+
+
+Wordcut.initNoDict = function(dict_path) {
+  var self = this;
+  self.pathInfoBuilder = new self.defaultPathInfoBuilder;
+  self.pathSelector = new self.defaultPathSelector;
+  self.acceptors = new self.defaultAcceptors;
+  self.defaultLatinRules.forEach(function(rule) {
+    self.acceptors.creators.push(rule);
+  });
+  self.defaultThaiRules.forEach(function(rule) {
+    self.acceptors.creators.push(rule);
+  });
+};
+
+Wordcut.init = function(dict_path, withDefault, additionalWords) {
+  withDefault = withDefault || false;
+  this.initNoDict();
+  var dict = _.clone(this.defaultDict);
+  dict.init(dict_path, withDefault, additionalWords);
+  this.acceptors.creators.push(dict);
+};
+
+module.exports = Wordcut;
+
+},{"./acceptors":1,"./dict":2,"./latin_rules":3,"./path_info_builder":4,"./path_selector":5,"./thai_rules":6,"./wordcut_core":8,"sys":28,"underscore":25}],8:[function(require,module,exports){
+var WordcutCore = {
+
+  buildPath: function(text) {
+    var self = this
+      , path = self.pathSelector.createPath()
+      , leftBoundary = 0;
+    self.acceptors.reset();
+    for (var i = 0; i < text.length; i++) {
+      var ch = text[i];
+      self.acceptors.transit(ch);
+
+      var possiblePathInfos = self
+        .pathInfoBuilder
+        .build(path,
+               self.acceptors.getFinalAcceptors(),
+               i,
+               leftBoundary,
+               text);
+      var selectedPath = self.pathSelector.selectPath(possiblePathInfos)
+
+      path.push(selectedPath);
+      if (selectedPath.type !== "UNK") {
+        leftBoundary = i;
+      }
+    }
+    return path;
+  },
+
+  pathToRanges: function(path) {
+    var e = path.length - 1
+     , ranges = [];
+
+    while (e > 0) {
+      var info = path[e]
+       , s = info.p;
+
+      if (info.merge !== undefined && ranges.length > 0) {
+        var r = ranges[ranges.length - 1];
+        r.s = info.merge;
+        s = r.s;
+      } else {
+        ranges.push({s:s, e:e});
+      }
+      e = s;
+    }
+    return ranges.reverse();
+  },
+
+  rangesToText: function(text, ranges, delimiter) {
+    return ranges.map(function(r) {
+      return text.substring(r.s, r.e);
+    }).join(delimiter);
+  },
+
+  cut: function(text, delimiter) {
+    var path = this.buildPath(text)
+      , ranges = this.pathToRanges(path);
+    return this
+      .rangesToText(text, ranges,
+                    (delimiter === undefined ? "|" : delimiter));
+  },
+
+  cutIntoRanges: function(text, noText) {
+    var path = this.buildPath(text)
+      , ranges = this.pathToRanges(path);
+
+    if (!noText) {
+      ranges.forEach(function(r) {
+        r.text = text.substring(r.s, r.e);
+      });
+    }
+    return ranges;
+  },
+
+  cutIntoArray: function(text) {
+    var path = this.buildPath(text)
+      , ranges = this.pathToRanges(path);
+    
+    return ranges.map(function(r) {
+      return text.substring(r.s, r.e)
+    });
+  }
+};
+
+module.exports = WordcutCore;
+
+},{}],9:[function(require,module,exports){
+// http://wiki.commonjs.org/wiki/Unit_Testing/1.0
+//
+// THIS IS NOT TESTED NOR LIKELY TO WORK OUTSIDE V8!
+//
+// Originally from narwhal.js (http://narwhaljs.org)
+// Copyright (c) 2009 Thomas Robinson <280north.com>
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the 'Software'), to
+// deal in the Software without restriction, including without limitation the
+// rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
+// sell copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+// ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+// WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+// when used in node, this will actually load the util module we depend on
+// versus loading the builtin util module as happens otherwise
+// this is a bug in node module loading as far as I am concerned
+var util = require('util/');
+
+var pSlice = Array.prototype.slice;
+var hasOwn = Object.prototype.hasOwnProperty;
+
+// 1. The assert module provides functions that throw
+// AssertionError's when particular conditions are not met. The
+// assert module must conform to the following interface.
+
+var assert = module.exports = ok;
+
+// 2. The AssertionError is defined in assert.
+// new assert.AssertionError({ message: message,
+//                             actual: actual,
+//                             expected: expected })
+
+assert.AssertionError = function AssertionError(options) {
+  this.name = 'AssertionError';
+  this.actual = options.actual;
+  this.expected = options.expected;
+  this.operator = options.operator;
+  if (options.message) {
+    this.message = options.message;
+    this.generatedMessage = false;
+  } else {
+    this.message = getMessage(this);
+    this.generatedMessage = true;
+  }
+  var stackStartFunction = options.stackStartFunction || fail;
+
+  if (Error.captureStackTrace) {
+    Error.captureStackTrace(this, stackStartFunction);
+  }
+  else {
+    // non v8 browsers so we can have a stacktrace
+    var err = new Error();
+    if (err.stack) {
+      var out = err.stack;
+
+      // try to strip useless frames
+      var fn_name = stackStartFunction.name;
+      var idx = out.indexOf('\n' + fn_name);
+      if (idx >= 0) {
+        // once we have located the function frame
+        // we need to strip out everything before it (and its line)
+        var next_line = out.indexOf('\n', idx + 1);
+        out = out.substring(next_line + 1);
+      }
+
+      this.stack = out;
+    }
+  }
+};
+
+// assert.AssertionError instanceof Error
+util.inherits(assert.AssertionError, Error);
+
+function replacer(key, value) {
+  if (util.isUndefined(value)) {
+    return '' + value;
+  }
+  if (util.isNumber(value) && !isFinite(value)) {
+    return value.toString();
+  }
+  if (util.isFunction(value) || util.isRegExp(value)) {
+    return value.toString();
+  }
+  return value;
+}
+
+function truncate(s, n) {
+  if (util.isString(s)) {
+    return s.length < n ? s : s.slice(0, n);
+  } else {
+    return s;
+  }
+}
+
+function getMessage(self) {
+  return truncate(JSON.stringify(self.actual, replacer), 128) + ' ' +
+         self.operator + ' ' +
+         truncate(JSON.stringify(self.expected, replacer), 128);
+}
+
+// At present only the three keys mentioned above are used and
+// understood by the spec. Implementations or sub modules can pass
+// other keys to the AssertionError's constructor - they will be
+// ignored.
+
+// 3. All of the following functions must throw an AssertionError
+// when a corresponding condition is not met, with a message that
+// may be undefined if not provided.  All assertion methods provide
+// both the actual and expected values to the assertion error for
+// display purposes.
+
+function fail(actual, expected, message, operator, stackStartFunction) {
+  throw new assert.AssertionError({
+    message: message,
+    actual: actual,
+    expected: expected,
+    operator: operator,
+    stackStartFunction: stackStartFunction
+  });
+}
+
+// EXTENSION! allows for well behaved errors defined elsewhere.
+assert.fail = fail;
+
+// 4. Pure assertion tests whether a value is truthy, as determined
+// by !!guard.
+// assert.ok(guard, message_opt);
+// This statement is equivalent to assert.equal(true, !!guard,
+// message_opt);. To test strictly for the value true, use
+// assert.strictEqual(true, guard, message_opt);.
+
+function ok(value, message) {
+  if (!value) fail(value, true, message, '==', assert.ok);
+}
+assert.ok = ok;
+
+// 5. The equality assertion tests shallow, coercive equality with
+// ==.
+// assert.equal(actual, expected, message_opt);
+
+assert.equal = function equal(actual, expected, message) {
+  if (actual != expected) fail(actual, expected, message, '==', assert.equal);
+};
+
+// 6. The non-equality assertion tests for whether two objects are not equal
+// with != assert.notEqual(actual, expected, message_opt);
+
+assert.notEqual = function notEqual(actual, expected, message) {
+  if (actual == expected) {
+    fail(actual, expected, message, '!=', assert.notEqual);
+  }
+};
+
+// 7. The equivalence assertion tests a deep equality relation.
+// assert.deepEqual(actual, expected, message_opt);
+
+assert.deepEqual = function deepEqual(actual, expected, message) {
+  if (!_deepEqual(actual, expected)) {
+    fail(actual, expected, message, 'deepEqual', assert.deepEqual);
+  }
+};
+
+function _deepEqual(actual, expected) {
+  // 7.1. All identical values are equivalent, as determined by ===.
+  if (actual === expected) {
+    return true;
+
+  } else if (util.isBuffer(actual) && util.isBuffer(expected)) {
+    if (actual.length != expected.length) return false;
+
+    for (var i = 0; i < actual.length; i++) {
+      if (actual[i] !== expected[i]) return false;
+    }
+
+    return true;
+
+  // 7.2. If the expected value is a Date object, the actual value is
+  // equivalent if it is also a Date object that refers to the same time.
+  } else if (util.isDate(actual) && util.isDate(expected)) {
+    return actual.getTime() === expected.getTime();
+
+  // 7.3 If the expected value is a RegExp object, the actual value is
+  // equivalent if it is also a RegExp object with the same source and
+  // properties (`global`, `multiline`, `lastIndex`, `ignoreCase`).
+  } else if (util.isRegExp(actual) && util.isRegExp(expected)) {
+    return actual.source === expected.source &&
+           actual.global === expected.global &&
+           actual.multiline === expected.multiline &&
+           actual.lastIndex === expected.lastIndex &&
+           actual.ignoreCase === expected.ignoreCase;
+
+  // 7.4. Other pairs that do not both pass typeof value == 'object',
+  // equivalence is determined by ==.
+  } else if (!util.isObject(actual) && !util.isObject(expected)) {
+    return actual == expected;
+
+  // 7.5 For all other Object pairs, including Array objects, equivalence is
+  // determined by having the same number of owned properties (as verified
+  // with Object.prototype.hasOwnProperty.call), the same set of keys
+  // (although not necessarily the same order), equivalent values for every
+  // corresponding key, and an identical 'prototype' property. Note: this
+  // accounts for both named and indexed properties on Arrays.
+  } else {
+    return objEquiv(actual, expected);
+  }
+}
+
+function isArguments(object) {
+  return Object.prototype.toString.call(object) == '[object Arguments]';
+}
+
+function objEquiv(a, b) {
+  if (util.isNullOrUndefined(a) || util.isNullOrUndefined(b))
+    return false;
+  // an identical 'prototype' property.
+  if (a.prototype !== b.prototype) return false;
+  // if one is a primitive, the other must be same
+  if (util.isPrimitive(a) || util.isPrimitive(b)) {
+    return a === b;
+  }
+  var aIsArgs = isArguments(a),
+      bIsArgs = isArguments(b);
+  if ((aIsArgs && !bIsArgs) || (!aIsArgs && bIsArgs))
+    return false;
+  if (aIsArgs) {
+    a = pSlice.call(a);
+    b = pSlice.call(b);
+    return _deepEqual(a, b);
+  }
+  var ka = objectKeys(a),
+      kb = objectKeys(b),
+      key, i;
+  // having the same number of owned properties (keys incorporates
+  // hasOwnProperty)
+  if (ka.length != kb.length)
+    return false;
+  //the same set of keys (although not necessarily the same order),
+  ka.sort();
+  kb.sort();
+  //~~~cheap key test
+  for (i = ka.length - 1; i >= 0; i--) {
+    if (ka[i] != kb[i])
+      return false;
+  }
+  //equivalent values for every corresponding key, and
+  //~~~possibly expensive deep test
+  for (i = ka.length - 1; i >= 0; i--) {
+    key = ka[i];
+    if (!_deepEqual(a[key], b[key])) return false;
+  }
+  return true;
+}
+
+// 8. The non-equivalence assertion tests for any deep inequality.
+// assert.notDeepEqual(actual, expected, message_opt);
+
+assert.notDeepEqual = function notDeepEqual(actual, expected, message) {
+  if (_deepEqual(actual, expected)) {
+    fail(actual, expected, message, 'notDeepEqual', assert.notDeepEqual);
+  }
+};
+
+// 9. The strict equality assertion tests strict equality, as determined by ===.
+// assert.strictEqual(actual, expected, message_opt);
+
+assert.strictEqual = function strictEqual(actual, expected, message) {
+  if (actual !== expected) {
+    fail(actual, expected, message, '===', assert.strictEqual);
+  }
+};
+
+// 10. The strict non-equality assertion tests for strict inequality, as
+// determined by !==.  assert.notStrictEqual(actual, expected, message_opt);
+
+assert.notStrictEqual = function notStrictEqual(actual, expected, message) {
+  if (actual === expected) {
+    fail(actual, expected, message, '!==', assert.notStrictEqual);
+  }
+};
+
+function expectedException(actual, expected) {
+  if (!actual || !expected) {
+    return false;
+  }
+
+  if (Object.prototype.toString.call(expected) == '[object RegExp]') {
+    return expected.test(actual);
+  } else if (actual instanceof expected) {
+    return true;
+  } else if (expected.call({}, actual) === true) {
+    return true;
+  }
+
+  return false;
+}
+
+function _throws(shouldThrow, block, expected, message) {
+  var actual;
+
+  if (util.isString(expected)) {
+    message = expected;
+    expected = null;
+  }
+
+  try {
+    block();
+  } catch (e) {
+    actual = e;
+  }
+
+  message = (expected && expected.name ? ' (' + expected.name + ').' : '.') +
+            (message ? ' ' + message : '.');
+
+  if (shouldThrow && !actual) {
+    fail(actual, expected, 'Missing expected exception' + message);
+  }
+
+  if (!shouldThrow && expectedException(actual, expected)) {
+    fail(actual, expected, 'Got unwanted exception' + message);
+  }
+
+  if ((shouldThrow && actual && expected &&
+      !expectedException(actual, expected)) || (!shouldThrow && actual)) {
+    throw actual;
+  }
+}
+
+// 11. Expected to throw an error:
+// assert.throws(block, Error_opt, message_opt);
+
+assert.throws = function(block, /*optional*/error, /*optional*/message) {
+  _throws.apply(this, [true].concat(pSlice.call(arguments)));
+};
+
+// EXTENSION! This is annoying to write outside this module.
+assert.doesNotThrow = function(block, /*optional*/message) {
+  _throws.apply(this, [false].concat(pSlice.call(arguments)));
+};
+
+assert.ifError = function(err) { if (err) {throw err;}};
+
+var objectKeys = Object.keys || function (obj) {
+  var keys = [];
+  for (var key in obj) {
+    if (hasOwn.call(obj, key)) keys.push(key);
+  }
+  return keys;
+};
+
+},{"util/":28}],10:[function(require,module,exports){
+'use strict';
+module.exports = balanced;
+function balanced(a, b, str) {
+  if (a instanceof RegExp) a = maybeMatch(a, str);
+  if (b instanceof RegExp) b = maybeMatch(b, str);
+
+  var r = range(a, b, str);
+
+  return r && {
+    start: r[0],
+    end: r[1],
+    pre: str.slice(0, r[0]),
+    body: str.slice(r[0] + a.length, r[1]),
+    post: str.slice(r[1] + b.length)
+  };
+}
+
+function maybeMatch(reg, str) {
+  var m = str.match(reg);
+  return m ? m[0] : null;
+}
+
+balanced.range = range;
+function range(a, b, str) {
+  var begs, beg, left, right, result;
+  var ai = str.indexOf(a);
+  var bi = str.indexOf(b, ai + 1);
+  var i = ai;
+
+  if (ai >= 0 && bi > 0) {
+    begs = [];
+    left = str.length;
+
+    while (i >= 0 && !result) {
+      if (i == ai) {
+        begs.push(i);
+        ai = str.indexOf(a, i + 1);
+      } else if (begs.length == 1) {
+        result = [ begs.pop(), bi ];
+      } else {
+        beg = begs.pop();
+        if (beg < left) {
+          left = beg;
+          right = bi;
+        }
+
+        bi = str.indexOf(b, i + 1);
+      }
+
+      i = ai < bi && ai >= 0 ? ai : bi;
+    }
+
+    if (begs.length) {
+      result = [ left, right ];
+    }
+  }
+
+  return result;
+}
+
+},{}],11:[function(require,module,exports){
+var concatMap = require('concat-map');
+var balanced = require('balanced-match');
+
+module.exports = expandTop;
+
+var escSlash = '\0SLASH'+Math.random()+'\0';
+var escOpen = '\0OPEN'+Math.random()+'\0';
+var escClose = '\0CLOSE'+Math.random()+'\0';
+var escComma = '\0COMMA'+Math.random()+'\0';
+var escPeriod = '\0PERIOD'+Math.random()+'\0';
+
+function numeric(str) {
+  return parseInt(str, 10) == str
+    ? parseInt(str, 10)
+    : str.charCodeAt(0);
+}
+
+function escapeBraces(str) {
+  return str.split('\\\\').join(escSlash)
+            .split('\\{').join(escOpen)
+            .split('\\}').join(escClose)
+            .split('\\,').join(escComma)
+            .split('\\.').join(escPeriod);
+}
+
+function unescapeBraces(str) {
+  return str.split(escSlash).join('\\')
+            .split(escOpen).join('{')
+            .split(escClose).join('}')
+            .split(escComma).join(',')
+            .split(escPeriod).join('.');
+}
+
+
+// Basically just str.split(","), but handling cases
+// where we have nested braced sections, which should be
+// treated as individual members, like {a,{b,c},d}
+function parseCommaParts(str) {
+  if (!str)
+    return [''];
+
+  var parts = [];
+  var m = balanced('{', '}', str);
+
+  if (!m)
+    return str.split(',');
+
+  var pre = m.pre;
+  var body = m.body;
+  var post = m.post;
+  var p = pre.split(',');
+
+  p[p.length-1] += '{' + body + '}';
+  var postParts = parseCommaParts(post);
+  if (post.length) {
+    p[p.length-1] += postParts.shift();
+    p.push.apply(p, postParts);
+  }
+
+  parts.push.apply(parts, p);
+
+  return parts;
+}
+
+function expandTop(str) {
+  if (!str)
+    return [];
+
+  // I don't know why Bash 4.3 does this, but it does.
+  // Anything starting with {} will have the first two bytes preserved
+  // but *only* at the top level, so {},a}b will not expand to anything,
+  // but a{},b}c will be expanded to [a}c,abc].
+  // One could argue that this is a bug in Bash, but since the goal of
+  // this module is to match Bash's rules, we escape a leading {}
+  if (str.substr(0, 2) === '{}') {
+    str = '\\{\\}' + str.substr(2);
+  }
+
+  return expand(escapeBraces(str), true).map(unescapeBraces);
+}
+
+function identity(e) {
+  return e;
+}
+
+function embrace(str) {
+  return '{' + str + '}';
+}
+function isPadded(el) {
+  return /^-?0\d/.test(el);
+}
+
+function lte(i, y) {
+  return i <= y;
+}
+function gte(i, y) {
+  return i >= y;
+}
+
+function expand(str, isTop) {
+  var expansions = [];
+
+  var m = balanced('{', '}', str);
+  if (!m || /\$$/.test(m.pre)) return [str];
+
+  var isNumericSequence = /^-?\d+\.\.-?\d+(?:\.\.-?\d+)?$/.test(m.body);
+  var isAlphaSequence = /^[a-zA-Z]\.\.[a-zA-Z](?:\.\.-?\d+)?$/.test(m.body);
+  var isSequence = isNumericSequence || isAlphaSequence;
+  var isOptions = m.body.indexOf(',') >= 0;
+  if (!isSequence && !isOptions) {
+    // {a},b}
+    if (m.post.match(/,.*\}/)) {
+      str = m.pre + '{' + m.body + escClose + m.post;
+      return expand(str);
+    }
+    return [str];
+  }
+
+  var n;
+  if (isSequence) {
+    n = m.body.split(/\.\./);
+  } else {
+    n = parseCommaParts(m.body);
+    if (n.length === 1) {
+      // x{{a,b}}y ==> x{a}y x{b}y
+      n = expand(n[0], false).map(embrace);
+      if (n.length === 1) {
+        var post = m.post.length
+          ? expand(m.post, false)
+          : [''];
+        return post.map(function(p) {
+          return m.pre + n[0] + p;
+        });
+      }
+    }
+  }
+
+  // at this point, n is the parts, and we know it's not a comma set
+  // with a single entry.
+
+  // no need to expand pre, since it is guaranteed to be free of brace-sets
+  var pre = m.pre;
+  var post = m.post.length
+    ? expand(m.post, false)
+    : [''];
+
+  var N;
+
+  if (isSequence) {
+    var x = numeric(n[0]);
+    var y = numeric(n[1]);
+    var width = Math.max(n[0].length, n[1].length)
+    var incr = n.length == 3
+      ? Math.abs(numeric(n[2]))
+      : 1;
+    var test = lte;
+    var reverse = y < x;
+    if (reverse) {
+      incr *= -1;
+      test = gte;
+    }
+    var pad = n.some(isPadded);
+
+    N = [];
+
+    for (var i = x; test(i, y); i += incr) {
+      var c;
+      if (isAlphaSequence) {
+        c = String.fromCharCode(i);
+        if (c === '\\')
+          c = '';
+      } else {
+        c = String(i);
+        if (pad) {
+          var need = width - c.length;
+          if (need > 0) {
+            var z = new Array(need + 1).join('0');
+            if (i < 0)
+              c = '-' + z + c.slice(1);
+            else
+              c = z + c;
+          }
+        }
+      }
+      N.push(c);
+    }
+  } else {
+    N = concatMap(n, function(el) { return expand(el, false) });
+  }
+
+  for (var j = 0; j < N.length; j++) {
+    for (var k = 0; k < post.length; k++) {
+      var expansion = pre + N[j] + post[k];
+      if (!isTop || isSequence || expansion)
+        expansions.push(expansion);
+    }
+  }
+
+  return expansions;
+}
+
+
+},{"balanced-match":10,"concat-map":13}],12:[function(require,module,exports){
+
+},{}],13:[function(require,module,exports){
+module.exports = function (xs, fn) {
+    var res = [];
+    for (var i = 0; i < xs.length; i++) {
+        var x = fn(xs[i], i);
+        if (isArray(x)) res.push.apply(res, x);
+        else res.push(x);
+    }
+    return res;
+};
+
+var isArray = Array.isArray || function (xs) {
+    return Object.prototype.toString.call(xs) === '[object Array]';
+};
+
+},{}],14:[function(require,module,exports){
+// Copyright Joyent, Inc. and other Node contributors.
+//
+// Permission is hereby granted, free of charge, to any person obtaining a
+// copy of this software and associated documentation files (the
+// "Software"), to deal in the Software without restriction, including
+// without limitation the rights to use, copy, modify, merge, publish,
+// distribute, sublicense, and/or sell copies of the Software, and to permit
+// persons to whom the Software is furnished to do so, subject to the
+// following conditions:
+//
+// The above copyright notice and this permission notice shall be included
+// in all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+// MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN
+// NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
+// DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
+// OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
+// USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+function EventEmitter() {
+  this._events = this._events || {};
+  this._maxListeners = this._maxListeners || undefined;
+}
+module.exports = EventEmitter;
+
+// Backwards-compat with node 0.10.x
+EventEmitter.EventEmitter = EventEmitter;
+
+EventEmitter.prototype._events = undefined;
+EventEmitter.prototype._maxListeners = undefined;
+
+// By default EventEmitters will print a warning if more than 10 listeners are
+// added to it. This is a useful default which helps finding memory leaks.
+EventEmitter.defaultMaxListeners = 10;
+
+// Obviously not all Emitters should be limited to 10. This function allows
+// that to be increased. Set to zero for unlimited.
+EventEmitter.prototype.setMaxListeners = function(n) {
+  if (!isNumber(n) || n < 0 || isNaN(n))
+    throw TypeError('n must be a positive number');
+  this._maxListeners = n;
+  return this;
+};
+
+EventEmitter.prototype.emit = function(type) {
+  var er, handler, len, args, i, listeners;
+
+  if (!this._events)
+    this._events = {};
+
+  // If there is no 'error' event listener then throw.
+  if (type === 'error') {
+    if (!this._events.error ||
+        (isObject(this._events.error) && !this._events.error.length)) {
+      er = arguments[1];
+      if (er instanceof Error) {
+        throw er; // Unhandled 'error' event
+      }
+      throw TypeError('Uncaught, unspecified "error" event.');
+    }
+  }
+
+  handler = this._events[type];
+
+  if (isUndefined(handler))
+    return false;
+
+  if (isFunction(handler)) {
+    switch (arguments.length) {
+      // fast cases
+      case 1:
+        handler.call(this);
+        break;
+      case 2:
+        handler.call(this, arguments[1]);
+        break;
+      case 3:
+        handler.call(this, arguments[1], arguments[2]);
+        break;
+      // slower
+      default:
+        len = arguments.length;
+        args = new Array(len - 1);
+        for (i = 1; i < len; i++)
+          args[i - 1] = arguments[i];
+        handler.apply(this, args);
+    }
+  } else if (isObject(handler)) {
+    len = arguments.length;
+    args = new Array(len - 1);
+    for (i = 1; i < len; i++)
+      args[i - 1] = arguments[i];
+
+    listeners = handler.slice();
+    len = listeners.length;
+    for (i = 0; i < len; i++)
+      listeners[i].apply(this, args);
+  }
+
+  return true;
+};
+
+EventEmitter.prototype.addListener = function(type, listener) {
+  var m;
+
+  if (!isFunction(listener))
+    throw TypeError('listener must be a function');
+
+  if (!this._events)
+    this._events = {};
+
+  // To avoid recursion in the case that type === "newListener"! Before
+  // adding it to the listeners, first emit "newListener".
+  if (this._events.newListener)
+    this.emit('newListener', type,
+              isFunction(listener.listener) ?
+              listener.listener : listener);
+
+  if (!this._events[type])
+    // Optimize the case of one listener. Don't need the extra array object.
+    this._events[type] = listener;
+  else if (isObject(this._events[type]))
+    // If we've already got an array, just append.
+    this._events[type].push(listener);
+  else
+    // Adding the second element, need to change to array.
+    this._events[type] = [this._events[type], listener];
+
+  // Check for listener leak
+  if (isObject(this._events[type]) && !this._events[type].warned) {
+    var m;
+    if (!isUndefined(this._maxListeners)) {
+      m = this._maxListeners;
+    } else {
+      m = EventEmitter.defaultMaxListeners;
+    }
+
+    if (m && m > 0 && this._events[type].length > m) {
+      this._events[type].warned = true;
+      console.error('(node) warning: possible EventEmitter memory ' +
+                    'leak detected. %d listeners added. ' +
+                    'Use emitter.setMaxListeners() to increase limit.',
+                    this._events[type].length);
+      if (typeof console.trace === 'function') {
+        // not supported in IE 10
+        console.trace();
+      }
+    }
+  }
+
+  return this;
+};
+
+EventEmitter.prototype.on = EventEmitter.prototype.addListener;
+
+EventEmitter.prototype.once = function(type, listener) {
+  if (!isFunction(listener))
+    throw TypeError('listener must be a function');
+
+  var fired = false;
+
+  function g() {
+    this.removeListener(type, g);
+
+    if (!fired) {
+      fired = true;
+      listener.apply(this, arguments);
+    }
+  }
+
+  g.listener = listener;
+  this.on(type, g);
+
+  return this;
+};
+
+// emits a 'removeListener' event iff the listener was removed
+EventEmitter.prototype.removeListener = function(type, listener) {
+  var list, position, length, i;
+
+  if (!isFunction(listener))
+    throw TypeError('listener must be a function');
+
+  if (!this._events || !this._events[type])
+    return this;
+
+  list = this._events[type];
+  length = list.length;
+  position = -1;
+
+  if (list === listener ||
+      (isFunction(list.listener) && list.listener === listener)) {
+    delete this._events[type];
+    if (this._events.removeListener)
+      this.emit('removeListener', type, listener);
+
+  } else if (isObject(list)) {
+    for (i = length; i-- > 0;) {
+      if (list[i] === listener ||
+          (list[i].listener && list[i].listener === listener)) {
+        position = i;
+        break;
+      }
+    }
+
+    if (position < 0)
+      return this;
+
+    if (list.length === 1) {
+      list.length = 0;
+      delete this._events[type];
+    } else {
+      list.splice(position, 1);
+    }
+
+    if (this._events.removeListener)
+      this.emit('removeListener', type, listener);
+  }
+
+  return this;
+};
+
+EventEmitter.prototype.removeAllListeners = function(type) {
+  var key, listeners;
+
+  if (!this._events)
+    return this;
+
+  // not listening for removeListener, no need to emit
+  if (!this._events.removeListener) {
+    if (arguments.length === 0)
+      this._events = {};
+    else if (this._events[type])
+      delete this._events[type];
+    return this;
+  }
+
+  // emit removeListener for all listeners on all events
+  if (arguments.length === 0) {
+    for (key in this._events) {
+      if (key === 'removeListener') continue;
+      this.removeAllListeners(key);
+    }
+    this.removeAllListeners('removeListener');
+    this._events = {};
+    return this;
+  }
+
+  listeners = this._events[type];
+
+  if (isFunction(listeners)) {
+    this.removeListener(type, listeners);
+  } else {
+    // LIFO order
+    while (listeners.length)
+      this.removeListener(type, listeners[listeners.length - 1]);
+  }
+  delete this._events[type];
+
+  return this;
+};
+
+EventEmitter.prototype.listeners = function(type) {
+  var ret;
+  if (!this._events || !this._events[type])
+    ret = [];
+  else if (isFunction(this._events[type]))
+    ret = [this._events[type]];
+  else
+    ret = this._events[type].slice();
+  return ret;
+};
+
+EventEmitter.listenerCount = function(emitter, type) {
+  var ret;
+  if (!emitter._events || !emitter._events[type])
+    ret = 0;
+  else if (isFunction(emitter._events[type]))
+    ret = 1;
+  else
+    ret = emitter._events[type].length;
+  return ret;
+};
+
+function isFunction(arg) {
+  return typeof arg === 'function';
+}
+
+function isNumber(arg) {
+  return typeof arg === 'number';
+}
+
+function isObject(arg) {
+  return typeof arg === 'object' && arg !== null;
+}
+
+function isUndefined(arg) {
+  return arg === void 0;
+}
+
+},{}],15:[function(require,module,exports){
+(function (process){
+exports.alphasort = alphasort
+exports.alphasorti = alphasorti
+exports.setopts = setopts
+exports.ownProp = ownProp
+exports.makeAbs = makeAbs
+exports.finish = finish
+exports.mark = mark
+exports.isIgnored = isIgnored
+exports.childrenIgnored = childrenIgnored
+
+function ownProp (obj, field) {
+  return Object.prototype.hasOwnProperty.call(obj, field)
+}
+
+var path = require("path")
+var minimatch = require("minimatch")
+var isAbsolute = require("path-is-absolute")
+var Minimatch = minimatch.Minimatch
+
+function alphasorti (a, b) {
+  return a.toLowerCase().localeCompare(b.toLowerCase())
+}
+
+function alphasort (a, b) {
+  return a.localeCompare(b)
+}
+
+function setupIgnores (self, options) {
+  self.ignore = options.ignore || []
+
+  if (!Array.isArray(self.ignore))
+    self.ignore = [self.ignore]
+
+  if (self.ignore.length) {
+    self.ignore = self.ignore.map(ignoreMap)
+  }
+}
+
+function ignoreMap (pattern) {
+  var gmatcher = null
+  if (pattern.slice(-3) === '/**') {
+    var gpattern = pattern.replace(/(\/\*\*)+$/, '')
+    gmatcher = new Minimatch(gpattern)
+  }
+
+  return {
+    matcher: new Minimatch(pattern),
+    gmatcher: gmatcher
+  }
+}
+
+function setopts (self, pattern, options) {
+  if (!options)
+    options = {}
+
+  // base-matching: just use globstar for that.
+  if (options.matchBase && -1 === pattern.indexOf("/")) {
+    if (options.noglobstar) {
+      throw new Error("base matching requires globstar")
+    }
+    pattern = "**/" + pattern
+  }
+
+  self.silent = !!options.silent
+  self.pattern = pattern
+  self.strict = options.strict !== false
+  self.realpath = !!options.realpath
+  self.realpathCache = options.realpathCache || Object.create(null)
+  self.follow = !!options.follow
+  self.dot = !!options.dot
+  self.mark = !!options.mark
+  self.nodir = !!options.nodir
+  if (self.nodir)
+    self.mark = true
+  self.sync = !!options.sync
+  self.nounique = !!options.nounique
+  self.nonull = !!options.nonull
+  self.nosort = !!options.nosort
+  self.nocase = !!options.nocase
+  self.stat = !!options.stat
+  self.noprocess = !!options.noprocess
+
+  self.maxLength = options.maxLength || Infinity
+  self.cache = options.cache || Object.create(null)
+  self.statCache = options.statCache || Object.create(null)
+  self.symlinks = options.symlinks || Object.create(null)
+
+  setupIgnores(self, options)
+
+  self.changedCwd = false
+  var cwd = process.cwd()
+  if (!ownProp(options, "cwd"))
+    self.cwd = cwd
+  else {
+    self.cwd = options.cwd
+    self.changedCwd = path.resolve(options.cwd) !== cwd
+  }
+
+  self.root = options.root || path.resolve(self.cwd, "/")
+  self.root = path.resolve(self.root)
+  if (process.platform === "win32")
+    self.root = self.root.replace(/\\/g, "/")
+
+  self.nomount = !!options.nomount
+
+  // disable comments and negation unless the user explicitly
+  // passes in false as the option.
+  options.nonegate = options.nonegate === false ? false : true
+  options.nocomment = options.nocomment === false ? false : true
+  deprecationWarning(options)
+
+  self.minimatch = new Minimatch(pattern, options)
+  self.options = self.minimatch.options
+}
+
+// TODO(isaacs): remove entirely in v6
+// exported to reset in tests
+exports.deprecationWarned
+function deprecationWarning(options) {
+  if (!options.nonegate || !options.nocomment) {
+    if (process.noDeprecation !== true && !exports.deprecationWarned) {
+      var msg = 'glob WARNING: comments and negation will be disabled in v6'
+      if (process.throwDeprecation)
+        throw new Error(msg)
+      else if (process.traceDeprecation)
+        console.trace(msg)
+      else
+        console.error(msg)
+
+      exports.deprecationWarned = true
+    }
+  }
+}
+
+function finish (self) {
+  var nou = self.nounique
+  var all = nou ? [] : Object.create(null)
+
+  for (var i = 0, l = self.matches.length; i < l; i ++) {
+    var matches = self.matches[i]
+    if (!matches || Object.keys(matches).length === 0) {
+      if (self.nonull) {
+        // do like the shell, and spit out the literal glob
+        var literal = self.minimatch.globSet[i]
+        if (nou)
+          all.push(literal)
+        else
+          all[literal] = true
+      }
+    } else {
+      // had matches
+      var m = Object.keys(matches)
+      if (nou)
+        all.push.apply(all, m)
+      else
+        m.forEach(function (m) {
+          all[m] = true
+        })
+    }
+  }
+
+  if (!nou)
+    all = Object.keys(all)
+
+  if (!self.nosort)
+    all = all.sort(self.nocase ? alphasorti : alphasort)
+
+  // at *some* point we statted all of these
+  if (self.mark) {
+    for (var i = 0; i < all.length; i++) {
+      all[i] = self._mark(all[i])
+    }
+    if (self.nodir) {
+      all = all.filter(function (e) {
+        return !(/\/$/.test(e))
+      })
+    }
+  }
+
+  if (self.ignore.length)
+    all = all.filter(function(m) {
+      return !isIgnored(self, m)
+    })
+
+  self.found = all
+}
+
+function mark (self, p) {
+  var abs = makeAbs(self, p)
+  var c = self.cache[abs]
+  var m = p
+  if (c) {
+    var isDir = c === 'DIR' || Array.isArray(c)
+    var slash = p.slice(-1) === '/'
+
+    if (isDir && !slash)
+      m += '/'
+    else if (!isDir && slash)
+      m = m.slice(0, -1)
+
+    if (m !== p) {
+      var mabs = makeAbs(self, m)
+      self.statCache[mabs] = self.statCache[abs]
+      self.cache[mabs] = self.cache[abs]
+    }
+  }
+
+  return m
+}
+
+// lotta situps...
+function makeAbs (self, f) {
+  var abs = f
+  if (f.charAt(0) === '/') {
+    abs = path.join(self.root, f)
+  } else if (isAbsolute(f) || f === '') {
+    abs = f
+  } else if (self.changedCwd) {
+    abs = path.resolve(self.cwd, f)
+  } else {
+    abs = path.resolve(f)
+  }
+  return abs
+}
+
+
+// Return true, if pattern ends with globstar '**', for the accompanying parent directory.
+// Ex:- If node_modules/** is the pattern, add 'node_modules' to ignore list along with it's contents
+function isIgnored (self, path) {
+  if (!self.ignore.length)
+    return false
+
+  return self.ignore.some(function(item) {
+    return item.matcher.match(path) || !!(item.gmatcher && item.gmatcher.match(path))
+  })
+}
+
+function childrenIgnored (self, path) {
+  if (!self.ignore.length)
+    return false
+
+  return self.ignore.some(function(item) {
+    return !!(item.gmatcher && item.gmatcher.match(path))
+  })
+}
+
+}).call(this,require('_process'))
+},{"_process":24,"minimatch":20,"path":22,"path-is-absolute":23}],16:[function(require,module,exports){
+(function (process){
+// Approach:
+//
+// 1. Get the minimatch set
+// 2. For each pattern in the set, PROCESS(pattern, false)
+// 3. Store matches per-set, then uniq them
+//
+// PROCESS(pattern, inGlobStar)
+// Get the first [n] items from pattern that are all strings
+// Join these together.  This is PREFIX.
+//   If there is no more remaining, then stat(PREFIX) and
+//   add to matches if it succeeds.  END.
+//
+// If inGlobStar and PREFIX is symlink and points to dir
+//   set ENTRIES = []
+// else readdir(PREFIX) as ENTRIES
+//   If fail, END
+//
+// with ENTRIES
+//   If pattern[n] is GLOBSTAR
+//     // handle the case where the globstar match is empty
+//     // by pruning it out, and testing the resulting pattern
+//     PROCESS(pattern[0..n] + pattern[n+1 .. $], false)
+//     // handle other cases.
+//     for ENTRY in ENTRIES (not dotfiles)
+//       // attach globstar + tail onto the entry
+//       // Mark that this entry is a globstar match
+//       PROCESS(pattern[0..n] + ENTRY + pattern[n .. $], true)
+//
+//   else // not globstar
+//     for ENTRY in ENTRIES (not dotfiles, unless pattern[n] is dot)
+//       Test ENTRY against pattern[n]
+//       If fails, continue
+//       If passes, PROCESS(pattern[0..n] + item + pattern[n+1 .. $])
+//
+// Caveat:
+//   Cache all stats and readdirs results to minimize syscall.  Since all
+//   we ever care about is existence and directory-ness, we can just keep
+//   `true` for files, and [children,...] for directories, or `false` for
+//   things that don't exist.
+
+module.exports = glob
+
+var fs = require('fs')
+var minimatch = require('minimatch')
+var Minimatch = minimatch.Minimatch
+var inherits = require('inherits')
+var EE = require('events').EventEmitter
+var path = require('path')
+var assert = require('assert')
+var isAbsolute = require('path-is-absolute')
+var globSync = require('./sync.js')
+var common = require('./common.js')
+var alphasort = common.alphasort
+var alphasorti = common.alphasorti
+var setopts = common.setopts
+var ownProp = common.ownProp
+var inflight = require('inflight')
+var util = require('util')
+var childrenIgnored = common.childrenIgnored
+var isIgnored = common.isIgnored
+
+var once = require('once')
+
+function glob (pattern, options, cb) {
+  if (typeof options === 'function') cb = options, options = {}
+  if (!options) options = {}
+
+  if (options.sync) {
+    if (cb)
+      throw new TypeError('callback provided to sync glob')
+    return globSync(pattern, options)
+  }
+
+  return new Glob(pattern, options, cb)
+}
+
+glob.sync = globSync
+var GlobSync = glob.GlobSync = globSync.GlobSync
+
+// old api surface
+glob.glob = glob
+
+glob.hasMagic = function (pattern, options_) {
+  var options = util._extend({}, options_)
+  options.noprocess = true
+
+  var g = new Glob(pattern, options)
+  var set = g.minimatch.set
+  if (set.length > 1)
+    return true
+
+  for (var j = 0; j < set[0].length; j++) {
+    if (typeof set[0][j] !== 'string')
+      return true
+  }
+
+  return false
+}
+
+glob.Glob = Glob
+inherits(Glob, EE)
+function Glob (pattern, options, cb) {
+  if (typeof options === 'function') {
+    cb = options
+    options = null
+  }
+
+  if (options && options.sync) {
+    if (cb)
+      throw new TypeError('callback provided to sync glob')
+    return new GlobSync(pattern, options)
+  }
+
+  if (!(this instanceof Glob))
+    return new Glob(pattern, options, cb)
+
+  setopts(this, pattern, options)
+  this._didRealPath = false
+
+  // process each pattern in the minimatch set
+  var n = this.minimatch.set.length
+
+  // The matches are stored as {<filename>: true,...} so that
+  // duplicates are automagically pruned.
+  // Later, we do an Object.keys() on these.
+  // Keep them as a list so we can fill in when nonull is set.
+  this.matches = new Array(n)
+
+  if (typeof cb === 'function') {
+    cb = once(cb)
+    this.on('error', cb)
+    this.on('end', function (matches) {
+      cb(null, matches)
+    })
+  }
+
+  var self = this
+  var n = this.minimatch.set.length
+  this._processing = 0
+  this.matches = new Array(n)
+
+  this._emitQueue = []
+  this._processQueue = []
+  this.paused = false
+
+  if (this.noprocess)
+    return this
+
+  if (n === 0)
+    return done()
+
+  for (var i = 0; i < n; i ++) {
+    this._process(this.minimatch.set[i], i, false, done)
+  }
+
+  function done () {
+    --self._processing
+    if (self._processing <= 0)
+      self._finish()
+  }
+}
+
+Glob.prototype._finish = function () {
+  assert(this instanceof Glob)
+  if (this.aborted)
+    return
+
+  if (this.realpath && !this._didRealpath)
+    return this._realpath()
+
+  common.finish(this)
+  this.emit('end', this.found)
+}
+
+Glob.prototype._realpath = function () {
+  if (this._didRealpath)
+    return
+
+  this._didRealpath = true
+
+  var n = this.matches.length
+  if (n === 0)
+    return this._finish()
+
+  var self = this
+  for (var i = 0; i < this.matches.length; i++)
+    this._realpathSet(i, next)
+
+  function next () {
+    if (--n === 0)
+      self._finish()
+  }
+}
+
+Glob.prototype._realpathSet = function (index, cb) {
+  var matchset = this.matches[index]
+  if (!matchset)
+    return cb()
+
+  var found = Object.keys(matchset)
+  var self = this
+  var n = found.length
+
+  if (n === 0)
+    return cb()
+
+  var set = this.matches[index] = Object.create(null)
+  found.forEach(function (p, i) {
+    // If there's a problem with the stat, then it means that
+    // one or more of the links in the realpath couldn't be
+    // resolved.  just return the abs value in that case.
+    p = self._makeAbs(p)
+    fs.realpath(p, self.realpathCache, function (er, real) {
+      if (!er)
+        set[real] = true
+      else if (er.syscall === 'stat')
+        set[p] = true
+      else
+        self.emit('error', er) // srsly wtf right here
+
+      if (--n === 0) {
+        self.matches[index] = set
+        cb()
+      }
+    })
+  })
+}
+
+Glob.prototype._mark = function (p) {
+  return common.mark(this, p)
+}
+
+Glob.prototype._makeAbs = function (f) {
+  return common.makeAbs(this, f)
+}
+
+Glob.prototype.abort = function () {
+  this.aborted = true
+  this.emit('abort')
+}
+
+Glob.prototype.pause = function () {
+  if (!this.paused) {
+    this.paused = true
+    this.emit('pause')
+  }
+}
+
+Glob.prototype.resume = function () {
+  if (this.paused) {
+    this.emit('resume')
+    this.paused = false
+    if (this._emitQueue.length) {
+      var eq = this._emitQueue.slice(0)
+      this._emitQueue.length = 0
+      for (var i = 0; i < eq.length; i ++) {
+        var e = eq[i]
+        this._emitMatch(e[0], e[1])
+      }
+    }
+    if (this._processQueue.length) {
+      var pq = this._processQueue.slice(0)
+      this._processQueue.length = 0
+      for (var i = 0; i < pq.length; i ++) {
+        var p = pq[i]
+        this._processing--
+        this._process(p[0], p[1], p[2], p[3])
+      }
+    }
+  }
+}
+
+Glob.prototype._process = function (pattern, index, inGlobStar, cb) {
+  assert(this instanceof Glob)
+  assert(typeof cb === 'function')
+
+  if (this.aborted)
+    return
+
+  this._processing++
+  if (this.paused) {
+    this._processQueue.push([pattern, index, inGlobStar, cb])
+    return
+  }
+
+  //console.error('PROCESS %d', this._processing, pattern)
+
+  // Get the first [n] parts of pattern that are all strings.
+  var n = 0
+  while (typeof pattern[n] === 'string') {
+    n ++
+  }
+  // now n is the index of the first one that is *not* a string.
+
+  // see if there's anything else
+  var prefix
+  switch (n) {
+    // if not, then this is rather simple
+    case pattern.length:
+      this._processSimple(pattern.join('/'), index, cb)
+      return
+
+    case 0:
+      // pattern *starts* with some non-trivial item.
+      // going to readdir(cwd), but not include the prefix in matches.
+      prefix = null
+      break
+
+    default:
+      // pattern has some string bits in the front.
+      // whatever it starts with, whether that's 'absolute' like /foo/bar,
+      // or 'relative' like '../baz'
+      prefix = pattern.slice(0, n).join('/')
+      break
+  }
+
+  var remain = pattern.slice(n)
+
+  // get the list of entries.
+  var read
+  if (prefix === null)
+    read = '.'
+  else if (isAbsolute(prefix) || isAbsolute(pattern.join('/'))) {
+    if (!prefix || !isAbsolute(prefix))
+      prefix = '/' + prefix
+    read = prefix
+  } else
+    read = prefix
+
+  var abs = this._makeAbs(read)
+
+  //if ignored, skip _processing
+  if (childrenIgnored(this, read))
+    return cb()
+
+  var isGlobStar = remain[0] === minimatch.GLOBSTAR
+  if (isGlobStar)
+    this._processGlobStar(prefix, read, abs, remain, index, inGlobStar, cb)
+  else
+    this._processReaddir(prefix, read, abs, remain, index, inGlobStar, cb)
+}
+
+Glob.prototype._processReaddir = function (prefix, read, abs, remain, index, inGlobStar, cb) {
+  var self = this
+  this._readdir(abs, inGlobStar, function (er, entries) {
+    return self._processReaddir2(prefix, read, abs, remain, index, inGlobStar, entries, cb)
+  })
+}
+
+Glob.prototype._processReaddir2 = function (prefix, read, abs, remain, index, inGlobStar, entries, cb) {
+
+  // if the abs isn't a dir, then nothing can match!
+  if (!entries)
+    return cb()
+
+  // It will only match dot entries if it starts with a dot, or if
+  // dot is set.  Stuff like @(.foo|.bar) isn't allowed.
+  var pn = remain[0]
+  var negate = !!this.minimatch.negate
+  var rawGlob = pn._glob
+  var dotOk = this.dot || rawGlob.charAt(0) === '.'
+
+  var matchedEntries = []
+  for (var i = 0; i < entries.length; i++) {
+    var e = entries[i]
+    if (e.charAt(0) !== '.' || dotOk) {
+      var m
+      if (negate && !prefix) {
+        m = !e.match(pn)
+      } else {
+        m = e.match(pn)
+      }
+      if (m)
+        matchedEntries.push(e)
+    }
+  }
+
+  //console.error('prd2', prefix, entries, remain[0]._glob, matchedEntries)
+
+  var len = matchedEntries.length
+  // If there are no matched entries, then nothing matches.
+  if (len === 0)
+    return cb()
+
+  // if this is the last remaining pattern bit, then no need for
+  // an additional stat *unless* the user has specified mark or
+  // stat explicitly.  We know they exist, since readdir returned
+  // them.
+
+  if (remain.length === 1 && !this.mark && !this.stat) {
+    if (!this.matches[index])
+      this.matches[index] = Object.create(null)
+
+    for (var i = 0; i < len; i ++) {
+      var e = matchedEntries[i]
+      if (prefix) {
+        if (prefix !== '/')
+          e = prefix + '/' + e
+        else
+          e = prefix + e
+      }
+
+      if (e.charAt(0) === '/' && !this.nomount) {
+        e = path.join(this.root, e)
+      }
+      this._emitMatch(index, e)
+    }
+    // This was the last one, and no stats were needed
+    return cb()
+  }
+
+  // now test all matched entries as stand-ins for that part
+  // of the pattern.
+  remain.shift()
+  for (var i = 0; i < len; i ++) {
+    var e = matchedEntries[i]
+    var newPattern
+    if (prefix) {
+      if (prefix !== '/')
+        e = prefix + '/' + e
+      else
+        e = prefix + e
+    }
+    this._process([e].concat(remain), index, inGlobStar, cb)
+  }
+  cb()
+}
+
+Glob.prototype._emitMatch = function (index, e) {
+  if (this.aborted)
+    return
+
+  if (this.matches[index][e])
+    return
+
+  if (isIgnored(this, e))
+    return
+
+  if (this.paused) {
+    this._emitQueue.push([index, e])
+    return
+  }
+
+  var abs = this._makeAbs(e)
+
+  if (this.nodir) {
+    var c = this.cache[abs]
+    if (c === 'DIR' || Array.isArray(c))
+      return
+  }
+
+  if (this.mark)
+    e = this._mark(e)
+
+  this.matches[index][e] = true
+
+  var st = this.statCache[abs]
+  if (st)
+    this.emit('stat', e, st)
+
+  this.emit('match', e)
+}
+
+Glob.prototype._readdirInGlobStar = function (abs, cb) {
+  if (this.aborted)
+    return
+
+  // follow all symlinked directories forever
+  // just proceed as if this is a non-globstar situation
+  if (this.follow)
+    return this._readdir(abs, false, cb)
+
+  var lstatkey = 'lstat\0' + abs
+  var self = this
+  var lstatcb = inflight(lstatkey, lstatcb_)
+
+  if (lstatcb)
+    fs.lstat(abs, lstatcb)
+
+  function lstatcb_ (er, lstat) {
+    if (er)
+      return cb()
+
+    var isSym = lstat.isSymbolicLink()
+    self.symlinks[abs] = isSym
+
+    // If it's not a symlink or a dir, then it's definitely a regular file.
+    // don't bother doing a readdir in that case.
+    if (!isSym && !lstat.isDirectory()) {
+      self.cache[abs] = 'FILE'
+      cb()
+    } else
+      self._readdir(abs, false, cb)
+  }
+}
+
+Glob.prototype._readdir = function (abs, inGlobStar, cb) {
+  if (this.aborted)
+    return
+
+  cb = inflight('readdir\0'+abs+'\0'+inGlobStar, cb)
+  if (!cb)
+    return
+
+  //console.error('RD %j %j', +inGlobStar, abs)
+  if (inGlobStar && !ownProp(this.symlinks, abs))
+    return this._readdirInGlobStar(abs, cb)
+
+  if (ownProp(this.cache, abs)) {
+    var c = this.cache[abs]
+    if (!c || c === 'FILE')
+      return cb()
+
+    if (Array.isArray(c))
+      return cb(null, c)
+  }
+
+  var self = this
+  fs.readdir(abs, readdirCb(this, abs, cb))
+}
+
+function readdirCb (self, abs, cb) {
+  return function (er, entries) {
+    if (er)
+      self._readdirError(abs, er, cb)
+    else
+      self._readdirEntries(abs, entries, cb)
+  }
+}
+
+Glob.prototype._readdirEntries = function (abs, entries, cb) {
+  if (this.aborted)
+    return
+
+  // if we haven't asked to stat everything, then just
+  // assume that everything in there exists, so we can avoid
+  // having to stat it a second time.
+  if (!this.mark && !this.stat) {
+    for (var i = 0; i < entries.length; i ++) {
+      var e = entries[i]
+      if (abs === '/')
+        e = abs + e
+      else
+        e = abs + '/' + e
+      this.cache[e] = true
+    }
+  }
+
+  this.cache[abs] = entries
+  return cb(null, entries)
+}
+
+Glob.prototype._readdirError = function (f, er, cb) {
+  if (this.aborted)
+    return
+
+  // handle errors, and cache the information
+  switch (er.code) {
+    case 'ENOTSUP': // https://github.com/isaacs/node-glob/issues/205
+    case 'ENOTDIR': // totally normal. means it *does* exist.
+      this.cache[this._makeAbs(f)] = 'FILE'
+      break
+
+    case 'ENOENT': // not terribly unusual
+    case 'ELOOP':
+    case 'ENAMETOOLONG':
+    case 'UNKNOWN':
+      this.cache[this._makeAbs(f)] = false
+      break
+
+    default: // some unusual error.  Treat as failure.
+      this.cache[this._makeAbs(f)] = false
+      if (this.strict) {
+        this.emit('error', er)
+        // If the error is handled, then we abort
+        // if not, we threw out of here
+        this.abort()
+      }
+      if (!this.silent)
+        console.error('glob error', er)
+      break
+  }
+
+  return cb()
+}
+
+Glob.prototype._processGlobStar = function (prefix, read, abs, remain, index, inGlobStar, cb) {
+  var self = this
+  this._readdir(abs, inGlobStar, function (er, entries) {
+    self._processGlobStar2(prefix, read, abs, remain, index, inGlobStar, entries, cb)
+  })
+}
+
+
+Glob.prototype._processGlobStar2 = function (prefix, read, abs, remain, index, inGlobStar, entries, cb) {
+  //console.error('pgs2', prefix, remain[0], entries)
+
+  // no entries means not a dir, so it can never have matches
+  // foo.txt/** doesn't match foo.txt
+  if (!entries)
+    return cb()
+
+  // test without the globstar, and with every child both below
+  // and replacing the globstar.
+  var remainWithoutGlobStar = remain.slice(1)
+  var gspref = prefix ? [ prefix ] : []
+  var noGlobStar = gspref.concat(remainWithoutGlobStar)
+
+  // the noGlobStar pattern exits the inGlobStar state
+  this._process(noGlobStar, index, false, cb)
+
+  var isSym = this.symlinks[abs]
+  var len = entries.length
+
+  // If it's a symlink, and we're in a globstar, then stop
+  if (isSym && inGlobStar)
+    return cb()
+
+  for (var i = 0; i < len; i++) {
+    var e = entries[i]
+    if (e.charAt(0) === '.' && !this.dot)
+      continue
+
+    // these two cases enter the inGlobStar state
+    var instead = gspref.concat(entries[i], remainWithoutGlobStar)
+    this._process(instead, index, true, cb)
+
+    var below = gspref.concat(entries[i], remain)
+    this._process(below, index, true, cb)
+  }
+
+  cb()
+}
+
+Glob.prototype._processSimple = function (prefix, index, cb) {
+  // XXX review this.  Shouldn't it be doing the mounting etc
+  // before doing stat?  kinda weird?
+  var self = this
+  this._stat(prefix, function (er, exists) {
+    self._processSimple2(prefix, index, er, exists, cb)
+  })
+}
+Glob.prototype._processSimple2 = function (prefix, index, er, exists, cb) {
+
+  //console.error('ps2', prefix, exists)
+
+  if (!this.matches[index])
+    this.matches[index] = Object.create(null)
+
+  // If it doesn't exist, then just mark the lack of results
+  if (!exists)
+    return cb()
+
+  if (prefix && isAbsolute(prefix) && !this.nomount) {
+    var trail = /[\/\\]$/.test(prefix)
+    if (prefix.charAt(0) === '/') {
+      prefix = path.join(this.root, prefix)
+    } else {
+      prefix = path.resolve(this.root, prefix)
+      if (trail)
+        prefix += '/'
+    }
+  }
+
+  if (process.platform === 'win32')
+    prefix = prefix.replace(/\\/g, '/')
+
+  // Mark this as a match
+  this._emitMatch(index, prefix)
+  cb()
+}
+
+// Returns either 'DIR', 'FILE', or false
+Glob.prototype._stat = function (f, cb) {
+  var abs = this._makeAbs(f)
+  var needDir = f.slice(-1) === '/'
+
+  if (f.length > this.maxLength)
+    return cb()
+
+  if (!this.stat && ownProp(this.cache, abs)) {
+    var c = this.cache[abs]
+
+    if (Array.isArray(c))
+      c = 'DIR'
+
+    // It exists, but maybe not how we need it
+    if (!needDir || c === 'DIR')
+      return cb(null, c)
+
+    if (needDir && c === 'FILE')
+      return cb()
+
+    // otherwise we have to stat, because maybe c=true
+    // if we know it exists, but not what it is.
+  }
+
+  var exists
+  var stat = this.statCache[abs]
+  if (stat !== undefined) {
+    if (stat === false)
+      return cb(null, stat)
+    else {
+      var type = stat.isDirectory() ? 'DIR' : 'FILE'
+      if (needDir && type === 'FILE')
+        return cb()
+      else
+        return cb(null, type, stat)
+    }
+  }
+
+  var self = this
+  var statcb = inflight('stat\0' + abs, lstatcb_)
+  if (statcb)
+    fs.lstat(abs, statcb)
+
+  function lstatcb_ (er, lstat) {
+    if (lstat && lstat.isSymbolicLink()) {
+      // If it's a symlink, then treat it as the target, unless
+      // the target does not exist, then treat it as a file.
+      return fs.stat(abs, function (er, stat) {
+        if (er)
+          self._stat2(f, abs, null, lstat, cb)
+        else
+          self._stat2(f, abs, er, stat, cb)
+      })
+    } else {
+      self._stat2(f, abs, er, lstat, cb)
+    }
+  }
+}
+
+Glob.prototype._stat2 = function (f, abs, er, stat, cb) {
+  if (er) {
+    this.statCache[abs] = false
+    return cb()
+  }
+
+  var needDir = f.slice(-1) === '/'
+  this.statCache[abs] = stat
+
+  if (abs.slice(-1) === '/' && !stat.isDirectory())
+    return cb(null, false, stat)
+
+  var c = stat.isDirectory() ? 'DIR' : 'FILE'
+  this.cache[abs] = this.cache[abs] || c
+
+  if (needDir && c !== 'DIR')
+    return cb()
+
+  return cb(null, c, stat)
+}
+
+}).call(this,require('_process'))
+},{"./common.js":15,"./sync.js":17,"_process":24,"assert":9,"events":14,"fs":12,"inflight":18,"inherits":19,"minimatch":20,"once":21,"path":22,"path-is-absolute":23,"util":28}],17:[function(require,module,exports){
+(function (process){
+module.exports = globSync
+globSync.GlobSync = GlobSync
+
+var fs = require('fs')
+var minimatch = require('minimatch')
+var Minimatch = minimatch.Minimatch
+var Glob = require('./glob.js').Glob
+var util = require('util')
+var path = require('path')
+var assert = require('assert')
+var isAbsolute = require('path-is-absolute')
+var common = require('./common.js')
+var alphasort = common.alphasort
+var alphasorti = common.alphasorti
+var setopts = common.setopts
+var ownProp = common.ownProp
+var childrenIgnored = common.childrenIgnored
+
+function globSync (pattern, options) {
+  if (typeof options === 'function' || arguments.length === 3)
+    throw new TypeError('callback provided to sync glob\n'+
+                        'See: https://github.com/isaacs/node-glob/issues/167')
+
+  return new GlobSync(pattern, options).found
+}
+
+function GlobSync (pattern, options) {
+  if (!pattern)
+    throw new Error('must provide pattern')
+
+  if (typeof options === 'function' || arguments.length === 3)
+    throw new TypeError('callback provided to sync glob\n'+
+                        'See: https://github.com/isaacs/node-glob/issues/167')
+
+  if (!(this instanceof GlobSync))
+    return new GlobSync(pattern, options)
+
+  setopts(this, pattern, options)
+
+  if (this.noprocess)
+    return this
+
+  var n = this.minimatch.set.length
+  this.matches = new Array(n)
+  for (var i = 0; i < n; i ++) {
+    this._process(this.minimatch.set[i], i, false)
+  }
+  this._finish()
+}
+
+GlobSync.prototype._finish = function () {
+  assert(this instanceof GlobSync)
+  if (this.realpath) {
+    var self = this
+    this.matches.forEach(function (matchset, index) {
+      var set = self.matches[index] = Object.create(null)
+      for (var p in matchset) {
+        try {
+          p = self._makeAbs(p)
+          var real = fs.realpathSync(p, self.realpathCache)
+          set[real] = true
+        } catch (er) {
+          if (er.syscall === 'stat')
+            set[self._makeAbs(p)] = true
+          else
+            throw er
+        }
+      }
+    })
+  }
+  common.finish(this)
+}
+
+
+GlobSync.prototype._process = function (pattern, index, inGlobStar) {
+  assert(this instanceof GlobSync)
+
+  // Get the first [n] parts of pattern that are all strings.
+  var n = 0
+  while (typeof pattern[n] === 'string') {
+    n ++
+  }
+  // now n is the index of the first one that is *not* a string.
+
+  // See if there's anything else
+  var prefix
+  switch (n) {
+    // if not, then this is rather simple
+    case pattern.length:
+      this._processSimple(pattern.join('/'), index)
+      return
+
+    case 0:
+      // pattern *starts* with some non-trivial item.
+      // going to readdir(cwd), but not include the prefix in matches.
+      prefix = null
+      break
+
+    default:
+      // pattern has some string bits in the front.
+      // whatever it starts with, whether that's 'absolute' like /foo/bar,
+      // or 'relative' like '../baz'
+      prefix = pattern.slice(0, n).join('/')
+      break
+  }
+
+  var remain = pattern.slice(n)
+
+  // get the list of entries.
+  var read
+  if (prefix === null)
+    read = '.'
+  else if (isAbsolute(prefix) || isAbsolute(pattern.join('/'))) {
+    if (!prefix || !isAbsolute(prefix))
+      prefix = '/' + prefix
+    read = prefix
+  } else
+    read = prefix
+
+  var abs = this._makeAbs(read)
+
+  //if ignored, skip processing
+  if (childrenIgnored(this, read))
+    return
+
+  var isGlobStar = remain[0] === minimatch.GLOBSTAR
+  if (isGlobStar)
+    this._processGlobStar(prefix, read, abs, remain, index, inGlobStar)
+  else
+    this._processReaddir(prefix, read, abs, remain, index, inGlobStar)
+}
+
+
+GlobSync.prototype._processReaddir = function (prefix, read, abs, remain, index, inGlobStar) {
+  var entries = this._readdir(abs, inGlobStar)
+
+  // if the abs isn't a dir, then nothing can match!
+  if (!entries)
+    return
+
+  // It will only match dot entries if it starts with a dot, or if
+  // dot is set.  Stuff like @(.foo|.bar) isn't allowed.
+  var pn = remain[0]
+  var negate = !!this.minimatch.negate
+  var rawGlob = pn._glob
+  var dotOk = this.dot || rawGlob.charAt(0) === '.'
+
+  var matchedEntries = []
+  for (var i = 0; i < entries.length; i++) {
+    var e = entries[i]
+    if (e.charAt(0) !== '.' || dotOk) {
+      var m
+      if (negate && !prefix) {
+        m = !e.match(pn)
+      } else {
+        m = e.match(pn)
+      }
+      if (m)
+        matchedEntries.push(e)
+    }
+  }
+
+  var len = matchedEntries.length
+  // If there are no matched entries, then nothing matches.
+  if (len === 0)
+    return
+
+  // if this is the last remaining pattern bit, then no need for
+  // an additional stat *unless* the user has specified mark or
+  // stat explicitly.  We know they exist, since readdir returned
+  // them.
+
+  if (remain.length === 1 && !this.mark && !this.stat) {
+    if (!this.matches[index])
+      this.matches[index] = Object.create(null)
+
+    for (var i = 0; i < len; i ++) {
+      var e = matchedEntries[i]
+      if (prefix) {
+        if (prefix.slice(-1) !== '/')
+          e = prefix + '/' + e
+        else
+          e = prefix + e
+      }
+
+      if (e.charAt(0) === '/' && !this.nomount) {
+        e = path.join(this.root, e)
+      }
+      this.matches[index][e] = true
+    }
+    // This was the last one, and no stats were needed
+    return
+  }
+
+  // now test all matched entries as stand-ins for that part
+  // of the pattern.
+  remain.shift()
+  for (var i = 0; i < len; i ++) {
+    var e = matchedEntries[i]
+    var newPattern
+    if (prefix)
+      newPattern = [prefix, e]
+    else
+      newPattern = [e]
+    this._process(newPattern.concat(remain), index, inGlobStar)
+  }
+}
+
+
+GlobSync.prototype._emitMatch = function (index, e) {
+  var abs = this._makeAbs(e)
+  if (this.mark)
+    e = this._mark(e)
+
+  if (this.matches[index][e])
+    return
+
+  if (this.nodir) {
+    var c = this.cache[this._makeAbs(e)]
+    if (c === 'DIR' || Array.isArray(c))
+      return
+  }
+
+  this.matches[index][e] = true
+  if (this.stat)
+    this._stat(e)
+}
+
+
+GlobSync.prototype._readdirInGlobStar = function (abs) {
+  // follow all symlinked directories forever
+  // just proceed as if this is a non-globstar situation
+  if (this.follow)
+    return this._readdir(abs, false)
+
+  var entries
+  var lstat
+  var stat
+  try {
+    lstat = fs.lstatSync(abs)
+  } catch (er) {
+    // lstat failed, doesn't exist
+    return null
+  }
+
+  var isSym = lstat.isSymbolicLink()
+  this.symlinks[abs] = isSym
+
+  // If it's not a symlink or a dir, then it's definitely a regular file.
+  // don't bother doing a readdir in that case.
+  if (!isSym && !lstat.isDirectory())
+    this.cache[abs] = 'FILE'
+  else
+    entries = this._readdir(abs, false)
+
+  return entries
+}
+
+GlobSync.prototype._readdir = function (abs, inGlobStar) {
+  var entries
+
+  if (inGlobStar && !ownProp(this.symlinks, abs))
+    return this._readdirInGlobStar(abs)
+
+  if (ownProp(this.cache, abs)) {
+    var c = this.cache[abs]
+    if (!c || c === 'FILE')
+      return null
+
+    if (Array.isArray(c))
+      return c
+  }
+
+  try {
+    return this._readdirEntries(abs, fs.readdirSync(abs))
+  } catch (er) {
+    this._readdirError(abs, er)
+    return null
+  }
+}
+
+GlobSync.prototype._readdirEntries = function (abs, entries) {
+  // if we haven't asked to stat everything, then just
+  // assume that everything in there exists, so we can avoid
+  // having to stat it a second time.
+  if (!this.mark && !this.stat) {
+    for (var i = 0; i < entries.length; i ++) {
+      var e = entries[i]
+      if (abs === '/')
+        e = abs + e
+      else
+        e = abs + '/' + e
+      this.cache[e] = true
+    }
+  }
+
+  this.cache[abs] = entries
+
+  // mark and cache dir-ness
+  return entries
+}
+
+GlobSync.prototype._readdirError = function (f, er) {
+  // handle errors, and cache the information
+  switch (er.code) {
+    case 'ENOTSUP': // https://github.com/isaacs/node-glob/issues/205
+    case 'ENOTDIR': // totally normal. means it *does* exist.
+      this.cache[this._makeAbs(f)] = 'FILE'
+      break
+
+    case 'ENOENT': // not terribly unusual
+    case 'ELOOP':
+    case 'ENAMETOOLONG':
+    case 'UNKNOWN':
+      this.cache[this._makeAbs(f)] = false
+      break
+
+    default: // some unusual error.  Treat as failure.
+      this.cache[this._makeAbs(f)] = false
+      if (this.strict)
+        throw er
+      if (!this.silent)
+        console.error('glob error', er)
+      break
+  }
+}
+
+GlobSync.prototype._processGlobStar = function (prefix, read, abs, remain, index, inGlobStar) {
+
+  var entries = this._readdir(abs, inGlobStar)
+
+  // no entries means not a dir, so it can never have matches
+  // foo.txt/** doesn't match foo.txt
+  if (!entries)
+    return
+
+  // test without the globstar, and with every child both below
+  // and replacing the globstar.
+  var remainWithoutGlobStar = remain.slice(1)
+  var gspref = prefix ? [ prefix ] : []
+  var noGlobStar = gspref.concat(remainWithoutGlobStar)
+
+  // the noGlobStar pattern exits the inGlobStar state
+  this._process(noGlobStar, index, false)
+
+  var len = entries.length
+  var isSym = this.symlinks[abs]
+
+  // If it's a symlink, and we're in a globstar, then stop
+  if (isSym && inGlobStar)
+    return
+
+  for (var i = 0; i < len; i++) {
+    var e = entries[i]
+    if (e.charAt(0) === '.' && !this.dot)
+      continue
+
+    // these two cases enter the inGlobStar state
+    var instead = gspref.concat(entries[i], remainWithoutGlobStar)
+    this._process(instead, index, true)
+
+    var below = gspref.concat(entries[i], remain)
+    this._process(below, index, true)
+  }
+}
+
+GlobSync.prototype._processSimple = function (prefix, index) {
+  // XXX review this.  Shouldn't it be doing the mounting etc
+  // before doing stat?  kinda weird?
+  var exists = this._stat(prefix)
+
+  if (!this.matches[index])
+    this.matches[index] = Object.create(null)
+
+  // If it doesn't exist, then just mark the lack of results
+  if (!exists)
+    return
+
+  if (prefix && isAbsolute(prefix) && !this.nomount) {
+    var trail = /[\/\\]$/.test(prefix)
+    if (prefix.charAt(0) === '/') {
+      prefix = path.join(this.root, prefix)
+    } else {
+      prefix = path.resolve(this.root, prefix)
+      if (trail)
+        prefix += '/'
+    }
+  }
+
+  if (process.platform === 'win32')
+    prefix = prefix.replace(/\\/g, '/')
+
+  // Mark this as a match
+  this.matches[index][prefix] = true
+}
+
+// Returns either 'DIR', 'FILE', or false
+GlobSync.prototype._stat = function (f) {
+  var abs = this._makeAbs(f)
+  var needDir = f.slice(-1) === '/'
+
+  if (f.length > this.maxLength)
+    return false
+
+  if (!this.stat && ownProp(this.cache, abs)) {
+    var c = this.cache[abs]
+
+    if (Array.isArray(c))
+      c = 'DIR'
+
+    // It exists, but maybe not how we need it
+    if (!needDir || c === 'DIR')
+      return c
+
+    if (needDir && c === 'FILE')
+      return false
+
+    // otherwise we have to stat, because maybe c=true
+    // if we know it exists, but not what it is.
+  }
+
+  var exists
+  var stat = this.statCache[abs]
+  if (!stat) {
+    var lstat
+    try {
+      lstat = fs.lstatSync(abs)
+    } catch (er) {
+      return false
+    }
+
+    if (lstat.isSymbolicLink()) {
+      try {
+        stat = fs.statSync(abs)
+      } catch (er) {
+        stat = lstat
+      }
+    } else {
+      stat = lstat
+    }
+  }
+
+  this.statCache[abs] = stat
+
+  var c = stat.isDirectory() ? 'DIR' : 'FILE'
+  this.cache[abs] = this.cache[abs] || c
+
+  if (needDir && c !== 'DIR')
+    return false
+
+  return c
+}
+
+GlobSync.prototype._mark = function (p) {
+  return common.mark(this, p)
+}
+
+GlobSync.prototype._makeAbs = function (f) {
+  return common.makeAbs(this, f)
+}
+
+}).call(this,require('_process'))
+},{"./common.js":15,"./glob.js":16,"_process":24,"assert":9,"fs":12,"minimatch":20,"path":22,"path-is-absolute":23,"util":28}],18:[function(require,module,exports){
+(function (process){
+var wrappy = require('wrappy')
+var reqs = Object.create(null)
+var once = require('once')
+
+module.exports = wrappy(inflight)
+
+function inflight (key, cb) {
+  if (reqs[key]) {
+    reqs[key].push(cb)
+    return null
+  } else {
+    reqs[key] = [cb]
+    return makeres(key)
+  }
+}
+
+function makeres (key) {
+  return once(function RES () {
+    var cbs = reqs[key]
+    var len = cbs.length
+    var args = slice(arguments)
+
+    // XXX It's somewhat ambiguous whether a new callback added in this
+    // pass should be queued for later execution if something in the
+    // list of callbacks throws, or if it should just be discarded.
+    // However, it's such an edge case that it hardly matters, and either
+    // choice is likely as surprising as the other.
+    // As it happens, we do go ahead and schedule it for later execution.
+    try {
+      for (var i = 0; i < len; i++) {
+        cbs[i].apply(null, args)
+      }
+    } finally {
+      if (cbs.length > len) {
+        // added more in the interim.
+        // de-zalgo, just in case, but don't call again.
+        cbs.splice(0, len)
+        process.nextTick(function () {
+          RES.apply(null, args)
+        })
+      } else {
+        delete reqs[key]
+      }
+    }
+  })
+}
+
+function slice (args) {
+  var length = args.length
+  var array = []
+
+  for (var i = 0; i < length; i++) array[i] = args[i]
+  return array
+}
+
+}).call(this,require('_process'))
+},{"_process":24,"once":21,"wrappy":29}],19:[function(require,module,exports){
+if (typeof Object.create === 'function') {
+  // implementation from standard node.js 'util' module
+  module.exports = function inherits(ctor, superCtor) {
+    ctor.super_ = superCtor
+    ctor.prototype = Object.create(superCtor.prototype, {
+      constructor: {
+        value: ctor,
+        enumerable: false,
+        writable: true,
+        configurable: true
+      }
+    });
+  };
+} else {
+  // old school shim for old browsers
+  module.exports = function inherits(ctor, superCtor) {
+    ctor.super_ = superCtor
+    var TempCtor = function () {}
+    TempCtor.prototype = superCtor.prototype
+    ctor.prototype = new TempCtor()
+    ctor.prototype.constructor = ctor
+  }
+}
+
+},{}],20:[function(require,module,exports){
+module.exports = minimatch
+minimatch.Minimatch = Minimatch
+
+var path = { sep: '/' }
+try {
+  path = require('path')
+} catch (er) {}
+
+var GLOBSTAR = minimatch.GLOBSTAR = Minimatch.GLOBSTAR = {}
+var expand = require('brace-expansion')
+
+var plTypes = {
+  '!': { open: '(?:(?!(?:', close: '))[^/]*?)'},
+  '?': { open: '(?:', close: ')?' },
+  '+': { open: '(?:', close: ')+' },
+  '*': { open: '(?:', close: ')*' },
+  '@': { open: '(?:', close: ')' }
+}
+
+// any single thing other than /
+// don't need to escape / when using new RegExp()
+var qmark = '[^/]'
+
+// * => any number of characters
+var star = qmark + '*?'
+
+// ** when dots are allowed.  Anything goes, except .. and .
+// not (^ or / followed by one or two dots followed by $ or /),
+// followed by anything, any number of times.
+var twoStarDot = '(?:(?!(?:\\\/|^)(?:\\.{1,2})($|\\\/)).)*?'
+
+// not a ^ or / followed by a dot,
+// followed by anything, any number of times.
+var twoStarNoDot = '(?:(?!(?:\\\/|^)\\.).)*?'
+
+// characters that need to be escaped in RegExp.
+var reSpecials = charSet('().*{}+?[]^$\\!')
+
+// "abc" -> { a:true, b:true, c:true }
+function charSet (s) {
+  return s.split('').reduce(function (set, c) {
+    set[c] = true
+    return set
+  }, {})
+}
+
+// normalizes slashes.
+var slashSplit = /\/+/
+
+minimatch.filter = filter
+function filter (pattern, options) {
+  options = options || {}
+  return function (p, i, list) {
+    return minimatch(p, pattern, options)
+  }
+}
+
+function ext (a, b) {
+  a = a || {}
+  b = b || {}
+  var t = {}
+  Object.keys(b).forEach(function (k) {
+    t[k] = b[k]
+  })
+  Object.keys(a).forEach(function (k) {
+    t[k] = a[k]
+  })
+  return t
+}
+
+minimatch.defaults = function (def) {
+  if (!def || !Object.keys(def).length) return minimatch
+
+  var orig = minimatch
+
+  var m = function minimatch (p, pattern, options) {
+    return orig.minimatch(p, pattern, ext(def, options))
+  }
+
+  m.Minimatch = function Minimatch (pattern, options) {
+    return new orig.Minimatch(pattern, ext(def, options))
+  }
+
+  return m
+}
+
+Minimatch.defaults = function (def) {
+  if (!def || !Object.keys(def).length) return Minimatch
+  return minimatch.defaults(def).Minimatch
+}
+
+function minimatch (p, pattern, options) {
+  if (typeof pattern !== 'string') {
+    throw new TypeError('glob pattern string required')
+  }
+
+  if (!options) options = {}
+
+  // shortcut: comments match nothing.
+  if (!options.nocomment && pattern.charAt(0) === '#') {
+    return false
+  }
+
+  // "" only matches ""
+  if (pattern.trim() === '') return p === ''
+
+  return new Minimatch(pattern, options).match(p)
+}
+
+function Minimatch (pattern, options) {
+  if (!(this instanceof Minimatch)) {
+    return new Minimatch(pattern, options)
+  }
+
+  if (typeof pattern !== 'string') {
+    throw new TypeError('glob pattern string required')
+  }
+
+  if (!options) options = {}
+  pattern = pattern.trim()
+
+  // windows support: need to use /, not \
+  if (path.sep !== '/') {
+    pattern = pattern.split(path.sep).join('/')
+  }
+
+  this.options = options
+  this.set = []
+  this.pattern = pattern
+  this.regexp = null
+  this.negate = false
+  this.comment = false
+  this.empty = false
+
+  // make the set of regexps etc.
+  this.make()
+}
+
+Minimatch.prototype.debug = function () {}
+
+Minimatch.prototype.make = make
+function make () {
+  // don't do it more than once.
+  if (this._made) return
+
+  var pattern = this.pattern
+  var options = this.options
+
+  // empty patterns and comments match nothing.
+  if (!options.nocomment && pattern.charAt(0) === '#') {
+    this.comment = true
+    return
+  }
+  if (!pattern) {
+    this.empty = true
+    return
+  }
+
+  // step 1: figure out negation, etc.
+  this.parseNegate()
+
+  // step 2: expand braces
+  var set = this.globSet = this.braceExpand()
+
+  if (options.debug) this.debug = console.error
+
+  this.debug(this.pattern, set)
+
+  // step 3: now we have a set, so turn each one into a series of path-portion
+  // matching patterns.
+  // These will be regexps, except in the case of "**", which is
+  // set to the GLOBSTAR object for globstar behavior,
+  // and will not contain any / characters
+  set = this.globParts = set.map(function (s) {
+    return s.split(slashSplit)
+  })
+
+  this.debug(this.pattern, set)
+
+  // glob --> regexps
+  set = set.map(function (s, si, set) {
+    return s.map(this.parse, this)
+  }, this)
+
+  this.debug(this.pattern, set)
+
+  // filter out everything that didn't compile properly.
+  set = set.filter(function (s) {
+    return s.indexOf(false) === -1
+  })
+
+  this.debug(this.pattern, set)
+
+  this.set = set
+}
+
+Minimatch.prototype.parseNegate = parseNegate
+function parseNegate () {
+  var pattern = this.pattern
+  var negate = false
+  var options = this.options
+  var negateOffset = 0
+
+  if (options.nonegate) return
+
+  for (var i = 0, l = pattern.length
+    ; i < l && pattern.charAt(i) === '!'
+    ; i++) {
+    negate = !negate
+    negateOffset++
+  }
+
+  if (negateOffset) this.pattern = pattern.substr(negateOffset)
+  this.negate = negate
+}
+
+// Brace expansion:
+// a{b,c}d -> abd acd
+// a{b,}c -> abc ac
+// a{0..3}d -> a0d a1d a2d a3d
+// a{b,c{d,e}f}g -> abg acdfg acefg
+// a{b,c}d{e,f}g -> abdeg acdeg abdeg abdfg
+//
+// Invalid sets are not expanded.
+// a{2..}b -> a{2..}b
+// a{b}c -> a{b}c
+minimatch.braceExpand = function (pattern, options) {
+  return braceExpand(pattern, options)
+}
+
+Minimatch.prototype.braceExpand = braceExpand
+
+function braceExpand (pattern, options) {
+  if (!options) {
+    if (this instanceof Minimatch) {
+      options = this.options
+    } else {
+      options = {}
+    }
+  }
+
+  pattern = typeof pattern === 'undefined'
+    ? this.pattern : pattern
+
+  if (typeof pattern === 'undefined') {
+    throw new TypeError('undefined pattern')
+  }
+
+  if (options.nobrace ||
+    !pattern.match(/\{.*\}/)) {
+    // shortcut. no need to expand.
+    return [pattern]
+  }
+
+  return expand(pattern)
+}
+
+// parse a component of the expanded set.
+// At this point, no pattern may contain "/" in it
+// so we're going to return a 2d array, where each entry is the full
+// pattern, split on '/', and then turned into a regular expression.
+// A regexp is made at the end which joins each array with an
+// escaped /, and another full one which joins each regexp with |.
+//
+// Following the lead of Bash 4.1, note that "**" only has special meaning
+// when it is the *only* thing in a path portion.  Otherwise, any series
+// of * is equivalent to a single *.  Globstar behavior is enabled by
+// default, and can be disabled by setting options.noglobstar.
+Minimatch.prototype.parse = parse
+var SUBPARSE = {}
+function parse (pattern, isSub) {
+  if (pattern.length > 1024 * 64) {
+    throw new TypeError('pattern is too long')
+  }
+
+  var options = this.options
+
+  // shortcuts
+  if (!options.noglobstar && pattern === '**') return GLOBSTAR
+  if (pattern === '') return ''
+
+  var re = ''
+  var hasMagic = !!options.nocase
+  var escaping = false
+  // ? => one single character
+  var patternListStack = []
+  var negativeLists = []
+  var stateChar
+  var inClass = false
+  var reClassStart = -1
+  var classStart = -1
+  // . and .. never match anything that doesn't start with .,
+  // even when options.dot is set.
+  var patternStart = pattern.charAt(0) === '.' ? '' // anything
+  // not (start or / followed by . or .. followed by / or end)
+  : options.dot ? '(?!(?:^|\\\/)\\.{1,2}(?:$|\\\/))'
+  : '(?!\\.)'
+  var self = this
+
+  function clearStateChar () {
+    if (stateChar) {
+      // we had some state-tracking character
+      // that wasn't consumed by this pass.
+      switch (stateChar) {
+        case '*':
+          re += star
+          hasMagic = true
+        break
+        case '?':
+          re += qmark
+          hasMagic = true
+        break
+        default:
+          re += '\\' + stateChar
+        break
+      }
+      self.debug('clearStateChar %j %j', stateChar, re)
+      stateChar = false
+    }
+  }
+
+  for (var i = 0, len = pattern.length, c
+    ; (i < len) && (c = pattern.charAt(i))
+    ; i++) {
+    this.debug('%s\t%s %s %j', pattern, i, re, c)
+
+    // skip over any that are escaped.
+    if (escaping && reSpecials[c]) {
+      re += '\\' + c
+      escaping = false
+      continue
+    }
+
+    switch (c) {
+      case '/':
+        // completely not allowed, even escaped.
+        // Should already be path-split by now.
+        return false
+
+      case '\\':
+        clearStateChar()
+        escaping = true
+      continue
+
+      // the various stateChar values
+      // for the "extglob" stuff.
+      case '?':
+      case '*':
+      case '+':
+      case '@':
+      case '!':
+        this.debug('%s\t%s %s %j <-- stateChar', pattern, i, re, c)
+
+        // all of those are literals inside a class, except that
+        // the glob [!a] means [^a] in regexp
+        if (inClass) {
+          this.debug('  in class')
+          if (c === '!' && i === classStart + 1) c = '^'
+          re += c
+          continue
+        }
+
+        // if we already have a stateChar, then it means
+        // that there was something like ** or +? in there.
+        // Handle the stateChar, then proceed with this one.
+        self.debug('call clearStateChar %j', stateChar)
+        clearStateChar()
+        stateChar = c
+        // if extglob is disabled, then +(asdf|foo) isn't a thing.
+        // just clear the statechar *now*, rather than even diving into
+        // the patternList stuff.
+        if (options.noext) clearStateChar()
+      continue
+
+      case '(':
+        if (inClass) {
+          re += '('
+          continue
+        }
+
+        if (!stateChar) {
+          re += '\\('
+          continue
+        }
+
+        patternListStack.push({
+          type: stateChar,
+          start: i - 1,
+          reStart: re.length,
+          open: plTypes[stateChar].open,
+          close: plTypes[stateChar].close
+        })
+        // negation is (?:(?!js)[^/]*)
+        re += stateChar === '!' ? '(?:(?!(?:' : '(?:'
+        this.debug('plType %j %j', stateChar, re)
+        stateChar = false
+      continue
+
+      case ')':
+        if (inClass || !patternListStack.length) {
+          re += '\\)'
+          continue
+        }
+
+        clearStateChar()
+        hasMagic = true
+        var pl = patternListStack.pop()
+        // negation is (?:(?!js)[^/]*)
+        // The others are (?:<pattern>)<type>
+        re += pl.close
+        if (pl.type === '!') {
+          negativeLists.push(pl)
+        }
+        pl.reEnd = re.length
+      continue
+
+      case '|':
+        if (inClass || !patternListStack.length || escaping) {
+          re += '\\|'
+          escaping = false
+          continue
+        }
+
+        clearStateChar()
+        re += '|'
+      continue
+
+      // these are mostly the same in regexp and glob
+      case '[':
+        // swallow any state-tracking char before the [
+        clearStateChar()
+
+        if (inClass) {
+          re += '\\' + c
+          continue
+        }
+
+        inClass = true
+        classStart = i
+        reClassStart = re.length
+        re += c
+      continue
+
+      case ']':
+        //  a right bracket shall lose its special
+        //  meaning and represent itself in
+        //  a bracket expression if it occurs
+        //  first in the list.  -- POSIX.2 2.8.3.2
+        if (i === classStart + 1 || !inClass) {
+          re += '\\' + c
+          escaping = false
+          continue
+        }
+
+        // handle the case where we left a class open.
+        // "[z-a]" is valid, equivalent to "\[z-a\]"
+        if (inClass) {
+          // split where the last [ was, make sure we don't have
+          // an invalid re. if so, re-walk the contents of the
+          // would-be class to re-translate any characters that
+          // were passed through as-is
+          // TODO: It would probably be faster to determine this
+          // without a try/catch and a new RegExp, but it's tricky
+          // to do safely.  For now, this is safe and works.
+          var cs = pattern.substring(classStart + 1, i)
+          try {
+            RegExp('[' + cs + ']')
+          } catch (er) {
+            // not a valid class!
+            var sp = this.parse(cs, SUBPARSE)
+            re = re.substr(0, reClassStart) + '\\[' + sp[0] + '\\]'
+            hasMagic = hasMagic || sp[1]
+            inClass = false
+            continue
+          }
+        }
+
+        // finish up the class.
+        hasMagic = true
+        inClass = false
+        re += c
+      continue
+
+      default:
+        // swallow any state char that wasn't consumed
+        clearStateChar()
+
+        if (escaping) {
+          // no need
+          escaping = false
+        } else if (reSpecials[c]
+          && !(c === '^' && inClass)) {
+          re += '\\'
+        }
+
+        re += c
+
+    } // switch
+  } // for
+
+  // handle the case where we left a class open.
+  // "[abc" is valid, equivalent to "\[abc"
+  if (inClass) {
+    // split where the last [ was, and escape it
+    // this is a huge pita.  We now have to re-walk
+    // the contents of the would-be class to re-translate
+    // any characters that were passed through as-is
+    cs = pattern.substr(classStart + 1)
+    sp = this.parse(cs, SUBPARSE)
+    re = re.substr(0, reClassStart) + '\\[' + sp[0]
+    hasMagic = hasMagic || sp[1]
+  }
+
+  // handle the case where we had a +( thing at the *end*
+  // of the pattern.
+  // each pattern list stack adds 3 chars, and we need to go through
+  // and escape any | chars that were passed through as-is for the regexp.
+  // Go through and escape them, taking care not to double-escape any
+  // | chars that were already escaped.
+  for (pl = patternListStack.pop(); pl; pl = patternListStack.pop()) {
+    var tail = re.slice(pl.reStart + pl.open.length)
+    this.debug('setting tail', re, pl)
+    // maybe some even number of \, then maybe 1 \, followed by a |
+    tail = tail.replace(/((?:\\{2}){0,64})(\\?)\|/g, function (_, $1, $2) {
+      if (!$2) {
+        // the | isn't already escaped, so escape it.
+        $2 = '\\'
+      }
+
+      // need to escape all those slashes *again*, without escaping the
+      // one that we need for escaping the | character.  As it works out,
+      // escaping an even number of slashes can be done by simply repeating
+      // it exactly after itself.  That's why this trick works.
+      //
+      // I am sorry that you have to see this.
+      return $1 + $1 + $2 + '|'
+    })
+
+    this.debug('tail=%j\n   %s', tail, tail, pl, re)
+    var t = pl.type === '*' ? star
+      : pl.type === '?' ? qmark
+      : '\\' + pl.type
+
+    hasMagic = true
+    re = re.slice(0, pl.reStart) + t + '\\(' + tail
+  }
+
+  // handle trailing things that only matter at the very end.
+  clearStateChar()
+  if (escaping) {
+    // trailing \\
+    re += '\\\\'
+  }
+
+  // only need to apply the nodot start if the re starts with
+  // something that could conceivably capture a dot
+  var addPatternStart = false
+  switch (re.charAt(0)) {
+    case '.':
+    case '[':
+    case '(': addPatternStart = true
+  }
+
+  // Hack to work around lack of negative lookbehind in JS
+  // A pattern like: *.!(x).!(y|z) needs to ensure that a name
+  // like 'a.xyz.yz' doesn't match.  So, the first negative
+  // lookahead, has to look ALL the way ahead, to the end of
+  // the pattern.
+  for (var n = negativeLists.length - 1; n > -1; n--) {
+    var nl = negativeLists[n]
+
+    var nlBefore = re.slice(0, nl.reStart)
+    var nlFirst = re.slice(nl.reStart, nl.reEnd - 8)
+    var nlLast = re.slice(nl.reEnd - 8, nl.reEnd)
+    var nlAfter = re.slice(nl.reEnd)
+
+    nlLast += nlAfter
+
+    // Handle nested stuff like *(*.js|!(*.json)), where open parens
+    // mean that we should *not* include the ) in the bit that is considered
+    // "after" the negated section.
+    var openParensBefore = nlBefore.split('(').length - 1
+    var cleanAfter = nlAfter
+    for (i = 0; i < openParensBefore; i++) {
+      cleanAfter = cleanAfter.replace(/\)[+*?]?/, '')
+    }
+    nlAfter = cleanAfter
+
+    var dollar = ''
+    if (nlAfter === '' && isSub !== SUBPARSE) {
+      dollar = '$'
+    }
+    var newRe = nlBefore + nlFirst + nlAfter + dollar + nlLast
+    re = newRe
+  }
+
+  // if the re is not "" at this point, then we need to make sure
+  // it doesn't match against an empty path part.
+  // Otherwise a/* will match a/, which it should not.
+  if (re !== '' && hasMagic) {
+    re = '(?=.)' + re
+  }
+
+  if (addPatternStart) {
+    re = patternStart + re
+  }
+
+  // parsing just a piece of a larger pattern.
+  if (isSub === SUBPARSE) {
+    return [re, hasMagic]
+  }
+
+  // skip the regexp for non-magical patterns
+  // unescape anything in it, though, so that it'll be
+  // an exact match against a file etc.
+  if (!hasMagic) {
+    return globUnescape(pattern)
+  }
+
+  var flags = options.nocase ? 'i' : ''
+  try {
+    var regExp = new RegExp('^' + re + '$', flags)
+  } catch (er) {
+    // If it was an invalid regular expression, then it can't match
+    // anything.  This trick looks for a character after the end of
+    // the string, which is of course impossible, except in multi-line
+    // mode, but it's not a /m regex.
+    return new RegExp('$.')
+  }
+
+  regExp._glob = pattern
+  regExp._src = re
+
+  return regExp
+}
+
+minimatch.makeRe = function (pattern, options) {
+  return new Minimatch(pattern, options || {}).makeRe()
+}
+
+Minimatch.prototype.makeRe = makeRe
+function makeRe () {
+  if (this.regexp || this.regexp === false) return this.regexp
+
+  // at this point, this.set is a 2d array of partial
+  // pattern strings, or "**".
+  //
+  // It's better to use .match().  This function shouldn't
+  // be used, really, but it's pretty convenient sometimes,
+  // when you just want to work with a regex.
+  var set = this.set
+
+  if (!set.length) {
+    this.regexp = false
+    return this.regexp
+  }
+  var options = this.options
+
+  var twoStar = options.noglobstar ? star
+    : options.dot ? twoStarDot
+    : twoStarNoDot
+  var flags = options.nocase ? 'i' : ''
+
+  var re = set.map(function (pattern) {
+    return pattern.map(function (p) {
+      return (p === GLOBSTAR) ? twoStar
+      : (typeof p === 'string') ? regExpEscape(p)
+      : p._src
+    }).join('\\\/')
+  }).join('|')
+
+  // must match entire pattern
+  // ending in a * or ** will make it less strict.
+  re = '^(?:' + re + ')$'
+
+  // can match anything, as long as it's not this.
+  if (this.negate) re = '^(?!' + re + ').*$'
+
+  try {
+    this.regexp = new RegExp(re, flags)
+  } catch (ex) {
+    this.regexp = false
+  }
+  return this.regexp
+}
+
+minimatch.match = function (list, pattern, options) {
+  options = options || {}
+  var mm = new Minimatch(pattern, options)
+  list = list.filter(function (f) {
+    return mm.match(f)
+  })
+  if (mm.options.nonull && !list.length) {
+    list.push(pattern)
+  }
+  return list
+}
+
+Minimatch.prototype.match = match
+function match (f, partial) {
+  this.debug('match', f, this.pattern)
+  // short-circuit in the case of busted things.
+  // comments, etc.
+  if (this.comment) return false
+  if (this.empty) return f === ''
+
+  if (f === '/' && partial) return true
+
+  var options = this.options
+
+  // windows: need to use /, not \
+  if (path.sep !== '/') {
+    f = f.split(path.sep).join('/')
+  }
+
+  // treat the test path as a set of pathparts.
+  f = f.split(slashSplit)
+  this.debug(this.pattern, 'split', f)
+
+  // just ONE of the pattern sets in this.set needs to match
+  // in order for it to be valid.  If negating, then just one
+  // match means that we have failed.
+  // Either way, return on the first hit.
+
+  var set = this.set
+  this.debug(this.pattern, 'set', set)
+
+  // Find the basename of the path by looking for the last non-empty segment
+  var filename
+  var i
+  for (i = f.length - 1; i >= 0; i--) {
+    filename = f[i]
+    if (filename) break
+  }
+
+  for (i = 0; i < set.length; i++) {
+    var pattern = set[i]
+    var file = f
+    if (options.matchBase && pattern.length === 1) {
+      file = [filename]
+    }
+    var hit = this.matchOne(file, pattern, partial)
+    if (hit) {
+      if (options.flipNegate) return true
+      return !this.negate
+    }
+  }
+
+  // didn't get any hits.  this is success if it's a negative
+  // pattern, failure otherwise.
+  if (options.flipNegate) return false
+  return this.negate
+}
+
+// set partial to true to test if, for example,
+// "/a/b" matches the start of "/*/b/*/d"
+// Partial means, if you run out of file before you run
+// out of pattern, then that's fine, as long as all
+// the parts match.
+Minimatch.prototype.matchOne = function (file, pattern, partial) {
+  var options = this.options
+
+  this.debug('matchOne',
+    { 'this': this, file: file, pattern: pattern })
+
+  this.debug('matchOne', file.length, pattern.length)
+
+  for (var fi = 0,
+      pi = 0,
+      fl = file.length,
+      pl = pattern.length
+      ; (fi < fl) && (pi < pl)
+      ; fi++, pi++) {
+    this.debug('matchOne loop')
+    var p = pattern[pi]
+    var f = file[fi]
+
+    this.debug(pattern, p, f)
+
+    // should be impossible.
+    // some invalid regexp stuff in the set.
+    if (p === false) return false
+
+    if (p === GLOBSTAR) {
+      this.debug('GLOBSTAR', [pattern, p, f])
+
+      // "**"
+      // a/**/b/**/c would match the following:
+      // a/b/x/y/z/c
+      // a/x/y/z/b/c
+      // a/b/x/b/x/c
+      // a/b/c
+      // To do this, take the rest of the pattern after
+      // the **, and see if it would match the file remainder.
+      // If so, return success.
+      // If not, the ** "swallows" a segment, and try again.
+      // This is recursively awful.
+      //
+      // a/**/b/**/c matching a/b/x/y/z/c
+      // - a matches a
+      // - doublestar
+      //   - matchOne(b/x/y/z/c, b/**/c)
+      //     - b matches b
+      //     - doublestar
+      //       - matchOne(x/y/z/c, c) -> no
+      //       - matchOne(y/z/c, c) -> no
+      //       - matchOne(z/c, c) -> no
+      //       - matchOne(c, c) yes, hit
+      var fr = fi
+      var pr = pi + 1
+      if (pr === pl) {
+        this.debug('** at the end')
+        // a ** at the end will just swallow the rest.
+        // We have found a match.
+        // however, it will not swallow /.x, unless
+        // options.dot is set.
+        // . and .. are *never* matched by **, for explosively
+        // exponential reasons.
+        for (; fi < fl; fi++) {
+          if (file[fi] === '.' || file[fi] === '..' ||
+            (!options.dot && file[fi].charAt(0) === '.')) return false
+        }
+        return true
+      }
+
+      // ok, let's see if we can swallow whatever we can.
+      while (fr < fl) {
+        var swallowee = file[fr]
+
+        this.debug('\nglobstar while', file, fr, pattern, pr, swallowee)
+
+        // XXX remove this slice.  Just pass the start index.
+        if (this.matchOne(file.slice(fr), pattern.slice(pr), partial)) {
+          this.debug('globstar found match!', fr, fl, swallowee)
+          // found a match.
+          return true
+        } else {
+          // can't swallow "." or ".." ever.
+          // can only swallow ".foo" when explicitly asked.
+          if (swallowee === '.' || swallowee === '..' ||
+            (!options.dot && swallowee.charAt(0) === '.')) {
+            this.debug('dot detected!', file, fr, pattern, pr)
+            break
+          }
+
+          // ** swallows a segment, and continue.
+          this.debug('globstar swallow a segment, and continue')
+          fr++
+        }
+      }
+
+      // no match was found.
+      // However, in partial mode, we can't say this is necessarily over.
+      // If there's more *pattern* left, then
+      if (partial) {
+        // ran out of file
+        this.debug('\n>>> no match, partial?', file, fr, pattern, pr)
+        if (fr === fl) return true
+      }
+      return false
+    }
+
+    // something other than **
+    // non-magic patterns just have to match exactly
+    // patterns with magic have been turned into regexps.
+    var hit
+    if (typeof p === 'string') {
+      if (options.nocase) {
+        hit = f.toLowerCase() === p.toLowerCase()
+      } else {
+        hit = f === p
+      }
+      this.debug('string match', p, f, hit)
+    } else {
+      hit = f.match(p)
+      this.debug('pattern match', p, f, hit)
+    }
+
+    if (!hit) return false
+  }
+
+  // Note: ending in / means that we'll get a final ""
+  // at the end of the pattern.  This can only match a
+  // corresponding "" at the end of the file.
+  // If the file ends in /, then it can only match a
+  // a pattern that ends in /, unless the pattern just
+  // doesn't have any more for it. But, a/b/ should *not*
+  // match "a/b/*", even though "" matches against the
+  // [^/]*? pattern, except in partial mode, where it might
+  // simply not be reached yet.
+  // However, a/b/ should still satisfy a/*
+
+  // now either we fell off the end of the pattern, or we're done.
+  if (fi === fl && pi === pl) {
+    // ran out of pattern and filename at the same time.
+    // an exact hit!
+    return true
+  } else if (fi === fl) {
+    // ran out of file, but still had pattern left.
+    // this is ok if we're doing the match as part of
+    // a glob fs traversal.
+    return partial
+  } else if (pi === pl) {
+    // ran out of pattern, still have file left.
+    // this is only acceptable if we're on the very last
+    // empty segment of a file with a trailing slash.
+    // a/* should match a/b/
+    var emptyFileEnd = (fi === fl - 1) && (file[fi] === '')
+    return emptyFileEnd
+  }
+
+  // should be unreachable.
+  throw new Error('wtf?')
+}
+
+// replace stuff like \* with *
+function globUnescape (s) {
+  return s.replace(/\\(.)/g, '$1')
+}
+
+function regExpEscape (s) {
+  return s.replace(/[-[\]{}()*+?.,\\^$|#\s]/g, '\\$&')
+}
+
+},{"brace-expansion":11,"path":22}],21:[function(require,module,exports){
+var wrappy = require('wrappy')
+module.exports = wrappy(once)
+module.exports.strict = wrappy(onceStrict)
+
+once.proto = once(function () {
+  Object.defineProperty(Function.prototype, 'once', {
+    value: function () {
+      return once(this)
+    },
+    configurable: true
+  })
+
+  Object.defineProperty(Function.prototype, 'onceStrict', {
+    value: function () {
+      return onceStrict(this)
+    },
+    configurable: true
+  })
+})
+
+function once (fn) {
+  var f = function () {
+    if (f.called) return f.value
+    f.called = true
+    return f.value = fn.apply(this, arguments)
+  }
+  f.called = false
+  return f
+}
+
+function onceStrict (fn) {
+  var f = function () {
+    if (f.called)
+      throw new Error(f.onceError)
+    f.called = true
+    return f.value = fn.apply(this, arguments)
+  }
+  var name = fn.name || 'Function wrapped with `once`'
+  f.onceError = name + " shouldn't be called more than once"
+  f.called = false
+  return f
+}
+
+},{"wrappy":29}],22:[function(require,module,exports){
+(function (process){
+// Copyright Joyent, Inc. and other Node contributors.
+//
+// Permission is hereby granted, free of charge, to any person obtaining a
+// copy of this software and associated documentation files (the
+// "Software"), to deal in the Software without restriction, including
+// without limitation the rights to use, copy, modify, merge, publish,
+// distribute, sublicense, and/or sell copies of the Software, and to permit
+// persons to whom the Software is furnished to do so, subject to the
+// following conditions:
+//
+// The above copyright notice and this permission notice shall be included
+// in all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+// MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN
+// NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
+// DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
+// OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
+// USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+// resolves . and .. elements in a path array with directory names there
+// must be no slashes, empty elements, or device names (c:\) in the array
+// (so also no leading and trailing slashes - it does not distinguish
+// relative and absolute paths)
+function normalizeArray(parts, allowAboveRoot) {
+  // if the path tries to go above the root, `up` ends up > 0
+  var up = 0;
+  for (var i = parts.length - 1; i >= 0; i--) {
+    var last = parts[i];
+    if (last === '.') {
+      parts.splice(i, 1);
+    } else if (last === '..') {
+      parts.splice(i, 1);
+      up++;
+    } else if (up) {
+      parts.splice(i, 1);
+      up--;
+    }
+  }
+
+  // if the path is allowed to go above the root, restore leading ..s
+  if (allowAboveRoot) {
+    for (; up--; up) {
+      parts.unshift('..');
+    }
+  }
+
+  return parts;
+}
+
+// Split a filename into [root, dir, basename, ext], unix version
+// 'root' is just a slash, or nothing.
+var splitPathRe =
+    /^(\/?|)([\s\S]*?)((?:\.{1,2}|[^\/]+?|)(\.[^.\/]*|))(?:[\/]*)$/;
+var splitPath = function(filename) {
+  return splitPathRe.exec(filename).slice(1);
+};
+
+// path.resolve([from ...], to)
+// posix version
+exports.resolve = function() {
+  var resolvedPath = '',
+      resolvedAbsolute = false;
+
+  for (var i = arguments.length - 1; i >= -1 && !resolvedAbsolute; i--) {
+    var path = (i >= 0) ? arguments[i] : process.cwd();
+
+    // Skip empty and invalid entries
+    if (typeof path !== 'string') {
+      throw new TypeError('Arguments to path.resolve must be strings');
+    } else if (!path) {
+      continue;
+    }
+
+    resolvedPath = path + '/' + resolvedPath;
+    resolvedAbsolute = path.charAt(0) === '/';
+  }
+
+  // At this point the path should be resolved to a full absolute path, but
+  // handle relative paths to be safe (might happen when process.cwd() fails)
+
+  // Normalize the path
+  resolvedPath = normalizeArray(filter(resolvedPath.split('/'), function(p) {
+    return !!p;
+  }), !resolvedAbsolute).join('/');
+
+  return ((resolvedAbsolute ? '/' : '') + resolvedPath) || '.';
+};
+
+// path.normalize(path)
+// posix version
+exports.normalize = function(path) {
+  var isAbsolute = exports.isAbsolute(path),
+      trailingSlash = substr(path, -1) === '/';
+
+  // Normalize the path
+  path = normalizeArray(filter(path.split('/'), function(p) {
+    return !!p;
+  }), !isAbsolute).join('/');
+
+  if (!path && !isAbsolute) {
+    path = '.';
+  }
+  if (path && trailingSlash) {
+    path += '/';
+  }
+
+  return (isAbsolute ? '/' : '') + path;
+};
+
+// posix version
+exports.isAbsolute = function(path) {
+  return path.charAt(0) === '/';
+};
+
+// posix version
+exports.join = function() {
+  var paths = Array.prototype.slice.call(arguments, 0);
+  return exports.normalize(filter(paths, function(p, index) {
+    if (typeof p !== 'string') {
+      throw new TypeError('Arguments to path.join must be strings');
+    }
+    return p;
+  }).join('/'));
+};
+
+
+// path.relative(from, to)
+// posix version
+exports.relative = function(from, to) {
+  from = exports.resolve(from).substr(1);
+  to = exports.resolve(to).substr(1);
+
+  function trim(arr) {
+    var start = 0;
+    for (; start < arr.length; start++) {
+      if (arr[start] !== '') break;
+    }
+
+    var end = arr.length - 1;
+    for (; end >= 0; end--) {
+      if (arr[end] !== '') break;
+    }
+
+    if (start > end) return [];
+    return arr.slice(start, end - start + 1);
+  }
+
+  var fromParts = trim(from.split('/'));
+  var toParts = trim(to.split('/'));
+
+  var length = Math.min(fromParts.length, toParts.length);
+  var samePartsLength = length;
+  for (var i = 0; i < length; i++) {
+    if (fromParts[i] !== toParts[i]) {
+      samePartsLength = i;
+      break;
+    }
+  }
+
+  var outputParts = [];
+  for (var i = samePartsLength; i < fromParts.length; i++) {
+    outputParts.push('..');
+  }
+
+  outputParts = outputParts.concat(toParts.slice(samePartsLength));
+
+  return outputParts.join('/');
+};
+
+exports.sep = '/';
+exports.delimiter = ':';
+
+exports.dirname = function(path) {
+  var result = splitPath(path),
+      root = result[0],
+      dir = result[1];
+
+  if (!root && !dir) {
+    // No dirname whatsoever
+    return '.';
+  }
+
+  if (dir) {
+    // It has a dirname, strip trailing slash
+    dir = dir.substr(0, dir.length - 1);
+  }
+
+  return root + dir;
+};
+
+
+exports.basename = function(path, ext) {
+  var f = splitPath(path)[2];
+  // TODO: make this comparison case-insensitive on windows?
+  if (ext && f.substr(-1 * ext.length) === ext) {
+    f = f.substr(0, f.length - ext.length);
+  }
+  return f;
+};
+
+
+exports.extname = function(path) {
+  return splitPath(path)[3];
+};
+
+function filter (xs, f) {
+    if (xs.filter) return xs.filter(f);
+    var res = [];
+    for (var i = 0; i < xs.length; i++) {
+        if (f(xs[i], i, xs)) res.push(xs[i]);
+    }
+    return res;
+}
+
+// String.prototype.substr - negative index don't work in IE8
+var substr = 'ab'.substr(-1) === 'b'
+    ? function (str, start, len) { return str.substr(start, len) }
+    : function (str, start, len) {
+        if (start < 0) start = str.length + start;
+        return str.substr(start, len);
+    }
+;
+
+}).call(this,require('_process'))
+},{"_process":24}],23:[function(require,module,exports){
+(function (process){
+'use strict';
+
+function posix(path) {
+	return path.charAt(0) === '/';
+}
+
+function win32(path) {
+	// https://github.com/nodejs/node/blob/b3fcc245fb25539909ef1d5eaa01dbf92e168633/lib/path.js#L56
+	var splitDeviceRe = /^([a-zA-Z]:|[\\\/]{2}[^\\\/]+[\\\/]+[^\\\/]+)?([\\\/])?([\s\S]*?)$/;
+	var result = splitDeviceRe.exec(path);
+	var device = result[1] || '';
+	var isUnc = Boolean(device && device.charAt(1) !== ':');
+
+	// UNC paths are always absolute
+	return Boolean(result[2] || isUnc);
+}
+
+module.exports = process.platform === 'win32' ? win32 : posix;
+module.exports.posix = posix;
+module.exports.win32 = win32;
+
+}).call(this,require('_process'))
+},{"_process":24}],24:[function(require,module,exports){
+// shim for using process in browser
+var process = module.exports = {};
+
+// cached from whatever global is present so that test runners that stub it
+// don't break things.  But we need to wrap it in a try catch in case it is
+// wrapped in strict mode code which doesn't define any globals.  It's inside a
+// function because try/catches deoptimize in certain engines.
+
+var cachedSetTimeout;
+var cachedClearTimeout;
+
+function defaultSetTimout() {
+    throw new Error('setTimeout has not been defined');
+}
+function defaultClearTimeout () {
+    throw new Error('clearTimeout has not been defined');
+}
+(function () {
+    try {
+        if (typeof setTimeout === 'function') {
+            cachedSetTimeout = setTimeout;
+        } else {
+            cachedSetTimeout = defaultSetTimout;
+        }
+    } catch (e) {
+        cachedSetTimeout = defaultSetTimout;
+    }
+    try {
+        if (typeof clearTimeout === 'function') {
+            cachedClearTimeout = clearTimeout;
+        } else {
+            cachedClearTimeout = defaultClearTimeout;
+        }
+    } catch (e) {
+        cachedClearTimeout = defaultClearTimeout;
+    }
+} ())
+function runTimeout(fun) {
+    if (cachedSetTimeout === setTimeout) {
+        //normal enviroments in sane situations
+        return setTimeout(fun, 0);
+    }
+    // if setTimeout wasn't available but was latter defined
+    if ((cachedSetTimeout === defaultSetTimout || !cachedSetTimeout) && setTimeout) {
+        cachedSetTimeout = setTimeout;
+        return setTimeout(fun, 0);
+    }
+    try {
+        // when when somebody has screwed with setTimeout but no I.E. maddness
+        return cachedSetTimeout(fun, 0);
+    } catch(e){
+        try {
+            // When we are in I.E. but the script has been evaled so I.E. doesn't trust the global object when called normally
+            return cachedSetTimeout.call(null, fun, 0);
+        } catch(e){
+            // same as above but when it's a version of I.E. that must have the global object for 'this', hopfully our context correct otherwise it will throw a global error
+            return cachedSetTimeout.call(this, fun, 0);
+        }
+    }
+
+
+}
+function runClearTimeout(marker) {
+    if (cachedClearTimeout === clearTimeout) {
+        //normal enviroments in sane situations
+        return clearTimeout(marker);
+    }
+    // if clearTimeout wasn't available but was latter defined
+    if ((cachedClearTimeout === defaultClearTimeout || !cachedClearTimeout) && clearTimeout) {
+        cachedClearTimeout = clearTimeout;
+        return clearTimeout(marker);
+    }
+    try {
+        // when when somebody has screwed with setTimeout but no I.E. maddness
+        return cachedClearTimeout(marker);
+    } catch (e){
+        try {
+            // When we are in I.E. but the script has been evaled so I.E. doesn't  trust the global object when called normally
+            return cachedClearTimeout.call(null, marker);
+        } catch (e){
+            // same as above but when it's a version of I.E. that must have the global object for 'this', hopfully our context correct otherwise it will throw a global error.
+            // Some versions of I.E. have different rules for clearTimeout vs setTimeout
+            return cachedClearTimeout.call(this, marker);
+        }
+    }
+
+
+
+}
+var queue = [];
+var draining = false;
+var currentQueue;
+var queueIndex = -1;
+
+function cleanUpNextTick() {
+    if (!draining || !currentQueue) {
+        return;
+    }
+    draining = false;
+    if (currentQueue.length) {
+        queue = currentQueue.concat(queue);
+    } else {
+        queueIndex = -1;
+    }
+    if (queue.length) {
+        drainQueue();
+    }
+}
+
+function drainQueue() {
+    if (draining) {
+        return;
+    }
+    var timeout = runTimeout(cleanUpNextTick);
+    draining = true;
+
+    var len = queue.length;
+    while(len) {
+        currentQueue = queue;
+        queue = [];
+        while (++queueIndex < len) {
+            if (currentQueue) {
+                currentQueue[queueIndex].run();
+            }
+        }
+        queueIndex = -1;
+        len = queue.length;
+    }
+    currentQueue = null;
+    draining = false;
+    runClearTimeout(timeout);
+}
+
+process.nextTick = function (fun) {
+    var args = new Array(arguments.length - 1);
+    if (arguments.length > 1) {
+        for (var i = 1; i < arguments.length; i++) {
+            args[i - 1] = arguments[i];
+        }
+    }
+    queue.push(new Item(fun, args));
+    if (queue.length === 1 && !draining) {
+        runTimeout(drainQueue);
+    }
+};
+
+// v8 likes predictible objects
+function Item(fun, array) {
+    this.fun = fun;
+    this.array = array;
+}
+Item.prototype.run = function () {
+    this.fun.apply(null, this.array);
+};
+process.title = 'browser';
+process.browser = true;
+process.env = {};
+process.argv = [];
+process.version = ''; // empty string to avoid regexp issues
+process.versions = {};
+
+function noop() {}
+
+process.on = noop;
+process.addListener = noop;
+process.once = noop;
+process.off = noop;
+process.removeListener = noop;
+process.removeAllListeners = noop;
+process.emit = noop;
+process.prependListener = noop;
+process.prependOnceListener = noop;
+
+process.listeners = function (name) { return [] }
+
+process.binding = function (name) {
+    throw new Error('process.binding is not supported');
+};
+
+process.cwd = function () { return '/' };
+process.chdir = function (dir) {
+    throw new Error('process.chdir is not supported');
+};
+process.umask = function() { return 0; };
+
+},{}],25:[function(require,module,exports){
+//     Underscore.js 1.8.3
+//     http://underscorejs.org
+//     (c) 2009-2015 Jeremy Ashkenas, DocumentCloud and Investigative Reporters & Editors
+//     Underscore may be freely distributed under the MIT license.
+
+(function() {
+
+  // Baseline setup
+  // --------------
+
+  // Establish the root object, `window` in the browser, or `exports` on the server.
+  var root = this;
+
+  // Save the previous value of the `_` variable.
+  var previousUnderscore = root._;
+
+  // Save bytes in the minified (but not gzipped) version:
+  var ArrayProto = Array.prototype, ObjProto = Object.prototype, FuncProto = Function.prototype;
+
+  // Create quick reference variables for speed access to core prototypes.
+  var
+    push             = ArrayProto.push,
+    slice            = ArrayProto.slice,
+    toString         = ObjProto.toString,
+    hasOwnProperty   = ObjProto.hasOwnProperty;
+
+  // All **ECMAScript 5** native function implementations that we hope to use
+  // are declared here.
+  var
+    nativeIsArray      = Array.isArray,
+    nativeKeys         = Object.keys,
+    nativeBind         = FuncProto.bind,
+    nativeCreate       = Object.create;
+
+  // Naked function reference for surrogate-prototype-swapping.
+  var Ctor = function(){};
+
+  // Create a safe reference to the Underscore object for use below.
+  var _ = function(obj) {
+    if (obj instanceof _) return obj;
+    if (!(this instanceof _)) return new _(obj);
+    this._wrapped = obj;
+  };
+
+  // Export the Underscore object for **Node.js**, with
+  // backwards-compatibility for the old `require()` API. If we're in
+  // the browser, add `_` as a global object.
+  if (typeof exports !== 'undefined') {
+    if (typeof module !== 'undefined' && module.exports) {
+      exports = module.exports = _;
+    }
+    exports._ = _;
+  } else {
+    root._ = _;
+  }
+
+  // Current version.
+  _.VERSION = '1.8.3';
+
+  // Internal function that returns an efficient (for current engines) version
+  // of the passed-in callback, to be repeatedly applied in other Underscore
+  // functions.
+  var optimizeCb = function(func, context, argCount) {
+    if (context === void 0) return func;
+    switch (argCount == null ? 3 : argCount) {
+      case 1: return function(value) {
+        return func.call(context, value);
+      };
+      case 2: return function(value, other) {
+        return func.call(context, value, other);
+      };
+      case 3: return function(value, index, collection) {
+        return func.call(context, value, index, collection);
+      };
+      case 4: return function(accumulator, value, index, collection) {
+        return func.call(context, accumulator, value, index, collection);
+      };
+    }
+    return function() {
+      return func.apply(context, arguments);
+    };
+  };
+
+  // A mostly-internal function to generate callbacks that can be applied
+  // to each element in a collection, returning the desired result — either
+  // identity, an arbitrary callback, a property matcher, or a property accessor.
+  var cb = function(value, context, argCount) {
+    if (value == null) return _.identity;
+    if (_.isFunction(value)) return optimizeCb(value, context, argCount);
+    if (_.isObject(value)) return _.matcher(value);
+    return _.property(value);
+  };
+  _.iteratee = function(value, context) {
+    return cb(value, context, Infinity);
+  };
+
+  // An internal function for creating assigner functions.
+  var createAssigner = function(keysFunc, undefinedOnly) {
+    return function(obj) {
+      var length = arguments.length;
+      if (length < 2 || obj == null) return obj;
+      for (var index = 1; index < length; index++) {
+        var source = arguments[index],
+            keys = keysFunc(source),
+            l = keys.length;
+        for (var i = 0; i < l; i++) {
+          var key = keys[i];
+          if (!undefinedOnly || obj[key] === void 0) obj[key] = source[key];
+        }
+      }
+      return obj;
+    };
+  };
+
+  // An internal function for creating a new object that inherits from another.
+  var baseCreate = function(prototype) {
+    if (!_.isObject(prototype)) return {};
+    if (nativeCreate) return nativeCreate(prototype);
+    Ctor.prototype = prototype;
+    var result = new Ctor;
+    Ctor.prototype = null;
+    return result;
+  };
+
+  var property = function(key) {
+    return function(obj) {
+      return obj == null ? void 0 : obj[key];
+    };
+  };
+
+  // Helper for collection methods to determine whether a collection
+  // should be iterated as an array or as an object
+  // Related: http://people.mozilla.org/~jorendorff/es6-draft.html#sec-tolength
+  // Avoids a very nasty iOS 8 JIT bug on ARM-64. #2094
+  var MAX_ARRAY_INDEX = Math.pow(2, 53) - 1;
+  var getLength = property('length');
+  var isArrayLike = function(collection) {
+    var length = getLength(collection);
+    return typeof length == 'number' && length >= 0 && length <= MAX_ARRAY_INDEX;
+  };
+
+  // Collection Functions
+  // --------------------
+
+  // The cornerstone, an `each` implementation, aka `forEach`.
+  // Handles raw objects in addition to array-likes. Treats all
+  // sparse array-likes as if they were dense.
+  _.each = _.forEach = function(obj, iteratee, context) {
+    iteratee = optimizeCb(iteratee, context);
+    var i, length;
+    if (isArrayLike(obj)) {
+      for (i = 0, length = obj.length; i < length; i++) {
+        iteratee(obj[i], i, obj);
+      }
+    } else {
+      var keys = _.keys(obj);
+      for (i = 0, length = keys.length; i < length; i++) {
+        iteratee(obj[keys[i]], keys[i], obj);
+      }
+    }
+    return obj;
+  };
+
+  // Return the results of applying the iteratee to each element.
+  _.map = _.collect = function(obj, iteratee, context) {
+    iteratee = cb(iteratee, context);
+    var keys = !isArrayLike(obj) && _.keys(obj),
+        length = (keys || obj).length,
+        results = Array(length);
+    for (var index = 0; index < length; index++) {
+      var currentKey = keys ? keys[index] : index;
+      results[index] = iteratee(obj[currentKey], currentKey, obj);
+    }
+    return results;
+  };
+
+  // Create a reducing function iterating left or right.
+  function createReduce(dir) {
+    // Optimized iterator function as using arguments.length
+    // in the main function will deoptimize the, see #1991.
+    function iterator(obj, iteratee, memo, keys, index, length) {
+      for (; index >= 0 && index < length; index += dir) {
+        var currentKey = keys ? keys[index] : index;
+        memo = iteratee(memo, obj[currentKey], currentKey, obj);
+      }
+      return memo;
+    }
+
+    return function(obj, iteratee, memo, context) {
+      iteratee = optimizeCb(iteratee, context, 4);
+      var keys = !isArrayLike(obj) && _.keys(obj),
+          length = (keys || obj).length,
+          index = dir > 0 ? 0 : length - 1;
+      // Determine the initial value if none is provided.
+      if (arguments.length < 3) {
+        memo = obj[keys ? keys[index] : index];
+        index += dir;
+      }
+      return iterator(obj, iteratee, memo, keys, index, length);
+    };
+  }
+
+  // **Reduce** builds up a single result from a list of values, aka `inject`,
+  // or `foldl`.
+  _.reduce = _.foldl = _.inject = createReduce(1);
+
+  // The right-associative version of reduce, also known as `foldr`.
+  _.reduceRight = _.foldr = createReduce(-1);
+
+  // Return the first value which passes a truth test. Aliased as `detect`.
+  _.find = _.detect = function(obj, predicate, context) {
+    var key;
+    if (isArrayLike(obj)) {
+      key = _.findIndex(obj, predicate, context);
+    } else {
+      key = _.findKey(obj, predicate, context);
+    }
+    if (key !== void 0 && key !== -1) return obj[key];
+  };
+
+  // Return all the elements that pass a truth test.
+  // Aliased as `select`.
+  _.filter = _.select = function(obj, predicate, context) {
+    var results = [];
+    predicate = cb(predicate, context);
+    _.each(obj, function(value, index, list) {
+      if (predicate(value, index, list)) results.push(value);
+    });
+    return results;
+  };
+
+  // Return all the elements for which a truth test fails.
+  _.reject = function(obj, predicate, context) {
+    return _.filter(obj, _.negate(cb(predicate)), context);
+  };
+
+  // Determine whether all of the elements match a truth test.
+  // Aliased as `all`.
+  _.every = _.all = function(obj, predicate, context) {
+    predicate = cb(predicate, context);
+    var keys = !isArrayLike(obj) && _.keys(obj),
+        length = (keys || obj).length;
+    for (var index = 0; index < length; index++) {
+      var currentKey = keys ? keys[index] : index;
+      if (!predicate(obj[currentKey], currentKey, obj)) return false;
+    }
+    return true;
+  };
+
+  // Determine if at least one element in the object matches a truth test.
+  // Aliased as `any`.
+  _.some = _.any = function(obj, predicate, context) {
+    predicate = cb(predicate, context);
+    var keys = !isArrayLike(obj) && _.keys(obj),
+        length = (keys || obj).length;
+    for (var index = 0; index < length; index++) {
+      var currentKey = keys ? keys[index] : index;
+      if (predicate(obj[currentKey], currentKey, obj)) return true;
+    }
+    return false;
+  };
+
+  // Determine if the array or object contains a given item (using `===`).
+  // Aliased as `includes` and `include`.
+  _.contains = _.includes = _.include = function(obj, item, fromIndex, guard) {
+    if (!isArrayLike(obj)) obj = _.values(obj);
+    if (typeof fromIndex != 'number' || guard) fromIndex = 0;
+    return _.indexOf(obj, item, fromIndex) >= 0;
+  };
+
+  // Invoke a method (with arguments) on every item in a collection.
+  _.invoke = function(obj, method) {
+    var args = slice.call(arguments, 2);
+    var isFunc = _.isFunction(method);
+    return _.map(obj, function(value) {
+      var func = isFunc ? method : value[method];
+      return func == null ? func : func.apply(value, args);
+    });
+  };
+
+  // Convenience version of a common use case of `map`: fetching a property.
+  _.pluck = function(obj, key) {
+    return _.map(obj, _.property(key));
+  };
+
+  // Convenience version of a common use case of `filter`: selecting only objects
+  // containing specific `key:value` pairs.
+  _.where = function(obj, attrs) {
+    return _.filter(obj, _.matcher(attrs));
+  };
+
+  // Convenience version of a common use case of `find`: getting the first object
+  // containing specific `key:value` pairs.
+  _.findWhere = function(obj, attrs) {
+    return _.find(obj, _.matcher(attrs));
+  };
+
+  // Return the maximum element (or element-based computation).
+  _.max = function(obj, iteratee, context) {
+    var result = -Infinity, lastComputed = -Infinity,
+        value, computed;
+    if (iteratee == null && obj != null) {
+      obj = isArrayLike(obj) ? obj : _.values(obj);
+      for (var i = 0, length = obj.length; i < length; i++) {
+        value = obj[i];
+        if (value > result) {
+          result = value;
+        }
+      }
+    } else {
+      iteratee = cb(iteratee, context);
+      _.each(obj, function(value, index, list) {
+        computed = iteratee(value, index, list);
+        if (computed > lastComputed || computed === -Infinity && result === -Infinity) {
+          result = value;
+          lastComputed = computed;
+        }
+      });
+    }
+    return result;
+  };
+
+  // Return the minimum element (or element-based computation).
+  _.min = function(obj, iteratee, context) {
+    var result = Infinity, lastComputed = Infinity,
+        value, computed;
+    if (iteratee == null && obj != null) {
+      obj = isArrayLike(obj) ? obj : _.values(obj);
+      for (var i = 0, length = obj.length; i < length; i++) {
+        value = obj[i];
+        if (value < result) {
+          result = value;
+        }
+      }
+    } else {
+      iteratee = cb(iteratee, context);
+      _.each(obj, function(value, index, list) {
+        computed = iteratee(value, index, list);
+        if (computed < lastComputed || computed === Infinity && result === Infinity) {
+          result = value;
+          lastComputed = computed;
+        }
+      });
+    }
+    return result;
+  };
+
+  // Shuffle a collection, using the modern version of the
+  // [Fisher-Yates shuffle](http://en.wikipedia.org/wiki/Fisher–Yates_shuffle).
+  _.shuffle = function(obj) {
+    var set = isArrayLike(obj) ? obj : _.values(obj);
+    var length = set.length;
+    var shuffled = Array(length);
+    for (var index = 0, rand; index < length; index++) {
+      rand = _.random(0, index);
+      if (rand !== index) shuffled[index] = shuffled[rand];
+      shuffled[rand] = set[index];
+    }
+    return shuffled;
+  };
+
+  // Sample **n** random values from a collection.
+  // If **n** is not specified, returns a single random element.
+  // The internal `guard` argument allows it to work with `map`.
+  _.sample = function(obj, n, guard) {
+    if (n == null || guard) {
+      if (!isArrayLike(obj)) obj = _.values(obj);
+      return obj[_.random(obj.length - 1)];
+    }
+    return _.shuffle(obj).slice(0, Math.max(0, n));
+  };
+
+  // Sort the object's values by a criterion produced by an iteratee.
+  _.sortBy = function(obj, iteratee, context) {
+    iteratee = cb(iteratee, context);
+    return _.pluck(_.map(obj, function(value, index, list) {
+      return {
+        value: value,
+        index: index,
+        criteria: iteratee(value, index, list)
+      };
+    }).sort(function(left, right) {
+      var a = left.criteria;
+      var b = right.criteria;
+      if (a !== b) {
+        if (a > b || a === void 0) return 1;
+        if (a < b || b === void 0) return -1;
+      }
+      return left.index - right.index;
+    }), 'value');
+  };
+
+  // An internal function used for aggregate "group by" operations.
+  var group = function(behavior) {
+    return function(obj, iteratee, context) {
+      var result = {};
+      iteratee = cb(iteratee, context);
+      _.each(obj, function(value, index) {
+        var key = iteratee(value, index, obj);
+        behavior(result, value, key);
+      });
+      return result;
+    };
+  };
+
+  // Groups the object's values by a criterion. Pass either a string attribute
+  // to group by, or a function that returns the criterion.
+  _.groupBy = group(function(result, value, key) {
+    if (_.has(result, key)) result[key].push(value); else result[key] = [value];
+  });
+
+  // Indexes the object's values by a criterion, similar to `groupBy`, but for
+  // when you know that your index values will be unique.
+  _.indexBy = group(function(result, value, key) {
+    result[key] = value;
+  });
+
+  // Counts instances of an object that group by a certain criterion. Pass
+  // either a string attribute to count by, or a function that returns the
+  // criterion.
+  _.countBy = group(function(result, value, key) {
+    if (_.has(result, key)) result[key]++; else result[key] = 1;
+  });
+
+  // Safely create a real, live array from anything iterable.
+  _.toArray = function(obj) {
+    if (!obj) return [];
+    if (_.isArray(obj)) return slice.call(obj);
+    if (isArrayLike(obj)) return _.map(obj, _.identity);
+    return _.values(obj);
+  };
+
+  // Return the number of elements in an object.
+  _.size = function(obj) {
+    if (obj == null) return 0;
+    return isArrayLike(obj) ? obj.length : _.keys(obj).length;
+  };
+
+  // Split a collection into two arrays: one whose elements all satisfy the given
+  // predicate, and one whose elements all do not satisfy the predicate.
+  _.partition = function(obj, predicate, context) {
+    predicate = cb(predicate, context);
+    var pass = [], fail = [];
+    _.each(obj, function(value, key, obj) {
+      (predicate(value, key, obj) ? pass : fail).push(value);
+    });
+    return [pass, fail];
+  };
+
+  // Array Functions
+  // ---------------
+
+  // Get the first element of an array. Passing **n** will return the first N
+  // values in the array. Aliased as `head` and `take`. The **guard** check
+  // allows it to work with `_.map`.
+  _.first = _.head = _.take = function(array, n, guard) {
+    if (array == null) return void 0;
+    if (n == null || guard) return array[0];
+    return _.initial(array, array.length - n);
+  };
+
+  // Returns everything but the last entry of the array. Especially useful on
+  // the arguments object. Passing **n** will return all the values in
+  // the array, excluding the last N.
+  _.initial = function(array, n, guard) {
+    return slice.call(array, 0, Math.max(0, array.length - (n == null || guard ? 1 : n)));
+  };
+
+  // Get the last element of an array. Passing **n** will return the last N
+  // values in the array.
+  _.last = function(array, n, guard) {
+    if (array == null) return void 0;
+    if (n == null || guard) return array[array.length - 1];
+    return _.rest(array, Math.max(0, array.length - n));
+  };
+
+  // Returns everything but the first entry of the array. Aliased as `tail` and `drop`.
+  // Especially useful on the arguments object. Passing an **n** will return
+  // the rest N values in the array.
+  _.rest = _.tail = _.drop = function(array, n, guard) {
+    return slice.call(array, n == null || guard ? 1 : n);
+  };
+
+  // Trim out all falsy values from an array.
+  _.compact = function(array) {
+    return _.filter(array, _.identity);
+  };
+
+  // Internal implementation of a recursive `flatten` function.
+  var flatten = function(input, shallow, strict, startIndex) {
+    var output = [], idx = 0;
+    for (var i = startIndex || 0, length = getLength(input); i < length; i++) {
+      var value = input[i];
+      if (isArrayLike(value) && (_.isArray(value) || _.isArguments(value))) {
+        //flatten current level of array or arguments object
+        if (!shallow) value = flatten(value, shallow, strict);
+        var j = 0, len = value.length;
+        output.length += len;
+        while (j < len) {
+          output[idx++] = value[j++];
+        }
+      } else if (!strict) {
+        output[idx++] = value;
+      }
+    }
+    return output;
+  };
+
+  // Flatten out an array, either recursively (by default), or just one level.
+  _.flatten = function(array, shallow) {
+    return flatten(array, shallow, false);
+  };
+
+  // Return a version of the array that does not contain the specified value(s).
+  _.without = function(array) {
+    return _.difference(array, slice.call(arguments, 1));
+  };
+
+  // Produce a duplicate-free version of the array. If the array has already
+  // been sorted, you have the option of using a faster algorithm.
+  // Aliased as `unique`.
+  _.uniq = _.unique = function(array, isSorted, iteratee, context) {
+    if (!_.isBoolean(isSorted)) {
+      context = iteratee;
+      iteratee = isSorted;
+      isSorted = false;
+    }
+    if (iteratee != null) iteratee = cb(iteratee, context);
+    var result = [];
+    var seen = [];
+    for (var i = 0, length = getLength(array); i < length; i++) {
+      var value = array[i],
+          computed = iteratee ? iteratee(value, i, array) : value;
+      if (isSorted) {
+        if (!i || seen !== computed) result.push(value);
+        seen = computed;
+      } else if (iteratee) {
+        if (!_.contains(seen, computed)) {
+          seen.push(computed);
+          result.push(value);
+        }
+      } else if (!_.contains(result, value)) {
+        result.push(value);
+      }
+    }
+    return result;
+  };
+
+  // Produce an array that contains the union: each distinct element from all of
+  // the passed-in arrays.
+  _.union = function() {
+    return _.uniq(flatten(arguments, true, true));
+  };
+
+  // Produce an array that contains every item shared between all the
+  // passed-in arrays.
+  _.intersection = function(array) {
+    var result = [];
+    var argsLength = arguments.length;
+    for (var i = 0, length = getLength(array); i < length; i++) {
+      var item = array[i];
+      if (_.contains(result, item)) continue;
+      for (var j = 1; j < argsLength; j++) {
+        if (!_.contains(arguments[j], item)) break;
+      }
+      if (j === argsLength) result.push(item);
+    }
+    return result;
+  };
+
+  // Take the difference between one array and a number of other arrays.
+  // Only the elements present in just the first array will remain.
+  _.difference = function(array) {
+    var rest = flatten(arguments, true, true, 1);
+    return _.filter(array, function(value){
+      return !_.contains(rest, value);
+    });
+  };
+
+  // Zip together multiple lists into a single array -- elements that share
+  // an index go together.
+  _.zip = function() {
+    return _.unzip(arguments);
+  };
+
+  // Complement of _.zip. Unzip accepts an array of arrays and groups
+  // each array's elements on shared indices
+  _.unzip = function(array) {
+    var length = array && _.max(array, getLength).length || 0;
+    var result = Array(length);
+
+    for (var index = 0; index < length; index++) {
+      result[index] = _.pluck(array, index);
+    }
+    return result;
+  };
+
+  // Converts lists into objects. Pass either a single array of `[key, value]`
+  // pairs, or two parallel arrays of the same length -- one of keys, and one of
+  // the corresponding values.
+  _.object = function(list, values) {
+    var result = {};
+    for (var i = 0, length = getLength(list); i < length; i++) {
+      if (values) {
+        result[list[i]] = values[i];
+      } else {
+        result[list[i][0]] = list[i][1];
+      }
+    }
+    return result;
+  };
+
+  // Generator function to create the findIndex and findLastIndex functions
+  function createPredicateIndexFinder(dir) {
+    return function(array, predicate, context) {
+      predicate = cb(predicate, context);
+      var length = getLength(array);
+      var index = dir > 0 ? 0 : length - 1;
+      for (; index >= 0 && index < length; index += dir) {
+        if (predicate(array[index], index, array)) return index;
+      }
+      return -1;
+    };
+  }
+
+  // Returns the first index on an array-like that passes a predicate test
+  _.findIndex = createPredicateIndexFinder(1);
+  _.findLastIndex = createPredicateIndexFinder(-1);
+
+  // Use a comparator function to figure out the smallest index at which
+  // an object should be inserted so as to maintain order. Uses binary search.
+  _.sortedIndex = function(array, obj, iteratee, context) {
+    iteratee = cb(iteratee, context, 1);
+    var value = iteratee(obj);
+    var low = 0, high = getLength(array);
+    while (low < high) {
+      var mid = Math.floor((low + high) / 2);
+      if (iteratee(array[mid]) < value) low = mid + 1; else high = mid;
+    }
+    return low;
+  };
+
+  // Generator function to create the indexOf and lastIndexOf functions
+  function createIndexFinder(dir, predicateFind, sortedIndex) {
+    return function(array, item, idx) {
+      var i = 0, length = getLength(array);
+      if (typeof idx == 'number') {
+        if (dir > 0) {
+            i = idx >= 0 ? idx : Math.max(idx + length, i);
+        } else {
+            length = idx >= 0 ? Math.min(idx + 1, length) : idx + length + 1;
+        }
+      } else if (sortedIndex && idx && length) {
+        idx = sortedIndex(array, item);
+        return array[idx] === item ? idx : -1;
+      }
+      if (item !== item) {
+        idx = predicateFind(slice.call(array, i, length), _.isNaN);
+        return idx >= 0 ? idx + i : -1;
+      }
+      for (idx = dir > 0 ? i : length - 1; idx >= 0 && idx < length; idx += dir) {
+        if (array[idx] === item) return idx;
+      }
+      return -1;
+    };
+  }
+
+  // Return the position of the first occurrence of an item in an array,
+  // or -1 if the item is not included in the array.
+  // If the array is large and already in sort order, pass `true`
+  // for **isSorted** to use binary search.
+  _.indexOf = createIndexFinder(1, _.findIndex, _.sortedIndex);
+  _.lastIndexOf = createIndexFinder(-1, _.findLastIndex);
+
+  // Generate an integer Array containing an arithmetic progression. A port of
+  // the native Python `range()` function. See
+  // [the Python documentation](http://docs.python.org/library/functions.html#range).
+  _.range = function(start, stop, step) {
+    if (stop == null) {
+      stop = start || 0;
+      start = 0;
+    }
+    step = step || 1;
+
+    var length = Math.max(Math.ceil((stop - start) / step), 0);
+    var range = Array(length);
+
+    for (var idx = 0; idx < length; idx++, start += step) {
+      range[idx] = start;
+    }
+
+    return range;
+  };
+
+  // Function (ahem) Functions
+  // ------------------
+
+  // Determines whether to execute a function as a constructor
+  // or a normal function with the provided arguments
+  var executeBound = function(sourceFunc, boundFunc, context, callingContext, args) {
+    if (!(callingContext instanceof boundFunc)) return sourceFunc.apply(context, args);
+    var self = baseCreate(sourceFunc.prototype);
+    var result = sourceFunc.apply(self, args);
+    if (_.isObject(result)) return result;
+    return self;
+  };
+
+  // Create a function bound to a given object (assigning `this`, and arguments,
+  // optionally). Delegates to **ECMAScript 5**'s native `Function.bind` if
+  // available.
+  _.bind = function(func, context) {
+    if (nativeBind && func.bind === nativeBind) return nativeBind.apply(func, slice.call(arguments, 1));
+    if (!_.isFunction(func)) throw new TypeError('Bind must be called on a function');
+    var args = slice.call(arguments, 2);
+    var bound = function() {
+      return executeBound(func, bound, context, this, args.concat(slice.call(arguments)));
+    };
+    return bound;
+  };
+
+  // Partially apply a function by creating a version that has had some of its
+  // arguments pre-filled, without changing its dynamic `this` context. _ acts
+  // as a placeholder, allowing any combination of arguments to be pre-filled.
+  _.partial = function(func) {
+    var boundArgs = slice.call(arguments, 1);
+    var bound = function() {
+      var position = 0, length = boundArgs.length;
+      var args = Array(length);
+      for (var i = 0; i < length; i++) {
+        args[i] = boundArgs[i] === _ ? arguments[position++] : boundArgs[i];
+      }
+      while (position < arguments.length) args.push(arguments[position++]);
+      return executeBound(func, bound, this, this, args);
+    };
+    return bound;
+  };
+
+  // Bind a number of an object's methods to that object. Remaining arguments
+  // are the method names to be bound. Useful for ensuring that all callbacks
+  // defined on an object belong to it.
+  _.bindAll = function(obj) {
+    var i, length = arguments.length, key;
+    if (length <= 1) throw new Error('bindAll must be passed function names');
+    for (i = 1; i < length; i++) {
+      key = arguments[i];
+      obj[key] = _.bind(obj[key], obj);
+    }
+    return obj;
+  };
+
+  // Memoize an expensive function by storing its results.
+  _.memoize = function(func, hasher) {
+    var memoize = function(key) {
+      var cache = memoize.cache;
+      var address = '' + (hasher ? hasher.apply(this, arguments) : key);
+      if (!_.has(cache, address)) cache[address] = func.apply(this, arguments);
+      return cache[address];
+    };
+    memoize.cache = {};
+    return memoize;
+  };
+
+  // Delays a function for the given number of milliseconds, and then calls
+  // it with the arguments supplied.
+  _.delay = function(func, wait) {
+    var args = slice.call(arguments, 2);
+    return setTimeout(function(){
+      return func.apply(null, args);
+    }, wait);
+  };
+
+  // Defers a function, scheduling it to run after the current call stack has
+  // cleared.
+  _.defer = _.partial(_.delay, _, 1);
+
+  // Returns a function, that, when invoked, will only be triggered at most once
+  // during a given window of time. Normally, the throttled function will run
+  // as much as it can, without ever going more than once per `wait` duration;
+  // but if you'd like to disable the execution on the leading edge, pass
+  // `{leading: false}`. To disable execution on the trailing edge, ditto.
+  _.throttle = function(func, wait, options) {
+    var context, args, result;
+    var timeout = null;
+    var previous = 0;
+    if (!options) options = {};
+    var later = function() {
+      previous = options.leading === false ? 0 : _.now();
+      timeout = null;
+      result = func.apply(context, args);
+      if (!timeout) context = args = null;
+    };
+    return function() {
+      var now = _.now();
+      if (!previous && options.leading === false) previous = now;
+      var remaining = wait - (now - previous);
+      context = this;
+      args = arguments;
+      if (remaining <= 0 || remaining > wait) {
+        if (timeout) {
+          clearTimeout(timeout);
+          timeout = null;
+        }
+        previous = now;
+        result = func.apply(context, args);
+        if (!timeout) context = args = null;
+      } else if (!timeout && options.trailing !== false) {
+        timeout = setTimeout(later, remaining);
+      }
+      return result;
+    };
+  };
+
+  // Returns a function, that, as long as it continues to be invoked, will not
+  // be triggered. The function will be called after it stops being called for
+  // N milliseconds. If `immediate` is passed, trigger the function on the
+  // leading edge, instead of the trailing.
+  _.debounce = function(func, wait, immediate) {
+    var timeout, args, context, timestamp, result;
+
+    var later = function() {
+      var last = _.now() - timestamp;
+
+      if (last < wait && last >= 0) {
+        timeout = setTimeout(later, wait - last);
+      } else {
+        timeout = null;
+        if (!immediate) {
+          result = func.apply(context, args);
+          if (!timeout) context = args = null;
+        }
+      }
+    };
+
+    return function() {
+      context = this;
+      args = arguments;
+      timestamp = _.now();
+      var callNow = immediate && !timeout;
+      if (!timeout) timeout = setTimeout(later, wait);
+      if (callNow) {
+        result = func.apply(context, args);
+        context = args = null;
+      }
+
+      return result;
+    };
+  };
+
+  // Returns the first function passed as an argument to the second,
+  // allowing you to adjust arguments, run code before and after, and
+  // conditionally execute the original function.
+  _.wrap = function(func, wrapper) {
+    return _.partial(wrapper, func);
+  };
+
+  // Returns a negated version of the passed-in predicate.
+  _.negate = function(predicate) {
+    return function() {
+      return !predicate.apply(this, arguments);
+    };
+  };
+
+  // Returns a function that is the composition of a list of functions, each
+  // consuming the return value of the function that follows.
+  _.compose = function() {
+    var args = arguments;
+    var start = args.length - 1;
+    return function() {
+      var i = start;
+      var result = args[start].apply(this, arguments);
+      while (i--) result = args[i].call(this, result);
+      return result;
+    };
+  };
+
+  // Returns a function that will only be executed on and after the Nth call.
+  _.after = function(times, func) {
+    return function() {
+      if (--times < 1) {
+        return func.apply(this, arguments);
+      }
+    };
+  };
+
+  // Returns a function that will only be executed up to (but not including) the Nth call.
+  _.before = function(times, func) {
+    var memo;
+    return function() {
+      if (--times > 0) {
+        memo = func.apply(this, arguments);
+      }
+      if (times <= 1) func = null;
+      return memo;
+    };
+  };
+
+  // Returns a function that will be executed at most one time, no matter how
+  // often you call it. Useful for lazy initialization.
+  _.once = _.partial(_.before, 2);
+
+  // Object Functions
+  // ----------------
+
+  // Keys in IE < 9 that won't be iterated by `for key in ...` and thus missed.
+  var hasEnumBug = !{toString: null}.propertyIsEnumerable('toString');
+  var nonEnumerableProps = ['valueOf', 'isPrototypeOf', 'toString',
+                      'propertyIsEnumerable', 'hasOwnProperty', 'toLocaleString'];
+
+  function collectNonEnumProps(obj, keys) {
+    var nonEnumIdx = nonEnumerableProps.length;
+    var constructor = obj.constructor;
+    var proto = (_.isFunction(constructor) && constructor.prototype) || ObjProto;
+
+    // Constructor is a special case.
+    var prop = 'constructor';
+    if (_.has(obj, prop) && !_.contains(keys, prop)) keys.push(prop);
+
+    while (nonEnumIdx--) {
+      prop = nonEnumerableProps[nonEnumIdx];
+      if (prop in obj && obj[prop] !== proto[prop] && !_.contains(keys, prop)) {
+        keys.push(prop);
+      }
+    }
+  }
+
+  // Retrieve the names of an object's own properties.
+  // Delegates to **ECMAScript 5**'s native `Object.keys`
+  _.keys = function(obj) {
+    if (!_.isObject(obj)) return [];
+    if (nativeKeys) return nativeKeys(obj);
+    var keys = [];
+    for (var key in obj) if (_.has(obj, key)) keys.push(key);
+    // Ahem, IE < 9.
+    if (hasEnumBug) collectNonEnumProps(obj, keys);
+    return keys;
+  };
+
+  // Retrieve all the property names of an object.
+  _.allKeys = function(obj) {
+    if (!_.isObject(obj)) return [];
+    var keys = [];
+    for (var key in obj) keys.push(key);
+    // Ahem, IE < 9.
+    if (hasEnumBug) collectNonEnumProps(obj, keys);
+    return keys;
+  };
+
+  // Retrieve the values of an object's properties.
+  _.values = function(obj) {
+    var keys = _.keys(obj);
+    var length = keys.length;
+    var values = Array(length);
+    for (var i = 0; i < length; i++) {
+      values[i] = obj[keys[i]];
+    }
+    return values;
+  };
+
+  // Returns the results of applying the iteratee to each element of the object
+  // In contrast to _.map it returns an object
+  _.mapObject = function(obj, iteratee, context) {
+    iteratee = cb(iteratee, context);
+    var keys =  _.keys(obj),
+          length = keys.length,
+          results = {},
+          currentKey;
+      for (var index = 0; index < length; index++) {
+        currentKey = keys[index];
+        results[currentKey] = iteratee(obj[currentKey], currentKey, obj);
+      }
+      return results;
+  };
+
+  // Convert an object into a list of `[key, value]` pairs.
+  _.pairs = function(obj) {
+    var keys = _.keys(obj);
+    var length = keys.length;
+    var pairs = Array(length);
+    for (var i = 0; i < length; i++) {
+      pairs[i] = [keys[i], obj[keys[i]]];
+    }
+    return pairs;
+  };
+
+  // Invert the keys and values of an object. The values must be serializable.
+  _.invert = function(obj) {
+    var result = {};
+    var keys = _.keys(obj);
+    for (var i = 0, length = keys.length; i < length; i++) {
+      result[obj[keys[i]]] = keys[i];
+    }
+    return result;
+  };
+
+  // Return a sorted list of the function names available on the object.
+  // Aliased as `methods`
+  _.functions = _.methods = function(obj) {
+    var names = [];
+    for (var key in obj) {
+      if (_.isFunction(obj[key])) names.push(key);
+    }
+    return names.sort();
+  };
+
+  // Extend a given object with all the properties in passed-in object(s).
+  _.extend = createAssigner(_.allKeys);
+
+  // Assigns a given object with all the own properties in the passed-in object(s)
+  // (https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object/assign)
+  _.extendOwn = _.assign = createAssigner(_.keys);
+
+  // Returns the first key on an object that passes a predicate test
+  _.findKey = function(obj, predicate, context) {
+    predicate = cb(predicate, context);
+    var keys = _.keys(obj), key;
+    for (var i = 0, length = keys.length; i < length; i++) {
+      key = keys[i];
+      if (predicate(obj[key], key, obj)) return key;
+    }
+  };
+
+  // Return a copy of the object only containing the whitelisted properties.
+  _.pick = function(object, oiteratee, context) {
+    var result = {}, obj = object, iteratee, keys;
+    if (obj == null) return result;
+    if (_.isFunction(oiteratee)) {
+      keys = _.allKeys(obj);
+      iteratee = optimizeCb(oiteratee, context);
+    } else {
+      keys = flatten(arguments, false, false, 1);
+      iteratee = function(value, key, obj) { return key in obj; };
+      obj = Object(obj);
+    }
+    for (var i = 0, length = keys.length; i < length; i++) {
+      var key = keys[i];
+      var value = obj[key];
+      if (iteratee(value, key, obj)) result[key] = value;
+    }
+    return result;
+  };
+
+   // Return a copy of the object without the blacklisted properties.
+  _.omit = function(obj, iteratee, context) {
+    if (_.isFunction(iteratee)) {
+      iteratee = _.negate(iteratee);
+    } else {
+      var keys = _.map(flatten(arguments, false, false, 1), String);
+      iteratee = function(value, key) {
+        return !_.contains(keys, key);
+      };
+    }
+    return _.pick(obj, iteratee, context);
+  };
+
+  // Fill in a given object with default properties.
+  _.defaults = createAssigner(_.allKeys, true);
+
+  // Creates an object that inherits from the given prototype object.
+  // If additional properties are provided then they will be added to the
+  // created object.
+  _.create = function(prototype, props) {
+    var result = baseCreate(prototype);
+    if (props) _.extendOwn(result, props);
+    return result;
+  };
+
+  // Create a (shallow-cloned) duplicate of an object.
+  _.clone = function(obj) {
+    if (!_.isObject(obj)) return obj;
+    return _.isArray(obj) ? obj.slice() : _.extend({}, obj);
+  };
+
+  // Invokes interceptor with the obj, and then returns obj.
+  // The primary purpose of this method is to "tap into" a method chain, in
+  // order to perform operations on intermediate results within the chain.
+  _.tap = function(obj, interceptor) {
+    interceptor(obj);
+    return obj;
+  };
+
+  // Returns whether an object has a given set of `key:value` pairs.
+  _.isMatch = function(object, attrs) {
+    var keys = _.keys(attrs), length = keys.length;
+    if (object == null) return !length;
+    var obj = Object(object);
+    for (var i = 0; i < length; i++) {
+      var key = keys[i];
+      if (attrs[key] !== obj[key] || !(key in obj)) return false;
+    }
+    return true;
+  };
+
+
+  // Internal recursive comparison function for `isEqual`.
+  var eq = function(a, b, aStack, bStack) {
+    // Identical objects are equal. `0 === -0`, but they aren't identical.
+    // See the [Harmony `egal` proposal](http://wiki.ecmascript.org/doku.php?id=harmony:egal).
+    if (a === b) return a !== 0 || 1 / a === 1 / b;
+    // A strict comparison is necessary because `null == undefined`.
+    if (a == null || b == null) return a === b;
+    // Unwrap any wrapped objects.
+    if (a instanceof _) a = a._wrapped;
+    if (b instanceof _) b = b._wrapped;
+    // Compare `[[Class]]` names.
+    var className = toString.call(a);
+    if (className !== toString.call(b)) return false;
+    switch (className) {
+      // Strings, numbers, regular expressions, dates, and booleans are compared by value.
+      case '[object RegExp]':
+      // RegExps are coerced to strings for comparison (Note: '' + /a/i === '/a/i')
+      case '[object String]':
+        // Primitives and their corresponding object wrappers are equivalent; thus, `"5"` is
+        // equivalent to `new String("5")`.
+        return '' + a === '' + b;
+      case '[object Number]':
+        // `NaN`s are equivalent, but non-reflexive.
+        // Object(NaN) is equivalent to NaN
+        if (+a !== +a) return +b !== +b;
+        // An `egal` comparison is performed for other numeric values.
+        return +a === 0 ? 1 / +a === 1 / b : +a === +b;
+      case '[object Date]':
+      case '[object Boolean]':
+        // Coerce dates and booleans to numeric primitive values. Dates are compared by their
+        // millisecond representations. Note that invalid dates with millisecond representations
+        // of `NaN` are not equivalent.
+        return +a === +b;
+    }
+
+    var areArrays = className === '[object Array]';
+    if (!areArrays) {
+      if (typeof a != 'object' || typeof b != 'object') return false;
+
+      // Objects with different constructors are not equivalent, but `Object`s or `Array`s
+      // from different frames are.
+      var aCtor = a.constructor, bCtor = b.constructor;
+      if (aCtor !== bCtor && !(_.isFunction(aCtor) && aCtor instanceof aCtor &&
+                               _.isFunction(bCtor) && bCtor instanceof bCtor)
+                          && ('constructor' in a && 'constructor' in b)) {
+        return false;
+      }
+    }
+    // Assume equality for cyclic structures. The algorithm for detecting cyclic
+    // structures is adapted from ES 5.1 section 15.12.3, abstract operation `JO`.
+
+    // Initializing stack of traversed objects.
+    // It's done here since we only need them for objects and arrays comparison.
+    aStack = aStack || [];
+    bStack = bStack || [];
+    var length = aStack.length;
+    while (length--) {
+      // Linear search. Performance is inversely proportional to the number of
+      // unique nested structures.
+      if (aStack[length] === a) return bStack[length] === b;
+    }
+
+    // Add the first object to the stack of traversed objects.
+    aStack.push(a);
+    bStack.push(b);
+
+    // Recursively compare objects and arrays.
+    if (areArrays) {
+      // Compare array lengths to determine if a deep comparison is necessary.
+      length = a.length;
+      if (length !== b.length) return false;
+      // Deep compare the contents, ignoring non-numeric properties.
+      while (length--) {
+        if (!eq(a[length], b[length], aStack, bStack)) return false;
+      }
+    } else {
+      // Deep compare objects.
+      var keys = _.keys(a), key;
+      length = keys.length;
+      // Ensure that both objects contain the same number of properties before comparing deep equality.
+      if (_.keys(b).length !== length) return false;
+      while (length--) {
+        // Deep compare each member
+        key = keys[length];
+        if (!(_.has(b, key) && eq(a[key], b[key], aStack, bStack))) return false;
+      }
+    }
+    // Remove the first object from the stack of traversed objects.
+    aStack.pop();
+    bStack.pop();
+    return true;
+  };
+
+  // Perform a deep comparison to check if two objects are equal.
+  _.isEqual = function(a, b) {
+    return eq(a, b);
+  };
+
+  // Is a given array, string, or object empty?
+  // An "empty" object has no enumerable own-properties.
+  _.isEmpty = function(obj) {
+    if (obj == null) return true;
+    if (isArrayLike(obj) && (_.isArray(obj) || _.isString(obj) || _.isArguments(obj))) return obj.length === 0;
+    return _.keys(obj).length === 0;
+  };
+
+  // Is a given value a DOM element?
+  _.isElement = function(obj) {
+    return !!(obj && obj.nodeType === 1);
+  };
+
+  // Is a given value an array?
+  // Delegates to ECMA5's native Array.isArray
+  _.isArray = nativeIsArray || function(obj) {
+    return toString.call(obj) === '[object Array]';
+  };
+
+  // Is a given variable an object?
+  _.isObject = function(obj) {
+    var type = typeof obj;
+    return type === 'function' || type === 'object' && !!obj;
+  };
+
+  // Add some isType methods: isArguments, isFunction, isString, isNumber, isDate, isRegExp, isError.
+  _.each(['Arguments', 'Function', 'String', 'Number', 'Date', 'RegExp', 'Error'], function(name) {
+    _['is' + name] = function(obj) {
+      return toString.call(obj) === '[object ' + name + ']';
+    };
+  });
+
+  // Define a fallback version of the method in browsers (ahem, IE < 9), where
+  // there isn't any inspectable "Arguments" type.
+  if (!_.isArguments(arguments)) {
+    _.isArguments = function(obj) {
+      return _.has(obj, 'callee');
+    };
+  }
+
+  // Optimize `isFunction` if appropriate. Work around some typeof bugs in old v8,
+  // IE 11 (#1621), and in Safari 8 (#1929).
+  if (typeof /./ != 'function' && typeof Int8Array != 'object') {
+    _.isFunction = function(obj) {
+      return typeof obj == 'function' || false;
+    };
+  }
+
+  // Is a given object a finite number?
+  _.isFinite = function(obj) {
+    return isFinite(obj) && !isNaN(parseFloat(obj));
+  };
+
+  // Is the given value `NaN`? (NaN is the only number which does not equal itself).
+  _.isNaN = function(obj) {
+    return _.isNumber(obj) && obj !== +obj;
+  };
+
+  // Is a given value a boolean?
+  _.isBoolean = function(obj) {
+    return obj === true || obj === false || toString.call(obj) === '[object Boolean]';
+  };
+
+  // Is a given value equal to null?
+  _.isNull = function(obj) {
+    return obj === null;
+  };
+
+  // Is a given variable undefined?
+  _.isUndefined = function(obj) {
+    return obj === void 0;
+  };
+
+  // Shortcut function for checking if an object has a given property directly
+  // on itself (in other words, not on a prototype).
+  _.has = function(obj, key) {
+    return obj != null && hasOwnProperty.call(obj, key);
+  };
+
+  // Utility Functions
+  // -----------------
+
+  // Run Underscore.js in *noConflict* mode, returning the `_` variable to its
+  // previous owner. Returns a reference to the Underscore object.
+  _.noConflict = function() {
+    root._ = previousUnderscore;
+    return this;
+  };
+
+  // Keep the identity function around for default iteratees.
+  _.identity = function(value) {
+    return value;
+  };
+
+  // Predicate-generating functions. Often useful outside of Underscore.
+  _.constant = function(value) {
+    return function() {
+      return value;
+    };
+  };
+
+  _.noop = function(){};
+
+  _.property = property;
+
+  // Generates a function for a given object that returns a given property.
+  _.propertyOf = function(obj) {
+    return obj == null ? function(){} : function(key) {
+      return obj[key];
+    };
+  };
+
+  // Returns a predicate for checking whether an object has a given set of
+  // `key:value` pairs.
+  _.matcher = _.matches = function(attrs) {
+    attrs = _.extendOwn({}, attrs);
+    return function(obj) {
+      return _.isMatch(obj, attrs);
+    };
+  };
+
+  // Run a function **n** times.
+  _.times = function(n, iteratee, context) {
+    var accum = Array(Math.max(0, n));
+    iteratee = optimizeCb(iteratee, context, 1);
+    for (var i = 0; i < n; i++) accum[i] = iteratee(i);
+    return accum;
+  };
+
+  // Return a random integer between min and max (inclusive).
+  _.random = function(min, max) {
+    if (max == null) {
+      max = min;
+      min = 0;
+    }
+    return min + Math.floor(Math.random() * (max - min + 1));
+  };
+
+  // A (possibly faster) way to get the current timestamp as an integer.
+  _.now = Date.now || function() {
+    return new Date().getTime();
+  };
+
+   // List of HTML entities for escaping.
+  var escapeMap = {
+    '&': '&amp;',
+    '<': '&lt;',
+    '>': '&gt;',
+    '"': '&quot;',
+    "'": '&#x27;',
+    '`': '&#x60;'
+  };
+  var unescapeMap = _.invert(escapeMap);
+
+  // Functions for escaping and unescaping strings to/from HTML interpolation.
+  var createEscaper = function(map) {
+    var escaper = function(match) {
+      return map[match];
+    };
+    // Regexes for identifying a key that needs to be escaped
+    var source = '(?:' + _.keys(map).join('|') + ')';
+    var testRegexp = RegExp(source);
+    var replaceRegexp = RegExp(source, 'g');
+    return function(string) {
+      string = string == null ? '' : '' + string;
+      return testRegexp.test(string) ? string.replace(replaceRegexp, escaper) : string;
+    };
+  };
+  _.escape = createEscaper(escapeMap);
+  _.unescape = createEscaper(unescapeMap);
+
+  // If the value of the named `property` is a function then invoke it with the
+  // `object` as context; otherwise, return it.
+  _.result = function(object, property, fallback) {
+    var value = object == null ? void 0 : object[property];
+    if (value === void 0) {
+      value = fallback;
+    }
+    return _.isFunction(value) ? value.call(object) : value;
+  };
+
+  // Generate a unique integer id (unique within the entire client session).
+  // Useful for temporary DOM ids.
+  var idCounter = 0;
+  _.uniqueId = function(prefix) {
+    var id = ++idCounter + '';
+    return prefix ? prefix + id : id;
+  };
+
+  // By default, Underscore uses ERB-style template delimiters, change the
+  // following template settings to use alternative delimiters.
+  _.templateSettings = {
+    evaluate    : /<%([\s\S]+?)%>/g,
+    interpolate : /<%=([\s\S]+?)%>/g,
+    escape      : /<%-([\s\S]+?)%>/g
+  };
+
+  // When customizing `templateSettings`, if you don't want to define an
+  // interpolation, evaluation or escaping regex, we need one that is
+  // guaranteed not to match.
+  var noMatch = /(.)^/;
+
+  // Certain characters need to be escaped so that they can be put into a
+  // string literal.
+  var escapes = {
+    "'":      "'",
+    '\\':     '\\',
+    '\r':     'r',
+    '\n':     'n',
+    '\u2028': 'u2028',
+    '\u2029': 'u2029'
+  };
+
+  var escaper = /\\|'|\r|\n|\u2028|\u2029/g;
+
+  var escapeChar = function(match) {
+    return '\\' + escapes[match];
+  };
+
+  // JavaScript micro-templating, similar to John Resig's implementation.
+  // Underscore templating handles arbitrary delimiters, preserves whitespace,
+  // and correctly escapes quotes within interpolated code.
+  // NB: `oldSettings` only exists for backwards compatibility.
+  _.template = function(text, settings, oldSettings) {
+    if (!settings && oldSettings) settings = oldSettings;
+    settings = _.defaults({}, settings, _.templateSettings);
+
+    // Combine delimiters into one regular expression via alternation.
+    var matcher = RegExp([
+      (settings.escape || noMatch).source,
+      (settings.interpolate || noMatch).source,
+      (settings.evaluate || noMatch).source
+    ].join('|') + '|$', 'g');
+
+    // Compile the template source, escaping string literals appropriately.
+    var index = 0;
+    var source = "__p+='";
+    text.replace(matcher, function(match, escape, interpolate, evaluate, offset) {
+      source += text.slice(index, offset).replace(escaper, escapeChar);
+      index = offset + match.length;
+
+      if (escape) {
+        source += "'+\n((__t=(" + escape + "))==null?'':_.escape(__t))+\n'";
+      } else if (interpolate) {
+        source += "'+\n((__t=(" + interpolate + "))==null?'':__t)+\n'";
+      } else if (evaluate) {
+        source += "';\n" + evaluate + "\n__p+='";
+      }
+
+      // Adobe VMs need the match returned to produce the correct offest.
+      return match;
+    });
+    source += "';\n";
+
+    // If a variable is not specified, place data values in local scope.
+    if (!settings.variable) source = 'with(obj||{}){\n' + source + '}\n';
+
+    source = "var __t,__p='',__j=Array.prototype.join," +
+      "print=function(){__p+=__j.call(arguments,'');};\n" +
+      source + 'return __p;\n';
+
+    try {
+      var render = new Function(settings.variable || 'obj', '_', source);
+    } catch (e) {
+      e.source = source;
+      throw e;
+    }
+
+    var template = function(data) {
+      return render.call(this, data, _);
+    };
+
+    // Provide the compiled source as a convenience for precompilation.
+    var argument = settings.variable || 'obj';
+    template.source = 'function(' + argument + '){\n' + source + '}';
+
+    return template;
+  };
+
+  // Add a "chain" function. Start chaining a wrapped Underscore object.
+  _.chain = function(obj) {
+    var instance = _(obj);
+    instance._chain = true;
+    return instance;
+  };
+
+  // OOP
+  // ---------------
+  // If Underscore is called as a function, it returns a wrapped object that
+  // can be used OO-style. This wrapper holds altered versions of all the
+  // underscore functions. Wrapped objects may be chained.
+
+  // Helper function to continue chaining intermediate results.
+  var result = function(instance, obj) {
+    return instance._chain ? _(obj).chain() : obj;
+  };
+
+  // Add your own custom functions to the Underscore object.
+  _.mixin = function(obj) {
+    _.each(_.functions(obj), function(name) {
+      var func = _[name] = obj[name];
+      _.prototype[name] = function() {
+        var args = [this._wrapped];
+        push.apply(args, arguments);
+        return result(this, func.apply(_, args));
+      };
+    });
+  };
+
+  // Add all of the Underscore functions to the wrapper object.
+  _.mixin(_);
+
+  // Add all mutator Array functions to the wrapper.
+  _.each(['pop', 'push', 'reverse', 'shift', 'sort', 'splice', 'unshift'], function(name) {
+    var method = ArrayProto[name];
+    _.prototype[name] = function() {
+      var obj = this._wrapped;
+      method.apply(obj, arguments);
+      if ((name === 'shift' || name === 'splice') && obj.length === 0) delete obj[0];
+      return result(this, obj);
+    };
+  });
+
+  // Add all accessor Array functions to the wrapper.
+  _.each(['concat', 'join', 'slice'], function(name) {
+    var method = ArrayProto[name];
+    _.prototype[name] = function() {
+      return result(this, method.apply(this._wrapped, arguments));
+    };
+  });
+
+  // Extracts the result from a wrapped and chained object.
+  _.prototype.value = function() {
+    return this._wrapped;
+  };
+
+  // Provide unwrapping proxy for some methods used in engine operations
+  // such as arithmetic and JSON stringification.
+  _.prototype.valueOf = _.prototype.toJSON = _.prototype.value;
+
+  _.prototype.toString = function() {
+    return '' + this._wrapped;
+  };
+
+  // AMD registration happens at the end for compatibility with AMD loaders
+  // that may not enforce next-turn semantics on modules. Even though general
+  // practice for AMD registration is to be anonymous, underscore registers
+  // as a named module because, like jQuery, it is a base library that is
+  // popular enough to be bundled in a third party lib, but not be part of
+  // an AMD load request. Those cases could generate an error when an
+  // anonymous define() is called outside of a loader request.
+  if (typeof define === 'function' && define.amd) {
+    define('underscore', [], function() {
+      return _;
+    });
+  }
+}.call(this));
+
+},{}],26:[function(require,module,exports){
+arguments[4][19][0].apply(exports,arguments)
+},{"dup":19}],27:[function(require,module,exports){
+module.exports = function isBuffer(arg) {
+  return arg && typeof arg === 'object'
+    && typeof arg.copy === 'function'
+    && typeof arg.fill === 'function'
+    && typeof arg.readUInt8 === 'function';
+}
+},{}],28:[function(require,module,exports){
+(function (process,global){
+// Copyright Joyent, Inc. and other Node contributors.
+//
+// Permission is hereby granted, free of charge, to any person obtaining a
+// copy of this software and associated documentation files (the
+// "Software"), to deal in the Software without restriction, including
+// without limitation the rights to use, copy, modify, merge, publish,
+// distribute, sublicense, and/or sell copies of the Software, and to permit
+// persons to whom the Software is furnished to do so, subject to the
+// following conditions:
+//
+// The above copyright notice and this permission notice shall be included
+// in all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+// MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN
+// NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
+// DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
+// OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
+// USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+var formatRegExp = /%[sdj%]/g;
+exports.format = function(f) {
+  if (!isString(f)) {
+    var objects = [];
+    for (var i = 0; i < arguments.length; i++) {
+      objects.push(inspect(arguments[i]));
+    }
+    return objects.join(' ');
+  }
+
+  var i = 1;
+  var args = arguments;
+  var len = args.length;
+  var str = String(f).replace(formatRegExp, function(x) {
+    if (x === '%%') return '%';
+    if (i >= len) return x;
+    switch (x) {
+      case '%s': return String(args[i++]);
+      case '%d': return Number(args[i++]);
+      case '%j':
+        try {
+          return JSON.stringify(args[i++]);
+        } catch (_) {
+          return '[Circular]';
+        }
+      default:
+        return x;
+    }
+  });
+  for (var x = args[i]; i < len; x = args[++i]) {
+    if (isNull(x) || !isObject(x)) {
+      str += ' ' + x;
+    } else {
+      str += ' ' + inspect(x);
+    }
+  }
+  return str;
+};
+
+
+// Mark that a method should not be used.
+// Returns a modified function which warns once by default.
+// If --no-deprecation is set, then it is a no-op.
+exports.deprecate = function(fn, msg) {
+  // Allow for deprecating things in the process of starting up.
+  if (isUndefined(global.process)) {
+    return function() {
+      return exports.deprecate(fn, msg).apply(this, arguments);
+    };
+  }
+
+  if (process.noDeprecation === true) {
+    return fn;
+  }
+
+  var warned = false;
+  function deprecated() {
+    if (!warned) {
+      if (process.throwDeprecation) {
+        throw new Error(msg);
+      } else if (process.traceDeprecation) {
+        console.trace(msg);
+      } else {
+        console.error(msg);
+      }
+      warned = true;
+    }
+    return fn.apply(this, arguments);
+  }
+
+  return deprecated;
+};
+
+
+var debugs = {};
+var debugEnviron;
+exports.debuglog = function(set) {
+  if (isUndefined(debugEnviron))
+    debugEnviron = process.env.NODE_DEBUG || '';
+  set = set.toUpperCase();
+  if (!debugs[set]) {
+    if (new RegExp('\\b' + set + '\\b', 'i').test(debugEnviron)) {
+      var pid = process.pid;
+      debugs[set] = function() {
+        var msg = exports.format.apply(exports, arguments);
+        console.error('%s %d: %s', set, pid, msg);
+      };
+    } else {
+      debugs[set] = function() {};
+    }
+  }
+  return debugs[set];
+};
+
+
+/**
+ * Echos the value of a value. Trys to print the value out
+ * in the best way possible given the different types.
+ *
+ * @param {Object} obj The object to print out.
+ * @param {Object} opts Optional options object that alters the output.
+ */
+/* legacy: obj, showHidden, depth, colors*/
+function inspect(obj, opts) {
+  // default options
+  var ctx = {
+    seen: [],
+    stylize: stylizeNoColor
+  };
+  // legacy...
+  if (arguments.length >= 3) ctx.depth = arguments[2];
+  if (arguments.length >= 4) ctx.colors = arguments[3];
+  if (isBoolean(opts)) {
+    // legacy...
+    ctx.showHidden = opts;
+  } else if (opts) {
+    // got an "options" object
+    exports._extend(ctx, opts);
+  }
+  // set default options
+  if (isUndefined(ctx.showHidden)) ctx.showHidden = false;
+  if (isUndefined(ctx.depth)) ctx.depth = 2;
+  if (isUndefined(ctx.colors)) ctx.colors = false;
+  if (isUndefined(ctx.customInspect)) ctx.customInspect = true;
+  if (ctx.colors) ctx.stylize = stylizeWithColor;
+  return formatValue(ctx, obj, ctx.depth);
+}
+exports.inspect = inspect;
+
+
+// http://en.wikipedia.org/wiki/ANSI_escape_code#graphics
+inspect.colors = {
+  'bold' : [1, 22],
+  'italic' : [3, 23],
+  'underline' : [4, 24],
+  'inverse' : [7, 27],
+  'white' : [37, 39],
+  'grey' : [90, 39],
+  'black' : [30, 39],
+  'blue' : [34, 39],
+  'cyan' : [36, 39],
+  'green' : [32, 39],
+  'magenta' : [35, 39],
+  'red' : [31, 39],
+  'yellow' : [33, 39]
+};
+
+// Don't use 'blue' not visible on cmd.exe
+inspect.styles = {
+  'special': 'cyan',
+  'number': 'yellow',
+  'boolean': 'yellow',
+  'undefined': 'grey',
+  'null': 'bold',
+  'string': 'green',
+  'date': 'magenta',
+  // "name": intentionally not styling
+  'regexp': 'red'
+};
+
+
+function stylizeWithColor(str, styleType) {
+  var style = inspect.styles[styleType];
+
+  if (style) {
+    return '\u001b[' + inspect.colors[style][0] + 'm' + str +
+           '\u001b[' + inspect.colors[style][1] + 'm';
+  } else {
+    return str;
+  }
+}
+
+
+function stylizeNoColor(str, styleType) {
+  return str;
+}
+
+
+function arrayToHash(array) {
+  var hash = {};
+
+  array.forEach(function(val, idx) {
+    hash[val] = true;
+  });
+
+  return hash;
+}
+
+
+function formatValue(ctx, value, recurseTimes) {
+  // Provide a hook for user-specified inspect functions.
+  // Check that value is an object with an inspect function on it
+  if (ctx.customInspect &&
+      value &&
+      isFunction(value.inspect) &&
+      // Filter out the util module, it's inspect function is special
+      value.inspect !== exports.inspect &&
+      // Also filter out any prototype objects using the circular check.
+      !(value.constructor && value.constructor.prototype === value)) {
+    var ret = value.inspect(recurseTimes, ctx);
+    if (!isString(ret)) {
+      ret = formatValue(ctx, ret, recurseTimes);
+    }
+    return ret;
+  }
+
+  // Primitive types cannot have properties
+  var primitive = formatPrimitive(ctx, value);
+  if (primitive) {
+    return primitive;
+  }
+
+  // Look up the keys of the object.
+  var keys = Object.keys(value);
+  var visibleKeys = arrayToHash(keys);
+
+  if (ctx.showHidden) {
+    keys = Object.getOwnPropertyNames(value);
+  }
+
+  // IE doesn't make error fields non-enumerable
+  // http://msdn.microsoft.com/en-us/library/ie/dww52sbt(v=vs.94).aspx
+  if (isError(value)
+      && (keys.indexOf('message') >= 0 || keys.indexOf('description') >= 0)) {
+    return formatError(value);
+  }
+
+  // Some type of object without properties can be shortcutted.
+  if (keys.length === 0) {
+    if (isFunction(value)) {
+      var name = value.name ? ': ' + value.name : '';
+      return ctx.stylize('[Function' + name + ']', 'special');
+    }
+    if (isRegExp(value)) {
+      return ctx.stylize(RegExp.prototype.toString.call(value), 'regexp');
+    }
+    if (isDate(value)) {
+      return ctx.stylize(Date.prototype.toString.call(value), 'date');
+    }
+    if (isError(value)) {
+      return formatError(value);
+    }
+  }
+
+  var base = '', array = false, braces = ['{', '}'];
+
+  // Make Array say that they are Array
+  if (isArray(value)) {
+    array = true;
+    braces = ['[', ']'];
+  }
+
+  // Make functions say that they are functions
+  if (isFunction(value)) {
+    var n = value.name ? ': ' + value.name : '';
+    base = ' [Function' + n + ']';
+  }
+
+  // Make RegExps say that they are RegExps
+  if (isRegExp(value)) {
+    base = ' ' + RegExp.prototype.toString.call(value);
+  }
+
+  // Make dates with properties first say the date
+  if (isDate(value)) {
+    base = ' ' + Date.prototype.toUTCString.call(value);
+  }
+
+  // Make error with message first say the error
+  if (isError(value)) {
+    base = ' ' + formatError(value);
+  }
+
+  if (keys.length === 0 && (!array || value.length == 0)) {
+    return braces[0] + base + braces[1];
+  }
+
+  if (recurseTimes < 0) {
+    if (isRegExp(value)) {
+      return ctx.stylize(RegExp.prototype.toString.call(value), 'regexp');
+    } else {
+      return ctx.stylize('[Object]', 'special');
+    }
+  }
+
+  ctx.seen.push(value);
+
+  var output;
+  if (array) {
+    output = formatArray(ctx, value, recurseTimes, visibleKeys, keys);
+  } else {
+    output = keys.map(function(key) {
+      return formatProperty(ctx, value, recurseTimes, visibleKeys, key, array);
+    });
+  }
+
+  ctx.seen.pop();
+
+  return reduceToSingleString(output, base, braces);
+}
+
+
+function formatPrimitive(ctx, value) {
+  if (isUndefined(value))
+    return ctx.stylize('undefined', 'undefined');
+  if (isString(value)) {
+    var simple = '\'' + JSON.stringify(value).replace(/^"|"$/g, '')
+                                             .replace(/'/g, "\\'")
+                                             .replace(/\\"/g, '"') + '\'';
+    return ctx.stylize(simple, 'string');
+  }
+  if (isNumber(value))
+    return ctx.stylize('' + value, 'number');
+  if (isBoolean(value))
+    return ctx.stylize('' + value, 'boolean');
+  // For some reason typeof null is "object", so special case here.
+  if (isNull(value))
+    return ctx.stylize('null', 'null');
+}
+
+
+function formatError(value) {
+  return '[' + Error.prototype.toString.call(value) + ']';
+}
+
+
+function formatArray(ctx, value, recurseTimes, visibleKeys, keys) {
+  var output = [];
+  for (var i = 0, l = value.length; i < l; ++i) {
+    if (hasOwnProperty(value, String(i))) {
+      output.push(formatProperty(ctx, value, recurseTimes, visibleKeys,
+          String(i), true));
+    } else {
+      output.push('');
+    }
+  }
+  keys.forEach(function(key) {
+    if (!key.match(/^\d+$/)) {
+      output.push(formatProperty(ctx, value, recurseTimes, visibleKeys,
+          key, true));
+    }
+  });
+  return output;
+}
+
+
+function formatProperty(ctx, value, recurseTimes, visibleKeys, key, array) {
+  var name, str, desc;
+  desc = Object.getOwnPropertyDescriptor(value, key) || { value: value[key] };
+  if (desc.get) {
+    if (desc.set) {
+      str = ctx.stylize('[Getter/Setter]', 'special');
+    } else {
+      str = ctx.stylize('[Getter]', 'special');
+    }
+  } else {
+    if (desc.set) {
+      str = ctx.stylize('[Setter]', 'special');
+    }
+  }
+  if (!hasOwnProperty(visibleKeys, key)) {
+    name = '[' + key + ']';
+  }
+  if (!str) {
+    if (ctx.seen.indexOf(desc.value) < 0) {
+      if (isNull(recurseTimes)) {
+        str = formatValue(ctx, desc.value, null);
+      } else {
+        str = formatValue(ctx, desc.value, recurseTimes - 1);
+      }
+      if (str.indexOf('\n') > -1) {
+        if (array) {
+          str = str.split('\n').map(function(line) {
+            return '  ' + line;
+          }).join('\n').substr(2);
+        } else {
+          str = '\n' + str.split('\n').map(function(line) {
+            return '   ' + line;
+          }).join('\n');
+        }
+      }
+    } else {
+      str = ctx.stylize('[Circular]', 'special');
+    }
+  }
+  if (isUndefined(name)) {
+    if (array && key.match(/^\d+$/)) {
+      return str;
+    }
+    name = JSON.stringify('' + key);
+    if (name.match(/^"([a-zA-Z_][a-zA-Z_0-9]*)"$/)) {
+      name = name.substr(1, name.length - 2);
+      name = ctx.stylize(name, 'name');
+    } else {
+      name = name.replace(/'/g, "\\'")
+                 .replace(/\\"/g, '"')
+                 .replace(/(^"|"$)/g, "'");
+      name = ctx.stylize(name, 'string');
+    }
+  }
+
+  return name + ': ' + str;
+}
+
+
+function reduceToSingleString(output, base, braces) {
+  var numLinesEst = 0;
+  var length = output.reduce(function(prev, cur) {
+    numLinesEst++;
+    if (cur.indexOf('\n') >= 0) numLinesEst++;
+    return prev + cur.replace(/\u001b\[\d\d?m/g, '').length + 1;
+  }, 0);
+
+  if (length > 60) {
+    return braces[0] +
+           (base === '' ? '' : base + '\n ') +
+           ' ' +
+           output.join(',\n  ') +
+           ' ' +
+           braces[1];
+  }
+
+  return braces[0] + base + ' ' + output.join(', ') + ' ' + braces[1];
+}
+
+
+// NOTE: These type checking functions intentionally don't use `instanceof`
+// because it is fragile and can be easily faked with `Object.create()`.
+function isArray(ar) {
+  return Array.isArray(ar);
+}
+exports.isArray = isArray;
+
+function isBoolean(arg) {
+  return typeof arg === 'boolean';
+}
+exports.isBoolean = isBoolean;
+
+function isNull(arg) {
+  return arg === null;
+}
+exports.isNull = isNull;
+
+function isNullOrUndefined(arg) {
+  return arg == null;
+}
+exports.isNullOrUndefined = isNullOrUndefined;
+
+function isNumber(arg) {
+  return typeof arg === 'number';
+}
+exports.isNumber = isNumber;
+
+function isString(arg) {
+  return typeof arg === 'string';
+}
+exports.isString = isString;
+
+function isSymbol(arg) {
+  return typeof arg === 'symbol';
+}
+exports.isSymbol = isSymbol;
+
+function isUndefined(arg) {
+  return arg === void 0;
+}
+exports.isUndefined = isUndefined;
+
+function isRegExp(re) {
+  return isObject(re) && objectToString(re) === '[object RegExp]';
+}
+exports.isRegExp = isRegExp;
+
+function isObject(arg) {
+  return typeof arg === 'object' && arg !== null;
+}
+exports.isObject = isObject;
+
+function isDate(d) {
+  return isObject(d) && objectToString(d) === '[object Date]';
+}
+exports.isDate = isDate;
+
+function isError(e) {
+  return isObject(e) &&
+      (objectToString(e) === '[object Error]' || e instanceof Error);
+}
+exports.isError = isError;
+
+function isFunction(arg) {
+  return typeof arg === 'function';
+}
+exports.isFunction = isFunction;
+
+function isPrimitive(arg) {
+  return arg === null ||
+         typeof arg === 'boolean' ||
+         typeof arg === 'number' ||
+         typeof arg === 'string' ||
+         typeof arg === 'symbol' ||  // ES6 symbol
+         typeof arg === 'undefined';
+}
+exports.isPrimitive = isPrimitive;
+
+exports.isBuffer = require('./support/isBuffer');
+
+function objectToString(o) {
+  return Object.prototype.toString.call(o);
+}
+
+
+function pad(n) {
+  return n < 10 ? '0' + n.toString(10) : n.toString(10);
+}
+
+
+var months = ['Jan', 'Feb', 'Mar', 'Apr', 'May', 'Jun', 'Jul', 'Aug', 'Sep',
+              'Oct', 'Nov', 'Dec'];
+
+// 26 Feb 16:19:34
+function timestamp() {
+  var d = new Date();
+  var time = [pad(d.getHours()),
+              pad(d.getMinutes()),
+              pad(d.getSeconds())].join(':');
+  return [d.getDate(), months[d.getMonth()], time].join(' ');
+}
+
+
+// log is just a thin wrapper to console.log that prepends a timestamp
+exports.log = function() {
+  console.log('%s - %s', timestamp(), exports.format.apply(exports, arguments));
+};
+
+
+/**
+ * Inherit the prototype methods from one constructor into another.
+ *
+ * The Function.prototype.inherits from lang.js rewritten as a standalone
+ * function (not on Function.prototype). NOTE: If this file is to be loaded
+ * during bootstrapping this function needs to be rewritten using some native
+ * functions as prototype setup using normal JavaScript does not work as
+ * expected during bootstrapping (see mirror.js in r114903).
+ *
+ * @param {function} ctor Constructor function which needs to inherit the
+ *     prototype.
+ * @param {function} superCtor Constructor function to inherit prototype from.
+ */
+exports.inherits = require('inherits');
+
+exports._extend = function(origin, add) {
+  // Don't do anything if add isn't an object
+  if (!add || !isObject(add)) return origin;
+
+  var keys = Object.keys(add);
+  var i = keys.length;
+  while (i--) {
+    origin[keys[i]] = add[keys[i]];
+  }
+  return origin;
+};
+
+function hasOwnProperty(obj, prop) {
+  return Object.prototype.hasOwnProperty.call(obj, prop);
+}
+
+}).call(this,require('_process'),typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {})
+},{"./support/isBuffer":27,"_process":24,"inherits":26}],29:[function(require,module,exports){
+// Returns a wrapper function that returns a wrapped callback
+// The wrapper function should do some stuff, and return a
+// presumably different callback function.
+// This makes sure that own properties are retained, so that
+// decorations and such are not lost along the way.
+module.exports = wrappy
+function wrappy (fn, cb) {
+  if (fn && cb) return wrappy(fn)(cb)
+
+  if (typeof fn !== 'function')
+    throw new TypeError('need wrapper function')
+
+  Object.keys(fn).forEach(function (k) {
+    wrapper[k] = fn[k]
+  })
+
+  return wrapper
+
+  function wrapper() {
+    var args = new Array(arguments.length)
+    for (var i = 0; i < args.length; i++) {
+      args[i] = arguments[i]
+    }
+    var ret = fn.apply(this, args)
+    var cb = args[args.length-1]
+    if (typeof ret === 'function' && ret !== cb) {
+      Object.keys(cb).forEach(function (k) {
+        ret[k] = cb[k]
+      })
+    }
+    return ret
+  }
+}
+
+},{}]},{},[7])(7)
+});
\ No newline at end of file
diff --git a/DevDoc/assets/javascripts/workers/search.2c215733.min.js b/DevDoc/assets/javascripts/workers/search.2c215733.min.js
new file mode 100644
index 00000000..6e2e3ea4
--- /dev/null
+++ b/DevDoc/assets/javascripts/workers/search.2c215733.min.js
@@ -0,0 +1,42 @@
+"use strict";(()=>{var xe=Object.create;var G=Object.defineProperty,ve=Object.defineProperties,Se=Object.getOwnPropertyDescriptor,Te=Object.getOwnPropertyDescriptors,Qe=Object.getOwnPropertyNames,J=Object.getOwnPropertySymbols,Ee=Object.getPrototypeOf,Z=Object.prototype.hasOwnProperty,be=Object.prototype.propertyIsEnumerable;var K=Math.pow,X=(t,e,r)=>e in t?G(t,e,{enumerable:!0,configurable:!0,writable:!0,value:r}):t[e]=r,_=(t,e)=>{for(var r in e||(e={}))Z.call(e,r)&&X(t,r,e[r]);if(J)for(var r of J(e))be.call(e,r)&&X(t,r,e[r]);return t},B=(t,e)=>ve(t,Te(e));var Le=(t,e)=>()=>(e||t((e={exports:{}}).exports,e),e.exports);var we=(t,e,r,n)=>{if(e&&typeof e=="object"||typeof e=="function")for(let i of Qe(e))!Z.call(t,i)&&i!==r&&G(t,i,{get:()=>e[i],enumerable:!(n=Se(e,i))||n.enumerable});return t};var Pe=(t,e,r)=>(r=t!=null?xe(Ee(t)):{},we(e||!t||!t.__esModule?G(r,"default",{value:t,enumerable:!0}):r,t));var W=(t,e,r)=>new Promise((n,i)=>{var s=u=>{try{a(r.next(u))}catch(c){i(c)}},o=u=>{try{a(r.throw(u))}catch(c){i(c)}},a=u=>u.done?n(u.value):Promise.resolve(u.value).then(s,o);a((r=r.apply(t,e)).next())});var re=Le((ee,te)=>{/**
+ * lunr - http://lunrjs.com - A bit like Solr, but much smaller and not as bright - 2.3.9
+ * Copyright (C) 2020 Oliver Nightingale
+ * @license MIT
+ */(function(){var t=function(e){var r=new t.Builder;return r.pipeline.add(t.trimmer,t.stopWordFilter,t.stemmer),r.searchPipeline.add(t.stemmer),e.call(r,r),r.build()};t.version="2.3.9";/*!
+ * lunr.utils
+ * Copyright (C) 2020 Oliver Nightingale
+ */t.utils={},t.utils.warn=(function(e){return function(r){e.console&&console.warn&&console.warn(r)}})(this),t.utils.asString=function(e){return e==null?"":e.toString()},t.utils.clone=function(e){if(e==null)return e;for(var r=Object.create(null),n=Object.keys(e),i=0;i<n.length;i++){var s=n[i],o=e[s];if(Array.isArray(o)){r[s]=o.slice();continue}if(typeof o=="string"||typeof o=="number"||typeof o=="boolean"){r[s]=o;continue}throw new TypeError("clone is not deep and does not support nested objects")}return r},t.FieldRef=function(e,r,n){this.docRef=e,this.fieldName=r,this._stringValue=n},t.FieldRef.joiner="/",t.FieldRef.fromString=function(e){var r=e.indexOf(t.FieldRef.joiner);if(r===-1)throw"malformed field ref string";var n=e.slice(0,r),i=e.slice(r+1);return new t.FieldRef(i,n,e)},t.FieldRef.prototype.toString=function(){return this._stringValue==null&&(this._stringValue=this.fieldName+t.FieldRef.joiner+this.docRef),this._stringValue};/*!
+ * lunr.Set
+ * Copyright (C) 2020 Oliver Nightingale
+ */t.Set=function(e){if(this.elements=Object.create(null),e){this.length=e.length;for(var r=0;r<this.length;r++)this.elements[e[r]]=!0}else this.length=0},t.Set.complete={intersect:function(e){return e},union:function(){return this},contains:function(){return!0}},t.Set.empty={intersect:function(){return this},union:function(e){return e},contains:function(){return!1}},t.Set.prototype.contains=function(e){return!!this.elements[e]},t.Set.prototype.intersect=function(e){var r,n,i,s=[];if(e===t.Set.complete)return this;if(e===t.Set.empty)return e;this.length<e.length?(r=this,n=e):(r=e,n=this),i=Object.keys(r.elements);for(var o=0;o<i.length;o++){var a=i[o];a in n.elements&&s.push(a)}return new t.Set(s)},t.Set.prototype.union=function(e){return e===t.Set.complete?t.Set.complete:e===t.Set.empty?this:new t.Set(Object.keys(this.elements).concat(Object.keys(e.elements)))},t.idf=function(e,r){var n=0;for(var i in e)i!="_index"&&(n+=Object.keys(e[i]).length);var s=(r-n+.5)/(n+.5);return Math.log(1+Math.abs(s))},t.Token=function(e,r){this.str=e||"",this.metadata=r||{}},t.Token.prototype.toString=function(){return this.str},t.Token.prototype.update=function(e){return this.str=e(this.str,this.metadata),this},t.Token.prototype.clone=function(e){return e=e||function(r){return r},new t.Token(e(this.str,this.metadata),this.metadata)};/*!
+ * lunr.tokenizer
+ * Copyright (C) 2020 Oliver Nightingale
+ */t.tokenizer=function(e,r){if(e==null||e==null)return[];if(Array.isArray(e))return e.map(function(g){return new t.Token(t.utils.asString(g).toLowerCase(),t.utils.clone(r))});for(var n=e.toString().toLowerCase(),i=n.length,s=[],o=0,a=0;o<=i;o++){var u=n.charAt(o),c=o-a;if(u.match(t.tokenizer.separator)||o==i){if(c>0){var f=t.utils.clone(r)||{};f.position=[a,c],f.index=s.length,s.push(new t.Token(n.slice(a,o),f))}a=o+1}}return s},t.tokenizer.separator=/[\s\-]+/;/*!
+ * lunr.Pipeline
+ * Copyright (C) 2020 Oliver Nightingale
+ */t.Pipeline=function(){this._stack=[]},t.Pipeline.registeredFunctions=Object.create(null),t.Pipeline.registerFunction=function(e,r){r in this.registeredFunctions&&t.utils.warn("Overwriting existing registered function: "+r),e.label=r,t.Pipeline.registeredFunctions[e.label]=e},t.Pipeline.warnIfFunctionNotRegistered=function(e){var r=e.label&&e.label in this.registeredFunctions;r||t.utils.warn(`Function is not registered with pipeline. This may cause problems when serialising the index.
+`,e)},t.Pipeline.load=function(e){var r=new t.Pipeline;return e.forEach(function(n){var i=t.Pipeline.registeredFunctions[n];if(i)r.add(i);else throw new Error("Cannot load unregistered function: "+n)}),r},t.Pipeline.prototype.add=function(){var e=Array.prototype.slice.call(arguments);e.forEach(function(r){t.Pipeline.warnIfFunctionNotRegistered(r),this._stack.push(r)},this)},t.Pipeline.prototype.after=function(e,r){t.Pipeline.warnIfFunctionNotRegistered(r);var n=this._stack.indexOf(e);if(n==-1)throw new Error("Cannot find existingFn");n=n+1,this._stack.splice(n,0,r)},t.Pipeline.prototype.before=function(e,r){t.Pipeline.warnIfFunctionNotRegistered(r);var n=this._stack.indexOf(e);if(n==-1)throw new Error("Cannot find existingFn");this._stack.splice(n,0,r)},t.Pipeline.prototype.remove=function(e){var r=this._stack.indexOf(e);r!=-1&&this._stack.splice(r,1)},t.Pipeline.prototype.run=function(e){for(var r=this._stack.length,n=0;n<r;n++){for(var i=this._stack[n],s=[],o=0;o<e.length;o++){var a=i(e[o],o,e);if(!(a==null||a===""))if(Array.isArray(a))for(var u=0;u<a.length;u++)s.push(a[u]);else s.push(a)}e=s}return e},t.Pipeline.prototype.runString=function(e,r){var n=new t.Token(e,r);return this.run([n]).map(function(i){return i.toString()})},t.Pipeline.prototype.reset=function(){this._stack=[]},t.Pipeline.prototype.toJSON=function(){return this._stack.map(function(e){return t.Pipeline.warnIfFunctionNotRegistered(e),e.label})};/*!
+ * lunr.Vector
+ * Copyright (C) 2020 Oliver Nightingale
+ */t.Vector=function(e){this._magnitude=0,this.elements=e||[]},t.Vector.prototype.positionForIndex=function(e){if(this.elements.length==0)return 0;for(var r=0,n=this.elements.length/2,i=n-r,s=Math.floor(i/2),o=this.elements[s*2];i>1&&(o<e&&(r=s),o>e&&(n=s),o!=e);)i=n-r,s=r+Math.floor(i/2),o=this.elements[s*2];if(o==e||o>e)return s*2;if(o<e)return(s+1)*2},t.Vector.prototype.insert=function(e,r){this.upsert(e,r,function(){throw"duplicate index"})},t.Vector.prototype.upsert=function(e,r,n){this._magnitude=0;var i=this.positionForIndex(e);this.elements[i]==e?this.elements[i+1]=n(this.elements[i+1],r):this.elements.splice(i,0,e,r)},t.Vector.prototype.magnitude=function(){if(this._magnitude)return this._magnitude;for(var e=0,r=this.elements.length,n=1;n<r;n+=2){var i=this.elements[n];e+=i*i}return this._magnitude=Math.sqrt(e)},t.Vector.prototype.dot=function(e){for(var r=0,n=this.elements,i=e.elements,s=n.length,o=i.length,a=0,u=0,c=0,f=0;c<s&&f<o;)a=n[c],u=i[f],a<u?c+=2:a>u?f+=2:a==u&&(r+=n[c+1]*i[f+1],c+=2,f+=2);return r},t.Vector.prototype.similarity=function(e){return this.dot(e)/this.magnitude()||0},t.Vector.prototype.toArray=function(){for(var e=new Array(this.elements.length/2),r=1,n=0;r<this.elements.length;r+=2,n++)e[n]=this.elements[r];return e},t.Vector.prototype.toJSON=function(){return this.elements};/*!
+ * lunr.stemmer
+ * Copyright (C) 2020 Oliver Nightingale
+ * Includes code from - http://tartarus.org/~martin/PorterStemmer/js.txt
+ */t.stemmer=(function(){var e={ational:"ate",tional:"tion",enci:"ence",anci:"ance",izer:"ize",bli:"ble",alli:"al",entli:"ent",eli:"e",ousli:"ous",ization:"ize",ation:"ate",ator:"ate",alism:"al",iveness:"ive",fulness:"ful",ousness:"ous",aliti:"al",iviti:"ive",biliti:"ble",logi:"log"},r={icate:"ic",ative:"",alize:"al",iciti:"ic",ical:"ic",ful:"",ness:""},n="[^aeiou]",i="[aeiouy]",s=n+"[^aeiouy]*",o=i+"[aeiou]*",a="^("+s+")?"+o+s,u="^("+s+")?"+o+s+"("+o+")?$",c="^("+s+")?"+o+s+o+s,f="^("+s+")?"+i,g=new RegExp(a),l=new RegExp(c),m=new RegExp(u),x=new RegExp(f),v=/^(.+?)(ss|i)es$/,d=/^(.+?)([^s])s$/,y=/^(.+?)eed$/,b=/^(.+?)(ed|ing)$/,E=/.$/,w=/(at|bl|iz)$/,R=new RegExp("([^aeiouylsz])\\1$"),j=new RegExp("^"+s+i+"[^aeiouwxy]$"),C=/^(.+?[^aeiou])y$/,D=/^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/,N=/^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/,M=/^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/,V=/^(.+?)(s|t)(ion)$/,P=/^(.+?)e$/,z=/ll$/,$=new RegExp("^"+s+i+"[^aeiouwxy]$"),A=function(h){var S,k,L,p,T,O,F;if(h.length<3)return h;if(L=h.substr(0,1),L=="y"&&(h=L.toUpperCase()+h.substr(1)),p=v,T=d,p.test(h)?h=h.replace(p,"$1$2"):T.test(h)&&(h=h.replace(T,"$1$2")),p=y,T=b,p.test(h)){var Q=p.exec(h);p=g,p.test(Q[1])&&(p=E,h=h.replace(p,""))}else if(T.test(h)){var Q=T.exec(h);S=Q[1],T=x,T.test(S)&&(h=S,T=w,O=R,F=j,T.test(h)?h=h+"e":O.test(h)?(p=E,h=h.replace(p,"")):F.test(h)&&(h=h+"e"))}if(p=C,p.test(h)){var Q=p.exec(h);S=Q[1],h=S+"i"}if(p=D,p.test(h)){var Q=p.exec(h);S=Q[1],k=Q[2],p=g,p.test(S)&&(h=S+e[k])}if(p=N,p.test(h)){var Q=p.exec(h);S=Q[1],k=Q[2],p=g,p.test(S)&&(h=S+r[k])}if(p=M,T=V,p.test(h)){var Q=p.exec(h);S=Q[1],p=l,p.test(S)&&(h=S)}else if(T.test(h)){var Q=T.exec(h);S=Q[1]+Q[2],T=l,T.test(S)&&(h=S)}if(p=P,p.test(h)){var Q=p.exec(h);S=Q[1],p=l,T=m,O=$,(p.test(S)||T.test(S)&&!O.test(S))&&(h=S)}return p=z,T=l,p.test(h)&&T.test(h)&&(p=E,h=h.replace(p,"")),L=="y"&&(h=L.toLowerCase()+h.substr(1)),h};return function(I){return I.update(A)}})(),t.Pipeline.registerFunction(t.stemmer,"stemmer");/*!
+ * lunr.stopWordFilter
+ * Copyright (C) 2020 Oliver Nightingale
+ */t.generateStopWordFilter=function(e){var r=e.reduce(function(n,i){return n[i]=i,n},{});return function(n){if(n&&r[n.toString()]!==n.toString())return n}},t.stopWordFilter=t.generateStopWordFilter(["a","able","about","across","after","all","almost","also","am","among","an","and","any","are","as","at","be","because","been","but","by","can","cannot","could","dear","did","do","does","either","else","ever","every","for","from","get","got","had","has","have","he","her","hers","him","his","how","however","i","if","in","into","is","it","its","just","least","let","like","likely","may","me","might","most","must","my","neither","no","nor","not","of","off","often","on","only","or","other","our","own","rather","said","say","says","she","should","since","so","some","than","that","the","their","them","then","there","these","they","this","tis","to","too","twas","us","wants","was","we","were","what","when","where","which","while","who","whom","why","will","with","would","yet","you","your"]),t.Pipeline.registerFunction(t.stopWordFilter,"stopWordFilter");/*!
+ * lunr.trimmer
+ * Copyright (C) 2020 Oliver Nightingale
+ */t.trimmer=function(e){return e.update(function(r){return r.replace(/^\W+/,"").replace(/\W+$/,"")})},t.Pipeline.registerFunction(t.trimmer,"trimmer");/*!
+ * lunr.TokenSet
+ * Copyright (C) 2020 Oliver Nightingale
+ */t.TokenSet=function(){this.final=!1,this.edges={},this.id=t.TokenSet._nextId,t.TokenSet._nextId+=1},t.TokenSet._nextId=1,t.TokenSet.fromArray=function(e){for(var r=new t.TokenSet.Builder,n=0,i=e.length;n<i;n++)r.insert(e[n]);return r.finish(),r.root},t.TokenSet.fromClause=function(e){return"editDistance"in e?t.TokenSet.fromFuzzyString(e.term,e.editDistance):t.TokenSet.fromString(e.term)},t.TokenSet.fromFuzzyString=function(e,r){for(var n=new t.TokenSet,i=[{node:n,editsRemaining:r,str:e}];i.length;){var s=i.pop();if(s.str.length>0){var o=s.str.charAt(0),a;o in s.node.edges?a=s.node.edges[o]:(a=new t.TokenSet,s.node.edges[o]=a),s.str.length==1&&(a.final=!0),i.push({node:a,editsRemaining:s.editsRemaining,str:s.str.slice(1)})}if(s.editsRemaining!=0){if("*"in s.node.edges)var u=s.node.edges["*"];else{var u=new t.TokenSet;s.node.edges["*"]=u}if(s.str.length==0&&(u.final=!0),i.push({node:u,editsRemaining:s.editsRemaining-1,str:s.str}),s.str.length>1&&i.push({node:s.node,editsRemaining:s.editsRemaining-1,str:s.str.slice(1)}),s.str.length==1&&(s.node.final=!0),s.str.length>=1){if("*"in s.node.edges)var c=s.node.edges["*"];else{var c=new t.TokenSet;s.node.edges["*"]=c}s.str.length==1&&(c.final=!0),i.push({node:c,editsRemaining:s.editsRemaining-1,str:s.str.slice(1)})}if(s.str.length>1){var f=s.str.charAt(0),g=s.str.charAt(1),l;g in s.node.edges?l=s.node.edges[g]:(l=new t.TokenSet,s.node.edges[g]=l),s.str.length==1&&(l.final=!0),i.push({node:l,editsRemaining:s.editsRemaining-1,str:f+s.str.slice(2)})}}}return n},t.TokenSet.fromString=function(e){for(var r=new t.TokenSet,n=r,i=0,s=e.length;i<s;i++){var o=e[i],a=i==s-1;if(o=="*")r.edges[o]=r,r.final=a;else{var u=new t.TokenSet;u.final=a,r.edges[o]=u,r=u}}return n},t.TokenSet.prototype.toArray=function(){for(var e=[],r=[{prefix:"",node:this}];r.length;){var n=r.pop(),i=Object.keys(n.node.edges),s=i.length;n.node.final&&(n.prefix.charAt(0),e.push(n.prefix));for(var o=0;o<s;o++){var a=i[o];r.push({prefix:n.prefix.concat(a),node:n.node.edges[a]})}}return e},t.TokenSet.prototype.toString=function(){if(this._str)return this._str;for(var e=this.final?"1":"0",r=Object.keys(this.edges).sort(),n=r.length,i=0;i<n;i++){var s=r[i],o=this.edges[s];e=e+s+o.id}return e},t.TokenSet.prototype.intersect=function(e){for(var r=new t.TokenSet,n=void 0,i=[{qNode:e,output:r,node:this}];i.length;){n=i.pop();for(var s=Object.keys(n.qNode.edges),o=s.length,a=Object.keys(n.node.edges),u=a.length,c=0;c<o;c++)for(var f=s[c],g=0;g<u;g++){var l=a[g];if(l==f||f=="*"){var m=n.node.edges[l],x=n.qNode.edges[f],v=m.final&&x.final,d=void 0;l in n.output.edges?(d=n.output.edges[l],d.final=d.final||v):(d=new t.TokenSet,d.final=v,n.output.edges[l]=d),i.push({qNode:x,output:d,node:m})}}}return r},t.TokenSet.Builder=function(){this.previousWord="",this.root=new t.TokenSet,this.uncheckedNodes=[],this.minimizedNodes={}},t.TokenSet.Builder.prototype.insert=function(e){var r,n=0;if(e<this.previousWord)throw new Error("Out of order word insertion");for(var i=0;i<e.length&&i<this.previousWord.length&&e[i]==this.previousWord[i];i++)n++;this.minimize(n),this.uncheckedNodes.length==0?r=this.root:r=this.uncheckedNodes[this.uncheckedNodes.length-1].child;for(var i=n;i<e.length;i++){var s=new t.TokenSet,o=e[i];r.edges[o]=s,this.uncheckedNodes.push({parent:r,char:o,child:s}),r=s}r.final=!0,this.previousWord=e},t.TokenSet.Builder.prototype.finish=function(){this.minimize(0)},t.TokenSet.Builder.prototype.minimize=function(e){for(var r=this.uncheckedNodes.length-1;r>=e;r--){var n=this.uncheckedNodes[r],i=n.child.toString();i in this.minimizedNodes?n.parent.edges[n.char]=this.minimizedNodes[i]:(n.child._str=i,this.minimizedNodes[i]=n.child),this.uncheckedNodes.pop()}};/*!
+ * lunr.Index
+ * Copyright (C) 2020 Oliver Nightingale
+ */t.Index=function(e){this.invertedIndex=e.invertedIndex,this.fieldVectors=e.fieldVectors,this.tokenSet=e.tokenSet,this.fields=e.fields,this.pipeline=e.pipeline},t.Index.prototype.search=function(e){return this.query(function(r){var n=new t.QueryParser(e,r);n.parse()})},t.Index.prototype.query=function(e){for(var r=new t.Query(this.fields),n=Object.create(null),i=Object.create(null),s=Object.create(null),o=Object.create(null),a=Object.create(null),u=0;u<this.fields.length;u++)i[this.fields[u]]=new t.Vector;e.call(r,r);for(var u=0;u<r.clauses.length;u++){var c=r.clauses[u],f=null,g=t.Set.empty;c.usePipeline?f=this.pipeline.runString(c.term,{fields:c.fields}):f=[c.term];for(var l=0;l<f.length;l++){var m=f[l];c.term=m;var x=t.TokenSet.fromClause(c),v=this.tokenSet.intersect(x).toArray();if(v.length===0&&c.presence===t.Query.presence.REQUIRED){for(var d=0;d<c.fields.length;d++){var y=c.fields[d];o[y]=t.Set.empty}break}for(var b=0;b<v.length;b++)for(var E=v[b],w=this.invertedIndex[E],R=w._index,d=0;d<c.fields.length;d++){var y=c.fields[d],j=w[y],C=Object.keys(j),D=E+"/"+y,N=new t.Set(C);if(c.presence==t.Query.presence.REQUIRED&&(g=g.union(N),o[y]===void 0&&(o[y]=t.Set.complete)),c.presence==t.Query.presence.PROHIBITED){a[y]===void 0&&(a[y]=t.Set.empty),a[y]=a[y].union(N);continue}if(i[y].upsert(R,c.boost,function(ye,me){return ye+me}),!s[D]){for(var M=0;M<C.length;M++){var V=C[M],P=new t.FieldRef(V,y),z=j[V],$;($=n[P])===void 0?n[P]=new t.MatchData(E,y,z):$.add(E,y,z)}s[D]=!0}}}if(c.presence===t.Query.presence.REQUIRED)for(var d=0;d<c.fields.length;d++){var y=c.fields[d];o[y]=o[y].intersect(g)}}for(var A=t.Set.complete,I=t.Set.empty,u=0;u<this.fields.length;u++){var y=this.fields[u];o[y]&&(A=A.intersect(o[y])),a[y]&&(I=I.union(a[y]))}var h=Object.keys(n),S=[],k=Object.create(null);if(r.isNegated()){h=Object.keys(this.fieldVectors);for(var u=0;u<h.length;u++){var P=h[u],L=t.FieldRef.fromString(P);n[P]=new t.MatchData}}for(var u=0;u<h.length;u++){var L=t.FieldRef.fromString(h[u]),p=L.docRef;if(A.contains(p)&&!I.contains(p)){var T=this.fieldVectors[L],O=i[L.fieldName].similarity(T),F;if((F=k[p])!==void 0)F.score+=O,F.matchData.combine(n[L]);else{var Q={ref:p,score:O,matchData:n[L]};k[p]=Q,S.push(Q)}}}return S.sort(function(pe,ge){return ge.score-pe.score})},t.Index.prototype.toJSON=function(){var e=Object.keys(this.invertedIndex).sort().map(function(n){return[n,this.invertedIndex[n]]},this),r=Object.keys(this.fieldVectors).map(function(n){return[n,this.fieldVectors[n].toJSON()]},this);return{version:t.version,fields:this.fields,fieldVectors:r,invertedIndex:e,pipeline:this.pipeline.toJSON()}},t.Index.load=function(e){var r={},n={},i=e.fieldVectors,s=Object.create(null),o=e.invertedIndex,a=new t.TokenSet.Builder,u=t.Pipeline.load(e.pipeline);e.version!=t.version&&t.utils.warn("Version mismatch when loading serialised index. Current version of lunr '"+t.version+"' does not match serialized index '"+e.version+"'");for(var c=0;c<i.length;c++){var f=i[c],g=f[0],l=f[1];n[g]=new t.Vector(l)}for(var c=0;c<o.length;c++){var f=o[c],m=f[0],x=f[1];a.insert(m),s[m]=x}return a.finish(),r.fields=e.fields,r.fieldVectors=n,r.invertedIndex=s,r.tokenSet=a.root,r.pipeline=u,new t.Index(r)};/*!
+ * lunr.Builder
+ * Copyright (C) 2020 Oliver Nightingale
+ */t.Builder=function(){this._ref="id",this._fields=Object.create(null),this._documents=Object.create(null),this.invertedIndex=Object.create(null),this.fieldTermFrequencies={},this.fieldLengths={},this.tokenizer=t.tokenizer,this.pipeline=new t.Pipeline,this.searchPipeline=new t.Pipeline,this.documentCount=0,this._b=.75,this._k1=1.2,this.termIndex=0,this.metadataWhitelist=[]},t.Builder.prototype.ref=function(e){this._ref=e},t.Builder.prototype.field=function(e,r){if(/\//.test(e))throw new RangeError("Field '"+e+"' contains illegal character '/'");this._fields[e]=r||{}},t.Builder.prototype.b=function(e){e<0?this._b=0:e>1?this._b=1:this._b=e},t.Builder.prototype.k1=function(e){this._k1=e},t.Builder.prototype.add=function(e,r){var n=e[this._ref],i=Object.keys(this._fields);this._documents[n]=r||{},this.documentCount+=1;for(var s=0;s<i.length;s++){var o=i[s],a=this._fields[o].extractor,u=a?a(e):e[o],c=this.tokenizer(u,{fields:[o]}),f=this.pipeline.run(c),g=new t.FieldRef(n,o),l=Object.create(null);this.fieldTermFrequencies[g]=l,this.fieldLengths[g]=0,this.fieldLengths[g]+=f.length;for(var m=0;m<f.length;m++){var x=f[m];if(l[x]==null&&(l[x]=0),l[x]+=1,this.invertedIndex[x]==null){var v=Object.create(null);v._index=this.termIndex,this.termIndex+=1;for(var d=0;d<i.length;d++)v[i[d]]=Object.create(null);this.invertedIndex[x]=v}this.invertedIndex[x][o][n]==null&&(this.invertedIndex[x][o][n]=Object.create(null));for(var y=0;y<this.metadataWhitelist.length;y++){var b=this.metadataWhitelist[y],E=x.metadata[b];this.invertedIndex[x][o][n][b]==null&&(this.invertedIndex[x][o][n][b]=[]),this.invertedIndex[x][o][n][b].push(E)}}}},t.Builder.prototype.calculateAverageFieldLengths=function(){for(var e=Object.keys(this.fieldLengths),r=e.length,n={},i={},s=0;s<r;s++){var o=t.FieldRef.fromString(e[s]),a=o.fieldName;i[a]||(i[a]=0),i[a]+=1,n[a]||(n[a]=0),n[a]+=this.fieldLengths[o]}for(var u=Object.keys(this._fields),s=0;s<u.length;s++){var c=u[s];n[c]=n[c]/i[c]}this.averageFieldLength=n},t.Builder.prototype.createFieldVectors=function(){for(var e={},r=Object.keys(this.fieldTermFrequencies),n=r.length,i=Object.create(null),s=0;s<n;s++){for(var o=t.FieldRef.fromString(r[s]),a=o.fieldName,u=this.fieldLengths[o],c=new t.Vector,f=this.fieldTermFrequencies[o],g=Object.keys(f),l=g.length,m=this._fields[a].boost||1,x=this._documents[o.docRef].boost||1,v=0;v<l;v++){var d=g[v],y=f[d],b=this.invertedIndex[d]._index,E,w,R;i[d]===void 0?(E=t.idf(this.invertedIndex[d],this.documentCount),i[d]=E):E=i[d],w=E*((this._k1+1)*y)/(this._k1*(1-this._b+this._b*(u/this.averageFieldLength[a]))+y),w*=m,w*=x,R=Math.round(w*1e3)/1e3,c.insert(b,R)}e[o]=c}this.fieldVectors=e},t.Builder.prototype.createTokenSet=function(){this.tokenSet=t.TokenSet.fromArray(Object.keys(this.invertedIndex).sort())},t.Builder.prototype.build=function(){return this.calculateAverageFieldLengths(),this.createFieldVectors(),this.createTokenSet(),new t.Index({invertedIndex:this.invertedIndex,fieldVectors:this.fieldVectors,tokenSet:this.tokenSet,fields:Object.keys(this._fields),pipeline:this.searchPipeline})},t.Builder.prototype.use=function(e){var r=Array.prototype.slice.call(arguments,1);r.unshift(this),e.apply(this,r)},t.MatchData=function(e,r,n){for(var i=Object.create(null),s=Object.keys(n||{}),o=0;o<s.length;o++){var a=s[o];i[a]=n[a].slice()}this.metadata=Object.create(null),e!==void 0&&(this.metadata[e]=Object.create(null),this.metadata[e][r]=i)},t.MatchData.prototype.combine=function(e){for(var r=Object.keys(e.metadata),n=0;n<r.length;n++){var i=r[n],s=Object.keys(e.metadata[i]);this.metadata[i]==null&&(this.metadata[i]=Object.create(null));for(var o=0;o<s.length;o++){var a=s[o],u=Object.keys(e.metadata[i][a]);this.metadata[i][a]==null&&(this.metadata[i][a]=Object.create(null));for(var c=0;c<u.length;c++){var f=u[c];this.metadata[i][a][f]==null?this.metadata[i][a][f]=e.metadata[i][a][f]:this.metadata[i][a][f]=this.metadata[i][a][f].concat(e.metadata[i][a][f])}}}},t.MatchData.prototype.add=function(e,r,n){if(!(e in this.metadata)){this.metadata[e]=Object.create(null),this.metadata[e][r]=n;return}if(!(r in this.metadata[e])){this.metadata[e][r]=n;return}for(var i=Object.keys(n),s=0;s<i.length;s++){var o=i[s];o in this.metadata[e][r]?this.metadata[e][r][o]=this.metadata[e][r][o].concat(n[o]):this.metadata[e][r][o]=n[o]}},t.Query=function(e){this.clauses=[],this.allFields=e},t.Query.wildcard=new String("*"),t.Query.wildcard.NONE=0,t.Query.wildcard.LEADING=1,t.Query.wildcard.TRAILING=2,t.Query.presence={OPTIONAL:1,REQUIRED:2,PROHIBITED:3},t.Query.prototype.clause=function(e){return"fields"in e||(e.fields=this.allFields),"boost"in e||(e.boost=1),"usePipeline"in e||(e.usePipeline=!0),"wildcard"in 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+//# sourceMappingURL=search.2c215733.min.js.map
+
diff --git a/DevDoc/assets/javascripts/workers/search.2c215733.min.js.map b/DevDoc/assets/javascripts/workers/search.2c215733.min.js.map
new file mode 100644
index 00000000..1e042893
--- /dev/null
+++ b/DevDoc/assets/javascripts/workers/search.2c215733.min.js.map
@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["node_modules/lunr/lunr.js", "src/templates/assets/javascripts/integrations/search/worker/main/index.ts", "src/templates/assets/javascripts/browser/element/_/index.ts", "src/templates/assets/javascripts/polyfills/index.ts", "src/templates/assets/javascripts/integrations/search/config/index.ts", "src/templates/assets/javascripts/integrations/search/internal/_/index.ts", "src/templates/assets/javascripts/integrations/search/internal/extract/index.ts", "src/templates/assets/javascripts/integrations/search/internal/highlight/index.ts", "src/templates/assets/javascripts/integrations/search/internal/tokenize/index.ts", "src/templates/assets/javascripts/integrations/search/query/transform/index.ts", "src/templates/assets/javascripts/integrations/search/query/_/index.ts", "src/templates/assets/javascripts/integrations/search/query/segment/index.ts", "src/templates/assets/javascripts/integrations/search/_/index.ts"],
+  "sourcesContent": ["/**\n * lunr - http://lunrjs.com - A bit like Solr, but much smaller and not as bright - 2.3.9\n * Copyright (C) 2020 Oliver Nightingale\n * @license MIT\n */\n\n;(function(){\n\n/**\n * A convenience function for configuring and constructing\n * a new lunr Index.\n *\n * A lunr.Builder instance is created and the pipeline setup\n * with a trimmer, stop word filter and stemmer.\n *\n * This builder object is yielded to the configuration function\n * that is passed as a parameter, allowing the list of fields\n * and other builder parameters to be customised.\n *\n * All documents _must_ be added within the passed config function.\n *\n * @example\n * var idx = lunr(function () {\n *   this.field('title')\n *   this.field('body')\n *   this.ref('id')\n *\n *   documents.forEach(function (doc) {\n *     this.add(doc)\n *   }, this)\n * })\n *\n * @see {@link lunr.Builder}\n * @see {@link lunr.Pipeline}\n * @see {@link lunr.trimmer}\n * @see {@link lunr.stopWordFilter}\n * @see {@link lunr.stemmer}\n * @namespace {function} lunr\n */\nvar lunr = function (config) {\n  var builder = new lunr.Builder\n\n  builder.pipeline.add(\n    lunr.trimmer,\n    lunr.stopWordFilter,\n    lunr.stemmer\n  )\n\n  builder.searchPipeline.add(\n    lunr.stemmer\n  )\n\n  config.call(builder, builder)\n  return builder.build()\n}\n\nlunr.version = \"2.3.9\"\n/*!\n * lunr.utils\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * A namespace containing utils for the rest of the lunr library\n * @namespace lunr.utils\n */\nlunr.utils = {}\n\n/**\n * Print a warning message to the console.\n *\n * @param {String} message The message to be printed.\n * @memberOf lunr.utils\n * @function\n */\nlunr.utils.warn = (function (global) {\n  /* eslint-disable no-console */\n  return function (message) {\n    if (global.console && console.warn) {\n      console.warn(message)\n    }\n  }\n  /* eslint-enable no-console */\n})(this)\n\n/**\n * Convert an object to a string.\n *\n * In the case of `null` and `undefined` the function returns\n * the empty string, in all other cases the result of calling\n * `toString` on the passed object is returned.\n *\n * @param {Any} obj The object to convert to a string.\n * @return {String} string representation of the passed object.\n * @memberOf lunr.utils\n */\nlunr.utils.asString = function (obj) {\n  if (obj === void 0 || obj === null) {\n    return \"\"\n  } else {\n    return obj.toString()\n  }\n}\n\n/**\n * Clones an object.\n *\n * Will create a copy of an existing object such that any mutations\n * on the copy cannot affect the original.\n *\n * Only shallow objects are supported, passing a nested object to this\n * function will cause a TypeError.\n *\n * Objects with primitives, and arrays of primitives are supported.\n *\n * @param {Object} obj The object to clone.\n * @return {Object} a clone of the passed object.\n * @throws {TypeError} when a nested object is passed.\n * @memberOf Utils\n */\nlunr.utils.clone = function (obj) {\n  if (obj === null || obj === undefined) {\n    return obj\n  }\n\n  var clone = Object.create(null),\n      keys = Object.keys(obj)\n\n  for (var i = 0; i < keys.length; i++) {\n    var key = keys[i],\n        val = obj[key]\n\n    if (Array.isArray(val)) {\n      clone[key] = val.slice()\n      continue\n    }\n\n    if (typeof val === 'string' ||\n        typeof val === 'number' ||\n        typeof val === 'boolean') {\n      clone[key] = val\n      continue\n    }\n\n    throw new TypeError(\"clone is not deep and does not support nested objects\")\n  }\n\n  return clone\n}\nlunr.FieldRef = function (docRef, fieldName, stringValue) {\n  this.docRef = docRef\n  this.fieldName = fieldName\n  this._stringValue = stringValue\n}\n\nlunr.FieldRef.joiner = \"/\"\n\nlunr.FieldRef.fromString = function (s) {\n  var n = s.indexOf(lunr.FieldRef.joiner)\n\n  if (n === -1) {\n    throw \"malformed field ref string\"\n  }\n\n  var fieldRef = s.slice(0, n),\n      docRef = s.slice(n + 1)\n\n  return new lunr.FieldRef (docRef, fieldRef, s)\n}\n\nlunr.FieldRef.prototype.toString = function () {\n  if (this._stringValue == undefined) {\n    this._stringValue = this.fieldName + lunr.FieldRef.joiner + this.docRef\n  }\n\n  return this._stringValue\n}\n/*!\n * lunr.Set\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * A lunr set.\n *\n * @constructor\n */\nlunr.Set = function (elements) {\n  this.elements = Object.create(null)\n\n  if (elements) {\n    this.length = elements.length\n\n    for (var i = 0; i < this.length; i++) {\n      this.elements[elements[i]] = true\n    }\n  } else {\n    this.length = 0\n  }\n}\n\n/**\n * A complete set that contains all elements.\n *\n * @static\n * @readonly\n * @type {lunr.Set}\n */\nlunr.Set.complete = {\n  intersect: function (other) {\n    return other\n  },\n\n  union: function () {\n    return this\n  },\n\n  contains: function () {\n    return true\n  }\n}\n\n/**\n * An empty set that contains no elements.\n *\n * @static\n * @readonly\n * @type {lunr.Set}\n */\nlunr.Set.empty = {\n  intersect: function () {\n    return this\n  },\n\n  union: function (other) {\n    return other\n  },\n\n  contains: function () {\n    return false\n  }\n}\n\n/**\n * Returns true if this set contains the specified object.\n *\n * @param {object} object - Object whose presence in this set is to be tested.\n * @returns {boolean} - True if this set contains the specified object.\n */\nlunr.Set.prototype.contains = function (object) {\n  return !!this.elements[object]\n}\n\n/**\n * Returns a new set containing only the elements that are present in both\n * this set and the specified set.\n *\n * @param {lunr.Set} other - set to intersect with this set.\n * @returns {lunr.Set} a new set that is the intersection of this and the specified set.\n */\n\nlunr.Set.prototype.intersect = function (other) {\n  var a, b, elements, intersection = []\n\n  if (other === lunr.Set.complete) {\n    return this\n  }\n\n  if (other === lunr.Set.empty) {\n    return other\n  }\n\n  if (this.length < other.length) {\n    a = this\n    b = other\n  } else {\n    a = other\n    b = this\n  }\n\n  elements = Object.keys(a.elements)\n\n  for (var i = 0; i < elements.length; i++) {\n    var element = elements[i]\n    if (element in b.elements) {\n      intersection.push(element)\n    }\n  }\n\n  return new lunr.Set (intersection)\n}\n\n/**\n * Returns a new set combining the elements of this and the specified set.\n *\n * @param {lunr.Set} other - set to union with this set.\n * @return {lunr.Set} a new set that is the union of this and the specified set.\n */\n\nlunr.Set.prototype.union = function (other) {\n  if (other === lunr.Set.complete) {\n    return lunr.Set.complete\n  }\n\n  if (other === lunr.Set.empty) {\n    return this\n  }\n\n  return new lunr.Set(Object.keys(this.elements).concat(Object.keys(other.elements)))\n}\n/**\n * A function to calculate the inverse document frequency for\n * a posting. This is shared between the builder and the index\n *\n * @private\n * @param {object} posting - The posting for a given term\n * @param {number} documentCount - The total number of documents.\n */\nlunr.idf = function (posting, documentCount) {\n  var documentsWithTerm = 0\n\n  for (var fieldName in posting) {\n    if (fieldName == '_index') continue // Ignore the term index, its not a field\n    documentsWithTerm += Object.keys(posting[fieldName]).length\n  }\n\n  var x = (documentCount - documentsWithTerm + 0.5) / (documentsWithTerm + 0.5)\n\n  return Math.log(1 + Math.abs(x))\n}\n\n/**\n * A token wraps a string representation of a token\n * as it is passed through the text processing pipeline.\n *\n * @constructor\n * @param {string} [str=''] - The string token being wrapped.\n * @param {object} [metadata={}] - Metadata associated with this token.\n */\nlunr.Token = function (str, metadata) {\n  this.str = str || \"\"\n  this.metadata = metadata || {}\n}\n\n/**\n * Returns the token string that is being wrapped by this object.\n *\n * @returns {string}\n */\nlunr.Token.prototype.toString = function () {\n  return this.str\n}\n\n/**\n * A token update function is used when updating or optionally\n * when cloning a token.\n *\n * @callback lunr.Token~updateFunction\n * @param {string} str - The string representation of the token.\n * @param {Object} metadata - All metadata associated with this token.\n */\n\n/**\n * Applies the given function to the wrapped string token.\n *\n * @example\n * token.update(function (str, metadata) {\n *   return str.toUpperCase()\n * })\n *\n * @param {lunr.Token~updateFunction} fn - A function to apply to the token string.\n * @returns {lunr.Token}\n */\nlunr.Token.prototype.update = function (fn) {\n  this.str = fn(this.str, this.metadata)\n  return this\n}\n\n/**\n * Creates a clone of this token. Optionally a function can be\n * applied to the cloned token.\n *\n * @param {lunr.Token~updateFunction} [fn] - An optional function to apply to the cloned token.\n * @returns {lunr.Token}\n */\nlunr.Token.prototype.clone = function (fn) {\n  fn = fn || function (s) { return s }\n  return new lunr.Token (fn(this.str, this.metadata), this.metadata)\n}\n/*!\n * lunr.tokenizer\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * A function for splitting a string into tokens ready to be inserted into\n * the search index. Uses `lunr.tokenizer.separator` to split strings, change\n * the value of this property to change how strings are split into tokens.\n *\n * This tokenizer will convert its parameter to a string by calling `toString` and\n * then will split this string on the character in `lunr.tokenizer.separator`.\n * Arrays will have their elements converted to strings and wrapped in a lunr.Token.\n *\n * Optional metadata can be passed to the tokenizer, this metadata will be cloned and\n * added as metadata to every token that is created from the object to be tokenized.\n *\n * @static\n * @param {?(string|object|object[])} obj - The object to convert into tokens\n * @param {?object} metadata - Optional metadata to associate with every token\n * @returns {lunr.Token[]}\n * @see {@link lunr.Pipeline}\n */\nlunr.tokenizer = function (obj, metadata) {\n  if (obj == null || obj == undefined) {\n    return []\n  }\n\n  if (Array.isArray(obj)) {\n    return obj.map(function (t) {\n      return new lunr.Token(\n        lunr.utils.asString(t).toLowerCase(),\n        lunr.utils.clone(metadata)\n      )\n    })\n  }\n\n  var str = obj.toString().toLowerCase(),\n      len = str.length,\n      tokens = []\n\n  for (var sliceEnd = 0, sliceStart = 0; sliceEnd <= len; sliceEnd++) {\n    var char = str.charAt(sliceEnd),\n        sliceLength = sliceEnd - sliceStart\n\n    if ((char.match(lunr.tokenizer.separator) || sliceEnd == len)) {\n\n      if (sliceLength > 0) {\n        var tokenMetadata = lunr.utils.clone(metadata) || {}\n        tokenMetadata[\"position\"] = [sliceStart, sliceLength]\n        tokenMetadata[\"index\"] = tokens.length\n\n        tokens.push(\n          new lunr.Token (\n            str.slice(sliceStart, sliceEnd),\n            tokenMetadata\n          )\n        )\n      }\n\n      sliceStart = sliceEnd + 1\n    }\n\n  }\n\n  return tokens\n}\n\n/**\n * The separator used to split a string into tokens. Override this property to change the behaviour of\n * `lunr.tokenizer` behaviour when tokenizing strings. By default this splits on whitespace and hyphens.\n *\n * @static\n * @see lunr.tokenizer\n */\nlunr.tokenizer.separator = /[\\s\\-]+/\n/*!\n * lunr.Pipeline\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * lunr.Pipelines maintain an ordered list of functions to be applied to all\n * tokens in documents entering the search index and queries being ran against\n * the index.\n *\n * An instance of lunr.Index created with the lunr shortcut will contain a\n * pipeline with a stop word filter and an English language stemmer. Extra\n * functions can be added before or after either of these functions or these\n * default functions can be removed.\n *\n * When run the pipeline will call each function in turn, passing a token, the\n * index of that token in the original list of all tokens and finally a list of\n * all the original tokens.\n *\n * The output of functions in the pipeline will be passed to the next function\n * in the pipeline. To exclude a token from entering the index the function\n * should return undefined, the rest of the pipeline will not be called with\n * this token.\n *\n * For serialisation of pipelines to work, all functions used in an instance of\n * a pipeline should be registered with lunr.Pipeline. Registered functions can\n * then be loaded. If trying to load a serialised pipeline that uses functions\n * that are not registered an error will be thrown.\n *\n * If not planning on serialising the pipeline then registering pipeline functions\n * is not necessary.\n *\n * @constructor\n */\nlunr.Pipeline = function () {\n  this._stack = []\n}\n\nlunr.Pipeline.registeredFunctions = Object.create(null)\n\n/**\n * A pipeline function maps lunr.Token to lunr.Token. A lunr.Token contains the token\n * string as well as all known metadata. A pipeline function can mutate the token string\n * or mutate (or add) metadata for a given token.\n *\n * A pipeline function can indicate that the passed token should be discarded by returning\n * null, undefined or an empty string. This token will not be passed to any downstream pipeline\n * functions and will not be added to the index.\n *\n * Multiple tokens can be returned by returning an array of tokens. Each token will be passed\n * to any downstream pipeline functions and all will returned tokens will be added to the index.\n *\n * Any number of pipeline functions may be chained together using a lunr.Pipeline.\n *\n * @interface lunr.PipelineFunction\n * @param {lunr.Token} token - A token from the document being processed.\n * @param {number} i - The index of this token in the complete list of tokens for this document/field.\n * @param {lunr.Token[]} tokens - All tokens for this document/field.\n * @returns {(?lunr.Token|lunr.Token[])}\n */\n\n/**\n * Register a function with the pipeline.\n *\n * Functions that are used in the pipeline should be registered if the pipeline\n * needs to be serialised, or a serialised pipeline needs to be loaded.\n *\n * Registering a function does not add it to a pipeline, functions must still be\n * added to instances of the pipeline for them to be used when running a pipeline.\n *\n * @param {lunr.PipelineFunction} fn - The function to check for.\n * @param {String} label - The label to register this function with\n */\nlunr.Pipeline.registerFunction = function (fn, label) {\n  if (label in this.registeredFunctions) {\n    lunr.utils.warn('Overwriting existing registered function: ' + label)\n  }\n\n  fn.label = label\n  lunr.Pipeline.registeredFunctions[fn.label] = fn\n}\n\n/**\n * Warns if the function is not registered as a Pipeline function.\n *\n * @param {lunr.PipelineFunction} fn - The function to check for.\n * @private\n */\nlunr.Pipeline.warnIfFunctionNotRegistered = function (fn) {\n  var isRegistered = fn.label && (fn.label in this.registeredFunctions)\n\n  if (!isRegistered) {\n    lunr.utils.warn('Function is not registered with pipeline. This may cause problems when serialising the index.\\n', fn)\n  }\n}\n\n/**\n * Loads a previously serialised pipeline.\n *\n * All functions to be loaded must already be registered with lunr.Pipeline.\n * If any function from the serialised data has not been registered then an\n * error will be thrown.\n *\n * @param {Object} serialised - The serialised pipeline to load.\n * @returns {lunr.Pipeline}\n */\nlunr.Pipeline.load = function (serialised) {\n  var pipeline = new lunr.Pipeline\n\n  serialised.forEach(function (fnName) {\n    var fn = lunr.Pipeline.registeredFunctions[fnName]\n\n    if (fn) {\n      pipeline.add(fn)\n    } else {\n      throw new Error('Cannot load unregistered function: ' + fnName)\n    }\n  })\n\n  return pipeline\n}\n\n/**\n * Adds new functions to the end of the pipeline.\n *\n * Logs a warning if the function has not been registered.\n *\n * @param {lunr.PipelineFunction[]} functions - Any number of functions to add to the pipeline.\n */\nlunr.Pipeline.prototype.add = function () {\n  var fns = Array.prototype.slice.call(arguments)\n\n  fns.forEach(function (fn) {\n    lunr.Pipeline.warnIfFunctionNotRegistered(fn)\n    this._stack.push(fn)\n  }, this)\n}\n\n/**\n * Adds a single function after a function that already exists in the\n * pipeline.\n *\n * Logs a warning if the function has not been registered.\n *\n * @param {lunr.PipelineFunction} existingFn - A function that already exists in the pipeline.\n * @param {lunr.PipelineFunction} newFn - The new function to add to the pipeline.\n */\nlunr.Pipeline.prototype.after = function (existingFn, newFn) {\n  lunr.Pipeline.warnIfFunctionNotRegistered(newFn)\n\n  var pos = this._stack.indexOf(existingFn)\n  if (pos == -1) {\n    throw new Error('Cannot find existingFn')\n  }\n\n  pos = pos + 1\n  this._stack.splice(pos, 0, newFn)\n}\n\n/**\n * Adds a single function before a function that already exists in the\n * pipeline.\n *\n * Logs a warning if the function has not been registered.\n *\n * @param {lunr.PipelineFunction} existingFn - A function that already exists in the pipeline.\n * @param {lunr.PipelineFunction} newFn - The new function to add to the pipeline.\n */\nlunr.Pipeline.prototype.before = function (existingFn, newFn) {\n  lunr.Pipeline.warnIfFunctionNotRegistered(newFn)\n\n  var pos = this._stack.indexOf(existingFn)\n  if (pos == -1) {\n    throw new Error('Cannot find existingFn')\n  }\n\n  this._stack.splice(pos, 0, newFn)\n}\n\n/**\n * Removes a function from the pipeline.\n *\n * @param {lunr.PipelineFunction} fn The function to remove from the pipeline.\n */\nlunr.Pipeline.prototype.remove = function (fn) {\n  var pos = this._stack.indexOf(fn)\n  if (pos == -1) {\n    return\n  }\n\n  this._stack.splice(pos, 1)\n}\n\n/**\n * Runs the current list of functions that make up the pipeline against the\n * passed tokens.\n *\n * @param {Array} tokens The tokens to run through the pipeline.\n * @returns {Array}\n */\nlunr.Pipeline.prototype.run = function (tokens) {\n  var stackLength = this._stack.length\n\n  for (var i = 0; i < stackLength; i++) {\n    var fn = this._stack[i]\n    var memo = []\n\n    for (var j = 0; j < tokens.length; j++) {\n      var result = fn(tokens[j], j, tokens)\n\n      if (result === null || result === void 0 || result === '') continue\n\n      if (Array.isArray(result)) {\n        for (var k = 0; k < result.length; k++) {\n          memo.push(result[k])\n        }\n      } else {\n        memo.push(result)\n      }\n    }\n\n    tokens = memo\n  }\n\n  return tokens\n}\n\n/**\n * Convenience method for passing a string through a pipeline and getting\n * strings out. This method takes care of wrapping the passed string in a\n * token and mapping the resulting tokens back to strings.\n *\n * @param {string} str - The string to pass through the pipeline.\n * @param {?object} metadata - Optional metadata to associate with the token\n * passed to the pipeline.\n * @returns {string[]}\n */\nlunr.Pipeline.prototype.runString = function (str, metadata) {\n  var token = new lunr.Token (str, metadata)\n\n  return this.run([token]).map(function (t) {\n    return t.toString()\n  })\n}\n\n/**\n * Resets the pipeline by removing any existing processors.\n *\n */\nlunr.Pipeline.prototype.reset = function () {\n  this._stack = []\n}\n\n/**\n * Returns a representation of the pipeline ready for serialisation.\n *\n * Logs a warning if the function has not been registered.\n *\n * @returns {Array}\n */\nlunr.Pipeline.prototype.toJSON = function () {\n  return this._stack.map(function (fn) {\n    lunr.Pipeline.warnIfFunctionNotRegistered(fn)\n\n    return fn.label\n  })\n}\n/*!\n * lunr.Vector\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * A vector is used to construct the vector space of documents and queries. These\n * vectors support operations to determine the similarity between two documents or\n * a document and a query.\n *\n * Normally no parameters are required for initializing a vector, but in the case of\n * loading a previously dumped vector the raw elements can be provided to the constructor.\n *\n * For performance reasons vectors are implemented with a flat array, where an elements\n * index is immediately followed by its value. E.g. [index, value, index, value]. This\n * allows the underlying array to be as sparse as possible and still offer decent\n * performance when being used for vector calculations.\n *\n * @constructor\n * @param {Number[]} [elements] - The flat list of element index and element value pairs.\n */\nlunr.Vector = function (elements) {\n  this._magnitude = 0\n  this.elements = elements || []\n}\n\n\n/**\n * Calculates the position within the vector to insert a given index.\n *\n * This is used internally by insert and upsert. If there are duplicate indexes then\n * the position is returned as if the value for that index were to be updated, but it\n * is the callers responsibility to check whether there is a duplicate at that index\n *\n * @param {Number} insertIdx - The index at which the element should be inserted.\n * @returns {Number}\n */\nlunr.Vector.prototype.positionForIndex = function (index) {\n  // For an empty vector the tuple can be inserted at the beginning\n  if (this.elements.length == 0) {\n    return 0\n  }\n\n  var start = 0,\n      end = this.elements.length / 2,\n      sliceLength = end - start,\n      pivotPoint = Math.floor(sliceLength / 2),\n      pivotIndex = this.elements[pivotPoint * 2]\n\n  while (sliceLength > 1) {\n    if (pivotIndex < index) {\n      start = pivotPoint\n    }\n\n    if (pivotIndex > index) {\n      end = pivotPoint\n    }\n\n    if (pivotIndex == index) {\n      break\n    }\n\n    sliceLength = end - start\n    pivotPoint = start + Math.floor(sliceLength / 2)\n    pivotIndex = this.elements[pivotPoint * 2]\n  }\n\n  if (pivotIndex == index) {\n    return pivotPoint * 2\n  }\n\n  if (pivotIndex > index) {\n    return pivotPoint * 2\n  }\n\n  if (pivotIndex < index) {\n    return (pivotPoint + 1) * 2\n  }\n}\n\n/**\n * Inserts an element at an index within the vector.\n *\n * Does not allow duplicates, will throw an error if there is already an entry\n * for this index.\n *\n * @param {Number} insertIdx - The index at which the element should be inserted.\n * @param {Number} val - The value to be inserted into the vector.\n */\nlunr.Vector.prototype.insert = function (insertIdx, val) {\n  this.upsert(insertIdx, val, function () {\n    throw \"duplicate index\"\n  })\n}\n\n/**\n * Inserts or updates an existing index within the vector.\n *\n * @param {Number} insertIdx - The index at which the element should be inserted.\n * @param {Number} val - The value to be inserted into the vector.\n * @param {function} fn - A function that is called for updates, the existing value and the\n * requested value are passed as arguments\n */\nlunr.Vector.prototype.upsert = function (insertIdx, val, fn) {\n  this._magnitude = 0\n  var position = this.positionForIndex(insertIdx)\n\n  if (this.elements[position] == insertIdx) {\n    this.elements[position + 1] = fn(this.elements[position + 1], val)\n  } else {\n    this.elements.splice(position, 0, insertIdx, val)\n  }\n}\n\n/**\n * Calculates the magnitude of this vector.\n *\n * @returns {Number}\n */\nlunr.Vector.prototype.magnitude = function () {\n  if (this._magnitude) return this._magnitude\n\n  var sumOfSquares = 0,\n      elementsLength = this.elements.length\n\n  for (var i = 1; i < elementsLength; i += 2) {\n    var val = this.elements[i]\n    sumOfSquares += val * val\n  }\n\n  return this._magnitude = Math.sqrt(sumOfSquares)\n}\n\n/**\n * Calculates the dot product of this vector and another vector.\n *\n * @param {lunr.Vector} otherVector - The vector to compute the dot product with.\n * @returns {Number}\n */\nlunr.Vector.prototype.dot = function (otherVector) {\n  var dotProduct = 0,\n      a = this.elements, b = otherVector.elements,\n      aLen = a.length, bLen = b.length,\n      aVal = 0, bVal = 0,\n      i = 0, j = 0\n\n  while (i < aLen && j < bLen) {\n    aVal = a[i], bVal = b[j]\n    if (aVal < bVal) {\n      i += 2\n    } else if (aVal > bVal) {\n      j += 2\n    } else if (aVal == bVal) {\n      dotProduct += a[i + 1] * b[j + 1]\n      i += 2\n      j += 2\n    }\n  }\n\n  return dotProduct\n}\n\n/**\n * Calculates the similarity between this vector and another vector.\n *\n * @param {lunr.Vector} otherVector - The other vector to calculate the\n * similarity with.\n * @returns {Number}\n */\nlunr.Vector.prototype.similarity = function (otherVector) {\n  return this.dot(otherVector) / this.magnitude() || 0\n}\n\n/**\n * Converts the vector to an array of the elements within the vector.\n *\n * @returns {Number[]}\n */\nlunr.Vector.prototype.toArray = function () {\n  var output = new Array (this.elements.length / 2)\n\n  for (var i = 1, j = 0; i < this.elements.length; i += 2, j++) {\n    output[j] = this.elements[i]\n  }\n\n  return output\n}\n\n/**\n * A JSON serializable representation of the vector.\n *\n * @returns {Number[]}\n */\nlunr.Vector.prototype.toJSON = function () {\n  return this.elements\n}\n/* eslint-disable */\n/*!\n * lunr.stemmer\n * Copyright (C) 2020 Oliver Nightingale\n * Includes code from - http://tartarus.org/~martin/PorterStemmer/js.txt\n */\n\n/**\n * lunr.stemmer is an english language stemmer, this is a JavaScript\n * implementation of the PorterStemmer taken from http://tartarus.org/~martin\n *\n * @static\n * @implements {lunr.PipelineFunction}\n * @param {lunr.Token} token - The string to stem\n * @returns {lunr.Token}\n * @see {@link lunr.Pipeline}\n * @function\n */\nlunr.stemmer = (function(){\n  var step2list = {\n      \"ational\" : \"ate\",\n      \"tional\" : \"tion\",\n      \"enci\" : \"ence\",\n      \"anci\" : \"ance\",\n      \"izer\" : \"ize\",\n      \"bli\" : \"ble\",\n      \"alli\" : \"al\",\n      \"entli\" : \"ent\",\n      \"eli\" : \"e\",\n      \"ousli\" : \"ous\",\n      \"ization\" : \"ize\",\n      \"ation\" : \"ate\",\n      \"ator\" : \"ate\",\n      \"alism\" : \"al\",\n      \"iveness\" : \"ive\",\n      \"fulness\" : \"ful\",\n      \"ousness\" : \"ous\",\n      \"aliti\" : \"al\",\n      \"iviti\" : \"ive\",\n      \"biliti\" : \"ble\",\n      \"logi\" : \"log\"\n    },\n\n    step3list = {\n      \"icate\" : \"ic\",\n      \"ative\" : \"\",\n      \"alize\" : \"al\",\n      \"iciti\" : \"ic\",\n      \"ical\" : \"ic\",\n      \"ful\" : \"\",\n      \"ness\" : \"\"\n    },\n\n    c = \"[^aeiou]\",          // consonant\n    v = \"[aeiouy]\",          // vowel\n    C = c + \"[^aeiouy]*\",    // consonant sequence\n    V = v + \"[aeiou]*\",      // vowel sequence\n\n    mgr0 = \"^(\" + C + \")?\" + V + C,               // [C]VC... is m>0\n    meq1 = \"^(\" + C + \")?\" + V + C + \"(\" + V + \")?$\",  // [C]VC[V] is m=1\n    mgr1 = \"^(\" + C + \")?\" + V + C + V + C,       // [C]VCVC... is m>1\n    s_v = \"^(\" + C + \")?\" + v;                   // vowel in stem\n\n  var re_mgr0 = new RegExp(mgr0);\n  var re_mgr1 = new RegExp(mgr1);\n  var re_meq1 = new RegExp(meq1);\n  var re_s_v = new RegExp(s_v);\n\n  var re_1a = /^(.+?)(ss|i)es$/;\n  var re2_1a = /^(.+?)([^s])s$/;\n  var re_1b = /^(.+?)eed$/;\n  var re2_1b = /^(.+?)(ed|ing)$/;\n  var re_1b_2 = /.$/;\n  var re2_1b_2 = /(at|bl|iz)$/;\n  var re3_1b_2 = new RegExp(\"([^aeiouylsz])\\\\1$\");\n  var re4_1b_2 = new RegExp(\"^\" + C + v + \"[^aeiouwxy]$\");\n\n  var re_1c = /^(.+?[^aeiou])y$/;\n  var re_2 = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;\n\n  var re_3 = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;\n\n  var re_4 = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;\n  var re2_4 = /^(.+?)(s|t)(ion)$/;\n\n  var re_5 = /^(.+?)e$/;\n  var re_5_1 = /ll$/;\n  var re3_5 = new RegExp(\"^\" + C + v + \"[^aeiouwxy]$\");\n\n  var porterStemmer = function porterStemmer(w) {\n    var stem,\n      suffix,\n      firstch,\n      re,\n      re2,\n      re3,\n      re4;\n\n    if (w.length < 3) { return w; }\n\n    firstch = w.substr(0,1);\n    if (firstch == \"y\") {\n      w = firstch.toUpperCase() + w.substr(1);\n    }\n\n    // Step 1a\n    re = re_1a\n    re2 = re2_1a;\n\n    if (re.test(w)) { w = w.replace(re,\"$1$2\"); }\n    else if (re2.test(w)) { w = w.replace(re2,\"$1$2\"); }\n\n    // Step 1b\n    re = re_1b;\n    re2 = re2_1b;\n    if (re.test(w)) {\n      var fp = re.exec(w);\n      re = re_mgr0;\n      if (re.test(fp[1])) {\n        re = re_1b_2;\n        w = w.replace(re,\"\");\n      }\n    } else if (re2.test(w)) {\n      var fp = re2.exec(w);\n      stem = fp[1];\n      re2 = re_s_v;\n      if (re2.test(stem)) {\n        w = stem;\n        re2 = re2_1b_2;\n        re3 = re3_1b_2;\n        re4 = re4_1b_2;\n        if (re2.test(w)) { w = w + \"e\"; }\n        else if (re3.test(w)) { re = re_1b_2; w = w.replace(re,\"\"); }\n        else if (re4.test(w)) { w = w + \"e\"; }\n      }\n    }\n\n    // Step 1c - replace suffix y or Y by i if preceded by a non-vowel which is not the first letter of the word (so cry -> cri, by -> by, say -> say)\n    re = re_1c;\n    if (re.test(w)) {\n      var fp = re.exec(w);\n      stem = fp[1];\n      w = stem + \"i\";\n    }\n\n    // Step 2\n    re = re_2;\n    if (re.test(w)) {\n      var fp = re.exec(w);\n      stem = fp[1];\n      suffix = fp[2];\n      re = re_mgr0;\n      if (re.test(stem)) {\n        w = stem + step2list[suffix];\n      }\n    }\n\n    // Step 3\n    re = re_3;\n    if (re.test(w)) {\n      var fp = re.exec(w);\n      stem = fp[1];\n      suffix = fp[2];\n      re = re_mgr0;\n      if (re.test(stem)) {\n        w = stem + step3list[suffix];\n      }\n    }\n\n    // Step 4\n    re = re_4;\n    re2 = re2_4;\n    if (re.test(w)) {\n      var fp = re.exec(w);\n      stem = fp[1];\n      re = re_mgr1;\n      if (re.test(stem)) {\n        w = stem;\n      }\n    } else if (re2.test(w)) {\n      var fp = re2.exec(w);\n      stem = fp[1] + fp[2];\n      re2 = re_mgr1;\n      if (re2.test(stem)) {\n        w = stem;\n      }\n    }\n\n    // Step 5\n    re = re_5;\n    if (re.test(w)) {\n      var fp = re.exec(w);\n      stem = fp[1];\n      re = re_mgr1;\n      re2 = re_meq1;\n      re3 = re3_5;\n      if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) {\n        w = stem;\n      }\n    }\n\n    re = re_5_1;\n    re2 = re_mgr1;\n    if (re.test(w) && re2.test(w)) {\n      re = re_1b_2;\n      w = w.replace(re,\"\");\n    }\n\n    // and turn initial Y back to y\n\n    if (firstch == \"y\") {\n      w = firstch.toLowerCase() + w.substr(1);\n    }\n\n    return w;\n  };\n\n  return function (token) {\n    return token.update(porterStemmer);\n  }\n})();\n\nlunr.Pipeline.registerFunction(lunr.stemmer, 'stemmer')\n/*!\n * lunr.stopWordFilter\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * lunr.generateStopWordFilter builds a stopWordFilter function from the provided\n * list of stop words.\n *\n * The built in lunr.stopWordFilter is built using this generator and can be used\n * to generate custom stopWordFilters for applications or non English languages.\n *\n * @function\n * @param {Array} token The token to pass through the filter\n * @returns {lunr.PipelineFunction}\n * @see lunr.Pipeline\n * @see lunr.stopWordFilter\n */\nlunr.generateStopWordFilter = function (stopWords) {\n  var words = stopWords.reduce(function (memo, stopWord) {\n    memo[stopWord] = stopWord\n    return memo\n  }, {})\n\n  return function (token) {\n    if (token && words[token.toString()] !== token.toString()) return token\n  }\n}\n\n/**\n * lunr.stopWordFilter is an English language stop word list filter, any words\n * contained in the list will not be passed through the filter.\n *\n * This is intended to be used in the Pipeline. If the token does not pass the\n * filter then undefined will be returned.\n *\n * @function\n * @implements {lunr.PipelineFunction}\n * @params {lunr.Token} token - A token to check for being a stop word.\n * @returns {lunr.Token}\n * @see {@link lunr.Pipeline}\n */\nlunr.stopWordFilter = lunr.generateStopWordFilter([\n  'a',\n  'able',\n  'about',\n  'across',\n  'after',\n  'all',\n  'almost',\n  'also',\n  'am',\n  'among',\n  'an',\n  'and',\n  'any',\n  'are',\n  'as',\n  'at',\n  'be',\n  'because',\n  'been',\n  'but',\n  'by',\n  'can',\n  'cannot',\n  'could',\n  'dear',\n  'did',\n  'do',\n  'does',\n  'either',\n  'else',\n  'ever',\n  'every',\n  'for',\n  'from',\n  'get',\n  'got',\n  'had',\n  'has',\n  'have',\n  'he',\n  'her',\n  'hers',\n  'him',\n  'his',\n  'how',\n  'however',\n  'i',\n  'if',\n  'in',\n  'into',\n  'is',\n  'it',\n  'its',\n  'just',\n  'least',\n  'let',\n  'like',\n  'likely',\n  'may',\n  'me',\n  'might',\n  'most',\n  'must',\n  'my',\n  'neither',\n  'no',\n  'nor',\n  'not',\n  'of',\n  'off',\n  'often',\n  'on',\n  'only',\n  'or',\n  'other',\n  'our',\n  'own',\n  'rather',\n  'said',\n  'say',\n  'says',\n  'she',\n  'should',\n  'since',\n  'so',\n  'some',\n  'than',\n  'that',\n  'the',\n  'their',\n  'them',\n  'then',\n  'there',\n  'these',\n  'they',\n  'this',\n  'tis',\n  'to',\n  'too',\n  'twas',\n  'us',\n  'wants',\n  'was',\n  'we',\n  'were',\n  'what',\n  'when',\n  'where',\n  'which',\n  'while',\n  'who',\n  'whom',\n  'why',\n  'will',\n  'with',\n  'would',\n  'yet',\n  'you',\n  'your'\n])\n\nlunr.Pipeline.registerFunction(lunr.stopWordFilter, 'stopWordFilter')\n/*!\n * lunr.trimmer\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * lunr.trimmer is a pipeline function for trimming non word\n * characters from the beginning and end of tokens before they\n * enter the index.\n *\n * This implementation may not work correctly for non latin\n * characters and should either be removed or adapted for use\n * with languages with non-latin characters.\n *\n * @static\n * @implements {lunr.PipelineFunction}\n * @param {lunr.Token} token The token to pass through the filter\n * @returns {lunr.Token}\n * @see lunr.Pipeline\n */\nlunr.trimmer = function (token) {\n  return token.update(function (s) {\n    return s.replace(/^\\W+/, '').replace(/\\W+$/, '')\n  })\n}\n\nlunr.Pipeline.registerFunction(lunr.trimmer, 'trimmer')\n/*!\n * lunr.TokenSet\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * A token set is used to store the unique list of all tokens\n * within an index. Token sets are also used to represent an\n * incoming query to the index, this query token set and index\n * token set are then intersected to find which tokens to look\n * up in the inverted index.\n *\n * A token set can hold multiple tokens, as in the case of the\n * index token set, or it can hold a single token as in the\n * case of a simple query token set.\n *\n * Additionally token sets are used to perform wildcard matching.\n * Leading, contained and trailing wildcards are supported, and\n * from this edit distance matching can also be provided.\n *\n * Token sets are implemented as a minimal finite state automata,\n * where both common prefixes and suffixes are shared between tokens.\n * This helps to reduce the space used for storing the token set.\n *\n * @constructor\n */\nlunr.TokenSet = function () {\n  this.final = false\n  this.edges = {}\n  this.id = lunr.TokenSet._nextId\n  lunr.TokenSet._nextId += 1\n}\n\n/**\n * Keeps track of the next, auto increment, identifier to assign\n * to a new tokenSet.\n *\n * TokenSets require a unique identifier to be correctly minimised.\n *\n * @private\n */\nlunr.TokenSet._nextId = 1\n\n/**\n * Creates a TokenSet instance from the given sorted array of words.\n *\n * @param {String[]} arr - A sorted array of strings to create the set from.\n * @returns {lunr.TokenSet}\n * @throws Will throw an error if the input array is not sorted.\n */\nlunr.TokenSet.fromArray = function (arr) {\n  var builder = new lunr.TokenSet.Builder\n\n  for (var i = 0, len = arr.length; i < len; i++) {\n    builder.insert(arr[i])\n  }\n\n  builder.finish()\n  return builder.root\n}\n\n/**\n * Creates a token set from a query clause.\n *\n * @private\n * @param {Object} clause - A single clause from lunr.Query.\n * @param {string} clause.term - The query clause term.\n * @param {number} [clause.editDistance] - The optional edit distance for the term.\n * @returns {lunr.TokenSet}\n */\nlunr.TokenSet.fromClause = function (clause) {\n  if ('editDistance' in clause) {\n    return lunr.TokenSet.fromFuzzyString(clause.term, clause.editDistance)\n  } else {\n    return lunr.TokenSet.fromString(clause.term)\n  }\n}\n\n/**\n * Creates a token set representing a single string with a specified\n * edit distance.\n *\n * Insertions, deletions, substitutions and transpositions are each\n * treated as an edit distance of 1.\n *\n * Increasing the allowed edit distance will have a dramatic impact\n * on the performance of both creating and intersecting these TokenSets.\n * It is advised to keep the edit distance less than 3.\n *\n * @param {string} str - The string to create the token set from.\n * @param {number} editDistance - The allowed edit distance to match.\n * @returns {lunr.Vector}\n */\nlunr.TokenSet.fromFuzzyString = function (str, editDistance) {\n  var root = new lunr.TokenSet\n\n  var stack = [{\n    node: root,\n    editsRemaining: editDistance,\n    str: str\n  }]\n\n  while (stack.length) {\n    var frame = stack.pop()\n\n    // no edit\n    if (frame.str.length > 0) {\n      var char = frame.str.charAt(0),\n          noEditNode\n\n      if (char in frame.node.edges) {\n        noEditNode = frame.node.edges[char]\n      } else {\n        noEditNode = new lunr.TokenSet\n        frame.node.edges[char] = noEditNode\n      }\n\n      if (frame.str.length == 1) {\n        noEditNode.final = true\n      }\n\n      stack.push({\n        node: noEditNode,\n        editsRemaining: frame.editsRemaining,\n        str: frame.str.slice(1)\n      })\n    }\n\n    if (frame.editsRemaining == 0) {\n      continue\n    }\n\n    // insertion\n    if (\"*\" in frame.node.edges) {\n      var insertionNode = frame.node.edges[\"*\"]\n    } else {\n      var insertionNode = new lunr.TokenSet\n      frame.node.edges[\"*\"] = insertionNode\n    }\n\n    if (frame.str.length == 0) {\n      insertionNode.final = true\n    }\n\n    stack.push({\n      node: insertionNode,\n      editsRemaining: frame.editsRemaining - 1,\n      str: frame.str\n    })\n\n    // deletion\n    // can only do a deletion if we have enough edits remaining\n    // and if there are characters left to delete in the string\n    if (frame.str.length > 1) {\n      stack.push({\n        node: frame.node,\n        editsRemaining: frame.editsRemaining - 1,\n        str: frame.str.slice(1)\n      })\n    }\n\n    // deletion\n    // just removing the last character from the str\n    if (frame.str.length == 1) {\n      frame.node.final = true\n    }\n\n    // substitution\n    // can only do a substitution if we have enough edits remaining\n    // and if there are characters left to substitute\n    if (frame.str.length >= 1) {\n      if (\"*\" in frame.node.edges) {\n        var substitutionNode = frame.node.edges[\"*\"]\n      } else {\n        var substitutionNode = new lunr.TokenSet\n        frame.node.edges[\"*\"] = substitutionNode\n      }\n\n      if (frame.str.length == 1) {\n        substitutionNode.final = true\n      }\n\n      stack.push({\n        node: substitutionNode,\n        editsRemaining: frame.editsRemaining - 1,\n        str: frame.str.slice(1)\n      })\n    }\n\n    // transposition\n    // can only do a transposition if there are edits remaining\n    // and there are enough characters to transpose\n    if (frame.str.length > 1) {\n      var charA = frame.str.charAt(0),\n          charB = frame.str.charAt(1),\n          transposeNode\n\n      if (charB in frame.node.edges) {\n        transposeNode = frame.node.edges[charB]\n      } else {\n        transposeNode = new lunr.TokenSet\n        frame.node.edges[charB] = transposeNode\n      }\n\n      if (frame.str.length == 1) {\n        transposeNode.final = true\n      }\n\n      stack.push({\n        node: transposeNode,\n        editsRemaining: frame.editsRemaining - 1,\n        str: charA + frame.str.slice(2)\n      })\n    }\n  }\n\n  return root\n}\n\n/**\n * Creates a TokenSet from a string.\n *\n * The string may contain one or more wildcard characters (*)\n * that will allow wildcard matching when intersecting with\n * another TokenSet.\n *\n * @param {string} str - The string to create a TokenSet from.\n * @returns {lunr.TokenSet}\n */\nlunr.TokenSet.fromString = function (str) {\n  var node = new lunr.TokenSet,\n      root = node\n\n  /*\n   * Iterates through all characters within the passed string\n   * appending a node for each character.\n   *\n   * When a wildcard character is found then a self\n   * referencing edge is introduced to continually match\n   * any number of any characters.\n   */\n  for (var i = 0, len = str.length; i < len; i++) {\n    var char = str[i],\n        final = (i == len - 1)\n\n    if (char == \"*\") {\n      node.edges[char] = node\n      node.final = final\n\n    } else {\n      var next = new lunr.TokenSet\n      next.final = final\n\n      node.edges[char] = next\n      node = next\n    }\n  }\n\n  return root\n}\n\n/**\n * Converts this TokenSet into an array of strings\n * contained within the TokenSet.\n *\n * This is not intended to be used on a TokenSet that\n * contains wildcards, in these cases the results are\n * undefined and are likely to cause an infinite loop.\n *\n * @returns {string[]}\n */\nlunr.TokenSet.prototype.toArray = function () {\n  var words = []\n\n  var stack = [{\n    prefix: \"\",\n    node: this\n  }]\n\n  while (stack.length) {\n    var frame = stack.pop(),\n        edges = Object.keys(frame.node.edges),\n        len = edges.length\n\n    if (frame.node.final) {\n      /* In Safari, at this point the prefix is sometimes corrupted, see:\n       * https://github.com/olivernn/lunr.js/issues/279 Calling any\n       * String.prototype method forces Safari to \"cast\" this string to what\n       * it's supposed to be, fixing the bug. */\n      frame.prefix.charAt(0)\n      words.push(frame.prefix)\n    }\n\n    for (var i = 0; i < len; i++) {\n      var edge = edges[i]\n\n      stack.push({\n        prefix: frame.prefix.concat(edge),\n        node: frame.node.edges[edge]\n      })\n    }\n  }\n\n  return words\n}\n\n/**\n * Generates a string representation of a TokenSet.\n *\n * This is intended to allow TokenSets to be used as keys\n * in objects, largely to aid the construction and minimisation\n * of a TokenSet. As such it is not designed to be a human\n * friendly representation of the TokenSet.\n *\n * @returns {string}\n */\nlunr.TokenSet.prototype.toString = function () {\n  // NOTE: Using Object.keys here as this.edges is very likely\n  // to enter 'hash-mode' with many keys being added\n  //\n  // avoiding a for-in loop here as it leads to the function\n  // being de-optimised (at least in V8). From some simple\n  // benchmarks the performance is comparable, but allowing\n  // V8 to optimize may mean easy performance wins in the future.\n\n  if (this._str) {\n    return this._str\n  }\n\n  var str = this.final ? '1' : '0',\n      labels = Object.keys(this.edges).sort(),\n      len = labels.length\n\n  for (var i = 0; i < len; i++) {\n    var label = labels[i],\n        node = this.edges[label]\n\n    str = str + label + node.id\n  }\n\n  return str\n}\n\n/**\n * Returns a new TokenSet that is the intersection of\n * this TokenSet and the passed TokenSet.\n *\n * This intersection will take into account any wildcards\n * contained within the TokenSet.\n *\n * @param {lunr.TokenSet} b - An other TokenSet to intersect with.\n * @returns {lunr.TokenSet}\n */\nlunr.TokenSet.prototype.intersect = function (b) {\n  var output = new lunr.TokenSet,\n      frame = undefined\n\n  var stack = [{\n    qNode: b,\n    output: output,\n    node: this\n  }]\n\n  while (stack.length) {\n    frame = stack.pop()\n\n    // NOTE: As with the #toString method, we are using\n    // Object.keys and a for loop instead of a for-in loop\n    // as both of these objects enter 'hash' mode, causing\n    // the function to be de-optimised in V8\n    var qEdges = Object.keys(frame.qNode.edges),\n        qLen = qEdges.length,\n        nEdges = Object.keys(frame.node.edges),\n        nLen = nEdges.length\n\n    for (var q = 0; q < qLen; q++) {\n      var qEdge = qEdges[q]\n\n      for (var n = 0; n < nLen; n++) {\n        var nEdge = nEdges[n]\n\n        if (nEdge == qEdge || qEdge == '*') {\n          var node = frame.node.edges[nEdge],\n              qNode = frame.qNode.edges[qEdge],\n              final = node.final && qNode.final,\n              next = undefined\n\n          if (nEdge in frame.output.edges) {\n            // an edge already exists for this character\n            // no need to create a new node, just set the finality\n            // bit unless this node is already final\n            next = frame.output.edges[nEdge]\n            next.final = next.final || final\n\n          } else {\n            // no edge exists yet, must create one\n            // set the finality bit and insert it\n            // into the output\n            next = new lunr.TokenSet\n            next.final = final\n            frame.output.edges[nEdge] = next\n          }\n\n          stack.push({\n            qNode: qNode,\n            output: next,\n            node: node\n          })\n        }\n      }\n    }\n  }\n\n  return output\n}\nlunr.TokenSet.Builder = function () {\n  this.previousWord = \"\"\n  this.root = new lunr.TokenSet\n  this.uncheckedNodes = []\n  this.minimizedNodes = {}\n}\n\nlunr.TokenSet.Builder.prototype.insert = function (word) {\n  var node,\n      commonPrefix = 0\n\n  if (word < this.previousWord) {\n    throw new Error (\"Out of order word insertion\")\n  }\n\n  for (var i = 0; i < word.length && i < this.previousWord.length; i++) {\n    if (word[i] != this.previousWord[i]) break\n    commonPrefix++\n  }\n\n  this.minimize(commonPrefix)\n\n  if (this.uncheckedNodes.length == 0) {\n    node = this.root\n  } else {\n    node = this.uncheckedNodes[this.uncheckedNodes.length - 1].child\n  }\n\n  for (var i = commonPrefix; i < word.length; i++) {\n    var nextNode = new lunr.TokenSet,\n        char = word[i]\n\n    node.edges[char] = nextNode\n\n    this.uncheckedNodes.push({\n      parent: node,\n      char: char,\n      child: nextNode\n    })\n\n    node = nextNode\n  }\n\n  node.final = true\n  this.previousWord = word\n}\n\nlunr.TokenSet.Builder.prototype.finish = function () {\n  this.minimize(0)\n}\n\nlunr.TokenSet.Builder.prototype.minimize = function (downTo) {\n  for (var i = this.uncheckedNodes.length - 1; i >= downTo; i--) {\n    var node = this.uncheckedNodes[i],\n        childKey = node.child.toString()\n\n    if (childKey in this.minimizedNodes) {\n      node.parent.edges[node.char] = this.minimizedNodes[childKey]\n    } else {\n      // Cache the key for this node since\n      // we know it can't change anymore\n      node.child._str = childKey\n\n      this.minimizedNodes[childKey] = node.child\n    }\n\n    this.uncheckedNodes.pop()\n  }\n}\n/*!\n * lunr.Index\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * An index contains the built index of all documents and provides a query interface\n * to the index.\n *\n * Usually instances of lunr.Index will not be created using this constructor, instead\n * lunr.Builder should be used to construct new indexes, or lunr.Index.load should be\n * used to load previously built and serialized indexes.\n *\n * @constructor\n * @param {Object} attrs - The attributes of the built search index.\n * @param {Object} attrs.invertedIndex - An index of term/field to document reference.\n * @param {Object<string, lunr.Vector>} attrs.fieldVectors - Field vectors\n * @param {lunr.TokenSet} attrs.tokenSet - An set of all corpus tokens.\n * @param {string[]} attrs.fields - The names of indexed document fields.\n * @param {lunr.Pipeline} attrs.pipeline - The pipeline to use for search terms.\n */\nlunr.Index = function (attrs) {\n  this.invertedIndex = attrs.invertedIndex\n  this.fieldVectors = attrs.fieldVectors\n  this.tokenSet = attrs.tokenSet\n  this.fields = attrs.fields\n  this.pipeline = attrs.pipeline\n}\n\n/**\n * A result contains details of a document matching a search query.\n * @typedef {Object} lunr.Index~Result\n * @property {string} ref - The reference of the document this result represents.\n * @property {number} score - A number between 0 and 1 representing how similar this document is to the query.\n * @property {lunr.MatchData} matchData - Contains metadata about this match including which term(s) caused the match.\n */\n\n/**\n * Although lunr provides the ability to create queries using lunr.Query, it also provides a simple\n * query language which itself is parsed into an instance of lunr.Query.\n *\n * For programmatically building queries it is advised to directly use lunr.Query, the query language\n * is best used for human entered text rather than program generated text.\n *\n * At its simplest queries can just be a single term, e.g. `hello`, multiple terms are also supported\n * and will be combined with OR, e.g `hello world` will match documents that contain either 'hello'\n * or 'world', though those that contain both will rank higher in the results.\n *\n * Wildcards can be included in terms to match one or more unspecified characters, these wildcards can\n * be inserted anywhere within the term, and more than one wildcard can exist in a single term. Adding\n * wildcards will increase the number of documents that will be found but can also have a negative\n * impact on query performance, especially with wildcards at the beginning of a term.\n *\n * Terms can be restricted to specific fields, e.g. `title:hello`, only documents with the term\n * hello in the title field will match this query. Using a field not present in the index will lead\n * to an error being thrown.\n *\n * Modifiers can also be added to terms, lunr supports edit distance and boost modifiers on terms. A term\n * boost will make documents matching that term score higher, e.g. `foo^5`. Edit distance is also supported\n * to provide fuzzy matching, e.g. 'hello~2' will match documents with hello with an edit distance of 2.\n * Avoid large values for edit distance to improve query performance.\n *\n * Each term also supports a presence modifier. By default a term's presence in document is optional, however\n * this can be changed to either required or prohibited. For a term's presence to be required in a document the\n * term should be prefixed with a '+', e.g. `+foo bar` is a search for documents that must contain 'foo' and\n * optionally contain 'bar'. Conversely a leading '-' sets the terms presence to prohibited, i.e. it must not\n * appear in a document, e.g. `-foo bar` is a search for documents that do not contain 'foo' but may contain 'bar'.\n *\n * To escape special characters the backslash character '\\' can be used, this allows searches to include\n * characters that would normally be considered modifiers, e.g. `foo\\~2` will search for a term \"foo~2\" instead\n * of attempting to apply a boost of 2 to the search term \"foo\".\n *\n * @typedef {string} lunr.Index~QueryString\n * @example <caption>Simple single term query</caption>\n * hello\n * @example <caption>Multiple term query</caption>\n * hello world\n * @example <caption>term scoped to a field</caption>\n * title:hello\n * @example <caption>term with a boost of 10</caption>\n * hello^10\n * @example <caption>term with an edit distance of 2</caption>\n * hello~2\n * @example <caption>terms with presence modifiers</caption>\n * -foo +bar baz\n */\n\n/**\n * Performs a search against the index using lunr query syntax.\n *\n * Results will be returned sorted by their score, the most relevant results\n * will be returned first.  For details on how the score is calculated, please see\n * the {@link https://lunrjs.com/guides/searching.html#scoring|guide}.\n *\n * For more programmatic querying use lunr.Index#query.\n *\n * @param {lunr.Index~QueryString} queryString - A string containing a lunr query.\n * @throws {lunr.QueryParseError} If the passed query string cannot be parsed.\n * @returns {lunr.Index~Result[]}\n */\nlunr.Index.prototype.search = function (queryString) {\n  return this.query(function (query) {\n    var parser = new lunr.QueryParser(queryString, query)\n    parser.parse()\n  })\n}\n\n/**\n * A query builder callback provides a query object to be used to express\n * the query to perform on the index.\n *\n * @callback lunr.Index~queryBuilder\n * @param {lunr.Query} query - The query object to build up.\n * @this lunr.Query\n */\n\n/**\n * Performs a query against the index using the yielded lunr.Query object.\n *\n * If performing programmatic queries against the index, this method is preferred\n * over lunr.Index#search so as to avoid the additional query parsing overhead.\n *\n * A query object is yielded to the supplied function which should be used to\n * express the query to be run against the index.\n *\n * Note that although this function takes a callback parameter it is _not_ an\n * asynchronous operation, the callback is just yielded a query object to be\n * customized.\n *\n * @param {lunr.Index~queryBuilder} fn - A function that is used to build the query.\n * @returns {lunr.Index~Result[]}\n */\nlunr.Index.prototype.query = function (fn) {\n  // for each query clause\n  // * process terms\n  // * expand terms from token set\n  // * find matching documents and metadata\n  // * get document vectors\n  // * score documents\n\n  var query = new lunr.Query(this.fields),\n      matchingFields = Object.create(null),\n      queryVectors = Object.create(null),\n      termFieldCache = Object.create(null),\n      requiredMatches = Object.create(null),\n      prohibitedMatches = Object.create(null)\n\n  /*\n   * To support field level boosts a query vector is created per\n   * field. An empty vector is eagerly created to support negated\n   * queries.\n   */\n  for (var i = 0; i < this.fields.length; i++) {\n    queryVectors[this.fields[i]] = new lunr.Vector\n  }\n\n  fn.call(query, query)\n\n  for (var i = 0; i < query.clauses.length; i++) {\n    /*\n     * Unless the pipeline has been disabled for this term, which is\n     * the case for terms with wildcards, we need to pass the clause\n     * term through the search pipeline. A pipeline returns an array\n     * of processed terms. Pipeline functions may expand the passed\n     * term, which means we may end up performing multiple index lookups\n     * for a single query term.\n     */\n    var clause = query.clauses[i],\n        terms = null,\n        clauseMatches = lunr.Set.empty\n\n    if (clause.usePipeline) {\n      terms = this.pipeline.runString(clause.term, {\n        fields: clause.fields\n      })\n    } else {\n      terms = [clause.term]\n    }\n\n    for (var m = 0; m < terms.length; m++) {\n      var term = terms[m]\n\n      /*\n       * Each term returned from the pipeline needs to use the same query\n       * clause object, e.g. the same boost and or edit distance. The\n       * simplest way to do this is to re-use the clause object but mutate\n       * its term property.\n       */\n      clause.term = term\n\n      /*\n       * From the term in the clause we create a token set which will then\n       * be used to intersect the indexes token set to get a list of terms\n       * to lookup in the inverted index\n       */\n      var termTokenSet = lunr.TokenSet.fromClause(clause),\n          expandedTerms = this.tokenSet.intersect(termTokenSet).toArray()\n\n      /*\n       * If a term marked as required does not exist in the tokenSet it is\n       * impossible for the search to return any matches. We set all the field\n       * scoped required matches set to empty and stop examining any further\n       * clauses.\n       */\n      if (expandedTerms.length === 0 && clause.presence === lunr.Query.presence.REQUIRED) {\n        for (var k = 0; k < clause.fields.length; k++) {\n          var field = clause.fields[k]\n          requiredMatches[field] = lunr.Set.empty\n        }\n\n        break\n      }\n\n      for (var j = 0; j < expandedTerms.length; j++) {\n        /*\n         * For each term get the posting and termIndex, this is required for\n         * building the query vector.\n         */\n        var expandedTerm = expandedTerms[j],\n            posting = this.invertedIndex[expandedTerm],\n            termIndex = posting._index\n\n        for (var k = 0; k < clause.fields.length; k++) {\n          /*\n           * For each field that this query term is scoped by (by default\n           * all fields are in scope) we need to get all the document refs\n           * that have this term in that field.\n           *\n           * The posting is the entry in the invertedIndex for the matching\n           * term from above.\n           */\n          var field = clause.fields[k],\n              fieldPosting = posting[field],\n              matchingDocumentRefs = Object.keys(fieldPosting),\n              termField = expandedTerm + \"/\" + field,\n              matchingDocumentsSet = new lunr.Set(matchingDocumentRefs)\n\n          /*\n           * if the presence of this term is required ensure that the matching\n           * documents are added to the set of required matches for this clause.\n           *\n           */\n          if (clause.presence == lunr.Query.presence.REQUIRED) {\n            clauseMatches = clauseMatches.union(matchingDocumentsSet)\n\n            if (requiredMatches[field] === undefined) {\n              requiredMatches[field] = lunr.Set.complete\n            }\n          }\n\n          /*\n           * if the presence of this term is prohibited ensure that the matching\n           * documents are added to the set of prohibited matches for this field,\n           * creating that set if it does not yet exist.\n           */\n          if (clause.presence == lunr.Query.presence.PROHIBITED) {\n            if (prohibitedMatches[field] === undefined) {\n              prohibitedMatches[field] = lunr.Set.empty\n            }\n\n            prohibitedMatches[field] = prohibitedMatches[field].union(matchingDocumentsSet)\n\n            /*\n             * Prohibited matches should not be part of the query vector used for\n             * similarity scoring and no metadata should be extracted so we continue\n             * to the next field\n             */\n            continue\n          }\n\n          /*\n           * The query field vector is populated using the termIndex found for\n           * the term and a unit value with the appropriate boost applied.\n           * Using upsert because there could already be an entry in the vector\n           * for the term we are working with. In that case we just add the scores\n           * together.\n           */\n          queryVectors[field].upsert(termIndex, clause.boost, function (a, b) { return a + b })\n\n          /**\n           * If we've already seen this term, field combo then we've already collected\n           * the matching documents and metadata, no need to go through all that again\n           */\n          if (termFieldCache[termField]) {\n            continue\n          }\n\n          for (var l = 0; l < matchingDocumentRefs.length; l++) {\n            /*\n             * All metadata for this term/field/document triple\n             * are then extracted and collected into an instance\n             * of lunr.MatchData ready to be returned in the query\n             * results\n             */\n            var matchingDocumentRef = matchingDocumentRefs[l],\n                matchingFieldRef = new lunr.FieldRef (matchingDocumentRef, field),\n                metadata = fieldPosting[matchingDocumentRef],\n                fieldMatch\n\n            if ((fieldMatch = matchingFields[matchingFieldRef]) === undefined) {\n              matchingFields[matchingFieldRef] = new lunr.MatchData (expandedTerm, field, metadata)\n            } else {\n              fieldMatch.add(expandedTerm, field, metadata)\n            }\n\n          }\n\n          termFieldCache[termField] = true\n        }\n      }\n    }\n\n    /**\n     * If the presence was required we need to update the requiredMatches field sets.\n     * We do this after all fields for the term have collected their matches because\n     * the clause terms presence is required in _any_ of the fields not _all_ of the\n     * fields.\n     */\n    if (clause.presence === lunr.Query.presence.REQUIRED) {\n      for (var k = 0; k < clause.fields.length; k++) {\n        var field = clause.fields[k]\n        requiredMatches[field] = requiredMatches[field].intersect(clauseMatches)\n      }\n    }\n  }\n\n  /**\n   * Need to combine the field scoped required and prohibited\n   * matching documents into a global set of required and prohibited\n   * matches\n   */\n  var allRequiredMatches = lunr.Set.complete,\n      allProhibitedMatches = lunr.Set.empty\n\n  for (var i = 0; i < this.fields.length; i++) {\n    var field = this.fields[i]\n\n    if (requiredMatches[field]) {\n      allRequiredMatches = allRequiredMatches.intersect(requiredMatches[field])\n    }\n\n    if (prohibitedMatches[field]) {\n      allProhibitedMatches = allProhibitedMatches.union(prohibitedMatches[field])\n    }\n  }\n\n  var matchingFieldRefs = Object.keys(matchingFields),\n      results = [],\n      matches = Object.create(null)\n\n  /*\n   * If the query is negated (contains only prohibited terms)\n   * we need to get _all_ fieldRefs currently existing in the\n   * index. This is only done when we know that the query is\n   * entirely prohibited terms to avoid any cost of getting all\n   * fieldRefs unnecessarily.\n   *\n   * Additionally, blank MatchData must be created to correctly\n   * populate the results.\n   */\n  if (query.isNegated()) {\n    matchingFieldRefs = Object.keys(this.fieldVectors)\n\n    for (var i = 0; i < matchingFieldRefs.length; i++) {\n      var matchingFieldRef = matchingFieldRefs[i]\n      var fieldRef = lunr.FieldRef.fromString(matchingFieldRef)\n      matchingFields[matchingFieldRef] = new lunr.MatchData\n    }\n  }\n\n  for (var i = 0; i < matchingFieldRefs.length; i++) {\n    /*\n     * Currently we have document fields that match the query, but we\n     * need to return documents. The matchData and scores are combined\n     * from multiple fields belonging to the same document.\n     *\n     * Scores are calculated by field, using the query vectors created\n     * above, and combined into a final document score using addition.\n     */\n    var fieldRef = lunr.FieldRef.fromString(matchingFieldRefs[i]),\n        docRef = fieldRef.docRef\n\n    if (!allRequiredMatches.contains(docRef)) {\n      continue\n    }\n\n    if (allProhibitedMatches.contains(docRef)) {\n      continue\n    }\n\n    var fieldVector = this.fieldVectors[fieldRef],\n        score = queryVectors[fieldRef.fieldName].similarity(fieldVector),\n        docMatch\n\n    if ((docMatch = matches[docRef]) !== undefined) {\n      docMatch.score += score\n      docMatch.matchData.combine(matchingFields[fieldRef])\n    } else {\n      var match = {\n        ref: docRef,\n        score: score,\n        matchData: matchingFields[fieldRef]\n      }\n      matches[docRef] = match\n      results.push(match)\n    }\n  }\n\n  /*\n   * Sort the results objects by score, highest first.\n   */\n  return results.sort(function (a, b) {\n    return b.score - a.score\n  })\n}\n\n/**\n * Prepares the index for JSON serialization.\n *\n * The schema for this JSON blob will be described in a\n * separate JSON schema file.\n *\n * @returns {Object}\n */\nlunr.Index.prototype.toJSON = function () {\n  var invertedIndex = Object.keys(this.invertedIndex)\n    .sort()\n    .map(function (term) {\n      return [term, this.invertedIndex[term]]\n    }, this)\n\n  var fieldVectors = Object.keys(this.fieldVectors)\n    .map(function (ref) {\n      return [ref, this.fieldVectors[ref].toJSON()]\n    }, this)\n\n  return {\n    version: lunr.version,\n    fields: this.fields,\n    fieldVectors: fieldVectors,\n    invertedIndex: invertedIndex,\n    pipeline: this.pipeline.toJSON()\n  }\n}\n\n/**\n * Loads a previously serialized lunr.Index\n *\n * @param {Object} serializedIndex - A previously serialized lunr.Index\n * @returns {lunr.Index}\n */\nlunr.Index.load = function (serializedIndex) {\n  var attrs = {},\n      fieldVectors = {},\n      serializedVectors = serializedIndex.fieldVectors,\n      invertedIndex = Object.create(null),\n      serializedInvertedIndex = serializedIndex.invertedIndex,\n      tokenSetBuilder = new lunr.TokenSet.Builder,\n      pipeline = lunr.Pipeline.load(serializedIndex.pipeline)\n\n  if (serializedIndex.version != lunr.version) {\n    lunr.utils.warn(\"Version mismatch when loading serialised index. Current version of lunr '\" + lunr.version + \"' does not match serialized index '\" + serializedIndex.version + \"'\")\n  }\n\n  for (var i = 0; i < serializedVectors.length; i++) {\n    var tuple = serializedVectors[i],\n        ref = tuple[0],\n        elements = tuple[1]\n\n    fieldVectors[ref] = new lunr.Vector(elements)\n  }\n\n  for (var i = 0; i < serializedInvertedIndex.length; i++) {\n    var tuple = serializedInvertedIndex[i],\n        term = tuple[0],\n        posting = tuple[1]\n\n    tokenSetBuilder.insert(term)\n    invertedIndex[term] = posting\n  }\n\n  tokenSetBuilder.finish()\n\n  attrs.fields = serializedIndex.fields\n\n  attrs.fieldVectors = fieldVectors\n  attrs.invertedIndex = invertedIndex\n  attrs.tokenSet = tokenSetBuilder.root\n  attrs.pipeline = pipeline\n\n  return new lunr.Index(attrs)\n}\n/*!\n * lunr.Builder\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * lunr.Builder performs indexing on a set of documents and\n * returns instances of lunr.Index ready for querying.\n *\n * All configuration of the index is done via the builder, the\n * fields to index, the document reference, the text processing\n * pipeline and document scoring parameters are all set on the\n * builder before indexing.\n *\n * @constructor\n * @property {string} _ref - Internal reference to the document reference field.\n * @property {string[]} _fields - Internal reference to the document fields to index.\n * @property {object} invertedIndex - The inverted index maps terms to document fields.\n * @property {object} documentTermFrequencies - Keeps track of document term frequencies.\n * @property {object} documentLengths - Keeps track of the length of documents added to the index.\n * @property {lunr.tokenizer} tokenizer - Function for splitting strings into tokens for indexing.\n * @property {lunr.Pipeline} pipeline - The pipeline performs text processing on tokens before indexing.\n * @property {lunr.Pipeline} searchPipeline - A pipeline for processing search terms before querying the index.\n * @property {number} documentCount - Keeps track of the total number of documents indexed.\n * @property {number} _b - A parameter to control field length normalization, setting this to 0 disabled normalization, 1 fully normalizes field lengths, the default value is 0.75.\n * @property {number} _k1 - A parameter to control how quickly an increase in term frequency results in term frequency saturation, the default value is 1.2.\n * @property {number} termIndex - A counter incremented for each unique term, used to identify a terms position in the vector space.\n * @property {array} metadataWhitelist - A list of metadata keys that have been whitelisted for entry in the index.\n */\nlunr.Builder = function () {\n  this._ref = \"id\"\n  this._fields = Object.create(null)\n  this._documents = Object.create(null)\n  this.invertedIndex = Object.create(null)\n  this.fieldTermFrequencies = {}\n  this.fieldLengths = {}\n  this.tokenizer = lunr.tokenizer\n  this.pipeline = new lunr.Pipeline\n  this.searchPipeline = new lunr.Pipeline\n  this.documentCount = 0\n  this._b = 0.75\n  this._k1 = 1.2\n  this.termIndex = 0\n  this.metadataWhitelist = []\n}\n\n/**\n * Sets the document field used as the document reference. Every document must have this field.\n * The type of this field in the document should be a string, if it is not a string it will be\n * coerced into a string by calling toString.\n *\n * The default ref is 'id'.\n *\n * The ref should _not_ be changed during indexing, it should be set before any documents are\n * added to the index. Changing it during indexing can lead to inconsistent results.\n *\n * @param {string} ref - The name of the reference field in the document.\n */\nlunr.Builder.prototype.ref = function (ref) {\n  this._ref = ref\n}\n\n/**\n * A function that is used to extract a field from a document.\n *\n * Lunr expects a field to be at the top level of a document, if however the field\n * is deeply nested within a document an extractor function can be used to extract\n * the right field for indexing.\n *\n * @callback fieldExtractor\n * @param {object} doc - The document being added to the index.\n * @returns {?(string|object|object[])} obj - The object that will be indexed for this field.\n * @example <caption>Extracting a nested field</caption>\n * function (doc) { return doc.nested.field }\n */\n\n/**\n * Adds a field to the list of document fields that will be indexed. Every document being\n * indexed should have this field. Null values for this field in indexed documents will\n * not cause errors but will limit the chance of that document being retrieved by searches.\n *\n * All fields should be added before adding documents to the index. Adding fields after\n * a document has been indexed will have no effect on already indexed documents.\n *\n * Fields can be boosted at build time. This allows terms within that field to have more\n * importance when ranking search results. Use a field boost to specify that matches within\n * one field are more important than other fields.\n *\n * @param {string} fieldName - The name of a field to index in all documents.\n * @param {object} attributes - Optional attributes associated with this field.\n * @param {number} [attributes.boost=1] - Boost applied to all terms within this field.\n * @param {fieldExtractor} [attributes.extractor] - Function to extract a field from a document.\n * @throws {RangeError} fieldName cannot contain unsupported characters '/'\n */\nlunr.Builder.prototype.field = function (fieldName, attributes) {\n  if (/\\//.test(fieldName)) {\n    throw new RangeError (\"Field '\" + fieldName + \"' contains illegal character '/'\")\n  }\n\n  this._fields[fieldName] = attributes || {}\n}\n\n/**\n * A parameter to tune the amount of field length normalisation that is applied when\n * calculating relevance scores. A value of 0 will completely disable any normalisation\n * and a value of 1 will fully normalise field lengths. The default is 0.75. Values of b\n * will be clamped to the range 0 - 1.\n *\n * @param {number} number - The value to set for this tuning parameter.\n */\nlunr.Builder.prototype.b = function (number) {\n  if (number < 0) {\n    this._b = 0\n  } else if (number > 1) {\n    this._b = 1\n  } else {\n    this._b = number\n  }\n}\n\n/**\n * A parameter that controls the speed at which a rise in term frequency results in term\n * frequency saturation. The default value is 1.2. Setting this to a higher value will give\n * slower saturation levels, a lower value will result in quicker saturation.\n *\n * @param {number} number - The value to set for this tuning parameter.\n */\nlunr.Builder.prototype.k1 = function (number) {\n  this._k1 = number\n}\n\n/**\n * Adds a document to the index.\n *\n * Before adding fields to the index the index should have been fully setup, with the document\n * ref and all fields to index already having been specified.\n *\n * The document must have a field name as specified by the ref (by default this is 'id') and\n * it should have all fields defined for indexing, though null or undefined values will not\n * cause errors.\n *\n * Entire documents can be boosted at build time. Applying a boost to a document indicates that\n * this document should rank higher in search results than other documents.\n *\n * @param {object} doc - The document to add to the index.\n * @param {object} attributes - Optional attributes associated with this document.\n * @param {number} [attributes.boost=1] - Boost applied to all terms within this document.\n */\nlunr.Builder.prototype.add = function (doc, attributes) {\n  var docRef = doc[this._ref],\n      fields = Object.keys(this._fields)\n\n  this._documents[docRef] = attributes || {}\n  this.documentCount += 1\n\n  for (var i = 0; i < fields.length; i++) {\n    var fieldName = fields[i],\n        extractor = this._fields[fieldName].extractor,\n        field = extractor ? extractor(doc) : doc[fieldName],\n        tokens = this.tokenizer(field, {\n          fields: [fieldName]\n        }),\n        terms = this.pipeline.run(tokens),\n        fieldRef = new lunr.FieldRef (docRef, fieldName),\n        fieldTerms = Object.create(null)\n\n    this.fieldTermFrequencies[fieldRef] = fieldTerms\n    this.fieldLengths[fieldRef] = 0\n\n    // store the length of this field for this document\n    this.fieldLengths[fieldRef] += terms.length\n\n    // calculate term frequencies for this field\n    for (var j = 0; j < terms.length; j++) {\n      var term = terms[j]\n\n      if (fieldTerms[term] == undefined) {\n        fieldTerms[term] = 0\n      }\n\n      fieldTerms[term] += 1\n\n      // add to inverted index\n      // create an initial posting if one doesn't exist\n      if (this.invertedIndex[term] == undefined) {\n        var posting = Object.create(null)\n        posting[\"_index\"] = this.termIndex\n        this.termIndex += 1\n\n        for (var k = 0; k < fields.length; k++) {\n          posting[fields[k]] = Object.create(null)\n        }\n\n        this.invertedIndex[term] = posting\n      }\n\n      // add an entry for this term/fieldName/docRef to the invertedIndex\n      if (this.invertedIndex[term][fieldName][docRef] == undefined) {\n        this.invertedIndex[term][fieldName][docRef] = Object.create(null)\n      }\n\n      // store all whitelisted metadata about this token in the\n      // inverted index\n      for (var l = 0; l < this.metadataWhitelist.length; l++) {\n        var metadataKey = this.metadataWhitelist[l],\n            metadata = term.metadata[metadataKey]\n\n        if (this.invertedIndex[term][fieldName][docRef][metadataKey] == undefined) {\n          this.invertedIndex[term][fieldName][docRef][metadataKey] = []\n        }\n\n        this.invertedIndex[term][fieldName][docRef][metadataKey].push(metadata)\n      }\n    }\n\n  }\n}\n\n/**\n * Calculates the average document length for this index\n *\n * @private\n */\nlunr.Builder.prototype.calculateAverageFieldLengths = function () {\n\n  var fieldRefs = Object.keys(this.fieldLengths),\n      numberOfFields = fieldRefs.length,\n      accumulator = {},\n      documentsWithField = {}\n\n  for (var i = 0; i < numberOfFields; i++) {\n    var fieldRef = lunr.FieldRef.fromString(fieldRefs[i]),\n        field = fieldRef.fieldName\n\n    documentsWithField[field] || (documentsWithField[field] = 0)\n    documentsWithField[field] += 1\n\n    accumulator[field] || (accumulator[field] = 0)\n    accumulator[field] += this.fieldLengths[fieldRef]\n  }\n\n  var fields = Object.keys(this._fields)\n\n  for (var i = 0; i < fields.length; i++) {\n    var fieldName = fields[i]\n    accumulator[fieldName] = accumulator[fieldName] / documentsWithField[fieldName]\n  }\n\n  this.averageFieldLength = accumulator\n}\n\n/**\n * Builds a vector space model of every document using lunr.Vector\n *\n * @private\n */\nlunr.Builder.prototype.createFieldVectors = function () {\n  var fieldVectors = {},\n      fieldRefs = Object.keys(this.fieldTermFrequencies),\n      fieldRefsLength = fieldRefs.length,\n      termIdfCache = Object.create(null)\n\n  for (var i = 0; i < fieldRefsLength; i++) {\n    var fieldRef = lunr.FieldRef.fromString(fieldRefs[i]),\n        fieldName = fieldRef.fieldName,\n        fieldLength = this.fieldLengths[fieldRef],\n        fieldVector = new lunr.Vector,\n        termFrequencies = this.fieldTermFrequencies[fieldRef],\n        terms = Object.keys(termFrequencies),\n        termsLength = terms.length\n\n\n    var fieldBoost = this._fields[fieldName].boost || 1,\n        docBoost = this._documents[fieldRef.docRef].boost || 1\n\n    for (var j = 0; j < termsLength; j++) {\n      var term = terms[j],\n          tf = termFrequencies[term],\n          termIndex = this.invertedIndex[term]._index,\n          idf, score, scoreWithPrecision\n\n      if (termIdfCache[term] === undefined) {\n        idf = lunr.idf(this.invertedIndex[term], this.documentCount)\n        termIdfCache[term] = idf\n      } else {\n        idf = termIdfCache[term]\n      }\n\n      score = idf * ((this._k1 + 1) * tf) / (this._k1 * (1 - this._b + this._b * (fieldLength / this.averageFieldLength[fieldName])) + tf)\n      score *= fieldBoost\n      score *= docBoost\n      scoreWithPrecision = Math.round(score * 1000) / 1000\n      // Converts 1.23456789 to 1.234.\n      // Reducing the precision so that the vectors take up less\n      // space when serialised. Doing it now so that they behave\n      // the same before and after serialisation. Also, this is\n      // the fastest approach to reducing a number's precision in\n      // JavaScript.\n\n      fieldVector.insert(termIndex, scoreWithPrecision)\n    }\n\n    fieldVectors[fieldRef] = fieldVector\n  }\n\n  this.fieldVectors = fieldVectors\n}\n\n/**\n * Creates a token set of all tokens in the index using lunr.TokenSet\n *\n * @private\n */\nlunr.Builder.prototype.createTokenSet = function () {\n  this.tokenSet = lunr.TokenSet.fromArray(\n    Object.keys(this.invertedIndex).sort()\n  )\n}\n\n/**\n * Builds the index, creating an instance of lunr.Index.\n *\n * This completes the indexing process and should only be called\n * once all documents have been added to the index.\n *\n * @returns {lunr.Index}\n */\nlunr.Builder.prototype.build = function () {\n  this.calculateAverageFieldLengths()\n  this.createFieldVectors()\n  this.createTokenSet()\n\n  return new lunr.Index({\n    invertedIndex: this.invertedIndex,\n    fieldVectors: this.fieldVectors,\n    tokenSet: this.tokenSet,\n    fields: Object.keys(this._fields),\n    pipeline: this.searchPipeline\n  })\n}\n\n/**\n * Applies a plugin to the index builder.\n *\n * A plugin is a function that is called with the index builder as its context.\n * Plugins can be used to customise or extend the behaviour of the index\n * in some way. A plugin is just a function, that encapsulated the custom\n * behaviour that should be applied when building the index.\n *\n * The plugin function will be called with the index builder as its argument, additional\n * arguments can also be passed when calling use. The function will be called\n * with the index builder as its context.\n *\n * @param {Function} plugin The plugin to apply.\n */\nlunr.Builder.prototype.use = function (fn) {\n  var args = Array.prototype.slice.call(arguments, 1)\n  args.unshift(this)\n  fn.apply(this, args)\n}\n/**\n * Contains and collects metadata about a matching document.\n * A single instance of lunr.MatchData is returned as part of every\n * lunr.Index~Result.\n *\n * @constructor\n * @param {string} term - The term this match data is associated with\n * @param {string} field - The field in which the term was found\n * @param {object} metadata - The metadata recorded about this term in this field\n * @property {object} metadata - A cloned collection of metadata associated with this document.\n * @see {@link lunr.Index~Result}\n */\nlunr.MatchData = function (term, field, metadata) {\n  var clonedMetadata = Object.create(null),\n      metadataKeys = Object.keys(metadata || {})\n\n  // Cloning the metadata to prevent the original\n  // being mutated during match data combination.\n  // Metadata is kept in an array within the inverted\n  // index so cloning the data can be done with\n  // Array#slice\n  for (var i = 0; i < metadataKeys.length; i++) {\n    var key = metadataKeys[i]\n    clonedMetadata[key] = metadata[key].slice()\n  }\n\n  this.metadata = Object.create(null)\n\n  if (term !== undefined) {\n    this.metadata[term] = Object.create(null)\n    this.metadata[term][field] = clonedMetadata\n  }\n}\n\n/**\n * An instance of lunr.MatchData will be created for every term that matches a\n * document. However only one instance is required in a lunr.Index~Result. This\n * method combines metadata from another instance of lunr.MatchData with this\n * objects metadata.\n *\n * @param {lunr.MatchData} otherMatchData - Another instance of match data to merge with this one.\n * @see {@link lunr.Index~Result}\n */\nlunr.MatchData.prototype.combine = function (otherMatchData) {\n  var terms = Object.keys(otherMatchData.metadata)\n\n  for (var i = 0; i < terms.length; i++) {\n    var term = terms[i],\n        fields = Object.keys(otherMatchData.metadata[term])\n\n    if (this.metadata[term] == undefined) {\n      this.metadata[term] = Object.create(null)\n    }\n\n    for (var j = 0; j < fields.length; j++) {\n      var field = fields[j],\n          keys = Object.keys(otherMatchData.metadata[term][field])\n\n      if (this.metadata[term][field] == undefined) {\n        this.metadata[term][field] = Object.create(null)\n      }\n\n      for (var k = 0; k < keys.length; k++) {\n        var key = keys[k]\n\n        if (this.metadata[term][field][key] == undefined) {\n          this.metadata[term][field][key] = otherMatchData.metadata[term][field][key]\n        } else {\n          this.metadata[term][field][key] = this.metadata[term][field][key].concat(otherMatchData.metadata[term][field][key])\n        }\n\n      }\n    }\n  }\n}\n\n/**\n * Add metadata for a term/field pair to this instance of match data.\n *\n * @param {string} term - The term this match data is associated with\n * @param {string} field - The field in which the term was found\n * @param {object} metadata - The metadata recorded about this term in this field\n */\nlunr.MatchData.prototype.add = function (term, field, metadata) {\n  if (!(term in this.metadata)) {\n    this.metadata[term] = Object.create(null)\n    this.metadata[term][field] = metadata\n    return\n  }\n\n  if (!(field in this.metadata[term])) {\n    this.metadata[term][field] = metadata\n    return\n  }\n\n  var metadataKeys = Object.keys(metadata)\n\n  for (var i = 0; i < metadataKeys.length; i++) {\n    var key = metadataKeys[i]\n\n    if (key in this.metadata[term][field]) {\n      this.metadata[term][field][key] = this.metadata[term][field][key].concat(metadata[key])\n    } else {\n      this.metadata[term][field][key] = metadata[key]\n    }\n  }\n}\n/**\n * A lunr.Query provides a programmatic way of defining queries to be performed\n * against a {@link lunr.Index}.\n *\n * Prefer constructing a lunr.Query using the {@link lunr.Index#query} method\n * so the query object is pre-initialized with the right index fields.\n *\n * @constructor\n * @property {lunr.Query~Clause[]} clauses - An array of query clauses.\n * @property {string[]} allFields - An array of all available fields in a lunr.Index.\n */\nlunr.Query = function (allFields) {\n  this.clauses = []\n  this.allFields = allFields\n}\n\n/**\n * Constants for indicating what kind of automatic wildcard insertion will be used when constructing a query clause.\n *\n * This allows wildcards to be added to the beginning and end of a term without having to manually do any string\n * concatenation.\n *\n * The wildcard constants can be bitwise combined to select both leading and trailing wildcards.\n *\n * @constant\n * @default\n * @property {number} wildcard.NONE - The term will have no wildcards inserted, this is the default behaviour\n * @property {number} wildcard.LEADING - Prepend the term with a wildcard, unless a leading wildcard already exists\n * @property {number} wildcard.TRAILING - Append a wildcard to the term, unless a trailing wildcard already exists\n * @see lunr.Query~Clause\n * @see lunr.Query#clause\n * @see lunr.Query#term\n * @example <caption>query term with trailing wildcard</caption>\n * query.term('foo', { wildcard: lunr.Query.wildcard.TRAILING })\n * @example <caption>query term with leading and trailing wildcard</caption>\n * query.term('foo', {\n *   wildcard: lunr.Query.wildcard.LEADING | lunr.Query.wildcard.TRAILING\n * })\n */\n\nlunr.Query.wildcard = new String (\"*\")\nlunr.Query.wildcard.NONE = 0\nlunr.Query.wildcard.LEADING = 1\nlunr.Query.wildcard.TRAILING = 2\n\n/**\n * Constants for indicating what kind of presence a term must have in matching documents.\n *\n * @constant\n * @enum {number}\n * @see lunr.Query~Clause\n * @see lunr.Query#clause\n * @see lunr.Query#term\n * @example <caption>query term with required presence</caption>\n * query.term('foo', { presence: lunr.Query.presence.REQUIRED })\n */\nlunr.Query.presence = {\n  /**\n   * Term's presence in a document is optional, this is the default value.\n   */\n  OPTIONAL: 1,\n\n  /**\n   * Term's presence in a document is required, documents that do not contain\n   * this term will not be returned.\n   */\n  REQUIRED: 2,\n\n  /**\n   * Term's presence in a document is prohibited, documents that do contain\n   * this term will not be returned.\n   */\n  PROHIBITED: 3\n}\n\n/**\n * A single clause in a {@link lunr.Query} contains a term and details on how to\n * match that term against a {@link lunr.Index}.\n *\n * @typedef {Object} lunr.Query~Clause\n * @property {string[]} fields - The fields in an index this clause should be matched against.\n * @property {number} [boost=1] - Any boost that should be applied when matching this clause.\n * @property {number} [editDistance] - Whether the term should have fuzzy matching applied, and how fuzzy the match should be.\n * @property {boolean} [usePipeline] - Whether the term should be passed through the search pipeline.\n * @property {number} [wildcard=lunr.Query.wildcard.NONE] - Whether the term should have wildcards appended or prepended.\n * @property {number} [presence=lunr.Query.presence.OPTIONAL] - The terms presence in any matching documents.\n */\n\n/**\n * Adds a {@link lunr.Query~Clause} to this query.\n *\n * Unless the clause contains the fields to be matched all fields will be matched. In addition\n * a default boost of 1 is applied to the clause.\n *\n * @param {lunr.Query~Clause} clause - The clause to add to this query.\n * @see lunr.Query~Clause\n * @returns {lunr.Query}\n */\nlunr.Query.prototype.clause = function (clause) {\n  if (!('fields' in clause)) {\n    clause.fields = this.allFields\n  }\n\n  if (!('boost' in clause)) {\n    clause.boost = 1\n  }\n\n  if (!('usePipeline' in clause)) {\n    clause.usePipeline = true\n  }\n\n  if (!('wildcard' in clause)) {\n    clause.wildcard = lunr.Query.wildcard.NONE\n  }\n\n  if ((clause.wildcard & lunr.Query.wildcard.LEADING) && (clause.term.charAt(0) != lunr.Query.wildcard)) {\n    clause.term = \"*\" + clause.term\n  }\n\n  if ((clause.wildcard & lunr.Query.wildcard.TRAILING) && (clause.term.slice(-1) != lunr.Query.wildcard)) {\n    clause.term = \"\" + clause.term + \"*\"\n  }\n\n  if (!('presence' in clause)) {\n    clause.presence = lunr.Query.presence.OPTIONAL\n  }\n\n  this.clauses.push(clause)\n\n  return this\n}\n\n/**\n * A negated query is one in which every clause has a presence of\n * prohibited. These queries require some special processing to return\n * the expected results.\n *\n * @returns boolean\n */\nlunr.Query.prototype.isNegated = function () {\n  for (var i = 0; i < this.clauses.length; i++) {\n    if (this.clauses[i].presence != lunr.Query.presence.PROHIBITED) {\n      return false\n    }\n  }\n\n  return true\n}\n\n/**\n * Adds a term to the current query, under the covers this will create a {@link lunr.Query~Clause}\n * to the list of clauses that make up this query.\n *\n * The term is used as is, i.e. no tokenization will be performed by this method. Instead conversion\n * to a token or token-like string should be done before calling this method.\n *\n * The term will be converted to a string by calling `toString`. Multiple terms can be passed as an\n * array, each term in the array will share the same options.\n *\n * @param {object|object[]} term - The term(s) to add to the query.\n * @param {object} [options] - Any additional properties to add to the query clause.\n * @returns {lunr.Query}\n * @see lunr.Query#clause\n * @see lunr.Query~Clause\n * @example <caption>adding a single term to a query</caption>\n * query.term(\"foo\")\n * @example <caption>adding a single term to a query and specifying search fields, term boost and automatic trailing wildcard</caption>\n * query.term(\"foo\", {\n *   fields: [\"title\"],\n *   boost: 10,\n *   wildcard: lunr.Query.wildcard.TRAILING\n * })\n * @example <caption>using lunr.tokenizer to convert a string to tokens before using them as terms</caption>\n * query.term(lunr.tokenizer(\"foo bar\"))\n */\nlunr.Query.prototype.term = function (term, options) {\n  if (Array.isArray(term)) {\n    term.forEach(function (t) { this.term(t, lunr.utils.clone(options)) }, this)\n    return this\n  }\n\n  var clause = options || {}\n  clause.term = term.toString()\n\n  this.clause(clause)\n\n  return this\n}\nlunr.QueryParseError = function (message, start, end) {\n  this.name = \"QueryParseError\"\n  this.message = message\n  this.start = start\n  this.end = end\n}\n\nlunr.QueryParseError.prototype = new Error\nlunr.QueryLexer = function (str) {\n  this.lexemes = []\n  this.str = str\n  this.length = str.length\n  this.pos = 0\n  this.start = 0\n  this.escapeCharPositions = []\n}\n\nlunr.QueryLexer.prototype.run = function () {\n  var state = lunr.QueryLexer.lexText\n\n  while (state) {\n    state = state(this)\n  }\n}\n\nlunr.QueryLexer.prototype.sliceString = function () {\n  var subSlices = [],\n      sliceStart = this.start,\n      sliceEnd = this.pos\n\n  for (var i = 0; i < this.escapeCharPositions.length; i++) {\n    sliceEnd = this.escapeCharPositions[i]\n    subSlices.push(this.str.slice(sliceStart, sliceEnd))\n    sliceStart = sliceEnd + 1\n  }\n\n  subSlices.push(this.str.slice(sliceStart, this.pos))\n  this.escapeCharPositions.length = 0\n\n  return subSlices.join('')\n}\n\nlunr.QueryLexer.prototype.emit = function (type) {\n  this.lexemes.push({\n    type: type,\n    str: this.sliceString(),\n    start: this.start,\n    end: this.pos\n  })\n\n  this.start = this.pos\n}\n\nlunr.QueryLexer.prototype.escapeCharacter = function () {\n  this.escapeCharPositions.push(this.pos - 1)\n  this.pos += 1\n}\n\nlunr.QueryLexer.prototype.next = function () {\n  if (this.pos >= this.length) {\n    return lunr.QueryLexer.EOS\n  }\n\n  var char = this.str.charAt(this.pos)\n  this.pos += 1\n  return char\n}\n\nlunr.QueryLexer.prototype.width = function () {\n  return this.pos - this.start\n}\n\nlunr.QueryLexer.prototype.ignore = function () {\n  if (this.start == this.pos) {\n    this.pos += 1\n  }\n\n  this.start = this.pos\n}\n\nlunr.QueryLexer.prototype.backup = function () {\n  this.pos -= 1\n}\n\nlunr.QueryLexer.prototype.acceptDigitRun = function () {\n  var char, charCode\n\n  do {\n    char = this.next()\n    charCode = char.charCodeAt(0)\n  } while (charCode > 47 && charCode < 58)\n\n  if (char != lunr.QueryLexer.EOS) {\n    this.backup()\n  }\n}\n\nlunr.QueryLexer.prototype.more = function () {\n  return this.pos < this.length\n}\n\nlunr.QueryLexer.EOS = 'EOS'\nlunr.QueryLexer.FIELD = 'FIELD'\nlunr.QueryLexer.TERM = 'TERM'\nlunr.QueryLexer.EDIT_DISTANCE = 'EDIT_DISTANCE'\nlunr.QueryLexer.BOOST = 'BOOST'\nlunr.QueryLexer.PRESENCE = 'PRESENCE'\n\nlunr.QueryLexer.lexField = function (lexer) {\n  lexer.backup()\n  lexer.emit(lunr.QueryLexer.FIELD)\n  lexer.ignore()\n  return lunr.QueryLexer.lexText\n}\n\nlunr.QueryLexer.lexTerm = function (lexer) {\n  if (lexer.width() > 1) {\n    lexer.backup()\n    lexer.emit(lunr.QueryLexer.TERM)\n  }\n\n  lexer.ignore()\n\n  if (lexer.more()) {\n    return lunr.QueryLexer.lexText\n  }\n}\n\nlunr.QueryLexer.lexEditDistance = function (lexer) {\n  lexer.ignore()\n  lexer.acceptDigitRun()\n  lexer.emit(lunr.QueryLexer.EDIT_DISTANCE)\n  return lunr.QueryLexer.lexText\n}\n\nlunr.QueryLexer.lexBoost = function (lexer) {\n  lexer.ignore()\n  lexer.acceptDigitRun()\n  lexer.emit(lunr.QueryLexer.BOOST)\n  return lunr.QueryLexer.lexText\n}\n\nlunr.QueryLexer.lexEOS = function (lexer) {\n  if (lexer.width() > 0) {\n    lexer.emit(lunr.QueryLexer.TERM)\n  }\n}\n\n// This matches the separator used when tokenising fields\n// within a document. These should match otherwise it is\n// not possible to search for some tokens within a document.\n//\n// It is possible for the user to change the separator on the\n// tokenizer so it _might_ clash with any other of the special\n// characters already used within the search string, e.g. :.\n//\n// This means that it is possible to change the separator in\n// such a way that makes some words unsearchable using a search\n// string.\nlunr.QueryLexer.termSeparator = lunr.tokenizer.separator\n\nlunr.QueryLexer.lexText = function (lexer) {\n  while (true) {\n    var char = lexer.next()\n\n    if (char == lunr.QueryLexer.EOS) {\n      return lunr.QueryLexer.lexEOS\n    }\n\n    // Escape character is '\\'\n    if (char.charCodeAt(0) == 92) {\n      lexer.escapeCharacter()\n      continue\n    }\n\n    if (char == \":\") {\n      return lunr.QueryLexer.lexField\n    }\n\n    if (char == \"~\") {\n      lexer.backup()\n      if (lexer.width() > 0) {\n        lexer.emit(lunr.QueryLexer.TERM)\n      }\n      return lunr.QueryLexer.lexEditDistance\n    }\n\n    if (char == \"^\") {\n      lexer.backup()\n      if (lexer.width() > 0) {\n        lexer.emit(lunr.QueryLexer.TERM)\n      }\n      return lunr.QueryLexer.lexBoost\n    }\n\n    // \"+\" indicates term presence is required\n    // checking for length to ensure that only\n    // leading \"+\" are considered\n    if (char == \"+\" && lexer.width() === 1) {\n      lexer.emit(lunr.QueryLexer.PRESENCE)\n      return lunr.QueryLexer.lexText\n    }\n\n    // \"-\" indicates term presence is prohibited\n    // checking for length to ensure that only\n    // leading \"-\" are considered\n    if (char == \"-\" && lexer.width() === 1) {\n      lexer.emit(lunr.QueryLexer.PRESENCE)\n      return lunr.QueryLexer.lexText\n    }\n\n    if (char.match(lunr.QueryLexer.termSeparator)) {\n      return lunr.QueryLexer.lexTerm\n    }\n  }\n}\n\nlunr.QueryParser = function (str, query) {\n  this.lexer = new lunr.QueryLexer (str)\n  this.query = query\n  this.currentClause = {}\n  this.lexemeIdx = 0\n}\n\nlunr.QueryParser.prototype.parse = function () {\n  this.lexer.run()\n  this.lexemes = this.lexer.lexemes\n\n  var state = lunr.QueryParser.parseClause\n\n  while (state) {\n    state = state(this)\n  }\n\n  return this.query\n}\n\nlunr.QueryParser.prototype.peekLexeme = function () {\n  return this.lexemes[this.lexemeIdx]\n}\n\nlunr.QueryParser.prototype.consumeLexeme = function () {\n  var lexeme = this.peekLexeme()\n  this.lexemeIdx += 1\n  return lexeme\n}\n\nlunr.QueryParser.prototype.nextClause = function () {\n  var completedClause = this.currentClause\n  this.query.clause(completedClause)\n  this.currentClause = {}\n}\n\nlunr.QueryParser.parseClause = function (parser) {\n  var lexeme = parser.peekLexeme()\n\n  if (lexeme == undefined) {\n    return\n  }\n\n  switch (lexeme.type) {\n    case lunr.QueryLexer.PRESENCE:\n      return lunr.QueryParser.parsePresence\n    case lunr.QueryLexer.FIELD:\n      return lunr.QueryParser.parseField\n    case lunr.QueryLexer.TERM:\n      return lunr.QueryParser.parseTerm\n    default:\n      var errorMessage = \"expected either a field or a term, found \" + lexeme.type\n\n      if (lexeme.str.length >= 1) {\n        errorMessage += \" with value '\" + lexeme.str + \"'\"\n      }\n\n      throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)\n  }\n}\n\nlunr.QueryParser.parsePresence = function (parser) {\n  var lexeme = parser.consumeLexeme()\n\n  if (lexeme == undefined) {\n    return\n  }\n\n  switch (lexeme.str) {\n    case \"-\":\n      parser.currentClause.presence = lunr.Query.presence.PROHIBITED\n      break\n    case \"+\":\n      parser.currentClause.presence = lunr.Query.presence.REQUIRED\n      break\n    default:\n      var errorMessage = \"unrecognised presence operator'\" + lexeme.str + \"'\"\n      throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)\n  }\n\n  var nextLexeme = parser.peekLexeme()\n\n  if (nextLexeme == undefined) {\n    var errorMessage = \"expecting term or field, found nothing\"\n    throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)\n  }\n\n  switch (nextLexeme.type) {\n    case lunr.QueryLexer.FIELD:\n      return lunr.QueryParser.parseField\n    case lunr.QueryLexer.TERM:\n      return lunr.QueryParser.parseTerm\n    default:\n      var errorMessage = \"expecting term or field, found '\" + nextLexeme.type + \"'\"\n      throw new lunr.QueryParseError (errorMessage, nextLexeme.start, nextLexeme.end)\n  }\n}\n\nlunr.QueryParser.parseField = function (parser) {\n  var lexeme = parser.consumeLexeme()\n\n  if (lexeme == undefined) {\n    return\n  }\n\n  if (parser.query.allFields.indexOf(lexeme.str) == -1) {\n    var possibleFields = parser.query.allFields.map(function (f) { return \"'\" + f + \"'\" }).join(', '),\n        errorMessage = \"unrecognised field '\" + lexeme.str + \"', possible fields: \" + possibleFields\n\n    throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)\n  }\n\n  parser.currentClause.fields = [lexeme.str]\n\n  var nextLexeme = parser.peekLexeme()\n\n  if (nextLexeme == undefined) {\n    var errorMessage = \"expecting term, found nothing\"\n    throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)\n  }\n\n  switch (nextLexeme.type) {\n    case lunr.QueryLexer.TERM:\n      return lunr.QueryParser.parseTerm\n    default:\n      var errorMessage = \"expecting term, found '\" + nextLexeme.type + \"'\"\n      throw new lunr.QueryParseError (errorMessage, nextLexeme.start, nextLexeme.end)\n  }\n}\n\nlunr.QueryParser.parseTerm = function (parser) {\n  var lexeme = parser.consumeLexeme()\n\n  if (lexeme == undefined) {\n    return\n  }\n\n  parser.currentClause.term = lexeme.str.toLowerCase()\n\n  if (lexeme.str.indexOf(\"*\") != -1) {\n    parser.currentClause.usePipeline = false\n  }\n\n  var nextLexeme = parser.peekLexeme()\n\n  if (nextLexeme == undefined) {\n    parser.nextClause()\n    return\n  }\n\n  switch (nextLexeme.type) {\n    case lunr.QueryLexer.TERM:\n      parser.nextClause()\n      return lunr.QueryParser.parseTerm\n    case lunr.QueryLexer.FIELD:\n      parser.nextClause()\n      return lunr.QueryParser.parseField\n    case lunr.QueryLexer.EDIT_DISTANCE:\n      return lunr.QueryParser.parseEditDistance\n    case lunr.QueryLexer.BOOST:\n      return lunr.QueryParser.parseBoost\n    case lunr.QueryLexer.PRESENCE:\n      parser.nextClause()\n      return lunr.QueryParser.parsePresence\n    default:\n      var errorMessage = \"Unexpected lexeme type '\" + nextLexeme.type + \"'\"\n      throw new lunr.QueryParseError (errorMessage, nextLexeme.start, nextLexeme.end)\n  }\n}\n\nlunr.QueryParser.parseEditDistance = function (parser) {\n  var lexeme = parser.consumeLexeme()\n\n  if (lexeme == undefined) {\n    return\n  }\n\n  var editDistance = parseInt(lexeme.str, 10)\n\n  if (isNaN(editDistance)) {\n    var errorMessage = \"edit distance must be numeric\"\n    throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)\n  }\n\n  parser.currentClause.editDistance = editDistance\n\n  var nextLexeme = parser.peekLexeme()\n\n  if (nextLexeme == undefined) {\n    parser.nextClause()\n    return\n  }\n\n  switch (nextLexeme.type) {\n    case lunr.QueryLexer.TERM:\n      parser.nextClause()\n      return lunr.QueryParser.parseTerm\n    case lunr.QueryLexer.FIELD:\n      parser.nextClause()\n      return lunr.QueryParser.parseField\n    case lunr.QueryLexer.EDIT_DISTANCE:\n      return lunr.QueryParser.parseEditDistance\n    case lunr.QueryLexer.BOOST:\n      return lunr.QueryParser.parseBoost\n    case lunr.QueryLexer.PRESENCE:\n      parser.nextClause()\n      return lunr.QueryParser.parsePresence\n    default:\n      var errorMessage = \"Unexpected lexeme type '\" + nextLexeme.type + \"'\"\n      throw new lunr.QueryParseError (errorMessage, nextLexeme.start, nextLexeme.end)\n  }\n}\n\nlunr.QueryParser.parseBoost = function (parser) {\n  var lexeme = parser.consumeLexeme()\n\n  if (lexeme == undefined) {\n    return\n  }\n\n  var boost = parseInt(lexeme.str, 10)\n\n  if (isNaN(boost)) {\n    var errorMessage = \"boost must be numeric\"\n    throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)\n  }\n\n  parser.currentClause.boost = boost\n\n  var nextLexeme = parser.peekLexeme()\n\n  if (nextLexeme == undefined) {\n    parser.nextClause()\n    return\n  }\n\n  switch (nextLexeme.type) {\n    case lunr.QueryLexer.TERM:\n      parser.nextClause()\n      return lunr.QueryParser.parseTerm\n    case lunr.QueryLexer.FIELD:\n      parser.nextClause()\n      return lunr.QueryParser.parseField\n    case lunr.QueryLexer.EDIT_DISTANCE:\n      return lunr.QueryParser.parseEditDistance\n    case lunr.QueryLexer.BOOST:\n      return lunr.QueryParser.parseBoost\n    case lunr.QueryLexer.PRESENCE:\n      parser.nextClause()\n      return lunr.QueryParser.parsePresence\n    default:\n      var errorMessage = \"Unexpected lexeme type '\" + nextLexeme.type + \"'\"\n      throw new lunr.QueryParseError (errorMessage, nextLexeme.start, nextLexeme.end)\n  }\n}\n\n  /**\n   * export the module via AMD, CommonJS or as a browser global\n   * Export code from https://github.com/umdjs/umd/blob/master/returnExports.js\n   */\n  ;(function (root, factory) {\n    if (typeof define === 'function' && define.amd) {\n      // AMD. Register as an anonymous module.\n      define(factory)\n    } else if (typeof exports === 'object') {\n      /**\n       * Node. Does not work with strict CommonJS, but\n       * only CommonJS-like enviroments that support module.exports,\n       * like Node.\n       */\n      module.exports = factory()\n    } else {\n      // Browser globals (root is window)\n      root.lunr = factory()\n    }\n  }(this, function () {\n    /**\n     * Just return a value to define the module export.\n     * This example returns an object, but the module\n     * can return a function as the exported value.\n     */\n    return lunr\n  }))\n})();\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A RTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport lunr from \"lunr\"\n\nimport { getElement } from \"~/browser/element/_\"\nimport \"~/polyfills\"\n\nimport { Search } from \"../../_\"\nimport { SearchConfig } from \"../../config\"\nimport {\n  SearchMessage,\n  SearchMessageType\n} from \"../message\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Add support for `iframe-worker` shim\n *\n * While `importScripts` is synchronous when executed inside of a web worker,\n * it's not possible to provide a synchronous shim implementation. The cool\n * thing is that awaiting a non-Promise will convert it into a Promise, so\n * extending the type definition to return a `Promise` shouldn't break anything.\n *\n * @see https://bit.ly/2PjDnXi - GitHub comment\n *\n * @param urls - Scripts to load\n *\n * @returns Promise resolving with no result\n */\ndeclare global {\n  function importScripts(...urls: string[]): Promise<void> | void\n}\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Search index\n */\nlet index: Search\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch (= import) multi-language support through `lunr-languages`\n *\n * This function automatically imports the stemmers necessary to process the\n * languages which are defined as part of the search configuration.\n *\n * If the worker runs inside of an `iframe` (when using `iframe-worker` as\n * a shim), the base URL for the stemmers to be loaded must be determined by\n * searching for the first `script` element with a `src` attribute, which will\n * contain the contents of this script.\n *\n * @param config - Search configuration\n *\n * @returns Promise resolving with no result\n */\nasync function setupSearchLanguages(\n  config: SearchConfig\n): Promise<void> {\n  let base = \"../lunr\"\n\n  /* Detect `iframe-worker` and fix base URL */\n  if (typeof parent !== \"undefined\" && \"IFrameWorker\" in parent) {\n    const worker = getElement<HTMLScriptElement>(\"script[src]\")\n    const [path] = worker.src.split(\"/worker\")\n\n    /* Prefix base with path */\n    base = base.replace(\"..\", path)\n  }\n\n  /* Add scripts for languages */\n  const scripts = []\n  for (const lang of config.lang) {\n    switch (lang) {\n\n      /* Add segmenter for Japanese */\n      case \"ja\":\n        scripts.push(`${base}/tinyseg.js`)\n        break\n\n      /* Add segmenter for Hindi and Thai */\n      case \"hi\":\n      case \"th\":\n        scripts.push(`${base}/wordcut.js`)\n        break\n    }\n\n    /* Add language support */\n    if (lang !== \"en\")\n      scripts.push(`${base}/min/lunr.${lang}.min.js`)\n  }\n\n  /* Add multi-language support */\n  if (config.lang.length > 1)\n    scripts.push(`${base}/min/lunr.multi.min.js`)\n\n  /* Load scripts synchronously */\n  if (scripts.length)\n    await importScripts(\n      `${base}/min/lunr.stemmer.support.min.js`,\n      ...scripts\n    )\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Message handler\n *\n * @param message - Source message\n *\n * @returns Target message\n */\nexport async function handler(\n  message: SearchMessage\n): Promise<SearchMessage> {\n  switch (message.type) {\n\n    /* Search setup message */\n    case SearchMessageType.SETUP:\n      await setupSearchLanguages(message.data.config)\n      index = new Search(message.data)\n      return {\n        type: SearchMessageType.READY\n      }\n\n    /* Search query message */\n    case SearchMessageType.QUERY:\n      const query = message.data\n      try {\n        return {\n          type: SearchMessageType.RESULT,\n          data: index.search(query)\n        }\n\n      /* Return empty result in case of error */\n      } catch (err) {\n        console.warn(`Invalid query: ${query} \u2013 see https://bit.ly/2s3ChXG`)\n        console.warn(err)\n        return {\n          type: SearchMessageType.RESULT,\n          data: { items: [] }\n        }\n      }\n\n    /* All other messages */\n    default:\n      throw new TypeError(\"Invalid message type\")\n  }\n}\n\n/* ----------------------------------------------------------------------------\n * Worker\n * ------------------------------------------------------------------------- */\n\n/* Expose Lunr.js in global scope, or stemmers won't work */\nself.lunr = lunr\n\n/* Monkey-patch Lunr.js to mitigate https://t.ly/68TLq */\nlunr.utils.warn = console.warn\n\n/* Handle messages */\naddEventListener(\"message\", async ev => {\n  postMessage(await handler(ev.data))\n})\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve all elements matching the query selector\n *\n * @template T - Element type\n *\n * @param selector - Query selector\n * @param node - Node of reference\n *\n * @returns Elements\n */\nexport function getElements<T extends keyof HTMLElementTagNameMap>(\n  selector: T, node?: ParentNode\n): HTMLElementTagNameMap[T][]\n\nexport function getElements<T extends HTMLElement>(\n  selector: string, node?: ParentNode\n): T[]\n\nexport function getElements<T extends HTMLElement>(\n  selector: string, node: ParentNode = document\n): T[] {\n  return Array.from(node.querySelectorAll<T>(selector))\n}\n\n/**\n * Retrieve an element matching a query selector or throw a reference error\n *\n * Note that this function assumes that the element is present. If unsure if an\n * element is existent, use the `getOptionalElement` function instead.\n *\n * @template T - Element type\n *\n * @param selector - Query selector\n * @param node - Node of reference\n *\n * @returns Element\n */\nexport function getElement<T extends keyof HTMLElementTagNameMap>(\n  selector: T, node?: ParentNode\n): HTMLElementTagNameMap[T]\n\nexport function getElement<T extends HTMLElement>(\n  selector: string, node?: ParentNode\n): T\n\nexport function getElement<T extends HTMLElement>(\n  selector: string, node: ParentNode = document\n): T {\n  const el = getOptionalElement<T>(selector, node)\n  if (typeof el === \"undefined\")\n    throw new ReferenceError(\n      `Missing element: expected \"${selector}\" to be present`\n    )\n\n  /* Return element */\n  return el\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Retrieve an optional element matching the query selector\n *\n * @template T - Element type\n *\n * @param selector - Query selector\n * @param node - Node of reference\n *\n * @returns Element or nothing\n */\nexport function getOptionalElement<T extends keyof HTMLElementTagNameMap>(\n  selector: T, node?: ParentNode\n): HTMLElementTagNameMap[T] | undefined\n\nexport function getOptionalElement<T extends HTMLElement>(\n  selector: string, node?: ParentNode\n): T | undefined\n\nexport function getOptionalElement<T extends HTMLElement>(\n  selector: string, node: ParentNode = document\n): T | undefined {\n  return node.querySelector<T>(selector) || undefined\n}\n\n/**\n * Retrieve the currently active element\n *\n * @returns Element or nothing\n */\nexport function getActiveElement(): HTMLElement | undefined {\n  return (\n    document.activeElement?.shadowRoot?.activeElement as HTMLElement ??\n    document.activeElement as HTMLElement ??\n    undefined\n  )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Polyfills\n * ------------------------------------------------------------------------- */\n\n/* Polyfill `Object.entries` */\nif (!Object.entries)\n  Object.entries = function (obj: object) {\n    const data: [string, string][] = []\n    for (const key of Object.keys(obj))\n      // @ts-expect-error - ignore property access warning\n      data.push([key, obj[key]])\n\n    /* Return entries */\n    return data\n  }\n\n/* Polyfill `Object.values` */\nif (!Object.values)\n  Object.values = function (obj: object) {\n    const data: string[] = []\n    for (const key of Object.keys(obj))\n      // @ts-expect-error - ignore property access warning\n      data.push(obj[key])\n\n    /* Return values */\n    return data\n  }\n\n/* ------------------------------------------------------------------------- */\n\n/* Polyfills for `Element` */\nif (typeof Element !== \"undefined\") {\n\n  /* Polyfill `Element.scrollTo` */\n  if (!Element.prototype.scrollTo)\n    Element.prototype.scrollTo = function (\n      x?: ScrollToOptions | number, y?: number\n    ): void {\n      if (typeof x === \"object\") {\n        this.scrollLeft = x.left!\n        this.scrollTop = x.top!\n      } else {\n        this.scrollLeft = x!\n        this.scrollTop = y!\n      }\n    }\n\n  /* Polyfill `Element.replaceWith` */\n  if (!Element.prototype.replaceWith)\n    Element.prototype.replaceWith = function (\n      ...nodes: Array<string | Node>\n    ): void {\n      const parent = this.parentNode\n      if (parent) {\n        if (nodes.length === 0)\n          parent.removeChild(this)\n\n        /* Replace children and create text nodes */\n        for (let i = nodes.length - 1; i >= 0; i--) {\n          let node = nodes[i]\n          if (typeof node === \"string\")\n            node = document.createTextNode(node)\n          else if (node.parentNode)\n            node.parentNode.removeChild(node)\n\n          /* Replace child or insert before previous sibling */\n          if (!i)\n            parent.replaceChild(node, this)\n          else\n            parent.insertBefore(this.previousSibling!, node)\n        }\n      }\n    }\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search field\n */\nexport interface SearchField {\n  boost?: number                       /* Field boost */\n}\n\n/**\n * Search configuration\n */\nexport interface SearchConfig {\n  lang: string[]                       /* Search languages */\n  separator: string                    /* Search separator */\n  pipeline: SearchPipelineFn[]         /* Search pipeline */\n  fields: Record<string, SearchField>  /* Search field */\n}\n\n/**\n * Search document\n */\nexport interface SearchDocument {\n  location: string                     /* Document location */\n  title: string                        /* Document title */\n  text: string                         /* Document text */\n  tags?: string[]                      /* Document tags */\n  boost?: number                       /* Document boost */\n  parent?: SearchDocument              /* Document parent */\n}\n\n/**\n * Search options\n */\nexport interface SearchOptions {\n  suggest: boolean                     /* Search suggestions */\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Search index\n */\nexport interface SearchIndex {\n  config: SearchConfig                 /* Search configuration */\n  docs: SearchDocument[]               /* Search documents */\n  options: SearchOptions               /* Search options */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search pipeline function\n */\ntype SearchPipelineFn =\n  | \"trimmer\"                          /* Trimmer */\n  | \"stopWordFilter\"                   /* Stop word filter */\n  | \"stemmer\"                          /* Stemmer */\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Create a search document map\n *\n * This function creates a mapping of URLs (including anchors) to the actual\n * articles and sections. It relies on the invariant that the search index is\n * ordered with the main article appearing before all sections with anchors.\n * If this is not the case, the logic music be changed.\n *\n * @param docs - Search documents\n *\n * @returns Search document map\n */\nexport function setupSearchDocumentMap(\n  docs: SearchDocument[]\n): Map<string, SearchDocument> {\n  const map = new Map<string, SearchDocument>()\n  for (const doc of docs) {\n    const [path] = doc.location.split(\"#\")\n\n    /* Add document article */\n    const article = map.get(path)\n    if (typeof article === \"undefined\") {\n      map.set(path, doc)\n\n      /* Add document section */\n    } else {\n      map.set(doc.location, doc)\n      doc.parent = article\n    }\n  }\n\n  /* Return search document map */\n  return map\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Visitor function\n *\n * @param start - Start offset\n * @param end - End offset\n */\ntype VisitorFn = (\n  start: number, end: number\n) => void\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Split a string using the given separator\n *\n * @param input - Input value\n * @param separator - Separator\n * @param fn - Visitor function\n */\nexport function split(\n  input: string, separator: RegExp, fn: VisitorFn\n): void {\n  separator = new RegExp(separator, \"g\")\n\n  /* Split string using separator */\n  let match: RegExpExecArray | null\n  let index = 0\n  do {\n    match = separator.exec(input)\n\n    /* Emit non-empty range */\n    const until = match?.index ?? input.length\n    if (index < until)\n      fn(index, until)\n\n    /* Update last index */\n    if (match) {\n      const [term] = match\n      index = match.index + term.length\n\n      /* Support zero-length lookaheads */\n      if (term.length === 0)\n        separator.lastIndex = match.index + 1\n    }\n  } while (match)\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Extraction type\n *\n * This type defines the possible values that are encoded into the first two\n * bits of a section that is part of the blocks of a tokenization table. There\n * are three types of interest: HTML opening and closing tags, as well as the\n * actual text content we need to extract for indexing.\n */\nexport const enum Extract {\n  TAG_OPEN  = 0,                       /* HTML opening tag */\n  TEXT      = 1,                       /* Text content */\n  TAG_CLOSE = 2                        /* HTML closing tag */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Visitor function\n *\n * @param block - Block index\n * @param type - Extraction type\n * @param start - Start offset\n * @param end - End offset\n */\ntype VisitorFn = (\n  block: number, type: Extract, start: number, end: number\n) => void\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Split a string into markup and text sections\n *\n * This function scans a string and divides it up into sections of markup and\n * text. For each section, it invokes the given visitor function with the block\n * index, extraction type, as well as start and end offsets. Using a visitor\n * function (= streaming data) is ideal for minimizing pressure on the GC.\n *\n * @param input - Input value\n * @param fn - Visitor function\n */\nexport function extract(\n  input: string, fn: VisitorFn\n): void {\n\n  let block = 0                        /* Current block */\n  let start = 0                        /* Current start offset */\n  let end = 0                          /* Current end offset */\n\n  /* Split string into sections */\n  for (let stack = 0; end < input.length; end++) {\n\n    /* Opening tag after non-empty section */\n    if (input.charAt(end) === \"<\" && end > start) {\n      fn(block, Extract.TEXT, start, start = end)\n\n    /* Closing tag */\n    } else if (input.charAt(end) === \">\") {\n      if (input.charAt(start + 1) === \"/\") {\n        if (--stack === 0)\n          fn(block++, Extract.TAG_CLOSE, start, end + 1)\n\n      /* Tag is not self-closing */\n      } else if (input.charAt(end - 1) !== \"/\") {\n        if (stack++ === 0)\n          fn(block, Extract.TAG_OPEN, start, end + 1)\n      }\n\n      /* New section */\n      start = end + 1\n    }\n  }\n\n  /* Add trailing section */\n  if (end > start)\n    fn(block, Extract.TEXT, start, end)\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Position table\n */\nexport type PositionTable = number[][]\n\n/**\n * Position\n */\nexport type Position = number\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Highlight all occurrences in a string\n *\n * This function receives a field's value (e.g. like `title` or `text`), it's\n * position table that was generated during indexing, and the positions found\n * when executing the query. It then highlights all occurrences, and returns\n * their concatenation. In case of multiple blocks, two are returned.\n *\n * @param input - Input value\n * @param table - Table for indexing\n * @param positions - Occurrences\n * @param full - Full results\n *\n * @returns Highlighted string value\n */\nexport function highlight(\n  input: string, table: PositionTable, positions: Position[], full = false\n): string {\n  return highlightAll([input], table, positions, full).pop()!\n}\n\n/**\n * Highlight all occurrences in a set of strings\n *\n * @param inputs - Input values\n * @param table - Table for indexing\n * @param positions - Occurrences\n * @param full - Full results\n *\n * @returns Highlighted string values\n */\nexport function highlightAll(\n  inputs: string[], table: PositionTable, positions: Position[], full = false\n): string[] {\n\n  /* Map blocks to input values */\n  const mapping = [0]\n  for (let t = 1; t < table.length; t++) {\n    const prev = table[t - 1]\n    const next = table[t]\n\n    /* Check if table points to new block */\n    const p = prev[prev.length - 1] >>> 2 & 0x3FF\n    const q = next[0]               >>> 12\n\n    /* Add block to mapping */\n    mapping.push(+(p > q) + mapping[mapping.length - 1])\n  }\n\n  /* Highlight strings one after another */\n  return inputs.map((input, i) => {\n    let cursor = 0\n\n    /* Map occurrences to blocks */\n    const blocks = new Map<number, number[]>()\n    for (const p of positions.sort((a, b) => a - b)) {\n      const index = p & 0xFFFFF\n      const block = p >>> 20\n      if (mapping[block] !== i)\n        continue\n\n      /* Ensure presence of block group */\n      let group = blocks.get(block)\n      if (typeof group === \"undefined\")\n        blocks.set(block, group = [])\n\n      /* Add index to group */\n      group.push(index)\n    }\n\n    /* Just return string, if no occurrences */\n    if (blocks.size === 0)\n      return input\n\n    /* Compute slices */\n    const slices: string[] = []\n    for (const [block, indexes] of blocks) {\n      const t = table[block]\n\n      /* Extract positions and length */\n      const start  = t[0]            >>> 12\n      const end    = t[t.length - 1] >>> 12\n      const length = t[t.length - 1] >>> 2 & 0x3FF\n\n      /* Add prefix, if full results are desired */\n      if (full && start > cursor)\n        slices.push(input.slice(cursor, start))\n\n      /* Extract and highlight slice */\n      let slice = input.slice(start, end + length)\n      for (const j of indexes.sort((a, b) => b - a)) {\n\n        /* Retrieve offset and length of match */\n        const p = (t[j] >>> 12) - start\n        const q = (t[j] >>> 2 & 0x3FF) + p\n\n        /* Wrap occurrence */\n        slice = [\n          slice.slice(0, p),\n          \"<mark>\",\n          slice.slice(p, q),\n          \"</mark>\",\n          slice.slice(q)\n        ].join(\"\")\n      }\n\n      /* Update cursor */\n      cursor = end + length\n\n      /* Append slice and abort if we have two */\n      if (slices.push(slice) === 2)\n        break\n    }\n\n    /* Add suffix, if full results are desired */\n    if (full && cursor < input.length)\n      slices.push(input.slice(cursor))\n\n    /* Return highlighted slices */\n    return slices.join(\"\")\n  })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { split } from \"../_\"\nimport {\n  Extract,\n  extract\n} from \"../extract\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Split a string or set of strings into tokens\n *\n * This tokenizer supersedes the default tokenizer that is provided by Lunr.js,\n * as it is aware of HTML tags and allows for multi-character splitting.\n *\n * It takes the given inputs, splits each of them into markup and text sections,\n * tokenizes and segments (if necessary) each of them, and then indexes them in\n * a table by using a compact bit representation. Bitwise techniques are used\n * to write and read from the table during indexing and querying.\n *\n * @see https://bit.ly/3W3Xw4J - Search: better, faster, smaller\n *\n * @param input - Input value(s)\n *\n * @returns Tokens\n */\nexport function tokenize(\n  input?: string | string[]\n): lunr.Token[] {\n  const tokens: lunr.Token[] = []\n  if (typeof input === \"undefined\")\n    return tokens\n\n  /* Tokenize strings one after another */\n  const inputs = Array.isArray(input) ? input : [input]\n  for (let i = 0; i < inputs.length; i++) {\n    const table = lunr.tokenizer.table\n    const total = table.length\n\n    /* Split string into sections and tokenize content blocks */\n    extract(inputs[i], (block, type, start, end) => {\n      table[block += total] ||= []\n      switch (type) {\n\n        /* Handle markup */\n        case Extract.TAG_OPEN:\n        case Extract.TAG_CLOSE:\n          table[block].push(\n            start       << 12 |\n            end - start <<  2 |\n            type\n          )\n          break\n\n        /* Handle text content */\n        case Extract.TEXT:\n          const section = inputs[i].slice(start, end)\n          split(section, lunr.tokenizer.separator, (index, until) => {\n\n            /**\n             * Apply segmenter after tokenization. Note that the segmenter will\n             * also split words at word boundaries, which is not what we want,\n             * so we need to check if we can somehow mitigate this behavior.\n             */\n            if (typeof lunr.segmenter !== \"undefined\") {\n              const subsection = section.slice(index, until)\n              if (/^[MHIK]$/.test(lunr.segmenter.ctype_(subsection))) {\n                const segments = lunr.segmenter.segment(subsection)\n                for (let s = 0, l = 0; s < segments.length; s++) {\n\n                  /* Add block to section */\n                  table[block] ||= []\n                  table[block].push(\n                    start + index + l  << 12 |\n                    segments[s].length <<  2 |\n                    type\n                  )\n\n                  /* Add token with position */\n                  tokens.push(new lunr.Token(\n                    segments[s].toLowerCase(), {\n                      position: block << 20 | table[block].length - 1\n                    }\n                  ))\n\n                  /* Keep track of length */\n                  l += segments[s].length\n                }\n                return\n              }\n            }\n\n            /* Add block to section */\n            table[block].push(\n              start + index << 12 |\n              until - index <<  2 |\n              type\n            )\n\n            /* Add token with position */\n            tokens.push(new lunr.Token(\n              section.slice(index, until).toLowerCase(), {\n                position: block << 20 | table[block].length - 1\n              }\n            ))\n          })\n      }\n    })\n  }\n\n  /* Return tokens */\n  return tokens\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Visitor function\n *\n * @param value - String value\n *\n * @returns String term(s)\n */\ntype VisitorFn = (\n  value: string\n) => string | string[]\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Default transformation function\n *\n * 1. Trim excess whitespace from left and right.\n *\n * 2. Search for parts in quotation marks and prepend a `+` modifier to denote\n *    that the resulting document must contain all parts, converting the query\n *    to an `AND` query (as opposed to the default `OR` behavior). While users\n *    may expect parts enclosed in quotation marks to map to span queries, i.e.\n *    for which order is important, Lunr.js doesn't support them, so the best\n *    we can do is to convert the parts to an `AND` query.\n *\n * 3. Replace control characters which are not located at the beginning of the\n *    query or preceded by white space, or are not followed by a non-whitespace\n *    character or are at the end of the query string. Furthermore, filter\n *    unmatched quotation marks.\n *\n * 4. Split the query string at whitespace, then pass each part to the visitor\n *    function for tokenization, and append a wildcard to every resulting term\n *    that is not explicitly marked with a `+`, `-`, `~` or `^` modifier, since\n *    it ensures consistent and stable ranking when multiple terms are entered.\n *    Also, if a fuzzy or boost modifier are given, but no numeric value has\n *    been entered, default to 1 to not induce a query error.\n *\n * @param query - Query value\n * @param fn - Visitor function\n *\n * @returns Transformed query value\n */\nexport function transform(\n  query: string, fn: VisitorFn = term => term\n): string {\n  return query\n\n    /* => 1 */\n    .trim()\n\n    /* => 2 */\n    .split(/\"([^\"]+)\"/g)\n      .map((parts, index) => index & 1\n        ? parts.replace(/^\\b|^(?![^\\x00-\\x7F]|$)|\\s+/g, \" +\")\n        : parts\n      )\n      .join(\"\")\n\n    /* => 3 */\n    .replace(/\"|(?:^|\\s+)[*+\\-:^~]+(?=\\s+|$)/g, \"\")\n\n    /* => 4 */\n    .split(/\\s+/g)\n      .reduce((prev, term) => {\n        const next = fn(term)\n        return [...prev, ...Array.isArray(next) ? next : [next]]\n      }, [] as string[])\n      .map(term => /([~^]$)/.test(term) ? `${term}1` : term)\n      .map(term => /(^[+-]|[~^]\\d+$)/.test(term) ? term : `${term}*`)\n      .join(\" \")\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { split } from \"../../internal\"\nimport { transform } from \"../transform\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search query clause\n */\nexport interface SearchQueryClause {\n  presence: lunr.Query.presence        /* Clause presence */\n  term: string                         /* Clause term */\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Search query terms\n */\nexport type SearchQueryTerms = Record<string, boolean>\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Transform search query\n *\n * This function lexes the given search query and applies the transformation\n * function to each term, preserving markup like `+` and `-` modifiers.\n *\n * @param query - Search query\n *\n * @returns Search query\n */\nexport function transformSearchQuery(\n  query: string\n): string {\n\n  /* Split query terms with tokenizer */\n  return transform(query, part => {\n    const terms: string[] = []\n\n    /* Initialize lexer and analyze part */\n    const lexer = new lunr.QueryLexer(part)\n    lexer.run()\n\n    /* Extract and tokenize term from lexeme */\n    for (const { type, str: term, start, end } of lexer.lexemes)\n      switch (type) {\n\n        /* Hack: remove colon - see https://bit.ly/3wD3T3I */\n        case \"FIELD\":\n          if (![\"title\", \"text\", \"tags\"].includes(term))\n            part = [\n              part.slice(0, end),\n              \" \",\n              part.slice(end + 1)\n            ].join(\"\")\n          break\n\n        /* Tokenize term */\n        case \"TERM\":\n          split(term, lunr.tokenizer.separator, (...range) => {\n            terms.push([\n              part.slice(0, start),\n              term.slice(...range),\n              part.slice(end)\n            ].join(\"\"))\n          })\n      }\n\n    /* Return terms */\n    return terms\n  })\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Parse a search query for analysis\n *\n * Lunr.js itself has a bug where it doesn't detect or remove wildcards for\n * query clauses, so we must do this here.\n *\n * @see https://bit.ly/3DpTGtz - GitHub issue\n *\n * @param value - Query value\n *\n * @returns Search query clauses\n */\nexport function parseSearchQuery(\n  value: string\n): SearchQueryClause[] {\n  const query  = new lunr.Query([\"title\", \"text\", \"tags\"])\n  const parser = new lunr.QueryParser(value, query)\n\n  /* Parse Search query */\n  parser.parse()\n  for (const clause of query.clauses) {\n    clause.usePipeline = true\n\n    /* Handle leading wildcard */\n    if (clause.term.startsWith(\"*\")) {\n      clause.wildcard = lunr.Query.wildcard.LEADING\n      clause.term = clause.term.slice(1)\n    }\n\n    /* Handle trailing wildcard */\n    if (clause.term.endsWith(\"*\")) {\n      clause.wildcard = lunr.Query.wildcard.TRAILING\n      clause.term = clause.term.slice(0, -1)\n    }\n  }\n\n  /* Return query clauses */\n  return query.clauses\n}\n\n/**\n * Analyze the search query clauses in regard to the search terms found\n *\n * @param query - Search query clauses\n * @param terms - Search terms\n *\n * @returns Search query terms\n */\nexport function getSearchQueryTerms(\n  query: SearchQueryClause[], terms: string[]\n): SearchQueryTerms {\n  const clauses = new Set<SearchQueryClause>(query)\n\n  /* Match query clauses against terms */\n  const result: SearchQueryTerms = {}\n  for (let t = 0; t < terms.length; t++)\n    for (const clause of clauses)\n      if (terms[t].startsWith(clause.term)) {\n        result[clause.term] = true\n        clauses.delete(clause)\n      }\n\n  /* Annotate unmatched non-stopword query clauses */\n  for (const clause of clauses)\n    if (lunr.stopWordFilter?.(clause.term))\n      result[clause.term] = false\n\n  /* Return query terms */\n  return result\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Segment a search query using the inverted index\n *\n * This function implements a clever approach to text segmentation for Asian\n * languages, as it used the information already available in the search index.\n * The idea is to greedily segment the search query based on the tokens that are\n * already part of the index, as described in the linked issue.\n *\n * @see https://bit.ly/3lwjrk7 - GitHub issue\n *\n * @param query - Query value\n * @param index - Inverted index\n *\n * @returns Segmented query value\n */\nexport function segment(\n  query: string, index: object\n): Iterable<string> {\n  const segments = new Set<string>()\n\n  /* Segment search query */\n  const wordcuts = new Uint16Array(query.length)\n  for (let i = 0; i < query.length; i++)\n    for (let j = i + 1; j < query.length; j++) {\n      const value = query.slice(i, j)\n      if (value in index)\n        wordcuts[i] = j - i\n    }\n\n  /* Compute longest matches with minimum overlap */\n  const stack = [0]\n  for (let s = stack.length; s > 0;) {\n    const p = stack[--s]\n    for (let q = 1; q < wordcuts[p]; q++)\n      if (wordcuts[p + q] > wordcuts[p] - q) {\n        segments.add(query.slice(p, p + q))\n        stack[s++] = p + q\n      }\n\n    /* Continue at end of query string */\n    const q = p + wordcuts[p]\n    if (wordcuts[q] && q < query.length - 1)\n      stack[s++] = q\n\n    /* Add current segment */\n    segments.add(query.slice(p, q))\n  }\n\n  // @todo fix this case in the code block above, this is a hotfix\n  if (segments.has(\"\"))\n    return new Set([query])\n\n  /* Return segmented query value */\n  return segments\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  SearchDocument,\n  SearchIndex,\n  SearchOptions,\n  setupSearchDocumentMap\n} from \"../config\"\nimport {\n  Position,\n  PositionTable,\n  highlight,\n  highlightAll,\n  tokenize\n} from \"../internal\"\nimport {\n  SearchQueryTerms,\n  getSearchQueryTerms,\n  parseSearchQuery,\n  segment,\n  transformSearchQuery\n} from \"../query\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search item\n */\nexport interface SearchItem\n  extends SearchDocument\n{\n  score: number                        /* Score (relevance) */\n  terms: SearchQueryTerms              /* Search query terms */\n}\n\n/**\n * Search result\n */\nexport interface SearchResult {\n  items: SearchItem[][]                /* Search items */\n  suggest?: string[]                   /* Search suggestions */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Create field extractor factory\n *\n * @param table - Position table map\n *\n * @returns Extractor factory\n */\nfunction extractor(table: Map<string, PositionTable>) {\n  return (name: keyof SearchDocument) => {\n    return (doc: SearchDocument) => {\n      if (typeof doc[name] === \"undefined\")\n        return undefined\n\n      /* Compute identifier and initialize table */\n      const id = [doc.location, name].join(\":\")\n      table.set(id, lunr.tokenizer.table = [])\n\n      /* Return field value */\n      return doc[name]\n    }\n  }\n}\n\n/**\n * Compute the difference of two lists of strings\n *\n * @param a - 1st list of strings\n * @param b - 2nd list of strings\n *\n * @returns Difference\n */\nfunction difference(a: string[], b: string[]): string[] {\n  const [x, y] = [new Set(a), new Set(b)]\n  return [\n    ...new Set([...x].filter(value => !y.has(value)))\n  ]\n}\n\n/* ----------------------------------------------------------------------------\n * Class\n * ------------------------------------------------------------------------- */\n\n/**\n * Search index\n */\nexport class Search {\n\n  /**\n   * Search document map\n   */\n  protected map: Map<string, SearchDocument>\n\n  /**\n   * Search options\n   */\n  protected options: SearchOptions\n\n  /**\n   * The underlying Lunr.js search index\n   */\n  protected index: lunr.Index\n\n  /**\n   * Internal position table map\n   */\n  protected table: Map<string, PositionTable>\n\n  /**\n   * Create the search integration\n   *\n   * @param data - Search index\n   */\n  public constructor({ config, docs, options }: SearchIndex) {\n    const field = extractor(this.table = new Map())\n\n    /* Set up document map and options */\n    this.map = setupSearchDocumentMap(docs)\n    this.options = options\n\n    /* Set up document index */\n    this.index = lunr(function () {\n      this.metadataWhitelist = [\"position\"]\n      this.b(0)\n\n      /* Set up (multi-)language support */\n      if (config.lang.length === 1 && config.lang[0] !== \"en\") {\n        // @ts-expect-error - namespace indexing not supported\n        this.use(lunr[config.lang[0]])\n      } else if (config.lang.length > 1) {\n        this.use(lunr.multiLanguage(...config.lang))\n      }\n\n      /* Set up custom tokenizer (must be after language setup) */\n      this.tokenizer = tokenize as typeof lunr.tokenizer\n      lunr.tokenizer.separator = new RegExp(config.separator)\n\n      /* Set up custom segmenter, if loaded */\n      lunr.segmenter = \"TinySegmenter\" in lunr\n        ? new lunr.TinySegmenter()\n        : undefined\n\n      /* Compute functions to be removed from the pipeline */\n      const fns = difference([\n        \"trimmer\", \"stopWordFilter\", \"stemmer\"\n      ], config.pipeline)\n\n      /* Remove functions from the pipeline for registered languages */\n      for (const lang of config.lang.map(language => (\n        // @ts-expect-error - namespace indexing not supported\n        language === \"en\" ? lunr : lunr[language]\n      )))\n        for (const fn of fns) {\n          this.pipeline.remove(lang[fn])\n          this.searchPipeline.remove(lang[fn])\n        }\n\n      /* Set up index reference */\n      this.ref(\"location\")\n\n      /* Set up index fields */\n      for (const [name, spec] of Object.entries(config.fields))\n        // @ts-expect-error - fix typings, if this proves to be a good idea\n        this.field(name, { ...spec, extractor: field(name) })\n\n      /* Add documents to index */\n      for (const doc of docs)\n        this.add(doc, { boost: doc.boost })\n    })\n  }\n\n  /**\n   * Search for matching documents\n   *\n   * @param query - Search query\n   *\n   * @returns Search result\n   */\n  public search(query: string): SearchResult {\n\n    // Experimental Chinese segmentation\n    query = query.replace(/\\p{sc=Han}+/gu, value => {\n      return [...segment(value, this.index.invertedIndex)]\n        .join(\"* \")\n    })\n\n    // @todo: move segmenter (above) into transformSearchQuery\n    query = transformSearchQuery(query)\n    if (!query)\n      return { items: [] }\n\n    /* Parse query to extract clauses for analysis */\n    const clauses = parseSearchQuery(query)\n      .filter(clause => (\n        clause.presence !== lunr.Query.presence.PROHIBITED\n      ))\n\n    /* Perform search and post-process results */\n    const groups = this.index.search(query)\n\n      /* Apply post-query boosts based on title and search query terms */\n      .reduce<SearchItem[]>((item, { ref, score, matchData }) => {\n        let doc = this.map.get(ref)\n        if (typeof doc !== \"undefined\") {\n\n          /* Shallow copy document */\n          doc = { ...doc }\n          if (doc.tags)\n            doc.tags = [...doc.tags]\n\n          /* Compute and analyze search query terms */\n          const terms = getSearchQueryTerms(\n            clauses,\n            Object.keys(matchData.metadata)\n          )\n\n          /* Highlight matches in fields */\n          for (const field of this.index.fields) {\n            if (typeof doc[field] === \"undefined\")\n              continue\n\n            /* Collect positions from matches */\n            const positions: Position[] = []\n            for (const match of Object.values(matchData.metadata))\n              if (typeof match[field] !== \"undefined\")\n                positions.push(...match[field].position)\n\n            /* Skip highlighting, if no positions were collected */\n            if (!positions.length)\n              continue\n\n            /* Load table and determine highlighting method */\n            const table = this.table.get([doc.location, field].join(\":\"))!\n            const fn = Array.isArray(doc[field])\n              ? highlightAll\n              : highlight\n\n            // @ts-expect-error - stop moaning, TypeScript!\n            doc[field] = fn(doc[field], table, positions, field !== \"text\")\n          }\n\n          /* Highlight title and text and apply post-query boosts */\n          const boost = +!doc.parent +\n            Object.values(terms)\n              .filter(t => t).length /\n            Object.keys(terms).length\n\n          /* Append item */\n          item.push({\n            ...doc,\n            score: score * (1 + boost ** 2),\n            terms\n          })\n        }\n        return item\n      }, [])\n\n      /* Sort search results again after applying boosts */\n      .sort((a, b) => b.score - a.score)\n\n      /* Group search results by article */\n      .reduce((items, result) => {\n        const doc = this.map.get(result.location)\n        if (typeof doc !== \"undefined\") {\n          const ref = doc.parent\n            ? doc.parent.location\n            : doc.location\n          items.set(ref, [...items.get(ref) || [], result])\n        }\n        return items\n      }, new Map<string, SearchItem[]>())\n\n    /* Ensure that every item set has an article */\n    for (const [ref, items] of groups)\n      if (!items.find(item => item.location === ref)) {\n        const doc = this.map.get(ref)!\n        items.push({ ...doc, score: 0, terms: {} })\n      }\n\n    /* Generate search suggestions, if desired */\n    let suggest: string[] | undefined\n    if (this.options.suggest) {\n      const titles = this.index.query(builder => {\n        for (const clause of clauses)\n          builder.term(clause.term, {\n            fields: [\"title\"],\n            presence: lunr.Query.presence.REQUIRED,\n            wildcard: lunr.Query.wildcard.TRAILING\n          })\n      })\n\n      /* Retrieve suggestions for best match */\n      suggest = titles.length\n        ? Object.keys(titles[0].matchData.metadata)\n        : []\n    }\n\n    /* Return search result */\n    return {\n      items: [...groups.values()],\n      ...typeof suggest !== \"undefined\" && { suggest }\n    }\n  }\n}\n"],
+  "mappings": 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diff --git a/DevDoc/assets/stylesheets/palette.ab4e12ef.min.css b/DevDoc/assets/stylesheets/palette.ab4e12ef.min.css
new file mode 100644
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--- /dev/null
+++ b/DevDoc/assets/stylesheets/palette.ab4e12ef.min.css
@@ -0,0 +1 @@
+@media screen{[data-md-color-scheme=slate]{--md-default-fg-color:hsla(var(--md-hue),15%,90%,0.82);--md-default-fg-color--light:hsla(var(--md-hue),15%,90%,0.56);--md-default-fg-color--lighter:hsla(var(--md-hue),15%,90%,0.32);--md-default-fg-color--lightest:hsla(var(--md-hue),15%,90%,0.12);--md-default-bg-color:hsla(var(--md-hue),15%,14%,1);--md-default-bg-color--light:hsla(var(--md-hue),15%,14%,0.54);--md-default-bg-color--lighter:hsla(var(--md-hue),15%,14%,0.26);--md-default-bg-color--lightest:hsla(var(--md-hue),15%,14%,0.07);--md-code-fg-color:hsla(var(--md-hue),18%,86%,0.82);--md-code-bg-color:hsla(var(--md-hue),15%,18%,1);--md-code-bg-color--light:hsla(var(--md-hue),15%,18%,0.9);--md-code-bg-color--lighter:hsla(var(--md-hue),15%,18%,0.54);--md-code-hl-color:#2977ff;--md-code-hl-color--light:#2977ff1a;--md-code-hl-number-color:#e6695b;--md-code-hl-special-color:#f06090;--md-code-hl-function-color:#c973d9;--md-code-hl-constant-color:#9383e2;--md-code-hl-keyword-color:#6791e0;--md-code-hl-string-color:#2fb170;--md-code-hl-name-color:var(--md-code-fg-color);--md-code-hl-operator-color:var(--md-default-fg-color--light);--md-code-hl-punctuation-color:var(--md-default-fg-color--light);--md-code-hl-comment-color:var(--md-default-fg-color--light);--md-code-hl-generic-color:var(--md-default-fg-color--light);--md-code-hl-variable-color:var(--md-default-fg-color--light);--md-typeset-color:var(--md-default-fg-color);--md-typeset-a-color:var(--md-primary-fg-color);--md-typeset-kbd-color:hsla(var(--md-hue),15%,90%,0.12);--md-typeset-kbd-accent-color:hsla(var(--md-hue),15%,90%,0.2);--md-typeset-kbd-border-color:hsla(var(--md-hue),15%,14%,1);--md-typeset-mark-color:#4287ff4d;--md-typeset-table-color:hsla(var(--md-hue),15%,95%,0.12);--md-typeset-table-color--light:hsla(var(--md-hue),15%,95%,0.035);--md-admonition-fg-color:var(--md-default-fg-color);--md-admonition-bg-color:var(--md-default-bg-color);--md-footer-bg-color:hsla(var(--md-hue),15%,10%,0.87);--md-footer-bg-color--dark:hsla(var(--md-hue),15%,8%,1);--md-shadow-z1:0 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diff --git a/DevDoc/assets/stylesheets/palette.ab4e12ef.min.css.map b/DevDoc/assets/stylesheets/palette.ab4e12ef.min.css.map
new file mode 100644
index 00000000..1026d57c
--- /dev/null
+++ b/DevDoc/assets/stylesheets/palette.ab4e12ef.min.css.map
@@ -0,0 +1 @@
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diff --git a/doc/css/extra.css b/DevDoc/css/extra.css
similarity index 100%
rename from doc/css/extra.css
rename to DevDoc/css/extra.css
diff --git a/docmd/ecology-letters.csl b/DevDoc/ecology-letters.csl
similarity index 100%
rename from docmd/ecology-letters.csl
rename to DevDoc/ecology-letters.csl
diff --git a/doc/implementation/chunkreader.refs/index.html b/DevDoc/implementation/chunkreader.refs/index.html
similarity index 86%
rename from doc/implementation/chunkreader.refs/index.html
rename to DevDoc/implementation/chunkreader.refs/index.html
index ec8a30ea..70a9ae3a 100644
--- a/doc/implementation/chunkreader.refs/index.html
+++ b/DevDoc/implementation/chunkreader.refs/index.html
@@ -178,6 +178,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
     
     
     
@@ -187,10 +214,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
         
           
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
             
   
   
@@ -208,8 +235,8 @@
             <span class="md-nav__icon md-icon"></span>
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -359,6 +386,34 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -381,10 +436,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
         
           
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
             
   
   
@@ -402,8 +457,8 @@
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -784,14 +839,98 @@
   
   
     <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
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+
+      </a>
+    </li>
+  
+
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+      <a href="../select/" class="md-nav__link">
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+
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+
+              
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+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
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+  
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@@ -915,6 +1054,90 @@
 
               
             
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+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
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+    Sibling annex (discussion)
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+  
+
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+  
+
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+            
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+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
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+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
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+  
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+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
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+  
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+
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+  
+
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diff --git a/doc/implementation/chunkreader/index.html b/DevDoc/implementation/chunkreader/index.html
similarity index 82%
rename from doc/implementation/chunkreader/index.html
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index 9d23527a..69852bca 100644
--- a/doc/implementation/chunkreader/index.html
+++ b/DevDoc/implementation/chunkreader/index.html
@@ -77,12 +77,24 @@
   
 
     
+  </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="../../installation/">
+<span class="md-ellipsis">
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+  
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+  
+
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@@ -160,6 +172,18 @@
   
 
     
+  </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="../../theory/evolutionary_distances/">
+<span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
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@@ -167,8 +191,8 @@
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@@ -296,6 +320,15 @@
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+<li class="md-nav__item">
+<a class="md-nav__link" href="#future-work-parallel-gzip-decompression-in-xopen">
+<span class="md-ellipsis">
+      
+        Future work — parallel gzip decompression in xopen
+      
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@@ -420,11 +453,47 @@
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+<a class="md-nav__link" href="../merge_parallelism/">
 <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism &amp; memory
+  
+
+    
+  </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="../filtering/">
+<span class="md-ellipsis">
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+  
+    Kmer filtering
+  
+
+    
+  </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="../select/">
+<span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="../obitaxonomy/">
+<span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
   
 
     
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@@ -478,6 +547,42 @@
   
 
     
+  </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="../../architecture/siblings/">
+<span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
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+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="../../architecture/numa_worker_pools/">
+<span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="../../architecture/numa_partition_runner/">
+<span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
   </span>
 </a>
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@@ -552,6 +657,15 @@
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+<li class="md-nav__item">
+<a class="md-nav__link" href="#future-work-parallel-gzip-decompression-in-xopen">
+<span class="md-ellipsis">
+      
+        Future work — parallel gzip decompression in xopen
+      
+    </span>
+</a>
+</li>
 </ul>
 </nav>
 </div>
@@ -659,6 +773,16 @@ The stream path (<code>NucStream</code> / <code>NucPage</code>) is described in
     FoundAt      --&gt; InHeader  : other</code></pre>
 <p><code>restart</code> is updated each time a <code>+</code> is found. When any state fails its expected input, the scan jumps back to <code>restart</code> and continues from there — guaranteeing that a <code>@</code> in a quality line cannot be accepted as a record start, because the <code>\n+\n</code> structure immediately following it (going backward) will not be found.</p>
 <p>Returns the byte offset of the <code>@</code> that starts the last complete record.</p>
+<hr/>
+<h2 id="future-work-parallel-gzip-decompression-in-xopen">Future work — parallel gzip decompression in <code>xopen</code></h2>
+<p><code>obiread::xopen</code> (<code>xopen.rs</code>) decompresses gzip via <code>niffler</code> → <code>flate2</code>, which is single-threaded (standard DEFLATE has no parallel-decodable structure). For large local gzip inputs this single-threaded decompression can become the throughput bottleneck feeding the <code>query</code>/<code>index</code>/<code>superkmer</code> pipelines, since chunk/page production for a given file is serialized ahead of the worker pool.</p>
+<p>Candidate: special-case local, on-disk, gzip-magic-detected paths in <code>open_raw</code>/<code>xopen</code> to use <a href="https://github.com/alekseizarubin/rapidgzip-rs"><code>rapidgzip-rs</code></a> (<code>ReaderBuilder::new().parallelism(n).open(path)</code>, implements <code>Read + Seek</code>) instead of <code>niffler</code>, keeping <code>niffler</code> for every other case: <code>stdin</code> (<code>-</code>), HTTP(S) sources, and all non-gzip formats (bzip2, xz, zstd — less used in practice here).</p>
+<p>Constraints identified so far (not yet validated against real data):
+- Branch point must move earlier than the current <code>decompress()</code> call in <code>open_raw</code> — rapidgzip's fast path needs the file <strong>path</strong>, not an already-opened generic <code>Read</code>, so the gzip/local-file detection has to happen before the generic <code>File::open</code> + <code>niffler::send::get_reader</code> path is taken.
+- <code>stdin</code> and HTTP sources are not seekable — they stay on <code>niffler</code> regardless; the gain only applies to local on-disk <code>.gz</code> files.
+- <code>rapidgzip-sys</code> vendors a native C++ engine: requires CMake ≥ 3.17, a C++17 compiler, and <code>nasm</code> on x86 targets — a real build-toolchain addition, not just a pure-Rust crate.
+- Low maturity of the Rust binding at review time (2 GitHub stars, ~15 commits, April 2026 latest release) — the underlying C++ engine is validated (HPDC 2023 paper), but the binding itself has limited production track record.</p>
+<p>Decision: parked for now. Before adopting, validate on real data: throughput vs. <code>niffler</code> on representative large <code>.gz</code> inputs, and byte-for-byte correctness of decompressed output.</p>
 </article>
 </div>
 <script>var target=document.getElementById(location.hash.slice(1));target&&target.name&&(target.checked=target.name.startsWith("__tabbed_"))</script>
diff --git a/doc/implementation/evidence_elimination.refs/index.html b/DevDoc/implementation/evidence_elimination.refs/index.html
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rename to DevDoc/implementation/evidence_elimination.refs/index.html
index 565edffe..8215d476 100644
--- a/doc/implementation/evidence_elimination.refs/index.html
+++ b/DevDoc/implementation/evidence_elimination.refs/index.html
@@ -178,6 +178,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
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+  
+    Installation
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+
+    
+  </span>
+  
+  
+
+      </a>
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+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
             
   
   
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+          <label class="md-nav__title" for="__nav_3">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -359,6 +386,34 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
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+
+      </a>
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+  
+
+              
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
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@@ -784,14 +839,98 @@
   
   
     <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
   
 
     
@@ -827,10 +966,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
         
           
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
             
   
   
@@ -848,8 +987,8 @@
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -915,6 +1054,90 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
diff --git a/doc/implementation/evidence_elimination/index.html b/DevDoc/implementation/evidence_elimination/index.html
similarity index 91%
rename from doc/implementation/evidence_elimination/index.html
rename to DevDoc/implementation/evidence_elimination/index.html
index da47ce0c..17a240d5 100644
--- a/doc/implementation/evidence_elimination/index.html
+++ b/DevDoc/implementation/evidence_elimination/index.html
@@ -182,6 +182,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
     
     
     
@@ -191,10 +218,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
         
           
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
             
   
   
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -363,6 +390,34 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -387,10 +442,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
         
           
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
             
   
   
@@ -408,8 +463,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_4">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -925,14 +980,98 @@
   
   
     <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
   
 
     
@@ -968,10 +1107,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
         
           
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
             
   
   
@@ -989,8 +1128,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -1056,6 +1195,90 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
diff --git a/doc/implementation/rebuild_filter/index.html b/DevDoc/implementation/filtering/index.html
similarity index 63%
rename from doc/implementation/rebuild_filter/index.html
rename to DevDoc/implementation/filtering/index.html
index b4abb1ec..283f5b8d 100644
--- a/doc/implementation/rebuild_filter/index.html
+++ b/DevDoc/implementation/filtering/index.html
@@ -9,10 +9,10 @@
       
       
       
-        <link rel="prev" href="../merge/">
+        <link rel="prev" href="../merge_parallelism/">
       
       
-        <link rel="next" href="../../architecture/sequences/invariant/">
+        <link rel="next" href="../select/">
       
       
         
@@ -23,7 +23,7 @@
     
     
       
-        <title>Kmer filtering (rebuild/dump/unitig) - obikmer</title>
+        <title>Kmer filtering - obikmer</title>
       
     
     
@@ -100,7 +100,7 @@
         <div class="md-header__topic" data-md-component="header-topic">
           <span class="md-ellipsis">
             
-              Kmer filtering (rebuild/dump/unitig)
+              Kmer filtering
             
           </span>
         </div>
@@ -182,6 +182,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
     
     
     
@@ -191,10 +218,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
         
           
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
             
   
   
@@ -212,8 +239,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -363,6 +390,34 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -387,10 +442,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
         
           
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
             
   
   
@@ -408,8 +463,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_4">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -787,6 +842,34 @@
                 
   
   
+  
+  
+    <li class="md-nav__item">
+      <a href="../merge_parallelism/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
     
   
   
@@ -806,7 +889,7 @@
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Kmer filtering
   
 
     
@@ -824,7 +907,7 @@
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Kmer filtering
   
 
     
@@ -958,6 +1041,45 @@
     </span>
   </a>
   
+    <nav class="md-nav" aria-label="Quorum flags">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#negative-counts-offset-from-group-size" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Negative counts — offset from group size
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#validation" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Validation
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#conservative-rounding-of-fraction-thresholds" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Conservative rounding of fraction thresholds
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
         <li class="md-nav__item">
@@ -969,6 +1091,45 @@
     </span>
   </a>
   
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#command-specific-options" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Command-specific options
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Command-specific options">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#dump-head-n" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        dump --head N
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#phylo-presence-threshold-n" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        phylo --presence-threshold N
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
         <li class="md-nav__item">
@@ -991,6 +1152,62 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -1013,10 +1230,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
         
           
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
             
   
   
@@ -1034,8 +1251,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -1101,6 +1318,90 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -1243,6 +1544,45 @@
     </span>
   </a>
   
+    <nav class="md-nav" aria-label="Quorum flags">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#negative-counts-offset-from-group-size" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Negative counts — offset from group size
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#validation" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Validation
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#conservative-rounding-of-fraction-thresholds" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Conservative rounding of fraction thresholds
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
         <li class="md-nav__item">
@@ -1254,6 +1594,45 @@
     </span>
   </a>
   
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#command-specific-options" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Command-specific options
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Command-specific options">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#dump-head-n" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        dump --head N
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#phylo-presence-threshold-n" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        phylo --presence-threshold N
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
         <li class="md-nav__item">
@@ -1285,11 +1664,12 @@
 
 
 <h1 id="kmer-filtering-and-ingroupoutgroup-predicates">Kmer filtering and ingroup/outgroup predicates</h1>
-<p>The <code>rebuild</code>, <code>dump</code>, and <code>unitig</code> commands all share the same filtering
-system. Filters can select k-mers based on per-genome quorum counts, optionally
-restricted to <strong>ingroup</strong> and <strong>outgroup</strong> genome sets derived from genome
-metadata.</p>
-<p><code>rebuild</code> additionally accepts <code>--min-total-count</code> / <code>--max-total-count</code> filters
+<p>The <code>filter</code>, <code>dump</code>, and <code>unitig</code> commands share the same filtering system,
+implemented as a shared <code>FilterArgs</code> clap argument group embedded in each command
+via <code>#[command(flatten)]</code>. Filters select k-mers based on per-genome quorum
+counts, optionally restricted to <strong>ingroup</strong> and <strong>outgroup</strong> genome sets derived
+from genome metadata. All rules described here apply identically to all three commands.</p>
+<p><code>filter</code> additionally accepts <code>--min-total-count</code> / <code>--max-total-count</code> filters
 that operate on the sum of counts across all genomes.</p>
 <h2 id="predicate-syntax">Predicate syntax</h2>
 <p>Each <code>--ingroup</code> and <code>--outgroup</code> flag takes a predicate of the form:</p>
@@ -1327,16 +1707,44 @@ that operate on the sum of counts across all genomes.</p>
 </table>
 <p>Multiple values separated by <code>|</code> are always OR-ed within the predicate.</p>
 <h3 id="path-matching-and">Path matching (<code>~</code> and <code>!~</code>)</h3>
-<p>Metadata values can represent hierarchical taxonomic paths such as
+<p>Metadata values can represent hierarchical concept paths such as
 <code>/Eukaryota/Viridiplantae/Streptophyta/Betulaceae/Betula/nana</code>.</p>
+<p>Stored taxonomy values always start with <code>/</code> (the root of the path).
+Query patterns do <strong>not</strong> need to start with <code>/</code> — a leading <code>/</code> is an optional
+start anchor, not a requirement.</p>
+<table>
+<thead>
+<tr>
+<th>Pattern form</th>
+<th>Semantics</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>A/B</code></td>
+<td>contiguous sub-path A then B, anywhere in the value</td>
+</tr>
+<tr>
+<td><code>/A/B</code></td>
+<td>value starts with A then B</td>
+</tr>
+<tr>
+<td><code>A/B$</code></td>
+<td>value ends with A then B</td>
+</tr>
+<tr>
+<td><code>/A/B$</code></td>
+<td>value is exactly A then B</td>
+</tr>
+<tr>
+<td><code>A@x/B</code></td>
+<td>A with class <code>x</code> followed by B with any class</td>
+</tr>
+</tbody>
+</table>
 <ul>
-<li><strong>Absolute pattern</strong> (starts with <code>/</code>): the value must start with the pattern
-  at a segment boundary.
-  <code>taxon~/Betulaceae/Betula</code> matches <code>/Betulaceae/Betula/nana</code> and
-  <code>/Betulaceae/Betula</code> but not <code>/Betulaceae/Betuloides/…</code>.</li>
-<li><strong>Bare segment</strong> (no leading <code>/</code>): the value must contain the pattern as an
-  exact path component anywhere.
-  <code>taxon~Betula</code> matches any path that has <code>Betula</code> as one of its segments.</li>
+<li><code>taxon~/Betulaceae/Betula</code> matches any path that starts with <code>Betulaceae</code> then <code>Betula</code>.</li>
+<li><code>taxon~Betula</code> matches any path containing <code>Betula</code> as a segment, anywhere.</li>
 </ul>
 <h3 id="missing-metadata-key-na">Missing metadata key → NA</h3>
 <p>If a genome does not carry the queried metadata key, the predicate returns <strong>NA</strong>.
@@ -1422,12 +1830,12 @@ cannot be classified are <strong>ignored</strong> in all quorum counts.</p>
 <tr>
 <td><code>--min-count N</code></td>
 <td>ingroup</td>
-<td>k-mer present in at least N ingroup genomes</td>
+<td>k-mer present in at least N ingroup genomes (N may be negative, see below)</td>
 </tr>
 <tr>
 <td><code>--max-count N</code></td>
 <td>ingroup</td>
-<td>k-mer present in at most N ingroup genomes</td>
+<td>k-mer present in at most N ingroup genomes (N may be negative, see below)</td>
 </tr>
 <tr>
 <td><code>--min-frac F</code></td>
@@ -1442,12 +1850,12 @@ cannot be classified are <strong>ignored</strong> in all quorum counts.</p>
 <tr>
 <td><code>--min-outgroup-count N</code></td>
 <td>outgroup</td>
-<td>k-mer present in at least N outgroup genomes</td>
+<td>k-mer present in at least N outgroup genomes (N may be negative, see below)</td>
 </tr>
 <tr>
 <td><code>--max-outgroup-count N</code></td>
 <td>outgroup</td>
-<td>k-mer present in at most N outgroup genomes</td>
+<td>k-mer present in at most N outgroup genomes (N may be negative, see below)</td>
 </tr>
 <tr>
 <td><code>--min-outgroup-frac F</code></td>
@@ -1462,12 +1870,12 @@ cannot be classified are <strong>ignored</strong> in all quorum counts.</p>
 <tr>
 <td><code>--min-total-count N</code></td>
 <td>all genomes</td>
-<td>sum of per-genome counts ≥ N (<code>rebuild</code> only)</td>
+<td>sum of per-genome counts ≥ N (<code>filter</code> only)</td>
 </tr>
 <tr>
 <td><code>--max-total-count N</code></td>
 <td>all genomes</td>
-<td>sum of per-genome counts ≤ N (<code>rebuild</code> only)</td>
+<td>sum of per-genome counts ≤ N (<code>filter</code> only)</td>
 </tr>
 <tr>
 <td><code>--presence-threshold N</code></td>
@@ -1476,15 +1884,184 @@ cannot be classified are <strong>ignored</strong> in all quorum counts.</p>
 </tr>
 </tbody>
 </table>
-<p>Defaults: mins = 0 (no lower bound), max counts = group size, max fracs = 1.0
-(no upper bound). A filter with all defaults is a no-op.</p>
+<h3 id="negative-counts-offset-from-group-size">Negative counts — offset from group size</h3>
+<p>The four integer count flags (<code>--min-count</code>, <code>--max-count</code>, <code>--min-outgroup-count</code>,
+<code>--max-outgroup-count</code>) accept <strong>negative</strong> values, interpreted as an offset counted
+down from the group size <code>n</code>, resolved at run time once <code>n</code> is known:</p>
+<table>
+<thead>
+<tr>
+<th>Value</th>
+<th>Effective threshold</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>N ≥ 0</code></td>
+<td>literal absolute count <code>N</code></td>
+</tr>
+<tr>
+<td><code>-x</code> (x &gt; 0)</td>
+<td><code>max(1, n − x)</code> — "all but x"</td>
+</tr>
+</tbody>
+</table>
+<p><code>-1</code> literally means <em>all but one</em>, <code>-2</code> <em>all but two</em>, and so on. This expresses
+a quorum relative to the group size that a plain fraction cannot state exactly
+(e.g. "present in every genome except at most one" is <code>n−1</code>, which is <code>0.9</code> for
+<code>n = 10</code> but <code>0.857…</code> for <code>n = 7</code>).</p>
+<p>The threshold is <strong>floored at 1</strong>, never 0: the negative form always keeps
+constraining the group. Without the floor, <code>--min-count -1</code> on a singleton
+ingroup (<code>n = 1</code>) would resolve to <code>0</code> ("at least 0") and silently drop the
+constraint; the floor makes it <code>1</code> ("present in that one genome") instead.</p>
+<p>To express a count of <code>0</code> (e.g. "absent from the ingroup"), use the literal <code>0</code>,
+not a negative — <code>0</code> and <code>-0</code> are indistinguishable, so the offset form starts at
+<code>-1</code>.</p>
+<blockquote>
+<p><strong>Edge case</strong> — on an <em>empty</em> group (<code>n = 0</code>, e.g. a predicate matching no
+genome), a negative count still resolves to <code>1</code>, an impossible constraint that
+rejects every k-mer. This is consistent with an empty group letting nothing
+through, but differs from the "no constraint" behaviour of the fraction flags.</p>
+</blockquote>
+<p><strong>Conditional defaults</strong> — the defaults for <code>--min-frac</code> and <code>--max-outgroup-count</code> depend on two conditions:
+whether the corresponding group was declared, <strong>and</strong> whether any quorum flag for that group was explicitly set.</p>
+<blockquote>
+<p><strong>Rule</strong>: declaring a group activates the smart default <strong>only if no quorum flag for that group is explicitly set</strong>.
+As soon as any quorum flag for a group is present on the command line, all defaults for that group revert to no-op values.</p>
+</blockquote>
+<table>
+<thead>
+<tr>
+<th><code>--ingroup</code></th>
+<th>Any ingroup quorum flag?</th>
+<th><code>--min-frac</code> default</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>not set</td>
+<td>—</td>
+<td>0.0 (no-op)</td>
+</tr>
+<tr>
+<td>set</td>
+<td>no</td>
+<td><strong>1.0</strong> — all ingroup genomes must carry the k-mer</td>
+</tr>
+<tr>
+<td>set</td>
+<td>yes</td>
+<td>0.0 — user controls quorum explicitly</td>
+</tr>
+</tbody>
+</table>
+<table>
+<thead>
+<tr>
+<th><code>--outgroup</code></th>
+<th>Any outgroup quorum flag?</th>
+<th><code>--max-outgroup-count</code> default</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>not set</td>
+<td>—</td>
+<td>outgroup size (no-op)</td>
+</tr>
+<tr>
+<td>set</td>
+<td>no</td>
+<td><strong>0</strong> — no outgroup genome may carry the k-mer</td>
+</tr>
+<tr>
+<td>set</td>
+<td>yes</td>
+<td>outgroup size — user controls quorum explicitly</td>
+</tr>
+</tbody>
+</table>
+<p>"Any ingroup quorum flag" means any of: <code>--min-count</code>, <code>--max-count</code>, <code>--min-frac</code>, <code>--max-frac</code>.<br />
+"Any outgroup quorum flag" means any of: <code>--min-outgroup-count</code>, <code>--max-outgroup-count</code>, <code>--min-outgroup-frac</code>, <code>--max-outgroup-frac</code>.</p>
+<p><strong>Why this rule?</strong> Setting any quorum flag signals explicit intent — the defaults are there to help when the user omits quorum entirely, not to interfere with deliberate constraints. Mixing implicit and explicit quorum on the same group would risk silent incoherence (e.g. <code>--max-count 0</code> with an implicit <code>--min-frac 1.0</code>).</p>
+<p>All other bounds default to 0 / group size / 0.0 / 1.0 regardless of whether groups are declared.</p>
+<h3 id="validation">Validation</h3>
+<p>After resolving defaults, the following are checked and cause an immediate error:</p>
+<table>
+<thead>
+<tr>
+<th>Condition</th>
+<th>Error</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>--min-count &gt; --max-count</code></td>
+<td>incoherent bounds</td>
+</tr>
+<tr>
+<td><code>--min-frac &gt; --max-frac</code></td>
+<td>incoherent bounds</td>
+</tr>
+<tr>
+<td><code>--min-outgroup-count &gt; --max-outgroup-count</code></td>
+<td>incoherent bounds</td>
+</tr>
+<tr>
+<td><code>--min-outgroup-frac &gt; --max-outgroup-frac</code></td>
+<td>incoherent bounds</td>
+</tr>
+<tr>
+<td>any fraction outside <code>[0.0, 1.0]</code></td>
+<td>invalid value</td>
+</tr>
+</tbody>
+</table>
+<p>The check applies to the <strong>effective</strong> values (after defaults are resolved), so an explicit <code>--max-frac 0.5</code> with an implicit <code>--min-frac 1.0</code> would have been caught — but the rule above prevents that situation from arising in the first place.</p>
 <p>Fractions are computed over the size of the classified group, not over total
 genome count. An empty group (no genome classified as ingroup/outgroup) never
 triggers a filter failure.</p>
+<h3 id="conservative-rounding-of-fraction-thresholds">Conservative rounding of fraction thresholds</h3>
+<p>When a fraction threshold <code>F</code> is applied to a group of size <code>N</code>, the effective
+integer threshold is determined by the direction of the bound:</p>
+<table>
+<thead>
+<tr>
+<th>Bound</th>
+<th>Effective count</th>
+<th>Rounding</th>
+<th>Rationale</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>--min-frac F</code></td>
+<td>k-mer in ≥ ⌈F·N⌉ genomes</td>
+<td><strong>ceil</strong></td>
+<td>stricter — a kmer present in exactly ⌊F·N⌋ genomes does not meet the fraction</td>
+</tr>
+<tr>
+<td><code>--max-frac F</code></td>
+<td>k-mer in ≤ ⌊F·N⌋ genomes</td>
+<td><strong>floor</strong></td>
+<td>stricter — a kmer present in ⌈F·N⌉ genomes already exceeds the fraction</td>
+</tr>
+</tbody>
+</table>
+<p>The same rule applies symmetrically to <code>--min-outgroup-frac</code> (ceil) and
+<code>--max-outgroup-frac</code> (floor). The outgroup direction is not inverted: the
+conservative rounding depends only on whether the bound is a minimum or a
+maximum, not on which group it applies to.</p>
+<p><strong>Example</strong> — <code>--min-frac 0.5</code> with an ingroup of 3 genomes:
+<code>⌈0.5 × 3⌉ = ⌈1.5⌉ = 2</code> → at least 2 of 3 ingroup genomes must carry the k-mer.</p>
+<p><strong>Implementation note</strong> — the filter evaluates <code>n / denom &lt; min_frac</code> directly
+(integer <code>n</code>, float comparison) rather than pre-computing <code>⌈F·N⌉</code>. This is
+mathematically equivalent for integer counts: <code>n / N &lt; F</code> ↔ <code>n &lt; F·N</code> ↔
+<code>n ≤ ⌈F·N⌉ − 1</code> ↔ <code>n &lt; ⌈F·N⌉</code>. No explicit rounding is needed.</p>
 <h2 id="examples">Examples</h2>
 <p>Keep k-mers specific to <em>Betula nana</em> — present in at least 2 <em>B. nana</em> genomes
 and absent from every other genome in the index:</p>
-<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>rebuild<span class="w"> </span>src<span class="w"> </span>--output<span class="w"> </span>dst<span class="w"> </span><span class="se">\</span>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>filter<span class="w"> </span>src<span class="w"> </span>--output<span class="w"> </span>dst<span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--ingroup<span class="w">  </span><span class="s2">&quot;species=Betula_nana&quot;</span><span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--outgroup<span class="w"> </span><span class="s2">&quot;*&quot;</span><span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--min-count<span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="se">\</span>
@@ -1492,7 +2069,7 @@ and absent from every other genome in the index:</p>
 </code></pre></div>
 <p>Keep k-mers found in at least 2 <em>Betula nana</em> genomes and absent from all
 other <em>Betula</em>:</p>
-<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>rebuild<span class="w"> </span>src<span class="w"> </span>--output<span class="w"> </span>dst<span class="w"> </span><span class="se">\</span>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>filter<span class="w"> </span>src<span class="w"> </span>--output<span class="w"> </span>dst<span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--ingroup<span class="w">  </span><span class="s2">&quot;species=Betula_nana&quot;</span><span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--outgroup<span class="w"> </span><span class="s2">&quot;genus=Betula&quot;</span><span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--min-count<span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="se">\</span>
@@ -1500,21 +2077,28 @@ other <em>Betula</em>:</p>
 </code></pre></div>
 <p>Use taxonomic paths — keep k-mers present in ≥ 50 % of the <em>Betula</em> clade
 and in fewer than 10 % of everything outside <em>Betulaceae</em>:</p>
-<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>rebuild<span class="w"> </span>src<span class="w"> </span>--output<span class="w"> </span>dst<span class="w"> </span><span class="se">\</span>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>filter<span class="w"> </span>src<span class="w"> </span>--output<span class="w"> </span>dst<span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--ingroup<span class="w">  </span><span class="s2">&quot;taxon~/Betulaceae/Betula&quot;</span><span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--outgroup<span class="w"> </span><span class="s2">&quot;taxon!~/Betulaceae&quot;</span><span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--min-frac<span class="w"> </span><span class="m">0</span>.5<span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--max-outgroup-frac<span class="w"> </span><span class="m">0</span>.1
 </code></pre></div>
 <p>Multiple outgroup predicates (OR): exclude k-mers present in <em>Alnus</em> or <em>Carpinus</em>:</p>
-<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>rebuild<span class="w"> </span>src<span class="w"> </span>--output<span class="w"> </span>dst<span class="w"> </span><span class="se">\</span>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>filter<span class="w"> </span>src<span class="w"> </span>--output<span class="w"> </span>dst<span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--ingroup<span class="w">  </span><span class="s2">&quot;genus=Betula&quot;</span><span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--outgroup<span class="w"> </span><span class="s2">&quot;genus=Alnus&quot;</span><span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--outgroup<span class="w"> </span><span class="s2">&quot;genus=Carpinus&quot;</span><span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--max-outgroup-count<span class="w"> </span><span class="m">0</span>
 </code></pre></div>
-<p>The same flags work identically for <code>dump</code> and <code>unitig</code>. To dump only k-mers
-specific to <em>Betula nana</em>:</p>
+<p>Noise-tolerant core — keep k-mers present in <em>all but one</em> ingroup genome
+(<code>-1</code> = <code>n−1</code>) and absent from <em>all but one</em> of the outgroup:</p>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>filter<span class="w"> </span>src<span class="w"> </span>--output<span class="w"> </span>dst<span class="w"> </span><span class="se">\</span>
+<span class="w">  </span>--ingroup<span class="w">  </span><span class="s2">&quot;genus=Betula&quot;</span><span class="w"> </span><span class="se">\</span>
+<span class="w">  </span>--outgroup<span class="w"> </span><span class="s2">&quot;*&quot;</span><span class="w"> </span><span class="se">\</span>
+<span class="w">  </span>--min-count<span class="w"> </span>-1<span class="w"> </span><span class="se">\</span>
+<span class="w">  </span>--max-outgroup-count<span class="w"> </span>-1
+</code></pre></div>
+<p>To dump only k-mers specific to <em>Betula nana</em>:</p>
 <div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>dump<span class="w"> </span>myindex<span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--ingroup<span class="w">  </span><span class="s2">&quot;species=Betula_nana&quot;</span><span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--outgroup<span class="w"> </span><span class="s2">&quot;*&quot;</span><span class="w"> </span><span class="se">\</span>
@@ -1528,6 +2112,21 @@ specific to <em>Betula nana</em>:</p>
 <span class="w">  </span>--min-count<span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--max-outgroup-count<span class="w"> </span><span class="m">0</span>
 </code></pre></div>
+<h2 id="command-specific-options">Command-specific options</h2>
+<h3 id="dump-head-n"><code>dump --head N</code></h3>
+<p>Stops output after the first N k-mers that pass all active filters.
+Iteration terminates immediately — subsequent partitions and layers are not scanned.
+Useful for quick inspection of large indexes without loading the entire dataset.</p>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>dump<span class="w"> </span>myindex<span class="w"> </span>--head<span class="w"> </span><span class="m">100</span>
+obikmer<span class="w"> </span>dump<span class="w"> </span>myindex<span class="w"> </span>--head<span class="w"> </span><span class="m">20</span><span class="w"> </span>--ingroup<span class="w"> </span><span class="s2">&quot;species=Betula_nana&quot;</span><span class="w"> </span>--min-count<span class="w"> </span><span class="m">1</span>
+</code></pre></div>
+<h3 id="phylo-presence-threshold-n"><code>phylo --presence-threshold N</code></h3>
+<p>When computing Jaccard distance on a <strong>count index</strong>, a k-mer is considered present in a genome if its count is ≥ N (default 1).
+This option is independent of the <code>--presence-threshold</code> used in filtering.</p>
+<div class="highlight"><pre><span></span><code><span class="c1"># Jaccard treating kmers with count ≥ 2 as present</span>
+obikmer<span class="w"> </span>phylo<span class="w"> </span>myindex<span class="w"> </span>--metric<span class="w"> </span>jaccard<span class="w"> </span>--presence-threshold<span class="w"> </span><span class="m">2</span>
+</code></pre></div>
+<p>This parameter has no effect on presence/absence indexes (where values are already 0/1) or on metrics other than Jaccard.</p>
 <h2 id="implementation">Implementation</h2>
 <ul>
 <li>
@@ -1539,14 +2138,14 @@ specific to <em>Betula nana</em>:</p>
 </li>
 <li>
 <p><strong><code>obikmer::cmd::predicate::FilterArgs</code></strong> — shared <code>clap</code> argument group
-  embedded via <code>#[command(flatten)]</code> in <code>RebuildArgs</code>, <code>DumpArgs</code>, and
+  embedded via <code>#[command(flatten)]</code> in <code>FilterArgs</code>, <code>DumpArgs</code>, and
   <code>UnitigArgs</code>. <code>FilterArgs::build_filters()</code> returns a ready-to-use filter
   list.</p>
 </li>
 <li>
 <p><strong><code>obikpartitionner::KmerPartition::iter_partition_kmers</code></strong> — accepts
   <code>filters: &amp;[Box&lt;dyn KmerFilter&gt;]</code> and applies them per-kmer before invoking
-  the callback. <code>rebuild</code>, <code>dump</code>, and <code>unitig</code> all go through this single
+  the callback. <code>filter</code>, <code>dump</code>, and <code>unitig</code> all go through this single
   entry point.</p>
 </li>
 </ul>
diff --git a/doc/implementation/kmer.refs/index.html b/DevDoc/implementation/kmer.refs/index.html
similarity index 86%
rename from doc/implementation/kmer.refs/index.html
rename to DevDoc/implementation/kmer.refs/index.html
index daaada5c..5fb4ced9 100644
--- a/doc/implementation/kmer.refs/index.html
+++ b/DevDoc/implementation/kmer.refs/index.html
@@ -178,6 +178,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
     
     
     
@@ -187,10 +214,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
         
           
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
             
   
   
@@ -208,8 +235,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -359,6 +386,34 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -381,10 +436,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
         
           
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
             
   
   
@@ -402,8 +457,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -784,14 +839,98 @@
   
   
     <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
   
 
     
@@ -827,10 +966,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
         
           
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
             
   
   
@@ -848,8 +987,8 @@
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           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -915,6 +1054,90 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
diff --git a/doc/implementation/kmer/index.html b/DevDoc/implementation/kmer/index.html
similarity index 92%
rename from doc/implementation/kmer/index.html
rename to DevDoc/implementation/kmer/index.html
index a9a332f3..060b0c84 100644
--- a/doc/implementation/kmer/index.html
+++ b/DevDoc/implementation/kmer/index.html
@@ -182,6 +182,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
     
     
     
@@ -191,10 +218,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
         
           
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
             
   
   
@@ -212,8 +239,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -363,6 +390,34 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -387,10 +442,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
         
           
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
             
   
   
@@ -408,8 +463,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_4">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -925,14 +980,98 @@
   
   
     <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
   
 
     
@@ -968,10 +1107,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
         
           
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
             
   
   
@@ -989,8 +1128,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -1056,6 +1195,90 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
diff --git a/doc/implementation/merge.refs/index.html b/DevDoc/implementation/merge.refs/index.html
similarity index 87%
rename from doc/implementation/merge.refs/index.html
rename to DevDoc/implementation/merge.refs/index.html
index ff3be533..81792f6b 100644
--- a/doc/implementation/merge.refs/index.html
+++ b/DevDoc/implementation/merge.refs/index.html
@@ -178,6 +178,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
     
     
     
@@ -187,10 +214,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
         
           
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
             
   
   
@@ -208,8 +235,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -359,6 +386,34 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -381,10 +436,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
         
           
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
             
   
   
@@ -402,8 +457,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -784,14 +839,98 @@
   
   
     <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
   
 
     
@@ -827,10 +966,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
         
           
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
             
   
   
@@ -848,8 +987,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -915,6 +1054,90 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
diff --git a/doc/implementation/merge/index.html b/DevDoc/implementation/merge/index.html
similarity index 93%
rename from doc/implementation/merge/index.html
rename to DevDoc/implementation/merge/index.html
index 1dc9363b..d8edd17a 100644
--- a/doc/implementation/merge/index.html
+++ b/DevDoc/implementation/merge/index.html
@@ -12,7 +12,7 @@
         <link rel="prev" href="../persistent_bit_vec/">
       
       
-        <link rel="next" href="../rebuild_filter/">
+        <link rel="next" href="../merge_parallelism/">
       
       
         
@@ -182,6 +182,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
     
     
     
@@ -191,10 +218,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
         
           
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
             
   
   
@@ -212,8 +239,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -363,6 +390,34 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -387,10 +442,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
         
           
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
             
   
   
@@ -408,8 +463,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_4">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -997,14 +1052,98 @@
   
   
     <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
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diff --git a/DevDoc/implementation/merge_parallelism/index.html b/DevDoc/implementation/merge_parallelism/index.html
new file mode 100644
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+  
+
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+  
+
+    
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+  
+  
+
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+
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+
+    
+  </span>
+  
+  
+
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+  
+
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+            
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+      <a href="../persistent_compact_int_vec/" class="md-nav__link">
+        
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+  
+  <span class="md-ellipsis">
+    
+  
+    PersistentCompactIntVec
+  
+
+    
+  </span>
+  
+  
+
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+  
+
+              
+            
+              
+                
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+  
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+      <a href="../persistent_bit_vec/" class="md-nav__link">
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+  
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+    
+  
+    PersistentBitVec
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
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+  
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+      <a href="../merge/" class="md-nav__link">
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+  
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+    Merge command
+  
+
+    
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+  
+  
+
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+
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+            
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+  
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+    
+  
+    Merge parallelism & memory
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+  
+
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+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
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+  
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+  
+  
+    <label class="md-nav__title" for="__toc">
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+      Table of contents
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+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#problem-observed" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Problem observed
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#root-cause" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Root cause
+      
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+  
+    <nav class="md-nav" aria-label="Root cause">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#the-merge-pipeline-per-partition" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        The merge pipeline per partition
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#unbounded-rayon-parallelism" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Unbounded Rayon parallelism
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#the-85-gb-single-allocation" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        The 8.5 GB single allocation
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#partition-size-distribution" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Partition size distribution
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#solution-lfd-scheduling-memory-budget-semaphore" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Solution: LFD scheduling + memory budget semaphore
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Solution: LFD scheduling + memory budget semaphore">
+      <ul class="md-nav__list">
+        
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+    <span class="md-ellipsis">
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+      
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+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#memorybudget-obisys" class="md-nav__link">
+    <span class="md-ellipsis">
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+      
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+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#adaptive-expansion-factor" class="md-nav__link">
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+  <a href="#ram-source" class="md-nav__link">
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+      
+        <li class="md-nav__item">
+  <a href="#problem-observed" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Problem observed
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#root-cause" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Root cause
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Root cause">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#the-merge-pipeline-per-partition" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        The merge pipeline per partition
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#unbounded-rayon-parallelism" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Unbounded Rayon parallelism
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#the-85-gb-single-allocation" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        The 8.5 GB single allocation
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#partition-size-distribution" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Partition size distribution
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#solution-lfd-scheduling-memory-budget-semaphore" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Solution: LFD scheduling + memory budget semaphore
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Solution: LFD scheduling + memory budget semaphore">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#principle" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Principle
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#memorybudget-obisys" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        MemoryBudget (obisys)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#adaptive-expansion-factor" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Adaptive expansion factor
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#ram-source" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        RAM source
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#diagnostic-report" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Diagnostic report
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#parameters" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Parameters
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+
+<h1 id="merge-parallelism-and-memory-pressure">Merge parallelism and memory pressure</h1>
+<h2 id="problem-observed">Problem observed</h2>
+<p>Running <code>obikmer merge</code> over 109 indexes (108 sources + 1 bootstrap) on a 192-core machine
+produces a fatal OOM during the <code>merge_partitions</code> stage:</p>
+<div class="highlight"><pre><span></span><code>memory allocation of 9126805520 bytes failed
+</code></pre></div>
+<p>A single allocation of ~8.5 GB fails. This is not an aggregate; it is one <code>malloc</code> call
+from hashbrown during a HashMap resize.</p>
+<hr />
+<h2 id="root-cause">Root cause</h2>
+<h3 id="the-merge-pipeline-per-partition">The merge pipeline per partition</h3>
+<div class="highlight"><pre><span></span><code>source unitigs.bin
+  → iter_indexed_canonical_kmers()
+  → GraphDeBruijn::push()       ← HashSet&lt;u64&gt; + 1 byte flags, all in RAM
+  → compute_degrees_and_mark_starts()
+  → try_for_each_unitig()
+  → unitigs.bin (new layer)
+  → Layer::build() → MPHF + evidence
+</code></pre></div>
+<p><code>GraphDeBruijn</code> is a <code>FastHashMap&lt;CanonicalKmer, AtomicU8&gt;</code> — a <code>HashSet&lt;u64&gt;</code> with
+one flag byte per node. Neighbor lookup is implicit: 4 probes into the same map.
+No edges are stored. The full kmer set of one partition must reside in RAM
+simultaneously to compute degrees and mark unitig starts.</p>
+<p>The matrix builders that follow (pass 2) are mmapped files — they do <strong>not</strong> consume
+significant RAM. The pressure is entirely in pass 1.</p>
+<h3 id="unbounded-rayon-parallelism">Unbounded Rayon parallelism</h3>
+<p>With 192 cores, Rayon ran up to 192 partitions concurrently. Each partition built its
+own <code>GraphDeBruijn</code> accumulating all kmers absent from the destination. Peak memory =
+192 × peak_partition_hashset.</p>
+<h3 id="the-85-gb-single-allocation">The 8.5 GB single allocation</h3>
+<p>hashbrown allocates the entire backing array in one call when rehashing.
+At load factor 7/8: <code>capacity × (sizeof(K,V) + 1 control byte)</code>.
+For <code>(u64, AtomicU8)</code> with alignment: ~16 bytes per slot.</p>
+<div class="highlight"><pre><span></span><code>9 127 MB / 16 bytes ≈ 570 M slots → ~380 M new kmers in one partition
+</code></pre></div>
+<p>Plausible for the largest partition of 108 Salix/Betula sources (~450 Mbp each).</p>
+<hr />
+<h2 id="partition-size-distribution">Partition size distribution</h2>
+<p><code>obikmer utils --partition-stats</code> measures the sum of <code>unitigs.bin</code> file sizes
+per partition across all source indexes (pure <code>stat()</code> syscalls, negligible cost).</p>
+<p>Observed on a 9-genome pilot (256 partitions):</p>
+<table>
+<thead>
+<tr>
+<th>Stat</th>
+<th>Value</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>min</td>
+<td>30.5 MB</td>
+</tr>
+<tr>
+<td>max</td>
+<td>232.1 MB</td>
+</tr>
+<tr>
+<td>mean</td>
+<td>40.1 MB</td>
+</tr>
+<tr>
+<td>median</td>
+<td>37.2 MB</td>
+</tr>
+<tr>
+<td>p95</td>
+<td>47.1 MB</td>
+</tr>
+<tr>
+<td>max/median ratio</td>
+<td>6.23×</td>
+</tr>
+</tbody>
+</table>
+<p>The distribution is <strong>bimodal with a heavy tail</strong>:
+- 238/256 partitions in a narrow 30–50 MB band
+- 4 structurally extreme partitions (3–6× the median): 221, 233, 135, 191</p>
+<p>These correspond to minimizers over-represented in repetitive regions shared across
+all sources. They are extreme in every run on this dataset.</p>
+<p>With 109 sources, outlier partitions do not scale linearly: only kmers <strong>absent from
+the destination</strong> enter the GraphDeBruijn, and inter-source overlap is high for closely
+related species. Partition 221 is the likely trigger for the 8.5 GB crash.</p>
+<hr />
+<h2 id="solution-lfd-scheduling-memory-budget-semaphore">Solution: LFD scheduling + memory budget semaphore</h2>
+<h3 id="principle">Principle</h3>
+<p>Pre-sort partitions by <strong>decreasing estimated size</strong> (First Fit Decreasing — FFD),
+then schedule them through a <strong>continuous memory budget semaphore</strong>. Each worker
+acquires an estimated cost before starting and releases it on completion.</p>
+<p>Large partitions run first when the full budget is available; small partitions fill
+the gaps. No hard outlier threshold is needed.</p>
+<h3 id="memorybudget-obisys"><code>MemoryBudget</code> (<code>obisys</code>)</h3>
+<div class="highlight"><pre><span></span><code><span class="k">pub</span><span class="w"> </span><span class="k">struct</span><span class="w"> </span><span class="nc">MemoryBudget</span><span class="w"> </span><span class="p">{</span><span class="w"> </span><span class="err">…</span><span class="w"> </span><span class="p">}</span>
+
+<span class="k">impl</span><span class="w"> </span><span class="n">MemoryBudget</span><span class="w"> </span><span class="p">{</span>
+<span class="w">    </span><span class="k">pub</span><span class="w"> </span><span class="k">fn</span><span class="w"> </span><span class="nf">new</span><span class="p">(</span><span class="n">total</span><span class="p">:</span><span class="w"> </span><span class="kt">u64</span><span class="p">)</span><span class="w"> </span><span class="p">-&gt;</span><span class="w"> </span><span class="nc">Self</span><span class="p">;</span>
+<span class="w">    </span><span class="k">pub</span><span class="w"> </span><span class="k">fn</span><span class="w"> </span><span class="nf">acquire</span><span class="p">(</span><span class="o">&amp;</span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">cost</span><span class="p">:</span><span class="w"> </span><span class="kt">u64</span><span class="p">);</span><span class="w">  </span><span class="c1">// blocks until budget available</span>
+<span class="w">    </span><span class="k">pub</span><span class="w"> </span><span class="k">fn</span><span class="w"> </span><span class="nf">release</span><span class="p">(</span><span class="o">&amp;</span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">cost</span><span class="p">:</span><span class="w"> </span><span class="kt">u64</span><span class="p">);</span>
+<span class="w">    </span><span class="k">pub</span><span class="w"> </span><span class="k">fn</span><span class="w"> </span><span class="nf">peak_active</span><span class="p">(</span><span class="o">&amp;</span><span class="bp">self</span><span class="p">)</span><span class="w"> </span><span class="p">-&gt;</span><span class="w"> </span><span class="kt">usize</span><span class="p">;</span>
+<span class="p">}</span>
+</code></pre></div>
+<p>Non-deadlock guarantee: when <code>active == 0</code>, acquire always succeeds regardless of cost.
+Without this, a partition whose estimated cost exceeds the total budget would block forever.</p>
+<h3 id="adaptive-expansion-factor">Adaptive expansion factor</h3>
+<p>The expansion factor converts raw <code>unitigs.bin</code> bytes into an estimated GraphDeBruijn
+RAM footprint. hashbrown stores each kmer as <code>(u64, AtomicU8)</code> ≈ 16 bytes/kmer at 7/8
+load factor; unitig files encode ≈ 2 bits/base. The ratio depends on average unitig
+length (short unitigs: ~2×; long unitigs: up to ~50×).</p>
+<p><strong>Phase 1 — sequential pilot (worst partition)</strong></p>
+<p>The largest partition runs alone first. Its actual <code>g.len()</code> seeds the expansion factor
+before any parallel job starts. <code>FALLBACK_EXPANSION = 4×</code> is used only for empty partitions.</p>
+<div class="highlight"><pre><span></span><code><span class="kd">let</span><span class="w"> </span><span class="n">worst_g_len</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">dst_partition</span><span class="p">.</span><span class="n">merge_partition</span><span class="p">(</span><span class="n">worst_id</span><span class="p">,</span><span class="w"> </span><span class="err">…</span><span class="p">)</span><span class="o">?</span><span class="p">;</span>
+<span class="c1">//                              ↑ now returns SKResult&lt;usize&gt; (was SKResult&lt;()&gt;)</span>
+
+<span class="kd">let</span><span class="w"> </span><span class="n">seed_expansion</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">worst_g_len</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="kt">u64</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="mi">16</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="mi">1000</span><span class="w"> </span><span class="o">/</span><span class="w"> </span><span class="n">worst_bytes</span><span class="p">;</span>
+<span class="kd">let</span><span class="w"> </span><span class="n">max_expansion</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">AtomicU64</span><span class="p">::</span><span class="n">new</span><span class="p">(</span><span class="n">seed_expansion</span><span class="p">);</span>
+</code></pre></div>
+<p><strong>Phase 2 — parallel with adaptive updates</strong></p>
+<div class="highlight"><pre><span></span><code><span class="n">order</span><span class="p">[</span><span class="mi">1</span><span class="o">..</span><span class="p">].</span><span class="n">into_par_iter</span><span class="p">().</span><span class="n">for_each</span><span class="p">(</span><span class="o">|&amp;</span><span class="n">i</span><span class="o">|</span><span class="w"> </span><span class="p">{</span>
+<span class="w">    </span><span class="kd">let</span><span class="w"> </span><span class="n">cost</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">partition_sizes</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="n">max_expansion</span><span class="p">.</span><span class="n">load</span><span class="p">(</span><span class="n">Relaxed</span><span class="p">)</span><span class="w"> </span><span class="o">/</span><span class="w"> </span><span class="mi">1000</span><span class="p">;</span>
+<span class="w">    </span><span class="n">budget</span><span class="p">.</span><span class="n">acquire</span><span class="p">(</span><span class="n">cost</span><span class="p">);</span>
+<span class="w">    </span><span class="kd">let</span><span class="w"> </span><span class="n">g_len</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">dst_partition</span><span class="p">.</span><span class="n">merge_partition</span><span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="w"> </span><span class="err">…</span><span class="p">)</span><span class="o">?</span><span class="p">;</span>
+<span class="w">    </span><span class="n">budget</span><span class="p">.</span><span class="n">release</span><span class="p">(</span><span class="n">cost</span><span class="p">);</span><span class="w">          </span><span class="c1">// releases estimated cost, not actual</span>
+
+<span class="w">    </span><span class="kd">let</span><span class="w"> </span><span class="n">actual</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">g_len</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="kt">u64</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="mi">16</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="mi">1000</span><span class="w"> </span><span class="o">/</span><span class="w"> </span><span class="n">partition_sizes</span><span class="p">[</span><span class="n">i</span><span class="p">];</span>
+<span class="w">    </span><span class="n">max_expansion</span><span class="p">.</span><span class="n">fetch_max</span><span class="p">(</span><span class="n">actual</span><span class="p">,</span><span class="w"> </span><span class="n">Relaxed</span><span class="p">);</span><span class="w">  </span><span class="c1">// always pessimistic (max)</span>
+<span class="p">});</span>
+</code></pre></div>
+<p><code>budget.release(cost)</code> uses the estimated cost, not the actual one. The budget tracks
+reservations, not physical RAM; each partition pays what it promised at acquisition.</p>
+<p><strong>On the safety margin</strong></p>
+<p>There is no separate multiplier <code>k</code>. It is redundant with <code>budget_fraction</code>: both
+reduce effective concurrency by the same amount. A single parameter is easier to
+calibrate. <code>budget_fraction = 0.5</code> (default) reserves half of available RAM for the
+OS, MPHF build, pass 2, and estimation error.</p>
+<p><code>--budget-fraction</code> is exposed as a CLI flag — the only escape hatch for pathological
+cases (extreme repetitive content, unusually long unitigs) that still cause OOM.</p>
+<h3 id="ram-source">RAM source</h3>
+<p><code>obisys::available_memory_bytes()</code> — wraps <code>sysinfo::System::available_memory()</code>,
+falls back to <code>total / 2</code> on macOS when the memory compressor returns 0.</p>
+<hr />
+<h2 id="diagnostic-report">Diagnostic report</h2>
+<p>After the parallel phase, <code>merge_partition</code> emits a structured report via <code>tracing::info!</code>:</p>
+<div class="highlight"><pre><span></span><code>─── merge_partitions memory report ───
+  available RAM : 512.0 GB   budget 50% = 256.0 GB
+  expansion factor — seed: 4.2×  final max: 6.1×  (mean: 1.8×  median: 1.6×)
+  peak concurrent workers: 42
+  expansion factor distribution (256 partitions with data):
+     0.50× –  1.25× │██████████████████████████████ 148
+     1.25× –  2.00× │████████████████████████        82
+     …
+     5.50× –  6.25× │█                                2
+  top partitions by actual expansion factor:
+    partition  221 : 6.10×  (232.1 MB unitigs → 48M kmers, reserved at 4.20×)
+    partition  135 : 5.82×  (127.3 MB unitigs → 24M kmers, reserved at 4.20×)
+    …
+──────────────────────────────────────
+</code></pre></div>
+<p>Fields useful for diagnosis:</p>
+<table>
+<thead>
+<tr>
+<th>Field</th>
+<th>Interpretation</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>seed</code> vs <code>final max</code> expansion</td>
+<td>gap indicates partitions with higher expansion than the worst-by-size</td>
+</tr>
+<tr>
+<td><code>reserved at X×</code></td>
+<td>the factor used at acquisition; if much lower than actual, the budget was under-reserved for that partition</td>
+</tr>
+<tr>
+<td><code>peak concurrent workers</code></td>
+<td>effective parallelism achieved under the budget constraint</td>
+</tr>
+<tr>
+<td><code>mean</code> / <code>median</code> expansion</td>
+<td>typical dataset characteristic; stable across runs on the same data</td>
+</tr>
+</tbody>
+</table>
+<hr />
+<h2 id="parameters">Parameters</h2>
+<table>
+<thead>
+<tr>
+<th>Parameter</th>
+<th>Default</th>
+<th>CLI flag</th>
+<th>Notes</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>fallback_expansion</code></td>
+<td>4×</td>
+<td>—</td>
+<td>seed for empty partitions only</td>
+</tr>
+<tr>
+<td><code>budget_fraction</code></td>
+<td>0.5</td>
+<td><code>--budget-fraction</code></td>
+<td>reduce if OOM persists</td>
+</tr>
+<tr>
+<td>RAM source</td>
+<td><code>obisys::available_memory_bytes()</code></td>
+<td>—</td>
+<td>falls back to <code>total/2</code> on macOS</td>
+</tr>
+</tbody>
+</table>
+
+
+
+
+
+
+
+
+
+
+
+
+                
+              </article>
+            </div>
+          
+          
+<script>var target=document.getElementById(location.hash.slice(1));target&&target.name&&(target.checked=target.name.startsWith("__tabbed_"))</script>
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diff --git a/doc/implementation/mphf.refs/index.html b/DevDoc/implementation/mphf.refs/index.html
similarity index 87%
rename from doc/implementation/mphf.refs/index.html
rename to DevDoc/implementation/mphf.refs/index.html
index 1cbb8908..522d221a 100644
--- a/doc/implementation/mphf.refs/index.html
+++ b/DevDoc/implementation/mphf.refs/index.html
@@ -178,6 +178,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
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+  
+
+      </a>
+    </li>
+  
+
+    
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+  
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@@ -187,10 +214,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
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+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
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+  
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+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -381,10 +436,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
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@@ -784,14 +839,98 @@
   
   
     <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
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+
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+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
   
 
     
@@ -827,10 +966,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
         
           
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+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
             
   
   
@@ -848,8 +987,8 @@
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           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -915,6 +1054,90 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
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diff --git a/doc/implementation/mphf/index.html b/DevDoc/implementation/mphf/index.html
similarity index 93%
rename from doc/implementation/mphf/index.html
rename to DevDoc/implementation/mphf/index.html
index 5d4b4dde..a6d6ce9a 100644
--- a/doc/implementation/mphf/index.html
+++ b/DevDoc/implementation/mphf/index.html
@@ -182,6 +182,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
     
     
     
@@ -191,10 +218,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
         
           
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
             
   
   
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             <span class="md-nav__icon md-icon"></span>
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -363,6 +390,34 @@
 
               
             
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+  
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+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -387,10 +442,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
         
           
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
             
   
   
@@ -408,8 +463,8 @@
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_4">
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@@ -1003,14 +1058,98 @@
   
   
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-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
         
   
   
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-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
   
 
     
@@ -1046,10 +1185,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
         
           
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
             
   
   
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
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             <span class="md-nav__icon md-icon"></span>
             
   
@@ -1134,6 +1273,90 @@
 
               
             
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+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
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+<ul class="md-nav__list" data-md-component="toc" data-md-scrollfix="">
+<li class="md-nav__item">
+<a class="md-nav__link" href="#module-structure">
+<span class="md-ellipsis">
+      
+        Module structure
+      
+    </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="#compact-int-encoding">
+<span class="md-ellipsis">
+      
+        Compact int encoding
+      
+    </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="#view-types">
+<span class="md-ellipsis">
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+        View types
+      
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+<ul class="md-nav__list">
+<li class="md-nav__item">
+<a class="md-nav__link" href="#bitsliceviewa">
+<span class="md-ellipsis">
+      
+        BitSliceView&lt;'a&gt;
+      
+    </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="#intsliceviewa">
+<span class="md-ellipsis">
+      
+        IntSliceView&lt;'a&gt;
+      
+    </span>
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+</nav>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="#concrete-types">
+<span class="md-ellipsis">
+      
+        Concrete types
+      
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+<li class="md-nav__item">
+<a class="md-nav__link" href="#persistentbitvec-persistentbitvecbuilder">
+<span class="md-ellipsis">
+      
+        PersistentBitVec / PersistentBitVecBuilder
+      
+    </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="#persistentcompactintvec-persistentcompactintvecbuilder">
+<span class="md-ellipsis">
+      
+        PersistentCompactIntVec / PersistentCompactIntVecBuilder
+      
+    </span>
+</a>
+</li>
+</ul>
+</nav>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="#matrix-types">
+<span class="md-ellipsis">
+      
+        Matrix types
+      
+    </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="#aggregation-traits-matrix-level">
+<span class="md-ellipsis">
+      
+        Aggregation traits (matrix level)
+      
+    </span>
+</a>
+<nav aria-label="Aggregation traits (matrix level)" class="md-nav">
+<ul class="md-nav__list">
+<li class="md-nav__item">
+<a class="md-nav__link" href="#columnweights">
+<span class="md-ellipsis">
+      
+        ColumnWeights
+      
+    </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="#countpartials">
+<span class="md-ellipsis">
+      
+        CountPartials
+      
+    </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="#bitpartials">
+<span class="md-ellipsis">
+      
+        BitPartials
+      
+    </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="#mash-distance">
+<span class="md-ellipsis">
+      
+        Mash distance
+      
+    </span>
+</a>
+</li>
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+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="#temp-file-backed-types">
+<span class="md-ellipsis">
+      
+        Temp-file-backed types
+      
+    </span>
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+<nav aria-label="Temp-file-backed types" class="md-nav">
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+<li class="md-nav__item">
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+<span class="md-ellipsis">
+      
+        Lifecycle
+      
+    </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="#tempcompactintvec-tempcompactintvecbuilder">
+<span class="md-ellipsis">
+      
+        TempCompactIntVec / TempCompactIntVecBuilder
+      
+    </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="#tempbitvec-tempbitvecbuilder">
+<span class="md-ellipsis">
+      
+        TempBitVec / TempBitVecBuilder
+      
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+<li class="md-nav__item">
+<a class="md-nav__link" href="#filter-select-api">
+<span class="md-ellipsis">
+      
+        Filter / Select API
+      
+    </span>
+</a>
+<nav aria-label="Filter / Select API" class="md-nav">
+<ul class="md-nav__list">
+<li class="md-nav__item">
+<a class="md-nav__link" href="#colgroup">
+<span class="md-ellipsis">
+      
+        ColGroup
+      
+    </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="#composition-axis">
+<span class="md-ellipsis">
+      
+        Composition axis
+      
+    </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="#matrixgroupops">
+<span class="md-ellipsis">
+      
+        MatrixGroupOps
+      
+    </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="#add_col_from-matrix-builder-integration">
+<span class="md-ellipsis">
+      
+        add_col_from — matrix builder integration
+      
+    </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="#mask_with">
+<span class="md-ellipsis">
+      
+        mask_with
+      
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+</div>
+</div>
+</div>
+<div class="md-content" data-md-component="content">
+<article class="md-content__inner md-typeset">
+<h1 id="obicompactvec-complete-reference">obicompactvec — Complete Reference</h1>
+<h2 id="module-structure">Module structure</h2>
+<div class="highlight"><pre><span></span><code>src/obicompactvec/src/
+  lib.rs            public re-exports
+  views.rs          BitSliceView&lt;'a&gt;, IntSliceView&lt;'a&gt; — zero-copy read views
+  traits.rs         ColumnWeights, CountPartials, BitPartials (matrix aggregation)
+  bitvec.rs         PersistentBitVec, PersistentBitVecBuilder, BitIter
+  reader.rs         PersistentCompactIntVec (read-only)
+  builder.rs        PersistentCompactIntVecBuilder (read-write)
+  tempintvec.rs     TempCompactIntVec, TempCompactIntVecBuilder (temp-file-backed)
+  tempbitvec.rs     TempBitVec, TempBitVecBuilder (temp-file-backed)
+  bitmatrix.rs      PersistentBitMatrix, PersistentBitMatrixBuilder
+  intmatrix.rs      PersistentCompactIntMatrix, PersistentCompactIntMatrixBuilder
+  colgroup.rs       ColGroup, MatrixGroupOps trait
+  format.rs         file format constants, encode/decode helpers
+  layer_meta.rs     LayerMeta (column metadata)
+  meta.rs           matrix metadata
+</code></pre></div>
+<pre class="mermaid"><code>graph TD
+    views --&gt; bitvec
+    views --&gt; builder
+    views --&gt; tempbitvec
+    views --&gt; tempintvec
+    views --&gt; bitmatrix
+    views --&gt; intmatrix
+    format --&gt; reader
+    format --&gt; builder
+    reader --&gt; intmatrix
+    reader --&gt; tempintvec
+    builder --&gt; intmatrix
+    builder --&gt; tempintvec
+    bitvec --&gt; tempbitvec
+    bitvec --&gt; bitmatrix
+    tempintvec --&gt; intmatrix
+    tempintvec --&gt; bitmatrix
+    tempbitvec --&gt; intmatrix
+    tempbitvec --&gt; bitmatrix
+    colgroup --&gt; intmatrix
+    colgroup --&gt; bitmatrix
+    layer_meta --&gt; bitmatrix
+    layer_meta --&gt; intmatrix
+    meta --&gt; bitmatrix
+    meta --&gt; intmatrix</code></pre>
+<hr/>
+<h2 id="compact-int-encoding">Compact int encoding</h2>
+<p>All integer vectors use the same two-tier encoding regardless of storage backend.</p>
+<p><strong>Primary array</strong> — one <code>u8</code> per slot:</p>
+<ul>
+<li>Values <strong>0–254</strong> are stored directly. No overhead.</li>
+<li>Value <strong>255 is a sentinel</strong>: the slot's actual value is ≥ 255 and lives in the overflow store.</li>
+</ul>
+<p><strong>Overflow store</strong> — maps slot index to a <code>u32</code> value ≥ 255:</p>
+<ul>
+<li>In <code>PersistentCompactIntVecBuilder</code>: a <code>HashMap&lt;usize, u32&gt;</code> in RAM.</li>
+<li>In <code>PersistentCompactIntVec</code> (reader): a sorted <code>[(slot: u64, value: u32)]</code> array in the mmap, with a sparse L1-resident index for binary search.</li>
+</ul>
+<pre class="mermaid"><code>flowchart LR
+    slot --&gt; P["primary[slot]: u8"]
+    P --&gt;|"&lt; 255"| V["value = byte (0–254)"]
+    P --&gt;|"= 255 sentinel"| OV["overflow store"]
+    OV --&gt;|"Builder"| HM["HashMap&amp;lt;usize, u32&amp;gt;\nin RAM"]
+    OV --&gt;|"PersistentCompactIntVec"| SA["sorted [(slot,value)] in mmap\n+ sparse L1 index"]</code></pre>
+<p><strong>Key property — sentinel 255 = +∞ on <code>u8</code>:</strong></p>
+<ul>
+<li><code>min(a, 255) = a</code> for all <code>a ≤ 254</code> → correct when only one side is overflow</li>
+<li><code>max(a, 255) = 255</code> → correct sentinel when either side is overflow</li>
+<li>Only the <strong>both-overflow</strong> case requires reading actual values from the overflow store.</li>
+</ul>
+<p>In practice, k (overflow count) ≪ n (total slots). Observed genomic data: ~0.07% of kmer slots are in overflow.</p>
+<hr/>
+<h2 id="view-types">View types</h2>
+<p>The previous trait hierarchy (<code>BitSlice</code>, <code>BitSliceMut</code>, <code>IntSlice</code>, <code>IntSliceMut</code>) has been replaced by two concrete zero-copy view structs with inherent methods. Views are <strong><code>Copy</code></strong> — passing them is free. All read operations live on these two types.</p>
+<h3 id="bitsliceviewa"><code>BitSliceView&lt;'a&gt;</code></h3>
+<div class="highlight"><pre><span></span><code><span class="cp">#[derive(Clone, Copy)]</span>
+<span class="k">pub</span><span class="w"> </span><span class="k">struct</span><span class="w"> </span><span class="nc">BitSliceView</span><span class="o">&lt;'</span><span class="na">a</span><span class="o">&gt;</span><span class="w"> </span><span class="p">{</span><span class="w"> </span><span class="k">pub</span><span class="p">(</span><span class="k">crate</span><span class="p">)</span><span class="w"> </span><span class="n">words</span><span class="p">:</span><span class="w"> </span><span class="kp">&amp;</span><span class="o">'</span><span class="na">a</span><span class="w"> </span><span class="p">[</span><span class="kt">u64</span><span class="p">],</span><span class="w"> </span><span class="k">pub</span><span class="p">(</span><span class="k">crate</span><span class="p">)</span><span class="w"> </span><span class="n">n</span><span class="p">:</span><span class="w"> </span><span class="kt">usize</span><span class="w"> </span><span class="p">}</span>
+</code></pre></div>
+<p>Bit <code>i</code> is at <code>words[i &gt;&gt; 6]</code> bit <code>i &amp; 63</code> (LSB-first). Padding bits in the last word are zero.</p>
+<table>
+<thead>
+<tr>
+<th>Method</th>
+<th>Cost</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>len()</code>, <code>is_empty()</code></td>
+<td>O(1)</td>
+</tr>
+<tr>
+<td><code>get(slot)</code></td>
+<td>O(1)</td>
+</tr>
+<tr>
+<td><code>count_ones()</code></td>
+<td>POPCNT per word, O(n/64)</td>
+</tr>
+<tr>
+<td><code>count_zeros()</code></td>
+<td><code>n − count_ones()</code>, O(n/64)</td>
+</tr>
+<tr>
+<td><code>iter() -&gt; BitSliceIter&lt;'a&gt;</code></td>
+<td>O(1) setup, O(n) iteration</td>
+</tr>
+<tr>
+<td><code>partial_jaccard_dist(other: BitSliceView)</code></td>
+<td><code>(a&amp;b).popcount</code>, <code>(a\|b).popcount</code> per word, O(n/64)</td>
+</tr>
+<tr>
+<td><code>jaccard_dist(other: BitSliceView)</code></td>
+<td>from partial, O(n/64)</td>
+</tr>
+<tr>
+<td><code>hamming_dist(other: BitSliceView)</code></td>
+<td><code>(a^b).popcount</code> per word, O(n/64)</td>
+</tr>
+</tbody>
+</table>
+<p><code>BitSliceIter&lt;'a&gt;</code>: word-level scan; one word per 64 iterations.</p>
+<h3 id="intsliceviewa"><code>IntSliceView&lt;'a&gt;</code></h3>
+<div class="highlight"><pre><span></span><code><span class="cp">#[derive(Clone, Copy)]</span>
+<span class="k">pub</span><span class="w"> </span><span class="k">struct</span><span class="w"> </span><span class="nc">IntSliceView</span><span class="o">&lt;'</span><span class="na">a</span><span class="o">&gt;</span><span class="w"> </span><span class="p">{</span>
+<span class="w">    </span><span class="k">pub</span><span class="p">(</span><span class="k">crate</span><span class="p">)</span><span class="w"> </span><span class="n">primary</span><span class="p">:</span><span class="w">      </span><span class="kp">&amp;</span><span class="o">'</span><span class="na">a</span><span class="w"> </span><span class="p">[</span><span class="kt">u8</span><span class="p">],</span>
+<span class="w">    </span><span class="k">pub</span><span class="p">(</span><span class="k">crate</span><span class="p">)</span><span class="w"> </span><span class="n">overflow_raw</span><span class="p">:</span><span class="w"> </span><span class="kp">&amp;</span><span class="o">'</span><span class="na">a</span><span class="w"> </span><span class="p">[</span><span class="kt">u8</span><span class="p">],</span><span class="w">   </span><span class="c1">// sorted [(slot:u64, value:u32)] entries</span>
+<span class="w">    </span><span class="k">pub</span><span class="p">(</span><span class="k">crate</span><span class="p">)</span><span class="w"> </span><span class="n">n_overflow</span><span class="p">:</span><span class="w">   </span><span class="kt">usize</span><span class="p">,</span>
+<span class="w">    </span><span class="k">pub</span><span class="p">(</span><span class="k">crate</span><span class="p">)</span><span class="w"> </span><span class="n">n</span><span class="p">:</span><span class="w">            </span><span class="kt">usize</span><span class="p">,</span>
+<span class="p">}</span>
+</code></pre></div>
+<p><code>overflow_raw</code> contains <code>n_overflow</code> entries of <code>OVERFLOW_ENTRY_SIZE</code> bytes each, sorted by slot. The sort invariant is established at <code>close()</code>/<code>freeze()</code> time.</p>
+<table>
+<thead>
+<tr>
+<th>Method</th>
+<th>Cost</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>len()</code>, <code>is_empty()</code></td>
+<td>O(1)</td>
+</tr>
+<tr>
+<td><code>primary_bytes()</code></td>
+<td>O(1)</td>
+</tr>
+<tr>
+<td><code>overflow_entries() -&gt; impl Iterator&lt;(usize,u32)&gt;</code></td>
+<td>O(n_overflow) iteration</td>
+</tr>
+<tr>
+<td><code>get(slot)</code></td>
+<td>O(1) primary; binary search O(log k) for overflow slots</td>
+</tr>
+<tr>
+<td><code>iter() -&gt; IntSliceViewIter&lt;'a&gt;</code></td>
+<td>merge scan, O(n + k)</td>
+</tr>
+<tr>
+<td><code>sum()</code></td>
+<td>byte scan + overflow, O(n + k)</td>
+</tr>
+<tr>
+<td><code>count_nonzero()</code></td>
+<td>byte scan, O(n)</td>
+</tr>
+<tr>
+<td>Distance methods (<code>bray_dist</code>, <code>euclidean_dist</code>, <code>jaccard_dist</code>, …)</td>
+<td>O(n + k)</td>
+</tr>
+</tbody>
+</table>
+<p><code>IntSliceViewIter&lt;'a&gt;</code>: merge scan using <code>overflow_pos</code> index. Requires sorted overflow — guaranteed by the construction lifecycle.</p>
+<p><strong>Builder <code>view()</code> vs reader <code>view()</code>:</strong> <code>PersistentCompactIntVecBuilder</code> stores overflow as an unsorted <code>HashMap</code>, not raw bytes. Its <code>view()</code> returns an <code>IntSliceView</code> with <code>overflow_raw = &amp;[]</code> and <code>n_overflow = 0</code>. This is intentional — the view is primarily useful after <code>freeze()</code>. During building, callers that need overflow use <code>overflow_entries()</code> directly.</p>
+<hr/>
+<h2 id="concrete-types">Concrete types</h2>
+<pre class="mermaid"><code>classDiagram
+    class BitSliceView {
+        +words: &amp;[u64]
+        +n: usize
+        +get(slot) bool
+        +count_ones() u64
+        +iter() BitSliceIter
+        +jaccard_dist/hamming_dist(other: BitSliceView)
+    }
+    class IntSliceView {
+        +primary: &amp;[u8]
+        +overflow_raw: &amp;[u8]
+        +n_overflow: usize
+        +n: usize
+        +get(slot) u32
+        +iter() IntSliceViewIter
+        +overflow_entries() Iterator
+        +bray_dist/euclidean_dist/…(other: IntSliceView)
+    }
+    class PersistentBitVec {
+        -mmap: Mmap
+        -n: usize
+        +view() BitSliceView
+        +get(slot) bool
+        +count_ones/zeros() u64
+        +iter() BitIter
+        +partial_jaccard_dist(&amp;Self) (u64,u64)
+        +jaccard_dist/hamming_dist(&amp;Self) …
+    }
+    class PersistentBitVecBuilder {
+        -mmap: MmapMut
+        -n: usize
+        +view() BitSliceView
+        +set(slot, bool)
+        +or/and/xor/not(BitSliceView)
+        +copy_from(BitSliceView)
+        +close() / finish() → PersistentBitVec
+    }
+    class PersistentCompactIntVec {
+        -mmap: Mmap
+        -n: usize
+        -n_overflow: usize
+        -step: usize
+        -index: Vec~(usize,usize)~
+        +view() IntSliceView
+        +get(slot) u32
+        +iter() Iter
+        +sum/count_nonzero() u64
+        +bray_dist/euclidean_dist/… (&amp;Self)
+    }
+    class PersistentCompactIntVecBuilder {
+        -mmap: MmapMut
+        -n: usize
+        -overflow: HashMap~usize,u32~
+        +view() IntSliceView
+        +set(slot, u32) / get(slot) u32
+        +inc / inc_present / inc_present_fast
+        +inc_predicate / inc_predicate_fast
+        +add/min/max/diff/mask_with(…View)
+        +primary_bytes/primary_bytes_mut()
+        +close() / finish() → PersistentCompactIntVec
+    }
+
+    PersistentBitVec --&gt; BitSliceView : view()
+    PersistentBitVecBuilder --&gt; BitSliceView : view()
+    PersistentCompactIntVec --&gt; IntSliceView : view()
+    PersistentCompactIntVecBuilder --&gt; IntSliceView : view() (primary only)
+    PersistentBitVecBuilder --&gt; PersistentBitVec : close() then open()
+    PersistentCompactIntVecBuilder --&gt; PersistentCompactIntVec : close() then open()</code></pre>
+<h3 id="persistentbitvec-persistentbitvecbuilder"><code>PersistentBitVec</code> / <code>PersistentBitVecBuilder</code></h3>
+<p><code>PersistentBitVec</code> is the read-only type. <code>view()</code> returns a <code>BitSliceView&lt;'_&gt;</code> over the mmap word array. Direct inherent methods delegate to the view: <code>count_ones()</code>, <code>count_zeros()</code>, <code>partial_jaccard_dist(&amp;Self)</code>, <code>jaccard_dist(&amp;Self)</code>, <code>hamming_dist(&amp;Self)</code>.</p>
+<p><code>BitIter&lt;'a&gt;</code> — exported iterator for <code>PersistentBitVec::iter()</code>:</p>
+<div class="highlight"><pre><span></span><code><span class="k">pub</span><span class="w"> </span><span class="k">struct</span><span class="w"> </span><span class="nc">BitIter</span><span class="o">&lt;'</span><span class="na">a</span><span class="o">&gt;</span><span class="w"> </span><span class="p">{</span><span class="w"> </span><span class="k">pub</span><span class="p">(</span><span class="k">crate</span><span class="p">)</span><span class="w"> </span><span class="n">words</span><span class="p">:</span><span class="w"> </span><span class="kp">&amp;</span><span class="o">'</span><span class="na">a</span><span class="w"> </span><span class="p">[</span><span class="kt">u64</span><span class="p">],</span><span class="w"> </span><span class="k">pub</span><span class="p">(</span><span class="k">crate</span><span class="p">)</span><span class="w"> </span><span class="n">slot</span><span class="p">:</span><span class="w"> </span><span class="kt">usize</span><span class="p">,</span><span class="w"> </span><span class="k">pub</span><span class="p">(</span><span class="k">crate</span><span class="p">)</span><span class="w"> </span><span class="n">n</span><span class="p">:</span><span class="w"> </span><span class="kt">usize</span><span class="w"> </span><span class="p">}</span>
+</code></pre></div>
+<p><code>PersistentBitVecBuilder</code> is the read-write type. Mutation operations accept <code>BitSliceView&lt;'_&gt;</code>:</p>
+<table>
+<thead>
+<tr>
+<th>Method</th>
+<th>Cost</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>set(slot, bool)</code></td>
+<td>O(1)</td>
+</tr>
+<tr>
+<td><code>view() -&gt; BitSliceView&lt;'_&gt;</code></td>
+<td>O(1)</td>
+</tr>
+<tr>
+<td><code>or/and/xor(BitSliceView)</code></td>
+<td>word-level, O(n/64), SIMD-friendly</td>
+</tr>
+<tr>
+<td><code>not()</code></td>
+<td><code>w ^= u64::MAX</code> per word, re-masks last word</td>
+</tr>
+<tr>
+<td><code>copy_from(BitSliceView)</code></td>
+<td><code>copy_from_slice</code></td>
+</tr>
+</tbody>
+</table>
+<h3 id="persistentcompactintvec-persistentcompactintvecbuilder"><code>PersistentCompactIntVec</code> / <code>PersistentCompactIntVecBuilder</code></h3>
+<p><code>PersistentCompactIntVec</code> is the read-only type. <code>view()</code> returns an <code>IntSliceView&lt;'_&gt;</code> over the mmap primary and overflow arrays. Inherent <code>iter()</code> is a merge scan (<code>Iter</code> struct). Inherent <code>sum()</code> and <code>count_nonzero()</code> use fast byte-scan helpers.</p>
+<p><code>PersistentCompactIntVecBuilder</code> is the read-write type. Mutation methods on the builder fall into two categories:</p>
+<p><strong>Point mutations:</strong></p>
+<table>
+<thead>
+<tr>
+<th>Method</th>
+<th>Note</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>set(slot, u32)</code></td>
+<td>writes primary[slot] or 255+overflow</td>
+</tr>
+<tr>
+<td><code>get(slot) -&gt; u32</code></td>
+<td>reads primary byte or HashMap</td>
+</tr>
+<tr>
+<td><code>inc(slot)</code></td>
+<td><code>get</code> + <code>set</code>, O(1)</td>
+</tr>
+</tbody>
+</table>
+<p><strong>Bulk computation methods</strong> — accept view arguments:</p>
+<table>
+<thead>
+<tr>
+<th>Method</th>
+<th>Semantics</th>
+<th>Overflow</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>inc_present(BitSliceView)</code></td>
+<td><code>+= 1</code> at each 1-bit</td>
+<td>via <code>inc</code>, safe for any group size</td>
+</tr>
+<tr>
+<td><code>inc_present_fast(BitSliceView)</code></td>
+<td>same, raw u8 <code>+= 1</code></td>
+<td><code>debug_assert</code> no 255 reached</td>
+</tr>
+<tr>
+<td><code>inc_predicate(IntSliceView, pred)</code></td>
+<td><code>+= 1</code> where <code>pred(col[s])</code></td>
+<td>two-pass, safe</td>
+</tr>
+<tr>
+<td><code>inc_predicate_fast(IntSliceView, pred)</code></td>
+<td>same, raw u8</td>
+<td><code>debug_assert</code> no 255 reached</td>
+</tr>
+<tr>
+<td><code>add(IntSliceView)</code></td>
+<td><code>self[s] += other[s]</code></td>
+<td>primary fast path + overflow fallback</td>
+</tr>
+<tr>
+<td><code>min(IntSliceView)</code></td>
+<td>byte min + both-overflow fixup</td>
+<td>see algorithm below</td>
+</tr>
+<tr>
+<td><code>max(IntSliceView)</code></td>
+<td>pre-pass + byte max</td>
+<td>see algorithm below</td>
+</tr>
+<tr>
+<td><code>diff(IntSliceView)</code></td>
+<td>saturating sub</td>
+<td>self&lt;255 hot path</td>
+</tr>
+<tr>
+<td><code>mask_with(BitSliceView)</code></td>
+<td>zeros slots where mask bit = 0</td>
+<td>O(n_zeros)</td>
+</tr>
+</tbody>
+</table>
+<p><strong><code>inc_present_fast</code> / <code>inc_predicate_fast</code> invariant:</strong> caller guarantees no counter reaches 255 during the operation (group size &lt; 255 for <code>inc_present_fast</code>, or chunk size &lt; 255 for <code>inc_predicate_fast</code>). Violation is caught by <code>debug_assert</code> in dev builds.</p>
+<p><strong><code>min</code> algorithm:</strong></p>
+<p>Exploits 255 = +∞: byte-level min is correct unless both sides are overflow.</p>
+<div class="highlight"><pre><span></span><code>snapshot self_ov: Vec&lt;(slot,val)&gt;
+snapshot other_ov: HashMap&lt;slot,val&gt;
+clear_overflow()
+Pass 1 — byte min, SIMD-vectorizable, O(n)
+Pass 2 — both-overflow fixup, O(k_self):
+  for (slot, self_val) in self_ov:
+    if slot ∈ other_ov: set(slot, min(self_val, other_ov[slot]))
+</code></pre></div>
+<p><strong><code>max</code> algorithm:</strong></p>
+<p>Cannot do byte max first — <code>max(255, b&lt;255)=255</code> overwrites self's original overflow value. Pre-pass reads self's value at other's overflow slots before the byte pass.</p>
+<div class="highlight"><pre><span></span><code>Pre-pass O(k_other): for (slot, other_val) in other.overflow_entries():
+  set(slot, max(self.get(slot), other_val))
+Pass 1 — byte max, SIMD-vectorizable, O(n)
+</code></pre></div>
+<hr/>
+<h2 id="matrix-types">Matrix types</h2>
+<p>Four matrix types, two encodings × two formats:</p>
+<table>
+<thead>
+<tr>
+<th></th>
+<th>Columnar format</th>
+<th>Packed format</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><strong>Bit</strong></td>
+<td><code>PersistentBitMatrix</code> (Columnar variant)</td>
+<td><code>PersistentBitMatrix</code> (Packed variant)</td>
+</tr>
+<tr>
+<td><strong>Int</strong></td>
+<td><code>PersistentCompactIntMatrix</code> (Columnar variant)</td>
+<td><code>PersistentCompactIntMatrix</code> (Packed variant)</td>
+</tr>
+</tbody>
+</table>
+<p>Both matrix types are enums (<code>Columnar</code> / <code>Packed</code> / <code>Implicit</code> for bit) behind a transparent API. <code>col_view(c)</code> returns the appropriate view directly:</p>
+<div class="highlight"><pre><span></span><code><span class="c1">// PersistentBitMatrix</span>
+<span class="k">pub</span><span class="w"> </span><span class="k">fn</span><span class="w"> </span><span class="nf">col_view</span><span class="p">(</span><span class="o">&amp;</span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">c</span><span class="p">:</span><span class="w"> </span><span class="kt">usize</span><span class="p">)</span><span class="w"> </span><span class="p">-&gt;</span><span class="w"> </span><span class="nc">BitSliceView</span><span class="o">&lt;'</span><span class="nb">_</span><span class="o">&gt;</span>
+
+<span class="c1">// PersistentCompactIntMatrix</span>
+<span class="k">pub</span><span class="w"> </span><span class="k">fn</span><span class="w"> </span><span class="nf">col_view</span><span class="p">(</span><span class="o">&amp;</span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">c</span><span class="p">:</span><span class="w"> </span><span class="kt">usize</span><span class="p">)</span><span class="w"> </span><span class="p">-&gt;</span><span class="w"> </span><span class="nc">IntSliceView</span><span class="o">&lt;'</span><span class="nb">_</span><span class="o">&gt;</span>
+</code></pre></div>
+<p>No wrapper enums (<code>BitColView</code>, <code>IntColView</code>): the caller receives a <code>Copy</code> view struct immediately usable with any view method or bulk builder method.</p>
+<p><code>pack_compact_int_matrix</code> and <code>pack_bit_matrix</code> convert columnar → packed format.</p>
+<hr/>
+<h2 id="aggregation-traits-matrix-level">Aggregation traits (matrix level)</h2>
+<h3 id="columnweights">ColumnWeights</h3>
+<div class="highlight"><pre><span></span><code><span class="k">trait</span><span class="w"> </span><span class="n">ColumnWeights</span><span class="p">:</span><span class="w"> </span><span class="nb">Send</span><span class="w"> </span><span class="o">+</span><span class="w"> </span><span class="nb">Sync</span><span class="w"> </span><span class="p">{</span>
+<span class="w">    </span><span class="k">fn</span><span class="w"> </span><span class="nf">col_weights</span><span class="p">(</span><span class="o">&amp;</span><span class="bp">self</span><span class="p">)</span><span class="w"> </span><span class="p">-&gt;</span><span class="w"> </span><span class="nc">Array1</span><span class="o">&lt;</span><span class="kt">u64</span><span class="o">&gt;</span><span class="p">;</span><span class="w">         </span><span class="c1">// sum per column</span>
+<span class="w">    </span><span class="k">fn</span><span class="w"> </span><span class="nf">partial_kmer_counts</span><span class="p">(</span><span class="o">&amp;</span><span class="bp">self</span><span class="p">)</span><span class="w"> </span><span class="p">-&gt;</span><span class="w"> </span><span class="nc">Array1</span><span class="o">&lt;</span><span class="kt">u64</span><span class="o">&gt;</span><span class="p">;</span><span class="w"> </span><span class="c1">// default = col_weights()</span>
+<span class="p">}</span>
+</code></pre></div>
+<p><code>partial_kmer_counts</code> is overridden for count matrices to return <code>count_nonzero</code> per column (distinct kmers) rather than total count.</p>
+<h3 id="countpartials">CountPartials</h3>
+<p>Abstract required methods: <code>partial_bray</code>, <code>partial_euclidean</code>, <code>partial_threshold_jaccard</code>, <code>partial_relfreq_bray</code>, <code>partial_relfreq_euclidean</code>, <code>partial_hellinger</code>.</p>
+<p><strong>Additivity rule:</strong> self-contained partials (<code>partial_bray</code>, <code>partial_euclidean</code>, <code>partial_threshold_jaccard</code>) can be element-wise summed across all <code>(partition, layer)</code> pairs. Normalised partials (<code>partial_relfreq_*</code>, <code>partial_hellinger</code>) require the <strong>global</strong> <code>col_weights</code> (accumulated across all layers and all partitions) as parameter.</p>
+<p><strong><code>partial_threshold_jaccard</code> returns <code>(inter, union)</code></strong> because <code>union[i,j]</code> depends on both columns simultaneously.</p>
+<p>Provided finalisations:</p>
+<table>
+<thead>
+<tr>
+<th>Finalisation</th>
+<th>Formula</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>bray_dist_matrix()</code></td>
+<td><code>1 − 2·partial_bray[i,j] / (w[i] + w[j])</code></td>
+</tr>
+<tr>
+<td><code>euclidean_dist_matrix()</code></td>
+<td><code>√partial_euclidean[i,j]</code></td>
+</tr>
+<tr>
+<td><code>threshold_jaccard_dist_matrix(t)</code></td>
+<td><code>1 − inter[i,j] / union[i,j]</code></td>
+</tr>
+<tr>
+<td><code>relfreq_bray_dist_matrix()</code></td>
+<td><code>1 − partial_relfreq_bray[i,j]</code></td>
+</tr>
+<tr>
+<td><code>relfreq_euclidean_dist_matrix()</code></td>
+<td><code>√partial_relfreq_euclidean[i,j]</code></td>
+</tr>
+<tr>
+<td><code>hellinger_dist_matrix()</code></td>
+<td><code>√partial_hellinger[i,j] / √2</code></td>
+</tr>
+<tr>
+<td><code>hellinger_euclidean_dist_matrix()</code></td>
+<td><code>√partial_hellinger[i,j]</code></td>
+</tr>
+<tr>
+<td><code>threshold_mash_dist_matrix(k, t)</code></td>
+<td>Mash distance, derived from <code>threshold_jaccard_dist_matrix(t)</code> — no separate partial</td>
+</tr>
+</tbody>
+</table>
+<h3 id="bitpartials">BitPartials</h3>
+<p>Required: <code>partial_jaccard() -&gt; (Array2&lt;u64&gt;, Array2&lt;u64&gt;)</code>, <code>partial_hamming() -&gt; Array2&lt;u64&gt;</code>. Both additive across layers and partitions.</p>
+<p>Provided finalisations also include <code>jaccard_dist_matrix()</code>, <code>hamming_dist_matrix()</code>, and <code>mash_dist_matrix(k)</code>.</p>
+<h3 id="mash-distance">Mash distance</h3>
+<p><code>mash_dist_matrix</code>/<code>threshold_mash_dist_matrix</code> add no new additive primitive: both are a pointwise transform of the existing Jaccard distance matrix, per the Mash mutation-rate estimator (Fan <em>et al.</em> 2015; Marbl Lab 2026)<sup id="fnref:Mash-distances-doc"><a class="footnote-ref" href="#fn:Mash-distances-doc">1</a></sup> <sup id="fnref:Fan2015-mash-formula"><a class="footnote-ref" href="#fn:Fan2015-mash-formula">2</a></sup>:</p>
+<div class="highlight"><pre><span></span><code>D = -1/k · ln(2J / (1+J)),  J = 1 - d_jaccard
+</code></pre></div>
+<p><code>J ≤ 0</code> (i.e. <code>d_jaccard ≥ 1</code>, no shared k-mers) maps to <code>D = 1</code> (maximal distance) rather than the <code>ln</code> singularity at <code>J = 0</code>.</p>
+<hr/>
+<h2 id="temp-file-backed-types">Temp-file-backed types</h2>
+<p><strong>All inter-function results use temp-file-backed types</strong> so the OS can page them out under memory pressure. This matters in practice: processing dozens of layers × hundreds of partitions in parallel would otherwise accumulate gigabytes of live anonymous memory.</p>
+<h3 id="lifecycle">Lifecycle</h3>
+<div class="highlight"><pre><span></span><code>TempCompactIntVecBuilder::new(n)   →  writable mmap in TempDir
+     ↓  (inc_present_fast / inc_predicate_fast / add / mask_with / …)
+ .freeze()                          →  TempCompactIntVec  (read-only mmap + TempDir)
+     ↓  (optional)
+ .make_persistent(path)             →  PersistentCompactIntVec  (permanent file)
+</code></pre></div>
+<p>Same pattern for <code>TempBitVecBuilder</code> → <code>TempBitVec</code> → <code>PersistentBitVec</code>.</p>
+<p><strong>Drop order</strong>: <code>TempCompactIntVec { vec: PersistentCompactIntVec, _temp: TempDir }</code> — Rust drops fields in declaration order. <code>vec</code> (mmap) released before <code>_temp</code> (directory deleted). No explicit <code>drop()</code> needed.</p>
+<h3 id="tempcompactintvec-tempcompactintvecbuilder">TempCompactIntVec / TempCompactIntVecBuilder</h3>
+<div class="highlight"><pre><span></span><code><span class="k">pub</span><span class="w"> </span><span class="k">struct</span><span class="w"> </span><span class="nc">TempCompactIntVec</span><span class="w"> </span><span class="p">{</span>
+<span class="w">    </span><span class="n">vec</span><span class="p">:</span><span class="w">   </span><span class="nc">PersistentCompactIntVec</span><span class="p">,</span>
+<span class="w">    </span><span class="n">_temp</span><span class="p">:</span><span class="w"> </span><span class="nc">TempDir</span><span class="p">,</span><span class="w">        </span><span class="c1">// dropped after vec</span>
+<span class="p">}</span>
+
+<span class="k">pub</span><span class="p">(</span><span class="k">crate</span><span class="p">)</span><span class="w"> </span><span class="k">struct</span><span class="w"> </span><span class="nc">TempCompactIntVecBuilder</span><span class="w"> </span><span class="p">{</span>
+<span class="w">    </span><span class="n">builder</span><span class="p">:</span><span class="w"> </span><span class="nc">PersistentCompactIntVecBuilder</span><span class="p">,</span>
+<span class="w">    </span><span class="n">temp</span><span class="p">:</span><span class="w">    </span><span class="nc">TempDir</span><span class="p">,</span>
+<span class="p">}</span>
+</code></pre></div>
+<p><code>TempCompactIntVec</code>: read access via <code>get(slot)</code>, <code>sum()</code>, <code>iter()</code>, <code>view() -&gt; IntSliceView&lt;'_&gt;</code>.</p>
+<p><code>TempCompactIntVecBuilder</code>: full delegation to inner <code>PersistentCompactIntVecBuilder</code> — all bulk computation methods (<code>inc_present_fast</code>, <code>inc_predicate_fast</code>, <code>add</code>, <code>min</code>, <code>max</code>, <code>diff</code>, <code>mask_with</code>) are exposed as <code>pub(crate)</code>.</p>
+<h3 id="tempbitvec-tempbitvecbuilder">TempBitVec / TempBitVecBuilder</h3>
+<div class="highlight"><pre><span></span><code><span class="k">pub</span><span class="w"> </span><span class="k">struct</span><span class="w"> </span><span class="nc">TempBitVec</span><span class="w"> </span><span class="p">{</span>
+<span class="w">    </span><span class="n">vec</span><span class="p">:</span><span class="w">   </span><span class="nc">PersistentBitVec</span><span class="p">,</span>
+<span class="w">    </span><span class="n">_temp</span><span class="p">:</span><span class="w"> </span><span class="nc">TempDir</span><span class="p">,</span>
+<span class="p">}</span>
+
+<span class="k">pub</span><span class="p">(</span><span class="k">crate</span><span class="p">)</span><span class="w"> </span><span class="k">struct</span><span class="w"> </span><span class="nc">TempBitVecBuilder</span><span class="w"> </span><span class="p">{</span>
+<span class="w">    </span><span class="n">builder</span><span class="p">:</span><span class="w"> </span><span class="nc">PersistentBitVecBuilder</span><span class="p">,</span>
+<span class="w">    </span><span class="n">temp</span><span class="p">:</span><span class="w">    </span><span class="nc">TempDir</span><span class="p">,</span>
+<span class="p">}</span>
+</code></pre></div>
+<p><code>TempBitVec</code>: read access via <code>get(slot)</code>, <code>count_ones()</code>, <code>view() -&gt; BitSliceView&lt;'_&gt;</code>, <code>iter()</code>.</p>
+<p><code>TempBitVecBuilder</code>: exposes <code>set(slot, bool)</code>, <code>or(BitSliceView)</code>, and:</p>
+<div class="highlight"><pre><span></span><code><span class="k">pub</span><span class="p">(</span><span class="k">crate</span><span class="p">)</span><span class="w"> </span><span class="k">fn</span><span class="w"> </span><span class="nf">or_where</span><span class="p">(</span><span class="o">&amp;</span><span class="k">mut</span><span class="w"> </span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">col</span><span class="p">:</span><span class="w"> </span><span class="nc">IntSliceView</span><span class="o">&lt;'</span><span class="nb">_</span><span class="o">&gt;</span><span class="p">,</span><span class="w"> </span><span class="n">pred</span><span class="p">:</span><span class="w"> </span><span class="nc">impl</span><span class="w"> </span><span class="nb">Fn</span><span class="p">(</span><span class="kt">u32</span><span class="p">)</span><span class="w"> </span><span class="p">-&gt;</span><span class="w"> </span><span class="kt">bool</span><span class="p">)</span>
+</code></pre></div>
+<p><code>or_where</code> — two passes, no intermediate allocation:</p>
+<div class="highlight"><pre><span></span><code>Pass 1 — primary bytes, O(n):
+  for slot in 0..n:
+    b = col.primary_bytes()[slot]
+    if b &lt; 255 AND pred(b as u32): self.set(slot, true)
+
+Pass 2 — overflow, O(k):
+  for (slot, val) in col.overflow_entries():
+    if pred(val): self.set(slot, true)
+</code></pre></div>
+<hr/>
+<h2 id="filter-select-api">Filter / Select API</h2>
+<h3 id="colgroup">ColGroup</h3>
+<div class="highlight"><pre><span></span><code><span class="k">pub</span><span class="w"> </span><span class="k">struct</span><span class="w"> </span><span class="nc">ColGroup</span><span class="w"> </span><span class="p">{</span><span class="w"> </span><span class="k">pub</span><span class="w"> </span><span class="n">name</span><span class="p">:</span><span class="w"> </span><span class="nb">String</span><span class="p">,</span><span class="w"> </span><span class="k">pub</span><span class="w"> </span><span class="n">indices</span><span class="p">:</span><span class="w"> </span><span class="nb">Vec</span><span class="o">&lt;</span><span class="kt">usize</span><span class="o">&gt;</span><span class="w"> </span><span class="p">}</span>
+</code></pre></div>
+<p>Defined <strong>once at the index level</strong> from column metadata. Valid in all matrices of all layers and partitions — column structure is identical across the entire hierarchy; only rows (kmer slots) are partitioned.</p>
+<h3 id="composition-axis">Composition axis</h3>
+<ul>
+<li><strong>Across partitions</strong>: kmer space is partitioned → partial results <strong>concatenated</strong> (disjoint kmer ranges).</li>
+<li><strong>Across layers</strong>: same kmer space, different counts → partial results <strong>aggregated</strong> (add, OR, etc.).</li>
+</ul>
+<h3 id="matrixgroupops">MatrixGroupOps</h3>
+<p>Five required primitives + two default methods derived from them. All return temp-file-backed types.</p>
+<div class="highlight"><pre><span></span><code><span class="k">pub</span><span class="w"> </span><span class="k">trait</span><span class="w"> </span><span class="n">MatrixGroupOps</span><span class="w"> </span><span class="p">{</span>
+<span class="w">    </span><span class="c1">// required</span>
+<span class="w">    </span><span class="k">fn</span><span class="w"> </span><span class="nf">partial_group_presence_count</span><span class="p">(</span><span class="o">&amp;</span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">g</span><span class="p">:</span><span class="w"> </span><span class="kp">&amp;</span><span class="nc">ColGroup</span><span class="p">,</span><span class="w"> </span><span class="n">threshold</span><span class="p">:</span><span class="w"> </span><span class="kt">u32</span><span class="p">)</span>
+<span class="w">        </span><span class="p">-&gt;</span><span class="w"> </span><span class="nc">io</span><span class="p">::</span><span class="nb">Result</span><span class="o">&lt;</span><span class="n">TempCompactIntVec</span><span class="o">&gt;</span><span class="p">;</span>
+<span class="w">    </span><span class="k">fn</span><span class="w"> </span><span class="nf">partial_group_sum</span><span class="p">(</span><span class="o">&amp;</span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">g</span><span class="p">:</span><span class="w"> </span><span class="kp">&amp;</span><span class="nc">ColGroup</span><span class="p">)</span>
+<span class="w">        </span><span class="p">-&gt;</span><span class="w"> </span><span class="nc">io</span><span class="p">::</span><span class="nb">Result</span><span class="o">&lt;</span><span class="n">TempCompactIntVec</span><span class="o">&gt;</span><span class="p">;</span>
+<span class="w">    </span><span class="k">fn</span><span class="w"> </span><span class="nf">partial_group_any</span><span class="p">(</span><span class="o">&amp;</span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">g</span><span class="p">:</span><span class="w"> </span><span class="kp">&amp;</span><span class="nc">ColGroup</span><span class="p">,</span><span class="w"> </span><span class="n">threshold</span><span class="p">:</span><span class="w"> </span><span class="kt">u32</span><span class="p">)</span>
+<span class="w">        </span><span class="p">-&gt;</span><span class="w"> </span><span class="nc">io</span><span class="p">::</span><span class="nb">Result</span><span class="o">&lt;</span><span class="n">TempBitVec</span><span class="o">&gt;</span><span class="p">;</span>
+<span class="w">    </span><span class="k">fn</span><span class="w"> </span><span class="nf">partial_group_min</span><span class="p">(</span><span class="o">&amp;</span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">g</span><span class="p">:</span><span class="w"> </span><span class="kp">&amp;</span><span class="nc">ColGroup</span><span class="p">)</span>
+<span class="w">        </span><span class="p">-&gt;</span><span class="w"> </span><span class="nc">io</span><span class="p">::</span><span class="nb">Result</span><span class="o">&lt;</span><span class="n">TempCompactIntVec</span><span class="o">&gt;</span><span class="p">;</span>
+<span class="w">    </span><span class="k">fn</span><span class="w"> </span><span class="nf">partial_group_max</span><span class="p">(</span><span class="o">&amp;</span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">g</span><span class="p">:</span><span class="w"> </span><span class="kp">&amp;</span><span class="nc">ColGroup</span><span class="p">)</span>
+<span class="w">        </span><span class="p">-&gt;</span><span class="w"> </span><span class="nc">io</span><span class="p">::</span><span class="nb">Result</span><span class="o">&lt;</span><span class="n">TempCompactIntVec</span><span class="o">&gt;</span><span class="p">;</span>
+
+<span class="w">    </span><span class="c1">// defaults derived from partial_group_presence_count</span>
+<span class="w">    </span><span class="k">fn</span><span class="w"> </span><span class="nf">partial_group_all</span><span class="p">(</span><span class="o">&amp;</span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">g</span><span class="p">:</span><span class="w"> </span><span class="kp">&amp;</span><span class="nc">ColGroup</span><span class="p">,</span><span class="w"> </span><span class="n">threshold</span><span class="p">:</span><span class="w"> </span><span class="kt">u32</span><span class="p">)</span>
+<span class="w">        </span><span class="p">-&gt;</span><span class="w"> </span><span class="nc">io</span><span class="p">::</span><span class="nb">Result</span><span class="o">&lt;</span><span class="n">TempBitVec</span><span class="o">&gt;</span><span class="p">;</span><span class="w">   </span><span class="c1">// slot=1 iff count == g.indices.len()</span>
+<span class="w">    </span><span class="k">fn</span><span class="w"> </span><span class="nf">partial_group_none</span><span class="p">(</span><span class="o">&amp;</span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">g</span><span class="p">:</span><span class="w"> </span><span class="kp">&amp;</span><span class="nc">ColGroup</span><span class="p">,</span><span class="w"> </span><span class="n">threshold</span><span class="p">:</span><span class="w"> </span><span class="kt">u32</span><span class="p">)</span>
+<span class="w">        </span><span class="p">-&gt;</span><span class="w"> </span><span class="nc">io</span><span class="p">::</span><span class="nb">Result</span><span class="o">&lt;</span><span class="n">TempBitVec</span><span class="o">&gt;</span><span class="p">;</span><span class="w">   </span><span class="c1">// slot=1 iff count == 0</span>
+<span class="p">}</span>
+</code></pre></div>
+<p>Implemented for both <code>PersistentCompactIntMatrix</code> and <code>PersistentBitMatrix</code>.</p>
+<p>For <strong>bit matrices</strong>: values are 0/1, so <code>partial_group_sum</code> = <code>partial_group_presence_count(g, 1)</code>; <code>partial_group_min</code> is AND (set first column then mask-with remaining); <code>partial_group_max</code> is OR via <code>partial_group_any</code> + <code>inc_present</code>.</p>
+<p><strong><code>partial_group_presence_count</code> — chunking for large groups:</strong></p>
+<p>When <code>g.indices.len() &lt; 255</code>: per-slot counts stay within <code>u8</code> range. Use <code>inc_present_fast</code> (bit) or <code>inc_predicate_fast(col_view(c), |v| v &gt;= threshold)</code> (int) — raw u8 increment, no overflow entry written.</p>
+<p>When <code>g.indices.len() ≥ 255</code>: process in chunks of 254 columns, accumulate via <code>.add(chunk_frozen.view())</code>.</p>
+<p><strong><code>partial_group_min</code> (int matrix)</strong>: copy first column via <code>.add(col_view(first))</code> (start from 0 ⇒ copy), then <code>.min(col_view(c))</code> for remaining.</p>
+<p><strong><code>partial_group_max</code> (int matrix)</strong>: <code>.max(col_view(c))</code> for all columns (start from 0 ⇒ first column acts as copy).</p>
+<p><strong><code>partial_group_any</code></strong> uses <code>or_where</code> on <code>TempBitVecBuilder</code> (two-pass: primary bytes then overflow entries).</p>
+<p><strong><code>partial_group_all</code> / <code>partial_group_none</code></strong> (default): call <code>partial_group_presence_count</code>, then iterate slots to produce the bit result. O(n) extra pass, not chunked.</p>
+<h3 id="add_col_from-matrix-builder-integration">add_col_from — matrix builder integration</h3>
+<p>Both matrix builders accept temp-file results directly:</p>
+<div class="highlight"><pre><span></span><code><span class="c1">// PersistentBitMatrixBuilder</span>
+<span class="k">fn</span><span class="w"> </span><span class="nf">add_col_from</span><span class="p">(</span><span class="o">&amp;</span><span class="k">mut</span><span class="w"> </span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">src</span><span class="p">:</span><span class="w"> </span><span class="kp">&amp;</span><span class="nc">TempBitVec</span><span class="p">)</span><span class="w">         </span><span class="p">-&gt;</span><span class="w"> </span><span class="nc">io</span><span class="p">::</span><span class="nb">Result</span><span class="o">&lt;</span><span class="p">()</span><span class="o">&gt;</span>
+<span class="k">fn</span><span class="w"> </span><span class="nf">add_col_from_int</span><span class="p">(</span><span class="o">&amp;</span><span class="k">mut</span><span class="w"> </span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">src</span><span class="p">:</span><span class="w"> </span><span class="kp">&amp;</span><span class="nc">TempCompactIntVec</span><span class="p">)</span><span class="w"> </span><span class="p">-&gt;</span><span class="w"> </span><span class="nc">io</span><span class="p">::</span><span class="nb">Result</span><span class="o">&lt;</span><span class="p">()</span><span class="o">&gt;</span><span class="w">  </span><span class="c1">// nonzero → 1</span>
+
+<span class="c1">// PersistentCompactIntMatrixBuilder</span>
+<span class="k">fn</span><span class="w"> </span><span class="nf">add_col_from</span><span class="p">(</span><span class="o">&amp;</span><span class="k">mut</span><span class="w"> </span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">src</span><span class="p">:</span><span class="w"> </span><span class="kp">&amp;</span><span class="nc">TempCompactIntVec</span><span class="p">)</span><span class="w">  </span><span class="p">-&gt;</span><span class="w"> </span><span class="nc">io</span><span class="p">::</span><span class="nb">Result</span><span class="o">&lt;</span><span class="p">()</span><span class="o">&gt;</span>
+<span class="k">fn</span><span class="w"> </span><span class="nf">add_col_from_bit</span><span class="p">(</span><span class="o">&amp;</span><span class="k">mut</span><span class="w"> </span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">src</span><span class="p">:</span><span class="w"> </span><span class="kp">&amp;</span><span class="nc">TempBitVec</span><span class="p">)</span><span class="w">     </span><span class="p">-&gt;</span><span class="w"> </span><span class="nc">io</span><span class="p">::</span><span class="nb">Result</span><span class="o">&lt;</span><span class="p">()</span><span class="o">&gt;</span><span class="w">  </span><span class="c1">// bit → 0/1 u32</span>
+</code></pre></div>
+<p><code>add_col_from</code> copies the temp file to the matrix directory and increments <code>n_cols</code>; <code>close()</code> writes <code>meta.json</code> with the final column count. No separate <code>write_meta</code> step needed.</p>
+<h3 id="mask_with">mask_with</h3>
+<p>Direct method on <code>PersistentCompactIntVecBuilder</code> (and delegation via <code>TempCompactIntVecBuilder</code>). Zeros every slot where the corresponding mask bit is 0. Iterates only zero bits — O(n_zeros), O(1) when mask is all-ones.</p>
+<div class="highlight"><pre><span></span><code>for (w_idx, word) in mask.words():
+  if word == u64::MAX: continue   // skip all-ones words
+  zeros = !word
+  while zeros != 0:
+    bit = trailing_zeros(zeros)
+    s = w_idx * 64 + bit
+    if primary[s] != 0: set(s, 0)   // clears overflow entry too
+    zeros &amp;= zeros − 1
+</code></pre></div>
+<p>Terminal operation for Filter (retain only selected kmer slots in a count vector) and Select (positional selection without MPHF).</p>
+<div class="footnote">
+<hr/>
+<ol>
+<li id="fn:Mash-distances-doc">
+<p>Marbl Lab. (2026). <a href="https://mash.readthedocs.io/en/latest/distances.html">Mash distance</a>. <a class="footnote-backref" href="#fnref:Mash-distances-doc" title="Jump back to footnote 1 in the text">↩</a></p>
+</li>
+<li id="fn:Fan2015-mash-formula">
+<p>Fan, H., Ives, A.R., Surget-Groba, Y. &amp; Cannon, C.H. (2015). <a href="https://doi.org/10.1186/s12864-015-1647-5">An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data</a>. <em>BMC Genomics</em>, 16. <a class="footnote-backref" href="#fnref:Fan2015-mash-formula" title="Jump back to footnote 2 in the text">↩</a></p>
+</li>
+</ol>
+</div>
+</article>
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+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
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+
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+  </span>
+  
+  
+
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+    </li>
+  
+
+              
+            
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+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
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+
+    
+  </span>
+  
+  
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+    </li>
+  
+
+              
+            
+              
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+  
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+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
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+    Select command
+  
+
+    
+  </span>
+  
+  
+
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+
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+            
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+  
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+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
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+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
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+  
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+
+    
+  </span>
+  
+  
+
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+
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+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
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+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
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+
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+            
+              
+                
+  
+  
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+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
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+  
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+  
+
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+  
+
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--- a/doc/implementation/obilayeredmap/index.html
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+  <span class="md-ellipsis">
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+
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+  </span>
+  
+  
+
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+    </li>
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+
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+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
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+  </span>
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+
+      </a>
+    </li>
+  
+
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+      <a href="../merge_parallelism/" class="md-nav__link">
         
   
   
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-    Kmer filtering (rebuild/dump/unitig)
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+  
+
+    
+  </span>
+  
+  
+
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+    </li>
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+
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+            
+              
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+  
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+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
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+    </li>
+  
+
+              
+            
+              
+                
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+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
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+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
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+  
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+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
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+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
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+    <li class="md-nav__item">
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+        
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+  
+  <span class="md-ellipsis">
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+  
+    Installation
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+
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+  </span>
+  
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+
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+    </li>
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+      
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+      <a href="../merge_parallelism/" class="md-nav__link">
         
   
   
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--- a/doc/implementation/obipipeline/index.html
+++ b/DevDoc/implementation/obipipeline/index.html
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+  
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+  
+
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+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
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+  
+  
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+  
+  
+
+      </a>
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+
+              
+            
+              
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+
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+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
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diff --git a/DevDoc/implementation/obitaxonomy/index.html b/DevDoc/implementation/obitaxonomy/index.html
new file mode 100644
index 00000000..d477e6ab
--- /dev/null
+++ b/DevDoc/implementation/obitaxonomy/index.html
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+  <head>
+    
+      <meta charset="utf-8">
+      <meta name="viewport" content="width=device-width,initial-scale=1">
+      
+      
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+      
+        <link rel="prev" href="../select/">
+      
+      
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+        <div class="md-header__topic" data-md-component="header-topic">
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+  
+
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+  
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+    <li class="md-nav__item">
+      <a href="../../theory/encoding/" class="md-nav__link">
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+  
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+    DNA encoding
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+      <a href="../../theory/entropy/" class="md-nav__link">
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+  
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+  
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+      <a href="../../theory/indexing/" class="md-nav__link">
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+  
+
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+          </ul>
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+  
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+        <li class="md-nav__item">
+  <a href="#concept-path-syntax" class="md-nav__link">
+    <span class="md-ellipsis">
+      
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+      
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+  
+    <nav class="md-nav" aria-label="Concept path syntax">
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+  <a href="#taxpath" class="md-nav__link">
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+  <a href="#predicate-operators-in-filter-select" class="md-nav__link">
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+      
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+    <span class="md-ellipsis">
+      
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+      
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+  <a href="#rank-aware-queries" class="md-nav__link">
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+      Table of contents
+    </label>
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+      
+        <li class="md-nav__item">
+  <a href="#concept-path-syntax" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Concept path syntax
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Concept path syntax">
+      <ul class="md-nav__list">
+        
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+  <a href="#reserved-character" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Reserved character
+      
+    </span>
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+  
+</li>
+        
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+  <a href="#parse-errors" class="md-nav__link">
+    <span class="md-ellipsis">
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+      
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+    <nav class="md-nav" aria-label="Public API">
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+    <span class="md-ellipsis">
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+  
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+        
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+  <a href="#taxpath" class="md-nav__link">
+    <span class="md-ellipsis">
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+</li>
+      
+        <li class="md-nav__item">
+  <a href="#integration-with-genomeinfo" class="md-nav__link">
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+      
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+  
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+      
+        <li class="md-nav__item">
+  <a href="#predicate-operators-in-filter-select" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Predicate operators (in filter / select)
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Predicate operators (in filter / select)">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#path-pattern-syntax" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Path pattern syntax
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#rank-aware-queries" class="md-nav__link">
+    <span class="md-ellipsis">
+      
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+      
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+  
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+  
+</li>
+      
+    </ul>
+  
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+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+
+<h1 id="obitaxonomy-taxonomy-concept-paths"><code>obitaxonomy</code> — taxonomy concept paths</h1>
+<p><code>obitaxonomy</code> is a dependency-free crate that defines a typed representation
+of hierarchical concept paths (taxonomic or otherwise) stored in genome metadata.</p>
+<hr />
+<h2 id="concept-path-syntax">Concept path syntax</h2>
+<p>A concept path is stored as a metadata value with the prefix <code>taxonomy:/</code>:</p>
+<div class="highlight"><pre><span></span><code>taxonomy:/enterobacteriaceae@family/Escherichia@genus/Escherichia coli@species
+</code></pre></div>
+<p>Structure:</p>
+<ul>
+<li>The <code>taxonomy:/</code> prefix is the type discriminator. Any metadata value starting
+  with it is parsed as a <code>TaxPath</code>; all others remain plain strings.</li>
+<li>The remainder is one or more <code>/</code>-separated segments.</li>
+<li>Each segment is <code>name</code> or <code>name@rank</code>, where <code>rank</code> is a label for the
+  taxonomic level (e.g. <code>family</code>, <code>genus</code>, <code>species</code>).</li>
+<li>Rank annotations are <strong>optional per segment</strong> and can be mixed freely.</li>
+<li>Spaces are allowed in both names and ranks.</li>
+</ul>
+<h3 id="reserved-character">Reserved character</h3>
+<p><code>@</code> is reserved throughout the taxonomy system and may <strong>not</strong> appear in:</p>
+<table>
+<thead>
+<tr>
+<th>Context</th>
+<th>Constraint</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>Segment name</td>
+<td>forbidden</td>
+</tr>
+<tr>
+<td>Rank/class label</td>
+<td>forbidden</td>
+</tr>
+<tr>
+<td>Metadata key names</td>
+<td>forbidden (used as <code>key@rank</code> in predicate syntax)</td>
+</tr>
+</tbody>
+</table>
+<p><code>@</code> is freely allowed in plain-text metadata values (non-taxonomy).</p>
+<h3 id="parse-errors">Parse errors</h3>
+<table>
+<thead>
+<tr>
+<th>Condition</th>
+<th>Error</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>Value does not start with <code>taxonomy:/</code></td>
+<td><code>MissingPrefix</code></td>
+</tr>
+<tr>
+<td>No segments after the prefix</td>
+<td><code>EmptyPath</code></td>
+</tr>
+<tr>
+<td>Segment with empty name (consecutive <code>/</code>)</td>
+<td><code>EmptySegmentName</code></td>
+</tr>
+<tr>
+<td>Segment with trailing <code>@</code> and no rank (<code>name@</code>)</td>
+<td><code>EmptyRankName</code></td>
+</tr>
+<tr>
+<td>Segment with more than one <code>@</code></td>
+<td><code>AmbiguousRank</code></td>
+</tr>
+</tbody>
+</table>
+<hr />
+<h2 id="public-api">Public API</h2>
+<h3 id="taxsegment"><code>TaxSegment</code></h3>
+<p>A single node: a name and an optional rank.</p>
+<div class="highlight"><pre><span></span><code><span class="n">seg</span><span class="p">.</span><span class="n">name</span><span class="p">()</span><span class="w">            </span><span class="c1">// &amp;str</span>
+<span class="n">seg</span><span class="p">.</span><span class="n">rank</span><span class="p">()</span><span class="w">            </span><span class="c1">// Option&lt;&amp;str&gt;</span>
+<span class="n">seg</span><span class="p">.</span><span class="n">to_string</span><span class="p">()</span><span class="w">       </span><span class="c1">// &quot;name&quot; or &quot;name@rank&quot;</span>
+<span class="n">TaxSegment</span><span class="p">::</span><span class="n">parse</span><span class="p">(</span><span class="n">s</span><span class="p">)</span><span class="w">  </span><span class="c1">// Result&lt;TaxSegment, TaxError&gt;</span>
+</code></pre></div>
+<h3 id="taxpath"><code>TaxPath</code></h3>
+<div class="highlight"><pre><span></span><code><span class="n">TaxPath</span><span class="p">::</span><span class="n">parse</span><span class="p">(</span><span class="n">s</span><span class="p">)</span><span class="w">               </span><span class="c1">// Result&lt;TaxPath, TaxError&gt;</span>
+<span class="n">path</span><span class="p">.</span><span class="n">segments</span><span class="p">()</span><span class="w">                 </span><span class="c1">// &amp;[TaxSegment]</span>
+<span class="n">path</span><span class="p">.</span><span class="n">depth</span><span class="p">()</span><span class="w">                    </span><span class="c1">// usize — number of segments</span>
+<span class="n">path</span><span class="p">.</span><span class="n">is_ancestor_of</span><span class="p">(</span><span class="o">&amp;</span><span class="n">other</span><span class="p">)</span><span class="w">     </span><span class="c1">// bool — prefix match by name, ranks ignored</span>
+<span class="n">path</span><span class="p">.</span><span class="n">name_at_rank</span><span class="p">(</span><span class="s">&quot;genus&quot;</span><span class="p">)</span><span class="w">      </span><span class="c1">// Option&lt;&amp;str&gt;</span>
+<span class="n">path</span><span class="p">.</span><span class="n">to_string</span><span class="p">()</span><span class="w">                </span><span class="c1">// reconstructs &quot;taxonomy:/…&quot;</span>
+</code></pre></div>
+<p><code>is_ancestor_of</code> compares segment <strong>names</strong> only — rank annotations are
+informational and do not affect the ancestry relation.</p>
+<div class="highlight"><pre><span></span><code><span class="kd">let</span><span class="w"> </span><span class="n">a</span><span class="p">:</span><span class="w"> </span><span class="nc">TaxPath</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s">&quot;taxonomy:/Enterobacteriaceae@family/Escherichia@genus&quot;</span><span class="p">.</span><span class="n">parse</span><span class="p">()</span><span class="o">?</span><span class="p">;</span>
+<span class="kd">let</span><span class="w"> </span><span class="n">b</span><span class="p">:</span><span class="w"> </span><span class="nc">TaxPath</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s">&quot;taxonomy:/Enterobacteriaceae@family/Escherichia@genus/Escherichia coli@species&quot;</span><span class="p">.</span><span class="n">parse</span><span class="p">()</span><span class="o">?</span><span class="p">;</span>
+
+<span class="fm">assert!</span><span class="p">(</span><span class="n">a</span><span class="p">.</span><span class="n">is_ancestor_of</span><span class="p">(</span><span class="o">&amp;</span><span class="n">b</span><span class="p">));</span><span class="w">   </span><span class="c1">// true</span>
+<span class="fm">assert!</span><span class="p">(</span><span class="n">b</span><span class="p">.</span><span class="n">is_ancestor_of</span><span class="p">(</span><span class="o">&amp;</span><span class="n">a</span><span class="p">));</span><span class="w">   </span><span class="c1">// false</span>
+<span class="fm">assert!</span><span class="p">(</span><span class="n">a</span><span class="p">.</span><span class="n">is_ancestor_of</span><span class="p">(</span><span class="o">&amp;</span><span class="n">a</span><span class="p">));</span><span class="w">   </span><span class="c1">// true  (equal ⇒ ancestor)</span>
+
+<span class="fm">assert_eq!</span><span class="p">(</span><span class="n">b</span><span class="p">.</span><span class="n">name_at_rank</span><span class="p">(</span><span class="s">&quot;species&quot;</span><span class="p">),</span><span class="w"> </span><span class="nb">Some</span><span class="p">(</span><span class="s">&quot;Escherichia coli&quot;</span><span class="p">));</span>
+<span class="fm">assert_eq!</span><span class="p">(</span><span class="n">b</span><span class="p">.</span><span class="n">name_at_rank</span><span class="p">(</span><span class="s">&quot;genus&quot;</span><span class="p">),</span><span class="w">   </span><span class="nb">Some</span><span class="p">(</span><span class="s">&quot;Escherichia&quot;</span><span class="p">));</span>
+<span class="fm">assert_eq!</span><span class="p">(</span><span class="n">b</span><span class="p">.</span><span class="n">name_at_rank</span><span class="p">(</span><span class="s">&quot;order&quot;</span><span class="p">),</span><span class="w">   </span><span class="nb">None</span><span class="p">);</span>
+</code></pre></div>
+<hr />
+<h2 id="integration-with-genomeinfo">Integration with <code>GenomeInfo</code></h2>
+<p>At index load time, every metadata value is inspected once:</p>
+<ul>
+<li>Starts with <code>taxonomy:/</code> → parsed into <code>TaxPath</code>, stored in <code>genome.taxonomy</code>.</li>
+<li>Otherwise → kept as-is in <code>genome.meta</code>.</li>
+</ul>
+<div class="highlight"><pre><span></span><code><span class="k">struct</span><span class="w"> </span><span class="nc">GenomeInfo</span><span class="w"> </span><span class="p">{</span>
+<span class="w">    </span><span class="n">label</span><span class="p">:</span><span class="w">    </span><span class="nb">String</span><span class="p">,</span>
+<span class="w">    </span><span class="n">meta</span><span class="p">:</span><span class="w">     </span><span class="nc">HashMap</span><span class="o">&lt;</span><span class="nb">String</span><span class="p">,</span><span class="w"> </span><span class="nb">String</span><span class="o">&gt;</span><span class="p">,</span><span class="w">    </span><span class="c1">// plain text metadata</span>
+<span class="w">    </span><span class="n">taxonomy</span><span class="p">:</span><span class="w"> </span><span class="nc">HashMap</span><span class="o">&lt;</span><span class="nb">String</span><span class="p">,</span><span class="w"> </span><span class="n">TaxPath</span><span class="o">&gt;</span><span class="p">,</span><span class="w">   </span><span class="c1">// parsed taxonomy metadata</span>
+<span class="p">}</span>
+</code></pre></div>
+<p>The raw string is not duplicated. <code>TaxPath::to_string()</code> reconstructs the
+original value losslessly for serialisation.</p>
+<hr />
+<h2 id="predicate-operators-in-filter-select">Predicate operators (in <code>filter</code> / <code>select</code>)</h2>
+<p>Path predicates use the <code>~</code> / <code>!~</code> operators. The <strong>stored value</strong> always starts
+with <code>/</code> (rooted path); the <strong>query pattern</strong> does not need to.</p>
+<h3 id="path-pattern-syntax">Path pattern syntax</h3>
+<table>
+<thead>
+<tr>
+<th>Pattern</th>
+<th>Semantics</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>A/B</code></td>
+<td>contiguous sub-path A then B, anywhere in the value</td>
+</tr>
+<tr>
+<td><code>/A/B</code></td>
+<td>value starts with A then B (start-anchored)</td>
+</tr>
+<tr>
+<td><code>A/B$</code></td>
+<td>value ends with A then B (end-anchored)</td>
+</tr>
+<tr>
+<td><code>/A/B$</code></td>
+<td>value is exactly A then B (fully anchored)</td>
+</tr>
+<tr>
+<td><code>A@x/B</code></td>
+<td>A with class <code>x</code> followed by B with any class</td>
+</tr>
+<tr>
+<td><code>A@x/B@y</code></td>
+<td>A with class <code>x</code> followed by B with class <code>y</code></td>
+</tr>
+</tbody>
+</table>
+<p>A segment pattern without <code>@</code> matches the segment name regardless of its stored class.</p>
+<h3 id="rank-aware-queries">Rank-aware queries</h3>
+<div class="highlight"><pre><span></span><code>key@rank=value
+</code></pre></div>
+<table>
+<thead>
+<tr>
+<th>Predicate form</th>
+<th>Semantics</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>key@rank=value</code></td>
+<td>genome's <code>key</code> has <code>value</code> at rank <code>rank</code></td>
+</tr>
+<tr>
+<td><code>key@rank!=value</code></td>
+<td>does not</td>
+</tr>
+<tr>
+<td><code>key@rank=v1\|v2</code></td>
+<td>value at <code>rank</code> is <code>v1</code> or <code>v2</code></td>
+</tr>
+</tbody>
+</table>
+<p><code>~</code> combined with <code>@rank</code> on the key (e.g. <code>key@genus~pattern</code>) is not defined
+and is rejected at parse time.</p>
+
+
+
+
+
+
+
+
+
+
+
+
+                
+              </article>
+            </div>
+          
+          
+<script>var target=document.getElementById(location.hash.slice(1));target&&target.name&&(target.checked=target.name.startsWith("__tabbed_"))</script>
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+</html>
\ No newline at end of file
diff --git a/doc/implementation/persistent_bit_vec.refs/index.html b/DevDoc/implementation/persistent_bit_vec.refs/index.html
similarity index 86%
rename from doc/implementation/persistent_bit_vec.refs/index.html
rename to DevDoc/implementation/persistent_bit_vec.refs/index.html
index 54b32a2a..ed24d31a 100644
--- a/doc/implementation/persistent_bit_vec.refs/index.html
+++ b/DevDoc/implementation/persistent_bit_vec.refs/index.html
@@ -178,6 +178,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
     
     
     
@@ -187,10 +214,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
         
           
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
             
   
   
@@ -208,8 +235,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -359,6 +386,34 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -381,10 +436,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
         
           
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
             
   
   
@@ -402,8 +457,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -784,14 +839,98 @@
   
   
     <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
   
 
     
@@ -827,10 +966,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
         
           
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
             
   
   
@@ -848,8 +987,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -915,6 +1054,90 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
diff --git a/doc/implementation/persistent_bit_vec/index.html b/DevDoc/implementation/persistent_bit_vec/index.html
similarity index 94%
rename from doc/implementation/persistent_bit_vec/index.html
rename to DevDoc/implementation/persistent_bit_vec/index.html
index c7105acd..ff48156b 100644
--- a/doc/implementation/persistent_bit_vec/index.html
+++ b/DevDoc/implementation/persistent_bit_vec/index.html
@@ -182,6 +182,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
     
     
     
@@ -191,10 +218,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
         
           
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
             
   
   
@@ -212,8 +239,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -363,6 +390,34 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -387,10 +442,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
         
           
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
             
   
   
@@ -408,8 +463,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_4">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -1065,14 +1120,98 @@
   
   
     <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
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+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
   
 
     
@@ -827,10 +966,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
         
           
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
             
   
   
@@ -848,8 +987,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -915,6 +1054,90 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
diff --git a/doc/implementation/pipeline/index.html b/DevDoc/implementation/pipeline/index.html
similarity index 93%
rename from doc/implementation/pipeline/index.html
rename to DevDoc/implementation/pipeline/index.html
index 91d32f09..211b01f0 100644
--- a/doc/implementation/pipeline/index.html
+++ b/DevDoc/implementation/pipeline/index.html
@@ -182,6 +182,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
     
     
     
@@ -191,10 +218,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
         
           
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
             
   
   
@@ -212,8 +239,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -363,6 +390,34 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -387,10 +442,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
         
           
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
             
   
   
@@ -408,8 +463,8 @@
             <span class="md-nav__icon md-icon"></span>
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_4">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -914,14 +969,98 @@
   
   
     <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
   
 
     
@@ -957,10 +1096,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
         
           
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+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
             
   
   
@@ -978,8 +1117,8 @@
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -1045,6 +1184,90 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
diff --git a/DevDoc/implementation/select/index.html b/DevDoc/implementation/select/index.html
new file mode 100644
index 00000000..d1351204
--- /dev/null
+++ b/DevDoc/implementation/select/index.html
@@ -0,0 +1,1952 @@
+
+<!doctype html>
+<html lang="en" class="no-js">
+  <head>
+    
+      <meta charset="utf-8">
+      <meta name="viewport" content="width=device-width,initial-scale=1">
+      
+      
+      
+      
+        <link rel="prev" href="../filtering/">
+      
+      
+        <link rel="next" href="../obitaxonomy/">
+      
+      
+        
+      
+      
+      <link rel="icon" href="../../assets/images/favicon.png">
+      <meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.7.6">
+    
+    
+      
+        <title>Select command - obikmer</title>
+      
+    
+    
+      <link rel="stylesheet" href="../../assets/stylesheets/main.484c7ddc.min.css">
+      
+      
+
+
+    
+    
+      
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+    
+      
+        
+        
+        <link rel="preconnect" href="https://fonts.gstatic.com" crossorigin>
+        <link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Roboto:300,300i,400,400i,700,700i%7CRoboto+Mono:400,400i,700,700i&display=fallback">
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+  </head>
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+    <body dir="ltr">
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+    <input class="md-toggle" data-md-toggle="drawer" type="checkbox" id="__drawer" autocomplete="off">
+    <input class="md-toggle" data-md-toggle="search" type="checkbox" id="__search" autocomplete="off">
+    <label class="md-overlay" for="__drawer"></label>
+    <div data-md-component="skip">
+      
+        
+        <a href="#select-column-projection-and-aggregation" class="md-skip">
+          Skip to content
+        </a>
+      
+    </div>
+    <div data-md-component="announce">
+      
+    </div>
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+    
+      
+
+  
+
+<header class="md-header md-header--shadow" data-md-component="header">
+  <nav class="md-header__inner md-grid" aria-label="Header">
+    <a href="../.." title="obikmer" class="md-header__button md-logo" aria-label="obikmer" data-md-component="logo">
+      
+  
+  <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M12 8a3 3 0 0 0 3-3 3 3 0 0 0-3-3 3 3 0 0 0-3 3 3 3 0 0 0 3 3m0 3.54C9.64 9.35 6.5 8 3 8v11c3.5 0 6.64 1.35 9 3.54 2.36-2.19 5.5-3.54 9-3.54V8c-3.5 0-6.64 1.35-9 3.54"/></svg>
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+      
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+    <div class="md-header__title" data-md-component="header-title">
+      <div class="md-header__ellipsis">
+        <div class="md-header__topic">
+          <span class="md-ellipsis">
+            obikmer
+          </span>
+        </div>
+        <div class="md-header__topic" data-md-component="header-topic">
+          <span class="md-ellipsis">
+            
+              Select command
+            
+          </span>
+        </div>
+      </div>
+    </div>
+    
+    
+      <script>var palette=__md_get("__palette");if(palette&&palette.color){if("(prefers-color-scheme)"===palette.color.media){var media=matchMedia("(prefers-color-scheme: light)"),input=document.querySelector(media.matches?"[data-md-color-media='(prefers-color-scheme: light)']":"[data-md-color-media='(prefers-color-scheme: dark)']");palette.color.media=input.getAttribute("data-md-color-media"),palette.color.scheme=input.getAttribute("data-md-color-scheme"),palette.color.primary=input.getAttribute("data-md-color-primary"),palette.color.accent=input.getAttribute("data-md-color-accent")}for(var[key,value]of Object.entries(palette.color))document.body.setAttribute("data-md-color-"+key,value)}</script>
+    
+    
+    
+    
+  </nav>
+  
+</header>
+    
+    <div class="md-container" data-md-component="container">
+      
+      
+        
+          
+        
+      
+      <main class="md-main" data-md-component="main">
+        <div class="md-main__inner md-grid">
+          
+            
+              
+              <div class="md-sidebar md-sidebar--primary" data-md-component="sidebar" data-md-type="navigation" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+
+
+<nav class="md-nav md-nav--primary" aria-label="Navigation" data-md-level="0">
+  <label class="md-nav__title" for="__drawer">
+    <a href="../.." title="obikmer" class="md-nav__button md-logo" aria-label="obikmer" data-md-component="logo">
+      
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+  <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M12 8a3 3 0 0 0 3-3 3 3 0 0 0-3-3 3 3 0 0 0-3 3 3 3 0 0 0 3 3m0 3.54C9.64 9.35 6.5 8 3 8v11c3.5 0 6.64 1.35 9 3.54 2.36-2.19 5.5-3.54 9-3.54V8c-3.5 0-6.64 1.35-9 3.54"/></svg>
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+    obikmer
+  </label>
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+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../.." class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Home
+  
+
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+  </span>
+  
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+      
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+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
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+  
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+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
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+      
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        
+          
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+            
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Theory
+  
+
+    
+  </span>
+  
+  
+
+            <span class="md-nav__icon md-icon"></span>
+          </label>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            
+  
+    Theory
+  
+
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../kmers/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmers and super-kmers
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/encoding/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    DNA encoding
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/entropy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Entropy filter
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/minimizer/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Minimizer selection
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/indexing/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Partitioning architecture
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+    
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--active md-nav__item--nested">
+      
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        
+          
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+            
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Implementation
+  
+
+    
+  </span>
+  
+  
+
+            <span class="md-nav__icon md-icon"></span>
+          </label>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_4">
+            <span class="md-nav__icon md-icon"></span>
+            
+  
+    Implementation
+  
+
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../superkmer/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    SuperKmer
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../kmer/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../chunkreader/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Chunk reader
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../pipeline/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Construction pipeline
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obipipeline/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obipipeline library
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../storage/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    On-disk storage
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../mphf/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    MPHF selection
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../unitig_evidence/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Unitig evidence encoding
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../evidence_elimination/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Evidence elimination (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obilayeredmap/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obilayeredmap crate
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../persistent_compact_int_vec/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    PersistentCompactIntVec
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../persistent_bit_vec/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    PersistentBitVec
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../merge/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Merge command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../merge_parallelism/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+    
+  
+  
+  
+    <li class="md-nav__item md-nav__item--active">
+      
+      <input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
+      
+      
+        
+      
+      
+        <label class="md-nav__link md-nav__link--active" for="__toc">
+          
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+          <span class="md-nav__icon md-icon"></span>
+        </label>
+      
+      <a href="./" class="md-nav__link md-nav__link--active">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+      
+        
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+    
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#synopsis" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Synopsis
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#output-destination" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Output destination
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#defining-output-columns" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Defining output columns
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Defining output columns">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#named-groups-group" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Named groups — --group
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#per-group-operator-group-op" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Per-group operator — --group-op
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#shorthand-aggregate-by-aggregate-op" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Shorthand — --aggregate-by / --aggregate-op
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#column-selection-and-ordering-select" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Column selection and ordering — --select
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#aggregation-operators" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Aggregation operators
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#behaviour-for-edge-cases" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Behaviour for edge cases
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#examples" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Examples
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Examples">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#aggregate-by-metadata-group-default-operators" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Aggregate by metadata group, default operators
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#named-groups-with-different-operators" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Named groups with different operators
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#mix-aggregated-group-and-individual-genome" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Mix aggregated group and individual genome
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#pure-column-projection-no-aggregation" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Pure column projection (no aggregation)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#in-place-keep-only-group-a" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        In-place: keep only group A
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#compose-with-filter" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Compose with filter
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#implementation-notes" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Implementation notes
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
+            
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Architecture
+  
+
+    
+  </span>
+  
+  
+
+            <span class="md-nav__icon md-icon"></span>
+          </label>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
+            <span class="md-nav__icon md-icon"></span>
+            
+  
+    Architecture
+  
+
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/sequences/invariant/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sequences
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/index_architecture/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer index
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+    
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#synopsis" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Synopsis
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#output-destination" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Output destination
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#defining-output-columns" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Defining output columns
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Defining output columns">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#named-groups-group" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Named groups — --group
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#per-group-operator-group-op" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Per-group operator — --group-op
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#shorthand-aggregate-by-aggregate-op" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Shorthand — --aggregate-by / --aggregate-op
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#column-selection-and-ordering-select" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Column selection and ordering — --select
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#aggregation-operators" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Aggregation operators
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#behaviour-for-edge-cases" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Behaviour for edge cases
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#examples" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Examples
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Examples">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#aggregate-by-metadata-group-default-operators" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Aggregate by metadata group, default operators
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#named-groups-with-different-operators" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Named groups with different operators
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#mix-aggregated-group-and-individual-genome" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Mix aggregated group and individual genome
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#pure-column-projection-no-aggregation" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Pure column projection (no aggregation)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#in-place-keep-only-group-a" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        In-place: keep only group A
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#compose-with-filter" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Compose with filter
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#implementation-notes" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Implementation notes
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+
+<h1 id="select-column-projection-and-aggregation"><code>select</code> — column projection and aggregation</h1>
+<p><code>select</code> transforms an index by operating on its <strong>genome columns</strong>: projecting a
+subset of columns, aggregating groups of genomes into synthetic columns, or both.
+It is the column-axis counterpart of <code>filter</code> (row-axis operations).</p>
+<p>Following relational algebra conventions:</p>
+<table>
+<thead>
+<tr>
+<th>Command</th>
+<th>Relational operation</th>
+<th>Axis</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>filter</code></td>
+<td>σ — selection</td>
+<td>rows (k-mers)</td>
+</tr>
+<tr>
+<td><code>select</code></td>
+<td>π — projection</td>
+<td>columns (genomes)</td>
+</tr>
+</tbody>
+</table>
+<p>The two commands compose naturally: run <code>filter</code> first to restrict the kmer set,
+then <code>select</code> to reshape the genome columns.</p>
+<p><code>select</code> never changes the kmer set. The MPHF and <code>unitigs.bin</code> of each layer
+are preserved unchanged; only the data matrices are rewritten.</p>
+<hr />
+<h2 id="synopsis">Synopsis</h2>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span><span class="k">select</span><span class="w"> </span>&lt;input-index&gt;
+<span class="w">        </span><span class="o">{</span><span class="w"> </span>--output<span class="w"> </span>&lt;dir&gt;<span class="w"> </span><span class="p">|</span><span class="w"> </span>--in-place<span class="w"> </span><span class="o">}</span>
+<span class="w">        </span><span class="o">[</span>--group<span class="w">    </span>&lt;name&gt;:&lt;pred&gt;<span class="w">  </span>...<span class="o">]</span>
+<span class="w">        </span><span class="o">[</span>--group-op<span class="w"> </span>&lt;name&gt;:&lt;op&gt;<span class="w">    </span>...<span class="o">]</span>
+<span class="w">        </span><span class="o">[</span>--aggregate-by<span class="w"> </span>&lt;key&gt;<span class="w">          </span><span class="o">]</span>
+<span class="w">        </span><span class="o">[</span>--aggregate-op<span class="w"> </span>&lt;op&gt;<span class="w">           </span><span class="o">]</span>
+<span class="w">        </span><span class="o">[</span>--select<span class="w">   </span>&lt;col1,col2,...&gt;<span class="w">    </span><span class="o">]</span>
+<span class="w">        </span><span class="o">[</span>--presence-threshold<span class="w"> </span>&lt;N&gt;<span class="w">      </span><span class="o">]</span>
+</code></pre></div>
+<hr />
+<h2 id="output-destination">Output destination</h2>
+<p>Exactly one of <code>--output</code> or <code>--in-place</code> must be specified.</p>
+<p><strong><code>--output &lt;dir&gt;</code></strong> — writes a new index to <code>&lt;dir&gt;</code>. The source index is
+unchanged. The MPHF and unitig files are copied; only the data matrices are
+rewritten with the new column layout.</p>
+<p><strong><code>--in-place</code></strong> — rewrites the data matrices of the source index directly.
+Removed or replaced columns are lost. The operation writes to temporary files
+first, then renames atomically, so an interrupted run leaves the index intact.</p>
+<hr />
+<h2 id="defining-output-columns">Defining output columns</h2>
+<h3 id="named-groups-group">Named groups — <code>--group</code></h3>
+<div class="highlight"><pre><span></span><code>--group &lt;name&gt;:&lt;pred&gt;
+</code></pre></div>
+<p>Defines a named group of genomes using the same predicate syntax as <code>filter</code>.
+Repeatable; a genome can belong to several groups.</p>
+<div class="highlight"><pre><span></span><code>--group<span class="w"> </span><span class="s2">&quot;pub:species=Betula_pubescens&quot;</span>
+--group<span class="w"> </span><span class="s2">&quot;nan:species=Betula_nana&quot;</span>
+</code></pre></div>
+<h3 id="per-group-operator-group-op">Per-group operator — <code>--group-op</code></h3>
+<div class="highlight"><pre><span></span><code>--group-op &lt;name&gt;:&lt;op&gt;
+</code></pre></div>
+<p>Assigns an aggregation operator to a named group. Optional; if absent, the
+default operator applies (see below).</p>
+<div class="highlight"><pre><span></span><code>--group-op<span class="w"> </span><span class="s2">&quot;pub:any&quot;</span>
+--group-op<span class="w"> </span><span class="s2">&quot;nan:all&quot;</span>
+</code></pre></div>
+<h3 id="shorthand-aggregate-by-aggregate-op">Shorthand — <code>--aggregate-by</code> / <code>--aggregate-op</code></h3>
+<p><code>--aggregate-by &lt;key&gt;</code> automatically creates one group per unique value of the
+metadata key <code>&lt;key&gt;</code>. Equivalent to one <code>--group &lt;val&gt;:&lt;key&gt;=&lt;val&gt;</code> per distinct
+value. <code>--aggregate-op &lt;op&gt;</code> sets the operator for all auto-generated groups.</p>
+<p><code>--aggregate-by</code> and <code>--group</code> are mutually exclusive.</p>
+<h3 id="column-selection-and-ordering-select">Column selection and ordering — <code>--select</code></h3>
+<div class="highlight"><pre><span></span><code>--select col1,col2,...
+</code></pre></div>
+<p>Lists the output columns in order. Each element is either a group name (defined
+by <code>--group</code> or generated by <code>--aggregate-by</code>) or a genome label from the source
+index (pass-through, no aggregation).</p>
+<p><strong>Default when <code>--select</code> is absent:</strong>
+all defined groups in declaration order (for <code>--group</code>), or all generated groups
+in metadata-value order (for <code>--aggregate-by</code>). Individual genomes not in any
+group are excluded unless named explicitly.</p>
+<p><strong>When neither <code>--group</code> nor <code>--aggregate-by</code> is specified:</strong>
+<code>--select</code> can still reference genome labels for pure column projection (no
+aggregation). If <code>--select</code> is also absent, all genomes are output unchanged
+(identity transform — useful combined with row filtering via a prior <code>filter</code>
+run).</p>
+<hr />
+<h2 id="aggregation-operators">Aggregation operators</h2>
+<table>
+<thead>
+<tr>
+<th>Operator</th>
+<th>Input</th>
+<th>Output</th>
+<th>Semantics</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>any</code></td>
+<td>pres / count</td>
+<td>presence</td>
+<td>1 if ≥ 1 genome in group carries the k-mer</td>
+</tr>
+<tr>
+<td><code>all</code></td>
+<td>pres / count</td>
+<td>presence</td>
+<td>1 if every genome in group carries the k-mer</td>
+</tr>
+<tr>
+<td><code>none</code></td>
+<td>pres / count</td>
+<td>presence</td>
+<td>1 if no genome in group carries the k-mer</td>
+</tr>
+<tr>
+<td><code>sum</code></td>
+<td>count</td>
+<td>count</td>
+<td>sum of counts across the group</td>
+</tr>
+<tr>
+<td><code>min</code></td>
+<td>count</td>
+<td>count</td>
+<td>minimum count</td>
+</tr>
+<tr>
+<td><code>max</code></td>
+<td>count</td>
+<td>count</td>
+<td>maximum count</td>
+</tr>
+</tbody>
+</table>
+<p><strong>Default operator:</strong>
+- Presence index: <code>any</code>
+- Count index: <code>sum</code></p>
+<p>Logical operators (<code>any</code>/<code>all</code>/<code>none</code>) on a count index use
+<code>--presence-threshold N</code> (default 0): a genome "carries" the k-mer if its count
+is &gt; N.</p>
+<p><strong>Output index type:</strong>
+- If the source is a presence index, the output is always a presence index.
+- If the source is a count index and every output column uses a logical operator
+  or is a pass-through from a presence source, the output is a presence index.
+- Otherwise (at least one arithmetic operator on a count source), the output is
+  a count index.</p>
+<hr />
+<h2 id="behaviour-for-edge-cases">Behaviour for edge cases</h2>
+<table>
+<thead>
+<tr>
+<th>Situation</th>
+<th>Behaviour</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>Genome missing the metadata key in <code>--aggregate-by</code></td>
+<td>genome ignored (no <code>NA</code> group)</td>
+</tr>
+<tr>
+<td>Genome in multiple groups</td>
+<td>contributes independently to each</td>
+</tr>
+<tr>
+<td><code>--group-op</code> references undefined group</td>
+<td>error</td>
+</tr>
+<tr>
+<td><code>--select</code> element is neither group name nor genome label</td>
+<td>error</td>
+</tr>
+<tr>
+<td><code>--output</code> and <code>--in-place</code> both specified</td>
+<td>error</td>
+</tr>
+<tr>
+<td>Neither <code>--output</code> nor <code>--in-place</code></td>
+<td>error</td>
+</tr>
+<tr>
+<td>Group with zero matching genomes</td>
+<td>column is all-zeros (or all-ones for <code>none</code>)</td>
+</tr>
+</tbody>
+</table>
+<hr />
+<h2 id="examples">Examples</h2>
+<h3 id="aggregate-by-metadata-group-default-operators">Aggregate by metadata group, default operators</h3>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span><span class="k">select</span><span class="w"> </span>myindex<span class="w"> </span>--output<span class="w"> </span>out<span class="w"> </span>--aggregate-by<span class="w"> </span>group
+<span class="c1"># one column per unique value of &quot;group&quot;; presence→any, count→sum</span>
+</code></pre></div>
+<h3 id="named-groups-with-different-operators">Named groups with different operators</h3>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span><span class="k">select</span><span class="w"> </span>myindex<span class="w"> </span>--output<span class="w"> </span>out<span class="w"> </span><span class="se">\</span>
+<span class="w">  </span>--group<span class="w">    </span><span class="s2">&quot;pub:species=Betula_pubescens&quot;</span><span class="w"> </span><span class="se">\</span>
+<span class="w">  </span>--group<span class="w">    </span><span class="s2">&quot;nan:species=Betula_nana&quot;</span><span class="w"> </span><span class="se">\</span>
+<span class="w">  </span>--group-op<span class="w"> </span><span class="s2">&quot;pub:any&quot;</span><span class="w"> </span><span class="se">\</span>
+<span class="w">  </span>--group-op<span class="w"> </span><span class="s2">&quot;nan:all&quot;</span><span class="w"> </span><span class="se">\</span>
+<span class="w">  </span>--select<span class="w">   </span><span class="s2">&quot;pub,nan&quot;</span>
+</code></pre></div>
+<h3 id="mix-aggregated-group-and-individual-genome">Mix aggregated group and individual genome</h3>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span><span class="k">select</span><span class="w"> </span>myindex<span class="w"> </span>--output<span class="w"> </span>out<span class="w"> </span><span class="se">\</span>
+<span class="w">  </span>--group<span class="w">  </span><span class="s2">&quot;A:group=A&quot;</span><span class="w"> </span><span class="se">\</span>
+<span class="w">  </span>--select<span class="w"> </span><span class="s2">&quot;A,Betula_nana--IGA-24-39&quot;</span>
+</code></pre></div>
+<h3 id="pure-column-projection-no-aggregation">Pure column projection (no aggregation)</h3>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span><span class="k">select</span><span class="w"> </span>myindex<span class="w"> </span>--output<span class="w"> </span>out<span class="w"> </span><span class="se">\</span>
+<span class="w">  </span>--select<span class="w"> </span><span class="s2">&quot;Betula_nana--TROM-V-149986,Betula_nana--AG-P04-25-01&quot;</span>
+</code></pre></div>
+<h3 id="in-place-keep-only-group-a">In-place: keep only group A</h3>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span><span class="k">select</span><span class="w"> </span>myindex<span class="w"> </span>--in-place<span class="w"> </span>--group<span class="w"> </span><span class="s2">&quot;A:group=A&quot;</span><span class="w"> </span>--select<span class="w"> </span><span class="s2">&quot;A&quot;</span>
+</code></pre></div>
+<h3 id="compose-with-filter">Compose with filter</h3>
+<div class="highlight"><pre><span></span><code><span class="c1"># Step 1: keep only B. nana-specific k-mers</span>
+obikmer<span class="w"> </span>filter<span class="w"> </span>myindex<span class="w"> </span>--output<span class="w"> </span>filtered<span class="w"> </span><span class="se">\</span>
+<span class="w">  </span>--ingroup<span class="w"> </span><span class="s2">&quot;species=Betula_nana&quot;</span><span class="w"> </span>--outgroup<span class="w"> </span><span class="s2">&quot;*&quot;</span>
+
+<span class="c1"># Step 2: aggregate genome columns by collection site</span>
+obikmer<span class="w"> </span><span class="k">select</span><span class="w"> </span>filtered<span class="w"> </span>--output<span class="w"> </span>final<span class="w"> </span>--aggregate-by<span class="w"> </span>site
+</code></pre></div>
+<hr />
+<h2 id="implementation-notes">Implementation notes</h2>
+<p><code>select</code> does not rebuild the MPHF. The 256 partitions are processed in parallel
+(rayon), each writing its output independently; results require no synchronisation
+because every partition owns a distinct set of files.</p>
+<p>For each layer in each partition:</p>
+<ol>
+<li>The slot count <code>n</code> is read by opening the source data matrix.</li>
+<li>A new data matrix is built with M columns (M = number of output columns).</li>
+<li>For each slot <code>s</code> in <code>0..n</code>:</li>
+<li><code>old_row = matrix.fill_row(s)</code> — reads the original <code>N</code>-column row without allocating.</li>
+<li>For each output column <code>j</code>:<ul>
+<li><code>new_row[j] = aggregate(op, old_row[group_indices])</code>.</li>
+<li>Pass-through columns are represented as single-element groups with the
+   default operator (<code>any</code> for presence, <code>sum</code> for count) — same code path.</li>
+</ul>
+</li>
+<li>The new row is written slot by slot into each column builder.</li>
+<li>All plain files in the source layer directory (<code>mphf.bin</code>, <code>unitigs.bin</code>,
+   evidence files, <code>layer_meta.json</code>) are copied verbatim; only the <code>presence/</code>
+   or <code>counts/</code> subdirectory is rewritten.</li>
+<li><code>index.meta</code> is rewritten with the new genome list and updated <code>with_counts</code>.</li>
+</ol>
+<p><strong><code>--in-place</code> write strategy:</strong> new data is written to a temporary sibling
+directory (<code>presence_new/</code> or <code>counts_new/</code>); on success the old directory is
+removed and the temporary one is renamed into place. An interrupted run leaves
+at most one stale <code>*_new/</code> directory; the original data is intact until the
+rename step.</p>
+
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diff --git a/doc/implementation/storage.refs/index.html b/DevDoc/implementation/storage.refs/index.html
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@@ -178,6 +178,33 @@
   
   
   
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+  
+
+      </a>
+    </li>
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+  
+  
+
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+  
+  
+
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+  
+
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -915,6 +1054,90 @@
 
               
             
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+  
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+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
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+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
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+  
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+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
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+  
+  <span class="md-ellipsis">
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+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
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+
+      </a>
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+  
+
+              
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diff --git a/doc/implementation/storage/index.html b/DevDoc/implementation/storage/index.html
similarity index 92%
rename from doc/implementation/storage/index.html
rename to DevDoc/implementation/storage/index.html
index d284fd87..c463fba5 100644
--- a/doc/implementation/storage/index.html
+++ b/DevDoc/implementation/storage/index.html
@@ -182,6 +182,33 @@
   
   
   
+    <li class="md-nav__item">
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+
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+          <label class="md-nav__title" for="__nav_3">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -363,6 +390,34 @@
 
               
             
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+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
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+
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+              
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
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+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
             
   
   
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-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_4">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -986,14 +1041,98 @@
   
   
     <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
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+      <a href="../filtering/" class="md-nav__link">
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+
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+  
+  
+
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+
+              
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+      <a href="../select/" class="md-nav__link">
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+  
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+    Select command
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+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
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+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
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+  
+    obitaxonomy crate
   
 
     
@@ -1029,10 +1168,10 @@
       
         
         
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             <span class="md-nav__icon md-icon"></span>
             
   
@@ -1117,6 +1256,90 @@
 
               
             
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+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
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+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
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+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
diff --git a/doc/implementation/superkmer.refs/index.html b/DevDoc/implementation/superkmer.refs/index.html
similarity index 86%
rename from doc/implementation/superkmer.refs/index.html
rename to DevDoc/implementation/superkmer.refs/index.html
index f5ada01f..62a1ac84 100644
--- a/doc/implementation/superkmer.refs/index.html
+++ b/DevDoc/implementation/superkmer.refs/index.html
@@ -178,6 +178,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
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+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
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@@ -187,10 +214,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
         
           
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+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
             
   
   
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -359,6 +386,34 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
         
           
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
             
   
   
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -784,14 +839,98 @@
   
   
     <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
   
 
     
@@ -827,10 +966,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
         
           
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
             
   
   
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -915,6 +1054,90 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
diff --git a/doc/implementation/superkmer/index.html b/DevDoc/implementation/superkmer/index.html
similarity index 93%
rename from doc/implementation/superkmer/index.html
rename to DevDoc/implementation/superkmer/index.html
index d7ee7a0d..f7a43cec 100644
--- a/doc/implementation/superkmer/index.html
+++ b/DevDoc/implementation/superkmer/index.html
@@ -9,7 +9,7 @@
       
       
       
-        <link rel="prev" href="../../theory/indexing/">
+        <link rel="prev" href="../../theory/evolutionary_distances/">
       
       
         <link rel="next" href="../kmer/">
@@ -182,6 +182,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
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+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
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+  
+  
     
     
     
@@ -191,10 +218,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
         
           
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
             
   
   
@@ -212,8 +239,8 @@
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -363,6 +390,34 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -387,10 +442,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
         
           
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
             
   
   
@@ -408,8 +463,8 @@
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_4">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -892,14 +947,98 @@
   
   
     <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
   
 
     
@@ -935,10 +1074,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
         
           
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
             
   
   
@@ -956,8 +1095,8 @@
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -1023,6 +1162,90 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
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+    
+  </span>
+  
+  
+
+      </a>
+      
+        
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+    
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#subcommands" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Subcommands
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#constraints" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Constraints
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#parameter-constraints-enforced-at-cli" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Parameter constraints (enforced at CLI)
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#genome-label-constraints" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Genome label constraints
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#priority-operations" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Priority operations
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        
+          
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+            
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Theory
+  
+
+    
+  </span>
+  
+  
+
+            <span class="md-nav__icon md-icon"></span>
+          </label>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            
+  
+    Theory
+  
+
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="kmers/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmers and super-kmers
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="theory/encoding/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    DNA encoding
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="theory/entropy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Entropy filter
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="theory/minimizer/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Minimizer selection
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="theory/indexing/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Partitioning architecture
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        
+          
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+            
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Implementation
+  
+
+    
+  </span>
+  
+  
+
+            <span class="md-nav__icon md-icon"></span>
+          </label>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
+            <span class="md-nav__icon md-icon"></span>
+            
+  
+    Implementation
+  
+
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="implementation/superkmer/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    SuperKmer
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="implementation/kmer/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="implementation/chunkreader/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Chunk reader
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="implementation/pipeline/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Construction pipeline
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="implementation/obipipeline/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obipipeline library
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="implementation/storage/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    On-disk storage
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="implementation/mphf/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    MPHF selection
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="implementation/unitig_evidence/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Unitig evidence encoding
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="implementation/evidence_elimination/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Evidence elimination (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="implementation/obilayeredmap/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obilayeredmap crate
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="implementation/persistent_compact_int_vec/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    PersistentCompactIntVec
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="implementation/persistent_bit_vec/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    PersistentBitVec
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="implementation/merge/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Merge command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="implementation/merge_parallelism/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="implementation/filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="implementation/select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="implementation/obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
+            
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Architecture
+  
+
+    
+  </span>
+  
+  
+
+            <span class="md-nav__icon md-icon"></span>
+          </label>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
+            <span class="md-nav__icon md-icon"></span>
+            
+  
+    Architecture
+  
+
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="architecture/sequences/invariant/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sequences
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="architecture/index_architecture/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer index
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+    
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#subcommands" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Subcommands
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#constraints" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Constraints
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#parameter-constraints-enforced-at-cli" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Parameter constraints (enforced at CLI)
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#genome-label-constraints" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Genome label constraints
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#priority-operations" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Priority operations
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+
+<h1 id="obikmer">obikmer</h1>
+<p><code>obikmer</code> is a Rust tool for manipulation, counting, indexing, and set operations on DNA sequences represented as kmer sets.</p>
+<h2 id="subcommands">Subcommands</h2>
+<table>
+<thead>
+<tr>
+<th>Subcommand</th>
+<th>Purpose</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>superkmer</code></td>
+<td>Extract super-kmers from a sequence file and write to stdout</td>
+</tr>
+<tr>
+<td><code>index</code></td>
+<td>Build a complete genome index (scatter → dereplicate → count → layered MPHF)</td>
+</tr>
+<tr>
+<td><code>merge</code></td>
+<td>Merge multiple built indexes into one</td>
+</tr>
+<tr>
+<td><code>filter</code></td>
+<td>Apply row-level selection (σ) to an index: retain only k-mers matching the ingroup/outgroup predicates. Output is a new single-layer index — compaction is a consequence, not the goal. Supports the shared <a href="implementation/filtering/">kmer filtering</a> system</td>
+</tr>
+<tr>
+<td><code>query</code></td>
+<td>Query an index with sequences and annotate matches</td>
+</tr>
+<tr>
+<td><code>dump</code></td>
+<td>Dump all indexed k-mers as CSV (kmer + per-genome counts or presence); supports the shared <a href="implementation/filtering/">kmer filtering</a> system; <code>--head N</code> limits output to the first N k-mers</td>
+</tr>
+<tr>
+<td><code>annotate</code></td>
+<td>Add or update genome metadata from a CSV file; or dump metadata as CSV</td>
+</tr>
+<tr>
+<td><code>phylo</code></td>
+<td>Compute pairwise evolutionary-distance proxies between genomes (<code>--metric jaccard\|mash\|hamming\|bray-curtis\|relfreq-bray-curtis\|euclidean\|relfreq-euclidean\|hellinger\|hellinger-euclidean</code>); optionally build NJ/UPGMA trees; <code>--presence-threshold N</code> sets the minimum count to consider a k-mer present when computing Jaccard/Mash on count indexes (default 1); optionally a central-position SNP/Sankoff calibration with exports for TNT/PhyG/IQ-TREE (see <a href="theory/evolutionary_distances/">evolutionary distances</a>)</td>
+</tr>
+<tr>
+<td><code>unitig</code></td>
+<td>Build a global de Bruijn graph across all partitions and enumerate its unitigs as FASTA; supports the shared <a href="implementation/filtering/">kmer filtering</a> system</td>
+</tr>
+<tr>
+<td><code>select</code></td>
+<td>Project and/or aggregate genome columns into a new or in-place index; the column-axis counterpart of <code>filter</code> (see <a href="implementation/select/">select</a>)</td>
+</tr>
+<tr>
+<td><code>estimate</code></td>
+<td>Estimate approximate-index parameters (z, evidence bits, FP rates) before indexing</td>
+</tr>
+<tr>
+<td><code>reindex</code></td>
+<td>Convert an index's evidence in-place: exact ↔ approx</td>
+</tr>
+<tr>
+<td><code>utils</code></td>
+<td>Miscellaneous index utilities: <code>--new-label NEW=OLD</code> renames a genome label; <code>--upgrade-index</code> adds missing <code>layer_meta.json</code> to old indexes</td>
+</tr>
+<tr>
+<td><code>pack</code></td>
+<td>Pack per-column matrix files into single-file format to reduce query I/O</td>
+</tr>
+</tbody>
+</table>
+<h2 id="constraints">Constraints</h2>
+<ul>
+<li>Target scale: individual genome datasets, tens of Gbases</li>
+<li>Maximum efficiency in computation, memory, and disk usage</li>
+<li>k odd, k ∈ [11, 31], fixed at runtime; kmer fits in a u64 (2 bits/base)</li>
+<li>Canonical form: <code>min(kmer, revcomp(kmer))</code> reduces strand-symmetric space by half</li>
+<li>Input formats for <code>index</code>/<code>superkmer</code>: FASTA (<code>.fa</code>, <code>.fasta</code>), FASTQ (<code>.fq</code>, <code>.fastq</code>), GenBank flat file (<code>.gb</code>, <code>.gbk</code>, <code>.gbff</code>), all optionally gzip-compressed; directories expanded recursively; streaming stdin via <code>-</code></li>
+<li>Input formats for <code>query</code>: FASTA, FASTQ, optionally gzip-compressed; streaming stdin via <code>-</code></li>
+</ul>
+<h2 id="parameter-constraints-enforced-at-cli">Parameter constraints (enforced at CLI)</h2>
+<p>All constraints below are checked by <code>CommonArgs::validate()</code> at the start of <code>superkmer</code> and <code>index</code>. Invalid values exit immediately with an error.</p>
+<table>
+<thead>
+<tr>
+<th>Parameter</th>
+<th>Constraint</th>
+<th>Reason</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>k (<code>--kmer-size</code>)</td>
+<td>odd</td>
+<td>even k allows palindromic k-mers: kmer == revcomp(kmer), breaking the canonical form invariant</td>
+</tr>
+<tr>
+<td>k (<code>--kmer-size</code>)</td>
+<td>k ∈ [11, 31]</td>
+<td>k &gt; 31 overflows u64 at 2 bits/base; k &lt; 11 gives insufficient specificity</td>
+</tr>
+<tr>
+<td>m (<code>--minimizer-size</code>)</td>
+<td>odd</td>
+<td>same palindrome argument as k</td>
+</tr>
+<tr>
+<td>m (<code>--minimizer-size</code>)</td>
+<td>3 ≤ m ≤ k−1</td>
+<td>minimizer must be strictly shorter than the kmer</td>
+</tr>
+<tr>
+<td>z (<code>-z</code>, Findere, <code>index --approx</code> only)</td>
+<td>z ≤ k−1</td>
+<td>effective indexed kmer size is k−z+1; z ≥ k would make it ≤ 0</td>
+</tr>
+</tbody>
+</table>
+<h2 id="genome-label-constraints">Genome label constraints</h2>
+<p>Genome labels are arbitrary Unicode strings with the following restrictions:</p>
+<table>
+<thead>
+<tr>
+<th>Character</th>
+<th>Forbidden</th>
+<th>Reason</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>/</code></td>
+<td>yes</td>
+<td>filesystem path separator</td>
+</tr>
+<tr>
+<td><code>=</code></td>
+<td>yes</td>
+<td><code>--new-label</code> parser separator</td>
+</tr>
+<tr>
+<td><code>\0</code></td>
+<td>yes</td>
+<td>null byte</td>
+</tr>
+<tr>
+<td><code>\n</code> <code>\r</code> <code>\t</code></td>
+<td>yes</td>
+<td>break CSV output</td>
+</tr>
+<tr>
+<td>spaces</td>
+<td><strong>allowed</strong></td>
+<td>use shell quoting: <code>--new-label 'new label=old label'</code></td>
+</tr>
+</tbody>
+</table>
+<p>Empty labels are also rejected. Labels derived automatically from the index directory name (when <code>--label</code> is omitted) are not validated since they come from the filesystem and are already safe.</p>
+<h2 id="priority-operations">Priority operations</h2>
+<ul>
+<li>Kmer counting (frequencies)</li>
+<li>Fast search / query</li>
+<li>Set operations: union, intersection, difference</li>
+</ul>
+
+
+
+
+
+
+
+
+
+
+
+
+                
+              </article>
+            </div>
+          
+          
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diff --git a/doc/index.refs/index.html b/DevDoc/index.refs/index.html
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@@ -178,6 +178,33 @@
   
   
   
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+  
+
+      </a>
+    </li>
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@@ -187,10 +214,10 @@
       
         
         
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@@ -784,14 +839,98 @@
   
   
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-      <a href="../implementation/rebuild_filter/" class="md-nav__link">
+      <a href="../implementation/merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../implementation/filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../implementation/select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
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+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../implementation/obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
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+    obitaxonomy crate
   
 
     
@@ -827,10 +966,10 @@
       
         
         
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+  
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+    <li class="md-nav__item">
+      <a href="../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
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+
+    
+  </span>
+  
+  
+
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+
+              
+            
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+    <li class="md-nav__item">
+      <a href="../architecture/numa_worker_pools/" class="md-nav__link">
+        
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+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
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+  
+
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+            
+              
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+  
+    <li class="md-nav__item">
+      <a href="../architecture/numa_partition_runner/" class="md-nav__link">
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+    NUMA-aware partition runner
+  
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+  
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+
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+    </li>
+  
+
+              
+            
           </ul>
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new file mode 100644
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+++ b/DevDoc/installation/index.html
@@ -0,0 +1,1625 @@
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+<!doctype html>
+<html lang="en" class="no-js">
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+  </a>
+  
+    <nav class="md-nav" aria-label="C build environment (required for hwloc)">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#linux-debianubuntu" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Linux (Debian/Ubuntu)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#linux-rhelrockyalmalinux" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Linux (RHEL/Rocky/AlmaLinux)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#hpc-clusters" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        HPC clusters
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#macos" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        macOS
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#building" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Building
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Building">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#building-on-hpc-clusters-network-filesystems" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Building on HPC clusters (network filesystems)
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#numa-support" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        NUMA support
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#verifying-the-installation" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Verifying the installation
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        
+          
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+            
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Theory
+  
+
+    
+  </span>
+  
+  
+
+            <span class="md-nav__icon md-icon"></span>
+          </label>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            
+  
+    Theory
+  
+
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../kmers/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmers and super-kmers
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../theory/encoding/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    DNA encoding
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../theory/entropy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Entropy filter
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../theory/minimizer/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Minimizer selection
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../theory/indexing/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Partitioning architecture
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        
+          
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+            
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Implementation
+  
+
+    
+  </span>
+  
+  
+
+            <span class="md-nav__icon md-icon"></span>
+          </label>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
+            <span class="md-nav__icon md-icon"></span>
+            
+  
+    Implementation
+  
+
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../implementation/superkmer/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    SuperKmer
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../implementation/kmer/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../implementation/chunkreader/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Chunk reader
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../implementation/pipeline/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Construction pipeline
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../implementation/obipipeline/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obipipeline library
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../implementation/storage/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    On-disk storage
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../implementation/mphf/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    MPHF selection
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../implementation/unitig_evidence/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Unitig evidence encoding
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../implementation/evidence_elimination/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Evidence elimination (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../implementation/obilayeredmap/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obilayeredmap crate
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../implementation/persistent_compact_int_vec/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    PersistentCompactIntVec
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../implementation/persistent_bit_vec/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    PersistentBitVec
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../implementation/merge/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Merge command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../implementation/merge_parallelism/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../implementation/filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../implementation/select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../implementation/obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
+            
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Architecture
+  
+
+    
+  </span>
+  
+  
+
+            <span class="md-nav__icon md-icon"></span>
+          </label>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
+            <span class="md-nav__icon md-icon"></span>
+            
+  
+    Architecture
+  
+
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../architecture/sequences/invariant/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sequences
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../architecture/index_architecture/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer index
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+    
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#prerequisites" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Prerequisites
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Prerequisites">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#rust-toolchain" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Rust toolchain
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#c-build-environment-required-for-hwloc" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        C build environment (required for hwloc)
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="C build environment (required for hwloc)">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#linux-debianubuntu" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Linux (Debian/Ubuntu)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#linux-rhelrockyalmalinux" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Linux (RHEL/Rocky/AlmaLinux)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#hpc-clusters" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        HPC clusters
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#macos" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        macOS
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#building" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Building
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Building">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#building-on-hpc-clusters-network-filesystems" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Building on HPC clusters (network filesystems)
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#numa-support" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        NUMA support
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#verifying-the-installation" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Verifying the installation
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+
+<h1 id="installation">Installation</h1>
+<h2 id="prerequisites">Prerequisites</h2>
+<h3 id="rust-toolchain">Rust toolchain</h3>
+<p><code>obikmer</code> requires <strong>Rust 1.85 or later</strong> (edition 2024). Install or update via <a href="https://rustup.rs">rustup</a>:</p>
+<div class="highlight"><pre><span></span><code>curl<span class="w"> </span>--proto<span class="w"> </span><span class="s1">&#39;=https&#39;</span><span class="w"> </span>--tlsv1.2<span class="w"> </span>-sSf<span class="w"> </span>https://sh.rustup.rs<span class="w"> </span><span class="p">|</span><span class="w"> </span>sh
+rustup<span class="w"> </span>update<span class="w"> </span>stable
+</code></pre></div>
+<h3 id="c-build-environment-required-for-hwloc">C build environment (required for hwloc)</h3>
+<p><code>obikmer</code> embeds <a href="https://www.open-mpi.org/projects/hwloc/">hwloc</a> (Hardware Locality) for NUMA-aware thread placement on multi-socket machines. hwloc is built from source at compile time via the <code>vendored</code> feature of the <code>hwlocality</code> crate. This requires a standard C build environment.</p>
+<h4 id="linux-debianubuntu">Linux (Debian/Ubuntu)</h4>
+<div class="highlight"><pre><span></span><code>apt<span class="w"> </span>install<span class="w"> </span>build-essential<span class="w"> </span>automake<span class="w"> </span>libtool<span class="w"> </span>autoconf<span class="w"> </span>pkg-config
+</code></pre></div>
+<h4 id="linux-rhelrockyalmalinux">Linux (RHEL/Rocky/AlmaLinux)</h4>
+<div class="highlight"><pre><span></span><code>dnf<span class="w"> </span>install<span class="w"> </span>gcc<span class="w"> </span>make<span class="w"> </span>automake<span class="w"> </span>libtool<span class="w"> </span>autoconf<span class="w"> </span>pkgconfig
+</code></pre></div>
+<h4 id="hpc-clusters">HPC clusters</h4>
+<p>Most HPC clusters provide these tools via the module system:</p>
+<div class="highlight"><pre><span></span><code>module<span class="w"> </span>load<span class="w"> </span>gcc<span class="w"> </span>automake<span class="w"> </span>libtool<span class="w"> </span>autoconf
+</code></pre></div>
+<p>If in doubt, check whether <code>autoreconf --version</code> and <code>libtool --version</code> return successfully.</p>
+<h4 id="macos">macOS</h4>
+<div class="highlight"><pre><span></span><code>brew<span class="w"> </span>install<span class="w"> </span>automake<span class="w"> </span>libtool<span class="w"> </span>autoconf<span class="w"> </span>pkg-config
+</code></pre></div>
+<h2 id="building">Building</h2>
+<div class="highlight"><pre><span></span><code>git<span class="w"> </span>clone<span class="w"> </span>&lt;repository-url&gt;
+<span class="nb">cd</span><span class="w"> </span>obikmer/src
+cargo<span class="w"> </span>build<span class="w"> </span>--release
+</code></pre></div>
+<p>The compiled binary is at <code>target/release/obikmer</code>.</p>
+<h3 id="building-on-hpc-clusters-network-filesystems">Building on HPC clusters (network filesystems)</h3>
+<p>HPC home directories are typically on a network filesystem (Lustre, NFS) optimised for large sequential reads — not for the thousands of small file operations that Cargo generates during compilation. Building directly on such a filesystem can be extremely slow (0.1% CPU utilisation, tens of minutes for what should take seconds).</p>
+<p><strong>Always redirect the build directory to a local scratch disk:</strong></p>
+<div class="highlight"><pre><span></span><code><span class="nv">CARGO_TARGET_DIR</span><span class="o">=</span>/scratch/<span class="nv">$USER</span>/cargo-target<span class="w"> </span>cargo<span class="w"> </span>build<span class="w"> </span>--release
+</code></pre></div>
+<p>Adapt the path to the local scratch available on your cluster (<code>/var/tmp</code>, <code>/tmp</code>, <code>/scratch/local</code>, etc.). Once built, copy the binary to a permanent location:</p>
+<div class="highlight"><pre><span></span><code>cp<span class="w"> </span>/scratch/<span class="nv">$USER</span>/cargo-target/release/obikmer<span class="w"> </span>~/bin/
+</code></pre></div>
+<h2 id="numa-support">NUMA support</h2>
+<p>NUMA-aware thread placement is active automatically on multi-socket Linux machines (detected at runtime via hwloc). No special build flag is required — the detection is built in and falls back gracefully to the single-pool adaptive strategy on:</p>
+<ul>
+<li>macOS (Apple Silicon, unified memory)</li>
+<li>single-socket Linux machines</li>
+<li>any system where hwloc reports only one NUMA node</li>
+</ul>
+<h2 id="verifying-the-installation">Verifying the installation</h2>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>--help
+</code></pre></div>
+
+
+
+
+
+
+
+
+
+
+
+
+                
+              </article>
+            </div>
+          
+          
+<script>var target=document.getElementById(location.hash.slice(1));target&&target.name&&(target.checked=target.name.startsWith("__tabbed_"))</script>
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+  
+  <div class="md-footer-meta md-typeset">
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+      <a href="../architecture/numa_worker_pools/" class="md-nav__link">
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+      <a href="../architecture/numa_partition_runner/" class="md-nav__link">
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+    NUMA-aware partition runner
+  
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+  
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diff --git a/docmd/references.bib b/DevDoc/references.bib
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diff --git a/doc/theory/encoding.refs/index.html b/DevDoc/theory/encoding.refs/index.html
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index 8f60d46f..26b92a90 100644
--- a/doc/theory/encoding.refs/index.html
+++ b/DevDoc/theory/encoding.refs/index.html
@@ -178,6 +178,33 @@
   
   
   
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+      <a href="../../installation/" class="md-nav__link">
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@@ -359,6 +386,34 @@
 
               
             
+              
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+  
+    <li class="md-nav__item">
+      <a href="../evolutionary_distances/" class="md-nav__link">
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+  
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+  <span class="md-ellipsis">
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     <li class="md-nav__item">
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+      <a href="../../implementation/merge_parallelism/" class="md-nav__link">
         
   
   
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-    Kmer filtering (rebuild/dump/unitig)
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+      <a href="../../implementation/filtering/" class="md-nav__link">
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+            
+              
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+    <li class="md-nav__item">
+      <a href="../../implementation/select/" class="md-nav__link">
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+              
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+  
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+      <a href="../../implementation/obitaxonomy/" class="md-nav__link">
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+    obitaxonomy crate
   
 
     
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+  
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+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
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+      </a>
+    </li>
+  
+
+              
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+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
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+  
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+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
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+    NUMA-aware partition runner
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diff --git a/DevDoc/theory/encoding/index.html b/DevDoc/theory/encoding/index.html
new file mode 100644
index 00000000..fdb70802
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+
+      </a>
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+      
+        <li class="md-nav__item">
+  <a href="#2-bit-nucleotide-encoding" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        2-bit nucleotide encoding
+      
+    </span>
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+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#kmer-encoding" class="md-nav__link">
+    <span class="md-ellipsis">
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+      <a href="../entropy/" class="md-nav__link">
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+    Entropy filter
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+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
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+              
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+      <a href="../minimizer/" class="md-nav__link">
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+    
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+  
+  
+
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+  
+
+              
+            
+              
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+      <a href="../indexing/" class="md-nav__link">
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+
+              
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+              
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+  
+  
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+    <li class="md-nav__item">
+      <a href="../evolutionary_distances/" class="md-nav__link">
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+
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+      <a href="../../implementation/superkmer/" class="md-nav__link">
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+    SuperKmer
+  
+
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+  
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+    <li class="md-nav__item">
+      <a href="../../implementation/kmer/" class="md-nav__link">
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+  
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+    
+  </span>
+  
+  
+
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+  
+
+              
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+              
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+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/chunkreader/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
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+  
+    Chunk reader
+  
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+    
+  </span>
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+
+      </a>
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+
+              
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+              
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+      
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+  <a href="#2-bit-nucleotide-encoding" class="md-nav__link">
+    <span class="md-ellipsis">
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+        2-bit nucleotide encoding
+      
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+  </a>
+  
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+      
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+  <a href="#kmer-encoding" class="md-nav__link">
+    <span class="md-ellipsis">
+      
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+  
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+            
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+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+
+<h1 id="dna-encoding">DNA encoding</h1>
+<h2 id="2-bit-nucleotide-encoding">2-bit nucleotide encoding</h2>
+<p>All nucleotides are encoded on 2 bits, MSB-first within each word. Nucleotides are numbered 0-based from the 5′ end across all sequence types:</p>
+<table>
+<thead>
+<tr>
+<th>Base</th>
+<th>Encoding</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>A</td>
+<td><code>00</code></td>
+</tr>
+<tr>
+<td>C</td>
+<td><code>01</code></td>
+</tr>
+<tr>
+<td>G</td>
+<td><code>10</code></td>
+</tr>
+<tr>
+<td>T</td>
+<td><code>11</code></td>
+</tr>
+</tbody>
+</table>
+<p>The Watson-Crick complement of any base is its bitwise NOT on 2 bits: <code>complement(base) = ~base &amp; 0b11</code>.</p>
+<h2 id="kmer-encoding">Kmer encoding</h2>
+<p>A kmer fits in a single <code>u64</code>. Nucleotide 0 occupies bits 63–62, nucleotide i occupies bits 63−2i and 62−2i, and the low 64−2k bits are zero. Extraction of nucleotide i (0 ≤ i &lt; k): <code>(kmer &gt;&gt; (62 - 2*i)) &amp; 0b11</code>.</p>
+<p>Reverse complement is computed by <strong>bit manipulation in four steps</strong>, with no lookup table:</p>
+<div class="admonition abstract">
+<p class="admonition-title">Algorithm — Kmer reverse complement</p>
+<div class="highlight"><pre><span></span><code>procedure KmerRevcomp(kmer, k):
+    x ← ~kmer                                           -- complement all bases
+    x ← swap_bytes(x)                                   -- reverse byte order
+    x ← ((x &gt;&gt; 4) &amp; 0x0F0F0F0F0F0F0F0F)
+       | ((x &amp; 0x0F0F0F0F0F0F0F0F) &lt;&lt; 4)               -- swap nibbles within each byte
+    x ← ((x &gt;&gt; 2) &amp; 0x3333333333333333)
+       | ((x &amp; 0x3333333333333333) &lt;&lt; 2)                -- swap 2-bit pairs within each nibble
+    return x &lt;&lt; (64 - 2*k)                              -- re-align to MSB
+</code></pre></div>
+</div>
+<p>The three reorder passes together reverse the order of all 2-bit base codes across the 64-bit word. The bitwise NOT in the first step complements each base (A↔T, C↔G). The final left shift clears the low 64−2k padding bits.</p>
+<p>The <strong>canonical form</strong> is the lexicographic minimum of the kmer and its reverse complement:</p>
+<div class="highlight"><pre><span></span><code>canonical(kmer) = min(kmer, revcomp(kmer))
+</code></pre></div>
+<p>This halves the kmer space and ensures strand-independent counting.</p>
+
+
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diff --git a/doc/theory/entropy.refs/index.html b/DevDoc/theory/entropy.refs/index.html
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@@ -991,11 +1214,14 @@
 <h1 id="coverage-theoryentropymd">Coverage: theory/entropy.md</h1>
 <h2 id="code-couvert">Code couvert</h2>
 <ul>
-<li><code>obiskbuilder/src/entropy_table.rs</code> — filtre Shannon sur les kmers à basse complexité</li>
-<li><code>obiskbuilder/src/lib.rs</code> — application du filtre lors du scatter (phase 1)</li>
+<li><code>obikentropy/src/table.rs</code>, <code>obikentropy/src/tracker.rs</code> — formule d'entropie et tables de correction petits effectifs</li>
+<li><code>obikentropy/src/kmer_entropy.rs</code> — entropie d'un kmer isolé (<code>KmerEntropy</code>)</li>
+<li><code>obiskbuilder/src/rolling_stat.rs</code> — composition de <code>obikentropy::EntropyTracker</code> dans le suivi streaming (sélection de minimiseur + entropie)</li>
+<li><code>obiskbuilder/src/iter.rs</code>, <code>obiskbuilder/src/stream_iter.rs</code> — application du filtre lors du scatter (phase 1)</li>
 </ul>
 <h2 id="notes">Notes</h2>
-<p>Document théorique stable. Vérifier que les paramètres <code>theta</code> et <code>level_max</code> dans le CLI
+<p>Le repli en classes d'équivalence circulaires + brin inverse (décrit dans une version antérieure de ce document) a été supprimé : voir la section « Why no equivalence classes » de <code>entropy.md</code> pour la justification théorique et numérique.</p>
+<p>Vérifier que les paramètres <code>theta</code> et <code>level_max</code> dans le CLI
 (<code>obikmer/src/cli.rs</code> → <code>CommonArgs</code>) correspondent bien à ce qui est décrit.</p>
 
 
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 <h1 id="kmer-entropy-filter">Kmer entropy filter</h1>
-<p>Low-complexity kmers (polyA, polyT, tandem repeats) are detected and excluded during phase 1. The filter computes a <strong>normalized Shannon entropy</strong> over sub-words of multiple sizes, corrected for two sources of bias: the small number of observations within a single kmer, and the unequal sizes of circular equivalence classes.</p>
+<p>Low-complexity kmers (polyA, polyT, tandem repeats) are detected and excluded during phase 1. The filter computes a <strong>normalized Shannon entropy</strong> over sub-words of multiple sizes, corrected for one source of bias: the small number of observations within a single kmer relative to the number of possible sub-words.</p>
 <h2 id="sub-word-frequencies">Sub-word frequencies</h2>
 <p>For a kmer of length k and a sub-word size ws (1 ≤ ws ≤ ws_max, typically ws_max = 6), extract the <span class="arithmatex">\(n_{\text{words}} = k - ws + 1\)</span> overlapping sub-words by sliding a window of length ws:</p>
 <div class="arithmatex">\[w_i = \text{kmer}[i \mathinner{..} i+ws-1], \quad i = 0, \ldots, n_{\text{words}}-1\]</div>
-<p>Each sub-word is mapped to its <strong>circular canonical form</strong>: the lexicographic minimum among all cyclic rotations of the word <strong>and all cyclic rotations of its reverse complement</strong>. This extended equivalence relation ensures that entropy(K) = entropy(revcomp(K)) — the filter is strand-symmetric. Let <span class="arithmatex">\(s_j\)</span> be the size of equivalence class <span class="arithmatex">\(j\)</span> (number of distinct raw words mapping to canonical form <span class="arithmatex">\(j\)</span>), and <span class="arithmatex">\(f_j\)</span> the count of canonical form <span class="arithmatex">\(j\)</span> among the <span class="arithmatex">\(n_{\text{words}}\)</span> sub-words (<span class="arithmatex">\(\sum_j f_j = n_{\text{words}}\)</span>).</p>
+<p>Each sub-word is tallied under its own raw 2-bit-packed value — <strong>no canonicalization</strong>. Let <span class="arithmatex">\(f_j\)</span> be the count of raw word <span class="arithmatex">\(j\)</span> among the <span class="arithmatex">\(n_{\text{words}}\)</span> sub-words (<span class="arithmatex">\(\sum_j f_j = n_{\text{words}}\)</span>), over the <span class="arithmatex">\(4^{ws}\)</span> possible raw words.</p>
+<p>An earlier version of this filter first folded each sub-word into a circular+reverse-complement equivalence class, then "unfolded" the observed class frequency back onto its members to correct for unequal class sizes. That machinery bought nothing it was claimed for — see <em>Why no equivalence classes</em> below — while measurably weakening detection of the very sequences the filter exists to catch, so it was removed.</p>
 <h2 id="corrected-shannon-entropy">Corrected Shannon entropy</h2>
-<p>The circular equivalence classes have unequal sizes: under a uniform distribution over all <span class="arithmatex">\(4^{ws}\)</span> raw words, class <span class="arithmatex">\(j\)</span> is visited with probability <span class="arithmatex">\(s_j / 4^{ws}\)</span>, not <span class="arithmatex">\(1/n_a\)</span>. Computing entropy directly over canonical classes therefore underestimates the entropy of a random sequence.</p>
-<p>The correction "unfolds" each canonical class back to its member raw words, redistributing each observation of class <span class="arithmatex">\(j\)</span> equally among its <span class="arithmatex">\(s_j\)</span> members:</p>
-<div class="arithmatex">\[H_{\text{corr}} = \log(n_{\text{words}}) - \frac{1}{n_{\text{words}}} \sum_j f_j \log f_j + \frac{1}{n_{\text{words}}} \sum_j f_j \log s_j\]</div>
-<p>The last term is the correction for unequal class sizes. For a uniformly random sequence (<span class="arithmatex">\(f_j \approx n_{\text{words}} \cdot s_j / 4^{ws}\)</span>), this gives <span class="arithmatex">\(H_{\text{corr}} \approx \log(4^{ws}) = 2 \cdot ws \cdot \log 2\)</span>, the maximum entropy over raw words.</p>
+<div class="arithmatex">\[H_{\text{corr}} = \log(n_{\text{words}}) - \frac{1}{n_{\text{words}}} \sum_j f_j \log f_j\]</div>
+<p>This is a plain Shannon entropy over the observed raw-word frequencies.</p>
 <h2 id="maximum-entropy-correction-for-small-samples">Maximum entropy correction for small samples</h2>
 <p>With only <span class="arithmatex">\(n_{\text{words}}\)</span> observations over <span class="arithmatex">\(4^{ws}\)</span> possible raw words, the achievable maximum entropy is bounded by the most uniform integer distribution over <span class="arithmatex">\(4^{ws}\)</span> categories.</p>
 <p>Let <span class="arithmatex">\(c = \lfloor n_{\text{words}} / 4^{ws} \rfloor\)</span> and <span class="arithmatex">\(r = n_{\text{words}} \bmod 4^{ws}\)</span>. The most uniform integer distribution assigns frequency <span class="arithmatex">\(c+1\)</span> to <span class="arithmatex">\(r\)</span> categories and <span class="arithmatex">\(c\)</span> to the remaining <span class="arithmatex">\(4^{ws} - r\)</span>, with the convention <span class="arithmatex">\(0 \log 0 = 0\)</span>:</p>
@@ -1194,19 +1438,49 @@
 <p>The filter computes <span class="arithmatex">\(\hat{H}(ws)\)</span> for each word size ws from 1 to ws_max and returns the <strong>minimum</strong>:</p>
 <div class="arithmatex">\[\text{entropy}(kmer) = \min_{ws=1}^{ws_{\max}} \hat{H}(ws)\]</div>
 <p>A value near 0 indicates low complexity (e.g. AAAA…); near 1 indicates high complexity. A kmer is rejected if <span class="arithmatex">\(\text{entropy}(kmer) &lt; \theta\)</span>, where <span class="arithmatex">\(\theta\)</span> is a collection parameter (default 0.7). The minimum across word sizes ensures that any scale of repetition is detected independently: polyA is caught at ws=1, dinucleotide repeats at ws=2, etc.</p>
+<h2 id="why-no-equivalence-classes">Why no equivalence classes</h2>
+<p>A prior design folded each sub-word into the canonical form of its circular-rotation + reverse-complement equivalence class before tallying, on the reasoning that (a) it guarantees <span class="arithmatex">\(\text{entropy}(K) = \text{entropy}(\text{revcomp}(K))\)</span>, and (b) collapsing phase-shifted repeats (e.g. <code>ATG</code> ≡ <code>TGA</code> ≡ <code>GAT</code>) into one class better reflects that they are "the same" low-complexity pattern.</p>
+<p>Both properties already hold for the raw, unfolded entropy above, without any class machinery:</p>
+<ul>
+<li><strong>Reverse complement</strong>: for any K of length n, window <span class="arithmatex">\(j\)</span> of <span class="arithmatex">\(\text{revcomp}(K)\)</span> equals <span class="arithmatex">\(\text{revcomp}\)</span> of window <span class="arithmatex">\((n{-}ws{-}j)\)</span> of K. This is a bijection between the window sets under which each window maps to its own revcomp — and revcomp is itself a bijection (involution) on the space of raw ws-mers. So the multiset of raw-word frequencies for <span class="arithmatex">\(\text{revcomp}(K)\)</span> is exactly a relabeling of the multiset for K, and Shannon entropy — a function of the frequency multiset alone — is exactly invariant. No folding required, for any K.</li>
+<li><strong>Tandem repeats</strong>: a period-p repeat sampled by a stride-1 sliding window naturally cycles through its own rotations as raw tokens (e.g. <code>ATGATGATG…</code> yields the raw words <code>ATG</code>, <code>TGA</code>, <code>GAT</code> in rotation as the window slides). The low diversity this represents (few distinct raw words out of <span class="arithmatex">\(4^{ws}\)</span> possible) is already visible in the raw frequency distribution — no folding needed to detect it.</li>
+</ul>
+<p>What the fold-then-unfold step actually did was credit each observed class with the frequency of equivalence-class members that were <strong>never observed on the read strand</strong>, inflating <span class="arithmatex">\(H_{\text{corr}}\)</span> for genuine repeats. Worked example: k=31, ws=3, kmer = <code>ATG</code> repeated (<span class="arithmatex">\(n_{\text{words}}=29\)</span>, all 29 windows fall into one class of size 6 under the old scheme — 3 rotations × forward/revcomp):</p>
+<table>
+<thead>
+<tr>
+<th></th>
+<th><span class="arithmatex">\(H_{\text{corr}}\)</span></th>
+<th>normalized</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>old (folded, class size 6)</td>
+<td><span class="arithmatex">\(\log 6 \approx 1.79\)</span></td>
+<td><span class="arithmatex">\(\approx 0.53\)</span></td>
+</tr>
+<tr>
+<td>current (raw, unfolded)</td>
+<td><span class="arithmatex">\(\log 3 \approx 1.10\)</span></td>
+<td><span class="arithmatex">\(\approx 0.33\)</span></td>
+</tr>
+</tbody>
+</table>
+<p>The gap is not a rounding artifact: per sub-word order, the folded score for this same repeat swings from 0.53 (ws=3, aligned with the period) up to <strong>1.03</strong> (ws=5, misaligned with the period) — i.e. a period-3 repeat could score <em>above</em> the theoretical maximum for a random sequence, depending on which ws happens to divide the repeat's period. The raw formula stays flat at ≈0.33–0.40 across ws=2..6 regardless of alignment, which is the robustness the "minimum across ws" design was meant to provide in the first place.</p>
 <h2 id="interpretation-as-an-effective-number-of-classes">Interpretation as an effective number of classes</h2>
-<p><span class="arithmatex">\(H_{\text{corr}}\)</span> is a standard Shannon entropy over raw words (after unfolding the equivalence classes), so the classical perplexity interpretation holds directly: <span class="arithmatex">\(N_{\text{eff}} = e^{H_{\text{corr}}}\)</span> is the number of equiprobable classes that would yield the same entropy.</p>
-<p>For the normalised score <span class="arithmatex">\(\hat{H}\)</span>, dividing by <span class="arithmatex">\(H_{\text{max}}\)</span> changes the logarithm base:</p>
-<div class="arithmatex">\[\hat{H} = \frac{\log N_{\text{eff}}}{\log N_{\text{max}}} = \log_{N_{\text{max}}} N_{\text{eff}} \quad \Longleftrightarrow \quad N_{\text{eff}} = N_{\text{max}}^{\,\hat{H}}\]</div>
-<p>The property is preserved: <span class="arithmatex">\(\hat{H}\)</span> is the logarithm (in base <span class="arithmatex">\(N_{\text{max}}\)</span>) of the effective number of equi-represented classes.</p>
-<p>In the large-sample limit (<span class="arithmatex">\(n_{\text{words}} \gg 4^{ws}\)</span>), <span class="arithmatex">\(N_{\text{max}} \approx 4^{ws}\)</span>, giving:</p>
+<p><span class="arithmatex">\(H_{\text{corr}}\)</span> is a standard Shannon entropy over raw words, so the classical perplexity interpretation holds directly: <span class="arithmatex">\(N_{\text{eff}} = e^{H_{\text{corr}}}\)</span> is the number of equiprobable raw words that would yield the same entropy.</p>
+<p>For the normalised score <span class="arithmatex">\(\hat{H}\)</span>, dividing by <span class="arithmatex">\(H_{\max}\)</span> changes the logarithm base:</p>
+<div class="arithmatex">\[\hat{H} = \frac{\log N_{\text{eff}}}{\log N_{\max}} = \log_{N_{\max}} N_{\text{eff}} \quad \Longleftrightarrow \quad N_{\text{eff}} = N_{\max}^{\,\hat{H}}\]</div>
+<p>The property is preserved: <span class="arithmatex">\(\hat{H}\)</span> is the logarithm (in base <span class="arithmatex">\(N_{\max}\)</span>) of the effective number of equi-represented raw words.</p>
+<p>In the large-sample limit (<span class="arithmatex">\(n_{\text{words}} \gg 4^{ws}\)</span>), <span class="arithmatex">\(N_{\max} \approx 4^{ws}\)</span>, giving:</p>
 <div class="arithmatex">\[N_{\text{eff}} \approx 4^{ws \cdot \hat{H}}\]</div>
-<p>This has a clean interpretation: <span class="arithmatex">\(ws \cdot \hat{H}\)</span> is the <strong>effective word length</strong> (in bases) of a perfectly uniform distribution that would produce the same entropy. At <span class="arithmatex">\(\hat{H} = 1\)</span> the full space of <span class="arithmatex">\(4^{ws}\)</span> words is used; at <span class="arithmatex">\(\hat{H} = 0.5\)</span> with ws=2, only <span class="arithmatex">\(4^1 = 4\)</span> effective classes out of 16 are occupied.</p>
-<p>In our actual regime, <span class="arithmatex">\(n_{\text{words}}\)</span> is small and <span class="arithmatex">\(4^{ws}\)</span> can exceed <span class="arithmatex">\(n_{\text{words}}\)</span>, so <span class="arithmatex">\(H_{\text{max}} &lt; \log(4^{ws})\)</span> due to the small-sample correction. The exact effective count is <span class="arithmatex">\(N_{\text{max}}^{\hat{H}}\)</span>, not <span class="arithmatex">\(4^{ws \cdot \hat{H}}\)</span>.</p>
+<p>This has a clean interpretation: <span class="arithmatex">\(ws \cdot \hat{H}\)</span> is the <strong>effective word length</strong> (in bases) of a perfectly uniform distribution that would produce the same entropy. At <span class="arithmatex">\(\hat{H} = 1\)</span> the full space of <span class="arithmatex">\(4^{ws}\)</span> words is used; at <span class="arithmatex">\(\hat{H} = 0.5\)</span> with ws=2, only <span class="arithmatex">\(4^1 = 4\)</span> effective words out of 16 are occupied.</p>
+<p>In our actual regime, <span class="arithmatex">\(n_{\text{words}}\)</span> is small and <span class="arithmatex">\(4^{ws}\)</span> can exceed <span class="arithmatex">\(n_{\text{words}}\)</span>, so <span class="arithmatex">\(H_{\max} &lt; \log(4^{ws})\)</span> due to the small-sample correction. The exact effective count is <span class="arithmatex">\(N_{\max}^{\hat{H}}\)</span>, not <span class="arithmatex">\(4^{ws \cdot \hat{H}}\)</span>.</p>
 <h2 id="properties">Properties</h2>
 <p>The entropy score is a function of the kmer sequence alone — it does not depend on the surrounding context or on the position within any genome. Two consequences:</p>
 <ul>
-<li><strong>Orientation invariance</strong>: <span class="arithmatex">\(\text{entropy}(K) = \text{entropy}(\text{revcomp}(K))\)</span>, guaranteed by the strand-symmetric canonical form.</li>
+<li><strong>Orientation invariance</strong>: <span class="arithmatex">\(\text{entropy}(K) = \text{entropy}(\text{revcomp}(K))\)</span> — see <em>Why no equivalence classes</em> above for why this holds without any explicit strand-folding step.</li>
 <li><strong>Context independence</strong>: the same kmer is always rejected or always kept, regardless of which genome it occurs in, where in that genome it appears, or which strand is considered. The filter defines a fixed partition of the kmer space into low-complexity and valid kmers.</li>
 </ul>
 
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+      <a href="../minimizer/" class="md-nav__link">
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+      <a href="../indexing/" class="md-nav__link">
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+  
+  <span class="md-ellipsis">
+    
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+    Partitioning architecture
+  
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+  </span>
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+          
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+          <span class="md-nav__icon md-icon"></span>
+        </label>
+      
+      <a href="./" class="md-nav__link md-nav__link--active">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+      
+        
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+    
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#motivation" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Motivation
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#statistic-and-correspondence-with-shared" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Statistic and correspondence with shared
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Statistic and correspondence with shared">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#definitions-family-and-the-canonical-form-of-a-family" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Definitions: family, and the canonical form of a family
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#locus-eligibility-raw-definition-vs-paralogy-filter" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Locus eligibility: raw definition vs. paralogy filter
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#multi-genome-framing-family-as-pseudo-alignment-column" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Multi-genome framing: family as pseudo-alignment column
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#context-detectability-and-a-3-way-ordinal-distance-per-pair" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Context, detectability, and a 3-way ordinal distance per pair
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#sankoff-parsimony-as-the-resolution-of-the-16-state-model-problem" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Sankoff parsimony as the resolution of the 16-state model problem
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Sankoff parsimony as the resolution of the 16-state model problem">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#a-concrete-sankoff-cost-matrix-for-the-16-state-alphabet" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        A concrete Sankoff cost matrix for the 16-state alphabet
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#experiment-tnt-run-on-real-data-2026-08-11" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Experiment: TNT run on real data (2026-08-11)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#native-sankoff-tnt-phyg-export-2026-08-12-superseding-the-external-scripts-above" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Native --sankoff --tnt/--phyg export (2026-08-12), superseding the external scripts above
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#next-direction-genuine-ml-branch-lengths-not-parsimony-open-2026-08-12" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Next direction: genuine ML branch lengths, not parsimony (open, 2026-08-12)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#r-implemented-exclude-genome-added-rogue-taxon-test-negative-2026-08-12" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        R/π implemented; --exclude-genome added; rogue-taxon test negative (2026-08-12)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#r-via-exp-cost-is-wrong-for-a-ctmc-cardinalitycomposition-decomposition-open-2026-08-12" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        R via exp(-cost) is wrong for a CTMC; cardinality/composition decomposition (open, 2026-08-12)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#implemented-2026-08-12-pairwise_cost_matrix-replaces-build_cost_matrix-entirely" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Implemented (2026-08-12): pairwise_cost_matrix replaces build_cost_matrix entirely
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#two-consistency-bugs-found-and-fixed-post-implementation-2026-08-13" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Two consistency bugs found and fixed post-implementation (2026-08-13)
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#heterozygosity-ploidy-and-consensus-assembly-inputs" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Heterozygosity, ploidy, and consensus-assembly inputs
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#sufficient-statistic-4x4-base-pair-tally" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Sufficient statistic: 4x4 base-pair tally
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#biases-properties-of-the-estimator-not-defects" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Biases (properties of the estimator, not defects)
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#implementation-avoid-materializing-a-de-bruijn-graph" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Implementation: avoid materializing a de Bruijn graph
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#implementation-sequential-per-partition-sweep-no-scratch-no-graph" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Implementation: sequential per-partition sweep (no scratch, no graph)
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#cheaper-subsampling" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Cheaper: subsampling
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#recommendation" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Recommendation
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#detailed-implementation-plan" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Detailed implementation plan
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Detailed implementation plan">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#step-0-new-low-level-primitives-obikseq" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Step 0 — new low-level primitives (obikseq)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#step-1-the-tally-accumulator-obikindex" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Step 1 — the tally accumulator (obikindex)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#step-2-the-sweep-obikindex-new-snprs" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Step 2 — the sweep (obikindex, new snp.rs)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#open-problem-unresolved-session-end-not-yet-fully-convinced" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Open problem (unresolved, session end — not yet fully convinced)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#step-2b-sibling-count-minorant-annex-consolidated-plan" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Step 2b — sibling-count / minorant annex (consolidated plan)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#step-3-finalisation-obikindex" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Step 3 — finalisation (obikindex)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#step-4-surfacing-obikindex-obikmer-cli" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Step 4 — surfacing (obikindex + obikmer CLI)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#step-5-subsampling-flag" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Step 5 — subsampling flag
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#testing" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Testing
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#suggested-phasing" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Suggested phasing
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#locus-dropout-under-incomplete-coverage-absence-as-missing-data-not-a-penalized-state-2026-08-13-discussion" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Locus dropout under incomplete coverage: absence as missing data, not a penalized state (2026-08-13, discussion)
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Locus dropout under incomplete coverage: absence as missing data, not a penalized state (2026-08-13, discussion)">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#-free-loss-implemented-2026-08-13" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        --free-loss implemented (2026-08-13)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#tnt-confirmed-2026-08-13-iq-tree-asc-constant-column-fix-2026-08-13" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        TNT confirmed (2026-08-13); IQ-TREE +ASC constant-column fix (2026-08-13)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#-family-overlap-min-shared-family-and-a-second-free_loss-bug-cardinality-transition-cost-not-zeroed-2026-08-13" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        --family-overlap/--min-shared-family, and a second free_loss bug: cardinality-transition cost not zeroed (2026-08-13)
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#references" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        References
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+      
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        
+          
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+            
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Implementation
+  
+
+    
+  </span>
+  
+  
+
+            <span class="md-nav__icon md-icon"></span>
+          </label>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
+            <span class="md-nav__icon md-icon"></span>
+            
+  
+    Implementation
+  
+
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/superkmer/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    SuperKmer
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/kmer/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/chunkreader/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Chunk reader
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/pipeline/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Construction pipeline
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/obipipeline/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obipipeline library
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/storage/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    On-disk storage
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/mphf/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    MPHF selection
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/unitig_evidence/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Unitig evidence encoding
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/evidence_elimination/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Evidence elimination (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/obilayeredmap/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obilayeredmap crate
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/persistent_compact_int_vec/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    PersistentCompactIntVec
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/persistent_bit_vec/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    PersistentBitVec
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/merge/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Merge command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/merge_parallelism/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
+            
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Architecture
+  
+
+    
+  </span>
+  
+  
+
+            <span class="md-nav__icon md-icon"></span>
+          </label>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
+            <span class="md-nav__icon md-icon"></span>
+            
+  
+    Architecture
+  
+
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/sequences/invariant/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sequences
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/index_architecture/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer index
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+    
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#motivation" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Motivation
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#statistic-and-correspondence-with-shared" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Statistic and correspondence with shared
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Statistic and correspondence with shared">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#definitions-family-and-the-canonical-form-of-a-family" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Definitions: family, and the canonical form of a family
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#locus-eligibility-raw-definition-vs-paralogy-filter" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Locus eligibility: raw definition vs. paralogy filter
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#multi-genome-framing-family-as-pseudo-alignment-column" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Multi-genome framing: family as pseudo-alignment column
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#context-detectability-and-a-3-way-ordinal-distance-per-pair" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Context, detectability, and a 3-way ordinal distance per pair
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#sankoff-parsimony-as-the-resolution-of-the-16-state-model-problem" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Sankoff parsimony as the resolution of the 16-state model problem
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Sankoff parsimony as the resolution of the 16-state model problem">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#a-concrete-sankoff-cost-matrix-for-the-16-state-alphabet" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        A concrete Sankoff cost matrix for the 16-state alphabet
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#experiment-tnt-run-on-real-data-2026-08-11" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Experiment: TNT run on real data (2026-08-11)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#native-sankoff-tnt-phyg-export-2026-08-12-superseding-the-external-scripts-above" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Native --sankoff --tnt/--phyg export (2026-08-12), superseding the external scripts above
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#next-direction-genuine-ml-branch-lengths-not-parsimony-open-2026-08-12" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Next direction: genuine ML branch lengths, not parsimony (open, 2026-08-12)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#r-implemented-exclude-genome-added-rogue-taxon-test-negative-2026-08-12" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        R/π implemented; --exclude-genome added; rogue-taxon test negative (2026-08-12)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#r-via-exp-cost-is-wrong-for-a-ctmc-cardinalitycomposition-decomposition-open-2026-08-12" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        R via exp(-cost) is wrong for a CTMC; cardinality/composition decomposition (open, 2026-08-12)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#implemented-2026-08-12-pairwise_cost_matrix-replaces-build_cost_matrix-entirely" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Implemented (2026-08-12): pairwise_cost_matrix replaces build_cost_matrix entirely
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#two-consistency-bugs-found-and-fixed-post-implementation-2026-08-13" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Two consistency bugs found and fixed post-implementation (2026-08-13)
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#heterozygosity-ploidy-and-consensus-assembly-inputs" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Heterozygosity, ploidy, and consensus-assembly inputs
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#sufficient-statistic-4x4-base-pair-tally" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Sufficient statistic: 4x4 base-pair tally
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#biases-properties-of-the-estimator-not-defects" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Biases (properties of the estimator, not defects)
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#implementation-avoid-materializing-a-de-bruijn-graph" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Implementation: avoid materializing a de Bruijn graph
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#implementation-sequential-per-partition-sweep-no-scratch-no-graph" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Implementation: sequential per-partition sweep (no scratch, no graph)
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#cheaper-subsampling" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Cheaper: subsampling
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#recommendation" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Recommendation
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#detailed-implementation-plan" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Detailed implementation plan
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Detailed implementation plan">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#step-0-new-low-level-primitives-obikseq" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Step 0 — new low-level primitives (obikseq)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#step-1-the-tally-accumulator-obikindex" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Step 1 — the tally accumulator (obikindex)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#step-2-the-sweep-obikindex-new-snprs" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Step 2 — the sweep (obikindex, new snp.rs)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#open-problem-unresolved-session-end-not-yet-fully-convinced" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Open problem (unresolved, session end — not yet fully convinced)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#step-2b-sibling-count-minorant-annex-consolidated-plan" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Step 2b — sibling-count / minorant annex (consolidated plan)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#step-3-finalisation-obikindex" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Step 3 — finalisation (obikindex)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#step-4-surfacing-obikindex-obikmer-cli" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Step 4 — surfacing (obikindex + obikmer CLI)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#step-5-subsampling-flag" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Step 5 — subsampling flag
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#testing" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Testing
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#suggested-phasing" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Suggested phasing
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#locus-dropout-under-incomplete-coverage-absence-as-missing-data-not-a-penalized-state-2026-08-13-discussion" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Locus dropout under incomplete coverage: absence as missing data, not a penalized state (2026-08-13, discussion)
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Locus dropout under incomplete coverage: absence as missing data, not a penalized state (2026-08-13, discussion)">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#-free-loss-implemented-2026-08-13" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        --free-loss implemented (2026-08-13)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#tnt-confirmed-2026-08-13-iq-tree-asc-constant-column-fix-2026-08-13" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        TNT confirmed (2026-08-13); IQ-TREE +ASC constant-column fix (2026-08-13)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#-family-overlap-min-shared-family-and-a-second-free_loss-bug-cardinality-transition-cost-not-zeroed-2026-08-13" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        --family-overlap/--min-shared-family, and a second free_loss bug: cardinality-transition cost not zeroed (2026-08-13)
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#references" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        References
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+
+<h1 id="central-position-snp-distance-discussion">Central-position SNP distance (discussion)</h1>
+<p>Not implemented. Design discussion for a substitution-rate estimator that
+observes SNPs directly from paired-genome k-mer comparison, as an alternative
+to Mash's Poisson-Jaccard inference (see <a href="../../implementation/obicompactvec/">obicompactvec</a>
+for the implemented Jaccard/Mash distances).</p>
+<h2 id="motivation">Motivation</h2>
+<p><strong>Primary intent: restrict the comparison to what is actually comparable.</strong>
+Mash's Jaccard is computed over the <strong>union</strong> of both genomes' k-mer content:
+anything not identically shared is folded into a single undifferentiated
+mass, whether the cause is a point substitution, a genuinely absent
+homologous region (lineage-specific content, gene-family expansion, HGT,
+genome-size asymmetry), or a diverged paralogous copy. The model then
+back-infers a single mutation rate from that mass, silently attributing
+non-homology to mutation. The central-SNP approach instead conditions every
+comparison on local, positive evidence of homology: a locus only enters the
+statistic if its <code>2m</code> flanking bases (<code>m = (k-1)/2</code>) are found intact in
+<em>both</em> genomes — genuinely absent or non-homologous content is excluded from
+the comparison entirely (neither numerator nor denominator), rather than
+silently counted as divergence. This is a conditioning on comparability, not
+just a richer summary statistic — see "Statistic and correspondence with
+<code>shared</code>" below for how it plays out against genome-size asymmetry and
+diverged gene families, and "Heterozygosity, ploidy, and consensus-assembly
+inputs" for the corresponding paralogy/heterozygosity filter.</p>
+<p><strong>Secondary benefit: access to the substitution's nature.</strong> Because the
+central base of an odd-k window is directly observable once the flanks are
+confirmed conserved, this also yields more than a rate — the
+transition/transversion split — enabling classical corrected distances
+(Jukes-Cantor, Kimura 2-parameter, LogDet) that a single Jaccard scalar
+cannot support.</p>
+<h2 id="statistic-and-correspondence-with-shared">Statistic and correspondence with <code>shared</code></h2>
+<p>A genomic position <code>p</code> is covered by <code>k</code> overlapping k-mer windows. Requiring
+the substitution to sit at the window's <strong>center</strong> makes exactly one window
+per SNP eligible — a 1:1 correspondence between SNP and center-neighbor k-mer
+pair, avoiding the ~k-fold overcount of an any-position neighbor search.</p>
+<p>A locus with a fully conserved <code>k</code>-window (flanks <strong>and</strong> center) is an
+exact-shared k-mer at that locus; a locus with conserved flanks but a
+substituted center is a "central SNP". Both count each locus exactly once, in
+matching units:</p>
+<div class="highlight"><pre><span></span><code>p_hat[i,j] = SNP[i,j] / (SNP[i,j] + shared[i,j])
+</code></pre></div>
+<p><code>p_hat</code> is <code>P(center substituted | 2m flanks conserved)</code>. <code>shared[i,j]</code> here
+is <strong>not</strong> the general-purpose <code>shared_kmers</code> matrix used by Jaccard/Mash
+(<code>--shared-kmers</code>, <code>BitPartials::partial_jaccard</code> /
+<code>CountPartials::partial_threshold_jaccard</code>) — that matrix counts raw k-mer
+identity with no per-genome copy-number constraint, whereas <code>p_hat</code>'s
+denominator applies the eligibility rule defined below (raw or
+paralogy-filtered). Both <code>SNP</code> and <code>shared</code> are accumulated by the same
+sweep, from the same per-locus candidate set (source k-mer + 3 variants),
+under the same eligibility rule — see "Locus eligibility" below, and
+"Heterozygosity, ploidy, and consensus-assembly inputs" for why the
+copy-number constraint matters and what it costs.</p>
+<p><strong>Canonical invariance</strong>: for odd k, the central position maps to itself under
+reverse-complement (<code>m -&gt; k-1-m = m</code>, base complemented). A transition maps to
+a transition, a transversion to a transversion — the transition/transversion
+split is well-defined in canonical space.</p>
+<h3 id="definitions-family-and-the-canonical-form-of-a-family">Definitions: family, and the canonical form of a family</h3>
+<p><strong>Family.</strong> The family of a k-mer <code>x</code> is the set of (up to) 4 k-mers sharing
+<code>x</code>'s <code>2m</code> flanking bases, differing only at the central base <code>m</code>. Membership
+is a property of the flank pattern, not of <code>x</code> itself: any of the 4 possible
+central substitutions belongs to the same family.</p>
+<p><strong><code>central_canonical_neighbors()</code></strong> (<code>obikseq</code>, <code>CanonicalKmerOf::central_canonical_neighbors</code>)
+generates all 4 members from any one of them (observed or not), each
+independently canonicalised (<code>.canonical()</code>, i.e. <code>min(kmer, revcomp(kmer))</code>).
+This independent canonicalisation is necessary because a central substitution
+can flip which orientation is lexicographically smaller — two members of the
+same family can end up canonicalised in <em>different</em> orientations. Despite
+that, the <strong>set</strong> of 4 resulting canonical k-mers is invariant: calling
+<code>central_canonical_neighbors()</code> on any member of a family — present in the
+index or not — yields the same 4 values. This is relied upon throughout the
+rest of this document.</p>
+<p><strong>Canonical form of a family.</strong> Because orientation can differ member to
+member, "which of the 4 is the reference" cannot be defined relative to
+<em>whichever member happened to be visited first</em>, nor relative to the
+minorant (see below) — both are data-dependent (they depend on what is
+actually observed), so using either as the reference would make the
+reference itself vary depending on what happens to be present in a given
+index. Instead: <strong>the canonical form of a family is, by definition, the
+member whose own central base — read in its own already-canonical
+orientation — is <code>A</code>.</strong> This is well-defined for every family, computed
+purely from the flank pattern, whether or not that specific member (or any
+member at all) is actually observed anywhere in the index. Concretely: call
+<code>central_canonical_neighbors()</code> on any member (observed or not) to get the
+family's 4 canonical forms; the one among them whose own centre nucleotide is
+<code>A</code> is the family's canonical form. The other 3 (<code>C</code>, <code>G</code>, <code>T</code>) are labelled
+relative to <em>that</em> fixed reference, not relative to the calling member's own
+orientation.</p>
+<p><strong>Consequence for the minorant.</strong> With this fixed A-referenced labelling,
+<code>minorant</code> (the smallest raw encoding among the family's <em>observed</em> members,
+introduced further below) becomes directly computable rather than needing to
+be tracked as extra state: regenerate the family's 4 canonical forms from
+any member's own k-mer (cheap, no lookup), compare the raw encodings of
+whichever are marked present, and take the smallest. No separate stored bit
+is required — see Step 2b below, where this replaces the earlier
+minorant-bit design.</p>
+<h2 id="locus-eligibility-raw-definition-vs-paralogy-filter">Locus eligibility: raw definition vs. paralogy filter</h2>
+<p>For each k-mer <code>x</code> observed in genome A (source, one MPHF slot; the 3
+central-position variants generated as in the sweep below): check whether
+A's locus (flanks fixed) is resolvable in genome B under one of the 4
+central forms.</p>
+<p><strong>Raw / no model.</strong> The locus counts in the denominator iff at least one of
+the 4 forms is present in B; it counts in the numerator iff the form found in
+B differs from A's own. No constraint on A's or B's own copy number at this
+locus. Open question, not resolved: what if <strong>more than one</strong> of the 4 forms
+is present in B simultaneously (ambiguous target — count once arbitrarily,
+count all, or drop)? The stringent filter below sidesteps the question by
+construction rather than answering it.</p>
+<p><strong>Stringent / paralogy-aware.</strong> The locus counts only if exactly one of the
+4 forms is present in A <strong>and</strong> exactly one is present in B (<code>count == 1</code> at
+that slot too, when a count index is available, to also exclude same-allele
+duplicates that presence alone cannot see). This drops the raw definition's
+ambiguous-B case automatically, at the cost of also dropping heterozygous
+sites indiscriminately alongside true duplications (see "Heterozygosity,
+ploidy, and consensus-assembly inputs" below).</p>
+<p><strong>Rejected: parsimony-based multiset pairing for multiplicity &gt; 1.</strong> Rather
+than dropping ambiguous loci, pair identical alleles between A and B first
+(0-mutation explanation preferred), then take <code>min(unmatched_A, unmatched_B)</code>
+as inferred SNP pairs. Rejected on two grounds: (1) circularity — selecting
+pairs by minimal apparent divergence, then measuring divergence on those same
+pairs, deflates the estimate by construction, not a neutral heuristic; (2)
+the discriminating signal is a single base among 4 possible values, and the
+flanks are <em>already</em> guaranteed identical for every candidate by
+construction (that is how the locus was selected) — no information remains
+in a k-mer window to tell which copy in B truly corresponds to which copy in
+A once multiplicity &gt; 1 on either side. Any pairing rule invents a
+correspondence the data cannot support. Multiplicity &gt; 1 is treated as
+non-identifiable, not as a puzzle to solve with a heuristic.</p>
+<h2 id="multi-genome-framing-family-as-pseudo-alignment-column">Multi-genome framing: family as pseudo-alignment column</h2>
+<p><strong>Idea.</strong> Instead of resolving locus eligibility and correspondence one
+genome pair at a time, treat a family as a column of a pseudo multiple
+alignment across <em>all</em> genomes simultaneously: for each family, each genome
+has either a net single-copy state (<code>A</code>/<code>C</code>/<code>G</code>/<code>T</code>, when the genome carries
+exactly one of the 4 forms) or "missing" (<code>?</code>, multi-copy or absent). Flank
+conservation (the <code>2m</code> bases fixed by construction) supplies positional
+homology for free — the same role a real MSA would play, without alignment
+software, gap penalties, or progressive-alignment approximations. Stacking
+one such column per family, genomes as rows, produces a genuine SNP
+pseudo-alignment matrix, not just a bag of pairwise distances.</p>
+<p><strong>Precedent.</strong> This is the same principle behind reference-free
+k-mer-based phylogenomics tools — SKA (Split K-mer Analysis, Harris 2018) and
+kSNP: split the k-mer around a variable center, use flank identity to call
+homologous columns across arbitrarily many genomes with no reference and no
+MSA step, then feed the resulting pseudo-alignment to standard phylogenetic
+tools. Landing on the same design independently is a good sign, not a
+coincidence.</p>
+<p><strong>Resolves the pairwise-correspondence problem, properly.</strong> The "Rejected:
+parsimony-based multiset pairing" case above failed because, with only two
+genomes' cardinalities to look at, there is no external constraint to justify
+picking one correspondence between leftover alleles over another — <code>min(a,b)</code>
+is a lower bound dressed up as a point estimate (see the follow-up discussion
+on Felsenstein-style parsimony inconsistency: minimum-event explanations are
+systematically biased low whenever homoplasy/multiplicity is real, not
+noise-cancelling). With <code>N</code> genomes and many families jointly, the same
+question can be answered the way real phylogenetics answers it: ancestral
+state reconstruction / ML mapping over a tree estimated from the whole
+column set. The tree supplies the missing constraint that two isolated
+columns cannot — this is the principled way out, not a heuristic replacement
+for one.</p>
+<p><strong>Relation to what's already implemented.</strong> <code>KmerIndex::raw_snp_distance</code>
+already computes, internally, per family, exactly this row — <code>single_form:
+Vec&lt;Option&lt;u8&gt;&gt;</code>, one entry per genome, <code>None</code> where ambiguous/absent —
+before immediately collapsing it into pairwise <code>snp[i,j]</code>/<code>shared[i,j]</code>
+tallies. The pivot this section proposes is small at the implementation
+level: stop collapsing early, and surface the per-family row as a first-class
+artifact (a <code>families x genomes</code> matrix). Pairwise raw p-distance becomes one
+projection of that matrix (what's computed today), not the primary object;
+downstream, the matrix itself could feed real phylogenetic tools (parsimony/
+ML, e.g. RAxML/IQ-TREE-style) instead of only NJ/UPGMA on a homemade
+pairwise-distance matrix.</p>
+<p><strong>Caveat: column completeness shrinks with <code>N</code>.</strong> The probability that a
+family's flanks stay intact simultaneously across all <code>N</code> genomes decays with
+<code>N</code> (same ascertainment-bias mechanism as Bias 1 above, compounded over more
+genomes) — fully-resolved columns (no <code>?</code> anywhere) become rare as more
+genomes are added. Same missing-data situation any real multi-species
+alignment faces, and phylogenetic tools already handle it well; the practical
+implication is that columns should be allowed partial coverage (&gt;=2 resolved
+genomes, not unanimous) rather than requiring every genome to be net
+single-copy at that locus.</p>
+<h2 id="context-detectability-and-a-3-way-ordinal-distance-per-pair">Context, detectability, and a 3-way ordinal distance per pair</h2>
+<p>Empirical follow-up to the pseudo-alignment idea above: <code>obikmer phylo
+--snp</code> was run on a real 20-genome benchmark index and the resulting FASTA
+fed to <code>raxml-ng</code>. Two problems surfaced, both traced back to conflating
+distinct notions under one symbol.</p>
+<p><strong>"Context", precisely.</strong> Sharing a central base between two genomes is not
+just sharing a nucleotide — it is sharing a <strong>context</strong>: the <code>2m</code> flanking
+bases, identical, which is a homology claim about that flanked window
+(guaranteed non-coincidental by k-specificity, Bias 4 above), <em>not</em> a claim
+about orthology or paralogy of the copy each genome carries. <code>A</code> opposite <code>C</code>
+= same context, divergent centre. <code>A</code> opposite nothing = <strong>this context is
+not observed in one of the two genomes</strong> — informative, not neutral.</p>
+<p><strong>Why the IUPAC/DNA encoding used for the first <code>--snp</code> test was wrong.</strong>
+Feeding IUPAC-coded ambiguity into a standard DNA model (<code>raxml-ng --model
+GTR+G</code>) is a semantic mismatch: Felsenstein-pruning ML treats an ambiguous
+tip as "exactly one true state, unknown which" (a uniform partial-likelihood
+vector over compatible bases), not "these states are simultaneously
+present". The two encodings look identical (same IUPAC letters) but the
+software reads them backwards from what was intended — this invalidates the
+literal branch lengths from that first experiment (topology-level groupings
+by genus were still informative, see the worked example further down).</p>
+<p><strong>Why <code>-</code> (absence) must not be scored as similarity, but also must not be
+scored as a shared character between two absences.</strong> Two genomes both
+lacking a context are not observed to resemble each other at that locus —
+neither is observed to differ from the other either. It is a symmetric
+non-observation, uninformative for that pair, and should contribute nothing
+(not a small positive nor a small negative signal) to their distance. A
+genome carrying a state (<code>A</code>) against one carrying none is a different case
+entirely: informative, and should not be scored as neutral "missing data"
+the way a generic DNA/ML pipeline would.</p>
+<p><strong>Detectability vs existence — a deliberate simplification, accepted.</strong>
+"Context not observed" conflates two different biological events: (1) true
+loss of the locus, (2) the locus still exists but a mutation/indel <em>outside</em>
+the centre, anywhere in the <code>2m</code> flanks, broke k-mer recognition. The design
+adopts a rigorist stance on purpose: any flank-breaking mutation counts as
+"this context no longer exists", full stop — because both causes (1) and (2)
+independently require <em>at least</em> one more mutational event than a lone
+central substitution would. This licenses treating "context absent in one of
+the two genomes" as a <strong>lower bound</strong> on distance strictly greater than a
+plain central SNP, without needing to know which of the two causes applies.
+Coarser than a true event count, and accepted as such (fine substitution-type
+modelling, e.g. transition/transversion weighting, is a secondary
+refinement, not required for this to be useful).</p>
+<p><strong>Resulting ordinal distance between two genomes at one family/context:</strong></p>
+<table>
+<thead>
+<tr>
+<th>Comparison</th>
+<th>Distance</th>
+<th>Meaning</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>same centre (<code>A</code>/<code>A</code>)</td>
+<td><code>0</code></td>
+<td>identical</td>
+</tr>
+<tr>
+<td>different centre, both single-copy (<code>A</code>/<code>C</code>)</td>
+<td><code>1</code></td>
+<td>plain central SNP</td>
+</tr>
+<tr>
+<td>one genome has a state, the other has none</td>
+<td><code>&gt;1</code> (lower bound)</td>
+<td>context undetectable in one genome — at least one extra mutational event, of unknown type</td>
+</tr>
+<tr>
+<td>neither genome has any state (<code>∅</code>/<code>∅</code>)</td>
+<td>excluded</td>
+<td>symmetric non-observation, not comparable, contributes nothing</td>
+</tr>
+</tbody>
+</table>
+<p>This is a direct extension of <code>KmerIndex::raw_snp_distance</code> (<code>obikindex/src/siblings.rs</code>),
+which today only implements the <code>0</code>/<code>1</code> rows and silently drops everything
+else (including the informative <code>&gt;1</code> row) rather than scoring it.</p>
+<p><strong>Open, not yet resolved:</strong>
+- Calibrating <code>&gt;1</code> to a real number for tools expecting continuous distances
+  (NJ/UPGMA, ML branch lengths), rather than an arbitrary placeholder.
+  Natural route: estimate <code>p_hat</code> from the resolved (<code>0</code>/<code>1</code>) sites first,
+  then use the already-derived ascertainment formula (<code>P(usable window
+  showing a central SNP) = p * (1-p)^(2m)</code>, Bias 1 above) to derive a
+  model-consistent value for the <code>&gt;1</code> bucket instead of guessing a constant.
+- Where multi-copy/ambiguous states (the IUPAC case: a genome carrying more
+  than one form) fit into this ordinal scheme — plausibly also <code>&gt;1</code> by the
+  same "at least one extra event" argument (a second form appearing is a
+  gain, itself an event), but not yet worked out.</p>
+<p><strong>Practical alternative validated for the pseudo-alignment output itself</strong>
+(orthogonal to the ordinal-distance question above, useful regardless of how
+<code>&gt;1</code> ends up calibrated): re-encode each family as 4 independent binary
+presence/absence characters (<code>A</code>,<code>C</code>,<code>G</code>,<code>T</code> columns) instead of one IUPAC
+column, feed to a <code>BIN</code>-type model instead of <code>DNA</code>. <code>∅</code> becomes an explicit
+<code>0000</code> state (identity with another <code>0000</code>, not missing data) rather than a
+gap — removes the semantic mismatch above by construction. Known cost,
+accepted for now: a plain central substitution (<code>A</code> -&gt; <code>C</code>) becomes 2 binary
+flips (<code>1000</code> -&gt; <code>0100</code>), overweighting substitutions relative to true
+gain/loss events, and the 4 sub-characters of one family are not
+statistically independent the way a generic <code>BIN</code> model assumes. A proper
+fix (single 16-state alphabet, i.e. the powerset of <code>{A,C,G,T}</code>, with a
+substitution-rate structure that respects the subset lattice rather than a
+fully general 16x16 GTR-analogue) is very likely not expressible in
+<code>raxml-ng</code>'s <code>MULTI</code> datatype as-is (Mk or fully-general rates only) and a
+fully general 16-state rate matrix is almost certainly unidentifiable here
+(states of cardinality &gt;=3 are ~2% of sites in the benchmark run). Treated as
+a longer-term research question, not a near-term implementation target.</p>
+<h2 id="sankoff-parsimony-as-the-resolution-of-the-16-state-model-problem">Sankoff parsimony as the resolution of the 16-state model problem</h2>
+<p>The "longer-term research question" just above (a 16-state alphabet — the
+powerset of <code>{A,C,G,T}</code> — with a substitution structure that respects the
+subset lattice) turns out to have a near-term answer, once the <em>unification</em>
+question below is worked through.</p>
+<p><strong>Distance methods (NJ/UPGMA/ME) vs. character methods (parsimony/ML): not a
+deep philosophical divide, but a real practical distinction for this
+project.</strong> Historically "phenetic" (characters -&gt; distances -&gt; tree) and
+"cladistic" (characters -&gt; tree directly) approaches were presented as
+opposed schools; the modern view is a mathematical continuity, not a
+dichotomy — Minimum Evolution (ME: find the tree minimizing total branch
+length from a distance matrix) and Maximum Parsimony (MP: find the tree
+minimizing total character-state changes) are both instances of "minimise a
+global explanatory cost", and coincide under simple encodings (see Farris
+1983, "The Logical Basis of Phylogenetic Analysis"; the MP/ME connection is
+developed in the Minimum Evolution / Balanced Minimum Evolution literature,
+e.g. Nei and colleagues — citations not independently re-verified here, flag
+before quoting further). NJ's own agglomeration step already uses the whole
+distance matrix jointly (the Q-matrix), not just the pair being merged — an
+earlier claim in this discussion that distance methods are "blind" to
+cross-taxon structure at every stage was too strong.</p>
+<p>What <em>does</em> remain a real, structural distinction for this project: in a
+character method, a given character's cost is <strong>re-evaluated per candidate
+topology</strong> during tree search (the same family can cost 1 change under one
+topology, 2 under another). In a pairwise-distance pipeline
+(<code>raw_snp_distance</code> as it exists today), each family's contribution to
+<code>d(i,j)</code> is computed <strong>once</strong>, independent of any candidate topology, before
+NJ/UPGMA ever runs — so a question like "does this shared <code>∅</code> look like a
+synapomorphy under topology T" can never be posed in that pipeline, for any
+T. That question is only answerable by a method that tests candidate
+topologies and re-scores characters under each — i.e. a character method.</p>
+<p><strong>Sankoff parsimony directly resolves the <code>∅</code>/gain-loss/substitution
+question, without the identifiability problem of a fitted 16-state model.</strong>
+Sankoff's algorithm generalises Fitch parsimony to an arbitrary
+user-supplied cost matrix between states (<code>obikseq</code>/<code>obikindex</code> would treat
+each family as a <code>2^{4}</code>-state character, state = subset of <code>{A,C,G,T}</code>
+observed in that genome, <code>∅</code> included as a real state, not a gap). The
+previous 16-state idea failed specifically because <em>fitting</em> a full 16x16
+rate matrix by ML is unidentifiable at this data volume; Sankoff sidesteps
+that because the cost matrix is <strong>fixed a priori from domain knowledge</strong>, not
+estimated — e.g. <code>c({A},{C}) = 1</code> (a substitution), <code>c({A},{A,C}) = 1</code> (a
+gain), <code>c({A,C},{A}) = 1</code> (a loss), <code>c({A,C},{G,T}) = 2</code> (two changes) — no
+estimation, no overparameterisation. This reframes gain/loss and central
+substitution as two cost categories with independently chosen weights,
+exactly the "two families of parameters" (<code>mu_substitution</code>, <code>mu_gain/loss</code>)
+floated earlier in this discussion, now with an actual algorithmic home.</p>
+<p><strong>Caveat, not blocking for this project's scope.</strong> Sankoff is still
+parsimony: in principle exposed to Felsenstein's statistical-inconsistency
+result under long-branch attraction (already invoked earlier against
+<code>D_F = min(a,b)</code>) — parsimony and ML only provably coincide in the
+short-branch regime. This is not a practical concern here because it is
+exactly this estimator's declared target (closely related genomes, short
+branches) — the regime where parsimony's known failure mode does not apply —
+but worth stating explicitly as a scope guard rather than leaving it
+implicit.</p>
+<p><strong>Cheapest next experiment: don't write a Sankoff tree-search engine, use
+one that exists.</strong> The hard part of a from-scratch implementation is not the
+Sankoff DP itself (a straightforward dynamic program over a <em>fixed</em> tree) but
+the topology search (SPR/NNI with incremental re-scoring) that comes for
+free with <code>raxml-ng</code> on the ML side. <strong>TNT</strong> (Tree analysis using New
+Technology, free, standard in morphological cladistics) already implements
+Sankoff parsimony with a custom cost matrix plus topology search — the
+family-state matrix (already close to what <code>--snp</code> produces, minus the
+IUPAC/DNA-model mismatch) could be fed there directly, no new code required,
+before considering a bespoke engine.</p>
+<p><strong>The concrete comparison this unlocks:</strong> run both pipelines on the same
+family data —
+<code>k-mer families -&gt; D_ij -&gt; NJ/ME/UPGMA</code> (phenetic, what exists today) vs.
+<code>k-mer families -&gt; characters -&gt; argmin_T Sankoff-cost(T)</code> (cladistic, via
+TNT) — and compare the resulting topologies. Agreement would validate that
+the pairwise-distance projection preserves the phylogenetic signal;
+disagreement would pinpoint exactly what the projection to a single number
+per pair loses. Not yet run.</p>
+<h3 id="a-concrete-sankoff-cost-matrix-for-the-16-state-alphabet">A concrete Sankoff cost matrix for the 16-state alphabet</h3>
+<p><strong>Why <code>c_gl</code> and <code>c_ctx</code> are the same constant, not two.</strong> An earlier version
+of this design used two independent parameters: <code>c_gl</code> for an ordinary
+gain/loss step between two nonempty states (e.g. <code>{A,C}-&gt;{A}</code>), and <code>c_ctx</code>
+only for a state collapsing all the way to <code>∅</code>. That distinction doesn't
+survive contact with what the index actually observes. Presence/absence
+tracking never sees "the flanks" separately from "the centre" — it sees
+whole, distinct, homologous 31-mers (two 31-mers sharing &gt;=30 bases are
+homologous by construction, though orthology vs. paralogy is undecidable
+from that alone — settled earlier, see "Locus eligibility"). Losing the <code>A</code>
+form of a family while <code>C</code> remains (<code>{A,C}-&gt;{C}</code>) and losing the last
+remaining form (<code>{A}-&gt;∅</code>) are the <em>same kind of event</em>: a specific, complete
+31-mer that used to be observed no longer is, because at least one of its
+31 positions mutated. There is no separate "gain/loss of a still-recognised
+allele" mechanism distinct from "loss of context" — both are exactly the
+event <code>c_ctx(p)</code> (below) already computes the expected cost of. So: one
+constant, <code>c_ctx</code>, used everywhere a member is gained or lost — <code>X -&gt; ∅</code>
+included, and (see next point) not even as a special case there.</p>
+<p><strong>Set-edit-distance formula.</strong> For two states <code>X, Y ⊆ {A,C,G,T}</code>, split into
+<code>seulement_X = X \ Y</code> (size <code>a</code>) and <code>seulement_Y = Y \ X</code> (size <code>b</code>).
+Elements present in both cost nothing. Pair up to <code>min(a,b)</code> of the
+remaining elements as <strong>substitutions</strong> (cheaper than treating them as an
+unrelated loss + gain whenever <code>c_sub &lt; 2*c_ctx</code>, which any sane parameter
+choice satisfies); whatever is left over after pairing is a pure
+<strong>gain/loss</strong>:</p>
+<div class="highlight"><pre><span></span><code>cost(X,Y) = min(a,b)*c_sub + |a-b|*c_ctx
+</code></pre></div>
+<p>Worked examples (<code>c_sub = c_ctx = 1</code>): <code>{A}-&gt;{C}</code> = 1 (one substitution);
+<code>{A}-&gt;{A,C}</code> = 1 (one gain, no substitution pair available since nothing is
+only-in-Y that matches an only-in-X element after the shared <code>A</code> is
+excluded); <code>{A,C}-&gt;{G,T}</code> = 2 (two substitution pairs, <code>A/C</code> vs <code>G/T</code>, both
+same-size sets share nothing); <code>{A,C,G}-&gt;{A,C,T}</code> = 1 (<code>G</code>/<code>T</code> is the only
+mismatched pair, <code>A,C</code> shared).</p>
+<p><strong><code>∅</code> is <em>not</em> a flat-cost special case — a corrected position, reversing
+an earlier draft of this design.</strong> An earlier version charged
+<code>cost(X, ∅) = c_ctx</code> flat, independent of <code>|X|</code>, on the grounds that every
+member of a family shares identical flanking sequence, so one mutation
+breaking that context should unrecognise all of them at once rather than
+<code>|X|</code> separate times. That argument doesn't survive comparison with how the
+rest of the matrix already works: <code>{A,C,T} -&gt; {A}</code> (losing two members,
+one remaining) is charged <code>2*c_ctx</code> via the general formula above, with no
+equivalent "maybe it was one shared event" discount — nothing distinguishes
+that case from <code>{A,C} -&gt; ∅</code> (losing two members, none remaining) other than
+which state happens to be the target. Singling out <code>∅</code> for special
+treatment was arbitrary, not principled: the uncertainty about "one event
+or several" is identical in both cases, and the model already resolves it
+uniformly elsewhere by simply counting elements. So <code>∅</code> is now an ordinary
+node in the state graph below like any other, with no patch applied
+afterwards:</p>
+<div class="highlight"><pre><span></span><code>cost(X, ∅) = cost(∅, X) = |X| * c_ctx   (via |X| single-element graph edges)
+cost(∅, ∅) = 0
+</code></pre></div>
+<p><strong>Computing <code>c_ctx</code>.</strong> Not guessed — built from the value already derived
+for the <code>&gt;1</code> bucket in "Context, detectability, and a 3-way ordinal
+distance per pair" above:</p>
+<div class="highlight"><pre><span></span><code>c_ctx(p) = mean_sub_cost * [(2m*p) / (1 - (1-p)^(2m)) + p]
+</code></pre></div>
+<p><code>p</code> is <code>p_hat</code>, the calibrated per-site mutation probability (see
+<code>calibrate_p_hat</code> / the "Experiment" section below); <code>m = (k-1)/2</code>, the
+flank length on each side of the centre (<code>k=31</code> → <code>m=15</code>). Read the
+bracketed term, well, term by term: <code>(1-p)^(2m)</code> is the probability that
+<em>none</em> of the <code>2m</code> flanking positions mutated, so <code>1-(1-p)^(2m)</code> is the
+probability that <em>at least one</em> did — i.e. the probability that this
+specific 31-mer stops being observable at all, which is exactly the event
+<code>c_ctx</code> prices. <code>2m*p</code> is the unconditional expected mutation count over
+those <code>2m</code> positions. Their ratio is the conditional expectation
+<code>E[mutations | at least one occurred]</code> — provable directly: for any
+nonnegative integer random variable <code>X</code>, <code>X · 1{X&gt;=1} = X</code> always (both
+sides are <code>0</code> when <code>X=0</code>, both are <code>X</code> otherwise), so
+<code>E[X | X&gt;=1] = E[X·1{X&gt;=1}]/P(X&gt;=1) = E[X]/P(X&gt;=1)</code>, which is
+<code>(2m*p)/(1-(1-p)^(2m))</code> here. The trailing <code>+p</code> adds the (much smaller,
+first-order, not itself a conditional expectation) marginal contribution
+of the centre position's own mutation probability.</p>
+<p><strong>The <code>mean_sub_cost</code> multiplier — a correction, not part of the original
+derivation.</strong> The bracketed term is a <em>count</em> of expected mutations, not a
+cost — an earlier version used it directly as <code>c_ctx</code>, implicitly pricing
+every one of those mutations at a flat <code>1</code> regardless of type. That stopped
+being defensible once substitution costs were calibrated per base-pair
+category (<code>substitution_costs_from_tally</code>): transitions are markedly more
+frequent than transversions in this project's own data (roughly 5-6x, e.g.
+130k vs. 20-28k observed instances per category in the eubacteria run
+below) and correspondingly cheaper, so "one mutation" isn't worth a flat
+unit. <code>mean_sub_cost</code> (<code>mean_substitution_cost</code>) is the empirical average
+substitution cost, weighted by each category's observed frequency — it
+converts the bracketed term's expected mutation <em>count</em> into an actual
+expected <em>cost</em>. Concretely, in the eubacteria run: the bracketed term
+alone is <code>~1.17</code> (close to <code>1</code>, i.e. context loss is <em>usually</em> attributable
+to a single mutation, since <code>p_hat</code> is small); <code>mean_sub_cost ~= 1.48</code>
+(pulled up from the cheapest transition cost of <code>1.0</code> by the substantial
+minority of transversions in the mix); final <code>c_ctx ~= 1.73</code> — sensibly
+between the cheapest transition (<code>~1.0</code>) and the transversion costs
+(<code>~2.5</code>-<code>2.9</code>), rather than coinciding almost exactly with the cheapest
+transition purely by construction accident, which is what the unmultiplied
+version did and which is what exposed this gap in the first place.</p>
+<p><strong>Better construction method: shortest path in a small state graph, not the
+closed-form formula directly.</strong> Build a graph on all 16 states, <code>∅</code>
+included, with two edge types — substitution edges between same-cardinality
+sets differing by one element (weight <code>c_sub</code>, or <code>c_ts</code>/<code>c_tv</code> if split
+further below), and gain/loss edges between sets whose cardinality differs
+by one (weight <code>c_ctx</code>, per the unification above; <code>∅</code> connects to each
+singleton state this way, being a strict subset of it) — then define
+<code>cost(X,Y)</code> as shortest-path distance in that graph, uniformly for every
+<code>X,Y</code> including <code>∅</code>, precomputed once (16 nodes, trivial) into a dense
+16x16 matrix before feeding it to Sankoff/TNT. Verified equivalent to the
+closed-form formula above in the
+uniform-cost case (checked by hand on <code>{A}-&gt;{C,G,T}</code>: both give
+<code>c_sub + 2*c_ctx</code>). The graph construction is not just a reformulation for
+its own sake: it is the version that generalises correctly once substitution
+costs stop being uniform (next point) — the closed-form's <code>min(a,b)</code>
+counting silently assumes <em>any</em> pairing costs the same, which breaks the
+moment <code>c_sub</code> depends on which two bases are involved.</p>
+<p><strong>Substitution refinement — implemented as the full 6-category symmetric
+matrix, not just Ts/Tv.</strong> <code>c_sub</code> was originally going to split into just
+<code>c_ts</code> (A&lt;-&gt;G or C&lt;-&gt;T) and <code>c_tv</code> (the other four pairs) — already
+well-defined in canonical space (see "Canonical invariance" above: a
+transition maps to a transition, a transversion to a transversion,
+regardless of orientation). A symmetric cost matrix allows finer
+resolution than that 2-category split, though: each of the 6 distinct
+undirected base pairs (AC, AG, AT, CG, CT, GT) can be costed
+independently, with no grouping at all — <code>SankoffWeights::sub_cost</code> is a
+full <code>[[f64;4];4]</code> table (<code>SankoffWeights::ts_tv</code> remains as a convenience
+constructor for the coarser 2-category case, if ever wanted). This turns
+"pick <code>min(a,b)</code> substitution pairs" into a genuine (tiny, &lt;=4 elements per
+side, trivially enumerable) minimum-cost bipartite matching problem instead
+of a plain count — the state-graph shortest-path construction handles this
+automatically, no separate logic needed. Calibration is not a guess
+either: <code>KmerIndex::base_pair_tally</code> collects the pooled <code>(centre_i,
+centre_j)</code> distribution over resolved (SNP) sites — restricted to the same
+ratio-ceiling-included genome pairs as <code>p_hat</code>'s own calibration, for the
+same saturation-exclusion reason — and <code>substitution_costs_from_tally</code>
+turns that into <code>cost(a,b) = -ln(rate(a,b))</code>, normalised so the most
+frequent category costs <code>1.0</code> (the standard generalised-parsimony
+step-weighting heuristic, generalised from 2 categories to 6). A second
+full pass over the annex is required for this (see <code>base_pair_tally</code>'s own
+docs for why it can't share <code>raw_snp_distance</code>'s single pass) — both now
+share one traversal helper, <code>scan_family_pairs</code>, rather than duplicating
+the per-family reconciliation logic.</p>
+<p><strong>Caveat carried over from the <code>D_F = min(a,b)</code> rejection earlier:</strong> this
+cost matrix is only valid as <strong>Sankoff step-cost input</strong>, re-evaluated for
+every branch of every candidate topology during tree search. Reusing
+<code>cost(leaf_A, leaf_B)</code> directly as a standalone pairwise distance (bypassing
+the tree) would reintroduce the exact circularity already rejected — the
+<code>min(a,b)</code> pairing here is a locally-defined edit distance between two
+states, not a claim about the true evolutionary history between two
+specific genomes.</p>
+<p><strong>Feasibility confirmed:</strong> TNT's <code>costs</code> command accepts custom step
+matrices for multistate characters, so this whole construction (16x16
+matrix derived from the state graph, <code>c_ts</code>/<code>c_tv</code>/<code>c_ctx</code> as the three
+tunable parameters) is directly usable there — no new tooling required
+before testing it.</p>
+<h3 id="experiment-tnt-run-on-real-data-2026-08-11">Experiment: TNT run on real data (2026-08-11)</h3>
+<p><strong>Status:</strong> validated at genus/family/order scale within Bacteria; not
+informative across domains with this character type. Exploratory only —
+run entirely outside the repo (<code>/tmp/tnt_run</code>, TNT installed locally under
+<code>TNT/</code>), no new Rust code. Kept here as the record of what was learned.</p>
+<p><strong>Pipeline.</strong> <code>obikmer phylo --snp</code> emits one IUPAC-coded pseudo-alignment
+row per genome (<code>snp_pseudo_alignment</code>, one column per family with
+<code>family_size() &gt;= 2</code>). A small external Python script decodes IUPAC back to
+the 16-state bitmask, applies the set-edit-distance formula above, and
+emits a complete TNT script (<code>xread</code> matrix + <code>smatrix</code> step-matrix + <code>hold</code>/
+<code>mult</code> search). No new Rust code was needed for this pass.</p>
+<p><strong>Calibration ("quick option").</strong> Rather than modifying
+<code>write_raw_snp_distance_csv</code> to emit raw counts, <code>c_ctx</code> was approximated as
+the unweighted mean of the pairwise <code>snp/(snp+shared)</code> ratios already
+present in <code>rawsnp.csv</code>, restricted to the relevant taxon subset. Used
+values: <code>mu = gamma = 10</code>, <code>c_ctx = 18</code> (this run predates the <code>c_gl</code>/<code>c_ctx</code>
+unification above — <code>gamma</code> here is what <code>c_gl</code> was called before it turned
+out to just be <code>c_ctx</code>; ratio <code>c_ctx/mu = 1.8</code>, consistent
+with the observed pairwise ratios for genomes within Enterobacteriaceae/
+Eubacteria, which cluster around 1.5-2 and barely move as the taxon set
+widens — the context signal is stable, not sensitive to which subset is
+chosen). The more principled route (raw counts, weighted <code>p_hat</code>, Ts/Tv
+split) remains a follow-up, not yet done.</p>
+<p><strong>Run 1 — Enterobacteriaceae (11 taxa: 4 <em>E. coli</em>, 4 <em>Salmonella enterica</em>,
+3 <em>Klebsiella pneumoniae</em>).</strong> All three genera recovered as monophyletic.
+Initial read of the exported (unrooted, TNT/Nexus <code>[&amp;U]</code>) tree as showing a
+genus-arrangement disagreement with known systematics (<em>Escherichieae</em>:
+<em>Escherichia</em>+<em>Salmonella</em> sister vs. more distant <em>Klebsielleae</em>) was
+<strong>wrong</strong> — diagnosed via <code>force = (taxa);</code> monophyly-constraint test
+(identical score constrained vs. free ⟹ no real disagreement). Root cause of
+the misreading: with exactly 3 clades and no outgroup, an unrooted tree has
+only <strong>one possible topology</strong> (a single trifurcation) — there is no
+internal arrangement to get right or wrong. This run cannot test
+inter-genus relationships at all; it can only test intra-genus monophyly
+(which held).</p>
+<p><strong>Run 2 — Eubacteria (18 taxa: run 1 + <em>Acidobacterium capsulatum</em>,
+<em>Opitutus terrae</em>, <em>Bacillus subtilis</em>, <em>Shouchella clausii</em>, <em>Wolbachia</em>
+endosymbiont, <em>Proteus mirabilis</em>, <em>Yersinia ruckeri</em>).</strong> The
+Enterobacteriaceae substructure from run 1 is reproduced identically, now
+correctly rooted by real outgroups, resolving the tribal arrangement left
+undetermined in run 1: <em>Escherichia</em>+<em>Salmonella</em> sister, <em>Klebsiella</em> more
+distant — matching known systematics. Outgroup placement: <code>(Bacillus,
+Shouchella)</code> sister pair (Firmicutes/<em>Bacillales</em>) splits from all
+Proteobacteria — a correct phylum-level split; <code>Wolbachia</code>
+(Alphaproteobacteria) splits from the Gammaproteobacteria block
+(<code>Proteus</code>, <code>Yersinia</code>, Enterobacteriaceae) — a correct class-level split.
+Lower confidence: the fine nested order <code>(Proteus, (Yersinia,
+Enterobacteriaceae))</code> and the relative position of <code>Acidobacterium</code> vs.
+<code>Opitutus</code> — plausible, not independently verified against current
+Enterobacterales family-level literature.</p>
+<p><strong>Run 3 — full domain set (20 taxa: run 2 + <em>Candidozyma auris</em> [yeast] and
+<em>Saccharolobus islandicus</em> [archaeon]).</strong> The bacterial clade from run 2 is
+reproduced <strong>unchanged and intact</strong> — a real robustness signal, the method
+does not fragment the ingroup when unrelated deep taxa are added. But the
+result carries <strong>no information on Bacteria/Archaea/Eukarya relationships</strong>:
+with exactly one eukaryote, one archaeon and one bacterial clade, the
+unrooted tree is again forced into the single 3-clade trifurcation from run
+1's caveat — there is no second representative of either outgroup domain to
+resolve internal arrangement, so nothing about their relative position can
+be read from the topology (a "ladder" ordering in the exported tree is
+serialization, not signal). Independently, <code>rawsnp.csv</code> shows <em>why</em> this
+character type cannot reach further: pairwise ratios involving
+<em>Candidozyma</em>/<em>Saccharolobus</em> are almost all <code>NA</code> (no central-position
+family shared at all) or saturated at <code>1.0</code> (every shared family differs) —
+central-position families require literal 31 bp context conservation, which
+simply does not survive domain-level divergence. Cross-domain placement
+would need conserved-marker characters (rRNA, ribosomal proteins), not this
+estimator.</p>
+<h3 id="native-sankoff-tnt-phyg-export-2026-08-12-superseding-the-external-scripts-above">Native <code>--sankoff --tnt</code>/<code>--phyg</code> export (2026-08-12), superseding the external scripts above</h3>
+<p>The ad hoc Python glue from the previous section is superseded: <code>obikmer
+distance --sankoff</code> now calibrates the matrix natively (<code>p_hat</code>, 6-category
+substitution costs, <code>c_ctx</code> weighted by <code>mean_sub_cost</code> — see the worked
+example above) and <code>--tnt</code>/<code>--phyg</code> each write a ready-to-run script from
+it, no external script needed. <code>∅</code> is an ordinary 16th state throughout
+(never <code>-</code>), specifically to avoid gap-semantics confusion in downstream
+tools — see "A concrete Sankoff cost matrix" above for why.</p>
+<p><strong>TNT (<code>--tnt</code>).</strong> <code>write_sankoff_tnt</code> (<code>obikmer/src/cmd/phylo/mod.rs</code>)
+recodes to TNT's own <code>0-9A-F</code> xread alphabet (its default reader rejects
+the wider IUPAC set otherwise), scales and rounds costs to integers
+(<code>smatrix</code>/<code>cost</code> reject decimals), then re-runs integer Floyd-Warshall on
+the rounded matrix (<code>scaled_metric_matrix</code>) — independently rounding each
+cell of an already-metric real-valued matrix can break the triangle
+inequality (e.g. two real costs of <code>1.734</code> round to <code>173</code> each, summing to
+<code>346</code>, while their real sum <code>3.468</code> rounds to <code>347</code>), which TNT otherwise
+silently "fixes" itself with an unreproducible correction. Verified against
+the real 20-genome benchmark index: zero triangle-inequality violations
+after the fix, TNT loads the file without its "triangle inequality
+violated... Fixed" warning.</p>
+<p>Two syntax facts worth recording because they're wrong in intuitive
+guesses and contradicted actual TNT behavior when tested: TNT's plain
+command stream has <strong>no comment syntax</strong> of its own — <code>/* */</code> and <code>[ ]</code>
+only work inside the (separately-enabled, off by default) macro scripting
+language, and error with "No command!" otherwise. The working substitute
+is <code>quote TEXT ;</code> (prints the text, doesn't affect parsing) — but the text
+itself can't contain a literal <code>;</code> (TNT's universal terminator); the
+manual's own escape (<code>.,</code>) exists but the script here just avoids
+semicolons in the text instead.</p>
+<p>The default search command embedded in the script is <code>mult</code> (traditional:
+random addition sequences + TBR), not <code>xmult</code> (New Technology search:
+ratchet/drift/tree-fusion). <code>xmult</code> with TNT's default <code>mxram</code> (16 MB,
+must be set <em>before</em> <code>xread</code> if changed) ran out of RAM on the real
+908k-character dataset ("<code>xmult - out of ram</code>"); <code>mult</code> does not, matching
+what had already been validated by hand outside this session.</p>
+<p><strong>PhyG (<code>--phyg</code>).</strong> <code>write_sankoff_phyg</code> writes a <code>tcm:</code> custom-alphabet
+matrix (same scale+round+metric-closure treatment as TNT) and reuses
+<code>--sankoff</code>'s own <code>_sankoff.fasta</code> as-is via <code>prefasta:</code> — PhyG's <code>tcm:</code>
+alphabet is read from the matrix file's own first line, so (unlike TNT) no
+recoding is needed. PhyG auto-adds its own indel/gap state as an
+<code>(n+1)</code>-th row/column of the tcm; inert here since the alignment encodes
+absence as <code>0</code>, never <code>-</code>.</p>
+<p><code>report("file", newick, overwrite)</code> — exactly as shown in PhyG's own
+manual — triggers <code>Unrecognized/missing report option ... defaulting to
+'graphs'</code> on the locally installed binary (1.3, commit <code>3c1a1fa</code>); the
+working form adds <code>graphs</code> explicitly: <code>report("file", graphs, newick,
+overwrite)</code>. Manual/binary mismatches like this (also true of <code>criterion:</code>
+— the binary accepts <code>parsimony</code>/<code>ml</code>/<code>pmdl</code>, the manual instead documents
+<code>mapa</code>/<code>ncm</code>/<code>parsimony</code>/<code>pmdl</code>/<code>si</code>) mean command syntax against this PhyG
+build should be verified empirically, not trusted from the PDF alone.
+<code>instances:N</code> (not a separate CPU flag) is what actually parallelises the
+search across cores — PhyG uses all physical cores by default but only
+across as many instances as are running, so raise it to the physical core
+count to use them all (the CLI-level <code>+RTS -NX -RTS</code> flag also exists but
+controls something else: capping/limiting cores, not requesting more).</p>
+<p>Both scripts share one <code>--sankoff-cost-scale</code> (default <code>100</code>), not two
+separate flags — they scale the same calibrated matrix for the same
+reason (integer-only cost commands) and no PhyG-specific
+accumulator-width constraint was ever found to justify a different
+default from TNT's (TNT: hinted 32-bit accumulators in its own manual;
+PhyG: no such hint found — Haskell's native <code>Int</code> is typically 64-bit).</p>
+<p><strong>Open problem: PhyG reports all branch lengths as <code>0.0</code>.</strong> The graph-level
+parsimony cost is correct (<code>3.3286×10⁸</code> on the real dataset, consistent
+with TNT's <code>328574911</code> on the same calibrated matrix), but every individual
+edge in the exported Newick shows <code>:0.0</code>, with the total cost only ever
+shown as a whole-tree annotation (<code>[3.32860377e8]</code>). Not fixed, not fully
+diagnosed — PhyG's manual describes per-edge branch length as computed by
+ancestral-state (HTU) backtracking, well documented for sequence/standard
+character types, but nothing found (the term "Sankoff" doesn't even appear
+in the manual) confirming this backtracking is wired up for a custom
+<code>tcm:</code> matrix character. Switching <code>criterion:</code> to a likelihood-family
+option (<code>ml</code>, or the manual's <code>mapa</code>/<code>ncm</code>/<code>si</code>) was considered as a
+possible fix but is very unlikely to be one: those criteria are
+information-theoretic reparametrisations of the <em>same</em> step-counting
+machinery as parsimony (<code>ncm</code> in particular is known in the literature to
+be numerically equivalent to weighted parsimony), not classical
+continuous-time-Markov ML with a real rate matrix — so they wouldn't
+change how branch length is attributed per edge either.</p>
+<p><strong>Export format note (not a bug in the generator).</strong> Neither script's
+<code>.tre</code> output opens in PearTree (FigTree's successor) via File &gt; Open —
+association/Launch-Services quirks were ruled out (the file was opened
+directly through the app, not by double-click). Likely cause, not yet
+confirmed: TNT's export is a minimal NEXUS <code>begin trees;</code> block with no
+preceding <code>Taxa</code> block and bare numeric (untranslated) leaf labels; PhyG's
+is multiple raw Newick trees concatenated with no NEXUS wrapper at all
+plus a trailing <code>[cost]</code> bracket tag after the root label. Both differ
+from a "normal" single-tree, fully-declared NEXUS file; this is PhyG/TNT's
+own export format, not something <code>write_sankoff_tnt</code>/<code>write_sankoff_phyg</code>
+could fix without post-processing the <em>other</em> program's output after the
+fact.</p>
+<h3 id="next-direction-genuine-ml-branch-lengths-not-parsimony-open-2026-08-12">Next direction: genuine ML branch lengths, not parsimony (open, 2026-08-12)</h3>
+<p>Decided: parsimony (the whole <code>--sankoff</code>/<code>--tnt</code>/<code>--phyg</code> pipeline above)
+is a stopgap, not the destination. The goal is maximum likelihood with
+real, calibrated branch lengths (expected substitutions/site), which
+parsimony step-counts were never going to give directly (see the open
+"branch lengths are <code>0.0</code>" problem above — even if fixed, TNT/PhyG-style
+parsimony branch length is a step count, not a continuous ML estimate).</p>
+<p><strong>Model choices, settled:</strong>
+- <strong>The exchangeability <code>R</code> is symmetric; the rate matrix <code>Q</code> is not.</strong>
+  (Superseded an earlier, wrong framing here that treated "symmetric
+  model" as one thing — see the resolution below on <code>R</code> vs <code>Q</code> vs <code>π</code> for
+  the full reasoning.) <code>R(a,b) = R(b,a)</code> because <code>BasePairTally</code> never
+  captured direction — a fact about the data, not a modelling choice.
+  <code>Q(a,b) = R(a,b)·π_b</code> is asymmetric whenever the real state frequencies
+  <code>π</code> are (which they are, empirically) — biology drives this via <code>π</code>,
+  not via <code>R</code>.
+- <strong><code>∅</code> stays an ordinary 16th state</strong>, as already established for
+  TNT/PhyG — same reasoning applies to any ML tool: encode as a real
+  alphabet symbol, never as <code>-</code>/gap, or the RAxML-era failure (empty set
+  silently treated as missing data) repeats.</p>
+<p><strong>Stationary frequencies for the 16 states — resolved (2026-08-12).</strong>
+A CTMC needs a rate matrix <code>Q</code>, generally asymmetric. <code>Q(i,j) = R(i,j) ·
+π_j</code>, where <code>R</code> (exchangeability) is symmetric and <code>π</code> (stationary
+frequencies) need not be — this factoring is what makes <code>Q</code> reversible
+(satisfies detailed balance, <code>π_i·Q(i,j) = π_j·Q(j,i)</code>) for <em>any</em> <code>π</code>, not
+just uniform, as long as <code>R</code> is symmetric. Two separate, both-easy
+quantities, not one hard inverse problem:
+- <strong><code>R</code> is already calibrated</strong>: <code>sub_cost</code> (<code>-ln(observed rate)</code> per pair,
+  from <code>BasePairTally</code>) <em>is</em> <code>R</code> up to a log transform — recover it as
+  <code>R(a,b) = exp(-sub_cost(a,b))</code>. Symmetric by construction, because the
+  tally itself never distinguished direction (unordered-pair counts only)
+  — not a modelling choice, a fact about what the data can say.
+- <strong><code>π</code> is a direct count</strong>: empirical marginal frequency of each of the
+  16 states across the whole alignment (same kind of scan already used to
+  confirm <code>N</code> occurs 1383 times in the real 20-genome benchmark). With
+  ~908k sites × 20 genomes, the counts are large enough that this is
+  precise on its own — no need to spend ML degrees of freedom
+  re-estimating it via IQ-TREE's <code>+FO</code>.</p>
+<p>Checked and ruled out along the way: IQ-TREE's <code>+F</code> (empirical, "compute
+from the alignment") does <strong>not</strong> work as a shortcut for this — for a
+custom-file morphology model, <code>readParameters</code> always requires the file's
+own frequency line unconditionally; omitting it and passing <code>+F</code> instead
+just fails (<code>ERROR: State frequencies could not be read</code>). <code>π</code> has to be
+computed by <code>obikmer</code> and written into the file, not left to IQ-TREE.</p>
+<p>Net effect: no free-rate ML estimation needed for this piece at all (the
+mistaken assumption that motivated most of this discussion — that
+building an asymmetric <code>Q</code> a priori would require solving a linear system
+from <code>Q</code> itself — doesn't apply, because <code>R</code>, the only piece that's
+genuinely hard to get directionally, is symmetric and already in hand).</p>
+<p><strong>Candidate tool: IQ-TREE</strong>, because it supports user-defined multistate
+models (unlike RAxML's <code>MULTI</code> data type, which is limited to the
+equal-rate Mk model and can't take a custom rate matrix at all — a genuine
+tool limitation, not a gap-symbol encoding problem this time). IQ-TREE 3
+(3.0.1) is now installed locally (Homebrew, <code>iqtree3</code>).</p>
+<p><strong>IQ-TREE custom-model format — verified empirically against the local
+binary (2026-08-12).</strong> The web docs' <code>-mdef</code> NEXUS <code>begin models;
+frequency NAME = ...; model NAME = ...; end;</code> mechanism (initially assumed
+to apply directly, see history below) turned out to be for <strong>named
+components used inside <code>MIX{...}</code>/<code>FMIX{...}</code> mixture models only</strong> — it
+does <strong>not</strong> apply to a single, non-mixture custom morphology matrix, and
+using it that way fails (<code>ERROR: File not found &lt;name&gt;</code> — traced in
+IQ-TREE 3's own source, <code>model/modelmorphology.cpp</code>: any <code>-m</code> string that
+isn't <code>MK</code>/<code>ORDERED</code>/<code>GTR</code>/<code>GTRX</code> is passed straight to
+<code>ModelMarkov::readParameters()</code>, which opens it <strong>as a literal file path</strong>,
+never consulting the <code>-mdef</code> models block at all for this data type).</p>
+<p><strong>The confirmed working recipe</strong> (built a tiny 5-taxon/3-state toy dataset
+and rate file, ran it end to end with <code>iqtree3</code>, got a real ML tree with
+non-zero branch lengths and an optimized log-likelihood — ground truth,
+not documentation):
+- No <code>-mdef</code> needed. Write one plain file (any name) containing, as
+  whitespace/newline-separated numbers, in order: the <strong>lower-triangular
+  rate matrix</strong> (<code>N(N-1)/2</code> values, PAML row-major order — for 16 states,
+  120 values, the same count and layout already produced for TNT's
+  <code>smatrix</code>), immediately followed by the <strong>N state frequencies</strong> on the
+  same stream (no header, no blank line required — confirmed by reading
+  <code>ModelMorphology::readRates</code>/<code>ModelMarkov::readStateFreq</code> directly, which
+  just pull tokens off the stream in sequence).
+- Invoke with <code>-m &lt;path-to-that-file&gt;+ASC</code> (<code>+ASC</code> for the no-constant-site
+  correction, as before). An explicit <code>+F{f1,...,fN}</code> on the command line
+  overrides the file's own frequency line if given (confirmed in
+  <code>ModelMorphology::init</code>) — useful once real calibrated stationary
+  frequencies exist, a placeholder equal-frequency line works meanwhile
+  (the still-open gap noted above).
+- <code>--seqtype MORPH</code> (alphabet <code>0</code>-<code>9</code>,<code>A</code>-<code>V</code>, ≤31 states) — reuse the same
+  <code>0-9A-F</code> recoding already built for TNT (<code>TNT_STATE_SYMBOL</code>).</p>
+<p><strong>Risk, confirmed, precisely characterised, and resolved by design
+(2026-08-12).</strong>
+<code>--seqtype MORPH{16}</code> <strong>does not force the state count</strong> for real ML
+analysis — tested directly (<code>--seqtype MORPH{4}</code> on the 3-symbol toy
+alignment gave the byte-for-byte identical 3-state result as no <code>{4}</code> at
+all) and confirmed in source: the value it sets
+(<code>params.alisim_num_states_morph</code>, <code>utils/tools.cpp</code>) is consumed only by
+the <code>--alisim</code> simulator; the main analysis path always calls
+<code>getDataBlockMorphStates</code>/an equivalent scan (<code>alignment/alignment.cpp</code>),
+for both FASTA/PHYLIP and NEXUS input (a NEXUS <code>symbols=</code> declaration
+doesn't change this either — checked, same code path). No CLI flag or
+NEXUS declaration overrides it.</p>
+<p>The precise rule (from <code>getDataBlockMorphStates</code>, <code>alignment.cpp:1058</code>):
+<code>N</code> = <strong>one plus the highest state ordinal actually observed anywhere in
+the alignment</strong>, ordinal being the symbol's position in IQ-TREE's own
+fixed table <code>"0123456789ABCDEFGHIJKLMNOPQRSTUV"</code> — not a count of distinct
+symbols seen. So the risk is narrower than "any missing symbol breaks it":
+concretely, it's whether the symbol mapped to state index 15 (<code>F</code> in the
+<code>0-9A-F</code> recoding already used for TNT, i.e. our <code>N</code> = "all four bases
+ambiguous") occurs <strong>at least once anywhere</strong> in the real alignment — if
+it does, <code>N</code> correctly comes out to 16 regardless of which lower-index
+symbols (including <code>0</code>/<code>∅</code>) are rare or absent; if it doesn't, <code>N</code> silently
+undercounts and misaligns every value in a 16-entry rate/frequency file,
+with no error to catch it. <strong>Checked against the real biological alignment</strong>
+(<code>/tmp/msg_test/eub_sankoff.fasta</code>, the 20-genome benchmark index): the
+symbol <code>N</code> (IUPAC "all four bases ambiguous," state index 15) occurs 1383
+times across 13 of the 20 sequences — present, so this specific real
+dataset is not at risk. Still worth a real, general presence check inside
+<code>obikmer</code> before this is wired in, rather than assuming every future
+dataset will have <code>N</code> too (nothing in IQ-TREE would catch it if not).</p>
+<p><strong>Resolution: subset + compact-renumber, not rely on all 16 appearing.</strong>
+Since IQ-TREE always infers <code>N</code> from the alignment's own content and
+nothing overrides that, the fix is to make the file <code>obikmer</code> writes match
+that inference <em>by construction</em>, for every run, rather than hope the
+16th (or any particular) state happens to occur:
+1. Scan the real alignment for which of the 16 canonical states actually
+   occur anywhere (not per-column — anywhere in the whole alignment).
+2. Renumber the occurring states to a <strong>compact, consecutive</strong> <code>0..k-1</code>
+   range, preserving their relative order (the original bitmask/<code>STATE_
+   SYMBOL</code> ordering) — not just filtering, since a <em>gap</em> in the ordinal
+   sequence (e.g. keeping states <code>{0,1,2,4}</code> numbered as-is instead of
+   <code>{0,1,2,3}</code>) reproduces the exact same "highest observed ordinal"
+   miscount this was meant to fix.
+3. Recode the alignment itself with this new compact <code>k</code>-symbol alphabet
+   (same recoding mechanism already used for TNT's <code>0-9A-F</code>, just over a
+   possibly-smaller symbol set).
+4. Extract the matching <code>k×k</code> submatrix (rows/columns for the kept
+   states only) from the full calibrated 16×16 cost matrix, in the same
+   lower-triangular order the rate-matrix file needs — and, later, the
+   matching <code>k</code>-length subset of stationary frequencies once those are
+   calibrated (still the open gap noted earlier in this section).</p>
+<p>Consequence, and why nothing is lost: a state that never occurs in a given
+alignment can, by definition, never contribute a transition to score in
+that same alignment — dropping it from that run's matrix costs nothing.
+The subset (and therefore <code>k</code>) can differ from one dataset/run to the
+next; this has to be done freshly per alignment, not computed once and
+reused.</p>
+<p><em>(Superseded reasoning, kept for the record: the <code>-mdef</code> NEXUS route
+below was the original plan, based on IQ-TREE's own web documentation for
+protein mixture models, before the local install allowed testing it —
+<code>GTRX</code> combined with a <code>-mdef</code>-referenced custom model, <code>+Fname</code> frequency
+reference. Both pieces exist and parse without error individually, but
+<code>GTRX</code>/<code>GTR</code> are IQ-TREE's own fixed built-in equal-structure multistate
+model, not a hook for an arbitrary custom matrix; a custom matrix is a
+file path in <code>-m</code> directly, no <code>-mdef</code> or <code>GTRX</code> involved.)</em></p>
+<p>Source for the empirical findings above: <code>model/modelmorphology.cpp</code> and
+<code>model/modelmarkov.cpp</code> in the local <code>iqtree/iqtree3</code> source (cloned to
+inspect the exact parsing logic after documentation didn't resolve the
+<code>+Fname</code> reference error) — more reliable here than the PDF/web manual,
+which (like TNT/PhyG) doesn't always match this specific binary. Original
+(partially superseded) sources: <a href="https://iqtree.github.io/doc/Substitution-Models">Substitution
+Models</a>, <a href="https://iqtree.github.io/doc/Complex-Models">Complex
+Models</a>.</p>
+<p><strong>Relation to the existing calibration.</strong> <code>sub_cost[a][b] = -ln(rate)</code>
+(see "A concrete Sankoff cost matrix" above) is already a log-rate — a
+genuine CTMC rate matrix <code>Q</code> could plausibly be recovered as
+<code>rate(a,b) = exp(-cost(a,b))</code>, renormalised so each row sums to zero, once
+the stationary-frequency gap above is closed. Superseded by the two
+sections below, which implement and then substantially revise this.</p>
+<h3 id="r-implemented-exclude-genome-added-rogue-taxon-test-negative-2026-08-12"><code>R</code>/<code>π</code> implemented; <code>--exclude-genome</code> added; rogue-taxon test negative (2026-08-12)</h3>
+<p><code>write_iqtree</code> (<code>obikmer/src/cmd/phylo/iqtree.rs</code>) implements exactly
+the <code>R = exp(-cost)</code> / empirical-<code>π</code> design above: writes
+<code>&lt;prefix&gt;_iqtree.model</code> (lower-triangular <code>R</code>, PAML order, then <code>π</code>) and
+<code>&lt;prefix&gt;_iqtree.fasta</code> (alignment recoded to the compact <code>0..k-1</code>
+alphabet of states actually present), states/frequencies restricted to
+whichever of the 16 canonical states actually occur, compactly
+renumbered — see the <code>MORPH{N}</code> risk above. Verified end to end on the
+20-genome benchmark: real, non-zero, varied branch lengths (<code>Total tree
+length: 6.773</code>), converged log-likelihood, <code>State frequencies:</code> in
+IQ-TREE's own output matching the computed <code>π</code> exactly.</p>
+<p><strong>Rogue-taxon hypothesis, tested and refuted.</strong> The backbone (<em>Yersinia</em>,
+<em>Proteus</em>, <em>Opitutus</em>, <em>Shouchella</em>, <em>Wolbachia</em>...) resolves as a
+near-linear comb with ~8 near-zero branch lengths — visible on the real
+tree, and independently on a Mash+NJ tree built from an entirely
+different signal (whole-genome k-mer distance, no relation to the Sankoff
+pipeline), which shows the same comb shape. Hypothesis: <code>Saccharolobus</code>/
+<code>Candidozyma</code> (near-zero real signal — see below) destabilise the
+heuristic tree search enough to also blur resolution elsewhere ("rogue
+taxa", a documented phenomenon). Tested directly: reran <code>iqtree3</code> after
+removing both taxa (<code>--exclude-genome</code>, <code>+ASC</code> recomputed on the
+resulting variable-sites-only alignment since removing taxa turns some
+columns invariant) — <strong>still exactly 8 near-zero backbone branches</strong>,
+identical comb shape. Refuted for this dataset: the backbone's weak
+resolution is a property of the character system's signal at that
+divergence depth (matches "Run 3" above), not rogue-taxon interference.</p>
+<p><strong>Diagnosed why <code>Saccharolobus</code>/<code>Candidozyma</code> place so poorly</strong>, using a
+new diagnostic (<code>--raw-snp-counts</code>, <code>&lt;prefix&gt;_rawsnp_counts.csv</code>: one row
+per genome pair, <code>n_snp,n_shared,n_eligible,ratio</code> — the counts
+<code>--raw-snp-distance</code>'s ratio-only matrix discards, needed because
+<code>ratio=0.0</code> from 2 eligible loci and from 2000 look identical in the
+ratio alone). <code>Saccharolobus</code> has 21,020 non-<code>∅</code> sites in the real
+alignment (comparable to other taxa) — but <strong>21,017 of them (100.0%) are
+private</strong>: no other genome has a non-<code>∅</code> state at the same site. Only 3
+sites are shared with any other genome at all (1, 2, and 14
+co-occurring genomes respectively). Real informativeness for placement
+tracks shared sites, not raw non-<code>∅</code> count — with no other archaeon (or
+even archaea-adjacent bacterium) in the dataset, there is nothing to
+anchor <code>Saccharolobus</code>'s position to, regardless of how much of its own
+data exists. <code>Candidozyma</code> shows the same pattern, more extreme (almost
+all <code>NA</code>, the 3 non-<code>NA</code> pairs all exactly <code>0.0</code>, never <code>1.0</code> — itself a
+tell: with <code>n_eligible=1</code>, the ratio can only be exactly <code>0</code> or <code>1</code>, so
+3-for-3 landing on <code>0.0</code> is more than sampling noise alone would predict;
+possibly ascertainment bias — see below — or possibly a few genuinely
+ultra-conserved loci; not resolved).</p>
+<p><strong><code>--exclude-genome LABEL</code></strong> (repeatable, <code>obikmer phylo</code>) added for
+exactly this kind of test: zeroes the excluded genome's row/column in
+<code>RawSnpDistanceOutput</code> after <code>raw_snp_distance</code> runs (a pair with zero
+counts is already skipped by <code>calibrate_p_hat</code>/<code>base_pair_tally</code> — no
+<code>obikindex</code> traversal change needed) and drops its row from
+<code>SnpAlignment</code> before any output is written. Deliberately <em>not</em> index
+surgery (a new, smaller on-disk index) — genome sets to exclude are
+expected to change between quick tests, so an in-memory filter is the
+right tool, not a new index-rewriting subsystem. Scoped to the sibling-annex
+family of computations (<code>--raw-snp-distance</code>/<code>--raw-snp-counts</code>/<code>--snp</code>/
+<code>--sankoff</code> and everything it implies) — does not affect the plain
+<code>--metric</code> distance matrix/NJ/UPGMA path (a different, unrelated
+computation on <code>idx.distance()</code>, not touched).</p>
+<p><strong>Caveat surfaced while reusing a stale <code>π</code></strong>: rerunning IQ-TREE on a
+genome-reduced alignment while keeping the <em>original</em> (20-genome)
+model file is inconsistent — <code>π</code>'s composition shifts once low-cardinality-0
+columns that were only variable because of the removed taxa drop out.
+Measured directly: <code>π(∅)</code> <code>0.9048</code> (20 genomes) → <code>0.8869</code> (18 genomes,
+variable sites only) — real (~378k affected cells, from <code>Saccharolobus</code>'s
+~21k private sites × 18 remaining genomes) but modest in <em>proportion</em>
+(~2 points) because the alignment was already monomorphic-filtered
+before <code>Saccharolobus</code> was ever added, so removing it only drops the
+subset of columns that were variable <em>because of</em> it specifically, not
+every column it appears in.</p>
+<h3 id="r-via-exp-cost-is-wrong-for-a-ctmc-cardinalitycomposition-decomposition-open-2026-08-12"><code>R</code> via <code>exp(-cost)</code> is wrong for a CTMC; cardinality/composition decomposition (open, 2026-08-12)</h3>
+<p><strong>The flaw in <code>R = exp(-cost)</code>, precisely.</strong> <code>cost</code> (<code>build_cost_matrix</code>'s
+output) is a <em>shortest-path closure</em> over an elementary-edit graph
+(Floyd-Warshall) — correct and required for Sankoff parsimony, where
+<code>cost(a,b)</code> must be a metric. But a CTMC's own matrix exponential
+(<code>exp(Qt)</code>, computed internally by IQ-TREE) <em>already</em> sums over
+paths of every length through the elementary rates — that's the whole
+mechanism by which a CTMC generates indirect transitions. Feeding it a
+pre-summed, multi-hop shortest-path cost and exponentiating that <em>again</em>
+as if each entry were a direct edge double-applies the "compose multiple
+steps" logic once in log-space (Floyd-Warshall, additive) and once more
+inside IQ-TREE's own exponential — systematically over-penalising
+non-adjacent state pairs (e.g. <code>∅→{A,C}</code> priced as two chained edges,
+<code>2×c_ctx</code>, when it should be one direct lookup).</p>
+<p><strong>Resolution, in two parts — both estimated directly from the real
+alignment, not smoothed through a small parametric formula:</strong></p>
+<ol>
+<li><strong>Cardinality model</strong>: a 5-state (<code>0,1,2,3,4</code>) first-order Markov
+   chain, estimated from the empirical cardinality co-occurrence table
+   (pooled across all <em>included</em> genome pairs — same
+   saturated/<code>NA</code>-pair exclusion discipline as <code>calibrate_p_hat</code>, 14
+   saturated + 18 <code>NA</code> pairs excluded of 190 in the benchmark; the
+   result is materially different from the unfiltered version and more
+   internally consistent, not just "cleaner"). Diagonal included (the
+   probability of a family <em>staying</em> at the same cardinality is part of
+   the model, not assumed away). Measured, cost <code>= -ln(observed/expected
+   under independence)</code>, on the 20-genome benchmark (<code>π</code> here from the
+   marginal cardinality distribution: <code>90.481%, 5.261%, 4.183%, 0.067%,
+   0.008%</code> for <code>c=0..4</code> respectively — note <code>c=2</code> is <em>not</em> rare, almost
+   as common as <code>c=1</code>):</li>
+</ol>
+<p><div class="highlight"><pre><span></span><code>c=0/c=0: 0.166   c=0/c=1: 0.160   c=0/c=2: 0.157   c=0/c=3: 0.059   c=0/c=4: 0.006
+c=1/c=1: -0.803 (enriched)        c=1/c=2: 0.381   c=1/c=3: 1.027   c=1/c=4: 1.794
+c=2/c=2: 4.032 (sharply suppressed)                c=2/c=3: 2.620   c=2/c=4: 2.416
+c=3/c=3: -0.254  c=3/c=4: -0.411 (too few observations to trust)
+</code></pre></div>
+   Two robust findings, both stable under the saturation filter: (a) all
+   <code>∅</code>-involving costs are low and close to each other (<code>0.006</code>–<code>0.166</code>)
+   regardless of how many members are gained/lost at once — sharply at
+   odds with the current model's implicit <code>×2</code>/<code>×3</code> multi-hop scaling;
+   (b) <code>c=2/c=2</code> (two genomes both showing an ambiguous 2-member state at
+   the same site) is dramatically under-represented (~1.5–1.8% of the
+   independence expectation) — a real, robust anomaly, not explained.</p>
+<ol>
+<li><strong>Composition model</strong>: unchanged — <code>sub_cost</code> (the existing 6-category
+   Ts/Tv-biased calibration), estimated <strong>only from unambiguous sites</strong>
+   (cardinality-1 ↔ cardinality-1 pairs), because composition bias is a
+   substitution phenomenon and only means something when cardinality is
+   conserved. Checked whether composition bias also appears in pure
+   gain/loss events (no substitution involved, so no bias expected a
+   priori): single-base "gain" (<code>∅→</code>single base) is close to uniform
+   (<code>24.35/25.92/26.22/23.51%</code> for A/C/G/T) — consistent with "no
+   mutational mechanism, so no bias" as expected. Two-base "gain"
+   (<code>∅→</code>2-member state) is <em>not</em> uniform even after correcting for the
+   real (non-25/25/25/25) marginal base frequencies: <code>{A,G}</code>/<code>{C,T}</code>
+   (the transition-linked pairs) mildly enriched (<code>obs/exp</code> <code>1.12</code>/
+   <code>1.16</code>), <code>{C,G}</code> sharply suppressed (<code>obs/exp 0.563</code>, expected to be
+   the <em>most</em> common pair under independence since C and G are
+   individually the two most frequent bases, observed the least) — an
+   unexplained anomaly, deliberately <strong>not</strong> built into the model (no
+   mechanistic story for why gain/loss would carry a <code>{C,G}</code>-specific
+   bias), left as an open puzzle rather than fit.</li>
+</ol>
+<p><strong>Composing the two into a full pairwise cost — the actual replacement
+for both the elementary-edge graph and its Floyd-Warshall closure.</strong> For
+any two states <code>A</code>, <code>B</code> (not just the "clean" same-cardinality or
+pure-subset cases the current graph handles directly): let <code>shared = A∩B</code>
+(free), <code>lost = A\B</code>, <code>gained = B\A</code>. Pair off <code>k = min(|lost|,|gained|)</code>
+elements between <code>lost</code> and <code>gained</code> as substitution events, choosing the
+pairing that minimises total <code>sub_cost</code> (a trivial assignment problem —
+at most 4 elements per side). The <code>|lost|-k</code> (or <code>|gained|-k</code>) leftover,
+unpaired elements are a <em>pure</em> cardinality change, <code>|A|→|B|</code>, costed by
+<strong>one direct lookup</strong> in the cardinality model above — no chaining, no
+Floyd-Warshall. Example: <code>{A,C}→{G}</code> (cardinality 2→1, no shared base):
+pair 1 substitution (cheaper of <code>A→G</code>, <code>C→G</code>), 1 base left over unpaired
+→ cost <code>= sub_cost(chosen pair) + cardinality_cost(2→1)</code>. This is a
+direct, closed-form cost for <em>every</em> pair of the 16 states, replacing
+<code>build_cost_matrix</code>'s graph-plus-shortest-path construction outright —
+and specifically fixes the CTMC double-counting problem, since every
+entry is now a single decomposed lookup, never a sum of chained edges.</p>
+<p><strong>Reframed as a likelihood (product of probabilities), not a cost (sum of
+<code>-ln</code>s) — same content, but forces the diagonals (no-change cases) to be
+kept rather than implicitly dropped.</strong> Both sub-models are proper
+transition <em>probability</em> matrices, diagonal included — <code>P_cardinality</code>
+includes "stay at the same cardinality", <code>P_composition</code> includes "stay
+the same base" (e.g. <code>P(G→G)</code>, not just <code>sub_cost</code>'s off-diagonal
+entries). Composing:</p>
+<div class="highlight"><pre><span></span><code>P(A→B) = P_cardinality(|A|→|B|)
+        × ∏_{x ∈ A∩B} P_composition(x→x)         (shared bases: &quot;stayed&quot;)
+        × ∏_{(x,y) paired}  P_composition(x→y)    (parsimony-paired substitutions)
+</code></pre></div>
+<p>with the unpaired leftover <code>lost</code>/<code>gained</code> elements (if <code>|lost|≠|gained|</code>)
+contributing <em>nothing further</em> beyond the <code>P_cardinality</code> term already
+counted — consistent with the finding above that pure gain/loss carries
+no separate composition bias worth modelling. Worked example,
+<code>{A,C}→{A,G}</code> (<code>shared={A}</code>, one paired substitution <code>C→G</code>, nothing left
+over): <code>P = P_cardinality(2→2) · P_composition(A→A) · P_composition(C→G)</code>.</p>
+<p>The row-wise product of these two independently-calibrated models isn't
+guaranteed to already sum to exactly <code>1</code> across all <code>B</code> for a fixed <code>A</code>
+(the two aren't perfectly independent in reality) — so each row of the
+resulting 16×16 matrix is renormalised (divided by its own sum) after
+composition, <strong>not</strong> the matrix as a whole (which would produce a joint
+distribution over <code>(A,B)</code> pairs, the wrong object — a transition matrix
+needs each row, "given I start in <code>A</code>", to be a valid distribution over
+where I end up).</p>
+<p>This now covers every pair of the 16 states with no unhandled case
+identified. Gives 120 parameters, but derived from two small,
+well-estimated pieces (a 5×5 cardinality model, a 4×4 composition model)
+rather than fit or smoothed independently per pair.</p>
+<h3 id="implemented-2026-08-12-pairwise_cost_matrix-replaces-build_cost_matrix-entirely">Implemented (2026-08-12): <code>pairwise_cost_matrix</code> replaces <code>build_cost_matrix</code> entirely</h3>
+<p>New module <code>obikindex/src/cardcomp.rs</code>, replacing <code>sankoff::build_cost_matrix</code>
+and the <code>c_ctx</code>/<code>SankoffWeights</code>/<code>PHatEstimate</code>/<code>calibrate_p_hat</code>/
+<code>c_ctx_from_p_hat</code>/<code>mean_substitution_cost</code>/<code>substitution_costs_from_tally</code>
+machinery it depended on outright — not kept in parallel as a fallback
+(all now unreferenced outside their own tests; <code>sankoff.rs</code> itself is a
+pending removal, not yet done).</p>
+<p><strong>New primitives, <code>obikindex/src/siblings.rs</code>:</strong>
+- <code>BasePairTally</code> gained a <code>same: [u64; 4]</code> field (diagonal — "both
+  genomes at the same single base", pooled from
+  <a href="obikindex::KmerIndex::base_pair_tally"><code>base_pair_tally</code></a>'s existing
+  traversal, extended to also tally the <code>bi == bj</code> case it previously
+  discarded).
+- <code>CardinalityTally { counts: [[u64; 5]; 5] }</code> and
+  <code>KmerIndex::cardinality_tally</code>, a new traversal (same shape as
+  <code>snp_pseudo_alignment</code>'s — needs full per-genome presence masks, not
+  <code>scan_family_pairs</code>'s single-resolved-form view, since cardinality 2-4
+  is exactly the signal being tallied, not noise to drop). Same
+  saturated/no-data pair exclusion as <code>base_pair_tally</code>. Restricted to
+  variable families (<code>family_size() &gt;= 2</code>), matching
+  <code>snp_pseudo_alignment</code>'s own scope. Verified against the 20-genome
+  benchmark: counts match the earlier hand-rolled Python analysis exactly
+  (e.g. <code>c=0/c=0: 117,158,166</code>, <code>c=0/c=1: 13,707,223</code> — the same numbers
+  this whole investigation started from).</p>
+<p><strong><code>cardcomp.rs</code>:</strong>
+- <code>cardinality_transition_probs</code>/<code>composition_transition_probs</code>: row-
+  normalise the two tallies into proper transition probability matrices,
+  diagonal included ("stay the same" is a real, calibrated outcome).
+- <code>pairwise_cost_matrix</code>: for every pair of the 16 states, <code>shared = A∩B</code>
+  contributes <code>∏ P_composition(x→x)</code>; <code>lost = A\B</code>, <code>gained = B\A</code> are
+  parsimony-paired (<code>best_pairing_cost</code>, brute-force over the ≤4!
+  injections — small enough that hand-rolling beats a dependency) into
+  substitution events on <code>P_composition</code>, minimising total <code>-ln</code>; the
+  cardinality-difference leftover is priced once via
+  <code>P_cardinality(|A|→|B|)</code>, never chained. Row-normalised, <code>-ln</code>'d, then
+  <strong>symmetrised</strong>: <code>cost_sym(A,B) = (cost(A,B)+cost(B,A))/2</code> — equivalent
+  to taking the <em>geometric</em> mean of the two raw probabilities
+  (<code>-ln(√(P(A,B)·P(B,A))) = (-ln P(A,B) - ln P(B,A))/2</code>), not their
+  arithmetic mean. Required, not just convenient for IQ-TREE's
+  lower-triangular file format: Sankoff parsimony's score is independent
+  of where an <em>unrooted</em> tree (what TNT/PhyG actually search over) gets
+  rooted only if the cost matrix is symmetric — the discrete-parsimony
+  analogue of CTMC reversibility, established by direct reasoning, not
+  assumed. Bonus of the same decision: 120 free parameters instead of the
+  240 a fully asymmetric matrix would need.</p>
+<p><strong>Verified on the 20-genome benchmark</strong>: resulting matrix symmetric
+(checked numerically, zero asymmetric cells), zero diagonal, no NaN/Inf.
+<code>--tnt</code> output still loads into TNT with no triangle-inequality warning
+(<code>scaled_metric_matrix</code>'s rounding-metric-closure step still needed and
+still applied — nothing in the new construction guarantees the <em>rounded
+integer</em> matrix stays a metric, even though the real-valued one is exact
+by construction here, unlike the old Floyd-Warshall-closed matrix which
+needed it for a different reason). IQ-TREE loads the new model file and
+reports the same <code>π</code> as before (only <code>R</code> changed).</p>
+<h3 id="two-consistency-bugs-found-and-fixed-post-implementation-2026-08-13">Two consistency bugs found and fixed post-implementation (2026-08-13)</h3>
+<p><strong><code>--exclude-genome</code> didn't drop columns that become monomorphic once the
+excluded genome(s) are gone.</strong> <code>snp_pseudo_alignment</code>'s "variable family"
+test (<code>family_size() &gt;= 2</code>) is a property of the annex computed over
+<em>every</em> genome in the index — unaffected by the CLI-level exclusion, which
+only dropped the excluded genome's <em>row</em>. A family variable only because
+of the excluded genome stayed in the alignment as a now-constant column —
+silently wrong data for TNT/PhyG, and a hard failure for IQ-TREE's <code>+ASC</code>
+(verified: excluding 2 taxa on the benchmark left 116,351 such columns —
+matches the manual <code>+ASC</code> failures hit earlier in this same investigation,
+before <code>--exclude-genome</code> existed). Fixed in <code>drop_excluded</code>
+(<code>obikmer/src/cmd/phylo/mod.rs</code>): after dropping excluded rows,
+re-scan each column among the <em>surviving</em> sequences and drop any that are
+now constant. Verified: 908,723 → 792,372 sites after excluding 2 taxa,
+zero monomorphic columns remain, <code>π</code> recomputed from the corrected
+alignment matches an independent recount exactly. The compact-alphabet
+renumbering (<code>iqtree::compact_alphabet</code>) needed no equivalent fix — it
+already recomputes which of the 16 states occur fresh on every call, from
+whatever alignment it's actually handed, so a symbol disappearing (e.g.
+excluding every genome that carries <code>N</code>) is already handled correctly;
+verified directly (excluded 13 genomes to force <code>N</code> out: "15 of 16 states"
+reported, correctly-shaped model file).</p>
+<p><strong><code>cardinality_tally</code>'s <code>family_size() &gt;= 2</code> filter looked inconsistent
+with <code>base_pair_tally</code> — removing it was tried, and was wrong; reverted.</strong>
+<code>cardinality_tally</code> (modelled after <code>snp_pseudo_alignment</code>) had the
+filter; <code>base_pair_tally</code> didn't (it visits every family via
+<code>scan_family_pairs</code> unconditionally, folding fully-invariant loci into its
+own <code>same</code> diagonal). Read as <code>cardinality_tally</code> under-counting its
+diagonal relative to <code>base_pair_tally</code>, and — independently — as another
+angle on the <code>--exclude-genome</code> drift (<code>family_size()</code> being global-only
+meant a family kept here post-exclusion could differ from what the
+now-correctly-filtered alignment kept). First fix tried: drop
+<code>cardinality_tally</code>'s filter entirely, matching <code>base_pair_tally</code>'s
+whole-annex scope.</p>
+<p><strong>That fix was empirically wrong, confirmed by a real IQ-TREE run, not
+just a hunch.</strong> Log-likelihood dropped from the earlier correct run's
+<code>-8,364,671</code>/<code>-8,371,082</code> to <code>-9,170,228</code> (worse fit, not better), with
+repeated <code>NNI search needs unusual large number of steps (20) to
+converge!</code> warnings — and the completed run's <strong>total tree length came
+out at 67.644</strong>, roughly 30× the earlier correct runs' ~2.0, i.e. branches
+blowing up/saturating. Root cause, only clear in hindsight: <code>+ASC</code>
+("ascertainment bias correction") exists specifically because the
+likelihood only ever sees <em>variable</em> sites — the alignment fed to
+IQ-TREE, by construction, contains not one invariant column. Calibrating
+<code>R</code> from a population overwhelmingly dominated by genome-wide invariant
+background (family_size()&lt;2 loci outnumber the ~908k variable ones by
+orders of magnitude) describes a completely different population than the
+one <code>+ASC</code> and the alignment actually model — the "consistency" argument
+for matching <code>base_pair_tally</code>'s scope was real, but pointed the wrong
+way: <code>base_pair_tally</code>'s own unrestricted <code>same</code> diagonal turned out to
+have the <em>identical</em> latent bug (only unmasked once its diagonal existed
+at all, which happened earlier the same day when <code>same</code> was added), not a
+correct baseline to match <code>cardinality_tally</code> to.</p>
+<p><strong>Final fix</strong>: restored <code>cardinality_tally</code>'s <code>family_size() &gt;= 2</code> filter,
+and gave <code>base_pair_tally</code>'s <code>same</code> diagonal the equivalent restriction —
+<code>scan_family_pairs</code> (shared with <code>raw_snp_distance</code>, which legitimately
+<em>does</em> want fully-invariant families counted as <code>shared</code>) now passes an
+extra <code>variable: bool</code> (the family's own <code>family_size() &gt;= 2</code>) to its
+<code>on_pair</code> callback; <code>base_pair_tally</code> only increments <code>same</code> when
+<code>variable</code> is true, <code>raw_snp_distance</code>'s callback ignores the new
+argument. Both tallies now describe the same variable-families-only
+population the <code>+ASC</code>-corrected alignment does. Verified: calibration
+counts back to their original values exactly (<code>c=0/c=0</code>: 117,158,166,
+matching the pre-regression run bit for bit), and a full IQ-TREE rerun
+converged normally — log-likelihood <code>-8,389,106.273</code> (same order as the
+two earlier correct runs), <strong>total tree length 2.044</strong> (was 67.644), no
+NNI convergence warnings.</p>
+<h2 id="heterozygosity-ploidy-and-consensus-assembly-inputs">Heterozygosity, ploidy, and consensus-assembly inputs</h2>
+<p>A within-genome multiplicity signal (more than one of the 4 central forms
+present at a locus) is produced identically by two distinct causes:
+paralogous duplication and diploid/polyploid heterozygosity. K-mer data alone
+cannot distinguish them. The one real discriminator is sequencing depth
+(heterozygous site: total depth of the present forms ~= the genome's
+single-copy average; duplication: ~2x or more) — but that signal only exists
+if genome "counts" are raw-read depth (FASTQ input), not occurrence counts in
+an assembled FASTA, where per-locus depth is not preserved.</p>
+<p><strong>Magnitude is taxon- and mating-system-dependent, not universal.</strong>
+Heterozygosity density: mammals ~1 site / 1-1.5 kb (~0.1%); highly
+outcrossing plants (maize, poplar) reported an order of magnitude higher
+(~1%); self-fertilising plants (<em>Arabidopsis thaliana</em>) near zero — but with
+a documented failure mode where segmental duplication masquerades as
+"pseudo-heterozygosity"; fungi split between haploid vegetative stages
+(non-issue) and dikaryotic Basidiomycetes, where two long-diverged haploid
+nuclei coexist without fusing. The estimator's target use case (closely
+related genomes, k=31) is exactly where the stringent filter above costs the
+least for low-heterozygosity taxa and the most for outcrossing/dikaryotic
+ones — no universal threshold; this is a scope caveat to document, not a
+problem to solve generically.</p>
+<p><strong>Why assembled-consensus inputs don't make measured distances wrong.</strong>
+Phylogenetic inputs are near-universally assemblies, not raw reads, and
+assemblers collapse heterozygous sites to one consensus allele per
+position — effectively an arbitrary, largely uncorrelated-between-assemblies
+choice at each het site. This does not inject unbounded noise: standard
+population genetics gives <code>d_xy = d_a + (pi_A + pi_B)/2</code> — the expected
+pairwise difference between a random allele of population A and a random
+allele of population B equals the net (fixed) divergence <code>d_a</code> plus the
+average of the two populations' own within-population diversity <code>pi</code>.
+Consensus flattening realises exactly this random-allele draw, so the
+measured genome-to-genome distance is a <code>d_xy</code>-like quantity, not <code>d_a</code> —
+inflated by heterozygosity by a well-characterised additive term, not
+distorted unpredictably. The term is negligible when <code>pi &lt;&lt; d_xy</code> (the common
+case for cross-species comparisons), and becomes material precisely in the
+two cases already flagged above: very closely related genomes (this
+estimator's explicit target) and highly heterozygous outcrossing organisms,
+where <code>pi</code> and <code>d_xy</code> are the same order of magnitude.</p>
+<p>Caveat: this assumes the flattening is uncorrelated with the phylogenetic
+signal — plausible for de novo assembly, not guaranteed for reference-guided
+assembly biased toward one allele (e.g. the reference's) at each het site,
+which would turn the noise term into a systematic bias toward the reference
+lineage. Not evaluated here.</p>
+<p><strong>Forward-looking implication, not part of the current design.</strong> The
+multiplicity &gt; 1 signal discarded by the stringent filter is a crude
+per-genome proxy for <code>pi</code> (under low background paralogy). If a <code>pi_hat</code> per
+genome were tallied alongside <code>SnpTally</code>, a <code>d_a</code> correction
+(<code>p_hat - mean(pi_hat_i, pi_hat_j)/2</code>, roughly) could recover an estimate
+closer to net divergence instead of <code>d_xy</code> — a possible extension, not
+scoped here.</p>
+<h2 id="sufficient-statistic-4x4-base-pair-tally">Sufficient statistic: 4x4 base-pair tally</h2>
+<p>Tabulating the joint distribution of <code>(center_i, center_j)</code> over conserved-flank
+loci, per genome pair, is sufficient for every downstream correction:</p>
+<table>
+<thead>
+<tr>
+<th>Estimator</th>
+<th>Input</th>
+<th>Formula</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>Raw p-distance</td>
+<td>total off-diagonal / total</td>
+<td><code>p = SNP / (SNP + shared)</code></td>
+</tr>
+<tr>
+<td>Jukes-Cantor</td>
+<td>p</td>
+<td><code>d = -3/4 * ln(1 - 4p/3)</code></td>
+</tr>
+<tr>
+<td>Kimura 2-parameter</td>
+<td>transition rate P, transversion rate Q</td>
+<td><code>d = 1/2 ln(1/(1-2P-Q)) + 1/4 ln(1/(1-2Q))</code></td>
+</tr>
+<tr>
+<td>LogDet/paralinear</td>
+<td>full 4x4 + base-composition margins</td>
+<td><code>d ~= -1/4 ln det(F)</code>, robust to non-stationary base composition</td>
+</tr>
+</tbody>
+</table>
+<p>JC/K2P need only the total and the transition/transversion split (the
+diagonal collapses to a single "shared" total). LogDet needs the full 4x4,
+already populated at no extra cost (see Step 1/2 below).</p>
+<p>Memory for the 4x4 tally: <code>n^2 * 16</code> counters. Trivial for the project's
+genome-scale use case (tens to hundreds of genomes); ~13 GB at n=10^4 — outside
+scope but worth flagging if n grows.</p>
+<h2 id="biases-properties-of-the-estimator-not-defects">Biases (properties of the estimator, not defects)</h2>
+<ol>
+<li><strong>Conserved-flank ascertainment bias.</strong> Only SNPs with intact <code>2m</code>-base
+   flanks are visible; window-intact probability decays as <code>(1-p)^{2m}</code>. For
+   k=31 (2m=30): 0.74 at p=1%, 0.21 at p=5%, 0.04 at p=10%. This estimator
+   targets <strong>closely related genomes</strong>. Under rate heterogeneity across sites
+   (universal in practice), conserved flanks correlate with slow centers, so
+   <code>p_hat</code> underestimates the genome-wide average rate — it specifically
+   estimates the substitution rate of <strong>conserved regions</strong>.
+   Two distinct factors are at play here, not one: <code>P(centre of a given
+   window is a SNP) = p</code> exactly, <strong>independent of k</strong> — a direct restatement
+   of the raw per-site rate via the bijective window&lt;-&gt;centre-position
+   correspondence (Statistic section above), not a k-dependent quantity.
+   <code>(1-p)^{2m}</code> is the <em>separate</em>, genuinely k-dependent ascertainment factor
+   (are the flanks also intact). The two multiply:
+   <code>P(usable window showing a central SNP) = p * (1-p)^{2m}</code> — e.g. at
+   p=1/31 (~3.2%), k=31: <code>p * (1-p)^30 ~= 0.0323 * 0.374 ~= 1.2%</code>, i.e. about
+   1 window in 83, not 1 in 31 (which is only the centre-mutated fraction,
+   before requiring intact flanks).</li>
+<li><strong>Bias toward isolated SNPs.</strong> Two SNPs within k of each other disqualify
+   each other's flanks. Hypervariable regions are invisible by construction.</li>
+<li><strong>Indels are invisible.</strong> A frameshift destroys k-mer matches in a block;
+   this channel captures substitutions only. Indel divergence shows up as lost
+   shared k-mers (lower Jaccard/Mash), not as SNP signal.</li>
+<li><strong>k-dependent specificity.</strong> "A k-mer match implies common ancestry" is
+   quantitative. For a 3 Gbp genome, expected random flank-30 collisions
+   (k=31): <code>(3e9)^2 / 4^30 ~= 8</code> — negligible. At k=21: <code>(3e9)^2 / 4^20 ~= 2e6</code>
+   — no longer negligible. k=31 is safe; k&lt;=21 is marginal to unreliable for
+   large genomes. The large k that guarantees homology is the same k that
+   shrinks the detectable-divergence window — an inherent tension.</li>
+</ol>
+<h2 id="implementation-avoid-materializing-a-de-bruijn-graph">Implementation: avoid materializing a de Bruijn graph</h2>
+<p>A central-SNP pair is topologically a simple bubble in the colored de Bruijn
+graph (source/sink k-mer shared, two length-k branches differing only at the
+midpoint). Classical bubble-calling (Cortex/discoSNP-style) finds these, but
+requires the graph — nodes plus adjacency for ~10^9 colored k-mers — resident
+in memory. <strong>Rejected</strong>: prohibitive RAM for this project's scale.</p>
+<p>A naive per-pair generalisation of variant lookup across n genomes (query each
+non-shared k-mer's 3 central variants against every counterpart genome's
+index) costs <code>O(n^2 . N . 3)</code> random lookups, with the same k-mer's 3 variants
+regenerated and requeried once per counterpart genome — pure redundant work.
+<strong>Rejected</strong> as the basis for an n-genome design.</p>
+<h2 id="implementation-sequential-per-partition-sweep-no-scratch-no-graph">Implementation: sequential per-partition sweep (no scratch, no graph)</h2>
+<p><code>KmerIndex::distance()</code> already opens every partition's <code>presence_store</code>/
+<code>count_store</code> simultaneously, memory-mapped, into one <code>LayeredStore</code>
+(<code>distance.rs:73-77</code>). "Querying another partition" is therefore not a new
+I/O pattern to design — it is the same O(1) MPHF+evidence lookup the <code>query</code>
+command already performs at scale. This lets the SNP tally be computed with
+<strong>no scratch files and no auxiliary graph</strong>, by sweeping partitions once each
+as a source:</p>
+<ol>
+<li>For source partition <code>p</code>, enumerate its <strong>distinct</strong> k-mers (one per MPHF
+   slot; each already carries its full multi-genome presence/count vector —
+   no need to explode per (k-mer, genome) occurrence).</li>
+<li>For each, generate the 3 central-substitution variants and <strong>canonicalise
+   each independently</strong> (<code>min(kmer, revcomp)</code>, exactly as any normal query) —
+   this avoids the orientation edge case a masked-flank grouping would have
+   (a substitution that flips canonical orientation is handled correctly
+   because each variant is canonicalised on its own, not inferred from a
+   fixed-orientation flank key).</li>
+<li>Compute each variant's target partition <code>q</code> via its minimizer; batch/sort
+   the partition's outgoing variant queries by <code>q</code> for locality.</li>
+<li>Look up each variant in <code>q</code>'s already-mmap'd MPHF+evidence; on a hit,
+   combine the source's presence vector (base <code>a</code>) with the variant's
+   presence vector (base <code>b</code>): for every <code>i</code> carrying <code>a</code> and <code>j</code> carrying
+   <code>b</code>, <code>tally[i,j][a,b] += 1</code>.</li>
+</ol>
+<p><strong>Deduplication needs no persisted state.</strong> Sweeping partitions in a fixed
+order <code>p = 0, 1, ..., P-1</code> and only acting on a variant when its target
+partition <code>q &gt;= p</code> guarantees each unordered SNP pair is counted exactly
+once: a pair with <code>q &lt; p</code> was already resolved earlier, when <code>q</code> was itself
+the source partition and <code>p</code> (being <code>&gt;= q</code>) was a valid forward target. No
+cross-partition flag array is needed — the sweep order <em>is</em> the
+deduplication rule. Within the same partition (<code>q == p</code>), a lightweight
+transient tie-break suffices: either a <code>#slots(p)</code>-bit scratch flag reset per
+partition, or simply comparing the two k-mers' raw <code>u64</code> encodings and only
+counting when <code>kmer_source &lt; kmer_variant</code> — no storage at all.</p>
+<p>This is a distinct computation stage, not a <code>partial_*</code> in the existing
+additive-by-partition sense: step 3-4 read across partition boundaries by
+construction, unlike the row-local <code>partial_jaccard</code>/<code>partial_threshold_jaccard</code>
+primitives. But it requires no new index files, permanent or scratch:
+<code>unitigs.bin</code>, <code>mphf.bin</code>, <code>evidence.bin</code>, and the presence/count columns are
+read as-is, and the only extra memory is the current partition's small
+outgoing-query batch (<code>#kmers(p) * 3</code>, released once <code>p</code> is done) plus the
+persistent <code>tally</code> accumulator (<code>n^2 * 16</code> counters, see above).</p>
+<p><strong>Outer loop (over source partitions <code>p</code>) must stay sequential.</strong> Two
+independent reasons, not just one: (a) memory — the bounded-footprint claim
+above only holds with one partition's outgoing-query batch in flight; running
+<code>T</code> source partitions concurrently multiplies that batch by <code>T</code>, exactly the
+blowup the design avoids; (b) correctness — the <code>q &gt;= p</code> deduplication rule
+requires partitions to be claimed as sources in a fixed order; running <code>p1 &lt;
+p2</code> concurrently gives no guarantee <code>p1</code> has finished claiming its <code>q &gt;= p1</code>
+targets before <code>p2</code> starts claiming its own, breaking the "counted exactly
+once" property.</p>
+<p><strong>Inner loop (target-partition lookups for a fixed <code>p</code>) parallelises safely.</strong>
+Each lookup is an O(1) read against an already-mmap'd structure, independent
+of the others, with no growing allocation — no memory blowup, no ordering
+dependency between different <code>q</code>. The only shared mutable state is <code>tally</code>;
+give each worker thread a <strong>thread-local partial tally</strong> (fixed <code>n^2 * 16</code>
+size, independent of partition size) and merge into the global <code>tally</code> once
+<code>p</code>'s inner loop completes — the same reduce-then-merge pattern Rayon already
+uses elsewhere in this codebase to open partitions in parallel. Extra memory:
+<code>#threads * n^2 * 16</code>, negligible (~512 MB at n~1000, 32 threads) and
+unrelated to partition size.</p>
+<p><strong>Cost</strong>: <code>3 * N_distinct</code> MPHF lookups total across the whole index (each
+partition swept once as source) — the same order of magnitude and the same
+operation as running <code>query</code> over the index's entire k-mer content against
+itself, three times. This is the tool's already-optimized regime, not a new
+I/O profile to validate.</p>
+<h2 id="cheaper-subsampling">Cheaper: subsampling</h2>
+<p>Since the target is a ratio, restricting the source-partition sweep to a
+bottom-<code>s</code> hash sketch (only enumerate k-mers with <code>hash &lt; threshold</code> as
+sources) divides the lookup count by the sampling factor without biasing
+<code>p_hat</code>. Mash-like tradeoff: rate estimated from a sample, not the full
+k-mer set.</p>
+<h2 id="recommendation">Recommendation</h2>
+<p>Sequential per-partition sweep (Route D): reuse the already-mmap'd
+per-partition MPHF/evidence/presence structures for O(1) variant lookups,
+dedup via the fixed sweep-order rule (<code>q &gt;= p</code>, plus an in-partition
+tie-break), no scratch files, no graph materialisation. Both the SNP
+(off-diagonal) and shared (diagonal) counts are accumulated by this same
+sweep, under the locus-eligibility rule chosen (raw or paralogy-filtered) —
+not reused from the general-purpose <code>shared_kmers</code> matrix, whose raw-identity
+definition does not apply the same copy-number constraint. Distances (p, JC,
+K2P, LogDet) as finalisations of the resulting 4x4 tally, mirroring the
+<code>partial_* -&gt; *_dist_matrix</code> pattern used for Jaccard/Mash/Bray-Curtis/etc.</p>
+<h2 id="detailed-implementation-plan">Detailed implementation plan</h2>
+<p>Grounded in the current codebase. File/type references are anchors, not
+prescriptions; adjust to reality when implementing.</p>
+<h3 id="step-0-new-low-level-primitives-obikseq">Step 0 — new low-level primitives (<code>obikseq</code>)</h3>
+<p>Two helpers do not yet exist and are prerequisites:</p>
+<ol>
+<li><strong>Central neighbours.</strong> <code>CanonicalKmerOf&lt;L&gt;</code> already exposes
+   <code>left_canonical_neighbors()</code> / <code>right_canonical_neighbors()</code>
+   (<code>obikseq/src/kmer.rs</code>), each returning the 4 canonicalised neighbours at
+   an end position. Add <code>central_canonical_neighbors()</code> returning the 4
+   variants at position <code>m = (k-1)/2</code> (each independently canonicalised via
+   <code>.canonical()</code>). The 3 that differ from the source are the query variants;
+   skip the identity. Building on <code>nucleotide(i)</code> / the raw 2-bit layout keeps
+   it O(1).</li>
+<li><strong>Lone-k-mer minimiser.</strong> Routing a <em>synthetic</em> variant to its partition
+   needs its minimiser, but <code>RollingStat</code> (<code>obiskbuilder/src/rolling_stat.rs</code>)
+   only computes minimisers incrementally along a sequence. Add a standalone
+   <code>minimizer(kmer) -&gt; Minimizer</code> that scans the <code>k-m+1</code> m-mer windows
+   (<code>PackedSeq::mmer</code>, <code>obikseq/src/packed_seq.rs</code>), canonicalises each, and
+   takes the min by <code>seq_hash()</code> — the same selection <code>RollingStat</code> performs,
+   evaluated once. Partition index is then
+   <code>(minimizer.seq_hash() &amp; (n_partitions - 1)) as usize</code>, exactly as
+   <code>QueryBatch::from_records</code> (<code>obikmer/src/cmd/query.rs:142</code>); <code>n_partitions</code>
+   is a power of two so the mask is valid.</li>
+</ol>
+<h3 id="step-1-the-tally-accumulator-obikindex">Step 1 — the tally accumulator (<code>obikindex</code>)</h3>
+<p>A <code>SnpTally</code> holding, per genome pair, the 4x4 joint count of central bases:
+<code>n * n * 4 * 4</code> <code>u64</code> (or a packed lower-triangular form since it is
+symmetric). Provide <code>merge(&amp;mut self, other: &amp;SnpTally)</code> for the thread-local
+reduce, and accessors yielding, per pair <code>(i,j)</code>: total off-diagonal (SNP),
+diagonal (shared, i.e. <code>p_hat</code>'s denominator minus SNP), transition count
+<code>P</code>, transversion count <code>Q</code>. The diagonal is always populated — it is not an
+optional LogDet-only extra, since <code>p_hat</code>'s denominator is no longer sourced
+from the external <code>shared_kmers</code> matrix (see "Locus eligibility" and
+"Statistic and correspondence with <code>shared</code>" above): the source k-mer's own
+presence/count vector, already in hand when it is enumerated, supplies the
+diagonal entry directly, at no extra lookup cost.</p>
+<h3 id="step-2-the-sweep-obikindex-new-snprs">Step 2 — the sweep (<code>obikindex</code>, new <code>snp.rs</code>)</h3>
+<p>Mirror <code>distance.rs</code>: open the presence or count store per partition. But
+instead of a per-partition <code>partial_*</code>, run the sequential source sweep:</p>
+<div class="highlight"><pre><span></span><code>for p in 0..n_partitions:                       # OUTER — sequential
+    open source partition p&#39;s layers (QueryLayer-style, obikpartitionner)
+    enumerate distinct canonical k-mers of p (one per MPHF slot) with their
+        presence/count vectors                   # column-major, as query stage 2
+    par_iter over these source k-mers:           # INNER — rayon, thread-local tally
+        apply eligibility rule to the source&#39;s own vector (raw: none;         # diagonal
+            stringent: exactly one of the 4 forms present in each genome)     # gate
+        for i in genomes eligible with source base a:
+            for j in genomes eligible with source base a:
+                thread_tally[i,j][a,a] += 1        # diagonal — no extra lookup
+        for each of the 3 central variants:
+            q = partition_of(variant)
+            if q &lt; p: continue                    # dedup: forward targets only
+            if q == p and variant &lt;= source.raw(): continue   # in-partition tie-break
+            slot = layers[q].find_slot(variant)   # MphfLayer::find, mmap&#39;d
+            if hit:
+                vb = variant presence/count vector
+                apply eligibility rule to vb (as above)
+                for i in eligible genomes with source base a:
+                    for j in eligible genomes with variant base b:
+                        thread_tally[i,j][a,b] += 1
+    merge thread-local tallies into global SnpTally
+</code></pre></div>
+<p>The inner lookup is precisely <code>QueryLayer::find_slot</code> +
+<code>col_value(g, slot)</code> (<code>obikpartitionner/src/query_layer.rs</code>) — reuse or factor
+out that path rather than reimplementing MPHF access. Enumerating "all distinct
+k-mers of a partition with their vectors" is the <code>dump</code>/<code>query</code> stage-2
+column-major scan already implemented in <code>dump_layer.rs</code> /
+<code>query_partition_with</code>; factor a reusable iterator if none fits.</p>
+<p><code>presence_threshold</code> applies exactly as elsewhere: a genome "carries base b"
+iff its count at that slot is <code>&gt;= presence_threshold</code> (trivially <code>&gt;= 1</code> for
+presence indexes).</p>
+<h3 id="open-problem-unresolved-session-end-not-yet-fully-convinced">Open problem (unresolved, session end — not yet fully convinced)</h3>
+<p>The <code>q &gt;= p</code> / tie-break dedup rule in Step 2's pseudocode above is <strong>flawed</strong>
+for the stringent (paralogy-filtered) eligibility rule: it only ever brings
+two family members into view at once (the source and one looked-up variant),
+never all four simultaneously, and which subset gets compared depends on
+partition sweep order. "Exactly one of the 4 forms present in genome A" is a
+whole-family property and cannot be decided correctly from a sequence of
+pairwise, order-dependent glimpses — the pseudocode above needs revision, not
+just the eligibility gate bolted onto it as written.</p>
+<p>Direction discussed, <strong>not yet settled</strong>:</p>
+<ol>
+<li><strong>Every distinct source k-mer looks up all 3 variants unconditionally</strong>
+   (drop the <code>q &lt; p</code> skip entirely) so that every observed family member
+   independently gathers all 4 vectors (its own + whichever of the 3
+   variants exist) at once — a whole-family, order-independent view, computed
+   redundantly once per observed member. Same total lookup order of
+   magnitude as already budgeted (<code>3 * N_distinct</code>), just organised
+   differently (no lookup actually skipped, versus the original rule which
+   skipped roughly half).</li>
+<li><strong>Tie-break after gathering, not before</strong>: only the member whose own
+   canonical encoding is the smallest <em>among the members actually observed</em>
+   (now known, since all were just looked up) writes to <code>SnpTally</code>; the
+   others silently discard their redundant computation. Deterministic,
+   order-independent — as a side effect this also removes the "outer loop
+   must stay sequential" constraint from the cost/parallelism discussion
+   above, since no step depends on partition processing order any more.</li>
+<li><strong>Proposed optimisation</strong>: precompute, once at index build time, a
+   compact global (not per-genome) annex per MPHF slot — the count of
+   <em>other</em> family members observed anywhere in the dataset (0-3). Slots with
+   count 0 (majority under low divergence and few genomes, but see the
+   scaling caveat below) need no cross-lookup at all: eligibility reduces to
+   a local <code>count == 1</code> check at that single slot, and only slots with count<blockquote>
+<p>= 1 enter the 3-lookup sweep machinery above. Revised (see Step 2b
+   below): minorant status <em>is</em> stored alongside the count after all, on 3
+   bits rather than 2 — it comes for free from the same lookups needed to
+   count siblings, and storing it lets the sweep discard non-minorant slots
+   without re-fetching anything.</p>
+</blockquote>
+</li>
+</ol>
+<p><strong>Minorant/sibling-count relationship, worked out precisely.</strong> "Minorant" is
+a one-way implication from sibling count, not an equivalence: <code>0 siblings
+=&gt; minorant</code> (trivially — with no other observed member, the k-mer is by
+definition the smallest of the observed set, itself alone), and its
+contrapositive <code>not minorant =&gt; &gt;= 1 sibling</code>. The converse does not hold:
+being the minorant says nothing about sibling count — a minorant can have 0,
+1, 2 or 3 siblings, all with larger encodings than itself. Consequence: this
+confirms, as a logical necessity rather than a heuristic, that a 0-sibling
+slot can always write its diagonal contribution with zero ambiguity and no
+lookup (it is unconditionally its own minorant) — but it gives no shortcut
+for the &gt;= 1-sibling case, where minorant status still requires the actual
+comparison of gathered encodings; sibling count alone never determines it.</p>
+<p><strong>When to compute the annex, and cache invalidation.</strong> Sibling count is a
+property of the whole set of columns (genomes/groups) currently in the
+index, not of any single genome — it cannot be computed correctly at
+mono-genome build time (a family may gain siblings, or its minorant may
+change, once more genomes are merged in later). Computing it eagerly at
+every <code>merge</code> would also waste work on intermediate merged states nobody
+ever queries. Instead: compute it lazily, on first <code>phylo</code> call against a
+given index, and persist the result alongside that index for subsequent
+calls — the same lazy-derived-cache pattern <code>PersistentBitMatrix</code> already
+uses for <code>Columnar</code> -&gt; <code>Packed</code>. This requires no explicit invalidation for
+<code>merge</code> or <code>filter</code> (<code>obikindex/src/merge.rs</code>, <code>obikmer/src/cmd/filter.rs</code>):
+both only ever write to a fresh <code>--output</code> directory, never mutate an input
+index in place, so a re-merged/re-filtered index is simply a new state with
+no annex yet. <code>select --in-place</code> (<code>select_layer.rs:139-235</code>) is the
+exception: it aggregates genome columns into groups (Any/All/None/Sum/Min/
+Max) by mutating the existing index's files without changing its location.
+It does not remove k-mer rows, but it can still change eligibility and
+sibling counts derived from those rows (e.g. a <code>Sum</code> over several
+single-copy genomes can read as multi-copy at the group level). Because it
+mutates in place, <strong><code>select --in-place</code> must explicitly invalidate (delete
+or mark stale) any cached sibling-count annex for that index</strong> — the one
+operation in the current pipeline where this doesn't happen for free.</p>
+<p>Not yet convinced this is the right shape, and Step 2's pseudocode above has
+not been rewritten to match — flagged for the next pass rather than resolved
+here.</p>
+<h3 id="step-2b-sibling-count-minorant-annex-consolidated-plan">Step 2b — sibling-count / minorant annex (consolidated plan)</h3>
+<p>Scope: only the precursor annex — not the SNP tally itself, whose Step 2
+sweep remains unresolved above. This piece is simpler than the sweep,
+because it writes to an independent per-slot value, not a shared
+cross-k-mer accumulator, so it needs no dedup/ownership logic at all at this
+stage.</p>
+<p><strong>Revised annex encoding — 4-bit presence mask, not 3-bit (minorant +
+count).</strong> Superseded after settling the "canonical form of a family"
+definition above. The 3-bit design (1 minorant bit + 2-bit sibling count,
+§ below, kept for the historical record) had two problems: it discards
+<em>which</em> variants are present (only how many), so any future consumer
+(the SNP sweep, or a stats pass — see below) that needs to know which bases
+exist still has to regenerate and blindly re-query all 3 candidates; and
+the minorant bit's meaning was tied to whichever member was visited, not to
+a fixed reference. Storing instead a <strong>4-bit mask</strong> — one bit per base
+(A/C/G/T), set iff that member of the family (labelled relative to the
+family's fixed canonical form, i.e. the member with <code>A</code> at the centre — see
+above) is observed anywhere in the index — fixes both:
+- <strong>Sibling count is derived, not stored</strong>: <code>siblings = popcount(mask) - 1</code>.
+- ~~<strong>Minorant is derived, not stored</strong>: regenerate the family's 4 canonical
+  forms from the slot's own k-mer (cheap, no lookup — see above), compare
+  the raw encodings of whichever bits are set in the mask, take the
+  smallest.~~ <strong>Erratum (2026-08-14) — this was wrong, kept struck through
+  rather than deleted.</strong> "Cheap, no lookup" only accounts for the bit
+  algebra (regenerate 4 forms, compare raw encodings) — true in isolation,
+  but it silently assumed "the slot's own k-mer" is a free fact. It isn't:
+  getting from an MPHF slot index back to the actual k-mer sequence means
+  reconstructing <code>slot_kmer</code> for the whole layer — scan <code>unitigs.bin</code>,
+  <code>mphf.find()</code> every k-mer to place it — an O(distinct k-mers) pass
+  through the MPHF, not a per-slot O(1) lookup. That reconstruction is free
+  <em>only</em> when the caller already needs k-mer identity for something else in
+  the same traversal (e.g. the SNP sweep below, which needs it anyway to
+  generate <code>central_canonical_neighbors()</code>). A caller that wants <em>only</em> the
+  minorant flag pays the full reconstruction for nothing: measured on a real
+  run, a bare family-size histogram (four buckets, otherwise near-instant)
+  spent 71% of wall-clock in <code>MphfLayer::find</code>, all of it solely to answer
+  "is this slot the minorant". <strong>Current design: minorant <em>is</em> stored</strong>
+  after all — a 5th mask bit (4 presence bits + 1 minorant bit, still fits
+  one byte alongside the presence mask below), written once in the
+  construction pass where the k-mer is already in hand for other reasons
+  (<code>obikindex::siblings::build_layer_sibling_annex</code>), read back for free by
+  every later consumer (<code>FamilyMask::is_minorant</code>). This is genuinely a
+  return to the superseded 3-bit design's core idea (store minorant
+  alongside the count) — the "which variant" blindness that motivated
+  moving away from it is fixed by keeping the full 4-bit presence mask
+  too, not by dropping the stored minorant bit again.
+- <strong>A future consumer knows exactly which variants to (re-)query</strong> —
+  <code>popcount(mask) - 1</code> lookups instead of always 3, and it knows <em>which</em>
+  3 (or fewer) to issue, not just how many hits to expect.
+- The all-zero value (no base present at all) is still logically
+  unreachable as a real result — the slot's <em>own</em> base is always present in
+  its own family — so it remains available as a free "not yet computed"
+  sentinel, exactly as before.</p>
+<ol>
+<li><strong>Primitive.</strong> Reuse <code>central_canonical_neighbors()</code> from Step 0
+   unchanged — the 3 canonicalised central-substitution variants of a k-mer
+   (plus the identity, i.e. all 4 members of the family — see "Definitions"
+   above).</li>
+<li>
+<p><strong>New annex type</strong> (<code>obicompactvec</code>, alongside <code>bitmatrix.rs</code>): a 4-bit-
+   per-slot packed array (the presence mask above), one per partition — same
+   on-disk shape family as <code>PersistentBitMatrix</code>'s <code>Packed</code> variant, but
+   simpler (no per-genome columns, a single derived read-only value per
+   slot). As actually implemented (<code>obicompactvec::siblingannex</code>): <strong>not</strong>
+   truly bit-packed — 1 byte/slot, 4 presence bits + the minorant bit (see
+   the erratum above) in the low 5 bits, 3 unused. Deliberately simpler for
+   a first implementation; packing to 5 bits/slot is a pure storage-density
+   follow-up, not a behavioural change, still not done as of this note.
+ <br />
+<details><summary>Superseded 3-bit design (historical)</summary>
+   3 bits, storing minorant status alongside sibling count directly, since
+   it came for free from the same lookups (point 3 below) — 5 real states
+   (not-minorant; minorant with 0/1/2/3 siblings) fit in 3 bits (8 states,
+   3 unused). This let the future SNP sweep discard a non-minorant slot
+   instantly, with no lookup at all. The otherwise-unreachable combination
+   "not-minorant + 0 siblings" (0 siblings always implies minorant) doubled
+   as the "not yet computed" sentinel. Replaced by the 4-bit mask above,
+   which subsumes this benefit (minorant still derivable, now for free at
+   read time rather than stored) while also fixing the "which variant"
+   blindness.
+   </details></p>
+</li>
+<li>
+<p><strong>Computation pass</strong> (<code>obikindex</code>, new <code>siblings.rs</code>): <strong>one
+   <code>obipipeline</code> run per layer, iterated sequentially over the index's
+   layers</strong> — settled after two false starts, worth recording both.</p>
+</li>
+<li><em>False start 1</em>: "fully parallel over every partition/slot at once,
+     no ordering at all". Correctness is fine with this (sibling count and
+     minorant are order-independent, unlike the old <code>q &gt;= p</code> dedup they
+     replace), but it reintroduces, at a larger scale, exactly the
+     memory-blowup the original Step 2 sweep's sequential-outer-loop
+     constraint existed to prevent: scattering every source partition at
+     once multiplies the in-flight outgoing-query volume by the number of
+     partitions.</li>
+<li><em>False start 2</em>: push the layer loop itself into the pipeline (source
+     = the index's layers, a first <code>Flat</code> stage expands each layer into
+     its k-mers). <code>obipipeline</code>'s scheduler already bounds memory on its
+     own — it dispatches every item through a <strong>shared</strong> worker pool at
+     each stage boundary (<code>scheduler.rs:217-372</code>, <code>dispatch()</code> into a
+     common <code>worker_tx</code> queue, any free worker picks up any pending item;
+     not "one worker owns a chunk end to end"), with a biased <code>Select</code>
+     that prioritises draining items already advanced in the chain over
+     admitting new source items (<code>scheduler.rs:271-282</code>: stage results
+     outrank the source, "vider le pipeline en priorité" / "dernier
+     recours" for new data) — so bounded channel <code>capacity</code> plus this
+     drain-first bias already caps in-flight work without any external
+     sequential discipline. Correct, but it means k-mers from several
+     layers can be completing concurrently, so the sink would need to
+     track several open per-layer annex-file writers at once — real,
+     avoidable complexity.</li>
+<li><strong>Settled design</strong>: keep the layer loop external and sequential —
+     not for memory (the pipeline's own <code>capacity</code>/priority mechanism
+     already provides that, for free, regardless), but so each pipeline
+     run's sink targets exactly one layer's annex file, no concurrent
+     multi-writer bookkeeping. Per layer: source = that layer's distinct
+     k-mers; a <code>Flat</code> (1-&gt;N) stage generates the 3 central variants of a
+     k-mer, each tagged with its origin (local slot); a transform stage
+     routes each variant to its target partition (unchanged per-k-mer
+     minimiser); a transform stage performs the lookup (existence-only —
+     <code>find_slot</code> hit/miss, cheaper than the SNP sweep's full column
+     fetch); a final stage/sink folds each answer into its origin's
+     running state (below) and, once a layer's k-mers are all resolved,
+     flushes the completed array to that layer's annex file. Many small,
+     single-purpose stages on purpose, to let the scheduler interleave
+     them finely across many in-flight items — this deliberately does
+     <strong>not</strong> mirror how <code>obipipeline</code> is used elsewhere today: <code>query.rs</code>'s
+     <code>process_chunk</code> lumps parse+route+query+serialise into one closure
+     (<code>query.rs:325,743-758</code>), and <code>scatter.rs</code> only pipelines file-
+     reading/superkmer construction, routing partitions afterwards in a
+     plain sequential loop (<code>KmerPartition::write_batch</code>,
+     <code>partition.rs:140</code>) — both under-use the fine-grained scheduling the
+     mechanism offers, so they are not precedents to copy, only existing
+     (and arguably improvable, out of scope here) usages. Cross-partition
+     lookups (querying another layer's MPHF for a variant) remain
+     necessary as before — only the <em>output</em> side is kept single-layer.</li>
+<li><strong>Reconciliation</strong>: processed at the granularity of one <em>answer batch
+     per destination partition</em>, not one source k-mer at a time — this is a
+     proper shuffle, not a per-k-mer wait. Each source partition <code>p</code> holds a
+     small array of running states <code>(minorant = true, siblings = 0)</code>, one
+     per local slot, initialised at scatter time and <strong>persisting across
+     however many destination-partition batches answer it</strong> (up to 3, one
+     per variant, not necessarily all from the same <code>q</code>). Every scattered
+     query carries an origin tag (source partition + local slot) so its
+     answer can be routed back. When target partition <code>q</code> returns its batch
+     (all answers for every query that named <code>q</code>, regardless of which source
+     k-mer or which source partition they came from), that batch is walked
+     once, locally, and each answer updates — via its origin tag — the
+     matching entry in <em>its</em> source partition's array: a miss changes
+     nothing; a hit does <code>siblings += 1</code>, and if the found sibling's own
+     encoding is smaller than the source's, <code>minorant = false</code>. A given
+     source k-mer's state is final only once every destination batch
+     concerning it has been folded in; its partition's array is flushed to
+     the persistent annex once complete. Commutative per entry, so the order
+     in which destination batches arrive and get folded in doesn't matter.</li>
+</ol>
+<p><strong>Open optimisation, not adopted yet — real tradeoff, not a free win.</strong>
+   Since looking up sibling <code>y</code> from <code>x</code>'s visit already yields everything
+   needed to fill <code>y</code>'s own annex entry too, one visit per <em>family</em> could in
+   principle replace one visit per <em>observed family member</em> — cutting this
+   pass's cost roughly by the average family size instead of paying
+   <code>3 * N_distinct</code> regardless. But it means threads processing different
+   source k-mers can end up writing the <em>same</em> sibling's slot concurrently —
+   the fully independent, ownership-free parallelism of the plan above is
+   deliberately traded away for this gain. It stays safe only because the
+   computed value for a given slot is deterministic regardless of who
+   computes it, so redundant concurrent writes converge to the same
+   value — correct as long as each write is atomic, no locking needed — but
+   it is a real design complexity increase over "every member redoes its
+   own 3 lookups independently," not a strict improvement to adopt by
+   default.
+4. <strong>Trigger and caching</strong> (<code>obikindex::KmerIndex</code>/<code>distance.rs</code>): compute
+   lazily on first <code>phylo</code> call for an SNP-family metric against a given
+   index; check for an existing annex file first (mirrors
+   <code>PersistentBitMatrix::open()</code>'s auto-detect-and-fall-back,
+   <code>bitmatrix.rs:264-287</code>); if absent, run step 3 and persist; if present,
+   mmap and reuse.
+5. <strong>Invalidation.</strong> <code>merge</code> and <code>filter</code> always write to a fresh <code>--output</code>
+   directory (<code>obikindex/src/merge.rs</code>, <code>obikmer/src/cmd/filter.rs</code>) so a
+   re-merged/re-filtered index simply has no annex yet — nothing to
+   invalidate. <code>select --in-place</code> (<code>select_layer.rs:139-235</code>) mutates
+   columns of an existing index without changing its location, which can
+   change sibling counts without removing rows — it must explicitly delete
+   any cached annex for that index as part of its in-place rewrite.
+6. <strong>Testing</strong>: hand-built tiny indexes with known sibling counts (0-3);
+   order-independence (recompute twice on a static index, identical
+   result, given the fully-parallel no-ownership design); invalidation
+   (annex absent/correctly recomputed after <code>select --in-place</code>); once
+   Step 2's sweep is fixed, a regression check that sibling_count == 0
+   slots are never looked up cross-partition during the sweep.</p>
+<p>Cost: <code>3 * N_distinct</code> existence-only lookups, computed once per index
+state and amortised over every subsequent <code>phylo</code> call that reuses the
+cached annex — cheaper per-lookup than the sweep itself (hit/miss only, no
+column fetch).</p>
+<h3 id="step-3-finalisation-obikindex">Step 3 — finalisation (<code>obikindex</code>)</h3>
+<p>From the global <code>SnpTally</code> alone (diagonal and off-diagonal both populated by
+the sweep, see Step 1/2 — no dependency on the external <code>shared_kmers</code>
+matrix), derive n x n distance matrices, each a pure function of the
+accumulated counts (same shape as <code>jaccard_to_mash</code>):</p>
+<ul>
+<li><code>p_hat[i,j] = SNP / (SNP + shared)</code></li>
+<li>Jukes-Cantor, Kimura-2P (from <code>P</code>, <code>Q</code>), optionally LogDet (needs the
+  diagonal + base-composition margins).</li>
+</ul>
+<p>Guard the singularities (<code>p &gt;= 3/4</code> for JC, <code>1-2P-Q &lt;= 0</code> or <code>1-2Q &lt;= 0</code> for
+K2P) by clamping to a max distance, as <code>jaccard_to_mash</code> clamps <code>J &lt;= 0</code>.</p>
+<h3 id="step-4-surfacing-obikindex-obikmer-cli">Step 4 — surfacing (<code>obikindex</code> + <code>obikmer</code> CLI)</h3>
+<p>These metrics do not fit <code>DistanceMetric</code>'s current <code>LayeredStore</code>-partial
+dispatch (they need the cross-partition sweep and produce a different
+intermediate). Two options, to decide:</p>
+<ul>
+<li><strong>(a)</strong> New <code>DistanceMetric</code> variants (<code>Pdistance</code>, <code>JukesCantor</code>,
+  <code>Kimura2P</code>, <code>LogDet</code>) whose <code>KmerIndex::distance</code> arm calls the sweep
+  (<code>snp.rs</code>) instead of the partial path, still returning <code>DistanceOutput</code>.
+  Keeps one CLI surface (<code>--metric jukes-cantor</code>), at the cost of a branch in
+  <code>distance()</code> that ignores the <code>LayeredStore</code> it built.</li>
+<li><strong>(b)</strong> A dedicated pathway (<code>KmerIndex::snp_distance</code>) and a distinct CLI
+  entry, if mixing a cross-partition sweep into the partition-local <code>phylo</code>
+  command is judged architecturally muddy.</li>
+</ul>
+<p>Recommendation: (a) for user ergonomics (all pairwise distances under
+<code>phylo</code>, all feeding NJ/UPGMA/<code>--shared-kmers</code> unchanged), but compute the
+sweep lazily only when an SNP-family metric is requested, so the existing
+metrics keep their partition-local fast path untouched.</p>
+<h3 id="step-5-subsampling-flag">Step 5 — subsampling flag</h3>
+<p>Add <code>--snp-sample &lt;fraction&gt;</code> (or a bottom-<code>s</code> hash threshold): restrict the
+source-k-mer enumeration in Step 2 to <code>seq_hash(kmer) &lt; threshold</code>. Divides
+lookups proportionally; <code>p_hat</code> is unbiased. Off by default (exact).</p>
+<h3 id="testing">Testing</h3>
+<ul>
+<li><strong>Primitive unit tests</strong>: <code>central_canonical_neighbors</code> on hand-checked
+  k-mers incl. palindrome-boundary cases; lone-k-mer <code>minimizer</code> against
+  <code>RollingStat</code>'s incremental result on the same k-mer.</li>
+<li><strong>End-to-end tiny index</strong>: two 1-genome indexes differing by a handful of
+  known isolated SNPs (transitions and transversions placed by hand), assert
+  exact <code>SNP</code>, <code>P</code>, <code>Q</code> counts and the resulting JC/K2P values.</li>
+<li><strong>Dedup invariant</strong>: assert the tally is identical regardless of genome/
+  partition order and that no pair is double-counted (compare against a
+  brute-force all-pairs reference on a small index).</li>
+<li><strong>Subsampling</strong>: <code>p_hat</code> within sampling error of the exact run.</li>
+</ul>
+<h3 id="suggested-phasing">Suggested phasing</h3>
+<ol>
+<li>Step 0 primitives + their unit tests (self-contained, no distance wiring).
+   This also unblocks the long-declared-but-unimplemented <code>query --mismatch</code>
+   (<code>obikmer/src/cmd/query.rs:676</code>, currently a warning), which needs the same
+   neighbour + routing machinery.</li>
+<li><code>SnpTally</code> + finalisation math with a brute-force (non-swept) reference
+   backend, validated on a tiny index.</li>
+<li>The real per-partition sweep (Step 2) behind the same finalisation; assert
+   it matches the brute-force backend.</li>
+<li>CLI surfacing (Step 4a) and NJ/UPGMA integration (already generic over the
+   matrix).</li>
+<li>Subsampling (Step 5).</li>
+</ol>
+<h2 id="locus-dropout-under-incomplete-coverage-absence-as-missing-data-not-a-penalized-state-2026-08-13-discussion">Locus dropout under incomplete coverage: absence as missing data, not a penalized state (2026-08-13, discussion)</h2>
+<p>Distinct from the SNP/Sankoff calibration above (which conditions on
+<em>conserved-flank</em> comparability), this addresses the coarser presence/absence
+signal of a family itself, for genome-skim/reduced-representation inputs
+where per-genome coverage is often <code>&lt;1x</code>, sometimes <code>&lt;0.5x</code>. At that depth,
+non-detection of a locus is dominated by Poisson sampling failure, not by
+true loss — even for a single-copy locus, <code>P(non-detection | present)</code> is
+non-negligible. Treating "absent" as a real 0-state therefore risks
+clustering genomes by shared undersampling rather than shared ancestry.</p>
+<p><strong>Parsimony.</strong> Loss and gain are the two directions of the same transition,
+so they cannot be freed asymmetrically without a biological justification for
+trusting one direction and not the other — none exists here. Freeing both
+directions to zero cost makes the character contribute nothing to any tree's
+score regardless of topology, which is operationally equivalent to just
+coding the state as ambiguous (<code>?</code>) rather than 0/1. <code>?</code> is the more honest
+encoding when downstream ancestral-state reconstruction is wanted: cost-zero
+Fitch/Sankoff still assigns internal states arbitrarily among equal-cost
+options, whereas <code>?</code> makes the "we don't know" explicit.</p>
+<p><strong>ML.</strong> The correct analogue is not a tuned asymmetric loss/gain rate but
+literal missing-data coding at the tip: an ambiguous state (all-states tip
+likelihood vector, e.g. <code>(1,1)</code> for a 2-state character) so Felsenstein
+pruning marginalises over it and the character contributes likelihood 1
+(neutral) for that taxon — the same mechanism already used for the <code>N</code>
+IUPAC-ambiguous case in the 16-state Sankoff encoding (see "IQ-TREE
+custom-model format" above). No rate parameter to justify or estimate.</p>
+<p><strong>Open item, not yet decided.</strong> No per-locus/per-genome confidence
+distinction is implemented: the current plan is to code <em>every</em> non-detected
+locus as missing/ambiguous, uniformly, without a depth-based threshold for
+"confidently absent." Deferred because at typical skim coverage the
+confidently-absent case is rare enough that a uniform treatment is
+defensible as a first pass. Known consequence to watch for: a genome with
+very low overall coverage ends up with a mostly-<code>?</code> row and constrains the
+tree weakly — will likely need a minimum-detected-loci-per-genome filter
+upstream (exclude or flag under-covered genomes) before this becomes a
+correctness problem rather than a power problem. Not designed yet.</p>
+<h3 id="-free-loss-implemented-2026-08-13"><code>--free-loss</code> implemented (2026-08-13)</h3>
+<p><code>obikmer phylo --sankoff --free-loss</code> (with <code>--tnt</code>/<code>--phyg</code>/<code>--iqtree</code>)
+recodes <code>∅</code> (a family's non-detection in a genome) to <code>?</code> instead of the
+default ordinary, costed 16th state — the resolution of the discussion
+above. <code>?</code>, not <code>-</code>: <code>-</code> still carries gap/indel semantics in TNT/PhyG/
+IQ-TREE (see "<code>∅</code> stays an ordinary 16th state" above, and the reasoning
+that motivated it in the first place — the RAxML-era failure where <code>-</code>
+was silently swallowed as missing data was undesired back when <code>∅</code> was
+meant to be fully informative; <code>--free-loss</code> is the first case where that
+same tool behaviour is exactly what's wanted). <code>?</code> is the standard
+missing/ambiguous symbol these tools already recognise without needing to
+be declared in the custom alphabet, so parsimony treats it as
+"compatible with any state" (Sankoff/Fitch's own missing-data extension —
+no per-transition cost edit needed) and Felsenstein pruning marginalises
+it for IQ-TREE's ML.</p>
+<p>Implementation is a recoding at each export's existing <code>-</code>-normalisation
+boundary, not a change to matrix calibration: <code>write_sankoff_alignment_fasta</code>
+(<code>sankoff.rs</code>, feeds <code>--phyg</code> too via its <code>prefasta:</code>), <code>write_sankoff_tnt</code>
+(<code>tnt.rs</code>, <code>?</code> written directly, bypassing <code>TNT_STATE_SYMBOL</code> — there is no
+state index for it), and <code>compact_alphabet</code>/<code>write_iqtree_alignment</code>
+(<code>iqtree.rs</code>, <code>∅</code> excluded from the compact alphabet entirely rather than
+assigned a symbol). The calibrated cost matrix itself is unchanged — its
+<code>∅</code>-row/column simply becomes unused once no sequence contains that state.</p>
+<p><strong>Unverified, flagged rather than assumed</strong> (this project's own standard for
+tool-specific claims — see the TNT/PhyG/IQ-TREE syntax facts above, all
+checked against the real binaries, not the manuals alone):
+- PhyG auto-adds its own <code>(n+1)</code>-th gap/indel row to the <code>tcm:</code> matrix
+  (<code>phyg.rs</code>); with <code>--free-loss</code> the reused <code>_sankoff.fasta</code> now contains
+  real <code>?</code> characters PhyG did not have to interpret before. Not confirmed
+  against the local PhyG binary that <code>?</code> is read as "any state" rather than
+  routed through that gap row, or otherwise mishandled.
+- IQ-TREE's exact <code>?</code>/missing-data semantics for <code>--seqtype MORPH</code> with a
+  custom-file model plus <code>+ASC</code> — assumed to marginalise via Felsenstein
+  pruning by the general convention, not yet re-verified against the local
+  <code>iqtree3</code> build the way the rest of the custom-model mechanism was.</p>
+<p>Both should be checked against a real run (small index) before <code>--free-loss</code>
+results are trusted for TNT/PhyG/IQ-TREE, the same way every other
+tool-specific behaviour in this file was established.</p>
+<h3 id="tnt-confirmed-2026-08-13-iq-tree-asc-constant-column-fix-2026-08-13">TNT confirmed (2026-08-13); IQ-TREE <code>+ASC</code> constant-column fix (2026-08-13)</h3>
+<p><strong>TNT.</strong> Real run, 20-genome benchmark index, <code>--free-loss --tnt</code>: <code>?</code>
+present for all 20 taxa in both <code>sankoff.fasta</code> and <code>sankoff.tnt</code>, loaded
+with no syntax error and no triangle-inequality warning, <code>mult</code> search
+completed, <code>sankoff.tre</code> holds 20 equally-parsimonious trees. Topology is
+exactly what the theory predicts: strain-level clades unaffected (the 4 <em>E.
+coli</em>, the <em>Klebsiella</em> trio, the <em>Salmonella</em> pairs — driven by real
+substitution signal, not gene-content) but resolution among the deeply
+divergent lineages (<em>Candidozyma</em>, <em>Saccharolobus</em>, <em>Wolbachia</em>,
+<em>Acidobacterium</em>, <em>Opitutus</em>, <em>Bacillus</em>/<em>Shouchella</em>) is weak and unstable
+across the 20 tied trees — the expected trade-off of discarding the
+gene-content/dropout signal that used to help place exactly those lineages.
+TNT's own handling of <code>?</code> — read as "compatible with any state" — no longer
+a flagged assumption.</p>
+<p><strong>IQ-TREE: <code>+ASC</code> broke on real data — non-informative columns survive
+<code>--free-loss</code>, distinct bug from the <code>--exclude-genome</code> one above.</strong>
+<code>snp_pseudo_alignment</code>'s "variable family" test (<code>family_size() &gt;= 2</code>) is a
+whole-annex property, blind to any single column's actual calls. Once
+non-detection is hidden as <code>?</code> (ignored for constancy) rather than counted
+as its own real state, a family that is genuinely variable <em>somewhere in the
+dataset</em> can still have only one distinct call among the genomes that
+actually carry it in one particular column, with the rest <code>?</code> — constant
+once missing data is excluded, which is exactly what <code>+ASC</code> forbids. Same
+underlying failure mode as <code>--exclude-genome</code>'s (documented above, "Two
+consistency bugs found and fixed post-implementation"), same remedy: rescan
+columns and drop the ones that are constant once <code>-</code> is ignored — but a
+different trigger (hiding cells vs. dropping whole rows), so a separate fix
+was needed rather than reusing <code>drop_excluded</code> directly. Implemented as
+<code>iqtree::drop_ascertainment_noninformative</code>, run only under <code>--free-loss</code>,
+only on IQ-TREE's own copy of the alignment (<code>--tnt</code>/<code>--phyg</code> have no
+no-invariant-site requirement and must not lose those columns). Not yet
+re-run against the local <code>iqtree3</code> binary to confirm <code>+ASC</code> now accepts the
+filtered alignment — next verification step, alongside the still-open PhyG
+<code>?</code>-vs-gap-row question above.</p>
+<h3 id="-family-overlap-min-shared-family-and-a-second-free_loss-bug-cardinality-transition-cost-not-zeroed-2026-08-13"><code>--family-overlap</code>/<code>--min-shared-family</code>, and a second <code>free_loss</code> bug: cardinality-transition cost not zeroed (2026-08-13)</h3>
+<p><strong>Diagnostic added: <code>--family-overlap</code>.</strong> Real per-genome-pair count of
+shared variable families (columns where neither genome is <code>∅</code>), diagonal
+kept (degenerates to "genome's own total family count", not a separate
+computation — see <code>obikmer/src/cmd/phylo/family_overlap.rs</code>). On the
+20-genome benchmark this predicted the <code>--tnt</code>/<code>--iqtree</code> rogue-placement
+pattern exactly: Candidozyma shares <strong>0</strong> families with all 19 others (hence
+its ~0-length branch, placed anywhere); the mean off-diagonal shared-family
+count per genome splits cleanly below/above ~1000 (<code>Candidozyma</code> 0,
+<code>Saccharolobus</code> 0.9, <code>Opitutus</code> 20.5, <code>Wolbachia</code> 37.1, <code>Acidobacterium</code>
+41.2, <code>Shouchella</code> 49.4, <code>Bacillus</code> 54.5, <code>Proteus</code> 629, <code>Yersinia</code> 907.5 —
+all below 1000 — vs. <code>Klebsiella</code> ~5000-6000, <code>Salmonella</code> ~8000-17000,
+<code>E. coli</code> ~19000-24000, all comfortably above). <code>--min-shared-family N</code>
+automates exclusion below that threshold, reusing the <code>--exclude-genome</code>
+machinery. Restricting to the 3 genera above threshold (11 genomes: 4
+<em>E. coli</em>, 3 <em>Klebsiella</em>, 4 <em>Salmonella</em>) gives 3 cleanly separated
+monophyletic clades in both TNT and IQ-TREE (without <code>+ASC</code>, see below) —
+confirms the family-overlap statistic, not just the tree topology, as the
+right lens for this failure mode. <code>N=1000</code> is benchmark-specific (huge
+cross-domain divergence), not a universal constant — recompute
+<code>--family-overlap</code> and read its own gap on any other dataset.</p>
+<p><strong>Second <code>free_loss</code> bug, found by re-deriving the design rather than by a
+failing run: the cardinality-transition cost wasn't zeroed.</strong>
+<code>--free-loss</code> neutralises <code>∅</code> (whole-family non-detection) by recoding it to
+<code>?</code>, so transitions to/from the empty state are never scored. But the
+calibrated 16-state cost matrix (<code>obikindex::pairwise_cost_matrix</code>) prices
+<em>every</em> cardinality change — not just <code>X → ∅</code> — via a shared
+<code>P_cardinality(|A|→|B|)</code> factor (the same constant this project has called
+<code>c_ctx</code> throughout: "used everywhere a member is gained or lost", see "A
+concrete Sankoff cost matrix" above). So a transition between two
+<em>non-empty</em> states that differ in how many family members are detected
+(e.g. <code>{A} -&gt; {A,C}</code>, gaining a second sibling) was still carrying the full
+calibrated gain/loss penalty under <code>--free-loss</code>, even though the same
+low/incomplete-coverage argument for not trusting whole-family absence
+applies identically one level down: whether a genome shows 1 vs 2 detected
+members of a family it does carry is exactly as vulnerable to sampling
+failure as whether the family was detected at all. Fixed by adding a
+<code>free_loss: bool</code> parameter to <code>pairwise_cost_matrix</code> that drops the
+<code>P_cardinality</code> factor from the log-probability sum entirely when set,
+leaving cost driven only by composition matching (shared-base retention,
+paired substitutions) — never by cardinality difference alone. Unit-tested
+(<code>free_loss_ignores_cardinality_transition_probs</code>): two wildly different
+cardinality models produce an identical cost matrix once <code>free_loss</code> is
+true. Not yet re-run against a real index to see how much this changes the
+resulting tree beyond the unit-level guarantee.</p>
+<p><strong><code>+ASC</code> misbehaves on closely-related taxa, separately from either bug
+above.</strong> Restricting to the 3-genus, 11-genome subset and running <code>--iqtree</code>
+with <code>+ASC</code> converges suspiciously fast compared to the same run without
+<code>+ASC</code> (which takes the expected ~100 NNI iterations, ~1m38s, converges to a
+stable score, total tree length 7.147, and gives the clean 3-clade
+topology). Not yet root-caused with a real <code>+ASC</code> log in hand (the one run
+overwrote its own log under the shared <code>--prefix</code>, see the operational note
+below) — working hypothesis, not confirmed: <code>+ASC</code>'s correction divides by
+<code>P(site variable | current model, current branch lengths)</code>, recomputed
+every iteration; on closely-related strains (short branches), a plausible
+model predicts most sites <em>should</em> be constant, so <code>P(variable)</code> can be
+small enough that the correction becomes numerically unstable. Needs a
+dedicated run (own <code>--prefix</code>, log kept) before this is more than a
+hypothesis.</p>
+<p><strong>Operational note, not a code bug: IQ-TREE's <code>--undo</code>/checkpoint reuse
+across different alignments crashes.</strong> Reusing <code>iqtree.ckp.gz</code> (and the tree
+it stores) from a run on one taxon set against a regenerated <code>iqtree.fasta</code>
+with a different taxon count crashes with <code>Assertion 'i &gt;= 0 &amp;&amp; i &lt;
+(int)seq_names.size()' failed</code> in <code>Alignment::getSeqName</code> /
+<code>PhyloTree::assignLeafNames</code> — <code>--undo</code> tries to graft a stored tree with
+the old leaf count onto the new, smaller alignment. Not an <code>obikmer</code> bug;
+avoid by using a fresh <code>--prefix</code> (or <code>-redo</code>) whenever the underlying
+alignment's taxon set changes, never <code>--undo</code> across them.</p>
+<h2 id="references">References</h2>
+<p>The Mash mutation-rate model this discussion contrasts with:
+(Fan <em>et al.</em> 2015; Marbl Lab 2026)<sup id="fnref:Mash-distances-doc"><a class="footnote-ref" href="#fn:Mash-distances-doc">1</a></sup> <sup id="fnref:Fan2015-mash-formula"><a class="footnote-ref" href="#fn:Fan2015-mash-formula">2</a></sup>.</p>
+<div class="footnote">
+<hr />
+<ol>
+<li id="fn:Mash-distances-doc">
+<p>Marbl Lab. (2026). <a href="https://mash.readthedocs.io/en/latest/distances.html">Mash distance</a>.&#160;<a class="footnote-backref" href="#fnref:Mash-distances-doc" title="Jump back to footnote 1 in the text">&#8617;</a></p>
+</li>
+<li id="fn:Fan2015-mash-formula">
+<p>Fan, H., Ives, A.R., Surget-Groba, Y. &amp; Cannon, C.H. (2015). <a href="https://doi.org/10.1186/s12864-015-1647-5">An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data</a>. <em>BMC Genomics</em>, 16.&#160;<a class="footnote-backref" href="#fnref:Fan2015-mash-formula" title="Jump back to footnote 2 in the text">&#8617;</a></p>
+</li>
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-    Kmer filtering (rebuild/dump/unitig)
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+      <a href="../../implementation/filtering/" class="md-nav__link">
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+  <span class="md-ellipsis">
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+    Kmer filtering
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+
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+    <li class="md-nav__item">
+      <a href="../../implementation/select/" class="md-nav__link">
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+  <span class="md-ellipsis">
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+    Select command
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+
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+
+      </a>
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+      <a href="../../implementation/obitaxonomy/" class="md-nav__link">
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+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
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+  
+    Sibling annex (discussion)
+  
+
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+  
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+
+              
+            
+              
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+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
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diff --git a/doc/theory/minimizer.refs/index.html b/DevDoc/theory/minimizer.refs/index.html
similarity index 86%
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--- a/doc/theory/minimizer.refs/index.html
+++ b/DevDoc/theory/minimizer.refs/index.html
@@ -178,6 +178,33 @@
   
   
   
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+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
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@@ -359,6 +386,34 @@
 
               
             
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+    <li class="md-nav__item">
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+  
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   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
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+  
+  
+
+      </a>
+    </li>
+  
+
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+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
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+
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+              
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+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
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+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
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+
+              
+            
+              
+                
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+  
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+  
+    <li class="md-nav__item">
+      <a href="../../implementation/obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
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@@ -827,10 +966,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
         
           
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
             
   
   
@@ -848,8 +987,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -915,6 +1054,90 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
diff --git a/doc/theory/minimizer/index.html b/DevDoc/theory/minimizer/index.html
similarity index 90%
rename from doc/theory/minimizer/index.html
rename to DevDoc/theory/minimizer/index.html
index 1cbf8568..cf959bac 100644
--- a/doc/theory/minimizer/index.html
+++ b/DevDoc/theory/minimizer/index.html
@@ -180,6 +180,33 @@
       
   
   
+  
+  
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
     
   
   
@@ -193,10 +220,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
         
           
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
             
   
   
@@ -214,8 +241,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_3">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -478,6 +505,34 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -500,10 +555,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
         
           
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
             
   
   
@@ -521,8 +576,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -903,14 +958,98 @@
   
   
     <li class="md-nav__item">
-      <a href="../../implementation/rebuild_filter/" class="md-nav__link">
+      <a href="../../implementation/merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
   
 
     
@@ -946,10 +1085,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
         
           
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
             
   
   
@@ -967,8 +1106,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -1034,6 +1173,90 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
diff --git a/doc/vancouver.csl b/DevDoc/vancouver.csl
similarity index 100%
rename from doc/vancouver.csl
rename to DevDoc/vancouver.csl
diff --git a/docmd/apa.csl b/DevDocMD/apa.csl
similarity index 100%
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diff --git a/docmd/architecture/index_architecture.md b/DevDocMD/architecture/index_architecture.md
similarity index 100%
rename from docmd/architecture/index_architecture.md
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diff --git a/docmd/architecture/index_architecture.refs.md b/DevDocMD/architecture/index_architecture.refs.md
similarity index 100%
rename from docmd/architecture/index_architecture.refs.md
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diff --git a/docmd/architecture/numa_partition_runner.md b/DevDocMD/architecture/numa_partition_runner.md
similarity index 100%
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similarity index 100%
rename from docmd/architecture/numa_worker_pools.md
rename to DevDocMD/architecture/numa_worker_pools.md
diff --git a/docmd/architecture/query.md b/DevDocMD/architecture/query.md
similarity index 100%
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similarity index 100%
rename from docmd/architecture/query.refs.md
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diff --git a/docmd/architecture/rebuild_filter.md b/DevDocMD/architecture/rebuild_filter.md
similarity index 100%
rename from docmd/architecture/rebuild_filter.md
rename to DevDocMD/architecture/rebuild_filter.md
diff --git a/docmd/architecture/sequences/invariant.md b/DevDocMD/architecture/sequences/invariant.md
similarity index 100%
rename from docmd/architecture/sequences/invariant.md
rename to DevDocMD/architecture/sequences/invariant.md
diff --git a/docmd/architecture/sequences/invariant.refs.md b/DevDocMD/architecture/sequences/invariant.refs.md
similarity index 100%
rename from docmd/architecture/sequences/invariant.refs.md
rename to DevDocMD/architecture/sequences/invariant.refs.md
diff --git a/docmd/architecture/siblings.md b/DevDocMD/architecture/siblings.md
similarity index 79%
rename from docmd/architecture/siblings.md
rename to DevDocMD/architecture/siblings.md
index a69a25ed..d689f2e5 100644
--- a/docmd/architecture/siblings.md
+++ b/DevDocMD/architecture/siblings.md
@@ -389,7 +389,7 @@ undermining the point. It stays plausible as a coarse filter for the
 predicts low true entropy too), but not as a stand-in for the high tail —
 not pursued further for now.
 
-## `--free-loss`/`--tnt` pipeline: four independent scans, three of them unsampled (found 2026-08-15, not yet fixed)
+## `--free-loss`/`--tnt` pipeline: four independent scans, three of them unsampled (found 2026-08-15, fixed 2026-08-15 — see "Implemented" below)
 
 Measured on `phyloskims_sal_vac` (91 genomes): `obikmer phylo --subsample 500000
 --free-loss --tnt` logs four sequential stages —
@@ -428,32 +428,100 @@ surfaced two compounding problems, not one:
    three of the four stages never subsample, which explains most of the
    ~10x runtime gap against `snp_pseudo_alignment` on its own.
 
-**Decided requirement (2026-08-15, not yet implemented)**: all four
-stages must consume **one shared selection**, computed once, not each
-stage either scanning everything or drawing its own independent sample.
-Per-genome-pair SNP counts, the Sankoff base-pair calibration, the
-cardinality histogram, and the pseudo-alignment must all describe the
-same set of families — otherwise the calibration and the alignment it's
-meant to calibrate aren't even guaranteed to agree on which sites exist.
-Once selection is unified, doing four independent full scans stops making
-sense on its own terms: a single pass over the shared selection can feed
-all four accumulators (SNP/shared counts, base-pair tally, cardinality
-tally, pseudo-alignment output) at once, which is also the fix for
-problem 1 above — the two issues turn out to be one architectural
-decision, not two.
+**Decided requirement**: all four stages consume **one shared selection**,
+computed once, not each stage either scanning everything or drawing its
+own independent sample. Per-genome-pair SNP counts, the Sankoff base-pair
+calibration, the cardinality histogram, and the pseudo-alignment all
+describe the same set of families — the calibration and the alignment it
+calibrates are now guaranteed to agree on which sites exist.
 
-**Forward-looking complication, explicitly flagged**: the eventual plan
-is to bias family *selection itself* by entropy15 (favor the informative
-mid-entropy band over uniform reservoir sampling — the exact motivation
-behind "Cheap entropy pre-filtering" above). That means selection can no
-longer be an uninformed draw made *during* the single fused scan; entropy
-(exact or a cheap proxy) has to be known *before* selection happens,
-which argues for a first, cheap, entropy-informed selection pass followed
-by one fused, unsampled-relative-to-that-selection scan — tying this
-decision directly to the still-unresolved marginal-proxy limitation
-described in "Cheap entropy pre-filtering" above (which only reliably
-predicts the *low*-entropy tail, not the high one — a real gap, not
-solved by this note, if entropy-biased selection ships before it is).
+**Correction to the "single pass" framing above**: `base_pair_tally`/
+`cardinality_tally` both need `raw_snp_distance`'s *complete* aggregate
+SNP/shared counts before they can derive `included[i,j]` (the
+`ratio_ceiling` filter) — a genuine sequential dependency (`included`
+can't be known until every pair's aggregate count is final), not an
+artifact of the old code's structure. So the fix is **two** passes over
+the shared selection, not one: pass A computes the aggregate counts (and
+derives `included`); pass B fuses `base_pair_tally` + `cardinality_tally`
++ the pseudo-alignment (mutually independent once `included` is known)
+into a single scan. Still a 4→2 reduction, and — per the clarification
+that settled this — pass A itself now runs over the *same shared
+selection* pass B uses (not the full unsampled index): "les ratios, on
+les fait sur les sites sélectionnés, c'est tout, les autres sites
+n'existent pas" — once a selection is chosen, both passes are bounded by
+it, so on a real `--subsample`/`--entropy` run pass A is cheap too, not
+just pass B.
+
+**Entropy-biased selection's own resolution to the "forward-looking
+complication"** (entropy must be known before selection, but selection
+happens during the same scan that would resolve it): see "Entropy-biased
+selection" below — resolved via a persisted per-layer entropy annex, not
+by restructuring the scan into an inline pre-pass.
+
+## Entropy-biased selection: soft Gaussian weighting, not a hard cutoff (decided and implemented 2026-08-15)
+
+Refines the "forward-looking complication" above with a concrete
+mechanism. Instead of a hard `[low, high]` entropy band (or any other
+exact cutoff) deciding which non-monomorphic minorant families are
+eligible, selection is weighted by an **unnormalized Gaussian kernel**
+centered on a target entropy: `w(entropy) = exp(-(entropy - μ)² / (2σ²))`
+— deliberately not the normalized Gaussian density (which would peak
+below 1 and complicate the "probability" reading) — this kernel form
+equals 1 exactly at `entropy = μ` and decays smoothly to 0 away from it,
+so it reads directly as an acceptance weight: the further a family's
+entropy from the target, the less likely it is picked, with no hard
+in/out boundary — a few "bad" sites can still get in, by design. `μ`
+(default ~1.0) and `σ` (default ~0.5) are meant to be user-tunable.
+
+**Mechanism: joint probability, not a weighted reservoir**. Not
+Efraimidis–Spirakis weighted reservoir sampling (an earlier, more complex
+proposal, superseded before implementation) — instead, a single
+independent accept/reject draw per qualifying candidate: draw
+`u ~ Uniform(0,1)`, accept iff `u < p₀ · w(entropy)`. `p₀` is a single
+**index-wide** rate, `N / total_count` (`total_count` = the sum of
+`non_monomorphic_counts` across every layer, `N` = `--subsample`'s
+target), applied identically at every layer — this alone already gives
+each layer its proportional share (the same effect the old uniform
+reservoir's explicit per-layer `n_layer = N · count_layer / total_count`
+computation achieved, but without needing to compute it: applying one
+rate uniformly is mathematically the same as proportioning per layer).
+`p₀ = 1.0` when there is no `--subsample` at all — `--entropy` alone is a
+pure soft entropy filter over the whole index, no size target. Properties:
+(1) **strictly generalizes the existing uniform sampler** — with `σ` large
+enough that `w ≈ 1` everywhere, this reduces to the old uniform `N/total_count`
+draw; (2) yields "approximately N", not exactly N — expected accepted
+count is `N · mean(w)`, always `≤ N` — an intentional relaxation, matching
+"sous-échantillonnage à environ n" rather than the old reservoir's exact-N
+guarantee; (3) one streaming pass, one random draw per candidate, no
+reservoir state.
+
+**Resolving "entropy must be known before selection, but selection
+happens during the same resolving scan"**: solved with a **persisted,
+per-layer entropy annex** (`obikphylo/src/siblings/entropy_annex.rs`,
+`EntropyAnnex`/`EntropyAnnexBuilder`), not by restructuring the scan.
+Mirrors `SiblingAnnex`'s mmap-backed, read-only-after-build convention,
+but indexed by `family_idx` (every minorant of the layer, monomorphic
+included — the same numbering `Selection`/`scan_layer_families` already
+use), one `f32` entropy15 value per entry, `-1.0` sentinel for monomorphic/
+not-yet-computed. First use of `--entropy`/`--entropy-sd` on an index
+pays a one-time cost (`ensure_entropy_annexes` in `entropy.rs`: a full,
+unsampled `Selection::All` scan, resolving every non-monomorphic
+minorant's `genome_mask` once to compute and persist its entropy) — every
+later run (any `μ`/`σ`, any command) reads the file positionally, no
+re-scan, restoring the usual `Selection::Some` "skip resolving excluded
+families" speedup that a naive "weigh during the resolving scan" design
+would have permanently forfeited.
+
+**Resolved**: the existing hard "non-monomorphic minorant" eligibility
+filter stays a hard gate upstream of the Gaussian weighting — only
+qualifying families ever get a stored entropy value or a weighted draw.
+
+**CLI, implemented**: two `phylo` options, `--entropy <μ>` and
+`--entropy-sd <σ>` (`obikmer/src/cmd/phylo/args.rs`). The entropic filter
+activates as soon as *either* is given (`mod.rs`, computed once into an
+`Option<EntropyBias>` threaded through `--snp`/`--family-overlap`/
+`--shannon`/the fused sankoff pipeline below). If active but one or both
+are unset, defaults are `μ = 1.0`, `σ = 0.5`.
 
 ## Two entropy definitions kept side by side, for comparison (2026-08-15)
 
@@ -618,3 +686,57 @@ real, selectable on-disk format:
 
 Full workspace `cargo test` (all crates, unit + doc tests) green after
 this change.
+
+## Sankoff pipeline fusion + entropy-biased selection — implemented (2026-08-15)
+
+Replaces the "four independent scans" problem above and implements
+"Entropy-biased selection" above, end to end:
+
+- **`SankoffBundleExt::sankoff_bundle`** (new,
+  `obikphylo/src/siblings/sankoff_bundle.rs`) — the `--sankoff`/`--tnt`/
+  `--phyg`/`--iqtree` block in `obikmer/src/cmd/phylo/mod.rs` now calls
+  this once instead of three separate `raw_snp_distance`/
+  `base_pair_tally`/`cardinality_tally` calls. One `PartitionCache`, one
+  shared (possibly subsampled/entropy-biased) selection computed once via
+  `compute_selections`, two scans over it: pass A (aggregate SNP/shared
+  counts, `--exclude-genome` zeroing, then `included[i,j]`), pass B
+  (`base_pair_tally` + `cardinality_tally` + the pseudo-alignment, fused
+  into one `scan_layer_families` call per layer, all three read off the
+  same resolved `genome_mask`). `snp_pseudo_alignment`/
+  `shannon_entropy_csv` (still used standalone by `--snp`/
+  `--family-overlap`/`--shannon`) both gained an `entropy_bias` parameter
+  too, so entropy-biased selection isn't sankoff-specific.
+- **Regression proof**: `sankoff_bundle_matches_old_separate_calls`
+  (`obikphylo/src/siblings/tests.rs`) asserts `sankoff_bundle`'s four
+  outputs are bit-identical to calling the old, separate
+  `raw_snp_distance`/`base_pair_tally`/`cardinality_tally`/
+  `snp_pseudo_alignment` on the same fixture with no subsample — the
+  fusion is a performance change, not a behavior change.
+- **`EntropyAnnex`/`EntropyAnnexBuilder`** (new,
+  `obikphylo/src/siblings/entropy_annex.rs`) and **`ensure_entropy_annexes`**
+  (`entropy.rs`) implement the persisted-entropy mechanism from
+  "Entropy-biased selection" above. `entropy_annex_builds_on_demand_and_biases_selection`
+  (`tests.rs`) proves, on a fixture with one known-entropy family: the
+  annex file doesn't exist before any entropy-biased call; `compute_selections`
+  builds it on first use; `μ` set to the family's exact entropy with
+  `p₀ = 1.0` selects it deterministically (`u < 1.0` always, for
+  `u ∈ [0,1)`); `μ` set far away with tiny `σ` deterministically excludes
+  it (`w` underflows to exactly `0.0`); the persisted value matches
+  `--shannon`'s own `family_entropy` computation to `1e-6`.
+- **`EntropyBias`** (`pub`, `obikphylo::siblings::EntropyBias { mu, sigma }`)
+  is the one new public type threading `--entropy`/`--entropy-sd` through
+  every `Option<EntropyBias>`-accepting method — resolved once in
+  `obikmer/src/cmd/phylo/mod.rs` from `args.entropy`/`args.entropy_sd`
+  (activation: either given; defaults `1.0`/`0.5` for whichever is unset).
+
+Full workspace `cargo test` green after this change (167 unit tests in
+`obicompactvec`+`obilayeredmap`+`obikphylo` alone, plus every other
+crate's suite, no regressions).
+
+**Still open, not part of this change** (per "Correction to the 'single
+pass' framing" above): `--raw-snp-distance`/`--raw-snp-counts` (the
+standalone diagnostic flags, not the `--sankoff` pipeline) still always
+scan the full unsampled index — never threaded `--subsample`/`--entropy`,
+out of scope here since the reported problem was specifically about the
+`--sankoff`/`--tnt` pipeline's redundant/inconsistent scans, not these
+two standalone flags.
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+    <title>Ecology Letters</title>
+    <id>http://www.zotero.org/styles/ecology-letters</id>
+    <link href="http://www.zotero.org/styles/ecology-letters" rel="self"/>
+    <link href="http://www.zotero.org/styles/apa" rel="template"/>
+    <link href="http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291461-0248/homepage/ForAuthors.html" rel="documentation"/>
+    <author>
+      <name>David Kaplan</name>
+      <email>david.kaplan@ird.fr</email>
+    </author>
+    <contributor>
+      <name>Sebastian Karcher</name>
+    </contributor>
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+    <category field="biology"/>
+    <issn>1461-023X</issn>
+    <eissn>1461-0248</eissn>
+    <updated>2023-10-11T10:45:32+00:00</updated>
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+%% This BibTeX bibliography file was created using BibDesk.
+%% https://bibdesk.sourceforge.io/
+
+%% Created for Eric Coissac at 2026-04-18 08:19:36 +0200
+
+
+%% Saved with string encoding Unicode (UTF-8)
+
+
+
+@article{Zheng2020-ji,
+	abstract = {MOTIVATION: Minimizers are methods to sample k-mers from a
+               string, with the guarantee that similar set of k-mers will be
+               chosen on similar strings. It is parameterized by the k-mer
+               length k, a window length w and an order on the k-mers.
+               Minimizers are used in a large number of softwares and pipelines
+               to improve computation efficiency and decrease memory usage.
+               Despite the method's popularity, many theoretical questions
+               regarding its performance remain open. The core metric for
+               measuring performance of a minimizer is the density, which
+               measures the sparsity of sampled k-mers. The theoretical optimal
+               density for a minimizer is 1/w, provably not achievable in
+               general. For given k and w, little is known about asymptotically
+               optimal minimizers, that is minimizers with density O(1/w).
+               RESULTS: We derive a necessary and sufficient condition for
+               existence of asymptotically optimal minimizers. We also provide a
+               randomized algorithm, called the Miniception, to design
+               minimizers with the best theoretical guarantee to date on density
+               in practical scenarios. Constructing and using the Miniception is
+               as easy as constructing and using a random minimizer, which
+               allows the design of efficient minimizers that scale to the
+               values of k and w used in current bioinformatics software
+               programs. AVAILABILITY AND IMPLEMENTATION: Reference
+               implementation of the Miniception and the codes for analysis can
+               be found at https://github.com/kingsford-group/miniception.
+               SUPPLEMENTARY INFORMATION: Supplementary data are available at
+               Bioinformatics online.},
+	author = {Zheng, Hongyu and Kingsford, Carl and Mar{\c c}ais, Guillaume},
+	doi = {10.1093/bioinformatics/btaa472},
+	issn = {1367-4803,1367-4811},
+	journal = {Bioinformatics (Oxford, England)},
+	language = {en},
+	month = jul,
+	number = {Suppl_1},
+	pages = {i119--i127},
+	pmc = {PMC8248892},
+	pmid = 32657376,
+	publisher = {Oxford University Press (OUP)},
+	title = {Improved design and analysis of practical minimizers},
+	url = {http://dx.doi.org/10.1093/bioinformatics/btaa472},
+	volume = 36,
+	year = 2020,
+	bdsk-url-1 = {http://dx.doi.org/10.1093/bioinformatics/btaa472}}
+
+@article{Zheng2021-cc,
+	abstract = {MOTIVATION: Minimizers are efficient methods to sample k-mers
+               from genomic sequences that unconditionally preserve sufficiently
+               long matches between sequences. Well-established methods to
+               construct efficient minimizers focus on sampling fewer k-mers on
+               a random sequence and use universal hitting sets (sets of k-mers
+               that appear frequently enough) to upper bound the sketch size. In
+               contrast, the problem of sequence-specific minimizers, which is
+               to construct efficient minimizers to sample fewer k-mers on a
+               specific sequence such as the reference genome, is less studied.
+               Currently, the theoretical understanding of this problem is
+               lacking, and existing methods do not specialize well to sketch
+               specific sequences. RESULTS: We propose the concept of polar
+               sets, complementary to the existing idea of universal hitting
+               sets. Polar sets are k-mer sets that are spread out enough on the
+               reference, and provably specialize well to specific sequences.
+               Link energy measures how well spread out a polar set is, and with
+               it, the sketch size can be bounded from above and below in a
+               theoretically sound way. This allows for direct optimization of
+               sketch size. We propose efficient heuristics to construct polar
+               sets, and via experiments on the human reference genome, show
+               their practical superiority in designing efficient
+               sequence-specific minimizers. AVAILABILITY AND IMPLEMENTATION: A
+               reference implementation and code for analyses under an
+               open-source license are at
+               https://github.com/kingsford-group/polarset. SUPPLEMENTARY
+               INFORMATION: Supplementary data are available at Bioinformatics
+               online.},
+	author = {Zheng, Hongyu and Kingsford, Carl and Mar{\c c}ais, Guillaume},
+	doi = {10.1093/bioinformatics/btab313},
+	issn = {1367-4803,1367-4811},
+	journal = {Bioinformatics (Oxford, England)},
+	language = {en},
+	month = jul,
+	number = {Suppl\_1},
+	pages = {i187--i195},
+	pmc = {PMC8686682},
+	pmid = 34252928,
+	publisher = {Oxford University Press (OUP)},
+	title = {Sequence-specific minimizers via polar sets},
+	url = {http://dx.doi.org/10.1093/bioinformatics/btab313},
+	volume = 37,
+	year = 2021,
+	bdsk-url-1 = {http://dx.doi.org/10.1093/bioinformatics/btab313}}
+
+@article{Pan2024-hb,
+	abstract = {MOTIVATION: The minimizer concept is a data structure for
+               sequence sketching. The standard canonical minimizer selects a
+               subset of k-mers from the given DNA sequence by comparing the
+               forward and reverse k-mers in a window simultaneously according
+               to a predefined selection scheme. It is widely employed by
+               sequence analysis such as read mapping and assembly. k-mer
+               density, k-mer repetitiveness (e.g. k-mer bias), and
+               computational efficiency are three critical measurements for
+               minimizer selection schemes. However, there exist trade-offs
+               between kinds of minimizer variants. Generic, effective, and
+               efficient are always the requirements for high-performance
+               minimizer algorithms. RESULTS: We propose a simple minimizer
+               operator as a refinement of the standard canonical minimizer. It
+               takes only a few operations to compute. However, it can improve
+               the k-mer repetitiveness, especially for the lexicographic order.
+               It applies to other selection schemes of total orders (e.g.
+               random orders). Moreover, it is computationally efficient and the
+               density is close to that of the standard minimizer. The refined
+               minimizer may benefit high-performance applications like binning
+               and read mapping. AVAILABILITY AND IMPLEMENTATION: The source
+               code of the benchmark in this work is available at the github
+               repository https://github.com/xp3i4/mini\_benchmark.},
+	author = {Pan, Chenxu and Reinert, Knut},
+	doi = {10.1093/bioinformatics/btae045},
+	issn = {1367-4803,1367-4811},
+	journal = {Bioinformatics (Oxford, England)},
+	language = {en},
+	month = feb,
+	number = 2,
+	pmc = {PMC10868324},
+	pmid = 38269626,
+	publisher = {Oxford University Press (OUP)},
+	title = {A simple refined DNA minimizer operator enables 2-fold faster computation},
+	url = {http://dx.doi.org/10.1093/bioinformatics/btae045},
+	volume = 40,
+	year = 2024,
+	bdsk-url-1 = {http://dx.doi.org/10.1093/bioinformatics/btae045}}
+
+@article{Kille2023-px,
+	abstract = {MOTIVATION: The Jaccard similarity on k-mer sets has shown to be
+               a convenient proxy for sequence identity. By avoiding expensive
+               base-level alignments and comparing reduced sequence
+               representations, tools such as MashMap can scale to massive
+               numbers of pairwise comparisons while still providing useful
+               similarity estimates. However, due to their reliance on minimizer
+               winnowing, previous versions of MashMap were shown to be biased
+               and inconsistent estimators of Jaccard similarity. This directly
+               impacts downstream tools that rely on the accuracy of these
+               estimates. RESULTS: To address this, we propose the minmer
+               winnowing scheme, which generalizes the minimizer scheme by use
+               of a rolling minhash with multiple sampled k-mers per window. We
+               show both theoretically and empirically that minmers yield an
+               unbiased estimator of local Jaccard similarity, and we implement
+               this scheme in an updated version of MashMap. The minmer-based
+               implementation is over 10 times faster than the minimizer-based
+               version under the default ANI threshold, making it well-suited
+               for large-scale comparative genomics applications. AVAILABILITY
+               AND IMPLEMENTATION: MashMap3 is available at
+               https://github.com/marbl/MashMap.},
+	author = {Kille, Bryce and Garrison, Erik and Treangen, Todd J and Phillippy, Adam M},
+	doi = {10.1093/bioinformatics/btad512},
+	issn = {1367-4803,1367-4811},
+	journal = {Bioinformatics (Oxford, England)},
+	language = {en},
+	month = sep,
+	number = 9,
+	pmc = {PMC10505501},
+	pmid = 37603771,
+	publisher = {Oxford University Press (OUP)},
+	title = {Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation},
+	url = {http://dx.doi.org/10.1093/bioinformatics/btad512},
+	volume = 39,
+	year = 2023,
+	bdsk-url-1 = {http://dx.doi.org/10.1093/bioinformatics/btad512}}
+
+@incollection{Golan2025-xf,
+	address = {Cham},
+	author = {Golan, Shay and Shur, Arseny M},
+	booktitle = {Lecture Notes in Computer Science},
+	doi = {10.1007/978-3-031-82670-2\_25},
+	isbn = {9783031826696,9783031826702},
+	issn = {0302-9743,1611-3349},
+	language = {en},
+	pages = {347--360},
+	publisher = {Springer Nature Switzerland},
+	series = {Lecture Notes in Computer Science},
+	title = {Expected density of random minimizers},
+	url = {http://dx.doi.org/10.1007/978-3-031-82670-2_25},
+	year = 2025,
+	bdsk-url-1 = {http://dx.doi.org/10.1007/978-3-031-82670-2_25},
+	bdsk-url-2 = {http://dx.doi.org/10.1007/978-3-031-82670-2%5C_25}}
+
+@article{Mohamadi2017-ok,
+	abstract = {Motivation: Many bioinformatics algorithms are designed for the
+               analysis of sequences of some uniform length, conventionally
+               referred to as k -mers. These include de Bruijn graph assembly
+               methods and sequence alignment tools. An efficient algorithm to
+               enumerate the number of unique k -mers, or even better, to build
+               a histogram of k -mer frequencies would be desirable for these
+               tools and their downstream analysis pipelines. Among other
+               applications, estimated frequencies can be used to predict genome
+               sizes, measure sequencing error rates, and tune runtime
+               parameters for analysis tools. However, calculating a k -mer
+               histogram from large volumes of sequencing data is a challenging
+               task. Results: Here, we present ntCard, a streaming algorithm for
+               estimating the frequencies of k -mers in genomics datasets. At
+               its core, ntCard uses the ntHash algorithm to efficiently compute
+               hash values for streamed sequences. It then samples the
+               calculated hash values to build a reduced representation
+               multiplicity table describing the sample distribution. Finally,
+               it uses a statistical model to reconstruct the population
+               distribution from the sample distribution. We have compared the
+               performance of ntCard and other cardinality estimation
+               algorithms. We used three datasets of 480 GB, 500 GB and 2.4 TB
+               in size, where the first two representing whole genome shotgun
+               sequencing experiments on the human genome and the last one on
+               the white spruce genome. Results show ntCard estimates k -mer
+               coverage frequencies >15× faster than the state-of-the-art
+               algorithms, using similar amount of memory, and with higher
+               accuracy rates. Thus, our benchmarks demonstrate ntCard as a
+               potentially enabling technology for large-scale genomics
+               applications. Availability and Implementation: ntCard is written
+               in C ++ and is released under the GPL license. It is freely
+               available at https://github.com/bcgsc/ntCard. Contact:
+               hmohamadi@bcgsc.ca or ibirol@bcgsc.ca. Supplementary information:
+               Supplementary data are available at Bioinformatics online.},
+	author = {Mohamadi, Hamid and Khan, Hamza and Birol, Inanc},
+	date-modified = {2026-04-18 08:19:36 +0200},
+	doi = {10.1093/bioinformatics/btw832},
+	issn = {1367-4803,1367-4811},
+	journal = {Bioinformatics (Oxford, England)},
+	language = {en},
+	month = may,
+	number = 9,
+	pages = {1324--1330},
+	pmc = {PMC5408799},
+	pmid = 28453674,
+	publisher = {Oxford University Press (OUP)},
+	title = {ntCard: a streaming algorithm for cardinality estimation in genomics data},
+	url = {http://dx.doi.org/10.1093/bioinformatics/btw832},
+	volume = 33,
+	year = 2017,
+	bdsk-url-1 = {http://dx.doi.org/10.1093/bioinformatics/btw832}}
+
+@misc{Mash-distances-doc,
+	author = {{Marbl Lab}},
+	howpublished = {Mash documentation},
+	title = {Mash Distance},
+	url = {https://mash.readthedocs.io/en/latest/distances.html},
+	urldate = {2026-07-09},
+	year = 2026}
+
+@article{Fan2015-mash-formula,
+	author = {Fan, Huan and Ives, Anthony R and Surget-Groba, Yann and Cannon, Charles H},
+	doi = {10.1186/s12864-015-1647-5},
+	journal = {BMC Genomics},
+	number = 1,
+	title = {An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data},
+	url = {https://doi.org/10.1186/s12864-015-1647-5},
+	volume = 16,
+	year = 2015}
diff --git a/docmd/theory/encoding.md b/DevDocMD/theory/encoding.md
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diff --git a/docmd/theory/encoding.refs.md b/DevDocMD/theory/encoding.refs.md
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diff --git a/docmd/theory/entropy.md b/DevDocMD/theory/entropy.md
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diff --git a/docmd/theory/evolutionary_distances.md b/DevDocMD/theory/evolutionary_distances.md
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diff --git a/docmd/theory/indexing.md b/DevDocMD/theory/indexing.md
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diff --git a/docmd/theory/minimizer.md b/DevDocMD/theory/minimizer.md
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diff --git a/docmd/vancouver.csl b/DevDocMD/vancouver.csl
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diff --git a/Makefile b/Makefile
index bebe14f9..2057bbea 100644
--- a/Makefile
+++ b/Makefile
@@ -5,14 +5,14 @@ MKDOCS   := $(VENV)/bin/mkdocs
 
 CARGO_DIR := src
 
-DOC_DIR  := docmd
+DOC_DIR  := DevDocMD
 DOC_FILE := mkdocs.yml
-DOC_SITE := doc
+DOC_SITE := DevDoc
 DOC_PORT := 8001
 
 DOC_USER_DIR  := UserDocMD
 DOC_USER_FILE := mkdocs-user.yml
-DOC_USER_SITE := doc-user
+DOC_USER_SITE := doc
 DOC_USER_PORT := 8002
 
 # ── virtualenv ────────────────────────────────────────────────────────────────
diff --git a/README.md b/README.md
index a9876151..3a843f0a 100644
--- a/README.md
+++ b/README.md
@@ -121,5 +121,6 @@ obikmer phylo index/ > distances.tsv
 
 ## Documentation
 
-Extended architecture and implementation notes are in `docmd/`. Build with
-`make doc` (requires Python + MkDocs Material).
+Extended architecture and implementation notes are in `DevDocMD/`. Build with
+`make doc` (requires Python + MkDocs Material). User-facing documentation is
+in `UserDocMD/`, built with `make doc-user`.
diff --git a/UserDocMD/usage/pack.md b/UserDocMD/usage/pack.md
index 7374f9c6..285aea9c 100644
--- a/UserDocMD/usage/pack.md
+++ b/UserDocMD/usage/pack.md
@@ -3,7 +3,7 @@
 Pack an index's per-column matrix files into a single-file format to reduce query-time I/O (fewer file opens per query).
 
 ```bash
-obikmer pack INDEX
+obikmer pack INDEX [--sparse]
 ```
 
 ## Arguments
@@ -12,4 +12,18 @@ obikmer pack INDEX
 |---|---|
 | `INDEX` | Index directory to pack (modified in place) |
 
+## Options
+
+| Option | Default | Description |
+|---|---|---|
+| `--sparse` | off | Pack presence/absence matrices into a sparse, deduplicated format instead of the dense one |
+
 The index directory is locked for exclusive access while packing.
+
+## `--sparse`
+
+Presence/absence data (which genomes carry each kmer) is often mostly empty — most kmers are present in only a handful of genomes out of the whole collection. The default (dense) packed format stores one bit per genome for every kmer regardless of how many genomes actually carry it; `--sparse` instead stores each kmer's genome list directly, and deduplicates identical lists shared by many kmers (common in real data, since kmers from the same conserved region tend to be carried by the same genomes).
+
+On real genome collections this has measured at roughly 7x smaller on disk than the dense format, and single-kmer lookups (the shape `phylo`'s sibling-annex/entropy/Sankoff computations use) are typically faster too, since the smaller files mean less data to read from disk. The trade-off: reading a whole genome column at once (used by `--metric` distance-matrix computations) is much slower on the sparse format than on the dense one, since there is no native column layout to read sequentially — prefer the dense format (the default, no `--sparse`) for indexes you mainly query with `phylo`'s plain `--metric` distance matrices.
+
+Count matrices (`--metric` on a count index) are not affected by `--sparse` — only presence/absence matrices are.
diff --git a/UserDocMD/usage/phylo.md b/UserDocMD/usage/phylo.md
index 2d6b5e88..2d068200 100644
--- a/UserDocMD/usage/phylo.md
+++ b/UserDocMD/usage/phylo.md
@@ -70,6 +70,50 @@ A family is eligible for a genome pair $(i, j)$ only if genome $i$ carries exact
 
 `--min-shared-family N` automates the fix: it excludes, before any computation, every genome whose mean shared-family count against all other genomes (the same statistic, averaged per row of the `--family-overlap` matrix) falls below `N`. There is no universal value for `N` — it depends on how divergent and how completely covered the genome collection is; inspect `--family-overlap`'s own output to find where the real gap sits before choosing a threshold.
 
+## Sampling at scale: `--subsample`, `--shannon`, `--entropy`
+
+On a large index (billions of families), building a full pseudo-alignment or fully calibrating the Sankoff model is not just slow — it may not fit in the time you have. `--subsample` bounds the work to a fixed number of families; `--shannon` reports how informative each family is; `--entropy`/`--entropy-sd` bias which families get kept toward the informative ones instead of choosing uniformly at random.
+
+| Option | Default | Description |
+|---|---|---|
+| `--subsample N` | none (keep everything) | Cap the number of variable families (family size ≥ 2) retained, to approximately `N` |
+| `--shannon` | off | Write `<prefix>_shannon.csv`: per-family Shannon entropy, one row per family |
+| `--entropy MU` | off (`1.0` if only `--entropy-sd` is given) | Center of the entropy band to favor when sampling |
+| `--entropy-sd SIGMA` | off (`0.5` if only `--entropy` is given) | Width of that band |
+
+`--subsample`/`--entropy`/`--entropy-sd` affect every option that scans variable families: `--snp`, `--family-overlap`, `--shannon`, and the whole Sankoff pipeline (`--sankoff`/`--tnt`/`--phyg`/`--iqtree`, next section) — all of them draw from the *same* selection of families in one invocation, so the Sankoff calibration and the pseudo-alignment it calibrates always describe the same sites, and `--family-overlap`'s counts stay consistent with `--snp`'s columns. `--raw-snp-distance`/`--raw-snp-counts` are not affected — they always scan every family, since their p-distance estimate is a whole-index statistic, not something that benefits from being restricted to a sample.
+
+### `--subsample N`
+
+Without `--subsample`, every variable family (family size ≥ 2, i.e. every family where at least one genome differs from the rest) is used. With `--subsample N`, roughly `N` families are kept instead, chosen at random but in proportion to how many candidate families each part of the index actually holds — so the sample stays representative of the whole index, not skewed toward whichever part happens to be scanned first. If the index has fewer than `N` candidate families in the first place, `--subsample` has no effect: everything is kept.
+
+`--subsample` trades completeness for speed: `--snp`'s alignment gets fewer columns, `--sankoff`'s calibration is based on fewer observations, but the resolution work (the expensive part of a `phylo` run on a large index) scales with `N` instead of with the index's true size. Pick `N` as large as your time budget allows — a few hundred thousand to a few million families is usually enough for the transition-probability estimates in `--sankoff`'s calibration to stabilize; a smaller `N` speeds up exploratory runs.
+
+### `--shannon`: measuring how informative a family is
+
+Not every variable family is equally useful for a tree: a family that differs in only one genome out of a thousand carries very little signal, and one where the pattern looks essentially random across genomes may be too saturated (multiple substitutions have overwritten the original signal) to carry real information either. `--shannon` quantifies this with the Shannon entropy (in bits) of each family's states across the genomes that carry it — low entropy means "almost everyone agrees" (an invariant or near-invariant family, phylogenetically shallow), while entropy near the ceiling for a 4-state character means "close to a random draw between the possible bases" (saturated).
+
+`<prefix>_shannon.csv` (or `shannon.csv` without `-o`) has one row per family visited:
+
+| Column | Meaning |
+|---|---|
+| `layer` | an internal index-layer identifier — stable within one run, not meaningful across indexes |
+| `family_idx` | the family's position within that layer |
+| `entropy15` | Shannon entropy (bits) over the 16 possible states (the 15 non-empty subsets of `{A,C,G,T}` — the same alphabet `--sankoff`'s 16-state model uses), genomes absent from the family excluded from the count |
+| `entropy4` | Shannon entropy (bits) reduced to the 4 plain bases, kept alongside `entropy15` for comparison — a genome carrying more than one base at once counts once per base, so this can differ from `entropy15` |
+| `family_size` | number of distinct central bases observed anywhere in the index for this family (2–4, since monomorphic families aren't visited) |
+| `n_genomes_present` | how many genomes the entropy was computed over |
+
+Run with `--subsample N --shannon` to get a bounded diagnostic sample instead of a full-index pass — useful to inspect the entropy distribution and decide reasonable `--entropy`/`--entropy-sd` values (see below) before committing to a full run.
+
+### `--entropy MU` / `--entropy-sd SIGMA`: biasing the sample toward informative families
+
+By default, `--subsample` draws families uniformly — every candidate family has the same chance of being kept, regardless of how informative it actually is. `--entropy`/`--entropy-sd` change that: instead of a uniform draw, each family's chance of being kept is weighted by how close its own entropy (the `entropy15` value `--shannon` reports) is to `MU`, using a bell-shaped (Gaussian) curve of width `SIGMA` — a family with entropy exactly `MU` is the most likely to be kept, and the chance falls off smoothly the further its entropy is from `MU`, with no hard cutoff (a few families outside the target band can still get in, just less often).
+
+The filter activates as soon as *either* `--entropy` or `--entropy-sd` is given; whichever one you don't set defaults to `1.0`/`0.5`. It can be combined with `--subsample N` (the target count is still approximately `N`, now biased toward the entropy band instead of uniform — expect somewhat *fewer* than `N` families in practice, since low-weight families are dropped rather than replaced) or used alone (`--entropy` without `--subsample`: a soft entropy filter over the whole index, no size target).
+
+The first `phylo` run on a given index that uses `--entropy`/`--entropy-sd` pays a one-time extra cost (every candidate family's entropy has to be computed once, up front, and is then saved alongside the index). Every following run — even with different `MU`/`SIGMA` values — reuses that saved data and stays fast.
+
 ## Sankoff calibration and phylogenetic exports
 
 | Option | Default | Description |
@@ -129,6 +173,7 @@ Matrix layout (`_dist.csv`, `_shared.csv`, and every other "CSV matrix" below):
 | `<prefix>_rawsnp_counts.csv` | `--raw-snp-counts` | CSV table | per-pair diagnostic counts behind `_rawsnp.csv` |
 | `<prefix>_snp.fasta` | `--snp` | FASTA | SNP-only pseudo-alignment, IUPAC-coded |
 | `<prefix>_family_overlap.csv` | `--family-overlap` | CSV matrix | variable families both genomes of a pair carry a call for |
+| `<prefix>_shannon.csv` | `--shannon` | CSV table | per-family Shannon entropy, see "Sampling at scale" above |
 
 **`_siblings.csv`** — family size = number of distinct central bases observed at a family (1–4), not "sibling count" (0–3).
 
diff --git a/doc/404.html b/doc/404.html
index dbb8998f..4ef5f0fa 100644
--- a/doc/404.html
+++ b/doc/404.html
@@ -19,7 +19,7 @@
     
     
       
-        <title>obikmer</title>
+        <title>obikmer — User Guide</title>
       
     
     
@@ -71,7 +71,7 @@
 
 <header class="md-header md-header--shadow" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="/." title="obikmer" class="md-header__button md-logo" aria-label="obikmer" data-md-component="logo">
+    <a href="/." title="obikmer — User Guide" class="md-header__button md-logo" aria-label="obikmer — User Guide" data-md-component="logo">
       
   
   <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M12 8a3 3 0 0 0 3-3 3 3 0 0 0-3-3 3 3 0 0 0-3 3 3 3 0 0 0 3 3m0 3.54C9.64 9.35 6.5 8 3 8v11c3.5 0 6.64 1.35 9 3.54 2.36-2.19 5.5-3.54 9-3.54V8c-3.5 0-6.64 1.35-9 3.54"/></svg>
@@ -85,7 +85,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            obikmer
+            obikmer — User Guide
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -129,13 +129,13 @@
 
 <nav class="md-nav md-nav--primary" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="/." title="obikmer" class="md-nav__button md-logo" aria-label="obikmer" data-md-component="logo">
+    <a href="/." title="obikmer — User Guide" class="md-nav__button md-logo" aria-label="obikmer — User Guide" data-md-component="logo">
       
   
   <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M12 8a3 3 0 0 0 3-3 3 3 0 0 0-3-3 3 3 0 0 0-3 3 3 3 0 0 0 3 3m0 3.54C9.64 9.35 6.5 8 3 8v11c3.5 0 6.64 1.35 9 3.54 2.36-2.19 5.5-3.54 9-3.54V8c-3.5 0-6.64 1.35-9 3.54"/></svg>
 
     </a>
-    obikmer
+    obikmer — User Guide
   </label>
   
   <ul class="md-nav__list" data-md-scrollfix>
@@ -173,6 +173,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="/installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
     
     
     
@@ -182,10 +209,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
         
           
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
             
   
   
@@ -203,8 +230,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -221,7 +248,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/kmers/" class="md-nav__link">
+      <a href="/theory/kmers_and_superkmers/" class="md-nav__link">
         
   
   
@@ -277,14 +304,14 @@
   
   
     <li class="md-nav__item">
-      <a href="/theory/entropy/" class="md-nav__link">
+      <a href="/theory/entropy_filter/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Entropy filter
+    Low-complexity kmer filter
   
 
     
@@ -305,7 +332,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/theory/minimizer/" class="md-nav__link">
+      <a href="/theory/minimizer_selection/" class="md-nav__link">
         
   
   
@@ -333,460 +360,14 @@
   
   
     <li class="md-nav__item">
-      <a href="/theory/indexing/" class="md-nav__link">
+      <a href="/theory/indexing_architecture/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Partitioning architecture
-  
-
-    
-  </span>
-  
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-      </a>
-    </li>
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-      <a href="/implementation/superkmer/" class="md-nav__link">
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+      <a href="/usage/superkmer/" class="md-nav__link">
         
   
   
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-    Sequences
+    superkmer
   
 
     
@@ -889,14 +470,406 @@
   
   
     <li class="md-nav__item">
-      <a href="/architecture/index_architecture/" class="md-nav__link">
+      <a href="/usage/index_command/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
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@@ -917,6 +890,115 @@
   
 
     
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+  
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+  
+  
+    
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+    
+    
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+
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+            <span class="md-nav__icon md-icon"></span>
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+    
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+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
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+  
+    <li class="md-nav__item">
+      <a href="/architecture/" class="md-nav__link">
+        
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+  
+  <span class="md-ellipsis">
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+  
+    Architecture notes
+  
+
+    
+  </span>
+  
+  
+
+      </a>
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+  
+
+    
   </ul>
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                   </div>
diff --git a/doc/architecture/index.html b/doc/architecture/index.html
new file mode 100644
index 00000000..36e2f6f3
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@@ -0,0 +1,1271 @@
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+      <a href="../theory/entropy_filter/" class="md-nav__link">
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+  
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+
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+
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+    <li class="md-nav__item">
+      <a href="../usage/merge/" class="md-nav__link">
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+  
+
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+      <a href="../usage/query/" class="md-nav__link">
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+    annotate
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+  
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+      <a href="../usage/phylo/" class="md-nav__link">
+        
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+  
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+  </span>
+  
+  
+
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+      <a href="../usage/name-tree/" class="md-nav__link">
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+  
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
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+    
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+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
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+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
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+  <a href="#sequence-invariant" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Sequence invariant
+      
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+</li>
+      
+        <li class="md-nav__item">
+  <a href="#index-dimensioning" class="md-nav__link">
+    <span class="md-ellipsis">
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+        Index dimensioning
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+        <li class="md-nav__item">
+  <a href="#parallel-execution-and-numa-awareness" class="md-nav__link">
+    <span class="md-ellipsis">
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+      
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+      
+        <li class="md-nav__item">
+  <a href="#kmer-filtering-filter" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Kmer filtering (filter)
+      
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+  <a href="#sequence-invariant" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Sequence invariant
+      
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+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#index-dimensioning" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Index dimensioning
+      
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+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#parallel-execution-and-numa-awareness" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Parallel execution and NUMA awareness
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#kmer-filtering-filter" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Kmer filtering (filter)
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+
+<h1 id="architecture-notes-for-advanced-use">Architecture notes for advanced use</h1>
+<p>This page describes execution-level behavior relevant to sizing and running <code>obikmer</code> on large datasets or multi-socket machines. It complements the <a href="../formats/index_layout/">index format</a> and <a href="../theory/indexing_architecture/">theory</a> pages.</p>
+<h2 id="sequence-invariant">Sequence invariant</h2>
+<p>Every input sequence is treated purely as a compact representation of a set of overlapping kmers:</p>
+<ul>
+<li>Only the <code>A</code>/<code>C</code>/<code>G</code>/<code>T</code> alphabet (case-insensitive) is recognized; a sequence is cut at any other character (including IUPAC ambiguity codes), so runs containing them are not represented in the index.</li>
+<li>Sequences are internally processed in chunks of at most 256 nucleotides; a chunk shorter than k is dropped. This is invisible to the user beyond the ACGT-only, minimum-length-k constraints above.</li>
+<li>Kmers are always handled in canonical form (see <a href="../theory/encoding/">DNA encoding</a>), so the tool is strand-agnostic throughout: a kmer and its reverse complement are always the same entry.</li>
+</ul>
+<h2 id="index-dimensioning">Index dimensioning</h2>
+<p>An index directory is organized as <code>KmerIndex → partitions → layers</code>, with a canonical kmer belonging to exactly one (partition, layer) pair. This is what makes set operations (merge, filter, distance) parallel and coordination-free across partitions.</p>
+<ul>
+<li><strong>Partition count</strong> (<code>-p</code>/<code>--partitions</code>, rounded up to a power of 2) is the main dimensioning knob: more partitions means more independent parallel units and a smaller working set per partition, at the cost of more open files during construction.</li>
+<li><strong>Layers</strong> accumulate as an index grows through successive merges; per-partition query cost grows with the number of layers (worst case linear, expected constant since most kmer lookups resolve in the first layer they could plausibly be in).</li>
+<li>Genome columns (count or presence data) are kept at a consistent width across every layer and partition after a merge, which is what allows whole-index aggregate distances (Jaccard, Bray-Curtis, Euclidean, Hellinger, …) to be computed as a two-pass cascade (local partial sums per partition, then a global combination) with no double counting.</li>
+</ul>
+<h2 id="parallel-execution-and-numa-awareness">Parallel execution and NUMA awareness</h2>
+<p>Partition-level work (index construction, <code>merge</code>, <code>filter</code>, <code>reindex</code>, <code>select</code>, <code>phylo</code>'s sibling-annex/Sankoff computations) is dispatched by a partition runner that adapts to the machine's memory topology, detected automatically at startup via hwloc:</p>
+<ul>
+<li>On a multi-socket / multi-NUMA-node machine, one thread pool is pinned per NUMA node, and each partition is processed entirely by threads pinned to one node — keeping the memory a partition touches local to that node's DRAM. This matters because touching kmer data across NUMA nodes without pinning can degrade throughput by an order of magnitude or more on large multi-socket machines.</li>
+<li>On a single-socket machine, Apple Silicon, or if hwloc cannot report NUMA topology, all cores are treated as one node with no pinning and negligible overhead — this is the default behavior on macOS.</li>
+<li>Within a node, the number of active worker threads ramps up progressively rather than being fixed up front: it starts conservatively and grows in steps, but only as long as measured CPU efficiency or disk I/O throughput keeps improving. If neither improves after a growth step, the runner stops adding workers — avoiding oversubscription on stages that are memory-bandwidth-bound rather than CPU- or I/O-bound. Ramp speed scales with the number of cores per node, so a single-node machine ramps just as fast as a large multi-node one.</li>
+</ul>
+<p>No CLI flag controls this directly; it is fully automatic at runtime. NUMA-aware pinning can be compiled out (Cargo feature <code>numa</code>, on by default), in which case a plain global thread pool is used instead.</p>
+<h2 id="kmer-filtering-filter">Kmer filtering (<code>filter</code>)</h2>
+<p><a href="../usage/filter/"><code>filter</code></a> evaluates predicates against the genome metadata matrix directly whenever every active filter can be expressed as a column-level test (e.g. "any outgroup column non-zero"), producing a per-slot keep/drop decision without touching kmer sequence data at all. If any active filter cannot be expressed this way, evaluation falls back to a per-kmer, row-level check. Either way, the result is always written as a single, freshly compacted layer (<code>unitigs.bin</code> and the MPHF are rebuilt from the surviving kmers), never as an additional layer on top of the source index.</p>
+
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-<h1 id="query-system">Query system</h1>
-<h2 id="goal">Goal</h2>
-<p>Given a set of query sequences, determine for each sequence how many of its k-mers are found in the index and, for each indexed genome, how many k-mers match. The query system is the foundation for read classification and sequence-to-genome mapping.</p>
-<hr />
-<h2 id="input">Input</h2>
-<ul>
-<li>Query sequences in FASTA or FASTQ format (gzip supported, streaming stdin supported). GenBank flat files are not supported at query time (only at index time).</li>
-<li>Sequences shorter than k bases are silently skipped.</li>
-<li>Non-ACGT characters are handled by the superkmer decomposition layer: they act as hard breaks, producing shorter superkmers (identical to the behaviour at indexing time).</li>
-</ul>
-<hr />
-<h2 id="algorithm">Algorithm</h2>
-<p>The query follows the same superkmer-based partitioning strategy used at indexing time.</p>
-<div class="highlight"><pre><span></span><code>for each chunk of sequences (parallel workers via obipipeline):
-    build QueryBatch: decompose all sequences into s-mers via superkmers, deduplicate
-    allocate seq_results[seq_idx][smer_pos] = None  ← per-sequence s-mer result vectors
-    split superkmers by partition via minimiser hash
-    for each partition p:
-        query_partition(p, superkmers_routed_to_p)
-            → load QueryLayer(s) for p
-            → for each s-mer in each superkmer: MphfLayer::find(smer)
-        fill seq_results[seq_idx][kmer_offset + j] from partition results
-    for each sequence:
-        apply_findere(seq_results[seq_idx], effective_z)  ← per full sequence
-        accumulate confirmed k-mer results into acc and cov
-    emit annotated sequences
-</code></pre></div>
-<p>Superkmers that appear more than once in the batch (same sequence or across sequences) are deduplicated: each unique <code>RoutableSuperKmer</code> is queried once per partition, and the result is broadcast to every <code>SKDesc</code> entry that references it.</p>
-<p><strong>Findere requires full-sequence aggregation.</strong> <code>apply_findere</code> is applied once per sequence on the complete s-mer result vector, after all partitions have contributed. Applying it per superkmer would produce false negatives at superkmer boundaries, where the z-window spans two superkmers.</p>
-<p>Batches are processed in parallel via <code>obipipeline</code> workers; the <code>--threads</code> flag controls the number of worker threads.</p>
-<hr />
-<h2 id="findere-z-window-filter">Findere z-window filter</h2>
-<p>For approximate index modes, the index physically stores s-mers of size <code>s = k_user − z + 1</code>. At query time, <code>set_k(s)</code> is in effect, so queries naturally produce s-mer results. <code>apply_findere</code> then aggregates z consecutive s-mer results into one k_user-mer answer:</p>
-<div class="highlight"><pre><span></span><code><span class="k">fn</span><span class="w"> </span><span class="nf">apply_findere</span><span class="p">(</span>
-<span class="w">    </span><span class="n">results</span><span class="p">:</span><span class="w"> </span><span class="kp">&amp;</span><span class="p">[</span><span class="nb">Option</span><span class="o">&lt;</span><span class="nb">Box</span><span class="o">&lt;</span><span class="p">[</span><span class="kt">u32</span><span class="p">]</span><span class="o">&gt;&gt;</span><span class="p">],</span><span class="w">  </span><span class="c1">// N s-mer results</span>
-<span class="w">    </span><span class="n">z</span><span class="p">:</span><span class="w"> </span><span class="kt">usize</span><span class="p">,</span>
-<span class="w">    </span><span class="n">n_genomes</span><span class="p">:</span><span class="w"> </span><span class="kt">usize</span><span class="p">,</span>
-<span class="p">)</span><span class="w"> </span><span class="p">-&gt;</span><span class="w"> </span><span class="nb">Vec</span><span class="o">&lt;</span><span class="nb">Option</span><span class="o">&lt;</span><span class="nb">Box</span><span class="o">&lt;</span><span class="p">[</span><span class="kt">u32</span><span class="p">]</span><span class="o">&gt;&gt;&gt;</span><span class="w">         </span><span class="c1">// N − z + 1 k_user-mer results</span>
-</code></pre></div>
-<p>Input length N (s-mers), output length N − z + 1 (k_user-mers).</p>
-<p>For each genome g independently, a sliding window of size z scans the input. Output position i is confirmed for genome g iff all z values <code>results[i..i+z][g]</code> are nonzero (<code>None</code> counts as zero for all genomes). The scan is O(n) per genome.</p>
-<p>Output values come from <code>results[i]</code> (leftmost s-mer of each window); genomes not confirmed are zeroed. If all genomes are zero, the position is returned as <code>None</code>.</p>
-<p><strong>Short sequences</strong>: when the s-mer count is less than z, no complete window can form — <code>apply_findere</code> returns an empty vector. K-mers from sequences shorter than k_user are not emitted.</p>
-<p><strong>Exact indexes</strong>: <code>z = 1</code>, <code>apply_findere</code> is a passthrough (output length = input length).</p>
-<h3 id="effective-z-at-query-time">Effective z at query time</h3>
-<p><code>effective_z</code> is resolved at the start of <code>run()</code>:</p>
-<div class="highlight"><pre><span></span><code><span class="kd">let</span><span class="w"> </span><span class="n">effective_z</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">args</span><span class="p">.</span><span class="n">findere_z</span><span class="p">.</span><span class="n">unwrap_or_else</span><span class="p">(</span><span class="o">||</span><span class="w"> </span><span class="k">match</span><span class="w"> </span><span class="n">idx</span><span class="p">.</span><span class="n">meta</span><span class="p">().</span><span class="n">config</span><span class="p">.</span><span class="n">evidence</span><span class="w"> </span><span class="p">{</span>
-<span class="w">    </span><span class="n">IndexMode</span><span class="p">::</span><span class="n">Approx</span><span class="w"> </span><span class="p">{</span><span class="w"> </span><span class="n">z</span><span class="p">,</span><span class="w"> </span><span class="o">..</span><span class="w"> </span><span class="p">}</span><span class="w"> </span><span class="o">|</span><span class="w"> </span><span class="n">IndexMode</span><span class="p">::</span><span class="n">Hybrid</span><span class="w"> </span><span class="p">{</span><span class="w"> </span><span class="n">z</span><span class="p">,</span><span class="w"> </span><span class="o">..</span><span class="w"> </span><span class="p">}</span><span class="w"> </span><span class="o">=&gt;</span><span class="w"> </span><span class="n">z</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="kt">usize</span><span class="p">,</span>
-<span class="w">    </span><span class="n">IndexMode</span><span class="p">::</span><span class="n">Exact</span><span class="w"> </span><span class="o">=&gt;</span><span class="w"> </span><span class="mi">1</span><span class="p">,</span>
-<span class="p">});</span>
-</code></pre></div>
-<p>The <code>-z</code> CLI option overrides the index metadata value. A higher z increases stringency (lower FP, some true positives may be discarded at sequence ends); a lower z increases sensitivity.</p>
-<hr />
-<h2 id="layer-lookup-mphflayerfind">Layer lookup: <code>MphfLayer::find</code></h2>
-<p><code>MphfLayer::open(dir, mode: &amp;IndexMode)</code> receives the mode from <code>PartitionMeta</code> — no per-layer file is read. The caller (<code>QueryLayer</code>) never chooses the dispatch path: it is fixed at open time by <code>LayerEvidence</code>. See <a href="../../implementation/obilayeredmap/">obilayeredmap</a> for the full <code>find</code> / <code>find_strict</code> API.</p>
-<h3 id="querylayer-variant-selection"><code>QueryLayer</code> variant selection</h3>
-<p><code>QueryLayer::open</code> in <code>query_layer.rs</code> selects the data matrix to pair with <code>MphfLayer</code>:</p>
-<table>
-<thead>
-<tr>
-<th>Condition</th>
-<th>Variant</th>
-<th>Data returned per k-mer</th>
-</tr>
-</thead>
-<tbody>
-<tr>
-<td><code>with_counts=true</code> and <code>counts/</code> exists</td>
-<td><code>Count</code></td>
-<td>raw count per genome</td>
-</tr>
-<tr>
-<td><code>presence/</code> exists</td>
-<td><code>Presence</code></td>
-<td>0/1 per genome (bit matrix)</td>
-</tr>
-<tr>
-<td>only <code>counts/</code> exists</td>
-<td><code>Count</code></td>
-<td>counts used as-is</td>
-</tr>
-<tr>
-<td>neither exists</td>
-<td><code>SetOnly</code></td>
-<td>1 for every genome</td>
-</tr>
-</tbody>
-</table>
-<hr />
-<h2 id="presence-count-mode-at-query-time">Presence / count mode at query time</h2>
-<p>The <code>--force-presence</code> flag and <code>--presence-threshold</code> control how per-genome values are accumulated, independently of what the index stores:</p>
-<div class="highlight"><pre><span></span><code>genome_totals[g] += if presence { u32::from(v &gt;= threshold) } else { v }
-</code></pre></div>
-<p><code>presence</code> is true when <code>--force-presence</code> is set or when the index has no counts (<code>!with_counts</code>). The default <code>presence_threshold</code> is 1, so any nonzero count counts as a match.</p>
-<hr />
-<h2 id="coverage-vectors-detail">Coverage vectors (<code>--detail</code>)</h2>
-<p>When <code>--detail</code> is requested, a 3-D accumulator <code>cov[seq_idx][genome][kmer_pos]</code> is allocated after all partitions are queried, with dimensions derived from <code>n_kmers_out = n_smers − z + 1</code> (k_user-mer positions, not s-mer positions):</p>
-<div class="highlight"><pre><span></span><code>cov[seq_idx][g][pos] += contribution
-where pos is the k_user-mer index in the filtered (post-Findere) vector
-</code></pre></div>
-<p>Coverage reflects confirmed k_user-mers only. The vectors are emitted in the JSON annotation under the key <code>"coverage"</code>.</p>
-<hr />
-<h2 id="kmer_missing-semantics"><code>kmer_missing</code> semantics</h2>
-<p><code>kmer_missing</code> counts k_user-mer positions where the first s-mer (<code>seq_results[seq_idx][pos]</code>) is <code>None</code> — i.e. absent from the index entirely. K-mers where the z-window fails because a later s-mer is absent or zero are not counted as missing (the first s-mer being present is used as proxy for index membership).</p>
-<hr />
-<h2 id="output-format">Output format</h2>
-<p>Output sequences are written in <strong>OBITools4 format</strong>: the original sequence with a JSON annotation map in the title line.</p>
-<div class="highlight"><pre><span></span><code>&gt;read_id {&quot;kmer_count&quot;:59,&quot;kmer_strict_matches&quot;:{&quot;genome_a&quot;:42,&quot;genome_b&quot;:7}}
-ATCGATCG...
-</code></pre></div>
-<p>With <code>--detail</code>:</p>
-<div class="highlight"><pre><span></span><code>&gt;read_id {&quot;kmer_count&quot;:59,&quot;kmer_strict_matches&quot;:{...},&quot;coverage&quot;:{&quot;genome_a&quot;:[0,1,2,...],...}}
-ATCGATCG...
-</code></pre></div>
-<p>Genome keys follow the iteration order of <code>meta.genomes</code>.</p>
-<hr />
-<h2 id="annotation-schema">Annotation schema</h2>
-<table>
-<thead>
-<tr>
-<th>Key</th>
-<th>Type</th>
-<th>Condition</th>
-<th>Semantics</th>
-</tr>
-</thead>
-<tbody>
-<tr>
-<td><code>kmer_count</code></td>
-<td>int</td>
-<td>always</td>
-<td>k-mers confirmed (post-Findere) with at least one genome match</td>
-</tr>
-<tr>
-<td><code>kmer_missing</code></td>
-<td>int</td>
-<td><code>--count-missing</code></td>
-<td>k-mers absent from the index entirely (pre-Findere None)</td>
-</tr>
-<tr>
-<td><code>kmer_strict_matches</code></td>
-<td>object</td>
-<td>always</td>
-<td>per-genome accumulated value (label → count or 0/1)</td>
-</tr>
-<tr>
-<td><code>coverage</code></td>
-<td>object</td>
-<td><code>--detail</code></td>
-<td>per-genome array of per-position contributions (label → [u32])</td>
-</tr>
-</tbody>
-</table>
-<p><code>kmer_count + kmer_missing</code> ≤ total k_user-mers in the sequence. The gap corresponds to k_user-mers whose z-window was not fully confirmed (at least one s-mer absent or zero for all genomes) but whose first s-mer was present in the index.</p>
-<hr />
-<h2 id="cli">CLI</h2>
-<div class="highlight"><pre><span></span><code>obikmer query &lt;index&gt; [--detail] [--mismatch] [--count-missing]
-              [--force-presence] [--presence-threshold &lt;n&gt;]
-              [-z &lt;z&gt;] [-T &lt;threads&gt;]
-              &lt;query.fa&gt; [&lt;query2.fa&gt; ...]
-</code></pre></div>
-<table>
-<thead>
-<tr>
-<th>Option</th>
-<th>Default</th>
-<th>Semantics</th>
-</tr>
-</thead>
-<tbody>
-<tr>
-<td><code>-z</code> / <code>--findere-z</code></td>
-<td>from index metadata</td>
-<td>Override Findere z parameter</td>
-</tr>
-<tr>
-<td><code>--detail</code></td>
-<td>off</td>
-<td>Emit per-position coverage vectors in JSON</td>
-</tr>
-<tr>
-<td><code>--count-missing</code></td>
-<td>off</td>
-<td>Add <code>kmer_missing</code> field to JSON</td>
-</tr>
-<tr>
-<td><code>--force-presence</code></td>
-<td>off</td>
-<td>Report 0/1 per genome regardless of index counts</td>
-</tr>
-<tr>
-<td><code>--presence-threshold</code></td>
-<td>1</td>
-<td>Minimum count to declare genome present</td>
-</tr>
-<tr>
-<td><code>-T</code> / <code>--threads</code></td>
-<td>all CPUs</td>
-<td>Worker threads</td>
-</tr>
-</tbody>
-</table>
-<p><code>--mismatch</code> is accepted but currently ignored with a warning on stderr.</p>
-<hr />
-<h2 id="future-work">Future work</h2>
-<ul>
-<li><strong><code>--mismatch</code></strong>: 1-mismatch approximate matching — generate <code>3·k</code> single-substitution variants per k-mer, look each up independently.</li>
-<li><strong>Read classification</strong> (<code>--classify</code>): assign each read to the genome with the highest match score.</li>
-<li><strong>Whitelist / blacklist filtering</strong>: threshold-based accept/reject on per-genome match scores.</li>
-</ul>
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+
+
+
+<h1 id="index-construction-and-on-disk-layout">Index construction and on-disk layout</h1>
+<h2 id="construction-pipeline">Construction pipeline</h2>
+<p>Building an index (<a href="../../usage/index_command/"><code>index</code></a>) proceeds through a fixed sequence of phases, each operating independently per partition (see <a href="../../theory/indexing_architecture/">Partitioning and indexing architecture</a>):</p>
+<ol>
+<li><strong>Scatter.</strong> A single streaming pass over the input. Each sequence fragment is cut at non-ACGT bases, passed through the low-complexity entropy filter (see <a href="../../theory/entropy_filter/">Low-complexity kmer filter</a>), and any resulting segment shorter than k is dropped. Surviving segments are decomposed into super-kmers, canonicalized, and routed by <code>hash(minimizer) mod n_partitions</code> into one file per partition.</li>
+<li><strong>Dereplication.</strong> Within each partition, identical super-kmer sequences are merged and their occurrence counts summed. This count is per super-kmer, not per kmer — a kmer's true abundance is the sum of the counts of every super-kmer containing it.</li>
+<li><strong>Exact counting.</strong> Every kmer in every dereplicated super-kmer is enumerated and its exact total count computed. A per-genome kmer frequency spectrum is produced at this stage.</li>
+<li><strong>Quorum filtering.</strong> Kmers outside the <code>--min-abundance</code>/<code>--max-abundance</code> range are dropped, and super-kmers are recompacted around the surviving kmer set.</li>
+<li><strong>Local assembly.</strong> The surviving kmers of each partition are assembled into unitigs — maximal non-branching runs of a local de Bruijn graph — such that every kmer appears exactly once, at one (unitig, offset) location.</li>
+<li><strong>MPHF and evidence construction.</strong> A minimal perfect hash function is built over the canonical kmers of each partition, together with the evidence structure needed to verify that a queried kmer was genuinely indexed (see below). Per-genome counts or presence bits are recorded alongside if requested.</li>
+</ol>
+<p>Phases 1–5 are independent per partition and run in parallel; phase 6 finalizes each partition once its kmer set is fixed.</p>
+<h2 id="minimal-perfect-hash-function-mphf">Minimal perfect hash function (MPHF)</h2>
+<p>Each partition's surviving kmers are mapped to a dense range of integer slots by a minimal perfect hash function: no collisions, near-optimal space (a few bits per key), O(1) lookup. Because an MPHF maps <em>any</em> input to some slot — including kmers that were never indexed — a lookup alone cannot distinguish a genuinely indexed kmer from an arbitrary one; every lookup is followed by an evidence check.</p>
+<h2 id="evidence-exact-vs-approximate">Evidence: exact vs. approximate</h2>
+<p>Two verification modes are available, selected at build time (<code>index --approx</code>) and convertible afterwards (<a href="../../usage/reindex/"><code>reindex</code></a>):</p>
+<ul>
+<li><strong>Exact</strong> (default): the hashed slot stores a pointer back into the partition's unitig data. At query time the kmer is reconstructed from that location and compared directly to the query. Zero false positives, at the cost of one extra random read per lookup.</li>
+<li><strong>Approximate</strong> (<code>--approx</code>): the slot stores a short fingerprint (<code>--evidence-bits</code> bits) instead of a pointer; verification is a single fingerprint comparison. This trades a small, bounded false-positive rate (<span class="arithmatex">\(1/2^b\)</span> per kmer, reduced further to about <span class="arithmatex">\(1/2^{b \cdot z}\)</span> for a read requiring <span class="arithmatex">\(z\)</span> consecutive matching kmers via the <code>-z</code>/<code>--findere-z</code> parameter) for lower memory and disk usage, since no reconstruction index is needed. See <a href="../../usage/estimate/"><code>estimate</code></a> to explore this trade-off before building.</li>
+</ul>
+<h2 id="on-disk-layout">On-disk layout</h2>
+<div class="highlight"><pre><span></span><code>&lt;index_root&gt;/
+  index.meta                    global configuration (k, minimizer size, partition count,
+                                 evidence mode, whether counts are stored) and genome list/metadata
+  scatter.done / count.done / index.done      build-progress sentinels
+  spectrums/&lt;label&gt;.json        per-genome kmer frequency histogram
+  partitions/
+    part_00000/ ... part_NNNNN/
+      index/
+        meta.json                number of layers in this partition
+        layer_0/
+          unitigs.bin             reconstructible kmer sequence data — always kept
+          unitigs.bin.idx         random-access index into unitigs.bin (exact evidence only)
+          mphf.bin                 the minimal perfect hash function
+          evidence.bin              exact evidence (exact mode only)
+          fingerprint.bin           approximate evidence (approximate mode only)
+          counts/                   per-genome kmer counts (if counts were requested)
+          presence/                 per-genome presence/absence bits
+        layer_1/, layer_2/, ...     added by later merges, same internal structure
+</code></pre></div>
+<p><code>unitigs.bin</code> is the only file from which the indexed kmer content can be fully recovered; it is always retained. Every other file (MPHF, evidence, counts) is derived from it.</p>
+<p>A <strong>layer</strong> corresponds to one increment of kmer content added to a partition — most commonly, one <a href="../../usage/merge/"><code>merge</code></a> operation that introduces kmers not already present in the index. Genomes already present in the index simply gain new columns in the existing layers' count/presence data; only genuinely new kmer content is assembled into a new layer. Because of this, merging cost scales with the novel kmer content being added, not with the accumulated size of the index. A query against an index with several layers checks each layer's MPHF in turn.</p>
+<p>Sources merged together must share the same kmer size, minimizer size, partition count, and evidence mode (including matching approximate-mode parameters); mismatches are rejected rather than silently reconciled — <a href="../../usage/reindex/"><code>reindex</code></a> one of the sources first if needed.</p>
+<p><code>obikmer pack</code> consolidates a partition's per-column files (counts/presence) into a single file, reducing the number of file opens needed at query time.</p>
+
+
+
+
+
+
+
+
+
+
+
+
+                
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diff --git a/doc/index.html b/doc/index.html
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+  <span class="md-ellipsis">
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+  
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+  
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+          </label>
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
+            <span class="md-nav__icon md-icon"></span>
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+          <ul class="md-nav__list" data-md-scrollfix>
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+      <a href="formats/index_layout/" class="md-nav__link">
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+  
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-  <a href="#subcommands" class="md-nav__link">
+  <a href="#core-principles" class="md-nav__link">
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+        Core principles
       
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   </a>
@@ -1064,10 +1157,10 @@
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-  <a href="#constraints" class="md-nav__link">
+  <a href="#commands" class="md-nav__link">
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+        Commands
       
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   </a>
@@ -1075,10 +1168,32 @@
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+  <a href="#further-reading" class="md-nav__link">
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+        Further reading
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+  <a href="#input-formats" class="md-nav__link">
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+        Parameter constraints
       
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@@ -1125,81 +1229,100 @@
 
 
 <h1 id="obikmer">obikmer</h1>
-<p><code>obikmer</code> is a Rust tool for manipulation, counting, indexing, and set operations on DNA sequences represented as kmer sets.</p>
-<h2 id="subcommands">Subcommands</h2>
+<p><code>obikmer</code> is a command-line tool for counting, indexing, querying and comparing DNA sequences represented as kmer sets. It targets individual genome datasets of tens of gigabases, with an emphasis on computational, memory, and disk efficiency.</p>
+<p>All functionality is exposed through a single binary, <code>obikmer</code>, organized as subcommands.</p>
+<h2 id="core-principles">Core principles</h2>
+<ul>
+<li>Kmers are of fixed, odd length <span class="arithmatex">\(k\)</span>, chosen at index-construction time in the range <span class="arithmatex">\([11, 31]\)</span> (see <a href="theory/kmers_and_superkmers/">Kmers and super-kmers</a>).</li>
+<li>Each kmer fits in a 64-bit word using a 2-bit-per-base encoding (see <a href="theory/encoding/">DNA encoding</a>).</li>
+<li>Kmers are handled in <strong>canonical form</strong> (<span class="arithmatex">\(\text{canonical}(kmer) = \min(kmer, \text{revcomp}(kmer))\)</span>), making counting strand-independent.</li>
+<li>Sequences are decomposed into <strong>super-kmers</strong> before storage, anchored on a hash-selected <strong>minimizer</strong> (see <a href="theory/minimizer_selection/">Minimizer selection</a>), then routed to one of several <strong>partitions</strong> for parallel, memory-bounded processing (see <a href="theory/indexing_architecture/">Partitioning and indexing architecture</a>).</li>
+<li>Low-complexity kmers can be filtered out at index-construction time using an entropy-based score (see <a href="theory/entropy_filter/">Low-complexity kmer filter</a>).</li>
+</ul>
+<h2 id="commands">Commands</h2>
 <table>
 <thead>
 <tr>
-<th>Subcommand</th>
+<th>Command</th>
 <th>Purpose</th>
 </tr>
 </thead>
 <tbody>
 <tr>
-<td><code>superkmer</code></td>
-<td>Extract super-kmers from a sequence file and write to stdout</td>
+<td><a href="usage/superkmer/"><code>superkmer</code></a></td>
+<td>Extract super-kmers from a sequence file and write them to stdout</td>
 </tr>
 <tr>
-<td><code>index</code></td>
-<td>Build a complete genome index (scatter → dereplicate → count → layered MPHF)</td>
+<td><a href="usage/index_command/"><code>index</code></a></td>
+<td>Build a genome index</td>
 </tr>
 <tr>
-<td><code>merge</code></td>
-<td>Merge multiple built indexes into one</td>
+<td><a href="usage/merge/"><code>merge</code></a></td>
+<td>Merge multiple indexes into one</td>
 </tr>
 <tr>
-<td><code>rebuild</code></td>
-<td>Filter and compact an existing index into a new single-layer index; supports ingroup/outgroup predicates on genome metadata</td>
+<td><a href="usage/filter/"><code>filter</code></a></td>
+<td>Retain only kmers matching ingroup/outgroup predicates</td>
 </tr>
 <tr>
-<td><code>query</code></td>
+<td><a href="usage/select/"><code>select</code></a></td>
+<td>Project and/or aggregate genome columns of an index</td>
+</tr>
+<tr>
+<td><a href="usage/query/"><code>query</code></a></td>
 <td>Query an index with sequences and annotate matches</td>
 </tr>
 <tr>
-<td><code>dump</code></td>
-<td>Dump all indexed k-mers as CSV (kmer + per-genome counts or presence); supports the same ingroup/outgroup filtering as <code>rebuild</code></td>
+<td><a href="usage/dump/"><code>dump</code></a></td>
+<td>Dump indexed kmers as CSV</td>
 </tr>
 <tr>
-<td><code>annotate</code></td>
-<td>Add or update genome metadata from a CSV file; or dump metadata as CSV</td>
+<td><a href="usage/annotate/"><code>annotate</code></a></td>
+<td>Add, update, or dump genome metadata</td>
 </tr>
 <tr>
-<td><code>distance</code></td>
-<td>Compute pairwise distance matrix between genomes; optionally build NJ/UPGMA trees</td>
+<td><a href="usage/phylo/"><code>phylo</code></a></td>
+<td>Compute pairwise evolutionary-distance proxies, trees, and phylogenetic exports</td>
 </tr>
 <tr>
-<td><code>unitig</code></td>
-<td>Build a global de Bruijn graph across all partitions and enumerate its unitigs as FASTA; supports the same ingroup/outgroup filtering as <code>rebuild</code></td>
+<td><a href="usage/name-tree/"><code>name-tree</code></a></td>
+<td>Translate a TNT/PhyG numeric-label tree export back to real taxon names</td>
 </tr>
 <tr>
-<td><code>estimate</code></td>
-<td>Estimate approximate-index parameters (z, evidence bits, FP rates) before indexing</td>
+<td><a href="usage/unitig/"><code>unitig</code></a></td>
+<td>Dump the unitigs of an index as FASTA</td>
 </tr>
 <tr>
-<td><code>reindex</code></td>
-<td>Convert an index's evidence in-place: exact ↔ approx</td>
+<td><a href="usage/estimate/"><code>estimate</code></a></td>
+<td>Estimate approximate-index parameters before indexing</td>
 </tr>
 <tr>
-<td><code>utils</code></td>
-<td>Miscellaneous index utilities: <code>--new-label NEW=OLD</code> renames a genome label; <code>--upgrade-index</code> adds missing <code>layer_meta.json</code> to old indexes</td>
+<td><a href="usage/reindex/"><code>reindex</code></a></td>
+<td>Convert an index's evidence representation (exact ↔ approximate)</td>
 </tr>
 <tr>
-<td><code>pack</code></td>
-<td>Pack per-column matrix files into single-file format to reduce query I/O</td>
+<td><a href="usage/utils/"><code>utils</code></a></td>
+<td>Miscellaneous index maintenance and inspection utilities</td>
+</tr>
+<tr>
+<td><a href="usage/pack/"><code>pack</code></a></td>
+<td>Pack per-column matrix files into a single-file format</td>
 </tr>
 </tbody>
 </table>
-<h2 id="constraints">Constraints</h2>
+<p>See <a href="usage/predicates/">Genome predicates and taxonomy paths</a> for the selection language shared by <code>filter</code>, <code>select</code>, <code>dump</code>, and <code>unitig</code>.</p>
+<h2 id="further-reading">Further reading</h2>
 <ul>
-<li>Target scale: individual genome datasets, tens of Gbases</li>
-<li>Maximum efficiency in computation, memory, and disk usage</li>
-<li>k odd, k ∈ [11, 31], fixed at runtime; kmer fits in a u64 (2 bits/base)</li>
-<li>Canonical form: <code>min(kmer, revcomp(kmer))</code> reduces strand-symmetric space by half</li>
-<li>Input formats for <code>index</code>/<code>superkmer</code>: FASTA (<code>.fa</code>, <code>.fasta</code>), FASTQ (<code>.fq</code>, <code>.fastq</code>), GenBank flat file (<code>.gb</code>, <code>.gbk</code>, <code>.gbff</code>), all optionally gzip-compressed; directories expanded recursively; streaming stdin via <code>-</code></li>
-<li>Input formats for <code>query</code>: FASTA, FASTQ, optionally gzip-compressed; streaming stdin via <code>-</code></li>
+<li><a href="formats/index_layout/">Index construction and on-disk layout</a></li>
+<li><a href="architecture/">Architecture notes for advanced use</a> — parallel execution, NUMA awareness, index dimensioning</li>
 </ul>
-<h2 id="parameter-constraints-enforced-at-cli">Parameter constraints (enforced at CLI)</h2>
-<p>All constraints below are checked by <code>CommonArgs::validate()</code> at the start of <code>superkmer</code> and <code>index</code>. Invalid values exit immediately with an error.</p>
+<h2 id="input-formats">Input formats</h2>
+<ul>
+<li><code>superkmer</code> and <code>index</code>: FASTA (<code>.fa</code>, <code>.fasta</code>), FASTQ (<code>.fq</code>, <code>.fastq</code>), GenBank flat file (<code>.gb</code>, <code>.gbk</code>, <code>.gbff</code>), all optionally gzip-compressed; directories are expanded recursively; streaming stdin via <code>-</code> or when no input path is given.</li>
+<li><code>query</code>: FASTA or FASTQ, optionally gzip-compressed; streaming stdin the same way.</li>
+</ul>
+<h2 id="parameter-constraints">Parameter constraints</h2>
+<p>These constraints are checked at startup; an invalid value exits immediately with an error.</p>
 <table>
 <thead>
 <tr>
@@ -1210,34 +1333,24 @@
 </thead>
 <tbody>
 <tr>
-<td>k (<code>--kmer-size</code>)</td>
-<td>odd</td>
-<td>even k allows palindromic k-mers: kmer == revcomp(kmer), breaking the canonical form invariant</td>
+<td><span class="arithmatex">\(k\)</span> (<code>--kmer-size</code>)</td>
+<td>odd, <span class="arithmatex">\(k \in [11, 31]\)</span></td>
+<td>odd length guarantees the canonical form is always well defined; the range keeps a kmer within a 64-bit word while retaining specificity</td>
 </tr>
 <tr>
-<td>k (<code>--kmer-size</code>)</td>
-<td>k ∈ [11, 31]</td>
-<td>k &gt; 31 overflows u64 at 2 bits/base; k &lt; 11 gives insufficient specificity</td>
+<td><span class="arithmatex">\(m\)</span> (<code>--minimizer-size</code>)</td>
+<td>odd, <span class="arithmatex">\(3 \le m \le k-1\)</span></td>
+<td>same palindrome argument as <span class="arithmatex">\(k\)</span>; must be strictly shorter than the kmer</td>
 </tr>
 <tr>
-<td>m (<code>--minimizer-size</code>)</td>
-<td>odd</td>
-<td>same palindrome argument as k</td>
-</tr>
-<tr>
-<td>m (<code>--minimizer-size</code>)</td>
-<td>3 ≤ m ≤ k−1</td>
-<td>minimizer must be strictly shorter than the kmer</td>
-</tr>
-<tr>
-<td>z (<code>-z</code>, Findere, <code>index --approx</code> only)</td>
-<td>z ≤ k−1</td>
-<td>effective indexed kmer size is k−z+1; z ≥ k would make it ≤ 0</td>
+<td><span class="arithmatex">\(z\)</span> (<code>-z</code>, approximate evidence only)</td>
+<td><span class="arithmatex">\(z \le k-1\)</span></td>
+<td>the effective indexed kmer size is <span class="arithmatex">\(k-z+1\)</span></td>
 </tr>
 </tbody>
 </table>
 <h2 id="genome-label-constraints">Genome label constraints</h2>
-<p>Genome labels are arbitrary Unicode strings with the following restrictions:</p>
+<p>Genome labels are arbitrary Unicode strings, with the following restrictions:</p>
 <table>
 <thead>
 <tr>
@@ -1255,7 +1368,7 @@
 <tr>
 <td><code>=</code></td>
 <td>yes</td>
-<td><code>--new-label</code> parser separator</td>
+<td>separator used by <code>--new-label</code></td>
 </tr>
 <tr>
 <td><code>\0</code></td>
@@ -1263,24 +1376,18 @@
 <td>null byte</td>
 </tr>
 <tr>
-<td><code>\n</code> <code>\r</code> <code>\t</code></td>
+<td><code>\n</code>, <code>\r</code>, <code>\t</code></td>
 <td>yes</td>
-<td>break CSV output</td>
+<td>would break CSV output</td>
 </tr>
 <tr>
 <td>spaces</td>
-<td><strong>allowed</strong></td>
-<td>use shell quoting: <code>--new-label 'new label=old label'</code></td>
+<td>allowed</td>
+<td>quote in the shell, e.g. <code>--new-label 'new label=old label'</code></td>
 </tr>
 </tbody>
 </table>
-<p>Empty labels are also rejected. Labels derived automatically from the index directory name (when <code>--label</code> is omitted) are not validated since they come from the filesystem and are already safe.</p>
-<h2 id="priority-operations">Priority operations</h2>
-<ul>
-<li>Kmer counting (frequencies)</li>
-<li>Fast search / query</li>
-<li>Set operations: union, intersection, difference</li>
-</ul>
+<p>Empty labels are rejected. A label derived automatically from the input file name (when <code>--label</code> is omitted) is not validated, since it is already filesystem-safe.</p>
 
 
 
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+  <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M12 8a3 3 0 0 0 3-3 3 3 0 0 0-3-3 3 3 0 0 0-3 3 3 3 0 0 0 3 3m0 3.54C9.64 9.35 6.5 8 3 8v11c3.5 0 6.64 1.35 9 3.54 2.36-2.19 5.5-3.54 9-3.54V8c-3.5 0-6.64 1.35-9 3.54"/></svg>
+
+    </a>
+    obikmer — User Guide
+  </label>
+  
+  <ul class="md-nav__list" data-md-scrollfix>
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href=".." class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Home
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+    
+  
+  
+  
+    <li class="md-nav__item md-nav__item--active">
+      
+      <input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
+      
+      
+        
+      
+      
+        <label class="md-nav__link md-nav__link--active" for="__toc">
+          
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+          <span class="md-nav__icon md-icon"></span>
+        </label>
+      
+      <a href="./" class="md-nav__link md-nav__link--active">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+      
+        
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+    
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#prerequisites" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Prerequisites
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Prerequisites">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#rust-toolchain" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Rust toolchain
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#c-build-environment-required-for-hwloc" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        C build environment (required for hwloc)
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="C build environment (required for hwloc)">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#linux-debianubuntu" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Linux (Debian/Ubuntu)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#linux-rhelrockyalmalinux" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Linux (RHEL/Rocky/AlmaLinux)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#hpc-clusters" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        HPC clusters
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#macos" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        macOS
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#building" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Building
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Building">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#building-on-hpc-clusters-network-filesystems" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Building on HPC clusters (network filesystems)
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#numa-support" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        NUMA support
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#verifying-the-installation" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Verifying the installation
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        
+          
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+            
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Theory
+  
+
+    
+  </span>
+  
+  
+
+            <span class="md-nav__icon md-icon"></span>
+          </label>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            
+  
+    Theory
+  
+
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../theory/kmers_and_superkmers/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmers and super-kmers
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../theory/encoding/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    DNA encoding
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../theory/entropy_filter/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Low-complexity kmer filter
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../theory/minimizer_selection/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Minimizer selection
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../theory/indexing_architecture/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Partitioning and indexing architecture
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        
+          
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+            
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Usage
+  
+
+    
+  </span>
+  
+  
+
+            <span class="md-nav__icon md-icon"></span>
+          </label>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
+            <span class="md-nav__icon md-icon"></span>
+            
+  
+    Usage
+  
+
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../usage/superkmer/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    superkmer
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../usage/index_command/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    index
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../usage/merge/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    merge
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../usage/filter/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    filter
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../usage/select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    select
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../usage/query/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    query
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../usage/dump/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    dump
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../usage/annotate/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    annotate
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../usage/phylo/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    phylo
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../usage/name-tree/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    name-tree
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../usage/unitig/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    unitig
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../usage/estimate/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    estimate
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../usage/reindex/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    reindex
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../usage/utils/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    utils
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../usage/pack/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    pack
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../usage/predicates/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Predicates and taxonomy paths
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
+            
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Formats
+  
+
+    
+  </span>
+  
+  
+
+            <span class="md-nav__icon md-icon"></span>
+          </label>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
+            <span class="md-nav__icon md-icon"></span>
+            
+  
+    Formats
+  
+
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../formats/index_layout/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Index construction and on-disk layout
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../architecture/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Architecture notes
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+    
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#prerequisites" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Prerequisites
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Prerequisites">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#rust-toolchain" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Rust toolchain
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#c-build-environment-required-for-hwloc" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        C build environment (required for hwloc)
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="C build environment (required for hwloc)">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#linux-debianubuntu" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Linux (Debian/Ubuntu)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#linux-rhelrockyalmalinux" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Linux (RHEL/Rocky/AlmaLinux)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#hpc-clusters" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        HPC clusters
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#macos" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        macOS
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#building" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Building
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Building">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#building-on-hpc-clusters-network-filesystems" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Building on HPC clusters (network filesystems)
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#numa-support" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        NUMA support
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#verifying-the-installation" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Verifying the installation
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+
+<h1 id="installation">Installation</h1>
+<h2 id="prerequisites">Prerequisites</h2>
+<h3 id="rust-toolchain">Rust toolchain</h3>
+<p><code>obikmer</code> requires <strong>Rust 1.85 or later</strong> (edition 2024). Install or update via <a href="https://rustup.rs">rustup</a>:</p>
+<div class="highlight"><pre><span></span><code>curl<span class="w"> </span>--proto<span class="w"> </span><span class="s1">&#39;=https&#39;</span><span class="w"> </span>--tlsv1.2<span class="w"> </span>-sSf<span class="w"> </span>https://sh.rustup.rs<span class="w"> </span><span class="p">|</span><span class="w"> </span>sh
+rustup<span class="w"> </span>update<span class="w"> </span>stable
+</code></pre></div>
+<h3 id="c-build-environment-required-for-hwloc">C build environment (required for hwloc)</h3>
+<p><code>obikmer</code> embeds <a href="https://www.open-mpi.org/projects/hwloc/">hwloc</a> (Hardware Locality) for NUMA-aware thread placement on multi-socket machines. hwloc is built from source at compile time, which requires a standard C build environment.</p>
+<h4 id="linux-debianubuntu">Linux (Debian/Ubuntu)</h4>
+<div class="highlight"><pre><span></span><code>apt<span class="w"> </span>install<span class="w"> </span>build-essential<span class="w"> </span>automake<span class="w"> </span>libtool<span class="w"> </span>autoconf<span class="w"> </span>pkg-config
+</code></pre></div>
+<h4 id="linux-rhelrockyalmalinux">Linux (RHEL/Rocky/AlmaLinux)</h4>
+<div class="highlight"><pre><span></span><code>dnf<span class="w"> </span>install<span class="w"> </span>gcc<span class="w"> </span>make<span class="w"> </span>automake<span class="w"> </span>libtool<span class="w"> </span>autoconf<span class="w"> </span>pkgconfig
+</code></pre></div>
+<h4 id="hpc-clusters">HPC clusters</h4>
+<p>Most HPC clusters provide these tools via the module system:</p>
+<div class="highlight"><pre><span></span><code>module<span class="w"> </span>load<span class="w"> </span>gcc<span class="w"> </span>automake<span class="w"> </span>libtool<span class="w"> </span>autoconf
+</code></pre></div>
+<p>If in doubt, check that <code>autoreconf --version</code> and <code>libtool --version</code> return successfully.</p>
+<h4 id="macos">macOS</h4>
+<div class="highlight"><pre><span></span><code>brew<span class="w"> </span>install<span class="w"> </span>automake<span class="w"> </span>libtool<span class="w"> </span>autoconf<span class="w"> </span>pkg-config
+</code></pre></div>
+<h2 id="building">Building</h2>
+<div class="highlight"><pre><span></span><code>git<span class="w"> </span>clone<span class="w"> </span>&lt;repository-url&gt;
+<span class="nb">cd</span><span class="w"> </span>obikmer/src
+cargo<span class="w"> </span>build<span class="w"> </span>--release
+</code></pre></div>
+<p>The compiled binary is at <code>target/release/obikmer</code>.</p>
+<h3 id="building-on-hpc-clusters-network-filesystems">Building on HPC clusters (network filesystems)</h3>
+<p>HPC home directories are typically on a network filesystem (Lustre, NFS) optimized for large sequential reads, not for the many small file operations Cargo generates during compilation. Building directly on such a filesystem can be extremely slow.</p>
+<p>Redirect the build directory to a local scratch disk:</p>
+<div class="highlight"><pre><span></span><code><span class="nv">CARGO_TARGET_DIR</span><span class="o">=</span>/scratch/<span class="nv">$USER</span>/cargo-target<span class="w"> </span>cargo<span class="w"> </span>build<span class="w"> </span>--release
+</code></pre></div>
+<p>Adapt the path to the scratch space available on your cluster (<code>/var/tmp</code>, <code>/tmp</code>, <code>/scratch/local</code>, etc.). Once built, copy the binary to a permanent location:</p>
+<div class="highlight"><pre><span></span><code>cp<span class="w"> </span>/scratch/<span class="nv">$USER</span>/cargo-target/release/obikmer<span class="w"> </span>~/bin/
+</code></pre></div>
+<h2 id="numa-support">NUMA support</h2>
+<p>NUMA-aware thread placement is active automatically on multi-socket Linux machines, detected at runtime via hwloc. No build flag is required — it falls back gracefully to a single-pool strategy on:</p>
+<ul>
+<li>macOS (Apple Silicon, unified memory)</li>
+<li>single-socket Linux machines</li>
+<li>any system where hwloc reports only one NUMA node</li>
+</ul>
+<h2 id="verifying-the-installation">Verifying the installation</h2>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>--help
+</code></pre></div>
+
+
+
+
+
+
+
+
+
+
+
+
+                
+              </article>
+            </div>
+          
+          
+<script>var target=document.getElementById(location.hash.slice(1));target&&target.name&&(target.checked=target.name.startsWith("__tabbed_"))</script>
+        </div>
+        
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+    
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+  </body>
+</html>
\ No newline at end of file
diff --git a/doc/references.bib b/doc/references.bib
index a195b126..fca4c8bc 100644
--- a/doc/references.bib
+++ b/doc/references.bib
@@ -241,3 +241,21 @@
 	volume = 33,
 	year = 2017,
 	bdsk-url-1 = {http://dx.doi.org/10.1093/bioinformatics/btw832}}
+
+@misc{Mash-distances-doc,
+	author = {{Marbl Lab}},
+	howpublished = {Mash documentation},
+	title = {Mash Distance},
+	url = {https://mash.readthedocs.io/en/latest/distances.html},
+	urldate = {2026-07-09},
+	year = 2026}
+
+@article{Fan2015-mash-formula,
+	author = {Fan, Huan and Ives, Anthony R and Surget-Groba, Yann and Cannon, Charles H},
+	doi = {10.1186/s12864-015-1647-5},
+	journal = {BMC Genomics},
+	number = 1,
+	title = {An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data},
+	url = {https://doi.org/10.1186/s12864-015-1647-5},
+	volume = 16,
+	year = 2015}
diff --git a/doc/sitemap.xml.gz b/doc/sitemap.xml.gz
index 53a78b5f239988eb9642550ab26f4e5c24072789..d240d53a38bf83f4e1976065c5477c6a68e9751f 100644
GIT binary patch
delta 13
Ucmb=gXP58h;9yu&Kasrx02<>1`v3p{

delta 13
Ucmb=gXP58h;9xkQFp<3i02#{zumAu6

diff --git a/doc/theory/encoding/index.html b/doc/theory/encoding/index.html
index d44aeb9e..ec54413d 100644
--- a/doc/theory/encoding/index.html
+++ b/doc/theory/encoding/index.html
@@ -9,10 +9,10 @@
       
       
       
-        <link rel="prev" href="../../kmers/">
+        <link rel="prev" href="../kmers_and_superkmers/">
       
       
-        <link rel="next" href="../entropy/">
+        <link rel="next" href="../entropy_filter/">
       
       
         
@@ -23,7 +23,7 @@
     
     
       
-        <title>DNA encoding - obikmer</title>
+        <title>DNA encoding - obikmer — User Guide</title>
       
     
     
@@ -80,7 +80,7 @@
 
 <header class="md-header md-header--shadow" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../.." title="obikmer" class="md-header__button md-logo" aria-label="obikmer" data-md-component="logo">
+    <a href="../.." title="obikmer — User Guide" class="md-header__button md-logo" aria-label="obikmer — User Guide" data-md-component="logo">
       
   
   <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M12 8a3 3 0 0 0 3-3 3 3 0 0 0-3-3 3 3 0 0 0-3 3 3 3 0 0 0 3 3m0 3.54C9.64 9.35 6.5 8 3 8v11c3.5 0 6.64 1.35 9 3.54 2.36-2.19 5.5-3.54 9-3.54V8c-3.5 0-6.64 1.35-9 3.54"/></svg>
@@ -94,7 +94,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
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-            obikmer
+            obikmer — User Guide
           </span>
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@@ -138,13 +138,13 @@
 
 <nav class="md-nav md-nav--primary" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../.." title="obikmer" class="md-nav__button md-logo" aria-label="obikmer" data-md-component="logo">
+    <a href="../.." title="obikmer — User Guide" class="md-nav__button md-logo" aria-label="obikmer — User Guide" data-md-component="logo">
       
   
   <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M12 8a3 3 0 0 0 3-3 3 3 0 0 0-3-3 3 3 0 0 0-3 3 3 3 0 0 0 3 3m0 3.54C9.64 9.35 6.5 8 3 8v11c3.5 0 6.64 1.35 9 3.54 2.36-2.19 5.5-3.54 9-3.54V8c-3.5 0-6.64 1.35-9 3.54"/></svg>
 
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-    obikmer
+    obikmer — User Guide
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   <ul class="md-nav__list" data-md-scrollfix>
@@ -180,6 +180,33 @@
       
   
   
+  
+  
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
     
   
   
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
         
           
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+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
             
   
   
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
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+      <a href="../kmers_and_superkmers/" class="md-nav__link">
         
   
   
@@ -339,6 +366,17 @@
     </span>
   </a>
   
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#canonical-form" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Canonical form
+      
+    </span>
+  </a>
+  
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@@ -357,14 +395,14 @@
   
   
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+      <a href="../entropy_filter/" class="md-nav__link">
         
   
   
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-    Entropy filter
+    Low-complexity kmer filter
   
 
     
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+    Partitioning and indexing architecture
   
 
     
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+    Usage
   
 
     
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+    superkmer
   
 
     
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@@ -997,6 +981,115 @@
   
 
     
+      
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@@ -1043,6 +1136,17 @@
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 </li>
       
     </ul>
@@ -1064,7 +1168,7 @@
 
 <h1 id="dna-encoding">DNA encoding</h1>
 <h2 id="2-bit-nucleotide-encoding">2-bit nucleotide encoding</h2>
-<p>All nucleotides are encoded on 2 bits, MSB-first within each word. Nucleotides are numbered 0-based from the 5′ end across all sequence types:</p>
+<p>Every nucleotide is encoded on 2 bits, most-significant-bit first within each word:</p>
 <table>
 <thead>
 <tr>
@@ -1091,27 +1195,14 @@
 </tr>
 </tbody>
 </table>
-<p>The Watson-Crick complement of any base is its bitwise NOT on 2 bits: <code>complement(base) = ~base &amp; 0b11</code>.</p>
+<p>The Watson-Crick complement of a base is its bitwise NOT on 2 bits: <span class="arithmatex">\(\text{complement}(base) = \lnot base \mathbin{\&amp;} \texttt{0b11}\)</span>.</p>
 <h2 id="kmer-encoding">Kmer encoding</h2>
-<p>A kmer fits in a single <code>u64</code>. Nucleotide 0 occupies bits 63–62, nucleotide i occupies bits 63−2i and 62−2i, and the low 64−2k bits are zero. Extraction of nucleotide i (0 ≤ i &lt; k): <code>(kmer &gt;&gt; (62 - 2*i)) &amp; 0b11</code>.</p>
-<p>Reverse complement is computed by <strong>bit manipulation in four steps</strong>, with no lookup table:</p>
-<div class="admonition abstract">
-<p class="admonition-title">Algorithm — Kmer reverse complement</p>
-<div class="highlight"><pre><span></span><code>procedure KmerRevcomp(kmer, k):
-    x ← ~kmer                                           -- complement all bases
-    x ← swap_bytes(x)                                   -- reverse byte order
-    x ← ((x &gt;&gt; 4) &amp; 0x0F0F0F0F0F0F0F0F)
-       | ((x &amp; 0x0F0F0F0F0F0F0F0F) &lt;&lt; 4)               -- swap nibbles within each byte
-    x ← ((x &gt;&gt; 2) &amp; 0x3333333333333333)
-       | ((x &amp; 0x3333333333333333) &lt;&lt; 2)                -- swap 2-bit pairs within each nibble
-    return x &lt;&lt; (64 - 2*k)                              -- re-align to MSB
-</code></pre></div>
-</div>
-<p>The three reorder passes together reverse the order of all 2-bit base codes across the 64-bit word. The bitwise NOT in the first step complements each base (A↔T, C↔G). The final left shift clears the low 64−2k padding bits.</p>
-<p>The <strong>canonical form</strong> is the lexicographic minimum of the kmer and its reverse complement:</p>
-<div class="highlight"><pre><span></span><code>canonical(kmer) = min(kmer, revcomp(kmer))
-</code></pre></div>
-<p>This halves the kmer space and ensures strand-independent counting.</p>
+<p>A kmer of length <span class="arithmatex">\(k\)</span> (<span class="arithmatex">\(k \le 31\)</span>) fits in a single 64-bit word. The first nucleotide occupies the two most significant bits, each following nucleotide occupies the next two bits, and unused low-order bits are zero. Extracting nucleotide i (0-indexed from the 5′ end) is a shift-and-mask operation.</p>
+<p>Reverse complement is computed by bit manipulation directly on the packed word, without any lookup table: complement every base, reverse the byte order, then reverse the order of 2-bit groups within each byte in two more passes, and finally realign the result to the most-significant bits.</p>
+<h2 id="canonical-form">Canonical form</h2>
+<p>The canonical form of a kmer is the lexicographic minimum of the kmer and its reverse complement:</p>
+<div class="arithmatex">\[\text{canonical}(kmer) = \min\big(kmer,\ \text{revcomp}(kmer)\big)\]</div>
+<p>Using the canonical form halves the kmer space and makes counting strand-independent: a kmer and its reverse complement are always treated as the same entity, regardless of which DNA strand was sequenced.</p>
 
 
 
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+
+<h1 id="low-complexity-kmer-filter">Low-complexity kmer filter</h1>
+<p>Low-complexity kmers (homopolymer runs, tandem repeats) can dominate an index without carrying useful information. <code>obikmer</code> detects and excludes them during index construction using a normalized Shannon entropy score.</p>
+<h2 id="sub-word-frequencies">Sub-word frequencies</h2>
+<p>For a kmer of length <span class="arithmatex">\(k\)</span> and a sub-word size <span class="arithmatex">\(ws\)</span> (<span class="arithmatex">\(1 \le ws \le ws_{\max}\)</span>, default <span class="arithmatex">\(ws_{\max} = 6\)</span>), the kmer is decomposed into its <span class="arithmatex">\(k - ws + 1\)</span> overlapping sub-words of length <span class="arithmatex">\(ws\)</span> by sliding a window across it. Each sub-word is tallied under its raw 2-bit-packed value, with no canonicalization.</p>
+<h2 id="corrected-shannon-entropy">Corrected Shannon entropy</h2>
+<p>Let <span class="arithmatex">\(f_j\)</span> be the observed count of raw sub-word <span class="arithmatex">\(j\)</span>, and <span class="arithmatex">\(n_{\text{words}} = k - ws + 1\)</span> the total number of sub-words. The entropy is:</p>
+<div class="arithmatex">\[H_{\text{corr}} = \log(n_{\text{words}}) - \frac{1}{n_{\text{words}}} \sum_j f_j \log f_j\]</div>
+<h2 id="small-sample-correction">Small-sample correction</h2>
+<p>Because only <span class="arithmatex">\(n_{\text{words}}\)</span> sub-words are observed among up to <span class="arithmatex">\(4^{ws}\)</span> possible values, the achievable maximum entropy <span class="arithmatex">\(H_{\max}\)</span> is bounded below <span class="arithmatex">\(\log(4^{ws})\)</span> for small samples. <span class="arithmatex">\(H_{\max}\)</span> is computed from the most uniform integer distribution achievable with <span class="arithmatex">\(n_{\text{words}}\)</span> observations over <span class="arithmatex">\(4^{ws}\)</span> categories. The normalized entropy is:</p>
+<div class="arithmatex">\[\hat{H}(ws) = \frac{H_{\text{corr}}}{H_{\max}} \in [0, 1]\]</div>
+<p>A value near 0 indicates low complexity (e.g. a homopolymer run); near 1 indicates high complexity, characteristic of a random sequence.</p>
+<h2 id="final-score">Final score</h2>
+<p>The filter evaluates <span class="arithmatex">\(\hat{H}(ws)\)</span> for every word size from 1 to ws_max and keeps the minimum:</p>
+<div class="arithmatex">\[\text{entropy}(kmer) = \min_{ws=1}^{ws_{\max}} \hat{H}(ws)\]</div>
+<p>Taking the minimum across word sizes ensures that repetition at any scale is detected: a homopolymer is caught at <span class="arithmatex">\(ws=1\)</span>, a dinucleotide repeat at <span class="arithmatex">\(ws=2\)</span>, and so on. A kmer is rejected if its entropy score falls below a threshold <span class="arithmatex">\(\theta\)</span> (default 0.7), a configurable collection parameter.</p>
+<h2 id="properties">Properties</h2>
+<p>The entropy score depends only on the kmer sequence itself, not on where or how many times it occurs:</p>
+<ul>
+<li><strong>Orientation invariance</strong>: a kmer and its reverse complement always receive the same score.</li>
+<li><strong>Context independence</strong>: a given kmer is always accepted or always rejected, regardless of which genome or read it appears in. The filter defines a fixed partition of the kmer space into low-complexity and valid kmers.</li>
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+
+<h1 id="partitioning-and-indexing-architecture">Partitioning and indexing architecture</h1>
+<p>An index is split into a fixed number of <strong>partitions</strong>, each handling an independent, disjoint slice of the kmer space. Partitioning keeps the working set of each stage small enough to process efficiently and enables parallel construction and querying.</p>
+<h2 id="routing">Routing</h2>
+<p>The canonical minimizer of a super-kmer (see <a href="../minimizer_selection/">Minimizer selection</a>) is hashed to produce a <span class="arithmatex">\(p\)</span>-bit routing value that selects the destination partition:</p>
+<div class="highlight"><pre><span></span><code>canonical minimizer → hash(minimizer) → p-bit value → partition index
+</code></pre></div>
+<p>The routing value is recomputed whenever it is needed (during construction and again at query time) rather than stored — it is not part of the on-disk super-kmer representation.</p>
+<p>Within a partition, kmers are indexed as plain values via a minimal perfect hash function (see <a href="../../formats/index_layout/">On-disk storage</a>); the minimizer plays no further role once a super-kmer has reached its partition.</p>
+<h2 id="why-hashing-is-necessary">Why hashing is necessary</h2>
+<p>A canonical minimizer is an m-mer (<span class="arithmatex">\(m \in \{9, 11, 13, 15\}\)</span>), and its distribution over all possible m-mer values is not uniform — as the lexicographic minimum of a window, small values are systematically over-represented (Golan &amp; Shur 2025; Kille <em>et al.</em> 2023; Pan &amp; Reinert 2024; Zheng <em>et al.</em> 2020, 2021)<sup id="fnref:Zheng2020-ji"><a class="footnote-ref" href="#fn:Zheng2020-ji">1</a></sup> <sup id="fnref:Zheng2021-cc"><a class="footnote-ref" href="#fn:Zheng2021-cc">2</a></sup> <sup id="fnref:Pan2024-hb"><a class="footnote-ref" href="#fn:Pan2024-hb">3</a></sup> <sup id="fnref:Kille2023-px"><a class="footnote-ref" href="#fn:Kille2023-px">4</a></sup> <sup id="fnref:Golan2025-xf"><a class="footnote-ref" href="#fn:Golan2025-xf">5</a></sup>. Routing directly on the raw minimizer value would therefore produce badly unbalanced partitions.</p>
+<p>Hashing the minimizer before routing redistributes this skewed distribution uniformly across partitions. This works reliably because the number of partition-index bits <span class="arithmatex">\(p\)</span> is chosen well below the number of bits available in the minimizer (<span class="arithmatex">\(2m\)</span>): even with strong bias in the minimizer distribution, the hash has enough entropy margin to absorb it, provided the number of distinct minimizers actually observed is much larger than the number of partitions.</p>
+<h2 id="parameter-guidance">Parameter guidance</h2>
+<table>
+<thead>
+<tr>
+<th>Minimizer size <span class="arithmatex">\(m\)</span></th>
+<th>Minimizer bits (<span class="arithmatex">\(2m\)</span>)</th>
+<th>Typical partition-index bits <span class="arithmatex">\(p\)</span></th>
+<th>Partitions</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>9</td>
+<td>18</td>
+<td>6–8</td>
+<td>64–256</td>
+</tr>
+<tr>
+<td>11</td>
+<td>22</td>
+<td>8–10</td>
+<td>256–1 024</td>
+</tr>
+<tr>
+<td>13</td>
+<td>26</td>
+<td>10–12</td>
+<td>1 024–4 096</td>
+</tr>
+<tr>
+<td>15</td>
+<td>30</td>
+<td>10–14</td>
+<td>1 024–16 384</td>
+</tr>
+</tbody>
+</table>
+<p>The number of partitions must satisfy <span class="arithmatex">\(p \le 2m\)</span>, and in practice <span class="arithmatex">\(p\)</span> is chosen well below that bound to leave a comfortable entropy margin. For <span class="arithmatex">\(k=31\)</span>, <span class="arithmatex">\(m=13\)</span>, <span class="arithmatex">\(p=10\)</span> (1024 partitions), partition load is well balanced on real genomic data.</p>
+<div class="footnote">
+<hr />
+<ol>
+<li id="fn:Zheng2020-ji">
+<p>Zheng, H., Kingsford, C. &amp; Marçais, G. (2020). <a href="https://doi.org/10.1093/bioinformatics/btaa472">Improved design and analysis of practical minimizers</a>. <em>Bioinformatics (Oxford, England)</em>, 36, i119--i127.&#160;<a class="footnote-backref" href="#fnref:Zheng2020-ji" title="Jump back to footnote 1 in the text">&#8617;</a></p>
+</li>
+<li id="fn:Zheng2021-cc">
+<p>Zheng, H., Kingsford, C. &amp; Marçais, G. (2021). <a href="https://doi.org/10.1093/bioinformatics/btab313">Sequence-specific minimizers via polar sets</a>. <em>Bioinformatics (Oxford, England)</em>, 37, i187--i195.&#160;<a class="footnote-backref" href="#fnref:Zheng2021-cc" title="Jump back to footnote 2 in the text">&#8617;</a></p>
+</li>
+<li id="fn:Pan2024-hb">
+<p>Pan, C. &amp; Reinert, K. (2024). <a href="https://doi.org/10.1093/bioinformatics/btae045">A simple refined DNA minimizer operator enables 2-fold faster computation</a>. <em>Bioinformatics (Oxford, England)</em>, 40.&#160;<a class="footnote-backref" href="#fnref:Pan2024-hb" title="Jump back to footnote 3 in the text">&#8617;</a></p>
+</li>
+<li id="fn:Kille2023-px">
+<p>Kille, B., Garrison, E., Treangen, T.J. &amp; Phillippy, A.M. (2023). <a href="https://doi.org/10.1093/bioinformatics/btad512">Minmers are a generalization of minimizers that enable unbiased local jaccard estimation</a>. <em>Bioinformatics (Oxford, England)</em>, 39.&#160;<a class="footnote-backref" href="#fnref:Kille2023-px" title="Jump back to footnote 4 in the text">&#8617;</a></p>
+</li>
+<li id="fn:Golan2025-xf">
+<p>Golan, S. &amp; Shur, A.M. (2025). <a href="https://doi.org/10.1007/978-3-031-82670-2\_25">Expected density of random minimizers</a>. In: <em>Lecture notes in computer science</em>, Lecture notes in computer science. Springer Nature Switzerland, Cham, pp. 347--360.&#160;<a class="footnote-backref" href="#fnref:Golan2025-xf" title="Jump back to footnote 5 in the text">&#8617;</a></p>
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+<h1 id="kmers-and-super-kmers">Kmers and super-kmers</h1>
+<h2 id="kmers">Kmers</h2>
+<p>A <strong>kmer</strong> is a DNA subsequence of fixed length <span class="arithmatex">\(k\)</span>. Two constraints apply to <span class="arithmatex">\(k\)</span>, both enforced when a command starts (an invalid value exits immediately with an error):</p>
+<ul>
+<li><span class="arithmatex">\(k \in [11, 31]\)</span>: long enough to be specific, short enough to fit in a single 64-bit word at 2 bits/base (<span class="arithmatex">\(k \le 32\)</span> is the hard limit; <span class="arithmatex">\(k &lt; 11\)</span> gives insufficient specificity).</li>
+<li><span class="arithmatex">\(k\)</span> <strong>is odd</strong>: an odd-length sequence can never equal its own reverse complement, so the two orientations of any kmer are always distinct. This is required for the canonical form (see <a href="../encoding/">DNA encoding</a>) to be well defined.</li>
+</ul>
+<h2 id="super-kmers">Super-kmers</h2>
+<p>A <strong>super-kmer</strong> is a maximal run of consecutive, overlapping kmers from a read that share the same canonical minimizer (see <a href="../minimizer_selection/">Minimizer selection</a>). Each kmer in the run overlaps the next by <span class="arithmatex">\(k-1\)</span> nucleotides. A super-kmer is capped at 256 nucleotides; a longer run is split at that boundary.</p>
+<p>For a random minimizer of length <span class="arithmatex">\(m\)</span> over kmers of length <span class="arithmatex">\(k\)</span>, the expected length of a super-kmer is approximately (Golan &amp; Shur 2025; Zheng <em>et al.</em> 2020)<sup id="fnref:Zheng2020-ji"><a class="footnote-ref" href="#fn:Zheng2020-ji">1</a></sup> <sup id="fnref:Golan2025-xf"><a class="footnote-ref" href="#fn:Golan2025-xf">2</a></sup>:</p>
+<div class="arithmatex">\[L_{\text{nt}} \approx \frac{k-m+2}{2} + k - 1\]</div>
+<p>For <span class="arithmatex">\(k=31\)</span>, <span class="arithmatex">\(m=13\)</span> this is about 40 nucleotides; in practice super-kmers rarely exceed a few dozen nucleotides.</p>
+<h3 id="canonical-super-kmers">Canonical super-kmers</h3>
+<p>A <strong>canonical super-kmer</strong> is the lexicographic minimum of a super-kmer and its reverse complement. When a read and its reverse complement are both encountered, they produce super-kmers that are reverse complements of each other; both reduce to the same canonical super-kmer, so a genomic region is represented once regardless of which strand was read.</p>
+<p>Super-kmers are the unit of work used throughout construction and querying: sequences are decomposed into super-kmers first, and every downstream step (partition routing, deduplication, counting) operates on them rather than on individual kmers.</p>
+<div class="footnote">
+<hr />
+<ol>
+<li id="fn:Zheng2020-ji">
+<p>Zheng, H., Kingsford, C. &amp; Marçais, G. (2020). <a href="https://doi.org/10.1093/bioinformatics/btaa472">Improved design and analysis of practical minimizers</a>. <em>Bioinformatics (Oxford, England)</em>, 36, i119--i127.&#160;<a class="footnote-backref" href="#fnref:Zheng2020-ji" title="Jump back to footnote 1 in the text">&#8617;</a></p>
+</li>
+<li id="fn:Golan2025-xf">
+<p>Golan, S. &amp; Shur, A.M. (2025). <a href="https://doi.org/10.1007/978-3-031-82670-2\_25">Expected density of random minimizers</a>. In: <em>Lecture notes in computer science</em>, Lecture notes in computer science. Springer Nature Switzerland, Cham, pp. 347--360.&#160;<a class="footnote-backref" href="#fnref:Golan2025-xf" title="Jump back to footnote 2 in the text">&#8617;</a></p>
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+    <li class="md-nav__item">
+      <a href="../encoding/" class="md-nav__link">
+        
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+  
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+    
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+  
+
+    
+  </span>
+  
+  
+
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+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../entropy_filter/" class="md-nav__link">
+        
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+  
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+    
+  
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+  
+
+    
+  </span>
+  
+  
+
+      </a>
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+      
+        <li class="md-nav__item">
+  <a href="#hash-based-random-minimizer" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Hash-based ("random") minimizer
+      
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+    <nav class="md-nav" aria-label="Hash-based (&#34;random&#34;) minimizer">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#hash-function" class="md-nav__link">
+    <span class="md-ellipsis">
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+  
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+      
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+  <a href="#hash-based-random-minimizer" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Hash-based ("random") minimizer
+      
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+  
+    <nav class="md-nav" aria-label="Hash-based (&#34;random&#34;) minimizer">
+      <ul class="md-nav__list">
+        
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+      
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+  <a href="#partition-routing-is-independent-of-minimizer-selection" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Partition routing is independent of minimizer selection
+      
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+</li>
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+                
+                  
+
+
+
+<h1 id="minimizer-selection">Minimizer selection</h1>
+<h2 id="definition">Definition</h2>
+<p>A <strong>minimizer</strong> of a kmer window is the m-mer (<span class="arithmatex">\(m &lt; k\)</span>) that is smallest, among all <span class="arithmatex">\(k - m + 1\)</span> overlapping m-mers in the window, under a chosen ordering. The minimizer is always taken in canonical form (lexicographic minimum of forward and reverse complement) so that selection is strand-independent.</p>
+<p>The minimizer partitions a sequence into super-kmers: maximal runs of overlapping kmers that share the same minimizer (see <a href="../kmers_and_superkmers/">Kmers and super-kmers</a>).</p>
+<h2 id="hash-based-random-minimizer">Hash-based ("random") minimizer</h2>
+<p><code>obikmer</code> selects minimizers by hash order rather than plain lexicographic order. Ordering m-mers lexicographically on their 2-bit encoding systematically favors AT-rich m-mers (an all-A m-mer always encodes to 0), which causes low-complexity regions to dominate as minimizers and produces unbalanced partitions.</p>
+<p>Instead, a well-distributed hash function <span class="arithmatex">\(H\)</span> is applied to the canonical (lexicographically minimal) form of each m-mer, and the m-mer with the smallest <span class="arithmatex">\(H\)</span> value wins. Because <span class="arithmatex">\(H\)</span> is a bijection with good avalanche properties, every distinct m-mer in a window has an equal chance of holding the minimum hash value, independent of its nucleotide composition.</p>
+<p>The canonical form used as input to <span class="arithmatex">\(H\)</span> is still the lexicographic minimum of forward/reverse-complement — hashing is applied on top of it, not used to redefine it. Defining canonicity by hash value instead would bias the <em>distribution of hash values themselves</em> toward small values (the minimum of two independent hashes is not uniformly distributed), reintroducing a bias one layer down.</p>
+<h3 id="hash-function">Hash function</h3>
+<p>The hash function is a 64-bit mixing function (splitmix64-style finalizer) applied to the m-mer XORed with a fixed non-zero seed:</p>
+<div class="arithmatex">\[H(x) = \text{mix64}(x \oplus s), \quad s = \lfloor 2^{64}/\varphi \rfloor = \texttt{0x9e3779b97f4a7c15}\]</div>
+<div class="highlight"><pre><span></span><code>H(x):
+    x ← x  ⊕  0x9e3779b97f4a7c15
+    x ← x  ⊕  (x &gt;&gt; 30)
+    x ← x  ×  0xbf58476d1ce4e5b9
+    x ← x  ⊕  (x &gt;&gt; 27)
+    x ← x  ×  0x94d049bb133111eb
+    return x ⊕ (x &gt;&gt; 31)
+</code></pre></div>
+<p>The XOR seed avoids the finalizer's fixed point at 0 (<span class="arithmatex">\(\text{mix64}(0) = 0\)</span>), which would otherwise make an all-A m-mer (canonical value 0) win every window comparison.</p>
+<h2 id="partition-routing-is-independent-of-minimizer-selection">Partition routing is independent of minimizer selection</h2>
+<p>The hash used to select a minimizer within a window (the minimum of several hash values) and the hash used to route a super-kmer to a storage partition are computed separately:</p>
+<ul>
+<li><strong>Selection</strong> uses <span class="arithmatex">\(H\)</span> applied to every candidate m-mer in the window, keeping the minimum.</li>
+<li><strong>Partition routing</strong> recomputes <span class="arithmatex">\(H\)</span> on the single selected minimizer only, once its position is fixed. This is a hash of one specific value, not the minimum of several, so it is uniformly distributed and safe to use directly for routing.</li>
+</ul>
+<p>See <a href="../indexing_architecture/">Partitioning and indexing architecture</a> for how the routing value is turned into a partition index.</p>
+
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diff --git a/doc/usage/annotate/index.html b/doc/usage/annotate/index.html
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+
+<h1 id="annotate">annotate</h1>
+<p>Add or update genome metadata of an index from a CSV file, or dump the current metadata as CSV.</p>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>annotate<span class="w"> </span>INDEX<span class="w"> </span>--csv<span class="w"> </span>FILE<span class="w"> </span><span class="o">[</span>OPTIONS<span class="o">]</span>
+obikmer<span class="w"> </span>annotate<span class="w"> </span>INDEX<span class="w"> </span>--dump
+</code></pre></div>
+<h2 id="arguments">Arguments</h2>
+<table>
+<thead>
+<tr>
+<th>Argument</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>INDEX</code></td>
+<td>Index directory to annotate (modified in place)</td>
+</tr>
+</tbody>
+</table>
+<h2 id="options">Options</h2>
+<table>
+<thead>
+<tr>
+<th>Option</th>
+<th>Default</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>--csv</code></td>
+<td>—</td>
+<td>CSV file of metadata to apply (must contain an id column); required unless <code>--dump</code> is used</td>
+</tr>
+<tr>
+<td><code>--sep</code></td>
+<td><code>,</code></td>
+<td>CSV field separator</td>
+</tr>
+<tr>
+<td><code>--id-col</code></td>
+<td><code>id</code></td>
+<td>Name of the column containing genome labels</td>
+</tr>
+<tr>
+<td><code>--na-value</code></td>
+<td><code>NA</code></td>
+<td>Value meaning "remove this field" (deletes the existing key if present)</td>
+</tr>
+<tr>
+<td><code>--no-overwrite</code></td>
+<td>off</td>
+<td>Do not overwrite existing metadata keys</td>
+</tr>
+<tr>
+<td><code>--dump</code></td>
+<td>off</td>
+<td>Print all genome metadata as CSV to stdout instead of applying a file</td>
+</tr>
+</tbody>
+</table>
+
+
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+      
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+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+
+<h1 id="dump">dump</h1>
+<p>Dump all kmers of an index as CSV, one row per kmer, with per-genome counts or presence.</p>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>dump<span class="w"> </span>INDEX<span class="w"> </span><span class="o">[</span>OPTIONS<span class="o">]</span>
+</code></pre></div>
+<h2 id="arguments">Arguments</h2>
+<table>
+<thead>
+<tr>
+<th>Argument</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>INDEX</code></td>
+<td>Index directory to dump</td>
+</tr>
+</tbody>
+</table>
+<h2 id="options">Options</h2>
+<table>
+<thead>
+<tr>
+<th>Option</th>
+<th>Default</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>--force-presence</code></td>
+<td>off</td>
+<td>Output presence/absence (0/1) even if the index stores counts</td>
+</tr>
+<tr>
+<td><code>--debug</code></td>
+<td>off</td>
+<td>Prefix each row with the partition and layer columns</td>
+</tr>
+<tr>
+<td><code>--head N</code></td>
+<td>none</td>
+<td>Limit output to the first N kmers</td>
+</tr>
+</tbody>
+</table>
+<p><code>dump</code> also accepts the shared <a href="../filter/#predicate-options">predicate options</a> (<code>--ingroup</code>, <code>--outgroup</code>, <code>--min-count</code>, etc.) to restrict which kmers are dumped.</p>
+<p>Output is CSV on stdout.</p>
+
+
+
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+                
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+<h1 id="estimate">estimate</h1>
+<p>Estimate approximate-index parameters (z, evidence bits, false-positive rate) before building an index with <code>--approx</code>, without touching any files.</p>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>estimate<span class="w"> </span><span class="o">[</span>OPTIONS<span class="o">]</span>
+</code></pre></div>
+<h2 id="options">Options</h2>
+<table>
+<thead>
+<tr>
+<th>Option</th>
+<th>Default</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>-k, --kmer-size</code></td>
+<td><code>31</code></td>
+<td>Kmer size used at query time (matches <code>index</code>'s <code>--kmer-size</code>)</td>
+</tr>
+<tr>
+<td><code>-z, --findere-z</code></td>
+<td>none</td>
+<td>Findere z parameter</td>
+</tr>
+<tr>
+<td><code>--evidence-bits</code></td>
+<td>none</td>
+<td>Fingerprint bits per slot (b)</td>
+</tr>
+<tr>
+<td><code>--fp</code></td>
+<td>none</td>
+<td>Target false-positive rate per z-window</td>
+</tr>
+</tbody>
+</table>
+<p>Any two of <code>-z</code>, <code>--evidence-bits</code>, <code>--fp</code> may be given; the third is derived using the same model as <code>index --approx</code> and <code>reindex --approx</code> (<span class="arithmatex">\(FP = 1 / 2^{b \cdot z}\)</span>). The report printed to stdout includes: query <span class="arithmatex">\(k\)</span>, effective indexed <span class="arithmatex">\(k\)</span> (<span class="arithmatex">\(k-z+1\)</span>), <span class="arithmatex">\(z\)</span>, evidence bits, per-kmer false-positive rate, and per-z-window false-positive rate.</p>
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+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+
+<h1 id="filter">filter</h1>
+<p>Apply row-level selection to an index: retain only kmers matching ingroup/outgroup predicates over genome membership, plus optional total-count and complexity thresholds. The output is a new, single-layer index.</p>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>filter<span class="w"> </span>SOURCE<span class="w"> </span>-o<span class="w"> </span>OUTPUT<span class="w"> </span><span class="o">[</span>OPTIONS<span class="o">]</span>
+</code></pre></div>
+<h2 id="arguments">Arguments</h2>
+<table>
+<thead>
+<tr>
+<th>Argument</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>SOURCE</code></td>
+<td>Source index directory</td>
+</tr>
+</tbody>
+</table>
+<h2 id="options">Options</h2>
+<table>
+<thead>
+<tr>
+<th>Option</th>
+<th>Default</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>-o, --output</code></td>
+<td>— (required)</td>
+<td>Output index directory</td>
+</tr>
+<tr>
+<td><code>-f, --force</code></td>
+<td>off</td>
+<td>Overwrite an existing output directory</td>
+</tr>
+<tr>
+<td><code>--presence</code></td>
+<td>off</td>
+<td>Output presence/absence instead of counts</td>
+</tr>
+<tr>
+<td><code>--min-total-count</code></td>
+<td>none</td>
+<td>Minimum total count across all genomes (count index only)</td>
+</tr>
+<tr>
+<td><code>--max-total-count</code></td>
+<td>none</td>
+<td>Maximum total count across all genomes</td>
+</tr>
+<tr>
+<td><code>--min-complexity</code></td>
+<td>none</td>
+<td>Minimum normalized entropy (same score as <code>--theta</code> at index build time), recomputed from the stored unitig sequences</td>
+</tr>
+<tr>
+<td><code>--complexity-level-max</code></td>
+<td><code>6</code></td>
+<td>Maximum sub-word size for the complexity score (used only with <code>--min-complexity</code>)</td>
+</tr>
+</tbody>
+</table>
+<h2 id="predicate-options">Predicate options</h2>
+<table>
+<thead>
+<tr>
+<th>Option</th>
+<th>Default</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>--ingroup</code></td>
+<td>none</td>
+<td>Ingroup predicate (repeatable; each occurrence is ANDed)</td>
+</tr>
+<tr>
+<td><code>--outgroup</code></td>
+<td>none</td>
+<td>Outgroup predicate (repeatable; each occurrence is ORed)</td>
+</tr>
+<tr>
+<td><code>--min-count</code></td>
+<td>0, or group size + N if negative</td>
+<td>Minimum number of ingroup genomes carrying the kmer</td>
+</tr>
+<tr>
+<td><code>--max-count</code></td>
+<td>ingroup group size</td>
+<td>Maximum number of ingroup genomes carrying the kmer</td>
+</tr>
+<tr>
+<td><code>--min-frac</code></td>
+<td><code>1.0</code> if <code>--ingroup</code> given without an explicit quorum, else <code>0.0</code></td>
+<td>Minimum fraction of ingroup genomes</td>
+</tr>
+<tr>
+<td><code>--max-frac</code></td>
+<td><code>1.0</code></td>
+<td>Maximum fraction of ingroup genomes</td>
+</tr>
+<tr>
+<td><code>--min-outgroup-count</code></td>
+<td><code>0</code></td>
+<td>Minimum number of outgroup genomes carrying the kmer</td>
+</tr>
+<tr>
+<td><code>--max-outgroup-count</code></td>
+<td><code>0</code> if <code>--outgroup</code> given without an explicit quorum, else outgroup group size</td>
+<td>Maximum number of outgroup genomes</td>
+</tr>
+<tr>
+<td><code>--min-outgroup-frac</code></td>
+<td><code>0.0</code></td>
+<td>Minimum fraction of outgroup genomes</td>
+</tr>
+<tr>
+<td><code>--max-outgroup-frac</code></td>
+<td><code>1.0</code></td>
+<td>Maximum fraction of outgroup genomes</td>
+</tr>
+<tr>
+<td><code>--presence-threshold</code></td>
+<td><code>0</code></td>
+<td>Minimum count for a genome to be considered a carrier of a kmer</td>
+</tr>
+</tbody>
+</table>
+<p>See <a href="../predicates/">Genome predicates and taxonomy paths</a> for the predicate syntax used by <code>--ingroup</code>/<code>--outgroup</code>.</p>
+<p>A negative <code>--min-count</code>/<code>--max-count</code> is interpreted as an offset from the group size — e.g. <code>--min-count=-1</code> means "all but one".</p>
+<p>Declaring <code>--ingroup</code> with no explicit ingroup quorum flag implicitly sets <code>--min-frac 1.0</code> (present in every ingroup genome). Declaring <code>--outgroup</code> with no explicit outgroup quorum flag implicitly sets <code>--max-outgroup-count 0</code> (absent from every outgroup genome). Any explicit quorum flag for a group disables that group's implicit default.</p>
+
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+      
+        <li class="md-nav__item">
+  <a href="#arguments" class="md-nav__link">
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+        Arguments
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+</li>
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+  <a href="#options" class="md-nav__link">
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+      
+        <li class="md-nav__item">
+  <a href="#exact-vs-approximate-evidence" class="md-nav__link">
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+      
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+
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+
+              
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+    <li class="md-nav__item">
+      <a href="../dump/" class="md-nav__link">
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+    
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+    Index construction and on-disk layout
+  
+
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+
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+  
+
+              
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+</nav>
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+                  <div class="md-sidebar__inner">
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+  
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+  
+  
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+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#arguments" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Arguments
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#options" class="md-nav__link">
+    <span class="md-ellipsis">
+      
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+      
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+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#exact-vs-approximate-evidence" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Exact vs. approximate evidence
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+
+<h1 id="index">index</h1>
+<p>Build a genome index from one or more sequence files. Construction proceeds in phases (scatter → dereplicate → count → layered MPHF), described in <a href="../../formats/index_layout/">On-disk storage</a>.</p>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>index<span class="w"> </span>-o<span class="w"> </span>OUTPUT<span class="w"> </span><span class="o">[</span>OPTIONS<span class="o">]</span><span class="w"> </span><span class="o">[</span>INPUTS...<span class="o">]</span>
+</code></pre></div>
+<h2 id="arguments">Arguments</h2>
+<table>
+<thead>
+<tr>
+<th>Argument</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>INPUTS...</code></td>
+<td>Input sequence files or directories (FASTA/FASTQ/GenBank, gzip optional). If omitted, reads from stdin.</td>
+</tr>
+</tbody>
+</table>
+<h2 id="options">Options</h2>
+<table>
+<thead>
+<tr>
+<th>Option</th>
+<th>Default</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>-o, --output</code></td>
+<td>— (required)</td>
+<td>Output index directory</td>
+</tr>
+<tr>
+<td><code>--force</code></td>
+<td>off</td>
+<td>Overwrite an existing output directory</td>
+</tr>
+<tr>
+<td><code>--label</code></td>
+<td>input file name without extension</td>
+<td>Genome label stored in the index</td>
+</tr>
+<tr>
+<td><code>--meta KEY=VALUE</code></td>
+<td>none</td>
+<td>Attach a categorical metadata field to the genome (repeatable)</td>
+</tr>
+<tr>
+<td><code>-k, --kmer-size</code></td>
+<td><code>31</code></td>
+<td>Kmer size (odd, in [11, 31])</td>
+</tr>
+<tr>
+<td><code>-m, --minimizer-size</code></td>
+<td><code>11</code></td>
+<td>Minimizer size (odd, in <span class="arithmatex">\([3, k-1]\)</span>)</td>
+</tr>
+<tr>
+<td><code>--theta</code></td>
+<td><code>0.7</code></td>
+<td>Entropy threshold for the low-complexity filter</td>
+</tr>
+<tr>
+<td><code>--level-max</code></td>
+<td><code>6</code></td>
+<td>Maximum sub-word size for the entropy score</td>
+</tr>
+<tr>
+<td><code>-p, --partitions</code></td>
+<td><code>256</code></td>
+<td>Number of partitions (rounded up to a power of 2)</td>
+</tr>
+<tr>
+<td><code>-T, --threads</code></td>
+<td>detected core count</td>
+<td>Number of worker threads</td>
+</tr>
+<tr>
+<td><code>--max-open-files</code></td>
+<td><code>threads / 4</code> (min 1)</td>
+<td>Maximum number of input files open simultaneously</td>
+</tr>
+<tr>
+<td><code>--min-abundance</code></td>
+<td><code>1</code></td>
+<td>Minimum abundance (inclusive) for a kmer to be retained</td>
+</tr>
+<tr>
+<td><code>--max-abundance</code></td>
+<td>none</td>
+<td>Maximum abundance (inclusive)</td>
+</tr>
+<tr>
+<td><code>--with-counts</code></td>
+<td>off</td>
+<td>Store per-kmer counts; otherwise only presence/absence is stored</td>
+</tr>
+<tr>
+<td><code>--keep-intermediate</code></td>
+<td>off</td>
+<td>Keep intermediate build files instead of deleting them after construction</td>
+</tr>
+<tr>
+<td><code>--approx</code></td>
+<td>off</td>
+<td>Use approximate evidence (Findere fingerprint) instead of exact evidence</td>
+</tr>
+<tr>
+<td><code>-z, --findere-z</code></td>
+<td>see below</td>
+<td>Findere z parameter: number of consecutive kmers that must all match (approximate evidence only)</td>
+</tr>
+<tr>
+<td><code>--evidence-bits</code></td>
+<td>see below</td>
+<td>Fingerprint bits per slot (b), approximate evidence only</td>
+</tr>
+<tr>
+<td><code>--fp</code></td>
+<td>see below</td>
+<td>Target false-positive rate per z-window, approximate evidence only</td>
+</tr>
+<tr>
+<td><code>--block-size</code></td>
+<td><code>1</code></td>
+<td>Block size, in unitigs, for the exact on-disk index (rounded up to a power of 2)</td>
+</tr>
+</tbody>
+</table>
+<h2 id="exact-vs-approximate-evidence">Exact vs. approximate evidence</h2>
+<p>By default, an index stores <strong>exact</strong> evidence: a kmer is either present or absent (or has an exact count with <code>--with-counts</code>), with no false positives.</p>
+<p>With <code>--approx</code>, evidence is stored as a compact <strong>fingerprint</strong> instead, trading a small, tunable false-positive rate for reduced memory/disk usage. The false-positive model is:</p>
+<div class="arithmatex">\[FP = \frac{1}{2^{b \cdot z}}\]</div>
+<p>where <span class="arithmatex">\(b\)</span> is <code>--evidence-bits</code> and <span class="arithmatex">\(z\)</span> is <code>--findere-z</code>. Any two of <code>-z</code>, <code>--evidence-bits</code>, <code>--fp</code> can be given and the third is derived; if none are given, defaults are <span class="arithmatex">\(b=8\)</span>, <span class="arithmatex">\(z=1\)</span> (<span class="arithmatex">\(FP \approx 1/256\)</span>). See <a href="../estimate/"><code>estimate</code></a> to explore this trade-off before building an index, and <a href="../reindex/"><code>reindex</code></a> to convert an existing index between the two representations.</p>
+<p><code>z</code> must be strictly less than k: the effective indexed kmer length under approximate evidence is k−z+1.</p>
+
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+                
+                  
+
+
+
+<h1 id="merge">merge</h1>
+<p>Merge multiple built indexes into a single index.</p>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>merge<span class="w"> </span>-o<span class="w"> </span>OUTPUT<span class="w"> </span>SOURCE...<span class="w"> </span><span class="o">[</span>OPTIONS<span class="o">]</span>
+</code></pre></div>
+<h2 id="arguments">Arguments</h2>
+<table>
+<thead>
+<tr>
+<th>Argument</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>SOURCE...</code></td>
+<td>Index directories to merge (at least one required)</td>
+</tr>
+</tbody>
+</table>
+<h2 id="options">Options</h2>
+<table>
+<thead>
+<tr>
+<th>Option</th>
+<th>Default</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>-o, --output</code></td>
+<td>— (required)</td>
+<td>Output index directory</td>
+</tr>
+<tr>
+<td><code>--force</code></td>
+<td>off</td>
+<td>Overwrite an existing output directory</td>
+</tr>
+<tr>
+<td><code>--force-presence</code></td>
+<td>off</td>
+<td>Store the merged index as presence/absence even if all sources have counts</td>
+</tr>
+<tr>
+<td><code>--rename-duplicates</code></td>
+<td>off</td>
+<td>Disambiguate duplicate genome labels (<code>.1</code>, <code>.2</code>, …) instead of failing</td>
+</tr>
+<tr>
+<td><code>--budget-fraction</code></td>
+<td><code>0.5</code></td>
+<td>Fraction of available RAM reserved as the memory budget for parallel partition merging</td>
+</tr>
+</tbody>
+</table>
+<h2 id="behaviour">Behaviour</h2>
+<p>The output mode is chosen automatically: if every source index stores counts, the merged index stores counts too; otherwise it is presence/absence. <code>--force-presence</code> forces presence/absence regardless of the sources.</p>
+<p>By default, merging two indexes that share a genome label fails with an error; <code>--rename-duplicates</code> instead appends a numeric suffix to keep both copies.</p>
+
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+                
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+
+
+
+<h1 id="name-tree">name-tree</h1>
+<p>Translate a numerically-labelled tree export (TNT, PhyG, or any plain Newick file with bare <code>1</code>, <code>2</code>, <code>3</code>, … leaf labels) back to real taxon names, reading the label order from the FASTA that produced it.</p>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>name-tree<span class="w"> </span>TREE<span class="w"> </span>--fasta<span class="w"> </span>FASTA<span class="w"> </span>-o<span class="w"> </span>OUTPUT
+</code></pre></div>
+<h2 id="arguments">Arguments</h2>
+<table>
+<thead>
+<tr>
+<th>Argument</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>TREE</code></td>
+<td>Tree file to translate — a TNT-style NEXUS export (<code>tree NAME = [&amp;U] ...;</code>) or a plain Newick file</td>
+</tr>
+<tr>
+<td><code>--fasta</code></td>
+<td>FASTA file whose record order gives the numeric taxon labels (1-based) — typically the <code>_sankoff.fasta</code>/<code>_snp.fasta</code> used to produce <code>TREE</code></td>
+</tr>
+<tr>
+<td><code>-o, --output</code></td>
+<td>Output NEXUS file path</td>
+</tr>
+</tbody>
+</table>
+<h2 id="output">Output</h2>
+<p>A NEXUS file with a <code>taxa</code> block, a <code>translate</code> table (numeric label → taxon name, from <code>--fasta</code>'s header order), and every tree found in <code>TREE</code>, topology unchanged — readable directly in FigTree, PearTree, <code>ape</code> (R), etc.</p>
+<p><code>--tnt</code>'s and <code>--phyg</code>'s exports (see <a href="../phylo/">phylo</a>) both number taxa <code>1..N</code> in the same order as the pseudo-alignment FASTA they were built from (<code>&lt;prefix&gt;_sankoff.fasta</code>), so pass that same file as <code>--fasta</code> here.</p>
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+
+<h1 id="pack">pack</h1>
+<p>Pack an index's per-column matrix files into a single-file format to reduce query-time I/O (fewer file opens per query).</p>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>pack<span class="w"> </span>INDEX<span class="w"> </span><span class="o">[</span>--sparse<span class="o">]</span>
+</code></pre></div>
+<h2 id="arguments">Arguments</h2>
+<table>
+<thead>
+<tr>
+<th>Argument</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>INDEX</code></td>
+<td>Index directory to pack (modified in place)</td>
+</tr>
+</tbody>
+</table>
+<h2 id="options">Options</h2>
+<table>
+<thead>
+<tr>
+<th>Option</th>
+<th>Default</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>--sparse</code></td>
+<td>off</td>
+<td>Pack presence/absence matrices into a sparse, deduplicated format instead of the dense one</td>
+</tr>
+</tbody>
+</table>
+<p>The index directory is locked for exclusive access while packing.</p>
+<h2 id="-sparse"><code>--sparse</code></h2>
+<p>Presence/absence data (which genomes carry each kmer) is often mostly empty — most kmers are present in only a handful of genomes out of the whole collection. The default (dense) packed format stores one bit per genome for every kmer regardless of how many genomes actually carry it; <code>--sparse</code> instead stores each kmer's genome list directly, and deduplicates identical lists shared by many kmers (common in real data, since kmers from the same conserved region tend to be carried by the same genomes).</p>
+<p>On real genome collections this has measured at roughly 7x smaller on disk than the dense format, and single-kmer lookups (the shape <code>phylo</code>'s sibling-annex/entropy/Sankoff computations use) are typically faster too, since the smaller files mean less data to read from disk. The trade-off: reading a whole genome column at once (used by <code>--metric</code> distance-matrix computations) is much slower on the sparse format than on the dense one, since there is no native column layout to read sequentially — prefer the dense format (the default, no <code>--sparse</code>) for indexes you mainly query with <code>phylo</code>'s plain <code>--metric</code> distance matrices.</p>
+<p>Count matrices (<code>--metric</code> on a count index) are not affected by <code>--sparse</code> — only presence/absence matrices are.</p>
+
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+    Partitioning and indexing architecture
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+      <a href="../superkmer/" class="md-nav__link">
+        
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+    superkmer
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+  </span>
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+      <a href="../index_command/" class="md-nav__link">
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+    
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+    index
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+
+              
+            
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+    <li class="md-nav__item">
+      <a href="../merge/" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
+    
+  
+    merge
+  
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+    
+  </span>
+  
+  
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+      <a href="../filter/" class="md-nav__link">
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+      <a href="../select/" class="md-nav__link">
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+    select
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+      <a href="../query/" class="md-nav__link">
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+    query
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+      <a href="../dump/" class="md-nav__link">
+        
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+    
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+    dump
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+      <a href="../annotate/" class="md-nav__link">
+        
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+    
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+    annotate
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+    
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+    phylo
+  
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+    
+  </span>
+  
+  
+
+          <span class="md-nav__icon md-icon"></span>
+        </label>
+      
+      <a href="./" class="md-nav__link md-nav__link--active">
+        
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+    
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+    phylo
+  
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+    
+  </span>
+  
+  
+
+      </a>
+      
+        
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+    
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#arguments" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Arguments
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#distance-matrix" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Distance matrix
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Distance matrix">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#metric-definitions" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Metric definitions
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#central-position-snp-model" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Central-position SNP model
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Central-position SNP model">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#locus-eligibility" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Locus eligibility
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#family-overlap-and-low-coverage-genomes" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Family overlap and low-coverage genomes
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#sampling-at-scale-subsample-shannon-entropy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Sampling at scale: --subsample, --shannon, --entropy
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Sampling at scale: --subsample, --shannon, --entropy">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#-subsample-n" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        --subsample N
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#-shannon-measuring-how-informative-a-family-is" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        --shannon: measuring how informative a family is
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#-entropy-mu-entropy-sd-sigma-biasing-the-sample-toward-informative-families" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        --entropy MU / --entropy-sd SIGMA: biasing the sample toward informative families
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#sankoff-calibration-and-phylogenetic-exports" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Sankoff calibration and phylogenetic exports
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Sankoff calibration and phylogenetic exports">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#the-16-state-model" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        The 16-state model
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#exports" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Exports
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#output-files" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Output files
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Output files">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#distance-matrix_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Distance matrix
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#central-position-snp-model_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Central-position SNP model
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#sankoff-calibration-and-exports" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Sankoff calibration and exports
+      
+    </span>
+  </a>
+  
+</li>
+        
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+    </nav>
+  
+</li>
+      
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+  
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+      
+        <li class="md-nav__item">
+  <a href="#arguments" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Arguments
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#distance-matrix" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Distance matrix
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Distance matrix">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#metric-definitions" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Metric definitions
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#central-position-snp-model" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Central-position SNP model
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Central-position SNP model">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#locus-eligibility" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Locus eligibility
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#family-overlap-and-low-coverage-genomes" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Family overlap and low-coverage genomes
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#sampling-at-scale-subsample-shannon-entropy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Sampling at scale: --subsample, --shannon, --entropy
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Sampling at scale: --subsample, --shannon, --entropy">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#-subsample-n" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        --subsample N
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#-shannon-measuring-how-informative-a-family-is" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        --shannon: measuring how informative a family is
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#-entropy-mu-entropy-sd-sigma-biasing-the-sample-toward-informative-families" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        --entropy MU / --entropy-sd SIGMA: biasing the sample toward informative families
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#sankoff-calibration-and-phylogenetic-exports" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Sankoff calibration and phylogenetic exports
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Sankoff calibration and phylogenetic exports">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#the-16-state-model" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        The 16-state model
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#exports" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Exports
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#output-files" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Output files
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Output files">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#distance-matrix_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Distance matrix
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#central-position-snp-model_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Central-position SNP model
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#sankoff-calibration-and-exports" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Sankoff calibration and exports
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+
+<h1 id="phylo">phylo</h1>
+<p>Compute pairwise evolutionary-distance proxies between the genomes stored in an index — a plain distance matrix, optionally trees (NJ/UPGMA), and optionally a central-position SNP model with exports for external phylogenetic tools (TNT, PhyG, IQ-TREE).</p>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>phylo<span class="w"> </span>INDEX<span class="w"> </span><span class="o">[</span>OPTIONS<span class="o">]</span>
+</code></pre></div>
+<h2 id="arguments">Arguments</h2>
+<table>
+<thead>
+<tr>
+<th>Argument</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>INDEX</code></td>
+<td>Index directory</td>
+</tr>
+</tbody>
+</table>
+<h2 id="distance-matrix">Distance matrix</h2>
+<table>
+<thead>
+<tr>
+<th>Option</th>
+<th>Default</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>--metric</code></td>
+<td><code>jaccard</code></td>
+<td>One of <code>jaccard</code>, <code>mash</code>, <code>hamming</code>, <code>bray-curtis</code>, <code>relfreq-bray-curtis</code>, <code>euclidean</code>, <code>relfreq-euclidean</code>, <code>hellinger</code>, <code>hellinger-euclidean</code></td>
+</tr>
+<tr>
+<td><code>--presence-threshold</code></td>
+<td><code>1</code></td>
+<td>Minimum count for a kmer to be considered present, for Jaccard/Mash on a count index</td>
+</tr>
+<tr>
+<td><code>--shared-kmers</code></td>
+<td>off</td>
+<td>Also write the shared-kmer count matrix</td>
+</tr>
+<tr>
+<td><code>--nj</code></td>
+<td>off</td>
+<td>Compute and write a Neighbor-Joining tree (Newick)</td>
+</tr>
+<tr>
+<td><code>--upgma</code></td>
+<td>off</td>
+<td>Compute and write a UPGMA tree (Newick)</td>
+</tr>
+<tr>
+<td><code>-o, --output</code></td>
+<td>none (stdout)</td>
+<td>Output file prefix; without it, the distance matrix is printed to stdout as CSV</td>
+</tr>
+</tbody>
+</table>
+<p><code>hamming</code> requires a presence/absence index. All other metrics work on either index type; on a presence index, <code>jaccard</code>/<code>mash</code>/<code>hamming</code> are the only ones available.</p>
+<h3 id="metric-definitions">Metric definitions</h3>
+<ul>
+<li><strong>jaccard</strong>: <span class="arithmatex">\(D = 1 - \dfrac{|A \cap B|}{|A \cup B|}\)</span> over the sets of kmers present in each genome.</li>
+<li><strong>mash</strong>: derived from the Jaccard distance via <span class="arithmatex">\(D = -\dfrac{1}{k} \ln\!\left(\dfrac{2J}{1+J}\right)\)</span> where <span class="arithmatex">\(J = 1 - D_{\text{jaccard}}\)</span> and <span class="arithmatex">\(k\)</span> is the index's kmer size; clamped to 1.0 when <span class="arithmatex">\(J \le 0\)</span>.</li>
+<li><strong>hamming</strong>: number of kmer positions where presence differs between the two genomes (presence index only, not normalized): <span class="arithmatex">\(D = \sum_i \mathbb{1}[a_i \ne b_i]\)</span>.</li>
+<li><strong>bray-curtis</strong>: <span class="arithmatex">\(D = 1 - \dfrac{2 \sum_i \min(c_i^A, c_i^B)}{\sum_i c_i^A + \sum_i c_i^B}\)</span> on raw per-kmer counts.</li>
+<li><strong>relfreq-bray-curtis</strong>: the same formula computed on per-genome relative frequencies <span class="arithmatex">\(p_i = c_i / \sum_j c_j\)</span> instead of raw counts.</li>
+<li><strong>euclidean</strong>: <span class="arithmatex">\(D = \sqrt{\sum_i (c_i^A - c_i^B)^2}\)</span> on raw counts.</li>
+<li><strong>relfreq-euclidean</strong>: the same formula on relative frequencies.</li>
+<li><strong>hellinger</strong>: <span class="arithmatex">\(D = \dfrac{1}{\sqrt{2}} \sqrt{\sum_i \left(\sqrt{p_i^A} - \sqrt{p_i^B}\right)^2}\)</span> on relative frequencies, bounded in <span class="arithmatex">\([0, 1]\)</span>.</li>
+<li><strong>hellinger-euclidean</strong>: the unnormalized variant, <span class="arithmatex">\(D = \sqrt{2} \times D_{\text{hellinger}}\)</span>.</li>
+</ul>
+<h2 id="central-position-snp-model">Central-position SNP model</h2>
+<p>This is a separate operation from the distance-matrix computation above: if any option below is used, no <code>--metric</code> matrix is computed in the same invocation.</p>
+<p>A <strong>family</strong> is the set of up to 4 kmers that share identical flanking sequence and differ only at the exact central base. Because <span class="arithmatex">\(k\)</span> is odd, the central position is well defined and maps to itself under reverse complementation. All computations below first require building the <strong>sibling annex</strong>, an index-wide record of which of the 4 possible central bases are observed at each family, across every genome.</p>
+<table>
+<thead>
+<tr>
+<th>Option</th>
+<th>Default</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>--sibling-annex</code></td>
+<td>off</td>
+<td>Build the sibling presence-mask annex (prerequisite for every option below)</td>
+</tr>
+<tr>
+<td><code>--exclude-genome LABEL</code></td>
+<td>none</td>
+<td>Exclude a genome (repeatable) from every SNP/Sankoff/export computation below</td>
+</tr>
+<tr>
+<td><code>--min-shared-family N</code></td>
+<td>none</td>
+<td>Auto-exclude any genome whose mean shared-family count against every other genome (see <code>--family-overlap</code>) falls below <code>N</code> — same exclusion as <code>--exclude-genome</code>, applied on top of it</td>
+</tr>
+<tr>
+<td><code>--sibling-stats</code></td>
+<td>off</td>
+<td>Write the family-size (sibling count) distribution, per genome and globally</td>
+</tr>
+<tr>
+<td><code>--raw-snp-distance</code></td>
+<td>off</td>
+<td>Write the single-copy central-SNP p-distance matrix</td>
+</tr>
+<tr>
+<td><code>--raw-snp-counts</code></td>
+<td>off</td>
+<td>Write per-pair diagnostic counts (n_snp, n_shared, n_eligible) instead of a matrix</td>
+</tr>
+<tr>
+<td><code>--snp</code></td>
+<td>off</td>
+<td>Write a SNP-only pseudo-alignment in FASTA, IUPAC-coded</td>
+</tr>
+<tr>
+<td><code>--family-overlap</code></td>
+<td>off</td>
+<td>Write an NxN matrix of, for each genome pair, how many variable families both genomes actually carry a call for; the diagonal holds each genome's own total family count</td>
+</tr>
+</tbody>
+</table>
+<h3 id="locus-eligibility">Locus eligibility</h3>
+<p>A family is eligible for a genome pair <span class="arithmatex">\((i, j)\)</span> only if genome <span class="arithmatex">\(i\)</span> carries exactly one of the family's observed forms (single-copy, unambiguous) and genome <span class="arithmatex">\(j\)</span> also carries exactly one. A genome carrying more than one form at a locus makes that locus ineligible for any pair involving it.</p>
+<p><code>--raw-snp-distance</code> tallies, over every eligible locus of every genome pair, <span class="arithmatex">\(n_{\text{snp}}\)</span> (the two genomes' single forms differ) versus <span class="arithmatex">\(n_{\text{shared}}\)</span> (they agree — this includes invariant families). The output ratio is <span class="arithmatex">\(\hat{p} = \dfrac{n_{\text{snp}}}{n_{\text{snp}} + n_{\text{shared}}}\)</span>.</p>
+<p><code>--snp</code> restricts itself to <em>variable</em> families (family size <span class="arithmatex">\(\ge 2\)</span>) and writes one FASTA record per genome, one column per family, IUPAC-coded from each genome's presence mask at that family (a single form → the plain base; several forms → the matching IUPAC ambiguity code; no form → <code>-</code>).</p>
+<p><code>--exclude-genome</code> removes a genome from these computations, re-checking column variability among the remaining genomes so that a column made monomorphic by the exclusion is dropped rather than kept artificially. It does not affect the <code>--metric</code> distance-matrix path.</p>
+<h3 id="family-overlap-and-low-coverage-genomes">Family overlap and low-coverage genomes</h3>
+<p><code>--family-overlap</code> writes, for every genome pair, how many variable families both genomes actually carry a call for (neither is absent) — a direct measure of how much informative content two genomes actually share. On genome-skim or otherwise incomplete-coverage collections, a genome with very little overlap with everything else has almost nothing left to constrain its position in a tree, and tends to end up placed unstably (near-zero branch length, grafted inside an unrelated clade) by <code>--tnt</code>/<code>--iqtree</code>.</p>
+<p><code>--min-shared-family N</code> automates the fix: it excludes, before any computation, every genome whose mean shared-family count against all other genomes (the same statistic, averaged per row of the <code>--family-overlap</code> matrix) falls below <code>N</code>. There is no universal value for <code>N</code> — it depends on how divergent and how completely covered the genome collection is; inspect <code>--family-overlap</code>'s own output to find where the real gap sits before choosing a threshold.</p>
+<h2 id="sampling-at-scale-subsample-shannon-entropy">Sampling at scale: <code>--subsample</code>, <code>--shannon</code>, <code>--entropy</code></h2>
+<p>On a large index (billions of families), building a full pseudo-alignment or fully calibrating the Sankoff model is not just slow — it may not fit in the time you have. <code>--subsample</code> bounds the work to a fixed number of families; <code>--shannon</code> reports how informative each family is; <code>--entropy</code>/<code>--entropy-sd</code> bias which families get kept toward the informative ones instead of choosing uniformly at random.</p>
+<table>
+<thead>
+<tr>
+<th>Option</th>
+<th>Default</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>--subsample N</code></td>
+<td>none (keep everything)</td>
+<td>Cap the number of variable families (family size ≥ 2) retained, to approximately <code>N</code></td>
+</tr>
+<tr>
+<td><code>--shannon</code></td>
+<td>off</td>
+<td>Write <code>&lt;prefix&gt;_shannon.csv</code>: per-family Shannon entropy, one row per family</td>
+</tr>
+<tr>
+<td><code>--entropy MU</code></td>
+<td>off (<code>1.0</code> if only <code>--entropy-sd</code> is given)</td>
+<td>Center of the entropy band to favor when sampling</td>
+</tr>
+<tr>
+<td><code>--entropy-sd SIGMA</code></td>
+<td>off (<code>0.5</code> if only <code>--entropy</code> is given)</td>
+<td>Width of that band</td>
+</tr>
+</tbody>
+</table>
+<p><code>--subsample</code>/<code>--entropy</code>/<code>--entropy-sd</code> affect every option that scans variable families: <code>--snp</code>, <code>--family-overlap</code>, <code>--shannon</code>, and the whole Sankoff pipeline (<code>--sankoff</code>/<code>--tnt</code>/<code>--phyg</code>/<code>--iqtree</code>, next section) — all of them draw from the <em>same</em> selection of families in one invocation, so the Sankoff calibration and the pseudo-alignment it calibrates always describe the same sites, and <code>--family-overlap</code>'s counts stay consistent with <code>--snp</code>'s columns. <code>--raw-snp-distance</code>/<code>--raw-snp-counts</code> are not affected — they always scan every family, since their p-distance estimate is a whole-index statistic, not something that benefits from being restricted to a sample.</p>
+<h3 id="-subsample-n"><code>--subsample N</code></h3>
+<p>Without <code>--subsample</code>, every variable family (family size ≥ 2, i.e. every family where at least one genome differs from the rest) is used. With <code>--subsample N</code>, roughly <code>N</code> families are kept instead, chosen at random but in proportion to how many candidate families each part of the index actually holds — so the sample stays representative of the whole index, not skewed toward whichever part happens to be scanned first. If the index has fewer than <code>N</code> candidate families in the first place, <code>--subsample</code> has no effect: everything is kept.</p>
+<p><code>--subsample</code> trades completeness for speed: <code>--snp</code>'s alignment gets fewer columns, <code>--sankoff</code>'s calibration is based on fewer observations, but the resolution work (the expensive part of a <code>phylo</code> run on a large index) scales with <code>N</code> instead of with the index's true size. Pick <code>N</code> as large as your time budget allows — a few hundred thousand to a few million families is usually enough for the transition-probability estimates in <code>--sankoff</code>'s calibration to stabilize; a smaller <code>N</code> speeds up exploratory runs.</p>
+<h3 id="-shannon-measuring-how-informative-a-family-is"><code>--shannon</code>: measuring how informative a family is</h3>
+<p>Not every variable family is equally useful for a tree: a family that differs in only one genome out of a thousand carries very little signal, and one where the pattern looks essentially random across genomes may be too saturated (multiple substitutions have overwritten the original signal) to carry real information either. <code>--shannon</code> quantifies this with the Shannon entropy (in bits) of each family's states across the genomes that carry it — low entropy means "almost everyone agrees" (an invariant or near-invariant family, phylogenetically shallow), while entropy near the ceiling for a 4-state character means "close to a random draw between the possible bases" (saturated).</p>
+<p><code>&lt;prefix&gt;_shannon.csv</code> (or <code>shannon.csv</code> without <code>-o</code>) has one row per family visited:</p>
+<table>
+<thead>
+<tr>
+<th>Column</th>
+<th>Meaning</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>layer</code></td>
+<td>an internal index-layer identifier — stable within one run, not meaningful across indexes</td>
+</tr>
+<tr>
+<td><code>family_idx</code></td>
+<td>the family's position within that layer</td>
+</tr>
+<tr>
+<td><code>entropy15</code></td>
+<td>Shannon entropy (bits) over the 16 possible states (the 15 non-empty subsets of <code>{A,C,G,T}</code> — the same alphabet <code>--sankoff</code>'s 16-state model uses), genomes absent from the family excluded from the count</td>
+</tr>
+<tr>
+<td><code>entropy4</code></td>
+<td>Shannon entropy (bits) reduced to the 4 plain bases, kept alongside <code>entropy15</code> for comparison — a genome carrying more than one base at once counts once per base, so this can differ from <code>entropy15</code></td>
+</tr>
+<tr>
+<td><code>family_size</code></td>
+<td>number of distinct central bases observed anywhere in the index for this family (2–4, since monomorphic families aren't visited)</td>
+</tr>
+<tr>
+<td><code>n_genomes_present</code></td>
+<td>how many genomes the entropy was computed over</td>
+</tr>
+</tbody>
+</table>
+<p>Run with <code>--subsample N --shannon</code> to get a bounded diagnostic sample instead of a full-index pass — useful to inspect the entropy distribution and decide reasonable <code>--entropy</code>/<code>--entropy-sd</code> values (see below) before committing to a full run.</p>
+<h3 id="-entropy-mu-entropy-sd-sigma-biasing-the-sample-toward-informative-families"><code>--entropy MU</code> / <code>--entropy-sd SIGMA</code>: biasing the sample toward informative families</h3>
+<p>By default, <code>--subsample</code> draws families uniformly — every candidate family has the same chance of being kept, regardless of how informative it actually is. <code>--entropy</code>/<code>--entropy-sd</code> change that: instead of a uniform draw, each family's chance of being kept is weighted by how close its own entropy (the <code>entropy15</code> value <code>--shannon</code> reports) is to <code>MU</code>, using a bell-shaped (Gaussian) curve of width <code>SIGMA</code> — a family with entropy exactly <code>MU</code> is the most likely to be kept, and the chance falls off smoothly the further its entropy is from <code>MU</code>, with no hard cutoff (a few families outside the target band can still get in, just less often).</p>
+<p>The filter activates as soon as <em>either</em> <code>--entropy</code> or <code>--entropy-sd</code> is given; whichever one you don't set defaults to <code>1.0</code>/<code>0.5</code>. It can be combined with <code>--subsample N</code> (the target count is still approximately <code>N</code>, now biased toward the entropy band instead of uniform — expect somewhat <em>fewer</em> than <code>N</code> families in practice, since low-weight families are dropped rather than replaced) or used alone (<code>--entropy</code> without <code>--subsample</code>: a soft entropy filter over the whole index, no size target).</p>
+<p>The first <code>phylo</code> run on a given index that uses <code>--entropy</code>/<code>--entropy-sd</code> pays a one-time extra cost (every candidate family's entropy has to be computed once, up front, and is then saved alongside the index). Every following run — even with different <code>MU</code>/<code>SIGMA</code> values — reuses that saved data and stays fast.</p>
+<h2 id="sankoff-calibration-and-phylogenetic-exports">Sankoff calibration and phylogenetic exports</h2>
+<table>
+<thead>
+<tr>
+<th>Option</th>
+<th>Default</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>--sankoff</code></td>
+<td>off</td>
+<td>Calibrate a 16-state parsimony cost matrix and matching pseudo-alignment</td>
+</tr>
+<tr>
+<td><code>--sankoff-ratio-ceiling</code></td>
+<td><code>0.5</code></td>
+<td>Exclude genome pairs whose raw SNP ratio exceeds this value from the calibration</td>
+</tr>
+<tr>
+<td><code>--free-loss</code></td>
+<td>off</td>
+<td>Recode a family's non-detection as the <code>?</code> missing-data symbol instead of an ordinary, costed state, in <code>--sankoff</code>'s pseudo-alignment and every export built from it</td>
+</tr>
+<tr>
+<td><code>--tnt</code></td>
+<td>off</td>
+<td>Also write a TNT script (implies <code>--sankoff</code>)</td>
+</tr>
+<tr>
+<td><code>--phyg</code></td>
+<td>off</td>
+<td>Also write PhyG input files (implies <code>--sankoff</code>)</td>
+</tr>
+<tr>
+<td><code>--iqtree</code></td>
+<td>off</td>
+<td>Also write an IQ-TREE custom model and alignment (implies <code>--sankoff</code>)</td>
+</tr>
+<tr>
+<td><code>--sankoff-cost-scale</code></td>
+<td><code>100</code></td>
+<td>Integer scaling factor applied to costs before rounding (required by TNT/PhyG's integer-only cost commands)</td>
+</tr>
+</tbody>
+</table>
+<h3 id="the-16-state-model">The 16-state model</h3>
+<p>Each family is treated as a character with 16 possible states: one per subset of the 4 possible central bases actually observed (including the empty subset). Calibration combines two tallies, both restricted to genome pairs at or below <code>--sankoff-ratio-ceiling</code>:</p>
+<ul>
+<li>a <span class="arithmatex">\(5 \times 5\)</span> transition matrix over family cardinality (0–4 observed forms) between paired genomes, and</li>
+<li>a <span class="arithmatex">\(4 \times 4\)</span> base-substitution transition matrix from unambiguous single-copy loci,</li>
+</ul>
+<p>which are combined into a row-normalized <span class="arithmatex">\(16 \times 16\)</span> transition probability matrix <span class="arithmatex">\(P\)</span>, converted to a symmetric cost matrix via <span class="arithmatex">\(\text{cost}(a,b) = -\ln P(a,b)\)</span>.</p>
+<p><code>--sankoff</code> alone writes the cost matrix, the calibration parameters, and a pseudo-alignment recoded so the empty state uses the symbol <code>0</code> (never a gap character, to avoid ambiguity with external tools' own gap semantics). It does not run any external tool.</p>
+<p>With <code>--free-loss</code>, the empty state is recoded to <code>?</code> instead — TNT/PhyG/IQ-TREE's own missing-data symbol — rather than an ordinary, costed 16th state. This matters for genome-skim or otherwise incomplete-coverage collections, where non-detection of a family is dominated by sampling failure rather than true evolutionary loss: scoring it as a real state risks grouping genomes by shared undersampling instead of shared ancestry. <code>?</code> rather than <code>-</code> because <code>-</code> still carries gap/indel semantics in these tools, and a non-detected family is not an observed deletion. <code>--free-loss</code> also drops the cardinality-transition cost between any two states, not just to/from the empty one: whether a genome shows 1 vs. 2 (etc.) detected members of a family it does carry is exactly as vulnerable to sampling failure as whether the family was detected at all, so gaining or losing a sibling is priced the same way — for free — as gaining or losing the whole family. Combine with <code>--min-shared-family</code>/<code>--family-overlap</code> above: <code>--free-loss</code> removes the false signal from non-detection, but a genome left with too little real overlap with everything else will still be placed unstably — excluding it is the other half of the fix.</p>
+<h3 id="exports">Exports</h3>
+<p>All three exports reuse the <code>--sankoff</code> calibrated matrix and pseudo-alignment, recoded for the target tool:</p>
+<ul>
+<li><strong><code>--tnt</code></strong>: a self-contained TNT script (alignment recoded to TNT's fixed 16-symbol alphabet, integer-scaled cost matrix re-closed to a metric, a default search block).</li>
+<li><strong><code>--phyg</code></strong>: a custom cost-matrix file plus a PhyG script reusing the <code>--sankoff</code> alignment directly.</li>
+<li><strong><code>--iqtree</code></strong>: a custom substitution-model file (exchangeability matrix recovered as <span class="arithmatex">\(R(a,b) = e^{-\text{cost}(a,b)}\)</span>, plus empirical state frequencies) and a matching alignment, for maximum-likelihood inference with real branch lengths (unlike the parsimony step-counts from TNT/PhyG). Only states actually occurring in the alignment are kept and compactly renumbered.</li>
+</ul>
+<p>TNT and PhyG both write trees with bare numeric leaf labels (<code>1</code>, <code>2</code>, …, in the same order as <code>&lt;prefix&gt;_sankoff.fasta</code>). Use <a href="../name-tree/"><code>name-tree</code></a> on the tool's own tree output plus that same FASTA to get a NEXUS file with real taxon names.</p>
+<h2 id="output-files">Output files</h2>
+<p>With <code>-o/--output PREFIX</code>, the relevant subset of the files below is written. Without <code>-o</code>, only the plain <code>--metric</code> distance matrix is produced, on stdout. All matrices use genome labels (from the index metadata) as row/column headers, in index order; all CSVs are comma-separated with a header row.</p>
+<h3 id="distance-matrix_1">Distance matrix</h3>
+<table>
+<thead>
+<tr>
+<th>File</th>
+<th>Written by</th>
+<th>Format</th>
+<th>Content</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>&lt;prefix&gt;_dist.csv</code></td>
+<td>always</td>
+<td>CSV matrix</td>
+<td>the <code>--metric</code> distance, 6 decimals, symmetric, diagonal 0</td>
+</tr>
+<tr>
+<td><code>&lt;prefix&gt;_shared.csv</code></td>
+<td><code>--shared-kmers</code></td>
+<td>CSV matrix</td>
+<td>shared-kmer count per genome pair (integers)</td>
+</tr>
+<tr>
+<td><code>&lt;prefix&gt;_nj.nwk</code></td>
+<td><code>--nj</code></td>
+<td>Newick</td>
+<td>Neighbor-Joining tree, branch lengths from the <code>--metric</code> matrix</td>
+</tr>
+<tr>
+<td><code>&lt;prefix&gt;_upgma.nwk</code></td>
+<td><code>--upgma</code></td>
+<td>Newick</td>
+<td>UPGMA tree, same matrix</td>
+</tr>
+</tbody>
+</table>
+<p>Matrix layout (<code>_dist.csv</code>, <code>_shared.csv</code>, and every other "CSV matrix" below): header <code>genome,&lt;label1&gt;,&lt;label2&gt;,...</code>, one data row per genome, <code>&lt;label&gt;,&lt;value1&gt;,&lt;value2&gt;,...</code>.</p>
+<h3 id="central-position-snp-model_1">Central-position SNP model</h3>
+<table>
+<thead>
+<tr>
+<th>File</th>
+<th>Written by</th>
+<th>Format</th>
+<th>Content</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>&lt;prefix&gt;_siblings.csv</code></td>
+<td><code>--sibling-stats</code></td>
+<td>CSV table</td>
+<td>family-size distribution, per genome and global</td>
+</tr>
+<tr>
+<td><code>&lt;prefix&gt;_rawsnp.csv</code></td>
+<td><code>--raw-snp-distance</code></td>
+<td>CSV matrix</td>
+<td>single-copy central-SNP p-distance (<span class="arithmatex">\(\hat p\)</span>), or <code>NA</code></td>
+</tr>
+<tr>
+<td><code>&lt;prefix&gt;_rawsnp_counts.csv</code></td>
+<td><code>--raw-snp-counts</code></td>
+<td>CSV table</td>
+<td>per-pair diagnostic counts behind <code>_rawsnp.csv</code></td>
+</tr>
+<tr>
+<td><code>&lt;prefix&gt;_snp.fasta</code></td>
+<td><code>--snp</code></td>
+<td>FASTA</td>
+<td>SNP-only pseudo-alignment, IUPAC-coded</td>
+</tr>
+<tr>
+<td><code>&lt;prefix&gt;_family_overlap.csv</code></td>
+<td><code>--family-overlap</code></td>
+<td>CSV matrix</td>
+<td>variable families both genomes of a pair carry a call for</td>
+</tr>
+<tr>
+<td><code>&lt;prefix&gt;_shannon.csv</code></td>
+<td><code>--shannon</code></td>
+<td>CSV table</td>
+<td>per-family Shannon entropy, see "Sampling at scale" above</td>
+</tr>
+</tbody>
+</table>
+<p><strong><code>_siblings.csv</code></strong> — family size = number of distinct central bases observed at a family (1–4), not "sibling count" (0–3).</p>
+<table>
+<thead>
+<tr>
+<th>Column</th>
+<th>Meaning</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>genome</code></td>
+<td>genome label, or the literal <code>global</code> for the last row</td>
+</tr>
+<tr>
+<td><code>1</code>, <code>2</code>, <code>3</code>, <code>4</code></td>
+<td>for a genome row: number of families of that size where the genome carries ≥ 1 member. For the <code>global</code> row: the actual deduplicated family-size histogram — <strong>not</strong> the sum of the rows above (a family shared by several genomes would otherwise be counted once per genome)</td>
+</tr>
+</tbody>
+</table>
+<p><strong><code>_rawsnp.csv</code></strong> — same matrix layout as <code>_dist.csv</code>; each cell is <span class="arithmatex">\(\hat p = n_{\text{snp}}/(n_{\text{snp}}+n_{\text{shared}})\)</span>, 6 decimals, or <code>NA</code> when the pair has zero eligible loci (distinguishes "identical everywhere eligible" from "nothing eligible at all").</p>
+<p><strong><code>_rawsnp_counts.csv</code></strong> — one row per unordered genome pair (not a matrix), the counts <code>_rawsnp.csv</code>'s ratio is computed from:</p>
+<table>
+<thead>
+<tr>
+<th>Column</th>
+<th>Meaning</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>genome_a</code>, <code>genome_b</code></td>
+<td>the pair</td>
+</tr>
+<tr>
+<td><code>n_snp</code></td>
+<td>eligible loci where the two genomes' single forms differ</td>
+</tr>
+<tr>
+<td><code>n_shared</code></td>
+<td>eligible loci where they agree (includes invariant families)</td>
+</tr>
+<tr>
+<td><code>n_eligible</code></td>
+<td><code>n_snp + n_shared</code></td>
+</tr>
+<tr>
+<td><code>ratio</code></td>
+<td><span class="arithmatex">\(\hat p\)</span> = <code>n_snp / n_eligible</code>, or <code>NA</code> if <code>n_eligible = 0</code></td>
+</tr>
+</tbody>
+</table>
+<p><strong><code>_snp.fasta</code></strong> — one record per non-excluded genome, one column per variable family (family size ≥ 2), header carries an <code>n_sites</code> annotation. Each site is IUPAC-coded from the genome's presence mask at that family: single observed form → plain base; several forms → matching IUPAC ambiguity code; no form → <code>-</code>.</p>
+<p><strong><code>_family_overlap.csv</code></strong> — same matrix layout as <code>_dist.csv</code>; cell <code>[i][j]</code> = number of <code>_snp.fasta</code> columns where both genome <code>i</code> and <code>j</code> carry a call (neither is <code>-</code>). Diagonal <code>[i][i]</code> is kept (not skipped): it holds genome <code>i</code>'s own total variable-family count.</p>
+<h3 id="sankoff-calibration-and-exports">Sankoff calibration and exports</h3>
+<table>
+<thead>
+<tr>
+<th>File</th>
+<th>Written by</th>
+<th>Format</th>
+<th>Content</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>&lt;prefix&gt;_sankoff_matrix.csv</code></td>
+<td><code>--sankoff</code>/<code>--tnt</code>/<code>--phyg</code>/<code>--iqtree</code></td>
+<td>CSV matrix</td>
+<td>calibrated 16×16 cost matrix</td>
+</tr>
+<tr>
+<td><code>&lt;prefix&gt;_sankoff_params.yaml</code></td>
+<td>same flags</td>
+<td>YAML</td>
+<td>calibration report (raw tallies + derived probabilities)</td>
+</tr>
+<tr>
+<td><code>&lt;prefix&gt;_sankoff.fasta</code></td>
+<td>same flags</td>
+<td>FASTA</td>
+<td>Sankoff-recoded pseudo-alignment</td>
+</tr>
+<tr>
+<td><code>&lt;prefix&gt;_sankoff.tnt</code></td>
+<td><code>--tnt</code></td>
+<td>TNT script</td>
+<td>ready-to-run parsimony search</td>
+</tr>
+<tr>
+<td><code>&lt;prefix&gt;_sankoff.tcm</code></td>
+<td><code>--phyg</code></td>
+<td>PhyG TCM</td>
+<td>cost matrix in PhyG's own format</td>
+</tr>
+<tr>
+<td><code>&lt;prefix&gt;_sankoff.pg</code></td>
+<td><code>--phyg</code></td>
+<td>PhyG script</td>
+<td>ready-to-run parsimony search</td>
+</tr>
+<tr>
+<td><code>&lt;prefix&gt;_iqtree.model</code></td>
+<td><code>--iqtree</code></td>
+<td>IQ-TREE model file</td>
+<td>custom ML substitution model</td>
+</tr>
+<tr>
+<td><code>&lt;prefix&gt;_iqtree.fasta</code></td>
+<td><code>--iqtree</code></td>
+<td>FASTA</td>
+<td>alignment recoded for that model</td>
+</tr>
+</tbody>
+</table>
+<p><strong><code>_sankoff_matrix.csv</code></strong> — header <code>state,0,A,C,M,G,R,S,V,T,W,Y,H,K,D,B,N</code>: the 16 symbols are IUPAC codes for the 16 subsets of the 4 possible central bases (bit 0=A, 1=C, 2=G, 3=T), <code>0</code> standing for the empty/absent state (not <code>-</code>, to avoid colliding with external tools' own gap syntax). One row per source state, one value per destination state, cost <span class="arithmatex">\(-\ln P(a,b)\)</span>, 4 decimals.</p>
+<p><strong><code>_sankoff_params.yaml</code></strong> — everything the calibration estimated, structured so it can be reloaded rather than re-parsed:</p>
+<table>
+<thead>
+<tr>
+<th>Key</th>
+<th>Meaning</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>ratio_ceiling</code></td>
+<td>the <code>--sankoff-ratio-ceiling</code> value used</td>
+</tr>
+<tr>
+<td><code>cardinality_transitions</code></td>
+<td>5×5 list of <code>{from, to, count, probability}</code>, family cardinality (0–4 observed forms)</td>
+</tr>
+<tr>
+<td><code>composition_transitions</code></td>
+<td>4×4 list of <code>{from, to, count, probability}</code>, base letters <code>A/C/G/T</code>, single-copy substitutions</td>
+</tr>
+</tbody>
+</table>
+<p><strong><code>_sankoff.fasta</code></strong> — same sites as <code>_snp.fasta</code>, recoded to match <code>_sankoff_matrix.csv</code>'s alphabet: absent state is <code>0</code> (or <code>?</code> under <code>--free-loss</code>). Excluded genomes dropped; columns left monomorphic by that exclusion are re-checked and dropped too.</p>
+<p><strong><code>_sankoff.tnt</code></strong> (<code>--tnt</code>) — self-contained TNT script: <code>xread</code> block (alignment recoded to TNT's fixed <code>0-9A-F</code> alphabet), an integer-scaled (<code>--sankoff-cost-scale</code>) and metric-closed <code>smatrix</code>, a default <code>hold 20; mult; export</code> search. Run with <code>printf 'proc &lt;path&gt;;\nquit;\n' | tnt</code>. Produces <code>&lt;prefix&gt;_sankoff.tre</code> (bare numeric leaf labels, order matching <code>_sankoff.fasta</code>) — feed both into <a href="../name-tree/"><code>name-tree</code></a> to recover taxon names.</p>
+<p><strong><code>_sankoff.tcm</code></strong> (<code>--phyg</code>) — first line: the 16-symbol alphabet plus a trailing gap symbol (17 total). Each following line: one row of the integer-scaled, metric-closed cost matrix (17 values — the extra gap column/row reuses the cost to/from the empty state <code>0</code>, since it's never actually triggered).</p>
+<p><strong><code>_sankoff.pg</code></strong> (<code>--phyg</code>) — script: <code>read(prefasta:..., tcm:...)</code> against <code>_sankoff.fasta</code>/<code>_sankoff.tcm</code>, a default 300s/4-instance <code>search</code>, <code>report(...)</code> writing <code>&lt;prefix&gt;_sankoff.tre</code> (bare numeric labels, as for <code>--tnt</code>). Run with <code>phyg</code> from the output directory (the script uses relative file names). Feed the tree plus <code>_sankoff.fasta</code> into <a href="../name-tree/"><code>name-tree</code></a> for taxon names.</p>
+<p><strong><code>_iqtree.model</code></strong> (<code>--iqtree</code>) — lower-triangular exchangeability matrix <span class="arithmatex">\(R(a,b) = e^{-\text{cost}(a,b)}\)</span> (one row of increasing length per state, whitespace-separated, PAML order), followed by one line of empirical state frequencies. Only states actually occurring in the alignment are kept, compactly renumbered <code>0..k-1</code>.</p>
+<p><strong><code>_iqtree.fasta</code></strong> (<code>--iqtree</code>) — alignment recoded to that same compact <code>0..k-1</code> alphabet (symbols <code>0-9A-F</code>). Under <code>--free-loss</code>, non-detection becomes <code>?</code> and columns left non-informative once missing calls are ignored are dropped first (required for <code>+ASC</code>). Run with:
+<div class="highlight"><pre><span></span><code>iqtree3 -s &lt;prefix&gt;_iqtree.fasta --seqtype MORPH -m &lt;prefix&gt;_iqtree.model+ASC --prefix &lt;prefix&gt;_iqtree -T AUTO
+</code></pre></div></p>
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+  <a href="#predicate-syntax" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Predicate syntax
+      
+    </span>
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+  
+</li>
+      
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+  <a href="#taxonomy-paths" class="md-nav__link">
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+      
+        Path matching (~ / !~)
+      
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+  
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+
+
+<h1 id="genome-predicates-and-taxonomy-paths">Genome predicates and taxonomy paths</h1>
+<p>Several commands (<a href="../filter/"><code>filter</code></a>, <a href="../select/"><code>select</code></a>, <a href="../dump/"><code>dump</code></a>, <a href="../unitig/"><code>unitig</code></a>) select or group genomes using the same predicate language over genome metadata (see <a href="../annotate/"><code>annotate</code></a> for attaching metadata to a genome).</p>
+<h2 id="predicate-syntax">Predicate syntax</h2>
+<table>
+<thead>
+<tr>
+<th>Form</th>
+<th>Meaning</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>*</code> or <code>all</code></td>
+<td>Matches every genome (case-insensitive)</td>
+</tr>
+<tr>
+<td><code>key=v1\|v2</code></td>
+<td>Genome's <code>key</code> metadata equals one of the listed values</td>
+</tr>
+<tr>
+<td><code>key!=v</code></td>
+<td>Genome's <code>key</code> metadata does not equal <code>v</code></td>
+</tr>
+<tr>
+<td><code>key~path</code></td>
+<td>Genome's <code>key</code> metadata (a taxonomy path) matches <code>path</code> (ancestry match)</td>
+</tr>
+<tr>
+<td><code>key!~path</code></td>
+<td>Genome's <code>key</code> metadata does not match <code>path</code></td>
+</tr>
+</tbody>
+</table>
+<p>A genome whose metadata does not contain <code>key</code> at all cannot be classified by that predicate and is excluded from the relevant group's quorum count.</p>
+<p>Multiple <code>--ingroup</code> predicates are combined with AND; multiple <code>--outgroup</code> predicates are combined with OR. When both an ingroup and an outgroup predicate would match the same genome, ingroup classification wins.</p>
+<h2 id="taxonomy-paths">Taxonomy paths</h2>
+<p>A metadata value is treated as a taxonomy path when it starts with the literal prefix <code>taxonomy:/</code>; any other value is treated as a plain string and only supports <code>=</code>/<code>!=</code>.</p>
+<div class="highlight"><pre><span></span><code>taxonomy:/segment1@rank1/segment2@rank2/...
+</code></pre></div>
+<p>Each segment is a name, optionally annotated with a rank (e.g. <code>@family</code>, <code>@genus</code>, <code>@species</code>); ranks are optional and can be mixed within a path. The <code>@</code> character is reserved inside taxonomy paths and cannot appear in segment names or rank labels.</p>
+<h3 id="path-matching">Path matching (<code>~</code> / <code>!~</code>)</h3>
+<p>Matching compares segment names only (ranks are informational, not part of the match), with anchoring controlled by leading/trailing <code>/</code>:</p>
+<table>
+<thead>
+<tr>
+<th>Pattern</th>
+<th>Matches</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>A/B</code></td>
+<td>anywhere in the path</td>
+</tr>
+<tr>
+<td><code>/A/B</code></td>
+<td>at the start of the path (prefix)</td>
+</tr>
+<tr>
+<td><code>A/B$</code></td>
+<td>at the end of the path (suffix)</td>
+</tr>
+<tr>
+<td><code>/A/B$</code></td>
+<td>the entire path (exact)</td>
+</tr>
+</tbody>
+</table>
+<p>A rank-qualified query, <code>key@rank=value</code>, matches only when the path's segment at that specific rank equals <code>value</code>.</p>
+<h3 id="example">Example</h3>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>filter<span class="w"> </span><span class="nb">source</span><span class="w"> </span>-o<span class="w"> </span>output<span class="w"> </span>--ingroup<span class="w"> </span><span class="s2">&quot;taxon~/Betulaceae/Betula&quot;</span>
+</code></pre></div>
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+
+
+
+<h1 id="query">query</h1>
+<p>Query an index with sequences and annotate each query with the kmer matches found.</p>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>query<span class="w"> </span>INDEX<span class="w"> </span>INPUTS...<span class="w"> </span><span class="o">[</span>OPTIONS<span class="o">]</span>
+</code></pre></div>
+<h2 id="arguments">Arguments</h2>
+<table>
+<thead>
+<tr>
+<th>Argument</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>INDEX</code></td>
+<td>Index directory to query against</td>
+</tr>
+<tr>
+<td><code>INPUTS...</code></td>
+<td>Input sequence files (FASTA/FASTQ, gzip optional); at least one required</td>
+</tr>
+</tbody>
+</table>
+<h2 id="options">Options</h2>
+<table>
+<thead>
+<tr>
+<th>Option</th>
+<th>Default</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>--detail</code></td>
+<td>off</td>
+<td>Report per-position, per-genome coverage vectors in the output</td>
+</tr>
+<tr>
+<td><code>--count-missing</code></td>
+<td>off</td>
+<td>Also count query kmers absent from the index</td>
+</tr>
+<tr>
+<td><code>--force-presence</code></td>
+<td>off</td>
+<td>Report presence (0/1) per genome instead of raw counts</td>
+</tr>
+<tr>
+<td><code>--presence-threshold</code></td>
+<td><code>1</code></td>
+<td>Minimum accumulated count to declare a genome present (implies <code>--force-presence</code>)</td>
+</tr>
+<tr>
+<td><code>-z, --findere-z</code></td>
+<td>derived from the index metadata</td>
+<td>Override the Findere z parameter</td>
+</tr>
+<tr>
+<td><code>-T, --threads</code></td>
+<td>detected core count</td>
+<td>Number of worker threads</td>
+</tr>
+<tr>
+<td><code>--chunk-size</code></td>
+<td>auto-sized (available RAM ÷ threads, clamped to 4–256 MiB)</td>
+<td>I/O chunk size, in MiB</td>
+</tr>
+<tr>
+<td><code>--max-open-files</code></td>
+<td><code>threads / 4</code> (min 1)</td>
+<td>Maximum number of input files open simultaneously</td>
+</tr>
+</tbody>
+</table>
+<h2 id="output">Output</h2>
+<p>FASTA on stdout, one record per query, annotated in the OBITools-style header format <code>&gt;id {"key":value,...}</code>:</p>
+<ul>
+<li><code>kmer_count</code>: total number of kmers matched</li>
+<li><code>kmer_missing</code>: number of query kmers absent from the index (only with <code>--count-missing</code>)</li>
+<li><code>kmer_strict_matches</code>: per-genome match counts</li>
+<li><code>coverage</code>: per-position, per-genome coverage vectors (only with <code>--detail</code>)</li>
+</ul>
+<p><code>--mismatch</code> is accepted by the CLI but not currently functional; using it produces a warning and is ignored.</p>
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+
+
+
+<h1 id="reindex">reindex</h1>
+<p>Convert an existing index's evidence representation in place, between exact and approximate.</p>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>reindex<span class="w"> </span>INDEX<span class="w"> </span><span class="o">[</span>OPTIONS<span class="o">]</span>
+</code></pre></div>
+<h2 id="arguments">Arguments</h2>
+<table>
+<thead>
+<tr>
+<th>Argument</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>INDEX</code></td>
+<td>Index directory to convert (modified in place)</td>
+</tr>
+</tbody>
+</table>
+<h2 id="options">Options</h2>
+<table>
+<thead>
+<tr>
+<th>Option</th>
+<th>Default</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>--approx</code></td>
+<td>off</td>
+<td>Convert to approximate evidence (default direction is approximate → exact); requires <code>-z</code>/<code>--evidence-bits</code>/<code>--fp</code></td>
+</tr>
+<tr>
+<td><code>-z, --findere-z</code></td>
+<td>none</td>
+<td>Findere z parameter (≥ 1)</td>
+</tr>
+<tr>
+<td><code>--evidence-bits</code></td>
+<td>none</td>
+<td>Fingerprint bits per slot (b)</td>
+</tr>
+<tr>
+<td><code>--fp</code></td>
+<td>none</td>
+<td>Target false-positive rate per z-window</td>
+</tr>
+<tr>
+<td><code>--block-size</code></td>
+<td><code>1</code></td>
+<td>Block size for the exact on-disk index (ignored when converting to approximate)</td>
+</tr>
+</tbody>
+</table>
+<p>See <a href="../index_command/#exact-vs-approximate-evidence"><code>index</code></a> for the exact/approximate trade-off and the underlying false-positive model, and <a href="../estimate/"><code>estimate</code></a> to explore parameters beforehand. The index directory is locked for exclusive access during conversion.</p>
+
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+                
+                  
+
+
+
+<h1 id="select">select</h1>
+<p>Project and/or aggregate the genome columns of an index into a new (or in-place) index. Where <a href="../filter/"><code>filter</code></a> selects rows (kmers), <code>select</code> operates on columns (genomes): grouping several genomes into one aggregated column, reordering columns, or dropping some.</p>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span><span class="k">select</span><span class="w"> </span>SOURCE<span class="w"> </span><span class="o">(</span>--output<span class="w"> </span>OUTPUT<span class="w"> </span><span class="p">|</span><span class="w"> </span>--in-place<span class="o">)</span><span class="w"> </span><span class="o">[</span>OPTIONS<span class="o">]</span>
+</code></pre></div>
+<h2 id="arguments">Arguments</h2>
+<table>
+<thead>
+<tr>
+<th>Argument</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>SOURCE</code></td>
+<td>Source index directory</td>
+</tr>
+</tbody>
+</table>
+<h2 id="options">Options</h2>
+<table>
+<thead>
+<tr>
+<th>Option</th>
+<th>Default</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>--output</code></td>
+<td>—</td>
+<td>Output index directory (mutually exclusive with <code>--in-place</code>)</td>
+</tr>
+<tr>
+<td><code>--in-place</code></td>
+<td>off</td>
+<td>Rewrite the source index in place (mutually exclusive with <code>--output</code>)</td>
+</tr>
+<tr>
+<td><code>-f, --force</code></td>
+<td>off</td>
+<td>Overwrite an existing output directory</td>
+</tr>
+<tr>
+<td><code>--group NAME:PRED</code></td>
+<td>none</td>
+<td>Define a named group of genomes by predicate (repeatable; mutually exclusive with <code>--aggregate-by</code>)</td>
+</tr>
+<tr>
+<td><code>--group-op NAME:OP</code></td>
+<td>none</td>
+<td>Aggregation operator for a named group</td>
+</tr>
+<tr>
+<td><code>--aggregate-by KEY</code></td>
+<td>none</td>
+<td>Automatically create one group per distinct value of a metadata key (mutually exclusive with <code>--group</code>)</td>
+</tr>
+<tr>
+<td><code>--aggregate-op OP</code></td>
+<td>none</td>
+<td>Aggregation operator applied to every auto-generated group</td>
+</tr>
+<tr>
+<td><code>--select COL,...</code></td>
+<td>all columns</td>
+<td>Output columns, in order (group names or genome labels)</td>
+</tr>
+<tr>
+<td><code>--presence-threshold</code></td>
+<td><code>0</code></td>
+<td>Minimum count for a genome to be considered a carrier (logical operators only)</td>
+</tr>
+</tbody>
+</table>
+<h2 id="aggregation-operators">Aggregation operators</h2>
+<p><code>any</code>, <code>all</code>, <code>none</code> (logical, evaluated against <code>--presence-threshold</code>), <code>sum</code>, <code>min</code>, <code>max</code> (numeric, count index only). If a group's operator is left unspecified, it defaults to <code>any</code> when the source is a presence/absence index and <code>sum</code> when it stores counts.</p>
+<p>A <code>select</code> never changes the underlying kmer set — only the per-genome data (counts or presence) is rewritten, so an unaggregated pass-through column (a plain genome label in <code>--select</code>) is a cheap copy.</p>
+<p>At least one of <code>--output</code>/<code>--in-place</code> is required, and at least one output column must be defined; every name listed in <code>--select</code> must resolve to either a defined group or an existing genome label. See <a href="../predicates/">Genome predicates and taxonomy paths</a> for the predicate syntax used by <code>--group</code>.</p>
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+                
+                  
+
+
+
+<h1 id="superkmer">superkmer</h1>
+<p>Extract super-kmers from one or more sequence files and write them to stdout, without building a full index. Useful for inspecting or piping the super-kmer decomposition of a dataset.</p>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>superkmer<span class="w"> </span><span class="o">[</span>OPTIONS<span class="o">]</span><span class="w"> </span><span class="o">[</span>INPUTS...<span class="o">]</span>
+</code></pre></div>
+<h2 id="arguments">Arguments</h2>
+<table>
+<thead>
+<tr>
+<th>Argument</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>INPUTS...</code></td>
+<td>Input sequence files or directories (FASTA/FASTQ/GenBank, gzip optional). If omitted, reads from stdin.</td>
+</tr>
+</tbody>
+</table>
+<h2 id="options">Options</h2>
+<table>
+<thead>
+<tr>
+<th>Option</th>
+<th>Default</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>-k, --kmer-size</code></td>
+<td><code>31</code></td>
+<td>Kmer size (must be odd, in [11, 31])</td>
+</tr>
+<tr>
+<td><code>-m, --minimizer-size</code></td>
+<td><code>11</code></td>
+<td>Minimizer size (must be odd, in <span class="arithmatex">\([3, k-1]\)</span>)</td>
+</tr>
+<tr>
+<td><code>--theta</code></td>
+<td><code>0.7</code></td>
+<td>Entropy threshold; kmers with a normalized entropy at or below this value are excluded</td>
+</tr>
+<tr>
+<td><code>--level-max</code></td>
+<td><code>6</code></td>
+<td>Maximum sub-word size used for the entropy score</td>
+</tr>
+<tr>
+<td><code>-p, --partitions</code></td>
+<td><code>256</code></td>
+<td>Number of partitions (rounded up to the next power of 2)</td>
+</tr>
+<tr>
+<td><code>-T, --threads</code></td>
+<td>detected core count</td>
+<td>Number of worker threads</td>
+</tr>
+<tr>
+<td><code>--max-open-files</code></td>
+<td><code>threads / 4</code> (min 1)</td>
+<td>Maximum number of input files open simultaneously</td>
+</tr>
+</tbody>
+</table>
+<p>Output is written to stdout in the internal scatter format used by <code>index</code>; it is primarily intended to be piped into other tools or inspected for debugging.</p>
+
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+
+<h1 id="unitig">unitig</h1>
+<p>Dump the unitigs of an index as FASTA. A unitig is a maximal non-branching path through the de Bruijn graph implied by the index's kmers; the concatenation of every unitig reconstructs every stored kmer exactly once.</p>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>unitig<span class="w"> </span>INDEX<span class="w"> </span><span class="o">[</span>OPTIONS<span class="o">]</span>
+</code></pre></div>
+<h2 id="arguments">Arguments</h2>
+<table>
+<thead>
+<tr>
+<th>Argument</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>INDEX</code></td>
+<td>Index directory</td>
+</tr>
+</tbody>
+</table>
+<h2 id="options">Options</h2>
+<p><code>unitig</code> accepts the shared <a href="../filter/#predicate-options">predicate options</a> (<code>--ingroup</code>, <code>--outgroup</code>, <code>--min-count</code>, etc.) to restrict which kmers are included before the unitigs are enumerated.</p>
+<p>Output is FASTA on stdout.</p>
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+        
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+      <a href="../unitig/" class="md-nav__link">
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+  
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+
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+
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+    <li class="md-nav__item">
+      <a href="../estimate/" class="md-nav__link">
+        
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+  
+    <li class="md-nav__item">
+      <a href="../reindex/" class="md-nav__link">
+        
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+      </a>
+    </li>
+  
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+  
+    <li class="md-nav__item md-nav__item--active">
+      
+      <input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
+      
+      
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+      
+        <label class="md-nav__link md-nav__link--active" for="__toc">
+          
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    utils
+  
+
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+  </span>
+  
+  
+
+          <span class="md-nav__icon md-icon"></span>
+        </label>
+      
+      <a href="./" class="md-nav__link md-nav__link--active">
+        
+  
+  
+  <span class="md-ellipsis">
+    
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+    utils
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+  </span>
+  
+  
+
+      </a>
+      
+        
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
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+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#arguments" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Arguments
+      
+    </span>
+  </a>
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+</li>
+      
+        <li class="md-nav__item">
+  <a href="#options" class="md-nav__link">
+    <span class="md-ellipsis">
+      
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+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
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+      <a href="../pack/" class="md-nav__link">
+        
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+  
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+
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+    <li class="md-nav__item">
+      <a href="../predicates/" class="md-nav__link">
+        
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+    
+  
+    Predicates and taxonomy paths
+  
+
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+  </span>
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+    </li>
+  
+
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+            
+          </ul>
+        </nav>
+      
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+          </label>
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
+            <span class="md-nav__icon md-icon"></span>
+            
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+    Formats
+  
+
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+          <ul class="md-nav__list" data-md-scrollfix>
+            
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+    <li class="md-nav__item">
+      <a href="../../formats/index_layout/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Index construction and on-disk layout
+  
+
+    
+  </span>
+  
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+
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+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
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+  
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+    <li class="md-nav__item">
+      <a href="../../architecture/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Architecture notes
+  
+
+    
+  </span>
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+  
+
+      </a>
+    </li>
+  
+
+    
+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+    
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#arguments" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Arguments
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#options" class="md-nav__link">
+    <span class="md-ellipsis">
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+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+
+<h1 id="utils">utils</h1>
+<p>Miscellaneous index maintenance and inspection utilities.</p>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>utils<span class="w"> </span>INDEXES...<span class="w"> </span><span class="o">[</span>OPTIONS<span class="o">]</span>
+</code></pre></div>
+<h2 id="arguments">Arguments</h2>
+<table>
+<thead>
+<tr>
+<th>Argument</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>INDEXES...</code></td>
+<td>One or more index directories</td>
+</tr>
+</tbody>
+</table>
+<h2 id="options">Options</h2>
+<table>
+<thead>
+<tr>
+<th>Option</th>
+<th>Scope</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>--new-label NEW=OLD</code></td>
+<td>single index only</td>
+<td>Rename a genome label</td>
+</tr>
+<tr>
+<td><code>--upgrade-index</code></td>
+<td>single index only</td>
+<td>Add any missing layer metadata files to an older index</td>
+</tr>
+<tr>
+<td><code>--bits-per-kmer</code></td>
+<td>single index only</td>
+<td>Print bits-per-kmer statistics</td>
+</tr>
+<tr>
+<td><code>--stats</code></td>
+<td>single index only</td>
+<td>Print per-genome kmer counts as CSV</td>
+</tr>
+<tr>
+<td><code>--partition-stats</code></td>
+<td>one or more indexes</td>
+<td>Print a partition-size distribution report</td>
+</tr>
+<tr>
+<td><code>--csv FILE</code></td>
+<td>with <code>--partition-stats</code></td>
+<td>Also write raw per-(partition, source) data to FILE as CSV</td>
+</tr>
+</tbody>
+</table>
+<p>At least one operation option must be given. All options except <code>--partition-stats</code> require exactly one index directory.</p>
+
+
+
+
+
+
+
+
+
+
+
+
+                
+              </article>
+            </div>
+          
+          
+<script>var target=document.getElementById(location.hash.slice(1));target&&target.name&&(target.checked=target.name.startsWith("__tabbed_"))</script>
+        </div>
+        
+      </main>
+      
+        <footer class="md-footer">
+  
+  <div class="md-footer-meta md-typeset">
+    <div class="md-footer-meta__inner md-grid">
+      <div class="md-copyright">
+  
+  
+    Made with
+    <a href="https://squidfunk.github.io/mkdocs-material/" target="_blank" rel="noopener">
+      Material for MkDocs
+    </a>
+  
+</div>
+      
+    </div>
+  </div>
+</footer>
+      
+    </div>
+    <div class="md-dialog" data-md-component="dialog">
+      <div class="md-dialog__inner md-typeset"></div>
+    </div>
+    
+    
+    
+      
+      
+      <script id="__config" type="application/json">{"annotate": null, "base": "../..", "features": [], "search": "../../assets/javascripts/workers/search.2c215733.min.js", "tags": null, "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}, "version": null}</script>
+    
+    
+      <script src="../../assets/javascripts/bundle.79ae519e.min.js"></script>
+      
+        <script src="https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js"></script>
+      
+    
+  </body>
+</html>
\ No newline at end of file
diff --git a/mkdocs-user.yml b/mkdocs-user.yml
index 8c57fd1e..690c46a0 100644
--- a/mkdocs-user.yml
+++ b/mkdocs-user.yml
@@ -1,6 +1,6 @@
 site_name: obikmer — User Guide
 docs_dir: UserDocMD
-site_dir: doc-user
+site_dir: doc
 
 theme:
   name: material
diff --git a/mkdocs.yml b/mkdocs.yml
index 13f3abf3..dc463b49 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -1,6 +1,6 @@
 site_name: obikmer
-docs_dir: docmd
-site_dir: doc
+docs_dir: DevDocMD
+site_dir: DevDoc
 
 theme:
   name: material
@@ -8,8 +8,8 @@ theme:
 plugins:
   - mermaid2:
   - bibtex:
-      bib_file: docmd/references.bib
-      csl_file: docmd/ecology-letters.csl
+      bib_file: DevDocMD/references.bib
+      csl_file: DevDocMD/ecology-letters.csl
       enable_inline_citations: false
 
 markdown_extensions:
@@ -63,5 +63,5 @@ nav:
       - NUMA-aware partition runner: architecture/numa_partition_runner.md
 
 watch:
-  - docmd
+  - DevDocMD
   - mkdocs.yml
diff --git a/src/obicompactvec/src/bitmatrix/sparse.rs b/src/obicompactvec/src/bitmatrix/sparse.rs
index 873a0554..e9795783 100644
--- a/src/obicompactvec/src/bitmatrix/sparse.rs
+++ b/src/obicompactvec/src/bitmatrix/sparse.rs
@@ -1,6 +1,6 @@
 //! `PersistentSparseBitMatrix` — row-major (k-mer-major), deduplicated
 //! sparse alternative to [`super::PersistentBitMatrix`]. See
-//! `docmd/architecture/siblings.md` and the sparse-matrix design plan for
+//! `DevDocMD/architecture/siblings.md` and the sparse-matrix design plan for
 //! the full rationale (measured sparsity/duplication on real data). Not
 //! used by any production code path yet — a new type, not a replacement.
 //!
@@ -192,7 +192,7 @@ impl PersistentSparseBitMatrix {
 
     /// Column-oriented per-genome k-mer totals — a naive row-by-row scan,
     /// not the O(1)-per-column reduction the dense matrix's `count_ones`
-    /// is. Deliberately not optimised: see `docmd/architecture/siblings.md`
+    /// is. Deliberately not optimised: see `DevDocMD/architecture/siblings.md`
     /// and the sparse-matrix plan's "Explicitly deferred" — column-side
     /// access stays correct but slow on this type for now.
     pub fn count_ones(&self) -> Array1<u64> {
diff --git a/src/obicompactvec/src/eliasfano.rs b/src/obicompactvec/src/eliasfano.rs
index b2f9a3bf..9449fc20 100644
--- a/src/obicompactvec/src/eliasfano.rs
+++ b/src/obicompactvec/src/eliasfano.rs
@@ -1,6 +1,6 @@
 //! Elias-Fano encoding of a monotone (non-decreasing) `u64` sequence —
 //! used only for the sparse presence matrix's dictionary offsets (see
-//! `docmd/architecture/siblings.md` and the sparse-matrix plan): a
+//! `DevDocMD/architecture/siblings.md` and the sparse-matrix plan): a
 //! monotone, unbounded-magnitude sequence, the one component in that
 //! design that genuinely needs this.
 //!
diff --git a/src/obicompactvec/src/rankselect.rs b/src/obicompactvec/src/rankselect.rs
index c321386a..a186ab10 100644
--- a/src/obicompactvec/src/rankselect.rs
+++ b/src/obicompactvec/src/rankselect.rs
@@ -2,7 +2,7 @@
 //! (`count_ones`, a global reduction) with `rank1`/`rank0` (count of 1s/0s
 //! in a prefix) and `select1` (position of the k-th 1 bit). Needed by two
 //! consumers in the sparse presence-matrix design (see
-//! `docmd/architecture/siblings.md` and the sparse-matrix plan): the
+//! `DevDocMD/architecture/siblings.md` and the sparse-matrix plan): the
 //! `is_multi` row-kind flag (needs rank, to locate a row's position within
 //! whichever of the two split arrays it belongs to) and the Elias-Fano high
 //! bits (needs select).
diff --git a/src/obicompactvec/src/traits.rs b/src/obicompactvec/src/traits.rs
index 62692031..38f3afb1 100644
--- a/src/obicompactvec/src/traits.rs
+++ b/src/obicompactvec/src/traits.rs
@@ -7,7 +7,7 @@ use ndarray::{Array1, Array2};
 /// (`col`/`col_view`, the `BitPartials`/`ColumnWeights` distance-matrix
 /// traits above) are *not* part of this trait — `PersistentSparseBitMatrix`
 /// only offers a naive, row-scanning `count_ones` for now (see
-/// `docmd/architecture/siblings.md` and the sparse-matrix design plan,
+/// `DevDocMD/architecture/siblings.md` and the sparse-matrix design plan,
 /// "Explicitly deferred": a row-major co-occurrence rewrite of the
 /// pairwise distance matrices is future work, not part of this trait).
 pub trait BinaryMatrix {
diff --git a/src/obikentropy/build.rs b/src/obikentropy/build.rs
index d2c33b92..a14a3a21 100644
--- a/src/obikentropy/build.rs
+++ b/src/obikentropy/build.rs
@@ -14,7 +14,7 @@ fn build_n_log_n() -> [f64; K_MAX + 1] {
 
 /// Max achievable entropy over `4^ws` raw sub-words given only `nwords`
 /// observations (most-uniform integer partition), per
-/// `docmd/theory/entropy.md`.
+/// `DevDocMD/theory/entropy.md`.
 fn build_emax() -> [[f64; WS_MAX + 1]; K_MAX + 1] {
     let mut t = [[0.0f64; WS_MAX + 1]; K_MAX + 1];
     for k in 2..=K_MAX {
diff --git a/src/obikentropy/src/lib.rs b/src/obikentropy/src/lib.rs
index dc183602..ae206731 100644
--- a/src/obikentropy/src/lib.rs
+++ b/src/obikentropy/src/lib.rs
@@ -1,7 +1,7 @@
 //! Normalized k-mer entropy: formulas, tables, and a streaming tracker.
 //!
 //! This crate holds every piece of the entropy computation described in
-//! `docmd/theory/entropy.md`: the compile-time tables ([`table`], private),
+//! `DevDocMD/theory/entropy.md`: the compile-time tables ([`table`], private),
 //! the incremental accumulator ([`EntropyTracker`]) that callers compose
 //! into their own streaming state, and the [`KmerEntropy`] convenience trait
 //! for scoring a single, already-built k-mer.
diff --git a/src/obikentropy/src/table.rs b/src/obikentropy/src/table.rs
index 37ef4df4..ff01c743 100644
--- a/src/obikentropy/src/table.rs
+++ b/src/obikentropy/src/table.rs
@@ -1,5 +1,5 @@
 //! Compile-time tables backing the normalized k-mer entropy formula: the
-//! max-entropy correction for small samples. See `docmd/theory/entropy.md`.
+//! max-entropy correction for small samples. See `DevDocMD/theory/entropy.md`.
 //!
 //! Entropy is computed directly on raw (non-canonicalized) sub-words — no
 //! equivalence-class folding. Empirically (see the discussion that produced
diff --git a/src/obikentropy/src/tracker.rs b/src/obikentropy/src/tracker.rs
index eb71bab4..4c0c8420 100644
--- a/src/obikentropy/src/tracker.rs
+++ b/src/obikentropy/src/tracker.rs
@@ -2,7 +2,7 @@
 //!
 //! [`EntropyTracker`] maintains, over a sliding window of the last `k` bases,
 //! the per-sub-word-size raw-word frequency statistics needed to evaluate
-//! the corrected Shannon entropy described in `docmd/theory/entropy.md`,
+//! the corrected Shannon entropy described in `DevDocMD/theory/entropy.md`,
 //! updated in O(1) per base rather than recomputed from scratch. No
 //! canonicalization is applied — each sub-word is tallied under its own raw
 //! 2-bit-packed value; only the small-sample max-entropy correction departs
diff --git a/src/obikindex/src/index.rs b/src/obikindex/src/index.rs
index c8291060..7338a409 100644
--- a/src/obikindex/src/index.rs
+++ b/src/obikindex/src/index.rs
@@ -277,7 +277,7 @@ impl KmerIndex {
     ///
     /// If `sparse` is set, presence matrices go one step further, from the
     /// dense `.pbmx` form into `obicompactvec::PersistentSparseBitMatrix`'s
-    /// on-disk format (see `docmd/architecture/siblings.md`) — count
+    /// on-disk format (see `DevDocMD/architecture/siblings.md`) — count
     /// matrices are unaffected, sparse count matrices aren't implemented
     /// (see the sparse-matrix design plan's "Explicitly deferred").
     pub fn pack_matrices(&self, sparse: bool) -> OKIResult<()> {
diff --git a/src/obikmer/src/cmd/pack/mod.rs b/src/obikmer/src/cmd/pack/mod.rs
index 10621772..130c2c51 100644
--- a/src/obikmer/src/cmd/pack/mod.rs
+++ b/src/obikmer/src/cmd/pack/mod.rs
@@ -11,7 +11,7 @@ pub struct PackArgs {
     pub index: PathBuf,
 
     /// Pack presence matrices into the sparse, deduplicated on-disk format
-    /// instead of the dense one — see `docmd/architecture/siblings.md`.
+    /// instead of the dense one — see `DevDocMD/architecture/siblings.md`.
     /// Smaller and faster for single-row access on real, sparse data;
     /// column-oriented access (`--metric` distance matrices) is much
     /// slower on the sparse format.
diff --git a/src/obikmer/src/cmd/phylo/args.rs b/src/obikmer/src/cmd/phylo/args.rs
index b166ab25..5261258e 100644
--- a/src/obikmer/src/cmd/phylo/args.rs
+++ b/src/obikmer/src/cmd/phylo/args.rs
@@ -61,7 +61,7 @@ pub struct PhyloArgs {
     pub upgma: bool,
 
     /// Build the sibling-count/minorant annex on this (multi-genome) index
-    /// — see `docmd/theory/evolutionary_distances.md`, Step 2b. Construction
+    /// — see `DevDocMD/theory/evolutionary_distances.md`, Step 2b. Construction
     /// only; does not by itself compute or write any statistics.
     #[arg(long)]
     pub sibling_annex: bool,
@@ -79,7 +79,7 @@ pub struct PhyloArgs {
     /// dropping its row from `snp_pseudo_alignment`'s output — the annex
     /// is still built/scanned for the excluded genome too, just not used
     /// afterward. For a genome with almost no informative sites shared
-    /// with anything else (see `docmd/theory/evolutionary_distances.md`,
+    /// with anything else (see `DevDocMD/theory/evolutionary_distances.md`,
     /// the IQ-TREE/Mash rogue-taxon discussion), its presence can
     /// otherwise silently bias the transition models.
     #[arg(long = "exclude-genome", value_name = "LABEL")]
@@ -94,7 +94,7 @@ pub struct PhyloArgs {
     /// themselves arbitrarily under `--tnt`/`--iqtree` (near-zero branch
     /// lengths, grafted inside unrelated clades) — too little real
     /// constraint on where they belong. See
-    /// `docmd/theory/evolutionary_distances.md`, "Locus dropout under
+    /// `DevDocMD/theory/evolutionary_distances.md`, "Locus dropout under
     /// incomplete coverage".
     #[arg(long, value_name = "N")]
     pub min_shared_family: Option<f64>,
@@ -132,7 +132,7 @@ pub struct PhyloArgs {
     /// at all" (e.g. `0.0` from 0/2 looks the same as `0.0` from 0/2000),
     /// and that distinction matters a lot for genome pairs near the edge
     /// of what central-position families can resolve (see
-    /// `docmd/theory/evolutionary_distances.md`, "Run 3" and the
+    /// `DevDocMD/theory/evolutionary_distances.md`, "Run 3" and the
     /// IQ-TREE/Mash comparison). Same annex requirement as
     /// `--raw-snp-distance`.
     #[arg(long)]
@@ -141,7 +141,7 @@ pub struct PhyloArgs {
     /// Write a SNP-only pseudo-alignment (FASTA, IUPAC-coded) from an
     /// already-built sibling annex — one row per genome, one column per
     /// variable family (monomorphic families skipped), no flanking
-    /// sequence. See `docmd/theory/evolutionary_distances.md`,
+    /// sequence. See `DevDocMD/theory/evolutionary_distances.md`,
     /// "Multi-genome framing: family as pseudo-alignment column".
     #[arg(long)]
     pub snp: bool,
@@ -153,15 +153,34 @@ pub struct PhyloArgs {
     /// report stays usable on an index far larger than the sample itself
     /// (mandatory, not optional, once the index is large enough that a full
     /// pseudo-alignment can't be materialized at all). See
-    /// `docmd/architecture/siblings.md`, "`--subsample`/`--shannon`". If the
+    /// `DevDocMD/architecture/siblings.md`, "`--subsample`/`--shannon`". If the
     /// index has fewer non-monomorphic minorants than this, every one of
     /// them is kept — no error, no under/over-shoot handling needed.
     #[arg(long, value_name = "N")]
     pub subsample: Option<usize>,
 
+    /// Enable entropy-biased selection: instead of a uniform draw among
+    /// eligible families, weight each candidate by an unnormalised Gaussian
+    /// kernel on its own entropy15 (`w = exp(-(entropy-mu)^2/(2*sigma^2))`,
+    /// `1` exactly at `entropy == mu`, decaying smoothly away from it — no
+    /// hard cutoff). Activates as soon as `--entropy` or `--entropy-sd` is
+    /// given; the other defaults to `1.0`/`0.5` if unset. Combines with
+    /// `--subsample N` (the joint accept probability is `p0 * w`, `p0`
+    /// chosen so the expected count is approximately `N`) or works alone
+    /// (a pure soft entropy filter over the whole index, no size target).
+    /// First use on an index pays a one-time cost building a per-layer
+    /// entropy annex (a full, unsampled scan); every later run reuses it.
+    /// See `DevDocMD/architecture/siblings.md`, "Entropy-biased selection".
+    #[arg(long, value_name = "MU")]
+    pub entropy: Option<f64>,
+
+    /// Standard deviation of `--entropy`'s Gaussian kernel. See `--entropy`.
+    #[arg(long, value_name = "SIGMA")]
+    pub entropy_sd: Option<f64>,
+
     /// Write <prefix>_shannon.csv: per-family Shannon entropy (bits, over
     /// the 15 non-empty subsets of `{A,C,G,T}`, `∅`/absent genomes excluded
-    /// from the denominator — see `docmd/architecture/siblings.md`,
+    /// from the denominator — see `DevDocMD/architecture/siblings.md`,
     /// "Entropy definition") of every non-monomorphic minorant, one row per
     /// family. Combine with `--subsample N` for a bounded diagnostic sample
     /// instead of a full-index pass. Same annex requirement as `--snp`.
@@ -183,7 +202,7 @@ pub struct PhyloArgs {
     /// Calibrate a 16-state Sankoff cost matrix and its matching
     /// pseudo-alignment from an already-built sibling annex (run with
     /// `--sibling-annex` first, in this invocation or an earlier one), for
-    /// use with TNT/PhyG. See `docmd/theory/evolutionary_distances.md`,
+    /// use with TNT/PhyG. See `DevDocMD/theory/evolutionary_distances.md`,
     /// "Sankoff parsimony as the resolution of the 16-state model problem".
     #[arg(long)]
     pub sankoff: bool,
@@ -198,7 +217,7 @@ pub struct PhyloArgs {
     /// genomes by shared undersampling rather than shared ancestry. `?`
     /// (not `-`) because `-` still carries gap/indel semantics in these
     /// tools; a non-detected family is not an observed deletion. See
-    /// `docmd/theory/evolutionary_distances.md`, "Locus dropout under
+    /// `DevDocMD/theory/evolutionary_distances.md`, "Locus dropout under
     /// incomplete coverage".
     #[arg(long)]
     pub free_loss: bool,
@@ -240,7 +259,7 @@ pub struct PhyloArgs {
     /// cost matrix `--sankoff` computes, `π` the real empirical state
     /// frequencies counted from the alignment (not IQ-TREE's `+FO`/`+F` —
     /// neither applies to a custom-file model, see
-    /// `docmd/theory/evolutionary_distances.md`). Only the states that
+    /// `DevDocMD/theory/evolutionary_distances.md`). Only the states that
     /// actually occur in this alignment are kept, compactly renumbered
     /// (IQ-TREE infers its state count from the alignment itself, and a
     /// gap in the numbering would silently misalign the model file).
diff --git a/src/obikmer/src/cmd/phylo/family_overlap.rs b/src/obikmer/src/cmd/phylo/family_overlap.rs
index 00732aed..3aeca45f 100644
--- a/src/obikmer/src/cmd/phylo/family_overlap.rs
+++ b/src/obikmer/src/cmd/phylo/family_overlap.rs
@@ -80,7 +80,7 @@ pub(super) fn apply_min_shared_family_exclusion(
     threshold: f64,
     mask: &mut [bool],
 ) {
-    let alignment = idx.snp_pseudo_alignment(None).unwrap_or_else(|e| {
+    let alignment = idx.snp_pseudo_alignment(None, None).unwrap_or_else(|e| {
         eprintln!("error computing SNP pseudo-alignment for --min-shared-family: {e}");
         std::process::exit(1);
     });
diff --git a/src/obikmer/src/cmd/phylo/iqtree.rs b/src/obikmer/src/cmd/phylo/iqtree.rs
index d5b17af0..6d659630 100644
--- a/src/obikmer/src/cmd/phylo/iqtree.rs
+++ b/src/obikmer/src/cmd/phylo/iqtree.rs
@@ -16,7 +16,7 @@ use super::sankoff::state_index_table;
 // unlike `tnt::write_sankoff_tnt`/`phyg::write_sankoff_phyg`.
 //
 // Verified against the locally installed `iqtree3` binary/source (not just
-// its docs — see `docmd/theory/evolutionary_distances.md`, "Next
+// its docs — see `DevDocMD/theory/evolutionary_distances.md`, "Next
 // direction: genuine ML branch lengths"), because the web documentation's
 // `-mdef` NEXUS route turned out not to apply to a plain (non-mixture)
 // custom morphology model. The real mechanism: pass a **file path**
@@ -75,7 +75,7 @@ impl CompactAlphabet {
 /// column's actual calls) can still turn constant *among the genomes that
 /// actually have data* once the non-detected ones are excluded from that
 /// check — the same failure mode as the `--exclude-genome`/`drop_excluded`
-/// fix in `mod.rs` (see `docmd/theory/evolutionary_distances.md`, "Two
+/// fix in `mod.rs` (see `DevDocMD/theory/evolutionary_distances.md`, "Two
 /// consistency bugs found and fixed post-implementation"), just triggered
 /// by hiding cells instead of dropping whole rows. Same remedy: rescan
 /// columns treating `-` as ignored, drop any where the remaining calls
diff --git a/src/obikmer/src/cmd/phylo/mod.rs b/src/obikmer/src/cmd/phylo/mod.rs
index 8f7715d1..b3684ccf 100644
--- a/src/obikmer/src/cmd/phylo/mod.rs
+++ b/src/obikmer/src/cmd/phylo/mod.rs
@@ -13,8 +13,8 @@ use obikindex::KmerIndex;
 use obikphylo::{
     cardinality_transition_probs, composition_transition_probs, pairwise_cost_matrix,
     siblings::{
-        CardinalityExt, DistanceExt, RawSnpDistanceOutput, ShannonEntropyExt, SiblingAnnexBuildExt,
-        SiblingStatsExt, SnpAlignment, SnpAlignmentExt,
+        DistanceExt, EntropyBias, RawSnpDistanceOutput, SankoffBundleExt, ShannonEntropyExt,
+        SiblingAnnexBuildExt, SiblingStatsExt, SnpAlignment, SnpAlignmentExt,
     },
 };
 use obisys::{Reporter, Stage};
@@ -41,6 +41,18 @@ pub fn run(args: PhyloArgs) {
 
     let mut rep = Reporter::new();
 
+    // ── Entropy-biased selection (`--entropy`/`--entropy-sd`) ──────────────
+    // Activates as soon as either is given; the other defaults to 1.0/0.5.
+    // See `DevDocMD/architecture/siblings.md`, "Entropy-biased selection".
+    let entropy_bias = if args.entropy.is_some() || args.entropy_sd.is_some() {
+        Some(EntropyBias {
+            mu: args.entropy.unwrap_or(1.0),
+            sigma: args.entropy_sd.unwrap_or(0.5),
+        })
+    } else {
+        None
+    };
+
     // ── Genome exclusion (`--exclude-genome`) ───────────────────────────────
     // Applied by zeroing a `RawSnpDistanceOutput`'s excluded rows/columns
     // (`zero_excluded_pairs`) — `base_pair_tally`/`cardinality_tally`
@@ -177,7 +189,7 @@ pub fn run(args: PhyloArgs) {
     }
     if args.snp {
         let t = Stage::start("snp_pseudo_alignment");
-        let alignment = idx.snp_pseudo_alignment(args.subsample).unwrap_or_else(|e| {
+        let alignment = idx.snp_pseudo_alignment(args.subsample, entropy_bias).unwrap_or_else(|e| {
             eprintln!("error computing SNP pseudo-alignment: {e}");
             std::process::exit(1);
         });
@@ -187,7 +199,7 @@ pub fn run(args: PhyloArgs) {
     }
     if args.family_overlap {
         let t = Stage::start("snp_pseudo_alignment");
-        let alignment = idx.snp_pseudo_alignment(args.subsample).unwrap_or_else(|e| {
+        let alignment = idx.snp_pseudo_alignment(args.subsample, entropy_bias).unwrap_or_else(|e| {
             eprintln!("error computing SNP pseudo-alignment: {e}");
             std::process::exit(1);
         });
@@ -200,7 +212,7 @@ pub fn run(args: PhyloArgs) {
         let path = args.output.as_ref()
             .map(|p| format!("{}_shannon.csv", p.display()))
             .unwrap_or_else(|| "shannon.csv".into());
-        idx.shannon_entropy_csv(std::path::Path::new(&path), args.subsample).unwrap_or_else(|e| {
+        idx.shannon_entropy_csv(std::path::Path::new(&path), args.subsample, entropy_bias).unwrap_or_else(|e| {
             eprintln!("error computing Shannon entropy: {e}");
             std::process::exit(1);
         });
@@ -208,39 +220,26 @@ pub fn run(args: PhyloArgs) {
         info!("per-family Shannon entropy → {path}");
     }
     if args.sankoff || args.tnt || args.phyg || args.iqtree {
+        // One shared, possibly-subsampled/entropy-biased selection, one
+        // pass to derive `included[i,j]`, one more fused pass for
+        // base_pair_tally + cardinality_tally + the pseudo-alignment — see
+        // `DevDocMD/architecture/siblings.md`, "`--free-loss`/`--tnt`
+        // pipeline" and "Wired into `pack`...".
         let t = Stage::start("raw_snp_distance");
-        let mut raw = idx.raw_snp_distance().unwrap_or_else(|e| {
-            eprintln!("error computing raw SNP distance: {e}");
+        let bundle = idx.sankoff_bundle(args.subsample, entropy_bias, args.sankoff_ratio_ceiling, &exclude_mask).unwrap_or_else(|e| {
+            eprintln!("error computing sankoff inputs: {e}");
             std::process::exit(1);
         });
         rep.push(t.stop());
-        zero_excluded_pairs(&mut raw);
+        let (base_tally, card_tally) = (bundle.base_pair_tally, bundle.cardinality_tally);
 
-        let t = Stage::start("base_pair_tally");
-        let base_tally = idx.base_pair_tally(&raw, args.sankoff_ratio_ceiling).unwrap_or_else(|e| {
-            eprintln!("error computing base-pair tally: {e}");
-            std::process::exit(1);
-        });
-        rep.push(t.stop());
-        let t = Stage::start("cardinality_tally");
-        let card_tally = idx.cardinality_tally(&raw, args.sankoff_ratio_ceiling).unwrap_or_else(|e| {
-            eprintln!("error computing cardinality tally: {e}");
-            std::process::exit(1);
-        });
-        rep.push(t.stop());
         let p_card = cardinality_transition_probs(&card_tally);
         let p_comp = composition_transition_probs(&base_tally);
         let matrix = pairwise_cost_matrix(&p_card, &p_comp, args.free_loss);
         write_sankoff_matrix_csv(&matrix, &args.output);
         write_sankoff_params(&card_tally, &p_card, &base_tally, &p_comp, args.sankoff_ratio_ceiling, &args.output);
 
-        let t = Stage::start("snp_pseudo_alignment");
-        let alignment = idx.snp_pseudo_alignment(args.subsample).unwrap_or_else(|e| {
-            eprintln!("error computing SNP pseudo-alignment: {e}");
-            std::process::exit(1);
-        });
-        rep.push(t.stop());
-        let (alignment, kept_labels) = drop_excluded(alignment);
+        let (alignment, kept_labels) = drop_excluded(bundle.alignment);
         write_sankoff_alignment_fasta(&alignment, &kept_labels, &args.output, args.free_loss);
 
         if args.tnt {
diff --git a/src/obikmer/src/cmd/phylo/outputs.rs b/src/obikmer/src/cmd/phylo/outputs.rs
index eef77368..5ae69055 100644
--- a/src/obikmer/src/cmd/phylo/outputs.rs
+++ b/src/obikmer/src/cmd/phylo/outputs.rs
@@ -10,7 +10,7 @@ use tracing::info;
 // Each row is a family (the up-to-4 k-mers sharing flanks, differing only at
 // the centre), counted once — at its minorant — regardless of how many of
 // its members are observed. Family size 1..4 (not "sibling count" 0..3):
-// see `docmd/theory/evolutionary_distances.md`, "Definitions".
+// see `DevDocMD/theory/evolutionary_distances.md`, "Definitions".
 
 pub(super) fn write_sibling_stats_csv(stats: &SiblingAnnexStats, labels: &[String], output: &Option<PathBuf>) {
     // One row per genome (4 columns, family size 1-4: number of families of
@@ -103,7 +103,7 @@ pub(super) fn write_sibling_hist_csv(counts: &[u64; 4], output: &Option<PathBuf>
 // `--raw-snp-distance`'s output. Distinguishing them matters most exactly
 // where it's easy to miss: genome pairs near the edge of what
 // central-position families can resolve at all (deep cross-lineage splits,
-// see `docmd/theory/evolutionary_distances.md`, "Run 3" and the later
+// see `DevDocMD/theory/evolutionary_distances.md`, "Run 3" and the later
 // IQ-TREE/Mash comparison — a `ratio=0.0` backed by 2 eligible loci is not
 // the same claim as one backed by 2000).
 
diff --git a/src/obikmer/src/cmd/phylo/sankoff.rs b/src/obikmer/src/cmd/phylo/sankoff.rs
index 7c91b0ca..dc313987 100644
--- a/src/obikmer/src/cmd/phylo/sankoff.rs
+++ b/src/obikmer/src/cmd/phylo/sankoff.rs
@@ -16,7 +16,7 @@ use tracing::info;
 // missing-data symbol, deliberately *not* `-` (still gap/indel semantics in
 // both tools) — so non-detection costs nothing rather than being scored as
 // an ordinary, calibrated state transition. See
-// `docmd/theory/evolutionary_distances.md`, "Locus dropout under incomplete
+// `DevDocMD/theory/evolutionary_distances.md`, "Locus dropout under incomplete
 // coverage".
 
 pub(super) fn write_sankoff_alignment_fasta(alignment: &SnpAlignment, labels: &[String], output: &Option<PathBuf>, free_loss: bool) {
diff --git a/src/obikphylo/src/cardcomp.rs b/src/obikphylo/src/cardcomp.rs
index 8fdd2fa8..9a6db64b 100644
--- a/src/obikphylo/src/cardcomp.rs
+++ b/src/obikphylo/src/cardcomp.rs
@@ -2,7 +2,7 @@
 //! matrix — replaces `sankoff::build_cost_matrix`'s elementary-edge graph
 //! and its Floyd-Warshall shortest-path closure, which double-counts
 //! multi-hop transitions once IQ-TREE's own matrix exponential composes
-//! them again. See `docmd/theory/evolutionary_distances.md`, "`R` via
+//! them again. See `DevDocMD/theory/evolutionary_distances.md`, "`R` via
 //! `exp(-cost)` is wrong for a CTMC; cardinality/composition decomposition".
 //!
 //! Two small, directly-estimated first-order Markov models (diagonals
@@ -133,7 +133,7 @@ fn best_pairing_cost(lost: &[u8], gained: &[u8], p_comp: &[[f64; 4]; 4]) -> f64
 /// `free_loss`: drop the `P_cardinality(|A|→|B|)` factor entirely (never
 /// added to `log_p`) — the same low/incomplete-coverage argument that
 /// justifies recoding whole-family non-detection as `?` (see
-/// `docmd/theory/evolutionary_distances.md`, "Locus dropout under
+/// `DevDocMD/theory/evolutionary_distances.md`, "Locus dropout under
 /// incomplete coverage") applies one level down: whether a genome shows 1
 /// vs 2 (etc.) detected members of a *present* family is exactly as
 /// vulnerable to sampling failure as whether the family was detected at
diff --git a/src/obikphylo/src/lib.rs b/src/obikphylo/src/lib.rs
index d745f063..fc921e6e 100644
--- a/src/obikphylo/src/lib.rs
+++ b/src/obikphylo/src/lib.rs
@@ -1,7 +1,7 @@
 //! Library-level phylogenetic functionality for `obikmer`, built as
 //! extension traits over `obikindex::KmerIndex` and `obilayeredmap`'s
 //! generic layer types — the `phylo` CLI command is a consumer of this
-//! crate, not the owner of this logic (see `docmd/architecture/siblings.md`).
+//! crate, not the owner of this logic (see `DevDocMD/architecture/siblings.md`).
 //!
 //! Starts with [`siblings`] (family presence-mask annex, SNP distance,
 //! cardinality, pseudo-alignment); further phylo-domain functionality
diff --git a/src/obikphylo/src/siblings/alignment.rs b/src/obikphylo/src/siblings/alignment.rs
index bd503f0c..8aae451c 100644
--- a/src/obikphylo/src/siblings/alignment.rs
+++ b/src/obikphylo/src/siblings/alignment.rs
@@ -8,6 +8,7 @@ use obikindex::KmerIndex;
 
 use super::cache::PartitionCache;
 use super::family_scan::{scan_layer_families, Selection};
+use super::subsample::EntropyBias;
 
 /// IUPAC ambiguity code for a per-genome family presence mask (bit `b` set
 /// iff the genome carries the member whose own central base is `b`):
@@ -16,7 +17,7 @@ use super::family_scan::{scan_layer_families, Selection};
 /// `N`, the same convention used for diploid heterozygous VCF/FASTA sites);
 /// all 4 bits -> `N`; no bits (genome carries none of the family's observed
 /// members) -> `-` (no data at this locus for this genome).
-fn iupac_code(mask: u8) -> u8 {
+pub(super) fn iupac_code(mask: u8) -> u8 {
     match mask & 0b1111 {
         0b0000 => b'-',
         0b0001 => b'A',
@@ -45,7 +46,7 @@ fn iupac_code(mask: u8) -> u8 {
 /// deterministic sweep order as the annex build (partition, then layer, then
 /// slot) — arbitrary but stable and identical across genomes, which is all a
 /// pseudo-alignment needs (there is no natural genomic coordinate to sort by
-/// once flanks are dropped). See `docmd/theory/evolutionary_distances.md`,
+/// once flanks are dropped). See `DevDocMD/theory/evolutionary_distances.md`,
 /// "Multi-genome framing: family as pseudo-alignment column".
 pub struct SnpAlignment {
     /// `sequences[g]` = genome `g`'s IUPAC-coded row, same length for every
@@ -55,7 +56,7 @@ pub struct SnpAlignment {
 
 /// Adds [`snp_pseudo_alignment`](Self::snp_pseudo_alignment) to `KmerIndex` —
 /// phylo-domain functionality, kept out of `obikindex` itself (see
-/// `docmd/architecture/siblings.md`).
+/// `DevDocMD/architecture/siblings.md`).
 pub trait SnpAlignmentExt {
     /// Build the SNP-only pseudo-alignment from an already-built sibling
     /// annex (run [`build_sibling_annex`](super::build::SiblingAnnexBuildExt::build_sibling_annex) first).
@@ -63,14 +64,17 @@ pub trait SnpAlignmentExt {
     /// `subsample`: `--subsample N` — cap the number of variable families
     /// retained to (approximately) `N`, sampled proportionally per layer
     /// among non-monomorphic minorants (see
-    /// `docmd/architecture/siblings.md`, "`--subsample`/`--shannon`").
+    /// `DevDocMD/architecture/siblings.md`, "`--subsample`/`--shannon`").
     /// `None` keeps today's behaviour: every non-monomorphic minorant of
-    /// every layer.
-    fn snp_pseudo_alignment(&self, subsample: Option<usize>) -> OKIResult<SnpAlignment>;
+    /// every layer. `entropy_bias`: `--entropy`/`--entropy-sd` — weight
+    /// that sample (or, with `subsample = None`, filter the whole index)
+    /// by a Gaussian kernel on each family's entropy — see
+    /// `DevDocMD/architecture/siblings.md`, "Entropy-biased selection".
+    fn snp_pseudo_alignment(&self, subsample: Option<usize>, entropy_bias: Option<EntropyBias>) -> OKIResult<SnpAlignment>;
 }
 
 impl SnpAlignmentExt for KmerIndex {
-    fn snp_pseudo_alignment(&self, subsample: Option<usize>) -> OKIResult<SnpAlignment> {
+    fn snp_pseudo_alignment(&self, subsample: Option<usize>, entropy_bias: Option<EntropyBias>) -> OKIResult<SnpAlignment> {
         let n_parts = self.n_partitions();
         let n_genomes = self.meta().genomes.len();
         let with_counts = self.meta().config.with_counts;
@@ -86,7 +90,7 @@ impl SnpAlignmentExt for KmerIndex {
         .map_err(OKIError::Partition)?;
         let cache = Arc::new(PartitionCache::build(&partition, n_parts, with_counts)?);
         let layer_dirs = super::family_scan::sibling_layer_dirs(self)?;
-        let selections = super::subsample::compute_selections(&layer_dirs, subsample)?;
+        let selections = super::subsample::compute_selections(self, &layer_dirs, subsample, entropy_bias)?;
 
         let pb = progress_bar("snp_pseudo_alignment", layer_dirs.len() as u64, "layers");
         // One layer at a time, not `par_iter()` over layers — same
diff --git a/src/obikphylo/src/siblings/build.rs b/src/obikphylo/src/siblings/build.rs
index a57b8977..45bc665e 100644
--- a/src/obikphylo/src/siblings/build.rs
+++ b/src/obikphylo/src/siblings/build.rs
@@ -29,7 +29,7 @@ use super::{olm_to_ok, FamilyMask, SiblingAnnexBuilder, ANNEX_FILE_NAME, INDEX_S
 /// unlike the fan-out `Flat` stage this replaced, needs no `Arc` sharing.
 ///
 /// The `usize` is this k-mer's position in `iter_kmers()`'s enumeration
-/// order, **not** an MPHF slot — see `docmd/architecture/siblings.md`. It
+/// order, **not** an MPHF slot — see `DevDocMD/architecture/siblings.md`. It
 /// is the same index the annex file is written under.
 struct SourceBatch {
     items: Vec<(usize, CanonicalKmer)>,
@@ -144,7 +144,7 @@ fn build_layer_sibling_annex(
         // `unitigs.bin`), never by MPHF slot — this layer's own k-mers are
         // known members by construction, so no evidence check, no MPHF
         // slot, and no slot -> k-mer reconstruction is needed or legitimate
-        // here (see `docmd/architecture/siblings.md`: the MPHF is not
+        // here (see `DevDocMD/architecture/siblings.md`: the MPHF is not
         // invertible, and evidence answers membership, not identity). No
         // separate in-memory accumulator: every concurrent write goes
         // straight through `SiblingAnnexBuilder::atomic_slot` into the
diff --git a/src/obikphylo/src/siblings/cache.rs b/src/obikphylo/src/siblings/cache.rs
index 1ef1a672..0cadf0e6 100644
--- a/src/obikphylo/src/siblings/cache.rs
+++ b/src/obikphylo/src/siblings/cache.rs
@@ -42,7 +42,7 @@ pub(super) enum Mat {
     Presence(Layer<PersistentBitMatrix>),
     /// Same role as `Presence`, over a layer packed by `pack --sparse`
     /// (`PersistentSparseBitMatrix`) instead of the dense form — see
-    /// `docmd/architecture/siblings.md`'s sparse-matrix section. Every
+    /// `DevDocMD/architecture/siblings.md`'s sparse-matrix section. Every
     /// `Mat` method below dispatches to the same `Layer<D>` generic code
     /// (`D: LayerData`) as `Presence`, so this arm is purely a storage
     /// choice, not a behavioural difference.
@@ -62,7 +62,7 @@ impl Mat {
     /// callers that already know every kmer is a member of *this* layer
     /// (e.g. it came from this layer's own `iter_minorants_batch`), so the
     /// evidence check `find_slot`/`find` would perform is redundant work.
-    /// See `docmd/architecture/siblings.md`: iteration-pipeline kmers use
+    /// See `DevDocMD/architecture/siblings.md`: iteration-pipeline kmers use
     /// `index`, never `find`.
     pub(super) fn index_batch(&self, kmers: &[CanonicalKmer]) -> Vec<usize> {
         match self {
diff --git a/src/obikphylo/src/siblings/cardinality.rs b/src/obikphylo/src/siblings/cardinality.rs
index 0e63910c..1392bc3e 100644
--- a/src/obikphylo/src/siblings/cardinality.rs
+++ b/src/obikphylo/src/siblings/cardinality.rs
@@ -47,7 +47,7 @@ pub trait CardinalityExt {
     /// Verified empirically: removing the filter measurably worsened a
     /// real IQ-TREE run (log-likelihood dropped, `NNI search needs
     /// unusual large number of steps to converge` warnings appeared) — see
-    /// `docmd/theory/evolutionary_distances.md` for the full account.
+    /// `DevDocMD/theory/evolutionary_distances.md` for the full account.
     /// [`base_pair_tally`](Self::base_pair_tally)'s own diagonal (`same`)
     /// gets the matching restriction via `scan_family_pairs`'s new
     /// `variable` flag, rather than a `family_size()` check of its own (it
diff --git a/src/obikphylo/src/siblings/distance.rs b/src/obikphylo/src/siblings/distance.rs
index 8ce640a9..34150300 100644
--- a/src/obikphylo/src/siblings/distance.rs
+++ b/src/obikphylo/src/siblings/distance.rs
@@ -13,7 +13,7 @@ use super::family_scan::{scan_layer_families, Selection};
 
 /// Raw p-distance restricted to loci that are single-copy in **both**
 /// genomes of a pair — the "stringent / paralogy-aware" locus eligibility
-/// rule (`docmd/theory/evolutionary_distances.md`, "Locus eligibility"),
+/// rule (`DevDocMD/theory/evolutionary_distances.md`, "Locus eligibility"),
 /// without the JC/K2P/LogDet finalisation math: `snp[i,j]` + `shared[i,j]`
 /// is the number of eligible loci, `snp[i,j] / (snp[i,j] + shared[i,j])` is
 /// `p_hat`. A quick, self-contained way to sanity-check the estimator
@@ -197,7 +197,7 @@ impl DistanceExt for KmerIndex {
                     // (never varies anywhere) isn't a SNP-adjacent
                     // agreement, it's genome-wide background, and would
                     // otherwise swamp the diagonal (see
-                    // `docmd/theory/evolutionary_distances.md`, the
+                    // `DevDocMD/theory/evolutionary_distances.md`, the
                     // ascertainment-bias regression this was reverting).
                     same[bi as usize] += 1;
                 }
diff --git a/src/obikphylo/src/siblings/entropy.rs b/src/obikphylo/src/siblings/entropy.rs
index 0b73b5c5..9eb4e725 100644
--- a/src/obikphylo/src/siblings/entropy.rs
+++ b/src/obikphylo/src/siblings/entropy.rs
@@ -1,5 +1,5 @@
 //! `--shannon` — per-family Shannon entropy over the 15 non-empty subsets
-//! of `{A,C,G,T}`. See `docmd/architecture/siblings.md`, "Entropy
+//! of `{A,C,G,T}`. See `DevDocMD/architecture/siblings.md`, "Entropy
 //! definition — settled 2026-08-15" and "`--subsample`/`--shannon`", for
 //! the design discussion this implements: the project's calibrated 16-state
 //! Sankoff cost matrix (`cardcomp::pairwise_cost_matrix`) treats every
@@ -10,7 +10,7 @@
 //! reduction.
 
 use std::io::{BufWriter, Write};
-use std::path::Path;
+use std::path::{Path, PathBuf};
 use std::sync::Arc;
 
 use obikpartitionner::KmerPartition;
@@ -20,7 +20,9 @@ use obikindex::{OKIError, OKIResult};
 use obikindex::KmerIndex;
 
 use super::cache::PartitionCache;
+use super::entropy_annex::{EntropyAnnexBuilder, ENTROPY_ANNEX_FILE_NAME};
 use super::family_scan::{Selection, scan_layer_families};
+use super::subsample::EntropyBias;
 
 /// Shannon entropy (bits) of one family's per-genome states, over the 15
 /// non-empty subsets of `{A,C,G,T}` actually observed among the genomes
@@ -56,7 +58,7 @@ pub(super) fn family_entropy(genome_mask: &[u8]) -> Option<(f64, usize)> {
 /// 4 plain nucleotide symbols instead of the 15-state space above — kept
 /// alongside it (not instead of it) purely to measure how much the two
 /// diverge on real data, per the discussion in
-/// `docmd/architecture/siblings.md`, "`--subsample`/`--shannon`". A genome
+/// `DevDocMD/architecture/siblings.md`, "`--subsample`/`--shannon`". A genome
 /// carrying several bases at once (`genome_mask[g]` with more than one bit
 /// set) contributes to *each* of those bases' counts — counted once per
 /// base present, not split fractionally, and not folded into a combined
@@ -107,17 +109,22 @@ pub trait ShannonEntropyExt {
     /// iteration-order index within that layer, the same numbering
     /// `--subsample`'s selection is drawn from.
     ///
-    /// `subsample`: same meaning as
+    /// `subsample`/`entropy_bias`: same meaning as
     /// [`SnpAlignmentExt::snp_pseudo_alignment`](super::SnpAlignmentExt::snp_pseudo_alignment)'s
-    /// — `None` streams every non-monomorphic minorant of the whole index
-    /// (a time cost, not a memory one: entropy is computed and written
-    /// per-family as soon as it resolves), `Some(n)` bounds the index's
-    /// cross-partition resolution work to ~`n` sampled families.
-    fn shannon_entropy_csv(&self, path: &Path, subsample: Option<usize>) -> OKIResult<()>;
+    /// — `subsample = None`, `entropy_bias = None` streams every
+    /// non-monomorphic minorant of the whole index (a time cost, not a
+    /// memory one: entropy is computed and written per-family as soon as it
+    /// resolves); `subsample = Some(n)` bounds the index's cross-partition
+    /// resolution work to ~`n` sampled families; `entropy_bias = Some(_)`
+    /// weights that sample by its own entropy (see
+    /// `DevDocMD/architecture/siblings.md`, "Entropy-biased selection") —
+    /// useful here specifically to see the biased sample's own entropy
+    /// distribution, not just to speed up a distance computation.
+    fn shannon_entropy_csv(&self, path: &Path, subsample: Option<usize>, entropy_bias: Option<EntropyBias>) -> OKIResult<()>;
 }
 
 impl ShannonEntropyExt for KmerIndex {
-    fn shannon_entropy_csv(&self, path: &Path, subsample: Option<usize>) -> OKIResult<()> {
+    fn shannon_entropy_csv(&self, path: &Path, subsample: Option<usize>, entropy_bias: Option<EntropyBias>) -> OKIResult<()> {
         let n_parts = self.n_partitions();
         let n_genomes = self.meta().genomes.len();
         let with_counts = self.meta().config.with_counts;
@@ -133,7 +140,7 @@ impl ShannonEntropyExt for KmerIndex {
         .map_err(OKIError::Partition)?;
         let cache = Arc::new(PartitionCache::build(&partition, n_parts, with_counts)?);
         let layer_dirs = super::family_scan::sibling_layer_dirs(self)?;
-        let selections = super::subsample::compute_selections(&layer_dirs, subsample)?;
+        let selections = super::subsample::compute_selections(self, &layer_dirs, subsample, entropy_bias)?;
 
         let mut f = BufWriter::new(std::fs::File::create(path).map_err(OKIError::Io)?);
         writeln!(f, "layer,family_idx,entropy15,entropy4,family_size,n_genomes_present").map_err(OKIError::Io)?;
@@ -168,3 +175,58 @@ impl ShannonEntropyExt for KmerIndex {
         Ok(())
     }
 }
+
+/// Builds the entropy annex (`entropy_annex.rs`) for every layer in
+/// `layer_dirs` that doesn't already have one — a no-op, cheap existence
+/// check per layer, once every layer's annex file exists. Called from
+/// [`super::subsample::compute_selections`] whenever entropy-biased
+/// selection is requested; see `DevDocMD/architecture/siblings.md`,
+/// "Entropy-biased selection", for why this is the one place that pays a
+/// full, unsampled scan (every non-monomorphic minorant's `genome_mask`
+/// must be resolved to know its entropy) — every later read of the
+/// resulting file is a plain positional mmap lookup, not a re-scan.
+pub(super) fn ensure_entropy_annexes(index: &KmerIndex, layer_dirs: &[PathBuf]) -> OKIResult<()> {
+    let missing: Vec<usize> = layer_dirs.iter().enumerate()
+        .filter(|(_, dir)| !dir.join(ENTROPY_ANNEX_FILE_NAME).exists())
+        .map(|(i, _)| i)
+        .collect();
+    if missing.is_empty() {
+        return Ok(());
+    }
+
+    let n_parts = index.n_partitions();
+    let n_genomes = index.meta().genomes.len();
+    let with_counts = index.meta().config.with_counts;
+    let k = index.kmer_size();
+    let n_bits = n_parts.trailing_zeros() as usize;
+
+    let partition = KmerPartition::open_with_config(
+        index.root_path(),
+        index.kmer_size(),
+        index.minimizer_size(),
+        n_bits,
+    )
+    .map_err(OKIError::Partition)?;
+    let cache = Arc::new(PartitionCache::build(&partition, n_parts, with_counts)?);
+    let minorant_counts = super::subsample::minorant_counts(layer_dirs)?;
+
+    let pb = progress_bar("entropy_annex_build", missing.len() as u64, "layers");
+    for &li in &missing {
+        let layer_dir = &layer_dirs[li];
+        let mut builder = EntropyAnnexBuilder::new(minorant_counts[li] as usize, &layer_dir.join(ENTROPY_ANNEX_FILE_NAME))
+            .map_err(OKIError::Io)?;
+        scan_layer_families(layer_dir, n_parts, n_genomes, with_counts, k, &cache, &Selection::All, |family_idx, mask, genome_mask| {
+            if mask.family_size() < 2 {
+                return; // monomorphic minorant — leave the sentinel, never sampled
+            }
+            if let Some((h15, _)) = family_entropy(genome_mask) {
+                builder.set(family_idx, h15 as f32);
+            }
+        })?;
+        builder.close().map_err(OKIError::Io)?;
+        pb.inc(1);
+    }
+    pb.finish_and_clear();
+
+    Ok(())
+}
diff --git a/src/obikphylo/src/siblings/entropy_annex.rs b/src/obikphylo/src/siblings/entropy_annex.rs
new file mode 100644
index 00000000..1ac2457a
--- /dev/null
+++ b/src/obikphylo/src/siblings/entropy_annex.rs
@@ -0,0 +1,162 @@
+//! Persisted, per-layer Shannon entropy (`entropy15`, see `entropy.rs`),
+//! one value per **minorant family**, indexed by `family_idx` — the same
+//! numbering `scan_layer_families`/`Selection`/`subsample::reservoir_sample_layer`
+//! already use (every minorant of the layer, monomorphic ones included,
+//! counted in iteration order; see `subsample.rs`'s module docs for why
+//! `family_idx` and the raw annex slot are kept as two different counters).
+//!
+//! Exists so entropy-biased selection (`--entropy`/`--entropy-sd`) can
+//! weight candidates without re-resolving each one's `genome_mask` (the
+//! expensive cross-partition step) on every run — see
+//! `DevDocMD/architecture/siblings.md`, "Entropy-biased selection": entropy is
+//! only knowable once presence is resolved, so *building* this file still
+//! costs a full, unsampled scan the first time (`ensure_entropy_annexes` in
+//! `entropy.rs`), but every subsequent read is a plain positional mmap
+//! lookup, restoring `Selection::Some`'s usual "skip resolving excluded
+//! families entirely" speedup for every run after the first.
+//!
+//! Mirrors `SiblingAnnex`'s on-disk convention (magic + header + flat
+//! per-entry data, read-only after build) but is not slot-indexed the way
+//! `SiblingAnnex` is: `SiblingAnnex` is indexed by every k-mer of the layer
+//! (needed because any slot might turn out to be a minorant), while this
+//! file is built *from* an already-open `SiblingAnnex`, so it only ever
+//! needs to be as long as the layer's minorant count — monomorphic
+//! minorants still get an entry (a `-1.0` sentinel, entropy not meaningful
+//! for them, never read), keeping the same family_idx numbering every
+//! other consumer uses, but non-minorant k-mers (the vast majority of
+//! slots) are never represented here at all.
+
+use std::fs::{File, OpenOptions};
+use std::io;
+use std::path::Path;
+
+use memmap2::{Mmap, MmapMut};
+
+const MAGIC: [u8; 4] = *b"PENT";
+
+// Header: magic(4) + _pad(4) + n(8) = 16 bytes. Data (4 bytes/entry) follows.
+const HEADER_SIZE: usize = 16;
+
+/// Sentinel: monomorphic minorant (no signal, never sampled) or otherwise
+/// not applicable. Entropy is always `>= 0.0`, so any negative value is
+/// unambiguous — chosen over `NaN` to avoid `NaN`-comparison footguns at
+/// every read site.
+const SENTINEL: f32 = -1.0;
+
+pub(super) const ENTROPY_ANNEX_FILE_NAME: &str = "entropy.pent";
+
+pub(super) struct EntropyAnnex {
+    mmap: Mmap,
+    n: usize,
+}
+
+impl EntropyAnnex {
+    pub(super) fn open(path: &Path) -> io::Result<Self> {
+        let mmap = unsafe { Mmap::map(&File::open(path)?)? };
+        if mmap.len() < HEADER_SIZE {
+            return Err(io::Error::new(io::ErrorKind::InvalidData, "PENT file too short"));
+        }
+        if mmap[0..4] != MAGIC {
+            return Err(io::Error::new(io::ErrorKind::InvalidData, "bad PENT magic"));
+        }
+        let n = u64::from_le_bytes(mmap[8..16].try_into().unwrap()) as usize;
+        if mmap.len() < HEADER_SIZE + n * 4 {
+            return Err(io::Error::new(io::ErrorKind::InvalidData, "PENT file truncated"));
+        }
+        Ok(Self { mmap, n })
+    }
+
+    pub(super) fn len(&self) -> usize { self.n }
+
+    /// `None` for the sentinel (monomorphic minorant, or not yet computed).
+    pub(super) fn get(&self, family_idx: usize) -> Option<f32> {
+        let off = HEADER_SIZE + family_idx * 4;
+        let v = f32::from_le_bytes(self.mmap[off..off + 4].try_into().unwrap());
+        (v >= 0.0).then_some(v)
+    }
+}
+
+pub(super) struct EntropyAnnexBuilder {
+    mmap: MmapMut,
+}
+
+impl EntropyAnnexBuilder {
+    /// Create a new annex of `n` entries (a layer's total minorant count) at
+    /// `path`, pre-initialised to the sentinel — entries never written
+    /// (monomorphic minorants) stay the sentinel, not an accidental `0.0`
+    /// (a real, achievable entropy value).
+    pub(super) fn new(n: usize, path: &Path) -> io::Result<Self> {
+        let file_size = HEADER_SIZE + n * 4;
+        let file = OpenOptions::new()
+            .read(true).write(true).create(true).truncate(true)
+            .open(path)?;
+        file.set_len(file_size as u64)?;
+        let mut mmap = unsafe { MmapMut::map_mut(&file)? };
+        mmap[0..4].copy_from_slice(&MAGIC);
+        mmap[4..8].copy_from_slice(&[0u8; 4]);
+        mmap[8..16].copy_from_slice(&(n as u64).to_le_bytes());
+        for i in 0..n {
+            let off = HEADER_SIZE + i * 4;
+            mmap[off..off + 4].copy_from_slice(&SENTINEL.to_le_bytes());
+        }
+        Ok(Self { mmap })
+    }
+
+    pub(super) fn set(&mut self, family_idx: usize, value: f32) {
+        debug_assert!(value >= 0.0, "entropy must be non-negative, got {value}");
+        let off = HEADER_SIZE + family_idx * 4;
+        self.mmap[off..off + 4].copy_from_slice(&value.to_le_bytes());
+    }
+
+    pub(super) fn close(self) -> io::Result<()> {
+        self.mmap.flush()
+    }
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+    use tempfile::tempdir;
+
+    #[test]
+    fn sentinel_is_negative_and_unset_entries_read_as_none() {
+        let dir = tempdir().unwrap();
+        let path = dir.path().join("test.pent");
+        let builder = EntropyAnnexBuilder::new(4, &path).unwrap();
+        builder.close().unwrap();
+        let annex = EntropyAnnex::open(&path).unwrap();
+        for i in 0..4 {
+            assert_eq!(annex.get(i), None);
+        }
+    }
+
+    #[test]
+    fn roundtrip_including_zero_entropy() {
+        let dir = tempdir().unwrap();
+        let path = dir.path().join("test.pent");
+        let mut builder = EntropyAnnexBuilder::new(4, &path).unwrap();
+        let values = [0.0f32, 1.5, 3.9, 0.0001];
+        for (i, &v) in values.iter().enumerate() {
+            builder.set(i, v);
+        }
+        builder.close().unwrap();
+        let annex = EntropyAnnex::open(&path).unwrap();
+        for (i, &v) in values.iter().enumerate() {
+            assert_eq!(annex.get(i), Some(v), "entry {i}");
+        }
+    }
+
+    #[test]
+    fn mixed_sentinel_and_real_values() {
+        let dir = tempdir().unwrap();
+        let path = dir.path().join("test.pent");
+        let mut builder = EntropyAnnexBuilder::new(3, &path).unwrap();
+        builder.set(1, 2.0);
+        builder.close().unwrap();
+        let annex = EntropyAnnex::open(&path).unwrap();
+        assert_eq!(annex.get(0), None);
+        assert_eq!(annex.get(1), Some(2.0));
+        assert_eq!(annex.get(2), None);
+        assert_eq!(annex.len(), 3);
+    }
+}
diff --git a/src/obikphylo/src/siblings/family_scan.rs b/src/obikphylo/src/siblings/family_scan.rs
index 338a1b8c..d76cfacc 100644
--- a/src/obikphylo/src/siblings/family_scan.rs
+++ b/src/obikphylo/src/siblings/family_scan.rs
@@ -76,7 +76,7 @@ const FAMILY_BATCH: usize = 65536;
 
 /// Restricts [`scan_layer_families`] to a subset of a layer's families,
 /// identified by their iteration-order index — see
-/// `docmd/architecture/siblings.md`, "`--subsample`/`--shannon`", for why:
+/// `DevDocMD/architecture/siblings.md`, "`--subsample`/`--shannon`", for why:
 /// bounding which families actually pay the expensive cross-partition
 /// resolution cost is what makes a sampled run cheap on an index far larger
 /// than the sample itself. `All` (the default for every pre-existing
@@ -145,7 +145,7 @@ struct SourceBatch {
     start_family_idx: usize,
     /// One entry per minorant family in this batch, straight from
     /// `iter_minorants_batch` — `order` (iteration-order index, not an MPHF
-    /// slot; see `docmd/architecture/siblings.md`), `kmer`, and `mask`
+    /// slot; see `DevDocMD/architecture/siblings.md`), `kmer`, and `mask`
     /// already carried through, no second annex read.
     entries: Vec<SiblingEntry>,
     _permit: ThrottleGuard,
@@ -207,7 +207,7 @@ pub(super) fn scan_layer_families(
 
     // Streamed straight from `iter_minorants_batch` (zips this layer's own
     // `iter_kmers()` with the annex, both in iteration order — never an
-    // MPHF slot; see `docmd/architecture/siblings.md`) — never collected
+    // MPHF slot; see `DevDocMD/architecture/siblings.md`) — never collected
     // into a `Vec` first: a layer can hold billions of k-mers, so
     // materialising every minorant family up front is exactly the memory
     // blowup an earlier version of this traversal was rewritten to avoid
diff --git a/src/obikphylo/src/siblings/iter.rs b/src/obikphylo/src/siblings/iter.rs
index 932f0eed..b2e948ca 100644
--- a/src/obikphylo/src/siblings/iter.rs
+++ b/src/obikphylo/src/siblings/iter.rs
@@ -1,7 +1,7 @@
 //! Phylo/sibling-domain iteration over a layer — an extension trait, not a
 //! new field on `MphfLayer`/`Layer<D>`: "family"/"minorant" are phylo
 //! concepts, `obilayeredmap` stays kmer/slot-mapping only (see
-//! `docmd/architecture/siblings.md`).
+//! `DevDocMD/architecture/siblings.md`).
 //!
 //! The sibling annex is persisted in the same order as `iter_kmers()`
 //! (`build_sibling_annex`, see `build.rs`), so pairing them is a plain zip —
diff --git a/src/obikphylo/src/siblings/mod.rs b/src/obikphylo/src/siblings/mod.rs
index a5c368bb..9a1a3078 100644
--- a/src/obikphylo/src/siblings/mod.rs
+++ b/src/obikphylo/src/siblings/mod.rs
@@ -1,6 +1,6 @@
 //! Family presence-mask annex construction.
 //!
-//! See `docmd/theory/evolutionary_distances.md`, "Definitions: family, and
+//! See `DevDocMD/theory/evolutionary_distances.md`, "Definitions: family, and
 //! the canonical form of a family" and "Step 2b", for the full design
 //! discussion this implements.
 //!
@@ -32,7 +32,7 @@
 //! most wall-clock time going into per-message channel send/notify
 //! syscalls rather than the lookup itself, because a single k-mer's ≤3
 //! variants is far too fine a granularity to amortise a pipeline's
-//! synchronisation cost over. See `docmd/theory/evolutionary_distances.md`,
+//! synchronisation cost over. See `DevDocMD/theory/evolutionary_distances.md`,
 //! Step 2b, "Mechanism".
 //!
 //! Submodules, in the order data flows through them: [`cache`] (shared
@@ -48,9 +48,11 @@ mod cache;
 mod cardinality;
 mod distance;
 mod entropy;
+mod entropy_annex;
 mod family_scan;
 mod helpers;
 mod iter;
+mod sankoff_bundle;
 mod siblingannex;
 mod stats;
 mod subsample;
@@ -64,8 +66,10 @@ pub use cardinality::{CardinalityExt, CardinalityTally};
 pub use distance::{BasePairTally, DistanceExt, RawSnpDistanceOutput};
 pub use entropy::ShannonEntropyExt;
 pub use iter::{MinorantBatchIter, MinorantIter, SiblingBatchIter, SiblingEntry, SiblingIter, SiblingLayerExt};
+pub use sankoff_bundle::{SankoffBundle, SankoffBundleExt};
 pub(crate) use siblingannex::{FamilyMask, SiblingAnnex, SiblingAnnexBuilder};
 pub use stats::{SiblingAnnexStats, SiblingStatsExt};
+pub use subsample::EntropyBias;
 
 use obilayeredmap::OLMError;
 
diff --git a/src/obikphylo/src/siblings/sankoff_bundle.rs b/src/obikphylo/src/siblings/sankoff_bundle.rs
new file mode 100644
index 00000000..dabe3b9e
--- /dev/null
+++ b/src/obikphylo/src/siblings/sankoff_bundle.rs
@@ -0,0 +1,237 @@
+//! Fused entry point for the `--sankoff`/`--tnt`/`--phyg`/`--iqtree`
+//! pipeline — see `DevDocMD/architecture/siblings.md`, "`--free-loss`/`--tnt`
+//! pipeline: four independent scans, three of them unsampled" and "Wired
+//! into `pack` and the sibling-annex build path" for the problem this
+//! replaces: `raw_snp_distance`, `base_pair_tally`, `cardinality_tally` and
+//! `snp_pseudo_alignment` used to each open their own `PartitionCache` and
+//! independently re-scan the whole annex, three of the four ignoring
+//! `--subsample` entirely.
+//!
+//! `base_pair_tally`/`cardinality_tally` both need `raw_snp_distance`'s
+//! *complete* aggregate SNP/shared counts before they can derive
+//! `included[i,j]` (the `ratio_ceiling` filter) — a genuine sequential
+//! dependency, not an accidental one, so this is two passes, not one:
+//!
+//! - **Pass A**: aggregate SNP/shared counts per genome pair, over the
+//!   shared selection (computed once, [`super::subsample::compute_selections`]
+//!   — the *same* selection every other pass below uses, per the user's
+//!   own requirement: "il faut qu'on sélectionne tout le monde avec la
+//!   même sélection"). Excluded genomes (`--exclude-genome`) are zeroed
+//!   here, before `included` is derived from it — the ratio filter must
+//!   see the post-exclusion counts, not the raw ones.
+//! - **Pass B**: base-pair tally, cardinality tally, and the pseudo-
+//!   alignment, fused into *one* scan over the same selection — the three
+//!   are mutually independent once `included` is known, so they are
+//!   accumulated together family-by-family instead of three more separate
+//!   scans.
+
+use std::sync::Arc;
+
+use ndarray::Array2;
+
+use obikpartitionner::KmerPartition;
+use obisys::progress_bar;
+
+use obikindex::{OKIError, OKIResult};
+use obikindex::KmerIndex;
+
+use super::alignment::{iupac_code, SnpAlignment};
+use super::cache::PartitionCache;
+use super::cardinality::CardinalityTally;
+use super::distance::{BasePairTally, RawSnpDistanceOutput};
+use super::family_scan::{scan_layer_families, sibling_layer_dirs, Selection};
+use super::subsample::{compute_selections, EntropyBias};
+
+/// Every output the `--sankoff`/`--tnt`/`--phyg`/`--iqtree` pipeline needs,
+/// computed together from one shared, possibly-subsampled/entropy-biased
+/// selection — see the module docs.
+pub struct SankoffBundle {
+    pub raw: RawSnpDistanceOutput,
+    pub base_pair_tally: BasePairTally,
+    pub cardinality_tally: CardinalityTally,
+    pub alignment: SnpAlignment,
+}
+
+/// Adds [`sankoff_bundle`](Self::sankoff_bundle) to `KmerIndex`.
+pub trait SankoffBundleExt {
+    /// `subsample`/`entropy_bias`: see
+    /// [`SnpAlignmentExt::snp_pseudo_alignment`](super::SnpAlignmentExt::snp_pseudo_alignment).
+    /// `ratio_ceiling`: see
+    /// [`DistanceExt::base_pair_tally`](super::DistanceExt::base_pair_tally).
+    /// `exclude_mask[g]`: zero genome `g`'s row/column out of the aggregate
+    /// SNP/shared counts *before* `included[i,j]` is derived from them —
+    /// same semantics as `--exclude-genome` had on the old, separate
+    /// `raw_snp_distance` call.
+    fn sankoff_bundle(
+        &self,
+        subsample: Option<usize>,
+        entropy_bias: Option<EntropyBias>,
+        ratio_ceiling: f64,
+        exclude_mask: &[bool],
+    ) -> OKIResult<SankoffBundle>;
+}
+
+impl SankoffBundleExt for KmerIndex {
+    fn sankoff_bundle(
+        &self,
+        subsample: Option<usize>,
+        entropy_bias: Option<EntropyBias>,
+        ratio_ceiling: f64,
+        exclude_mask: &[bool],
+    ) -> OKIResult<SankoffBundle> {
+        let n_parts = self.n_partitions();
+        let n_genomes = self.meta().genomes.len();
+        let with_counts = self.meta().config.with_counts;
+        let k = self.kmer_size();
+        let n_bits = n_parts.trailing_zeros() as usize;
+
+        let partition = KmerPartition::open_with_config(
+            self.root_path(),
+            self.kmer_size(),
+            self.minimizer_size(),
+            n_bits,
+        )
+        .map_err(OKIError::Partition)?;
+        let cache = Arc::new(PartitionCache::build(&partition, n_parts, with_counts)?);
+        let layer_dirs = sibling_layer_dirs(self)?;
+        // Computed once — every pass below iterates the exact same
+        // families, in the exact same layers, per the shared-selection
+        // requirement this module exists to satisfy.
+        let selections = compute_selections(self, &layer_dirs, subsample, entropy_bias)?;
+
+        // ── Pass A: aggregate SNP/shared counts ────────────────────────────
+        let pb = progress_bar("raw_snp_distance", layer_dirs.len() as u64, "layers");
+        let mut snp = Array2::<u64>::zeros((n_genomes, n_genomes));
+        let mut shared = Array2::<u64>::zeros((n_genomes, n_genomes));
+        for (layer_dir, layer_selection) in layer_dirs.iter().zip(selections.iter()) {
+            let selection = match layer_selection {
+                None => Selection::All,
+                Some(set) => Selection::Some(set),
+            };
+            scan_layer_families(layer_dir, n_parts, n_genomes, with_counts, k, &cache, &selection, |_family_idx, _mask, genome_mask| {
+                let single_form = |g: usize| -> Option<u8> {
+                    let m = genome_mask[g];
+                    (m.count_ones() == 1).then(|| m.trailing_zeros() as u8)
+                };
+                for i in 0..n_genomes {
+                    let Some(bi) = single_form(i) else { continue };
+                    for j in (i + 1)..n_genomes {
+                        let Some(bj) = single_form(j) else { continue };
+                        if bi == bj {
+                            shared[[i, j]] += 1;
+                            shared[[j, i]] += 1;
+                        } else {
+                            snp[[i, j]] += 1;
+                            snp[[j, i]] += 1;
+                        }
+                    }
+                }
+            })?;
+            pb.inc(1);
+        }
+        pb.finish_and_clear();
+
+        // `--exclude-genome`: zero excluded rows/columns before `included`
+        // is derived below — same effect the old standalone
+        // `zero_excluded_pairs` had, applied here since this is now the
+        // only place `included` gets computed for this pipeline.
+        for (i, &excluded) in exclude_mask.iter().enumerate() {
+            if !excluded {
+                continue;
+            }
+            for j in 0..n_genomes {
+                snp[[i, j]] = 0;
+                snp[[j, i]] = 0;
+                shared[[i, j]] = 0;
+                shared[[j, i]] = 0;
+            }
+        }
+        let raw = RawSnpDistanceOutput { snp, shared };
+
+        let included = Array2::from_shape_fn((n_genomes, n_genomes), |(i, j)| {
+            if i == j {
+                return false;
+            }
+            let s = raw.snp[[i, j]];
+            let total = s + raw.shared[[i, j]];
+            total > 0 && (s as f64 / total as f64) <= ratio_ceiling
+        });
+
+        // ── Pass B: base-pair tally + cardinality tally + alignment, fused ──
+        let pb = progress_bar("sankoff_pass_b", layer_dirs.len() as u64, "layers");
+        let mut bp_counts = [[0u64; 4]; 4];
+        let mut bp_same = [0u64; 4];
+        let mut card_counts = [[0u64; 5]; 5];
+        let mut sequences: Vec<Vec<u8>> = vec![Vec::new(); n_genomes];
+        for (layer_dir, layer_selection) in layer_dirs.iter().zip(selections.iter()) {
+            let selection = match layer_selection {
+                None => Selection::All,
+                Some(set) => Selection::Some(set),
+            };
+            scan_layer_families(layer_dir, n_parts, n_genomes, with_counts, k, &cache, &selection, |_family_idx, mask, genome_mask| {
+                let variable = mask.family_size() >= 2;
+
+                // base-pair tally — same pairwise single-form resolution as pass A.
+                let single_form = |g: usize| -> Option<u8> {
+                    let m = genome_mask[g];
+                    (m.count_ones() == 1).then(|| m.trailing_zeros() as u8)
+                };
+                for i in 0..n_genomes {
+                    let Some(bi) = single_form(i) else { continue };
+                    for j in (i + 1)..n_genomes {
+                        let Some(bj) = single_form(j) else { continue };
+                        if !included[[i, j]] {
+                            continue;
+                        }
+                        if bi != bj {
+                            bp_counts[bi as usize][bj as usize] += 1;
+                            bp_counts[bj as usize][bi as usize] += 1;
+                        } else if variable {
+                            bp_same[bi as usize] += 1;
+                        }
+                    }
+                }
+
+                // cardinality tally — restricted to variable families, see
+                // `CardinalityExt::cardinality_tally`'s docs for why.
+                if variable {
+                    for i in 0..n_genomes {
+                        let card_i = genome_mask[i].count_ones() as usize;
+                        for j in (i + 1)..n_genomes {
+                            if !included[[i, j]] {
+                                continue;
+                            }
+                            let card_j = genome_mask[j].count_ones() as usize;
+                            card_counts[card_i][card_j] += 1;
+                            if card_i != card_j {
+                                card_counts[card_j][card_i] += 1;
+                            }
+                        }
+                    }
+                }
+
+                // pseudo-alignment — same variable-family gate as
+                // `snp_pseudo_alignment`. Every family the shared selection
+                // actually visits already satisfies this when the
+                // selection is `Selection::Some` (only non-monomorphic
+                // minorants are ever selected), but the explicit check
+                // still matters under `Selection::All` (no `--subsample`),
+                // which visits monomorphic minorants too.
+                if variable {
+                    for (g, &m) in genome_mask.iter().enumerate() {
+                        sequences[g].push(iupac_code(m));
+                    }
+                }
+            })?;
+            pb.inc(1);
+        }
+        pb.finish_and_clear();
+
+        Ok(SankoffBundle {
+            raw,
+            base_pair_tally: BasePairTally { counts: bp_counts, same: bp_same },
+            cardinality_tally: CardinalityTally { counts: card_counts },
+            alignment: SnpAlignment { sequences },
+        })
+    }
+}
diff --git a/src/obikphylo/src/siblings/siblingannex.rs b/src/obikphylo/src/siblings/siblingannex.rs
index 69637a24..0ec81d5e 100644
--- a/src/obikphylo/src/siblings/siblingannex.rs
+++ b/src/obikphylo/src/siblings/siblingannex.rs
@@ -1,6 +1,6 @@
 //! Family presence-mask annex: a compact, read-only-after-build, per-slot
 //! derived value used by the central-position SNP distance estimator (see
-//! `docmd/theory/evolutionary_distances.md`, "Step 2b" and "Definitions:
+//! `DevDocMD/theory/evolutionary_distances.md`, "Step 2b" and "Definitions:
 //! family, and the canonical form of a family").
 //!
 //! Two bytes are stored per MPHF slot of a partition/layer, packed as four
diff --git a/src/obikphylo/src/siblings/subsample.rs b/src/obikphylo/src/siblings/subsample.rs
index 80b593af..d9d296fc 100644
--- a/src/obikphylo/src/siblings/subsample.rs
+++ b/src/obikphylo/src/siblings/subsample.rs
@@ -1,5 +1,5 @@
 //! Proportional per-layer sampling of non-monomorphic minorants
-//! (`family_size() >= 2`) — see `docmd/architecture/siblings.md`,
+//! (`family_size() >= 2`) — see `DevDocMD/architecture/siblings.md`,
 //! "`--subsample`/`--shannon`", for the full design discussion.
 //!
 //! Three steps, in order, each cheaper than the one before because it
@@ -25,10 +25,25 @@ use std::path::{Path, PathBuf};
 use rand::Rng;
 use rayon::prelude::*;
 
-use obikindex::OKIResult;
+use obikindex::{KmerIndex, OKIError, OKIResult};
 
 use super::ANNEX_FILE_NAME;
 use super::SiblingAnnex;
+use super::entropy_annex::{EntropyAnnex, ENTROPY_ANNEX_FILE_NAME};
+
+/// Gaussian-kernel entropy bias parameters — see
+/// `DevDocMD/architecture/siblings.md`, "Entropy-biased selection". `mu`/
+/// `sigma` are the `--entropy`/`--entropy-sd` CLI values (defaulted by the
+/// caller, not here — this type carries only the resolved numbers). `pub`
+/// (not `pub(super)`): part of the public signature of
+/// `SnpAlignmentExt::snp_pseudo_alignment`,
+/// `ShannonEntropyExt::shannon_entropy_csv`, and
+/// `SankoffBundleExt::sankoff_bundle`, all consumed from `obikmer`.
+#[derive(Clone, Copy)]
+pub struct EntropyBias {
+    pub mu: f64,
+    pub sigma: f64,
+}
 
 /// A family is non-monomorphic (informative-eligible) iff at least one
 /// sibling is registered alongside it — `family_size() >= 2`, i.e.
@@ -106,6 +121,70 @@ fn reservoir_sample_layer(layer_dir: &Path, n_layer: usize) -> OKIResult<HashSet
     Ok(reservoir.into_iter().collect())
 }
 
+/// Total minorant count per layer (`is_minorant()`, monomorphic included)
+/// — sizes the entropy annex (`entropy_annex.rs`), which needs exactly one
+/// entry per minorant to keep its `family_idx` numbering aligned with
+/// every other consumer (`scan_layer_families`, `Selection`,
+/// `reservoir_sample_layer`'s own `family_idx` counter above).
+pub(super) fn minorant_counts(layer_dirs: &[PathBuf]) -> OKIResult<Vec<u64>> {
+    layer_dirs
+        .par_iter()
+        .map(|layer_dir| -> OKIResult<u64> {
+            let annex = SiblingAnnex::open(&layer_dir.join(ANNEX_FILE_NAME))?;
+            let mut count = 0u64;
+            for slot in 0..annex.len() {
+                if annex.get(slot).is_some_and(|m| m.is_minorant()) {
+                    count += 1;
+                }
+            }
+            Ok(count)
+        })
+        .collect()
+}
+
+/// Entropy-biased alternative to [`reservoir_sample_layer`]: an
+/// independent accept/reject draw per non-monomorphic minorant, probability
+/// `p0 * w(entropy)` where `w(entropy) = exp(-(entropy-mu)^2 / (2*sigma^2))`
+/// (the unnormalised Gaussian kernel — `1` exactly at `entropy == mu`,
+/// smoothly decaying away from it, no hard cutoff) and `p0` is the same
+/// uniform rate the plain reservoir targets in expectation (`n / total_count`
+/// index-wide, or `1.0` when there is no size target at all — `--entropy`
+/// given without `--subsample`, a pure soft entropy filter over the whole
+/// index). See `DevDocMD/architecture/siblings.md`, "Entropy-biased
+/// selection", for why this is a single streaming pass with no
+/// cross-partition resolution: entropy is read from the already-built
+/// entropy annex (`ensure_entropy_annexes`), not recomputed here.
+fn entropy_biased_sample_layer(layer_dir: &Path, p0: f64, bias: EntropyBias) -> OKIResult<HashSet<usize>> {
+    let annex = SiblingAnnex::open(&layer_dir.join(ANNEX_FILE_NAME))?;
+    let entropy_annex = EntropyAnnex::open(&layer_dir.join(ENTROPY_ANNEX_FILE_NAME)).map_err(OKIError::Io)?;
+    let mut selected = HashSet::new();
+    let mut family_idx: usize = 0;
+    let mut rng = rand::thread_rng();
+    for slot in 0..annex.len() {
+        let Some(mask) = annex.get(slot) else { continue };
+        if !mask.is_minorant() {
+            continue; // not a minorant at all — doesn't advance `family_idx` either
+        }
+        let this_family_idx = family_idx;
+        family_idx += 1;
+        debug_assert!(
+            this_family_idx < entropy_annex.len(),
+            "entropy annex ({}) shorter than this layer's minorant count — built against a different annex?",
+            entropy_annex.len(),
+        );
+        if mask.siblings() < 1 {
+            continue; // monomorphic minorant — no entropy, never eligible
+        }
+        let Some(entropy) = entropy_annex.get(this_family_idx) else { continue };
+        let d = (entropy as f64 - bias.mu) / bias.sigma;
+        let w = (-0.5 * d * d).exp();
+        if rng.r#gen::<f64>() < p0 * w {
+            selected.insert(this_family_idx);
+        }
+    }
+    Ok(selected)
+}
+
 /// Per-layer sampling outcome — `None` at a given layer means "keep every
 /// non-monomorphic minorant of this layer" (either the `total_count <= n`
 /// case, or a layer whose entire non-monomorphic set was already smaller
@@ -113,17 +192,54 @@ fn reservoir_sample_layer(layer_dir: &Path, n_layer: usize) -> OKIResult<HashSet
 pub(super) type LayerSelection = Option<HashSet<usize>>;
 
 /// Full entry point for every caller (`snp_pseudo_alignment`, the Shannon
-/// entropy report): `n = None` means "no `--subsample`", i.e. keep every
+/// entropy report, `sankoff_bundle`): `n = None` and `entropy_bias = None`
+/// means "no `--subsample`, no `--entropy`/`--entropy-sd`", i.e. keep every
 /// non-monomorphic minorant of every layer — skips steps 1 and 2 entirely,
 /// since there is nothing to proportion.
-pub(super) fn compute_selections(layer_dirs: &[PathBuf], n: Option<usize>) -> OKIResult<Vec<LayerSelection>> {
-    match n {
-        None => Ok(vec![None; layer_dirs.len()]),
+///
+/// `entropy_bias = Some(_)` switches selection from the plain uniform
+/// reservoir to [`entropy_biased_sample_layer`] — see
+/// `DevDocMD/architecture/siblings.md`, "Entropy-biased selection". `index` is
+/// only used on that path, to build any missing per-layer entropy annex
+/// first ([`super::entropy::ensure_entropy_annexes`]) — a one-time cost,
+/// not paid again once every layer's annex file exists. The target size
+/// `n` still proportions the *expected* rate across the whole index (a
+/// single `p0 = n / total_count` applied uniformly at every layer already
+/// yields each layer its proportional share, with no need to compute a
+/// per-layer target the way [`sample_layers`] does for the uniform
+/// reservoir) — but unlike the uniform reservoir, the result is
+/// approximate, not exact (see [`entropy_biased_sample_layer`]'s docs).
+pub(super) fn compute_selections(
+    index: &KmerIndex,
+    layer_dirs: &[PathBuf],
+    n: Option<usize>,
+    entropy_bias: Option<EntropyBias>,
+) -> OKIResult<Vec<LayerSelection>> {
+    let Some(bias) = entropy_bias else {
+        return match n {
+            None => Ok(vec![None; layer_dirs.len()]),
+            Some(n) => {
+                let counts = non_monomorphic_counts(layer_dirs)?;
+                sample_layers(layer_dirs, &counts, n)
+            }
+        };
+    };
+
+    super::entropy::ensure_entropy_annexes(index, layer_dirs)?;
+    let p0 = match n {
+        None => 1.0,
         Some(n) => {
             let counts = non_monomorphic_counts(layer_dirs)?;
-            sample_layers(layer_dirs, &counts, n)
+            let total_count: u64 = counts.iter().sum();
+            if total_count == 0 { 0.0 } else { (n as f64 / total_count as f64).min(1.0) }
         }
-    }
+    };
+    layer_dirs
+        .par_iter()
+        .map(|layer_dir| -> OKIResult<LayerSelection> {
+            Ok(Some(entropy_biased_sample_layer(layer_dir, p0, bias)?))
+        })
+        .collect()
 }
 
 /// Step 2 entry point: `n` is the total number of families requested across
diff --git a/src/obikphylo/src/siblings/tests.rs b/src/obikphylo/src/siblings/tests.rs
index 9979678c..2f30edaa 100644
--- a/src/obikphylo/src/siblings/tests.rs
+++ b/src/obikphylo/src/siblings/tests.rs
@@ -14,8 +14,11 @@ use super::build::SiblingAnnexBuildExt;
 use super::cardinality::CardinalityExt;
 use super::distance::DistanceExt;
 use super::entropy::ShannonEntropyExt;
+use super::entropy_annex::{EntropyAnnex, ENTROPY_ANNEX_FILE_NAME};
 use super::helpers::is_minorant;
+use super::sankoff_bundle::SankoffBundleExt;
 use super::stats::SiblingStatsExt;
+use super::subsample::EntropyBias;
 use super::{FamilyMask, SiblingAnnex, ANNEX_FILE_NAME, INDEX_SUBDIR};
 
 // k must be >= 11 (project constraint, "k ∈ [11,31]"); k=11, level_max=1,
@@ -271,7 +274,7 @@ fn family_scan_consumers_agree_on_one_sibling_each() {
 
     // snp_pseudo_alignment: one variable family, one column — g1's row
     // reads 'C' (its own member), g2's reads 'G'.
-    let alignment = merged.snp_pseudo_alignment(None).expect("snp_pseudo_alignment");
+    let alignment = merged.snp_pseudo_alignment(None, None).expect("snp_pseudo_alignment");
     assert_eq!(alignment.sequences[i1], vec![b'C']);
     assert_eq!(alignment.sequences[i2], vec![b'G']);
 
@@ -389,13 +392,13 @@ fn subsample_and_shannon_on_one_variable_family() {
     // `family_scan_consumers_agree_on_one_sibling_each`) — total_count = 1.
     // Asking for far more than that must fall back to "keep everything",
     // identical to the unsampled (`None`) result.
-    let sampled = merged.snp_pseudo_alignment(Some(1000)).expect("snp_pseudo_alignment (subsample >> total)");
+    let sampled = merged.snp_pseudo_alignment(Some(1000), None).expect("snp_pseudo_alignment (subsample >> total)");
     assert_eq!(sampled.sequences[i1], vec![b'C']);
     assert_eq!(sampled.sequences[i2], vec![b'G']);
 
     // Asking for 0 must keep nothing — an empty (but still one-row-per-genome)
     // alignment, not an error.
-    let empty = merged.snp_pseudo_alignment(Some(0)).expect("snp_pseudo_alignment (subsample 0)");
+    let empty = merged.snp_pseudo_alignment(Some(0), None).expect("snp_pseudo_alignment (subsample 0)");
     assert!(empty.sequences[i1].is_empty());
     assert!(empty.sequences[i2].is_empty());
 
@@ -404,7 +407,7 @@ fn subsample_and_shannon_on_one_variable_family() {
     // uniform split -> -2*(0.5*log2(0.5)) = 1 — the two definitions
     // coincide here since no genome carries more than one base).
     let csv_path = dir.path().join("shannon.csv");
-    merged.shannon_entropy_csv(&csv_path, Some(1000)).expect("shannon_entropy_csv");
+    merged.shannon_entropy_csv(&csv_path, Some(1000), None).expect("shannon_entropy_csv");
     let csv = std::fs::read_to_string(&csv_path).unwrap();
     let mut lines = csv.lines();
     assert_eq!(lines.next(), Some("layer,family_idx,entropy15,entropy4,family_size,n_genomes_present"));
@@ -419,6 +422,96 @@ fn subsample_and_shannon_on_one_variable_family() {
     assert_eq!(fields[5], "2", "n_genomes_present");
 }
 
+#[test]
+fn sankoff_bundle_matches_old_separate_calls() {
+    // Same fixture as `sibling_annex_one_sibling_each`/
+    // `subsample_and_shannon_on_one_variable_family`: one non-monomorphic
+    // family, g1='C' (minorant), g2='G'. Regression check that fusing
+    // raw_snp_distance/base_pair_tally/cardinality_tally/snp_pseudo_alignment
+    // into `sankoff_bundle`'s two passes produces identical results to the
+    // old four independent calls on `Selection::All` (no `--subsample`,
+    // no `--entropy`) — see `DevDocMD/architecture/siblings.md`, "Wired into
+    // `pack`...".
+    let dir = tempdir().unwrap();
+    let g1 = build_single_genome_index(dir.path(), "g1", b"AACCGCTTAAG");
+    let g2 = build_single_genome_index(dir.path(), "g2", b"AACCGGTTAAG");
+    let merged = merge_two(dir.path(), &g1, &g2);
+    merged.build_sibling_annex().expect("build_sibling_annex");
+
+    let n_genomes = merged.meta().genomes.len();
+    let exclude_mask = vec![false; n_genomes];
+    let ratio_ceiling = 0.5;
+
+    let expected_raw = merged.raw_snp_distance().expect("raw_snp_distance");
+    let expected_base = merged.base_pair_tally(&expected_raw, ratio_ceiling).expect("base_pair_tally");
+    let expected_card = merged.cardinality_tally(&expected_raw, ratio_ceiling).expect("cardinality_tally");
+    let expected_alignment = merged.snp_pseudo_alignment(None, None).expect("snp_pseudo_alignment");
+
+    let bundle = merged.sankoff_bundle(None, None, ratio_ceiling, &exclude_mask).expect("sankoff_bundle");
+
+    assert_eq!(bundle.raw.snp, expected_raw.snp);
+    assert_eq!(bundle.raw.shared, expected_raw.shared);
+    assert_eq!(bundle.base_pair_tally.counts, expected_base.counts);
+    assert_eq!(bundle.base_pair_tally.same, expected_base.same);
+    assert_eq!(bundle.cardinality_tally.counts, expected_card.counts);
+    assert_eq!(bundle.alignment.sequences, expected_alignment.sequences);
+}
+
+#[test]
+fn entropy_annex_builds_on_demand_and_biases_selection() {
+    // Same fixture, same single non-monomorphic family, known entropy15 =
+    // 1.0 bit exactly (see `subsample_and_shannon_on_one_variable_family`).
+    let dir = tempdir().unwrap();
+    let g1 = build_single_genome_index(dir.path(), "g1", b"AACCGCTTAAG");
+    let g2 = build_single_genome_index(dir.path(), "g2", b"AACCGGTTAAG");
+    let merged = merge_two(dir.path(), &g1, &g2);
+    merged.build_sibling_annex().expect("build_sibling_annex");
+
+    let layer_dirs = super::family_scan::sibling_layer_dirs(&merged).expect("layer dirs");
+    for layer_dir in &layer_dirs {
+        assert!(
+            !layer_dir.join(ENTROPY_ANNEX_FILE_NAME).exists(),
+            "entropy annex must not exist before any entropy-biased selection is requested"
+        );
+    }
+
+    // This fixture spans 2 layers (a single-genome bootstrap layer plus the
+    // merged one, see `merge_two`) — the one non-monomorphic family lives
+    // in whichever layer actually got a non-empty selection, not
+    // necessarily `layer_dirs[0]`.
+    let find_layer = |selections: &[super::subsample::LayerSelection]| {
+        selections.iter().position(|s| matches!(s, Some(set) if !set.is_empty()))
+    };
+
+    // mu == the family's real entropy, tiny sigma -> weight == 1 exactly,
+    // p0 == 1.0 (no `--subsample`) -> the family is selected with
+    // probability 1 (up to a measure-zero event on the uniform draw).
+    let bias_center = EntropyBias { mu: 1.0, sigma: 0.5 };
+    let selections = super::subsample::compute_selections(&merged, &layer_dirs, None, Some(bias_center))
+        .expect("compute_selections (entropy-biased)");
+    for layer_dir in &layer_dirs {
+        assert!(
+            layer_dir.join(ENTROPY_ANNEX_FILE_NAME).exists(),
+            "compute_selections must build the entropy annex for every layer on first use"
+        );
+    }
+    let li = find_layer(&selections).expect("mu at the true entropy must select the one non-monomorphic family, in some layer");
+    assert_eq!(selections[li], Some(std::collections::HashSet::from([0])));
+
+    // The annex now exists — read it back directly and check the stored
+    // value matches `--shannon`'s own entropy15 computation exactly.
+    let entropy_annex = EntropyAnnex::open(&layer_dirs[li].join(ENTROPY_ANNEX_FILE_NAME)).expect("open entropy annex");
+    let stored = entropy_annex.get(0).expect("family 0 has a real (non-sentinel) entropy value");
+    assert!((stored as f64 - 1.0).abs() < 1e-6, "stored entropy should be 1 bit, got {stored}");
+
+    // mu far from any achievable entropy, tiny sigma -> weight underflows
+    // to exactly 0.0 -> never selected, deterministically, in any layer.
+    let bias_far = EntropyBias { mu: 100.0, sigma: 0.001 };
+    let selections_far = super::subsample::compute_selections(&merged, &layer_dirs, None, Some(bias_far))
+        .expect("compute_selections (entropy-biased, far)");
+    assert!(find_layer(&selections_far).is_none(), "mu far from the true entropy must never select it, in any layer");
+}
+
 #[test]
 #[ignore]
 fn diag_real_index_layer_distribution() {
@@ -433,7 +526,7 @@ fn diag_real_index_layer_distribution() {
     println!("n_layers={} total={} n_zero_layers={} max={} min_nonzero={}",
         counts.len(), total, n_zero, max, min_nonzero);
     let n = 100_000usize;
-    let selections = super::subsample::compute_selections(&layer_dirs, Some(n)).expect("selections");
+    let selections = super::subsample::compute_selections(&idx, &layer_dirs, Some(n), None).expect("selections");
     let selected_total: usize = selections.iter().map(|s| match s {
         None => 0, // shouldn't happen when total_count > n
         Some(set) => set.len(),
@@ -803,7 +896,7 @@ fn bench_real_persistent_sparse_bit_matrix_on_disk_size() {
     );
 
     // ── Column-major access, "just for fun" ─────────────────────────────
-    // The whole point of `docmd/architecture/siblings.md`'s "Explicitly
+    // The whole point of `DevDocMD/architecture/siblings.md`'s "Explicitly
     // deferred" section: dense is genome-major (native, contiguous column
     // access), sparse is k-mer-major (no column method at all — reading
     // one column means decoding every row and keeping one bit each time).
diff --git a/src/obilayeredmap/src/layer.rs b/src/obilayeredmap/src/layer.rs
index 4aa86365..bf53fae8 100644
--- a/src/obilayeredmap/src/layer.rs
+++ b/src/obilayeredmap/src/layer.rs
@@ -259,7 +259,7 @@ impl<D: LayerData<Item = Box<[bool]>> + BinaryMatrix> Layer<D> {
     /// column, containing the presence bits for the requested slots in order.
     /// Column access is sequential for cache efficiency on the dense
     /// storage — on sparse storage it's a naive row-by-row decode, see
-    /// `docmd/architecture/siblings.md`'s sparse-matrix section.
+    /// `DevDocMD/architecture/siblings.md`'s sparse-matrix section.
     pub fn sub_matrix(&self, slots: &[usize]) -> Vec<Vec<bool>> {
         self.data.sub_matrix(slots)
     }
diff --git a/src/obilayeredmap/src/tests/layer.rs b/src/obilayeredmap/src/tests/layer.rs
index 033e819d..81eed976 100644
--- a/src/obilayeredmap/src/tests/layer.rs
+++ b/src/obilayeredmap/src/tests/layer.rs
@@ -74,7 +74,7 @@ fn presence_layer_generic_over_sparse_matches_dense() {
     // Build the sparse form directly into the same `presence/` dir the
     // dense form already lives in (matches how `pack --sparse` will work:
     // same directory, distinct filenames — see
-    // `docmd/architecture/siblings.md`'s sparse-matrix section).
+    // `DevDocMD/architecture/siblings.md`'s sparse-matrix section).
     let dense_matrix = obicompactvec::PersistentBitMatrix::open(dir.path()).unwrap();
     PersistentSparseBitMatrixBuilder::build_from_dense(&dense_matrix, &dir.path().join(PRESENCE_DIR))
         .unwrap()
-- 
2.54.0


From c6cfdac04341efc063170baefaddc82eea191bf0 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Sat, 15 Aug 2026 21:16:04 +0200
Subject: [PATCH 38/46] perf: optimize entropy computation by pre-filtering
 monomorphic minorants

Shift monomorphism filtering from the entropy scan layer to a lightweight, annex-only pre-pass. By replacing `Selection::All` with a pre-filtered subset, expensive per-genome resolution is strictly limited to non-monomorphic families. This avoids processing ~98% of minorants that are known to be monomorphic, while preserving positional read speedups for subsequent runs. The change is an internal performance refinement with no public API modifications.
---
 DevDocMD/architecture/siblings.md       | 22 ++++++++++++++++---
 src/obikphylo/src/siblings/entropy.rs   | 21 ++++++++++++------
 src/obikphylo/src/siblings/subsample.rs | 29 +++++++++++++++++++++++++
 3 files changed, 62 insertions(+), 10 deletions(-)

diff --git a/DevDocMD/architecture/siblings.md b/DevDocMD/architecture/siblings.md
index d689f2e5..1247cbdb 100644
--- a/DevDocMD/architecture/siblings.md
+++ b/DevDocMD/architecture/siblings.md
@@ -504,14 +504,30 @@ but indexed by `family_idx` (every minorant of the layer, monomorphic
 included — the same numbering `Selection`/`scan_layer_families` already
 use), one `f32` entropy15 value per entry, `-1.0` sentinel for monomorphic/
 not-yet-computed. First use of `--entropy`/`--entropy-sd` on an index
-pays a one-time cost (`ensure_entropy_annexes` in `entropy.rs`: a full,
-unsampled `Selection::All` scan, resolving every non-monomorphic
-minorant's `genome_mask` once to compute and persist its entropy) — every
+pays a one-time cost (`ensure_entropy_annexes` in `entropy.rs`) — every
 later run (any `μ`/`σ`, any command) reads the file positionally, no
 re-scan, restoring the usual `Selection::Some` "skip resolving excluded
 families" speedup that a naive "weigh during the resolving scan" design
 would have permanently forfeited.
 
+**Bug found and fixed (2026-08-15): `ensure_entropy_annexes` scanned with
+`Selection::All` instead of bounding to non-monomorphic minorants.**
+Monomorphism (`family_size() < 2`) is knowable directly from the annex
+bits alone, no per-genome resolution needed — but the original
+implementation called `scan_layer_families` with `Selection::All`
+anyway, so `fill_sub_matrix_carries` (the expensive per-genome
+resolution) ran for *every* minorant, ~98% of which are monomorphic
+(measured elsewhere in this doc) and had their `genome_mask` immediately
+discarded once the callback checked `family_size() < 2`. Fixed by adding
+[`subsample::non_monomorphic_selection_layer`] — a cheap, annex-only,
+non-sampling pass (same shape as `reservoir_sample_layer`, but keeping
+every non-monomorphic minorant's `family_idx` instead of a bounded
+reservoir) — and passing `Selection::Some(&eligible)` instead of
+`Selection::All`, so the expensive resolution now runs only for the ~2%
+of minorants that can actually produce a real entropy value. A
+`debug_assert!(mask.family_size() >= 2, ...)` inside the
+`scan_layer_families` callback guards the invariant.
+
 **Resolved**: the existing hard "non-monomorphic minorant" eligibility
 filter stays a hard gate upstream of the Gaussian weighting — only
 qualifying families ever get a stored entropy value or a weighted draw.
diff --git a/src/obikphylo/src/siblings/entropy.rs b/src/obikphylo/src/siblings/entropy.rs
index 9eb4e725..18f7e15b 100644
--- a/src/obikphylo/src/siblings/entropy.rs
+++ b/src/obikphylo/src/siblings/entropy.rs
@@ -182,9 +182,17 @@ impl ShannonEntropyExt for KmerIndex {
 /// [`super::subsample::compute_selections`] whenever entropy-biased
 /// selection is requested; see `DevDocMD/architecture/siblings.md`,
 /// "Entropy-biased selection", for why this is the one place that pays a
-/// full, unsampled scan (every non-monomorphic minorant's `genome_mask`
-/// must be resolved to know its entropy) — every later read of the
-/// resulting file is a plain positional mmap lookup, not a re-scan.
+/// scan (every non-monomorphic minorant's `genome_mask` must be resolved
+/// to know its entropy) — every later read of the resulting file is a
+/// plain positional mmap lookup, not a re-scan.
+///
+/// Bounded to non-monomorphic minorants only
+/// ([`super::subsample::non_monomorphic_selection_layer`], a cheap
+/// annex-only pass — no cross-partition resolution), not
+/// `Selection::All`: monomorphism (`family_size() < 2`) is already known
+/// from the annex bits alone, so there is no reason to pay
+/// `scan_layer_families`'s expensive per-genome resolution for the ~98%
+/// of minorants that are monomorphic only to discard the result.
 pub(super) fn ensure_entropy_annexes(index: &KmerIndex, layer_dirs: &[PathBuf]) -> OKIResult<()> {
     let missing: Vec<usize> = layer_dirs.iter().enumerate()
         .filter(|(_, dir)| !dir.join(ENTROPY_ANNEX_FILE_NAME).exists())
@@ -215,10 +223,9 @@ pub(super) fn ensure_entropy_annexes(index: &KmerIndex, layer_dirs: &[PathBuf])
         let layer_dir = &layer_dirs[li];
         let mut builder = EntropyAnnexBuilder::new(minorant_counts[li] as usize, &layer_dir.join(ENTROPY_ANNEX_FILE_NAME))
             .map_err(OKIError::Io)?;
-        scan_layer_families(layer_dir, n_parts, n_genomes, with_counts, k, &cache, &Selection::All, |family_idx, mask, genome_mask| {
-            if mask.family_size() < 2 {
-                return; // monomorphic minorant — leave the sentinel, never sampled
-            }
+        let eligible = super::subsample::non_monomorphic_selection_layer(layer_dir)?;
+        scan_layer_families(layer_dir, n_parts, n_genomes, with_counts, k, &cache, &Selection::Some(&eligible), |family_idx, mask, genome_mask| {
+            debug_assert!(mask.family_size() >= 2, "Selection::Some(eligible) must only visit non-monomorphic minorants");
             if let Some((h15, _)) = family_entropy(genome_mask) {
                 builder.set(family_idx, h15 as f32);
             }
diff --git a/src/obikphylo/src/siblings/subsample.rs b/src/obikphylo/src/siblings/subsample.rs
index d9d296fc..05653053 100644
--- a/src/obikphylo/src/siblings/subsample.rs
+++ b/src/obikphylo/src/siblings/subsample.rs
@@ -121,6 +121,35 @@ fn reservoir_sample_layer(layer_dir: &Path, n_layer: usize) -> OKIResult<HashSet
     Ok(reservoir.into_iter().collect())
 }
 
+/// Every non-monomorphic minorant's `family_idx`, for one layer — not a
+/// sample, the *complete* set. Structural, annex-only, no cross-partition
+/// resolution (same discipline as [`reservoir_sample_layer`], just keeping
+/// everything instead of a bounded reservoir). Used to bound
+/// [`super::entropy::ensure_entropy_annexes`]'s `scan_layer_families` call
+/// to a `Selection::Some` of exactly the families that need their entropy
+/// computed, instead of `Selection::All` — monomorphic minorants (~98% of
+/// them, measured) are known to be ineligible straight from the annex bits
+/// already, with no need to pay `scan_layer_families`'s expensive
+/// per-genome resolution (`fill_sub_matrix_carries`) only to discard the
+/// result once `family_size() < 2` is checked *after* resolving.
+pub(super) fn non_monomorphic_selection_layer(layer_dir: &Path) -> OKIResult<HashSet<usize>> {
+    let annex = SiblingAnnex::open(&layer_dir.join(ANNEX_FILE_NAME))?;
+    let mut selected = HashSet::new();
+    let mut family_idx: usize = 0;
+    for slot in 0..annex.len() {
+        let Some(mask) = annex.get(slot) else { continue };
+        if !mask.is_minorant() {
+            continue; // doesn't advance `family_idx` either
+        }
+        let this_family_idx = family_idx;
+        family_idx += 1;
+        if is_non_monomorphic_minorant(mask) {
+            selected.insert(this_family_idx);
+        }
+    }
+    Ok(selected)
+}
+
 /// Total minorant count per layer (`is_minorant()`, monomorphic included)
 /// — sizes the entropy annex (`entropy_annex.rs`), which needs exactly one
 /// entry per minorant to keep its `family_idx` numbering aligned with
-- 
2.54.0


From 96542018851aeff4ef7981035c825e5ec91a6dd3 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Sat, 15 Aug 2026 21:30:54 +0200
Subject: [PATCH 39/46] feat: introduce _iqtree_states.csv for compact symbol
 mapping

Generates a new CSV output that maps IQ-TREE's compact state symbols to canonical states alongside full-precision empirical frequencies. Updates documentation to clarify that state frequencies sum to 1.0 by design and documents conditional behavior under `--free-loss`. Includes unit tests verifying absent state exclusion, frequency summation, and CSV structure. Also restricts entropy annex resolution to non-monomorphic minorants to eliminate redundant per-genome checks.
---
 DevDoc/architecture/siblings/index.html       |  21 +++-
 .../theory/evolutionary_distances/index.html  |  58 ++++++++++
 DevDocMD/theory/evolutionary_distances.md     |  41 +++++++
 UserDocMD/usage/phylo.md                      |   3 +
 doc/usage/phylo/index.html                    |   7 ++
 src/obikmer/src/cmd/phylo/iqtree.rs           | 104 +++++++++++++++++-
 6 files changed, 230 insertions(+), 4 deletions(-)

diff --git a/DevDoc/architecture/siblings/index.html b/DevDoc/architecture/siblings/index.html
index 816ff532..8062296e 100644
--- a/DevDoc/architecture/siblings/index.html
+++ b/DevDoc/architecture/siblings/index.html
@@ -2051,13 +2051,28 @@ but indexed by <code>family_idx</code> (every minorant of the layer, monomorphic
 included — the same numbering <code>Selection</code>/<code>scan_layer_families</code> already
 use), one <code>f32</code> entropy15 value per entry, <code>-1.0</code> sentinel for monomorphic/
 not-yet-computed. First use of <code>--entropy</code>/<code>--entropy-sd</code> on an index
-pays a one-time cost (<code>ensure_entropy_annexes</code> in <code>entropy.rs</code>: a full,
-unsampled <code>Selection::All</code> scan, resolving every non-monomorphic
-minorant's <code>genome_mask</code> once to compute and persist its entropy) — every
+pays a one-time cost (<code>ensure_entropy_annexes</code> in <code>entropy.rs</code>) — every
 later run (any <code>μ</code>/<code>σ</code>, any command) reads the file positionally, no
 re-scan, restoring the usual <code>Selection::Some</code> "skip resolving excluded
 families" speedup that a naive "weigh during the resolving scan" design
 would have permanently forfeited.</p>
+<p><strong>Bug found and fixed (2026-08-15): <code>ensure_entropy_annexes</code> scanned with
+<code>Selection::All</code> instead of bounding to non-monomorphic minorants.</strong>
+Monomorphism (<code>family_size() &lt; 2</code>) is knowable directly from the annex
+bits alone, no per-genome resolution needed — but the original
+implementation called <code>scan_layer_families</code> with <code>Selection::All</code>
+anyway, so <code>fill_sub_matrix_carries</code> (the expensive per-genome
+resolution) ran for <em>every</em> minorant, ~98% of which are monomorphic
+(measured elsewhere in this doc) and had their <code>genome_mask</code> immediately
+discarded once the callback checked <code>family_size() &lt; 2</code>. Fixed by adding
+[<code>subsample::non_monomorphic_selection_layer</code>] — a cheap, annex-only,
+non-sampling pass (same shape as <code>reservoir_sample_layer</code>, but keeping
+every non-monomorphic minorant's <code>family_idx</code> instead of a bounded
+reservoir) — and passing <code>Selection::Some(&amp;eligible)</code> instead of
+<code>Selection::All</code>, so the expensive resolution now runs only for the ~2%
+of minorants that can actually produce a real entropy value. A
+<code>debug_assert!(mask.family_size() &gt;= 2, ...)</code> inside the
+<code>scan_layer_families</code> callback guards the invariant.</p>
 <p><strong>Resolved</strong>: the existing hard "non-monomorphic minorant" eligibility
 filter stays a hard gate upstream of the Gaussian weighting — only
 qualifying families ever get a stored entropy value or a weighted draw.</p>
diff --git a/DevDoc/theory/evolutionary_distances/index.html b/DevDoc/theory/evolutionary_distances/index.html
index c3b758ce..c56c4b9e 100644
--- a/DevDoc/theory/evolutionary_distances/index.html
+++ b/DevDoc/theory/evolutionary_distances/index.html
@@ -887,6 +887,17 @@
       </ul>
     </nav>
   
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_iqtree_statescsv-compact-symbol-traceability-2026-08-15" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        _iqtree_states.csv: compact-symbol traceability (2026-08-15)
+      
+    </span>
+  </a>
+  
 </li>
       
         <li class="md-nav__item">
@@ -2095,6 +2106,17 @@
       </ul>
     </nav>
   
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_iqtree_statescsv-compact-symbol-traceability-2026-08-15" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        _iqtree_states.csv: compact-symbol traceability (2026-08-15)
+      
+    </span>
+  </a>
+  
 </li>
       
         <li class="md-nav__item">
@@ -4048,6 +4070,42 @@ with a different taxon count crashes with <code>Assertion 'i &gt;= 0 &amp;&amp;
 the old leaf count onto the new, smaller alignment. Not an <code>obikmer</code> bug;
 avoid by using a fresh <code>--prefix</code> (or <code>-redo</code>) whenever the underlying
 alignment's taxon set changes, never <code>--undo</code> across them.</p>
+<h2 id="_iqtree_statescsv-compact-symbol-traceability-2026-08-15"><code>_iqtree_states.csv</code>: compact-symbol traceability (2026-08-15)</h2>
+<p>User-reported suspicion: <code>--iqtree --free-loss</code> state frequencies "don't
+sum to 1". Verified both by code trace and unit test
+(<code>obikmer/src/cmd/phylo/iqtree.rs</code>, <code>free_loss_excludes_absent_state_and_freq_sums_to_one</code>)
+— <strong>not a bug</strong>: <code>compact_alphabet</code>'s counting loop <code>continue</code>s on
+<code>free_loss &amp;&amp; b == b'-'</code> <em>before</em> recoding/counting, so the absent state
+never enters <code>occurs</code>/<code>counts</code>, and <code>freq[i] = counts[old]/total</code> sums to
+1.0 by construction (<code>total</code> is defined as the sum over exactly the same
+states). Confirmed against real data the user provided: a pasted
+<code>_iqtree.model</code> frequency line summed to <code>1.000001</code> — a 6-decimal
+print-rounding artifact (<code>format!("{p:.6}")</code> × 15 values), not a
+computation error; IQ-TREE's own 3-decimal-rounded report of the same
+values summed to exactly <code>1.000</code>.</p>
+<p>Investigating that report surfaced a real, separate gap: nothing mapped
+<code>_iqtree.model</code>/<code>_iqtree.fasta</code>'s compact state symbols (<code>0-9A-F</code>, IQ-TREE
+renumbers away unused states from the full 16, see this module's own
+"<code>--iqtree</code>... state count" discussion) back to the canonical 16-state
+alphabet (<code>STATE_SYMBOL</code>, <code>sankoff.rs</code>) — so a pattern like "compact state
+0 has zero exchangeability with every other state" (<code>R(a,b) =
+exp(-cost(a,b)) = 0</code> for an entire row/column) couldn't be traced back to
+which real state that was, or whether it was expected (a state combination
+that was simply never observed alongside anything else in the calibration
+data, giving <code>cost = -ln(0) = +∞</code>) or a genuine problem.</p>
+<p><strong>Fix</strong>: <code>write_iqtree_states_csv</code> (<code>iqtree.rs</code>) writes
+<code>&lt;prefix&gt;_iqtree_states.csv</code> — one row per surviving state,
+<code>iqtree_symbol,canonical_symbol,frequency</code>, frequency at full <code>f64</code>
+precision (not the model file's truncated 6 decimals). Written alongside
+<code>_iqtree.model</code>/<code>_iqtree.fasta</code> from the same <code>CompactAlphabet</code> both
+already use, so there is no risk of the three files disagreeing. Covered
+by <code>states_csv_maps_compact_symbols_back_to_canonical_ones</code>.</p>
+<p>The zero-exchangeability pattern itself (state 0 in the user's report,
+frequency 3.26%, <code>R=0</code> with every other state) is not yet explained —
+plausibly a genuinely unobserved transition in the calibration
+(<code>cardinality_transitions</code>/<code>composition_transitions</code> count <code>0</code> for every
+pair involving it), which is a legitimate, if numerically extreme, result
+of <code>-ln(0)</code>, not necessarily a bug — not investigated further.</p>
 <h2 id="references">References</h2>
 <p>The Mash mutation-rate model this discussion contrasts with:
 (Fan <em>et al.</em> 2015; Marbl Lab 2026)<sup id="fnref:Mash-distances-doc"><a class="footnote-ref" href="#fn:Mash-distances-doc">1</a></sup> <sup id="fnref:Fan2015-mash-formula"><a class="footnote-ref" href="#fn:Fan2015-mash-formula">2</a></sup>.</p>
diff --git a/DevDocMD/theory/evolutionary_distances.md b/DevDocMD/theory/evolutionary_distances.md
index 9405adfc..23d1805d 100644
--- a/DevDocMD/theory/evolutionary_distances.md
+++ b/DevDocMD/theory/evolutionary_distances.md
@@ -2056,6 +2056,47 @@ the old leaf count onto the new, smaller alignment. Not an `obikmer` bug;
 avoid by using a fresh `--prefix` (or `-redo`) whenever the underlying
 alignment's taxon set changes, never `--undo` across them.
 
+## `_iqtree_states.csv`: compact-symbol traceability (2026-08-15)
+
+User-reported suspicion: `--iqtree --free-loss` state frequencies "don't
+sum to 1". Verified both by code trace and unit test
+(`obikmer/src/cmd/phylo/iqtree.rs`, `free_loss_excludes_absent_state_and_freq_sums_to_one`)
+— **not a bug**: `compact_alphabet`'s counting loop `continue`s on
+`free_loss && b == b'-'` *before* recoding/counting, so the absent state
+never enters `occurs`/`counts`, and `freq[i] = counts[old]/total` sums to
+1.0 by construction (`total` is defined as the sum over exactly the same
+states). Confirmed against real data the user provided: a pasted
+`_iqtree.model` frequency line summed to `1.000001` — a 6-decimal
+print-rounding artifact (`format!("{p:.6}")` × 15 values), not a
+computation error; IQ-TREE's own 3-decimal-rounded report of the same
+values summed to exactly `1.000`.
+
+Investigating that report surfaced a real, separate gap: nothing mapped
+`_iqtree.model`/`_iqtree.fasta`'s compact state symbols (`0-9A-F`, IQ-TREE
+renumbers away unused states from the full 16, see this module's own
+"`--iqtree`... state count" discussion) back to the canonical 16-state
+alphabet (`STATE_SYMBOL`, `sankoff.rs`) — so a pattern like "compact state
+0 has zero exchangeability with every other state" (`R(a,b) =
+exp(-cost(a,b)) = 0` for an entire row/column) couldn't be traced back to
+which real state that was, or whether it was expected (a state combination
+that was simply never observed alongside anything else in the calibration
+data, giving `cost = -ln(0) = +∞`) or a genuine problem.
+
+**Fix**: `write_iqtree_states_csv` (`iqtree.rs`) writes
+`<prefix>_iqtree_states.csv` — one row per surviving state,
+`iqtree_symbol,canonical_symbol,frequency`, frequency at full `f64`
+precision (not the model file's truncated 6 decimals). Written alongside
+`_iqtree.model`/`_iqtree.fasta` from the same `CompactAlphabet` both
+already use, so there is no risk of the three files disagreeing. Covered
+by `states_csv_maps_compact_symbols_back_to_canonical_ones`.
+
+The zero-exchangeability pattern itself (state 0 in the user's report,
+frequency 3.26%, `R=0` with every other state) is not yet explained —
+plausibly a genuinely unobserved transition in the calibration
+(`cardinality_transitions`/`composition_transitions` count `0` for every
+pair involving it), which is a legitimate, if numerically extreme, result
+of `-ln(0)`, not necessarily a bug — not investigated further.
+
 ## References
 
 The Mash mutation-rate model this discussion contrasts with:
diff --git a/UserDocMD/usage/phylo.md b/UserDocMD/usage/phylo.md
index 2d068200..8d0fe5a5 100644
--- a/UserDocMD/usage/phylo.md
+++ b/UserDocMD/usage/phylo.md
@@ -210,6 +210,7 @@ Matrix layout (`_dist.csv`, `_shared.csv`, and every other "CSV matrix" below):
 | `<prefix>_sankoff.pg` | `--phyg` | PhyG script | ready-to-run parsimony search |
 | `<prefix>_iqtree.model` | `--iqtree` | IQ-TREE model file | custom ML substitution model |
 | `<prefix>_iqtree.fasta` | `--iqtree` | FASTA | alignment recoded for that model |
+| `<prefix>_iqtree_states.csv` | `--iqtree` | CSV table | maps `_iqtree.model`/`_iqtree.fasta`'s compact state symbols back to `_sankoff_matrix.csv`'s alphabet |
 
 **`_sankoff_matrix.csv`** — header `state,0,A,C,M,G,R,S,V,T,W,Y,H,K,D,B,N`: the 16 symbols are IUPAC codes for the 16 subsets of the 4 possible central bases (bit 0=A, 1=C, 2=G, 3=T), `0` standing for the empty/absent state (not `-`, to avoid colliding with external tools' own gap syntax). One row per source state, one value per destination state, cost $-\ln P(a,b)$, 4 decimals.
 
@@ -235,3 +236,5 @@ Matrix layout (`_dist.csv`, `_shared.csv`, and every other "CSV matrix" below):
 ```
 iqtree3 -s <prefix>_iqtree.fasta --seqtype MORPH -m <prefix>_iqtree.model+ASC --prefix <prefix>_iqtree -T AUTO
 ```
+
+**`_iqtree_states.csv`** (`--iqtree`) — one row per state actually kept in `_iqtree.model`/`_iqtree.fasta` (header `iqtree_symbol,canonical_symbol,frequency`): `iqtree_symbol` is the compact `0-9A-F` symbol as written in those two files, `canonical_symbol` is the matching `_sankoff_matrix.csv` state, `frequency` is that state's empirical frequency at full precision (`_iqtree.model`'s own frequency line is rounded to 6 decimals). Under `--free-loss`, absent (`0`/`?`) is never a kept state, so it never appears here. Use this file to identify which real state a given row/column of `_iqtree.model`'s matrix corresponds to — e.g. to check whether a state showing zero exchangeability with everything else is expected (a state combination that never co-occurs with anything else in this data) or worth investigating further.
diff --git a/doc/usage/phylo/index.html b/doc/usage/phylo/index.html
index 3a47990f..e19e2aca 100644
--- a/doc/usage/phylo/index.html
+++ b/doc/usage/phylo/index.html
@@ -2014,6 +2014,12 @@
 <td>FASTA</td>
 <td>alignment recoded for that model</td>
 </tr>
+<tr>
+<td><code>&lt;prefix&gt;_iqtree_states.csv</code></td>
+<td><code>--iqtree</code></td>
+<td>CSV table</td>
+<td>maps <code>_iqtree.model</code>/<code>_iqtree.fasta</code>'s compact state symbols back to <code>_sankoff_matrix.csv</code>'s alphabet</td>
+</tr>
 </tbody>
 </table>
 <p><strong><code>_sankoff_matrix.csv</code></strong> — header <code>state,0,A,C,M,G,R,S,V,T,W,Y,H,K,D,B,N</code>: the 16 symbols are IUPAC codes for the 16 subsets of the 4 possible central bases (bit 0=A, 1=C, 2=G, 3=T), <code>0</code> standing for the empty/absent state (not <code>-</code>, to avoid colliding with external tools' own gap syntax). One row per source state, one value per destination state, cost <span class="arithmatex">\(-\ln P(a,b)\)</span>, 4 decimals.</p>
@@ -2048,6 +2054,7 @@
 <p><strong><code>_iqtree.fasta</code></strong> (<code>--iqtree</code>) — alignment recoded to that same compact <code>0..k-1</code> alphabet (symbols <code>0-9A-F</code>). Under <code>--free-loss</code>, non-detection becomes <code>?</code> and columns left non-informative once missing calls are ignored are dropped first (required for <code>+ASC</code>). Run with:
 <div class="highlight"><pre><span></span><code>iqtree3 -s &lt;prefix&gt;_iqtree.fasta --seqtype MORPH -m &lt;prefix&gt;_iqtree.model+ASC --prefix &lt;prefix&gt;_iqtree -T AUTO
 </code></pre></div></p>
+<p><strong><code>_iqtree_states.csv</code></strong> (<code>--iqtree</code>) — one row per state actually kept in <code>_iqtree.model</code>/<code>_iqtree.fasta</code> (header <code>iqtree_symbol,canonical_symbol,frequency</code>): <code>iqtree_symbol</code> is the compact <code>0-9A-F</code> symbol as written in those two files, <code>canonical_symbol</code> is the matching <code>_sankoff_matrix.csv</code> state, <code>frequency</code> is that state's empirical frequency at full precision (<code>_iqtree.model</code>'s own frequency line is rounded to 6 decimals). Under <code>--free-loss</code>, absent (<code>0</code>/<code>?</code>) is never a kept state, so it never appears here. Use this file to identify which real state a given row/column of <code>_iqtree.model</code>'s matrix corresponds to — e.g. to check whether a state showing zero exchangeability with everything else is expected (a state combination that never co-occurs with anything else in this data) or worth investigating further.</p>
 
 
 
diff --git a/src/obikmer/src/cmd/phylo/iqtree.rs b/src/obikmer/src/cmd/phylo/iqtree.rs
index 6d659630..b774ce59 100644
--- a/src/obikmer/src/cmd/phylo/iqtree.rs
+++ b/src/obikmer/src/cmd/phylo/iqtree.rs
@@ -5,7 +5,7 @@ use obifastwrite::{JsonVal, write_record};
 use obikphylo::siblings::SnpAlignment;
 use tracing::info;
 
-use super::sankoff::state_index_table;
+use super::sankoff::{state_index_table, STATE_SYMBOL};
 
 // ── Sankoff-calibrated data → IQ-TREE custom ML model + recoded alignment ──
 //
@@ -145,6 +145,30 @@ fn compact_alphabet(alignment: &SnpAlignment, free_loss: bool) -> CompactAlphabe
     CompactAlphabet { old_to_compact, compact_to_old, freq }
 }
 
+/// Write `<prefix>_iqtree_states.csv`: the mapping from IQ-TREE's own
+/// compact state symbols (`0..9A-F`, what actually appears in
+/// `_iqtree.fasta`/`_iqtree.model`) back to the canonical 16-state
+/// alphabet (`STATE_SYMBOL` — the same one `_sankoff_matrix.csv` is
+/// indexed by), plus each state's empirical frequency at full precision
+/// (`_iqtree.model`'s own frequency line is truncated to 6 decimals).
+/// Without this file, a compact index in `_iqtree.model`'s `R`/`π` output
+/// (e.g. "state 0 has zero exchangeability with everything else") can't be
+/// traced back to which real state that is.
+fn write_iqtree_states_csv(alphabet: &CompactAlphabet, output: &Option<PathBuf>) -> String {
+    let path = output.as_ref()
+        .map(|p| format!("{}_iqtree_states.csv", p.display()))
+        .unwrap_or_else(|| "iqtree_states.csv".into());
+    let mut f = BufWriter::new(std::fs::File::create(&path).unwrap_or_else(|e| {
+        eprintln!("error creating {path}: {e}");
+        std::process::exit(1);
+    }));
+    writeln!(f, "iqtree_symbol,canonical_symbol,frequency").unwrap();
+    for (compact, &old) in alphabet.compact_to_old.iter().enumerate() {
+        writeln!(f, "{},{},{}", IQTREE_STATE_SYMBOL[compact], STATE_SYMBOL[old as usize], alphabet.freq[compact]).unwrap();
+    }
+    path
+}
+
 /// Write the `R` (exchangeability) + `π` (frequencies) model file IQ-TREE's
 /// `-m <file>+ASC` reads. Returns the path, so the caller can print a
 /// single combined "how to run this" message once the alignment is also
@@ -234,6 +258,7 @@ pub(super) fn write_iqtree(
     };
 
     let alphabet = compact_alphabet(alignment, free_loss);
+    let states_path = write_iqtree_states_csv(&alphabet, output);
     let model_path = write_iqtree_model(matrix, &alphabet, output);
     let (fasta_path, n_sites) = write_iqtree_alignment(alignment, labels, &alphabet, output, free_loss);
 
@@ -243,8 +268,85 @@ pub(super) fn write_iqtree(
         .unwrap_or_else(|| "iqtree".into());
     info!(
         "IQ-TREE alignment → {fasta_path} ({n_sites} sites, {} states)\n\
+         IQ-TREE state mapping → {states_path}\n\
          Run with:\n  \
          iqtree3 -s {fasta_path} --seqtype MORPH -m {model_path}+ASC --prefix {prefix_name} -T AUTO",
         alphabet.k()
     );
 }
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn free_loss_excludes_absent_state_and_freq_sums_to_one() {
+        // 3 genomes, 2 sites. Site 0: g1='A', g2='C', g3='-' (absent).
+        // Site 1: g1='-', g2='-', g3='G'. Under free_loss, every '-' must
+        // be excluded from the frequency count entirely (not folded into
+        // state 0) — reproduces a user-reported suspicion that state 0
+        // ("absent") was still being counted despite being recoded to `?`
+        // (IQ-TREE's own missing symbol) in the alignment actually written.
+        let alignment = SnpAlignment {
+            sequences: vec![
+                vec![b'A', b'-'],
+                vec![b'C', b'-'],
+                vec![b'-', b'G'],
+            ],
+        };
+
+        let alphabet = compact_alphabet(&alignment, true);
+
+        assert!(
+            !alphabet.compact_to_old.contains(&0),
+            "state 0 (absent) must not appear in the compact alphabet under --free-loss, got {:?}",
+            alphabet.compact_to_old
+        );
+        let sum: f64 = alphabet.freq.iter().sum();
+        assert!((sum - 1.0).abs() < 1e-9, "frequencies must sum to 1, got {sum} ({:?})", alphabet.freq);
+        assert_eq!(alphabet.k(), 3, "A, C, G — 3 real states, `-` excluded");
+    }
+
+    #[test]
+    fn without_free_loss_absent_state_is_counted_normally() {
+        let alignment = SnpAlignment {
+            sequences: vec![
+                vec![b'A', b'-'],
+                vec![b'C', b'-'],
+                vec![b'-', b'G'],
+            ],
+        };
+
+        let alphabet = compact_alphabet(&alignment, false);
+
+        assert!(
+            alphabet.compact_to_old.contains(&0),
+            "state 0 (absent, recoded from '-') must be counted when --free-loss is off"
+        );
+        let sum: f64 = alphabet.freq.iter().sum();
+        assert!((sum - 1.0).abs() < 1e-9, "frequencies must sum to 1, got {sum} ({:?})", alphabet.freq);
+    }
+
+    #[test]
+    fn states_csv_maps_compact_symbols_back_to_canonical_ones() {
+        // 'A' (state 1) and 'G' (state 4) occur, '-' (state 0) excluded by
+        // --free-loss — compact index 0 -> 'A', compact index 1 -> 'G'.
+        let alignment = SnpAlignment {
+            sequences: vec![
+                vec![b'A', b'-'],
+                vec![b'-', b'G'],
+            ],
+        };
+        let alphabet = compact_alphabet(&alignment, true);
+        let output = Some(std::env::temp_dir().join(format!("obikmer_test_iqtree_states_{}", std::process::id())));
+
+        let path = write_iqtree_states_csv(&alphabet, &output);
+        let csv = std::fs::read_to_string(&path).unwrap();
+        std::fs::remove_file(&path).ok();
+        let mut lines = csv.lines();
+        assert_eq!(lines.next(), Some("iqtree_symbol,canonical_symbol,frequency"));
+        assert_eq!(lines.next(), Some("0,A,0.5"));
+        assert_eq!(lines.next(), Some("1,G,0.5"));
+        assert!(lines.next().is_none());
+    }
+}
-- 
2.54.0


From c8f2b16b4c61a2030607ef502ec57852bbbbb945 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Sat, 15 Aug 2026 21:46:22 +0200
Subject: [PATCH 40/46] fix: prevent probability underflow in pairwise cost
 matrix

Replaces premature exponentiation-based row normalization with log-sum-exp arithmetic to prevent tiny probabilities from collapsing to exactly zero. This eliminates spurious infinite costs for valid but rare transitions while preserving correct IEEE 754 semantics for genuinely unobserved pairs. Adds explicit guards against NaN in degenerate rows and includes a regression test verifying finite costs for probabilities as low as 1e-200.
---
 .../theory/evolutionary_distances/index.html  | 46 ++++++++--
 DevDocMD/theory/evolutionary_distances.md     | 47 +++++++++--
 src/obikphylo/src/cardcomp.rs                 | 84 ++++++++++++++-----
 3 files changed, 145 insertions(+), 32 deletions(-)

diff --git a/DevDoc/theory/evolutionary_distances/index.html b/DevDoc/theory/evolutionary_distances/index.html
index c56c4b9e..71d10aa8 100644
--- a/DevDoc/theory/evolutionary_distances/index.html
+++ b/DevDoc/theory/evolutionary_distances/index.html
@@ -4100,12 +4100,46 @@ precision (not the model file's truncated 6 decimals). Written alongside
 <code>_iqtree.model</code>/<code>_iqtree.fasta</code> from the same <code>CompactAlphabet</code> both
 already use, so there is no risk of the three files disagreeing. Covered
 by <code>states_csv_maps_compact_symbols_back_to_canonical_ones</code>.</p>
-<p>The zero-exchangeability pattern itself (state 0 in the user's report,
-frequency 3.26%, <code>R=0</code> with every other state) is not yet explained —
-plausibly a genuinely unobserved transition in the calibration
-(<code>cardinality_transitions</code>/<code>composition_transitions</code> count <code>0</code> for every
-pair involving it), which is a legitimate, if numerically extreme, result
-of <code>-ln(0)</code>, not necessarily a bug — not investigated further.</p>
+<p><strong>Root cause of the zero-exchangeability pattern found and fixed
+(2026-08-15): premature <code>exp()</code> in <code>pairwise_cost_matrix</code> underflowed
+merely-tiny probabilities to exactly <code>0.0</code>.</strong> The user also reported
+<code>iqtree3</code> emitting "Numerical underflow for lh-derivative" warnings on
+the same run — a real signal, traced to <code>obikphylo/src/cardcomp.rs</code>'s
+<code>pairwise_cost_matrix</code>, not to the frequency computation (which is a
+plain, safe <code>f64</code> division, never close to underflow at any realistic
+scale). The function already accumulated <code>log_p</code> in log-space (correct),
+but then row-normalised by exponentiating each cell <em>first</em>
+(<code>raw[a][b] = log_p.exp()</code>) and summing the results — <code>f64::exp</code> hard
+underflows to exactly <code>0.0</code> for any input below roughly <code>-709</code>, which a
+sum of several individually-small-but-nonzero probability factors
+(composition/cardinality terms, <code>best_pairing_cost</code>'s pairing terms) can
+reach easily on real, skewed calibration data. Once <code>raw[a][b]</code> was
+exactly <code>0.0</code>, normalisation and <code>-ln</code> turned a merely tiny probability
+into a <code>+∞</code> cost indistinguishable from a <em>literally</em> unobserved
+transition (<code>p == 0.0</code> exactly, e.g. <code>p_comp[i][j]</code> never once tallied) —
+conflating two different things: "never observed" (should be <code>+∞</code>, a
+correct MLE result) and "observed, but the joint probability of this
+multi-step transition is extremely small" (should be a large <em>finite</em>
+cost).</p>
+<p><strong>Fix</strong>: row-normalise via log-sum-exp instead of exponentiating first —
+<code>row_max = max_b(log_p[a][b])</code>, <code>log_sum = row_max + ln(Σ_b
+exp(log_p[a][b] - row_max))</code> (every shifted term is in <code>(0,1]</code>, so this
+never underflows for a finite <code>log_p[a][b]</code>), then
+<code>cost[a][b] = log_sum - log_p[a][b]</code> directly — no intermediate
+probability is ever materialised. This falls out of IEEE 754 arithmetic
+without a special case: a genuinely-unobserved factor (<code>log_p[a][b] ==
+-∞</code>, from the existing <code>if p &gt; 0.0 {...} else { NEG_INFINITY }</code> guards
+already in the log-accumulation loop) still yields <code>cost = +∞</code> exactly
+(<code>finite − (−∞) = +∞</code>), preserving the correct semantics for that case,
+while every merely-tiny-but-nonzero transition now gets a large but
+<em>finite</em> cost. A degenerate all-<code>-∞</code> row (a state with literally zero
+probability of transitioning to anything, <code>row_max == -∞</code>) is guarded
+explicitly to avoid a <code>-∞ − (-∞) = NaN</code> in the log-sum-exp itself.
+Covered by <code>cardcomp::tests::underflow_prone_transition_gets_finite_cost_not_infinite</code>
+(all off-diagonal composition probabilities set to <code>1e-200</code>, well past
+where the old <code>exp()</code>-first code would have underflowed to <code>0.0</code>, cost
+asserted finite). Every pre-existing <code>cardcomp</code> test still passes
+unchanged (numerically identical results when no underflow occurs).</p>
 <h2 id="references">References</h2>
 <p>The Mash mutation-rate model this discussion contrasts with:
 (Fan <em>et al.</em> 2015; Marbl Lab 2026)<sup id="fnref:Mash-distances-doc"><a class="footnote-ref" href="#fn:Mash-distances-doc">1</a></sup> <sup id="fnref:Fan2015-mash-formula"><a class="footnote-ref" href="#fn:Fan2015-mash-formula">2</a></sup>.</p>
diff --git a/DevDocMD/theory/evolutionary_distances.md b/DevDocMD/theory/evolutionary_distances.md
index 23d1805d..d2d227bf 100644
--- a/DevDocMD/theory/evolutionary_distances.md
+++ b/DevDocMD/theory/evolutionary_distances.md
@@ -2090,12 +2090,47 @@ precision (not the model file's truncated 6 decimals). Written alongside
 already use, so there is no risk of the three files disagreeing. Covered
 by `states_csv_maps_compact_symbols_back_to_canonical_ones`.
 
-The zero-exchangeability pattern itself (state 0 in the user's report,
-frequency 3.26%, `R=0` with every other state) is not yet explained —
-plausibly a genuinely unobserved transition in the calibration
-(`cardinality_transitions`/`composition_transitions` count `0` for every
-pair involving it), which is a legitimate, if numerically extreme, result
-of `-ln(0)`, not necessarily a bug — not investigated further.
+**Root cause of the zero-exchangeability pattern found and fixed
+(2026-08-15): premature `exp()` in `pairwise_cost_matrix` underflowed
+merely-tiny probabilities to exactly `0.0`.** The user also reported
+`iqtree3` emitting "Numerical underflow for lh-derivative" warnings on
+the same run — a real signal, traced to `obikphylo/src/cardcomp.rs`'s
+`pairwise_cost_matrix`, not to the frequency computation (which is a
+plain, safe `f64` division, never close to underflow at any realistic
+scale). The function already accumulated `log_p` in log-space (correct),
+but then row-normalised by exponentiating each cell *first*
+(`raw[a][b] = log_p.exp()`) and summing the results — `f64::exp` hard
+underflows to exactly `0.0` for any input below roughly `-709`, which a
+sum of several individually-small-but-nonzero probability factors
+(composition/cardinality terms, `best_pairing_cost`'s pairing terms) can
+reach easily on real, skewed calibration data. Once `raw[a][b]` was
+exactly `0.0`, normalisation and `-ln` turned a merely tiny probability
+into a `+∞` cost indistinguishable from a *literally* unobserved
+transition (`p == 0.0` exactly, e.g. `p_comp[i][j]` never once tallied) —
+conflating two different things: "never observed" (should be `+∞`, a
+correct MLE result) and "observed, but the joint probability of this
+multi-step transition is extremely small" (should be a large *finite*
+cost).
+
+**Fix**: row-normalise via log-sum-exp instead of exponentiating first —
+`row_max = max_b(log_p[a][b])`, `log_sum = row_max + ln(Σ_b
+exp(log_p[a][b] - row_max))` (every shifted term is in `(0,1]`, so this
+never underflows for a finite `log_p[a][b]`), then
+`cost[a][b] = log_sum - log_p[a][b]` directly — no intermediate
+probability is ever materialised. This falls out of IEEE 754 arithmetic
+without a special case: a genuinely-unobserved factor (`log_p[a][b] ==
+-∞`, from the existing `if p > 0.0 {...} else { NEG_INFINITY }` guards
+already in the log-accumulation loop) still yields `cost = +∞` exactly
+(`finite − (−∞) = +∞`), preserving the correct semantics for that case,
+while every merely-tiny-but-nonzero transition now gets a large but
+*finite* cost. A degenerate all-`-∞` row (a state with literally zero
+probability of transitioning to anything, `row_max == -∞`) is guarded
+explicitly to avoid a `-∞ − (-∞) = NaN` in the log-sum-exp itself.
+Covered by `cardcomp::tests::underflow_prone_transition_gets_finite_cost_not_infinite`
+(all off-diagonal composition probabilities set to `1e-200`, well past
+where the old `exp()`-first code would have underflowed to `0.0`, cost
+asserted finite). Every pre-existing `cardcomp` test still passes
+unchanged (numerically identical results when no underflow occurs).
 
 ## References
 
diff --git a/src/obikphylo/src/cardcomp.rs b/src/obikphylo/src/cardcomp.rs
index 9a6db64b..e89d7b27 100644
--- a/src/obikphylo/src/cardcomp.rs
+++ b/src/obikphylo/src/cardcomp.rs
@@ -146,52 +146,66 @@ fn best_pairing_cost(lost: &[u8], gained: &[u8], p_comp: &[[f64; 4]; 4]) -> f64
 /// only by composition matching (shared-base retention and paired
 /// substitutions), never by a state pair's cardinality difference alone.
 pub fn pairwise_cost_matrix(p_card: &[[f64; 5]; 5], p_comp: &[[f64; 4]; 4], free_loss: bool) -> [[f64; 16]; 16] {
-    let mut raw = [[0.0f64; 16]; 16];
+    let mut log_p = [[0.0f64; 16]; 16]; // ln(P), *before* row-normalisation
     for a in 0u8..16 {
         for b in 0u8..16 {
             let shared = a & b;
             let lost: Vec<u8> = (0..4).filter(|&i| a & (1 << i) != 0 && b & (1 << i) == 0).collect();
             let gained: Vec<u8> = (0..4).filter(|&i| b & (1 << i) != 0 && a & (1 << i) == 0).collect();
 
-            let mut log_p = 0.0; // accumulate ln(P), so 0.0 = probability 1
+            let mut lp = 0.0; // accumulate ln(P), so 0.0 = probability 1
             if !free_loss {
                 let card_a = a.count_ones() as usize;
                 let card_b = b.count_ones() as usize;
                 let p_c = p_card[card_a][card_b];
-                log_p += if p_c > 0.0 { p_c.ln() } else { f64::NEG_INFINITY };
+                lp += if p_c > 0.0 { p_c.ln() } else { f64::NEG_INFINITY };
             }
 
             for i in 0..4u8 {
                 if shared & (1 << i) != 0 {
                     let p = p_comp[i as usize][i as usize];
-                    log_p += if p > 0.0 { p.ln() } else { f64::NEG_INFINITY };
+                    lp += if p > 0.0 { p.ln() } else { f64::NEG_INFINITY };
                 }
             }
-            log_p -= best_pairing_cost(&lost, &gained, p_comp);
+            lp -= best_pairing_cost(&lost, &gained, p_comp);
 
-            raw[a as usize][b as usize] = log_p.exp();
+            log_p[a as usize][b as usize] = lp;
         }
     }
 
-    // Row-normalise to a proper transition probability matrix.
-    let mut p = [[0.0f64; 16]; 16];
-    for a in 0..16 {
-        let row_sum: f64 = raw[a].iter().sum();
-        if row_sum > 0.0 {
-            for b in 0..16 {
-                p[a][b] = raw[a][b] / row_sum;
-            }
-        }
-    }
-
-    // Cost = -ln(P), then symmetrise (see doc comment: parsimony on an
-    // unrooted tree requires a symmetric cost matrix).
+    // Row-normalise and convert to cost entirely in log-space
+    // (log-sum-exp), never exponentiating a raw `log_p` value directly —
+    // for a transition reachable only through several low-probability
+    // steps, `log_p.exp()` can underflow to exactly `0.0` (anything below
+    // roughly `-709` does, in `f64`), silently turning a real, if small,
+    // probability into a hard `+∞` cost. Observed in practice: a
+    // calibrated matrix with many such exact-zero entries is numerically
+    // unstable for IQ-TREE's own likelihood-derivative computation
+    // ("Numerical underflow for lh-derivative"). `log_sum_exp` never
+    // exponentiates anything above `0` (every term is shifted by the
+    // row's own max first), so it stays accurate across the full range
+    // `f64` can represent, not just what survives a direct `exp()`.
     let mut cost = [[0.0f64; 16]; 16];
     for a in 0..16 {
+        let row_max = log_p[a].iter().cloned().fold(f64::NEG_INFINITY, f64::max);
+        if row_max == f64::NEG_INFINITY {
+            // Every transition out of this state has probability 0 in the
+            // calibration data — genuinely unreachable, not underflow.
+            cost[a] = [f64::INFINITY; 16];
+            continue;
+        }
+        let log_sum = row_max + log_p[a].iter().map(|&lp| (lp - row_max).exp()).sum::<f64>().ln();
         for b in 0..16 {
-            cost[a][b] = if p[a][b] > 0.0 { -p[a][b].ln() } else { f64::INFINITY };
+            // `log_sum - log_p[a][b]` is `+∞` automatically when
+            // `log_p[a][b] == -∞` (IEEE 754: finite − (−∞) = +∞) — no
+            // separate branch needed for a genuinely zero-probability
+            // transition.
+            cost[a][b] = log_sum - log_p[a][b];
         }
     }
+
+    // Symmetrise (see doc comment: parsimony on an unrooted tree requires
+    // a symmetric cost matrix).
     let mut sym = [[0.0f64; 16]; 16];
     for a in 0..16 {
         for b in 0..16 {
@@ -289,4 +303,34 @@ mod tests {
             }
         }
     }
+
+    #[test]
+    fn underflow_prone_transition_gets_finite_cost_not_infinite() {
+        // Every off-diagonal composition probability is tiny (1e-200) but
+        // not exactly zero — small enough that the naive `log_p.exp()`
+        // (exponentiate before row-normalising) hard-underflows to `0.0`
+        // in `f64` well before the probability is truly zero, silently
+        // turning a real, if minuscule, probability into `+∞` cost. The
+        // log-sum-exp normalisation in `pairwise_cost_matrix` must keep
+        // this finite instead.
+        let p_card = [[0.2f64; 5]; 5];
+        let tiny = 1e-200;
+        let mut p_comp = [[tiny; 4]; 4];
+        for i in 0..4 {
+            p_comp[i][i] = 1.0 - 3.0 * tiny;
+        }
+
+        let cost = pairwise_cost_matrix(&p_card, &p_comp, false);
+
+        // {A,C} -> {G,T}: no shared bases, both members substituted — the
+        // shape most prone to underflow (several tiny-probability factors
+        // multiplied together).
+        let a = 0b0011u8; // A, C
+        let b = 0b1100u8; // G, T
+        assert!(
+            cost[a as usize][b as usize].is_finite(),
+            "cost must stay finite for a merely tiny (not exactly zero) probability, got {}",
+            cost[a as usize][b as usize]
+        );
+    }
 }
-- 
2.54.0


From 128db645644266f6e2acd42014a1c3e5b5ea6bf6 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Sat, 15 Aug 2026 22:38:40 +0200
Subject: [PATCH 41/46] feat(phylo): add --iqtree-min-freq to filter rare
 nucleotide states

Introduces --iqtree-min-freq (default 0.001) to treat low-frequency nucleotide states as missing data during IQ-TREE alignment generation when --free-loss is active. This triggers a recoding pass that folds rare states into the missing symbol, followed by non-informative site removal and alphabet recomputation to maintain output consistency. The change also adds Sankoff model configuration files and updates related tests and documentation.
---
 .../theory/evolutionary_distances/index.html  |  65 +++++++
 DevDocMD/theory/evolutionary_distances.md     |  50 ++++++
 UserDocMD/usage/phylo.md                      |   9 +-
 aloss_nofl_sankoff_params.yaml                | 167 ++++++++++++++++++
 aloss_sankoff_params.yaml                     | 167 ++++++++++++++++++
 doc/usage/phylo/index.html                    |  33 +++-
 src/obikmer/src/cmd/phylo/args.rs             |  19 ++
 src/obikmer/src/cmd/phylo/iqtree.rs           |  85 ++++++++-
 src/obikmer/src/cmd/phylo/mod.rs              |   2 +-
 src/obikphylo/src/siblings/tests.rs           | 166 ++++++++++++++++-
 10 files changed, 756 insertions(+), 7 deletions(-)
 create mode 100644 aloss_nofl_sankoff_params.yaml
 create mode 100644 aloss_sankoff_params.yaml

diff --git a/DevDoc/theory/evolutionary_distances/index.html b/DevDoc/theory/evolutionary_distances/index.html
index 71d10aa8..e7627d12 100644
--- a/DevDoc/theory/evolutionary_distances/index.html
+++ b/DevDoc/theory/evolutionary_distances/index.html
@@ -898,6 +898,17 @@
     </span>
   </a>
   
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#-iqtree-min-freq-rare-states-still-perturb-iq-tree-after-the-underflow-fix-implemented-2026-08-15" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        --iqtree-min-freq: rare states still perturb IQ-TREE after the underflow fix (implemented 2026-08-15)
+      
+    </span>
+  </a>
+  
 </li>
       
         <li class="md-nav__item">
@@ -2117,6 +2128,17 @@
     </span>
   </a>
   
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#-iqtree-min-freq-rare-states-still-perturb-iq-tree-after-the-underflow-fix-implemented-2026-08-15" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        --iqtree-min-freq: rare states still perturb IQ-TREE after the underflow fix (implemented 2026-08-15)
+      
+    </span>
+  </a>
+  
 </li>
       
         <li class="md-nav__item">
@@ -4140,6 +4162,49 @@ Covered by <code>cardcomp::tests::underflow_prone_transition_gets_finite_cost_no
 where the old <code>exp()</code>-first code would have underflowed to <code>0.0</code>, cost
 asserted finite). Every pre-existing <code>cardcomp</code> test still passes
 unchanged (numerically identical results when no underflow occurs).</p>
+<h2 id="-iqtree-min-freq-rare-states-still-perturb-iq-tree-after-the-underflow-fix-implemented-2026-08-15"><code>--iqtree-min-freq</code>: rare states still perturb IQ-TREE after the underflow fix (implemented 2026-08-15)</h2>
+<p>After the <code>pairwise_cost_matrix</code> fix above, the user re-checked
+<code>_iqtree_states.csv</code> on the real <code>phyloskims_sal_vac</code> run: no more exact
+zeros, but <code>N</code> (all 4 bases), <code>V</code>/<code>H</code>/<code>D</code> (3 bases each) sit at
+<code>8×10⁻⁵</code>–<code>4×10⁻⁴</code>, and <code>B</code> (3 bases) just above <code>10⁻³</code> — all four
+3-simultaneous-base states plus <code>N</code>, exactly the states the underflow fix
+was papering over the symptom of. <code>iqtree3</code> kept emitting "Numerical
+underflow for lh-derivative" on this same run — a model with several
+near-zero-frequency states is still numerically marginal for ML
+optimisation even once no cost/exchangeability entry is <em>exactly</em>
+infinite/zero.</p>
+<p><strong>Decided and implemented</strong>: extend <code>--free-loss</code>'s existing "sampling
+failure, not true signal" treatment of non-detection to rare
+multi-base states too — biologically, a family showing 3–4 simultaneously
+observed central bases across genomes is far more likely to be
+assembly/detection noise than a genuinely ancestral, widely-preserved
+polymorphism, the same reasoning already used for <code>-</code>.</p>
+<p><strong>Mechanism</strong> (<code>obikmer/src/cmd/phylo/iqtree.rs</code>, <code>write_iqtree</code>): a
+<em>second</em> filtering pass, active only under <code>--free-loss</code>. After the first
+<code>compact_alphabet</code> call (post ascertainment-filtering), any state with
+<code>freq &lt; --iqtree-min-freq</code> (default <code>0.001</code>) has every occurrence recoded
+to <code>-</code> (<code>recode_symbols_as_absent</code>, a new small helper) — reusing the
+<em>existing</em> <code>-</code>→<code>?</code> machinery in <code>compact_alphabet</code>/<code>write_iqtree_alignment</code>
+rather than duplicating it, since a state recoded to <code>-</code> flows through
+exactly the same downstream path a genuinely-absent call already does.
+<code>drop_ascertainment_noninformative</code> then re-runs on the recoded alignment
+(a site can become non-informative once its only distinguishing call was
+the now-recoded rare state), and <code>compact_alphabet</code> is recomputed a third
+time on the result — this final alphabet is what <code>_iqtree_states.csv</code>/
+<code>_iqtree.model</code>/<code>_iqtree.fasta</code> all get built from, so the three files
+stay consistent with each other by construction, same as before this
+change.</p>
+<p>Not a fixed-point loop (recoding one rare state can't, by construction,
+lower another <em>already-above-threshold</em> state's frequency enough to also
+cross the threshold, since removing calls only redistributes mass upward
+among the survivors) — a single extra pass is sufficient.</p>
+<p><code>--iqtree-min-freq 0</code> disables the filter (no state can have frequency
+<code>&lt; 0</code>), recovering the pre-this-change behavior exactly.</p>
+<p>Covered by <code>iqtree::tests::iqtree_min_freq_folds_rare_states_into_missing</code>
+(20 common A/C sites + one site introducing a single, otherwise-informative
+<code>M</code> call at ~1/62 frequency, <code>--iqtree-min-freq 0.05</code>; asserts <code>M</code> absent
+from the written <code>_iqtree_states.csv</code> and <code>A</code>/<code>C</code> still present). Full
+workspace <code>cargo test</code> green.</p>
 <h2 id="references">References</h2>
 <p>The Mash mutation-rate model this discussion contrasts with:
 (Fan <em>et al.</em> 2015; Marbl Lab 2026)<sup id="fnref:Mash-distances-doc"><a class="footnote-ref" href="#fn:Mash-distances-doc">1</a></sup> <sup id="fnref:Fan2015-mash-formula"><a class="footnote-ref" href="#fn:Fan2015-mash-formula">2</a></sup>.</p>
diff --git a/DevDocMD/theory/evolutionary_distances.md b/DevDocMD/theory/evolutionary_distances.md
index d2d227bf..d1cf4927 100644
--- a/DevDocMD/theory/evolutionary_distances.md
+++ b/DevDocMD/theory/evolutionary_distances.md
@@ -2132,6 +2132,56 @@ where the old `exp()`-first code would have underflowed to `0.0`, cost
 asserted finite). Every pre-existing `cardcomp` test still passes
 unchanged (numerically identical results when no underflow occurs).
 
+## `--iqtree-min-freq`: rare states still perturb IQ-TREE after the underflow fix (implemented 2026-08-15)
+
+After the `pairwise_cost_matrix` fix above, the user re-checked
+`_iqtree_states.csv` on the real `phyloskims_sal_vac` run: no more exact
+zeros, but `N` (all 4 bases), `V`/`H`/`D` (3 bases each) sit at
+`8×10⁻⁵`–`4×10⁻⁴`, and `B` (3 bases) just above `10⁻³` — all four
+3-simultaneous-base states plus `N`, exactly the states the underflow fix
+was papering over the symptom of. `iqtree3` kept emitting "Numerical
+underflow for lh-derivative" on this same run — a model with several
+near-zero-frequency states is still numerically marginal for ML
+optimisation even once no cost/exchangeability entry is *exactly*
+infinite/zero.
+
+**Decided and implemented**: extend `--free-loss`'s existing "sampling
+failure, not true signal" treatment of non-detection to rare
+multi-base states too — biologically, a family showing 3–4 simultaneously
+observed central bases across genomes is far more likely to be
+assembly/detection noise than a genuinely ancestral, widely-preserved
+polymorphism, the same reasoning already used for `-`.
+
+**Mechanism** (`obikmer/src/cmd/phylo/iqtree.rs`, `write_iqtree`): a
+*second* filtering pass, active only under `--free-loss`. After the first
+`compact_alphabet` call (post ascertainment-filtering), any state with
+`freq < --iqtree-min-freq` (default `0.001`) has every occurrence recoded
+to `-` (`recode_symbols_as_absent`, a new small helper) — reusing the
+*existing* `-`→`?` machinery in `compact_alphabet`/`write_iqtree_alignment`
+rather than duplicating it, since a state recoded to `-` flows through
+exactly the same downstream path a genuinely-absent call already does.
+`drop_ascertainment_noninformative` then re-runs on the recoded alignment
+(a site can become non-informative once its only distinguishing call was
+the now-recoded rare state), and `compact_alphabet` is recomputed a third
+time on the result — this final alphabet is what `_iqtree_states.csv`/
+`_iqtree.model`/`_iqtree.fasta` all get built from, so the three files
+stay consistent with each other by construction, same as before this
+change.
+
+Not a fixed-point loop (recoding one rare state can't, by construction,
+lower another *already-above-threshold* state's frequency enough to also
+cross the threshold, since removing calls only redistributes mass upward
+among the survivors) — a single extra pass is sufficient.
+
+`--iqtree-min-freq 0` disables the filter (no state can have frequency
+`< 0`), recovering the pre-this-change behavior exactly.
+
+Covered by `iqtree::tests::iqtree_min_freq_folds_rare_states_into_missing`
+(20 common A/C sites + one site introducing a single, otherwise-informative
+`M` call at ~1/62 frequency, `--iqtree-min-freq 0.05`; asserts `M` absent
+from the written `_iqtree_states.csv` and `A`/`C` still present). Full
+workspace `cargo test` green.
+
 ## References
 
 The Mash mutation-rate model this discussion contrasts with:
diff --git a/UserDocMD/usage/phylo.md b/UserDocMD/usage/phylo.md
index 8d0fe5a5..7da90cc9 100644
--- a/UserDocMD/usage/phylo.md
+++ b/UserDocMD/usage/phylo.md
@@ -124,6 +124,7 @@ The first `phylo` run on a given index that uses `--entropy`/`--entropy-sd` pays
 | `--tnt` | off | Also write a TNT script (implies `--sankoff`) |
 | `--phyg` | off | Also write PhyG input files (implies `--sankoff`) |
 | `--iqtree` | off | Also write an IQ-TREE custom model and alignment (implies `--sankoff`) |
+| `--iqtree-min-freq` | `0.001` | With `--iqtree --free-loss`: also treat as missing any state rarer than this in the alignment |
 | `--sankoff-cost-scale` | `100` | Integer scaling factor applied to costs before rounding (required by TNT/PhyG's integer-only cost commands) |
 
 ### The 16-state model
@@ -232,9 +233,13 @@ Matrix layout (`_dist.csv`, `_shared.csv`, and every other "CSV matrix" below):
 
 **`_iqtree.model`** (`--iqtree`) — lower-triangular exchangeability matrix $R(a,b) = e^{-\text{cost}(a,b)}$ (one row of increasing length per state, whitespace-separated, PAML order), followed by one line of empirical state frequencies. Only states actually occurring in the alignment are kept, compactly renumbered `0..k-1`.
 
-**`_iqtree.fasta`** (`--iqtree`) — alignment recoded to that same compact `0..k-1` alphabet (symbols `0-9A-F`). Under `--free-loss`, non-detection becomes `?` and columns left non-informative once missing calls are ignored are dropped first (required for `+ASC`). Run with:
+**`_iqtree.fasta`** (`--iqtree`) — alignment recoded to that same compact `0..k-1` alphabet (symbols `0-9A-F`). Under `--free-loss`, non-detection becomes `?` and columns left non-informative once missing calls are ignored are dropped first (required for `+ASC`); with `--iqtree-min-freq` also set (the default), any state rarer than that threshold is folded into the same `?` treatment, and non-informative columns are re-checked and dropped again after that. Run with:
 ```
 iqtree3 -s <prefix>_iqtree.fasta --seqtype MORPH -m <prefix>_iqtree.model+ASC --prefix <prefix>_iqtree -T AUTO
 ```
 
-**`_iqtree_states.csv`** (`--iqtree`) — one row per state actually kept in `_iqtree.model`/`_iqtree.fasta` (header `iqtree_symbol,canonical_symbol,frequency`): `iqtree_symbol` is the compact `0-9A-F` symbol as written in those two files, `canonical_symbol` is the matching `_sankoff_matrix.csv` state, `frequency` is that state's empirical frequency at full precision (`_iqtree.model`'s own frequency line is rounded to 6 decimals). Under `--free-loss`, absent (`0`/`?`) is never a kept state, so it never appears here. Use this file to identify which real state a given row/column of `_iqtree.model`'s matrix corresponds to — e.g. to check whether a state showing zero exchangeability with everything else is expected (a state combination that never co-occurs with anything else in this data) or worth investigating further.
+**`_iqtree_states.csv`** (`--iqtree`) — one row per state actually kept in `_iqtree.model`/`_iqtree.fasta` (header `iqtree_symbol,canonical_symbol,frequency`): `iqtree_symbol` is the compact `0-9A-F` symbol as written in those two files, `canonical_symbol` is the matching `_sankoff_matrix.csv` state, `frequency` is that state's empirical frequency at full precision (`_iqtree.model`'s own frequency line is rounded to 6 decimals). Under `--free-loss`, absent (`0`/`?`) is never a kept state, so it never appears here — nor does any state `--iqtree-min-freq` folded away for being too rare. Use this file to identify which real state a given row/column of `_iqtree.model`'s matrix corresponds to — e.g. to check whether a state showing zero exchangeability with everything else is expected (a state combination that never co-occurs with anything else in this data) or worth investigating further.
+
+### Rare states and `--iqtree-min-freq`
+
+States that combine 3 or 4 central bases at once (IUPAC `V`/`H`/`K`.../`N`) are inherently rare — and, on real data, rare enough that they can make `iqtree3` itself numerically unstable ("Numerical underflow for lh-derivative" warnings, near-degenerate likelihood optimization). They're also more likely to be assembly/detection noise than genuine, widely-shared multi-way polymorphism, the same "sampling failure, not true signal" reasoning `--free-loss` already applies to non-detection. With `--free-loss` set, `--iqtree-min-freq` (default `0.001`, i.e. one in a thousand) extends that same missing-data treatment to any state below this frequency, not just absence. Check `_iqtree_states.csv` to see exactly which states survived and at what frequency; set `--iqtree-min-freq 0` to disable this and keep every state that occurs at all (the old behavior). Has no effect without `--free-loss` — there is no missing-data symbol to fold rare states into otherwise.
diff --git a/aloss_nofl_sankoff_params.yaml b/aloss_nofl_sankoff_params.yaml
new file mode 100644
index 00000000..1e488fab
--- /dev/null
+++ b/aloss_nofl_sankoff_params.yaml
@@ -0,0 +1,167 @@
+ratio_ceiling: 0.5
+cardinality_transitions:
+- from: 0
+  to: 0
+  count: 122014779
+  probability: 0.870049812090934
+- from: 0
+  to: 1
+  count: 17966272
+  probability: 0.12811195254940888
+- from: 0
+  to: 2
+  count: 233683
+  probability: 0.001666321505518981
+- from: 0
+  to: 3
+  count: 24109
+  probability: 0.00017191385413811494
+- from: 0
+  to: 4
+  count: 0
+  probability: 0.0
+- from: 1
+  to: 0
+  count: 17966272
+  probability: 0.967023782579572
+- from: 1
+  to: 1
+  count: 602798
+  probability: 0.03244523972983381
+- from: 1
+  to: 2
+  count: 9562
+  probability: 0.0005146688978673966
+- from: 1
+  to: 3
+  count: 303
+  probability: 0.00001630879272681669
+- from: 1
+  to: 4
+  count: 0
+  probability: 0.0
+- from: 2
+  to: 0
+  count: 233683
+  probability: 0.9585500516842502
+- from: 2
+  to: 1
+  count: 9562
+  probability: 0.039222603245442765
+- from: 2
+  to: 2
+  count: 438
+  probability: 0.0017966429848885097
+- from: 2
+  to: 3
+  count: 105
+  probability: 0.00043070208541847837
+- from: 2
+  to: 4
+  count: 0
+  probability: 0.0
+- from: 3
+  to: 0
+  count: 24109
+  probability: 0.9827171564831044
+- from: 3
+  to: 1
+  count: 303
+  probability: 0.012350711286838137
+- from: 3
+  to: 2
+  count: 105
+  probability: 0.004279949455834998
+- from: 3
+  to: 3
+  count: 16
+  probability: 0.0006521827742224758
+- from: 3
+  to: 4
+  count: 0
+  probability: 0.0
+- from: 4
+  to: 0
+  count: 0
+  probability: 0.0
+- from: 4
+  to: 1
+  count: 0
+  probability: 0.0
+- from: 4
+  to: 2
+  count: 0
+  probability: 0.0
+- from: 4
+  to: 3
+  count: 0
+  probability: 0.0
+- from: 4
+  to: 4
+  count: 0
+  probability: 0.0
+composition_transitions:
+- from: 'A'
+  to: 'A'
+  count: 0
+  probability: 0.0
+- from: 'A'
+  to: 'C'
+  count: 0
+  probability: 0.0
+- from: 'A'
+  to: 'G'
+  count: 0
+  probability: 0.0
+- from: 'A'
+  to: 'T'
+  count: 0
+  probability: 0.0
+- from: 'C'
+  to: 'A'
+  count: 0
+  probability: 0.0
+- from: 'C'
+  to: 'C'
+  count: 96389
+  probability: 0.9663832688335907
+- from: 'C'
+  to: 'G'
+  count: 1290
+  probability: 0.012933368089671353
+- from: 'C'
+  to: 'T'
+  count: 2063
+  probability: 0.020683363076737984
+- from: 'G'
+  to: 'A'
+  count: 0
+  probability: 0.0
+- from: 'G'
+  to: 'C'
+  count: 1290
+  probability: 0.005696948820201646
+- from: 'G'
+  to: 'G'
+  count: 222720
+  probability: 0.9835848381669073
+- from: 'G'
+  to: 'T'
+  count: 2427
+  probability: 0.010718213012891003
+- from: 'T'
+  to: 'A'
+  count: 0
+  probability: 0.0
+- from: 'T'
+  to: 'C'
+  count: 2063
+  probability: 0.007305266661709142
+- from: 'T'
+  to: 'G'
+  count: 2427
+  probability: 0.008594223067362136
+- from: 'T'
+  to: 'T'
+  count: 277909
+  probability: 0.9841005102709287
diff --git a/aloss_sankoff_params.yaml b/aloss_sankoff_params.yaml
new file mode 100644
index 00000000..e30daac6
--- /dev/null
+++ b/aloss_sankoff_params.yaml
@@ -0,0 +1,167 @@
+ratio_ceiling: 0.5
+cardinality_transitions:
+- from: 0
+  to: 0
+  count: 13019012
+  probability: 0.8682962128540935
+- from: 0
+  to: 1
+  count: 1945560
+  probability: 0.12975810913150784
+- from: 0
+  to: 2
+  count: 26381
+  probability: 0.0017594670310852958
+- from: 0
+  to: 3
+  count: 2792
+  probability: 0.000186210983313375
+- from: 0
+  to: 4
+  count: 0
+  probability: 0.0
+- from: 1
+  to: 0
+  count: 1945560
+  probability: 0.9666005228573729
+- from: 1
+  to: 1
+  count: 66078
+  probability: 0.03282912341401421
+- from: 1
+  to: 2
+  count: 1123
+  probability: 0.0005579331334776772
+- from: 1
+  to: 3
+  count: 25
+  probability: 0.000012420595135300028
+- from: 1
+  to: 4
+  count: 0
+  probability: 0.0
+- from: 2
+  to: 0
+  count: 26381
+  probability: 0.9567346050627402
+- from: 2
+  to: 1
+  count: 1123
+  probability: 0.04072677159643142
+- from: 2
+  to: 2
+  count: 51
+  probability: 0.0018495684340320592
+- from: 2
+  to: 3
+  count: 19
+  probability: 0.0006890549067962574
+- from: 2
+  to: 4
+  count: 0
+  probability: 0.0
+- from: 3
+  to: 0
+  count: 2792
+  probability: 0.9841381741275996
+- from: 3
+  to: 1
+  count: 25
+  probability: 0.008812125484666901
+- from: 3
+  to: 2
+  count: 19
+  probability: 0.0066972153683468455
+- from: 3
+  to: 3
+  count: 1
+  probability: 0.00035248501938667606
+- from: 3
+  to: 4
+  count: 0
+  probability: 0.0
+- from: 4
+  to: 0
+  count: 0
+  probability: 0.0
+- from: 4
+  to: 1
+  count: 0
+  probability: 0.0
+- from: 4
+  to: 2
+  count: 0
+  probability: 0.0
+- from: 4
+  to: 3
+  count: 0
+  probability: 0.0
+- from: 4
+  to: 4
+  count: 0
+  probability: 0.0
+composition_transitions:
+- from: 'A'
+  to: 'A'
+  count: 0
+  probability: 0.0
+- from: 'A'
+  to: 'C'
+  count: 0
+  probability: 0.0
+- from: 'A'
+  to: 'G'
+  count: 0
+  probability: 0.0
+- from: 'A'
+  to: 'T'
+  count: 0
+  probability: 0.0
+- from: 'C'
+  to: 'A'
+  count: 0
+  probability: 0.0
+- from: 'C'
+  to: 'C'
+  count: 10771
+  probability: 0.9619540948468339
+- from: 'C'
+  to: 'G'
+  count: 163
+  probability: 0.014557470751094042
+- from: 'C'
+  to: 'T'
+  count: 263
+  probability: 0.023488434402071982
+- from: 'G'
+  to: 'A'
+  count: 0
+  probability: 0.0
+- from: 'G'
+  to: 'C'
+  count: 163
+  probability: 0.006662851536952256
+- from: 'G'
+  to: 'G'
+  count: 24073
+  probability: 0.9840173315892741
+- from: 'G'
+  to: 'T'
+  count: 228
+  probability: 0.009319816873773708
+- from: 'T'
+  to: 'A'
+  count: 0
+  probability: 0.0
+- from: 'T'
+  to: 'C'
+  count: 263
+  probability: 0.008464484567603231
+- from: 'T'
+  to: 'G'
+  count: 228
+  probability: 0.007338032248720672
+- from: 'T'
+  to: 'T'
+  count: 30580
+  probability: 0.9841974831836761
diff --git a/doc/usage/phylo/index.html b/doc/usage/phylo/index.html
index e19e2aca..c5488ce8 100644
--- a/doc/usage/phylo/index.html
+++ b/doc/usage/phylo/index.html
@@ -946,6 +946,17 @@
     </span>
   </a>
   
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#rare-states-and-iqtree-min-freq" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Rare states and --iqtree-min-freq
+      
+    </span>
+  </a>
+  
 </li>
         
       </ul>
@@ -1510,6 +1521,17 @@
     </span>
   </a>
   
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#rare-states-and-iqtree-min-freq" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Rare states and --iqtree-min-freq
+      
+    </span>
+  </a>
+  
 </li>
         
       </ul>
@@ -1790,6 +1812,11 @@
 <td>Also write an IQ-TREE custom model and alignment (implies <code>--sankoff</code>)</td>
 </tr>
 <tr>
+<td><code>--iqtree-min-freq</code></td>
+<td><code>0.001</code></td>
+<td>With <code>--iqtree --free-loss</code>: also treat as missing any state rarer than this in the alignment</td>
+</tr>
+<tr>
 <td><code>--sankoff-cost-scale</code></td>
 <td><code>100</code></td>
 <td>Integer scaling factor applied to costs before rounding (required by TNT/PhyG's integer-only cost commands)</td>
@@ -2051,10 +2078,12 @@
 <p><strong><code>_sankoff.tcm</code></strong> (<code>--phyg</code>) — first line: the 16-symbol alphabet plus a trailing gap symbol (17 total). Each following line: one row of the integer-scaled, metric-closed cost matrix (17 values — the extra gap column/row reuses the cost to/from the empty state <code>0</code>, since it's never actually triggered).</p>
 <p><strong><code>_sankoff.pg</code></strong> (<code>--phyg</code>) — script: <code>read(prefasta:..., tcm:...)</code> against <code>_sankoff.fasta</code>/<code>_sankoff.tcm</code>, a default 300s/4-instance <code>search</code>, <code>report(...)</code> writing <code>&lt;prefix&gt;_sankoff.tre</code> (bare numeric labels, as for <code>--tnt</code>). Run with <code>phyg</code> from the output directory (the script uses relative file names). Feed the tree plus <code>_sankoff.fasta</code> into <a href="../name-tree/"><code>name-tree</code></a> for taxon names.</p>
 <p><strong><code>_iqtree.model</code></strong> (<code>--iqtree</code>) — lower-triangular exchangeability matrix <span class="arithmatex">\(R(a,b) = e^{-\text{cost}(a,b)}\)</span> (one row of increasing length per state, whitespace-separated, PAML order), followed by one line of empirical state frequencies. Only states actually occurring in the alignment are kept, compactly renumbered <code>0..k-1</code>.</p>
-<p><strong><code>_iqtree.fasta</code></strong> (<code>--iqtree</code>) — alignment recoded to that same compact <code>0..k-1</code> alphabet (symbols <code>0-9A-F</code>). Under <code>--free-loss</code>, non-detection becomes <code>?</code> and columns left non-informative once missing calls are ignored are dropped first (required for <code>+ASC</code>). Run with:
+<p><strong><code>_iqtree.fasta</code></strong> (<code>--iqtree</code>) — alignment recoded to that same compact <code>0..k-1</code> alphabet (symbols <code>0-9A-F</code>). Under <code>--free-loss</code>, non-detection becomes <code>?</code> and columns left non-informative once missing calls are ignored are dropped first (required for <code>+ASC</code>); with <code>--iqtree-min-freq</code> also set (the default), any state rarer than that threshold is folded into the same <code>?</code> treatment, and non-informative columns are re-checked and dropped again after that. Run with:
 <div class="highlight"><pre><span></span><code>iqtree3 -s &lt;prefix&gt;_iqtree.fasta --seqtype MORPH -m &lt;prefix&gt;_iqtree.model+ASC --prefix &lt;prefix&gt;_iqtree -T AUTO
 </code></pre></div></p>
-<p><strong><code>_iqtree_states.csv</code></strong> (<code>--iqtree</code>) — one row per state actually kept in <code>_iqtree.model</code>/<code>_iqtree.fasta</code> (header <code>iqtree_symbol,canonical_symbol,frequency</code>): <code>iqtree_symbol</code> is the compact <code>0-9A-F</code> symbol as written in those two files, <code>canonical_symbol</code> is the matching <code>_sankoff_matrix.csv</code> state, <code>frequency</code> is that state's empirical frequency at full precision (<code>_iqtree.model</code>'s own frequency line is rounded to 6 decimals). Under <code>--free-loss</code>, absent (<code>0</code>/<code>?</code>) is never a kept state, so it never appears here. Use this file to identify which real state a given row/column of <code>_iqtree.model</code>'s matrix corresponds to — e.g. to check whether a state showing zero exchangeability with everything else is expected (a state combination that never co-occurs with anything else in this data) or worth investigating further.</p>
+<p><strong><code>_iqtree_states.csv</code></strong> (<code>--iqtree</code>) — one row per state actually kept in <code>_iqtree.model</code>/<code>_iqtree.fasta</code> (header <code>iqtree_symbol,canonical_symbol,frequency</code>): <code>iqtree_symbol</code> is the compact <code>0-9A-F</code> symbol as written in those two files, <code>canonical_symbol</code> is the matching <code>_sankoff_matrix.csv</code> state, <code>frequency</code> is that state's empirical frequency at full precision (<code>_iqtree.model</code>'s own frequency line is rounded to 6 decimals). Under <code>--free-loss</code>, absent (<code>0</code>/<code>?</code>) is never a kept state, so it never appears here — nor does any state <code>--iqtree-min-freq</code> folded away for being too rare. Use this file to identify which real state a given row/column of <code>_iqtree.model</code>'s matrix corresponds to — e.g. to check whether a state showing zero exchangeability with everything else is expected (a state combination that never co-occurs with anything else in this data) or worth investigating further.</p>
+<h3 id="rare-states-and-iqtree-min-freq">Rare states and <code>--iqtree-min-freq</code></h3>
+<p>States that combine 3 or 4 central bases at once (IUPAC <code>V</code>/<code>H</code>/<code>K</code>.../<code>N</code>) are inherently rare — and, on real data, rare enough that they can make <code>iqtree3</code> itself numerically unstable ("Numerical underflow for lh-derivative" warnings, near-degenerate likelihood optimization). They're also more likely to be assembly/detection noise than genuine, widely-shared multi-way polymorphism, the same "sampling failure, not true signal" reasoning <code>--free-loss</code> already applies to non-detection. With <code>--free-loss</code> set, <code>--iqtree-min-freq</code> (default <code>0.001</code>, i.e. one in a thousand) extends that same missing-data treatment to any state below this frequency, not just absence. Check <code>_iqtree_states.csv</code> to see exactly which states survived and at what frequency; set <code>--iqtree-min-freq 0</code> to disable this and keep every state that occurs at all (the old behavior). Has no effect without <code>--free-loss</code> — there is no missing-data symbol to fold rare states into otherwise.</p>
 
 
 
diff --git a/src/obikmer/src/cmd/phylo/args.rs b/src/obikmer/src/cmd/phylo/args.rs
index 5261258e..32468a3c 100644
--- a/src/obikmer/src/cmd/phylo/args.rs
+++ b/src/obikmer/src/cmd/phylo/args.rs
@@ -267,6 +267,25 @@ pub struct PhyloArgs {
     #[arg(long)]
     pub iqtree: bool,
 
+    /// Under `--iqtree --free-loss`, also recode to `?` (the same
+    /// missing-data treatment as `-`) any state whose empirical frequency
+    /// in the alignment falls below this threshold — not just genuinely
+    /// absent calls. States encoding 3 or 4 simultaneously-observed
+    /// central bases (IUPAC `V`/`H`/`K`.../`N` for 3, `N` for 4) are rare
+    /// by construction and, on real data, land in exactly this low-frequency
+    /// range — more likely assembly/detection noise than a genuine,
+    /// widely-preserved multi-way polymorphism, the same "sampling failure,
+    /// not true signal" reasoning `--free-loss` already applies to absence.
+    /// Confirmed on real data to matter: `iqtree3`'s own "Numerical
+    /// underflow for lh-derivative" warnings and the exact-zero
+    /// exchangeability rows this was meant to fix (see
+    /// `DevDocMD/theory/evolutionary_distances.md`) both trace back to
+    /// states this thin. No effect without `--free-loss` (there is no
+    /// missing-data symbol to recode to otherwise). `<prefix>_iqtree_states.csv`
+    /// reports the frequency actually used to decide.
+    #[arg(long, default_value = "0.001")]
+    pub iqtree_min_freq: f64,
+
     /// Scale factor applied before rounding real-valued costs to the
     /// integers both `--tnt`'s smatrix/cost commands and `--phyg`'s `tcm:`
     /// matrix require. Keep this small: the total tree score is this scale
diff --git a/src/obikmer/src/cmd/phylo/iqtree.rs b/src/obikmer/src/cmd/phylo/iqtree.rs
index b774ce59..3ec1b712 100644
--- a/src/obikmer/src/cmd/phylo/iqtree.rs
+++ b/src/obikmer/src/cmd/phylo/iqtree.rs
@@ -107,6 +107,19 @@ fn drop_ascertainment_noninformative(alignment: &SnpAlignment) -> SnpAlignment {
     SnpAlignment { sequences }
 }
 
+/// Recode every occurrence of a byte in `symbols` to `-` — the same
+/// "absent" byte `drop_ascertainment_noninformative`/`compact_alphabet`
+/// already treat specially under `--free-loss` (recoded to `?` further
+/// downstream). Used by `--iqtree-min-freq` to fold rare, likely-noisy
+/// states into the missing-data treatment before a second
+/// `compact_alphabet` pass, without duplicating that treatment's logic.
+fn recode_symbols_as_absent(alignment: &SnpAlignment, symbols: &[u8]) -> SnpAlignment {
+    let sequences = alignment.sequences.iter()
+        .map(|seq| seq.iter().map(|&b| if symbols.contains(&b) { b'-' } else { b }).collect())
+        .collect();
+    SnpAlignment { sequences }
+}
+
 fn compact_alphabet(alignment: &SnpAlignment, free_loss: bool) -> CompactAlphabet {
     let iupac_to_state = state_index_table();
 
@@ -240,6 +253,7 @@ pub(super) fn write_iqtree(
     labels: &[String],
     output: &Option<PathBuf>,
     free_loss: bool,
+    min_freq: f64,
 ) {
     let filtered;
     let alignment = if free_loss {
@@ -257,7 +271,41 @@ pub(super) fn write_iqtree(
         alignment
     };
 
-    let alphabet = compact_alphabet(alignment, free_loss);
+    let mut alphabet = compact_alphabet(alignment, free_loss);
+
+    // `--iqtree-min-freq`: fold rare (likely-noisy) states into the same
+    // missing-data treatment `-` already gets under `--free-loss`, then
+    // recompute the alphabet on the further-filtered alignment — see
+    // `args.rs`'s docs on `--iqtree-min-freq` and
+    // `DevDocMD/theory/evolutionary_distances.md` for why (real data:
+    // states encoding 3-4 simultaneous central bases land in exactly this
+    // low-frequency range and correlate with `iqtree3`'s own numerical
+    // instability warnings).
+    let refiltered;
+    let alignment = if free_loss {
+        let low_freq_symbols: Vec<u8> = alphabet.compact_to_old.iter().zip(alphabet.freq.iter())
+            .filter(|&(_, &f)| f < min_freq)
+            .map(|(&old, _)| STATE_SYMBOL[old as usize] as u8)
+            .collect();
+        if low_freq_symbols.is_empty() {
+            alignment
+        } else {
+            let recoded = recode_symbols_as_absent(alignment, &low_freq_symbols);
+            let before = recoded.sequences.first().map(|s| s.len()).unwrap_or(0);
+            refiltered = drop_ascertainment_noninformative(&recoded);
+            let after = refiltered.sequences.first().map(|s| s.len()).unwrap_or(0);
+            info!(
+                "--iqtree-min-freq {min_freq}: {} rare state(s) ({}) recoded as missing, {before} → {after} sites",
+                low_freq_symbols.len(),
+                low_freq_symbols.iter().map(|&b| b as char).collect::<String>(),
+            );
+            alphabet = compact_alphabet(&refiltered, free_loss);
+            &refiltered
+        }
+    } else {
+        alignment
+    };
+
     let states_path = write_iqtree_states_csv(&alphabet, output);
     let model_path = write_iqtree_model(matrix, &alphabet, output);
     let (fasta_path, n_sites) = write_iqtree_alignment(alignment, labels, &alphabet, output, free_loss);
@@ -349,4 +397,39 @@ mod tests {
         assert_eq!(lines.next(), Some("1,G,0.5"));
         assert!(lines.next().is_none());
     }
+
+    #[test]
+    fn iqtree_min_freq_folds_rare_states_into_missing() {
+        // 20 common A/C sites (60 calls total across 3 genomes) plus one
+        // site where genome 0 carries the rare ambiguity state `M` and
+        // genome 1 carries `A` (kept informative by the first
+        // ascertainment filter: two distinct non-`-` calls) — `M` ends up
+        // at 1/62, well below the 0.05 threshold used here.
+        let mut sequences: Vec<Vec<u8>> = vec![Vec::new(); 3];
+        for i in 0..20 {
+            let (a, b, c) = if i % 2 == 0 { (b'A', b'C', b'A') } else { (b'C', b'A', b'C') };
+            sequences[0].push(a);
+            sequences[1].push(b);
+            sequences[2].push(c);
+        }
+        sequences[0].push(b'M');
+        sequences[1].push(b'A');
+        sequences[2].push(b'-');
+        let alignment = SnpAlignment { sequences };
+        let labels = vec!["g1".to_string(), "g2".to_string(), "g3".to_string()];
+        let matrix = [[0.0f64; 16]; 16];
+        let prefix = std::env::temp_dir().join(format!("obikmer_test_iqtree_minfreq_{}", std::process::id()));
+        let output = Some(prefix.clone());
+
+        write_iqtree(&matrix, &alignment, &labels, &output, true, 0.05);
+
+        let states_path = format!("{}_iqtree_states.csv", prefix.display());
+        let csv = std::fs::read_to_string(&states_path).unwrap();
+        assert!(!csv.contains(",M,"), "M (freq ~1/62) must be folded into missing under --iqtree-min-freq 0.05, got:\n{csv}");
+        assert!(csv.contains(",A,") && csv.contains(",C,"), "A/C must survive (well above threshold), got:\n{csv}");
+
+        for suffix in ["_iqtree_states.csv", "_iqtree.model", "_iqtree.fasta"] {
+            std::fs::remove_file(format!("{}{suffix}", prefix.display())).ok();
+        }
+    }
 }
diff --git a/src/obikmer/src/cmd/phylo/mod.rs b/src/obikmer/src/cmd/phylo/mod.rs
index b3684ccf..cfeaf816 100644
--- a/src/obikmer/src/cmd/phylo/mod.rs
+++ b/src/obikmer/src/cmd/phylo/mod.rs
@@ -249,7 +249,7 @@ pub fn run(args: PhyloArgs) {
             write_sankoff_phyg(&matrix, &args.output, args.sankoff_cost_scale);
         }
         if args.iqtree {
-            write_iqtree(&matrix, &alignment, &kept_labels, &args.output, args.free_loss);
+            write_iqtree(&matrix, &alignment, &kept_labels, &args.output, args.free_loss, args.iqtree_min_freq);
         }
     }
 
diff --git a/src/obikphylo/src/siblings/tests.rs b/src/obikphylo/src/siblings/tests.rs
index 2f30edaa..f984a376 100644
--- a/src/obikphylo/src/siblings/tests.rs
+++ b/src/obikphylo/src/siblings/tests.rs
@@ -15,7 +15,7 @@ use super::cardinality::CardinalityExt;
 use super::distance::DistanceExt;
 use super::entropy::ShannonEntropyExt;
 use super::entropy_annex::{EntropyAnnex, ENTROPY_ANNEX_FILE_NAME};
-use super::helpers::is_minorant;
+use super::helpers::{central_base, is_minorant};
 use super::sankoff_bundle::SankoffBundleExt;
 use super::stats::SiblingStatsExt;
 use super::subsample::EntropyBias;
@@ -457,6 +457,44 @@ fn sankoff_bundle_matches_old_separate_calls() {
     assert_eq!(bundle.alignment.sequences, expected_alignment.sequences);
 }
 
+#[test]
+fn base_pair_tally_accumulates_base_a_diagnostic() {
+    // Diagnostic for a user-reported observation on real data:
+    // `composition_transitions`'s row/column for base 'A' (index 0) was
+    // *entirely* zero, including the diagonal (`same[0]`, "A stays A"),
+    // despite 'A' appearing at ~6% frequency in the pseudo-alignment
+    // itself. g1/g2 are identical (both central base 'A'), g3 differs
+    // (central base 'C') at the same family — makes the family variable
+    // (family_size=2) while g1/g2 form an eligible (ratio 0), ordinary
+    // pair both resolving `single_form` to `Some(0)` = 'A'.
+    let dir = tempdir().unwrap();
+    let g1 = build_single_genome_index(dir.path(), "g1", b"AAAAAAAAAAA");
+    let g2 = build_single_genome_index(dir.path(), "g2", b"AAAAAAAAAAA");
+    let g3 = build_single_genome_index(dir.path(), "g3", b"AAAAACAAAAA");
+    let mut rep = Reporter::new();
+    let merged = KmerIndex::merge(
+        &dir.path().join("merged.idx"),
+        &[&g1, &g2, &g3],
+        MergeMode::Presence,
+        false,
+        false,
+        1.0,
+        &mut rep,
+    ).expect("merge");
+    merged.build_sibling_annex().expect("build_sibling_annex");
+
+    let n_genomes = merged.meta().genomes.len();
+    let exclude_mask = vec![false; n_genomes];
+    let bundle = merged.sankoff_bundle(None, None, 0.5, &exclude_mask).expect("sankoff_bundle");
+
+    assert!(
+        bundle.base_pair_tally.same[0] >= 1,
+        "base 'A' (index 0) must accumulate in BasePairTally.same for an identical, included g1/g2 \
+         pair both resolving to 'A' — got same={:?}, counts={:?}",
+        bundle.base_pair_tally.same, bundle.base_pair_tally.counts,
+    );
+}
+
 #[test]
 fn entropy_annex_builds_on_demand_and_biases_selection() {
     // Same fixture, same single non-monomorphic family, known entropy15 =
@@ -537,6 +575,132 @@ fn diag_real_index_layer_distribution() {
     println!("top10 counts: {:?}", &sorted_counts[..10.min(sorted_counts.len())]);
 }
 
+#[test]
+#[ignore]
+fn diag_real_index_base_a_representation() {
+    // Diagnostic for a user-reported observation, reproduced on two
+    // unrelated real datasets (a plant and this bacterial index):
+    // `composition_transitions`'s row/column for base 'A' is entirely
+    // zero, even though 'A' appears at real (~6-22%) frequency in the
+    // pseudo-alignment itself. A minimal synthetic reproduction
+    // (`base_pair_tally_accumulates_base_a_diagnostic`) showed the
+    // pairwise tally mechanism itself works correctly for base A in
+    // isolation — so this checks one level lower, purely structural
+    // (annex bits only, no cross-partition/genome-level resolution): does
+    // base A even show up as *present* in minorant families' own
+    // `FamilyMask`s at all, at a rate proportional to the other 3 bases?
+    // If yes, the anomaly is specific to the pairwise/`single_form`
+    // resolution stage; if `has_base[0]` is itself near-zero here, the
+    // anomaly originates earlier, in `build_sibling_annex`/`central_base`.
+    let idx = KmerIndex::open("/Users/coissac/Sync/travail/__MOI__/obikmer/benchmark/global_index_presence")
+        .expect("open real index");
+    let layer_dirs = super::family_scan::sibling_layer_dirs(&idx).expect("layer dirs");
+    let mut has_base = [0u64; 4];
+    let mut minorant_total = 0u64;
+    let mut minorant_central_a = 0u64;
+    for layer_dir in &layer_dirs {
+        let annex = SiblingAnnex::open(&layer_dir.join(ANNEX_FILE_NAME)).unwrap();
+        for slot in 0..annex.len() {
+            let Some(mask) = annex.get(slot) else { continue };
+            if !mask.is_minorant() {
+                continue;
+            }
+            minorant_total += 1;
+            for b in 0..4u8 {
+                if mask.has(b) {
+                    has_base[b as usize] += 1;
+                }
+            }
+        }
+        // Cross-check: for a sample of this layer's minorants, is the
+        // slot's *own* central base ever actually 'A' (bit 0)? — reads
+        // the real k-mer via the layer's MPHF, not just the mask.
+        let meta = PartitionMeta::load(layer_dir.parent().unwrap()).unwrap();
+        let mphf = MphfLayer::open(layer_dir, &meta.mode).unwrap();
+        for (order, kmer) in mphf.enumerate_kmers().take(2_000_000) {
+            let Some(mask) = annex.get(order) else { continue };
+            if mask.is_minorant() && central_base(kmer, idx.kmer_size()) == 0 {
+                minorant_central_a += 1;
+            }
+        }
+    }
+    println!(
+        "minorant_total={minorant_total} has_base(A,C,G,T)={has_base:?} minorant_central_a_sampled={minorant_central_a}"
+    );
+}
+
+#[test]
+#[ignore]
+fn diag_real_index_sankoff_bundle_base_a() {
+    // Structural check (`diag_real_index_base_a_representation`) shows
+    // base A fully, proportionally represented at the family level (~23M
+    // minorants, the *highest* of the four bases) — so the anomaly must
+    // be downstream, in `sankoff_bundle`'s actual pairwise resolution.
+    // Reproduces through the real cross-partition code path (not the
+    // minimal synthetic fixture, which showed the mechanism working in
+    // isolation), bounded by `--subsample` to stay fast.
+    let idx = KmerIndex::open("/Users/coissac/Sync/travail/__MOI__/obikmer/benchmark/global_index_presence")
+        .expect("open real index");
+    let n_genomes = idx.meta().genomes.len();
+    let exclude_mask = vec![false; n_genomes];
+    let bundle = idx.sankoff_bundle(Some(1_000_000), None, 0.5, &exclude_mask).expect("sankoff_bundle");
+    println!("base_pair_tally.same={:?}", bundle.base_pair_tally.same);
+    println!("base_pair_tally.counts={:?}", bundle.base_pair_tally.counts);
+    let alignment_a_count: usize = bundle.alignment.sequences.iter()
+        .map(|seq| seq.iter().filter(|&&b| b == b'A').count())
+        .sum();
+    println!("alignment raw 'A' byte count={alignment_a_count}");
+}
+
+#[test]
+#[ignore]
+fn diag_real_index_genome_mask_for_base_a_families() {
+    // Directly inspects the raw `genome_mask` array `sankoff_bundle`'s
+    // closures see, for the first few variable families where base A is
+    // present — to check whether A ever co-occurs as `single_form` in two
+    // *different* genomes at the same family at all (the precondition for
+    // `bp_same`/`bp_counts` to ever increment for base A), rather than
+    // reasoning about it further.
+    use std::sync::Arc;
+    let idx = KmerIndex::open("/Users/coissac/Sync/travail/__MOI__/obikmer/benchmark/global_index_presence")
+        .expect("open real index");
+    let n_parts = idx.n_partitions();
+    let n_genomes = idx.meta().genomes.len();
+    let with_counts = idx.meta().config.with_counts;
+    let k = idx.kmer_size();
+    let n_bits = n_parts.trailing_zeros() as usize;
+    let partition = obikpartitionner::KmerPartition::open_with_config(
+        idx.root_path(), idx.kmer_size(), idx.minimizer_size(), n_bits,
+    ).unwrap();
+    let cache = Arc::new(super::cache::PartitionCache::build(&partition, n_parts, with_counts).unwrap());
+    let layer_dirs = super::family_scan::sibling_layer_dirs(&idx).unwrap();
+
+    let mut printed = 0usize;
+    for layer_dir in &layer_dirs {
+        super::family_scan::scan_layer_families(
+            layer_dir, n_parts, n_genomes, with_counts, k, &cache, &super::family_scan::Selection::All,
+            |_family_idx, mask, genome_mask| {
+                if printed >= 15 || !mask.has(0) || mask.family_size() < 2 {
+                    return;
+                }
+                let single_a: Vec<usize> = (0..n_genomes).filter(|&g| genome_mask[g] == 1).collect();
+                let others: Vec<(usize, u8)> = (0..n_genomes)
+                    .filter(|&g| genome_mask[g] != 0 && genome_mask[g] != 1)
+                    .map(|g| (g, genome_mask[g]))
+                    .collect();
+                println!(
+                    "family bits={:#06b} size={} single_A_genomes={:?} other_nonzero_genomes={:?}",
+                    mask.bits(), mask.family_size(), single_a, others,
+                );
+                printed += 1;
+            },
+        ).unwrap();
+        if printed >= 15 {
+            break;
+        }
+    }
+}
+
 #[test]
 #[ignore]
 fn diag_plant_index_presence_matrix_sparsity() {
-- 
2.54.0


From 1f9c6388eb5e922b91e52e3ea81b1a189861a677 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Sun, 16 Aug 2026 09:22:41 +0200
Subject: [PATCH 42/46] Introduce compare_sparse CLI tool to verify index
 consistency

Adds a new binary that validates bit-level consistency between dense and sparse K-mer index representations by sampling slots across partitions and reporting discrepancies. Refactors sibling cache matrix initialization into a centralized factory method to simplify control flow and standardize error handling. Introduces diagnostic configurations, benchmark scripts, and an ignored test case to support k-mer resolution analysis.
---
 .DS_Store                                     | Bin 14340 -> 14340 bytes
 .gitignore                                    |   2 +
 Le_bug_des_A.md                               |  43 +++++
 benchmark/test_transition_sankoff_params.yaml | 167 ++++++++++++++++++
 benchmark/transition.awk                      |  18 ++
 src/Cargo.lock                                |  10 ++
 src/Cargo.toml                                |   2 +-
 src/bin/compare_sparse.rs                     | 130 ++++++++++++++
 src/compare_sparse/Cargo.toml                 |  14 ++
 src/compare_sparse/src/main.rs                | 100 +++++++++++
 src/obikphylo/src/siblings/cache.rs           |  47 +++--
 src/obikphylo/src/siblings/family_scan.rs     |   9 +-
 src/obikphylo/src/siblings/tests.rs           |  93 ++++++++++
 src/sankoff_params.yaml                       | 167 ++++++++++++++++++
 14 files changed, 776 insertions(+), 26 deletions(-)
 create mode 100644 Le_bug_des_A.md
 create mode 100644 benchmark/test_transition_sankoff_params.yaml
 create mode 100755 benchmark/transition.awk
 create mode 100644 src/bin/compare_sparse.rs
 create mode 100644 src/compare_sparse/Cargo.toml
 create mode 100644 src/compare_sparse/src/main.rs
 create mode 100644 src/sankoff_params.yaml

diff --git a/.DS_Store b/.DS_Store
index 4373600fa9ad52b079125e98c415ac6ae5447bf4..eeb93388e96a5632f84ac905c6d25dbe339dfb46 100644
GIT binary patch
delta 1102
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delta 120
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diff --git a/.gitignore b/.gitignore
index 5bb83c6d..b19afb41 100644
--- a/.gitignore
+++ b/.gitignore
@@ -12,10 +12,12 @@ data-stress
 *.csv
 Betula_exilis--IGA-24-33
 benchmark/genomes
+benchmark/genomes_orig
 benchmark/simulated_data
 benchmark/specimen_index_presence
 benchmark/specimen_index_count
 benchmark/global_index_presence
+benchmark/global_index_presence_orig
 benchmark/global_index_presence_sav
 benchmark/all_specific
 benchmark/global_index_count
diff --git a/Le_bug_des_A.md b/Le_bug_des_A.md
new file mode 100644
index 00000000..3f25b9c2
--- /dev/null
+++ b/Le_bug_des_A.md
@@ -0,0 +1,43 @@
+Voici la version corrigée :
+
+---
+
+**Bug** : dans `base_pair_tally`, toutes les transitions/comptes depuis/vers A valent 0 dans `_sankoff_params.yaml`, alors que C/G/T sont corrects.
+
+**Contexte** : obikmer, pipeline phylogénétique `--sankoff`. L’index est construit sur 20 génomes bactériens. Même symptôme sur un jeu de 100 génomes de plantes : A est toujours à 0.
+
+**Fichier clé** : `src/obikphylo/src/siblings/sankoff_bundle.rs` (Pass A + Pass B).
+
+**Ce qui a été vérifié** :
+- Le fichier de sortie `_sankoff_params.yaml` montre bien `composition_transitions` avec A à 0 partout.
+- L’index contient bien des familles avec A (`mask.has(0) == true`), et même des familles où A co-existe avec d’autres bases (`mask == 0b0011` par ex.).
+- Un k-mer propriétaire de famille avec `mask == 0b0001` (A seul) a été identifié : forward `GAACAAGAGATCTCGATCTTGTCTACAAGGA`, revcomp `TCCTTGTAGACAAGATCGAGATCTCTTGTTC`.
+- Le diagnostic CLI sur l’index réel donne :
+  - Pass A : `a_pairs=623342 a_snp=623342 a_shared=0 a_both_a=0`
+  - Pass B : `families_with_a=22965521 a_single_form_genomes=22913238 a_included_pairs=0 a_same_incremented=0 bp_same=[0, 96389, 222720, 277909] bp_counts[0]=[0, 0, 0, 0]`
+
+**Interprétation** : A est fréquemment en `single_form` (mask == 1) chez certains génomes, mais **jamais simultanément** chez deux génomes différents dans la même famille. Donc toutes les paires “avec A” sont 100% SNP → ratio = 1.0 > `ratio_ceiling=0.5` → toutes exclues par le filtre `included`. C’est pourquoi `bp_same[0]` et `bp_counts[0][*]` restent à 0.
+
+**Point crucial** : le bug n’apparaît **que sur l’index compacté sparse**. Sur le même index avant compaction (matrice dense `matrix.pbmx`), `--sankoff` produit des tallies corrects pour A. Dès qu’on compacte avec `pack --sparse`, A disparaît.
+
+**Vérifications supplémentaires (diagnostic sparse)** :
+- La compaction `pack --sparse` produit une matrice `PersistentSparseBitMatrix` dont le contenu est **strictement identique** à la matrice dense d'origine : vérification exhaustive coordonnée par coordonnée sur **1 804 774 880 cellules** (512 partitions × 2 layers), **zéro différence**.
+- `fill_row` et `fill_sub_matrix` (les deux chemins de lecture utilisés par le pipeline phylogénétique) restituent les mêmes bits sur dense et sparse.
+- **Conclusion** : le bug n'est **pas** dans la compaction sparse elle-même, ni dans les chemins de lecture individuels. La structure stocke correctement A, C, G, T.
+
+**Conséquence logique** :
+Si les matrices sont identiques mais que le résultat final diffère, le bug se situe dans l'**intersection** des informations — c'est-à-dire dans le code qui **combine** les lectures des deux matrices (ou qui transforme les résultats bruts en tallies). Deux endroits possibles :
+1. **Le scan `sankoff_bundle`** (`family_scan.rs` + `sankoff_bundle.rs`) : la boucle qui lit les matrices, construit `genome_mask`, et accumule `bp_counts` / `same`. C'est l'étape d'intersection proprement dite.
+2. **La conversion des tallies en YAML** (`obikmer/src/cmd/phylo/sankoff.rs`) : moins probable, mais possible si quelque chose sélectionne/filtre les transitions avant écriture.
+
+**Hypothèse la plus probable** : bug dans la résolution cross-partition lors de la construction de l'annex sibling (`build_sibling_annex`). A (bit 0) serait systématiquement manquant ou mal résolu quand on interroge les variants d'une famille depuis une partition différente. À vérifier dans `src/obikphylo/src/siblings/build.rs` et `src/obikphylo/src/siblings/cache.rs` (`PartitionCache::find` / `find_presence_batch`).
+
+**Prochaine étape logique** :
+1. Inspecter `build_sibling_annex` pour voir si les variants avec base A sont bien générés et bien recherchés dans `cache.find`.
+2. Vérifier `PartitionCache::find` et `resolve_layer_hits` pour un éventuel biais contre le bit 0.
+3. Si besoin, ajouter un diagnostic ciblé (compteurs par base) **uniquement** dans `cache.rs` ou `build.rs`, pas dans `sankoff_bundle.rs` qui est déjà propre.
+
+**Contraintes** :
+- Ne pas modifier `sankoff_bundle.rs` davantage.
+- Ne pas toucher à git.
+- Faire des diagnostics minimaux et ciblés.
diff --git a/benchmark/test_transition_sankoff_params.yaml b/benchmark/test_transition_sankoff_params.yaml
new file mode 100644
index 00000000..721e01d7
--- /dev/null
+++ b/benchmark/test_transition_sankoff_params.yaml
@@ -0,0 +1,167 @@
+ratio_ceiling: 0.5
+cardinality_transitions:
+- from: 0
+  to: 0
+  count: 115955295
+  probability: 0.8297007290571883
+- from: 0
+  to: 1
+  count: 12901663
+  probability: 0.0923159153460836
+- from: 0
+  to: 2
+  count: 10519367
+  probability: 0.07526975347801175
+- from: 0
+  to: 3
+  count: 339782
+  probability: 0.0024312591600108434
+- from: 0
+  to: 4
+  count: 39459
+  probability: 0.00028234295870548727
+- from: 1
+  to: 0
+  count: 12901663
+  probability: 0.9007741539906029
+- from: 1
+  to: 1
+  count: 973491
+  probability: 0.0679676357956696
+- from: 1
+  to: 2
+  count: 444884
+  probability: 0.031061112720426456
+- from: 1
+  to: 3
+  count: 2739
+  probability: 0.00019123274323474897
+- from: 1
+  to: 4
+  count: 84
+  probability: 5.864750066344985e-6
+- from: 2
+  to: 0
+  count: 10519367
+  probability: 0.9590597257562327
+- from: 2
+  to: 1
+  count: 444884
+  probability: 0.04056045644508228
+- from: 2
+  to: 2
+  count: 3796
+  probability: 0.00034608458084699006
+- from: 2
+  to: 3
+  count: 327
+  probability: 0.000029812870900149037
+- from: 2
+  to: 4
+  count: 43
+  probability: 3.920346937940087e-6
+- from: 3
+  to: 0
+  count: 339782
+  probability: 0.9908029486551426
+- from: 3
+  to: 1
+  count: 2739
+  probability: 0.007986913010007698
+- from: 3
+  to: 2
+  count: 327
+  probability: 0.0009535306879417734
+- from: 3
+  to: 3
+  count: 58
+  probability: 0.00016912776728019222
+- from: 3
+  to: 4
+  count: 30
+  probability: 0.00008747987962768563
+- from: 4
+  to: 0
+  count: 39459
+  probability: 0.9957604663487016
+- from: 4
+  to: 1
+  count: 84
+  probability: 0.0021197668256491787
+- from: 4
+  to: 2
+  count: 43
+  probability: 0.0010851187321775557
+- from: 4
+  to: 3
+  count: 30
+  probability: 0.0007570595805889924
+- from: 4
+  to: 4
+  count: 11
+  probability: 0.0002775885128826305
+composition_transitions:
+- from: 'A'
+  to: 'A'
+  count: 169043
+  probability: 0.49442957633191476
+- from: 'A'
+  to: 'C'
+  count: 27672
+  probability: 0.08093712982055894
+- from: 'A'
+  to: 'G'
+  count: 124160
+  probability: 0.36315242983957063
+- from: 'A'
+  to: 'T'
+  count: 21020
+  probability: 0.06148086400795566
+- from: 'C'
+  to: 'A'
+  count: 27672
+  probability: 0.08651690662664728
+- from: 'C'
+  to: 'C'
+  count: 145183
+  probability: 0.4539167409213838
+- from: 'C'
+  to: 'G'
+  count: 23425
+  probability: 0.07323859994684925
+- from: 'C'
+  to: 'T'
+  count: 123565
+  probability: 0.3863277525051197
+- from: 'G'
+  to: 'A'
+  count: 124160
+  probability: 0.3846082361177367
+- from: 'G'
+  to: 'C'
+  count: 23425
+  probability: 0.07256320820761906
+- from: 'G'
+  to: 'G'
+  count: 148125
+  probability: 0.4588441927749658
+- from: 'G'
+  to: 'T'
+  count: 27112
+  probability: 0.08398436289967846
+- from: 'T'
+  to: 'A'
+  count: 21020
+  probability: 0.06258131551760583
+- from: 'T'
+  to: 'C'
+  count: 123565
+  probability: 0.3678810776371534
+- from: 'T'
+  to: 'G'
+  count: 27112
+  probability: 0.08071858355439246
+- from: 'T'
+  to: 'T'
+  count: 164186
+  probability: 0.4888190232908483
diff --git a/benchmark/transition.awk b/benchmark/transition.awk
new file mode 100755
index 00000000..93fcbd79
--- /dev/null
+++ b/benchmark/transition.awk
@@ -0,0 +1,18 @@
+#!/usr/bin/awk -f
+
+/^>/ {
+    print
+    next
+}
+
+{
+    gsub(/[Aa]/, "a")
+    gsub(/[Gg]/, "A")
+    gsub(/a/, "G")
+
+    gsub(/[Cc]/, "c")
+    gsub(/[Tt]/, "C")
+    gsub(/c/, "T")
+
+    print
+}
diff --git a/src/Cargo.lock b/src/Cargo.lock
index 1c8798ad..d3a61d54 100644
--- a/src/Cargo.lock
+++ b/src/Cargo.lock
@@ -493,6 +493,16 @@ dependencies = [
  "impl-tools",
 ]
 
+[[package]]
+name = "compare_sparse"
+version = "0.1.0"
+dependencies = [
+ "anyhow",
+ "fastrand",
+ "obicompactvec",
+ "obikindex",
+]
+
 [[package]]
 name = "console"
 version = "0.15.11"
diff --git a/src/Cargo.toml b/src/Cargo.toml
index f34f6918..84935806 100644
--- a/src/Cargo.toml
+++ b/src/Cargo.toml
@@ -1,5 +1,5 @@
 [workspace]
 resolver = "3"
-members = ["obikseq", "obiread", "obiskbuilder", "obifastwrite", "obikmer","obikrope","obipipeline", "obikpartitionner","obiskio","obidebruinj","obilayeredmap", "obicompactvec", "obisys", "obikindex", "obitaxonomy", "obikentropy", "obikphylo"]
+members = ["obikseq", "obiread", "obiskbuilder", "obifastwrite", "obikmer","obikrope","obipipeline", "obikpartitionner","obiskio","obidebruinj","obilayeredmap", "obicompactvec", "obisys", "obikindex", "obitaxonomy", "obikentropy", "obikphylo", "compare_sparse"]
 [profile.release]
 debug = 1
diff --git a/src/bin/compare_sparse.rs b/src/bin/compare_sparse.rs
new file mode 100644
index 00000000..372116b0
--- /dev/null
+++ b/src/bin/compare_sparse.rs
@@ -0,0 +1,130 @@
+use std::path::PathBuf;
+
+use obicompactvec::{BinaryMatrix, PersistentBitMatrix, PersistentSparseBitMatrix};
+use obikindex::KmerIndex;
+
+fn main() -> anyhow::Result<()> {
+    let orig_root = std::env::args().nth(1).expect("usage: compare_sparse <orig_dense> <sparse>");
+    let sparse_root = std::env::args().nth(2).expect("usage: compare_sparse <orig_dense> <sparse>");
+
+    let orig = KmerIndex::open(&orig_root)?;
+    let sparse = KmerIndex::open(&sparse_root)?;
+
+    let n_parts = orig.n_partitions();
+    let n_layers = orig.n_layers_per_partition()?;
+    let n_genomes = orig.meta().genomes.len();
+
+    println!("index orig:  {} partitions, {} layers, {} genomes", n_parts, n_layers, n_genomes);
+    println!("index sparse:{} partitions, {} layers, {} genomes", sparse.n_partitions(), sparse.n_layers_per_partition()?, sparse.meta().genomes.len());
+
+    let mut total_layers = 0usize;
+    let mut mismatches = 0usize;
+    let mut slot_checked = 0usize;
+
+    for part in 0..n_parts {
+        let part_dir_orig = orig.partition().part_dir(part);
+        let part_dir_sparse = sparse.partition().part_dir(part);
+
+        if !part_dir_orig.join("index").exists() || !part_dir_sparse.join("index").exists() {
+            continue;
+        }
+
+        for layer in 0..n_layers {
+            let layer_dir_orig = part_dir_orig.join("index").join(format!("layer_{layer}"));
+            let layer_dir_sparse = part_dir_sparse.join("index").join(format!("layer_{layer}"));
+
+            if !layer_dir_orig.exists() || !layer_dir_sparse.exists() {
+                continue;
+            }
+
+            let presence_orig = layer_dir_orig.join("presence");
+            let presence_sparse = layer_dir_sparse.join("presence");
+
+            if !presence_orig.exists() || !presence_sparse.exists() {
+                continue;
+            }
+
+            // Ouvrir la matrice dense (PackedBitMatrix) depuis l'original
+            let dense = match PersistentBitMatrix::open(&presence_orig) {
+                Ok(m) => m,
+                Err(e) => {
+                    eprintln!("ERREUR ouverture dense part={part} layer={layer}: {e}");
+                    continue;
+                }
+            };
+
+            // Ouvrir la matrice sparse
+            let sp = match PersistentSparseBitMatrix::open(&presence_sparse) {
+                Ok(m) => m,
+                Err(e) => {
+                    eprintln!("ERREUR ouverture sparse part={part} layer={layer}: {e}");
+                    continue;
+                }
+            };
+
+            if dense.n_cols() != sp.n_cols() {
+                eprintln!("ERREUR n_cols différent part={part} layer={layer}: dense={} sparse={}", dense.n_cols(), sp.n_cols());
+                continue;
+            }
+
+            let n = dense.n();
+            if n != sp.n() {
+                eprintln!("ERREUR n différent part={part} layer={layer}: dense={} sparse={}", n, sp.n());
+                continue;
+            }
+
+            if n == 0 {
+                continue;
+            }
+
+            // Échantillon de 100 slots aléatoires par layer
+            let mut rng = fastrand::Rng::with_seed(part as u64 * 1000 + layer as u64);
+            let sample_size = 100.min(n);
+            let mut checked_any = false;
+
+            for _ in 0..sample_size {
+                let slot = rng.usize(0..n);
+                let mut dense_row = vec![0u32; dense.n_cols()];
+                let mut sparse_row = vec![0u32; sp.n_cols()];
+
+                dense.fill_row(slot, &mut dense_row);
+                sp.fill_row(slot, &mut sparse_row);
+
+                if dense_row != sparse_row {
+                    // Premier mismatch pour ce layer : diagnostiquer la colonne A
+                    if !checked_any {
+                        let a_col = 0; // A est la colonne 0
+                        let mut a_dense = 0u32;
+                        let mut a_sparse = 0u32;
+                        // scanner tous les slots pour compter les différences sur la colonne A
+                        let mut diff_a = 0usize;
+                        for s in 0..n {
+                            let mut d = vec![0u32; dense.n_cols()];
+                            let mut s2 = vec![0u32; sp.n_cols()];
+                            dense.fill_row(s, &mut d);
+                            sp.fill_row(s, &mut s2);
+                            if d[a_col] != s2[a_col] {
+                                diff_a += 1;
+                            }
+                        }
+                        eprintln!("MISMATCH part={part} layer={layer} slot={slot}: colonne A différente sur {diff_a}/{n} slots");
+                        mismatches += 1;
+                        checked_any = true;
+                    }
+                }
+                slot_checked += 1;
+            }
+
+            total_layers += 1;
+        }
+    }
+
+    println!("Vérifié {} layers, {} slots échantillonnés", total_layers, slot_checked);
+    if mismatches == 0 {
+        println!("OK : aucune différence détectée.");
+    } else {
+        println!("MISMATCHES détectés dans {} layers", mismatches);
+    }
+
+    Ok(())
+}
diff --git a/src/compare_sparse/Cargo.toml b/src/compare_sparse/Cargo.toml
new file mode 100644
index 00000000..f11f19d0
--- /dev/null
+++ b/src/compare_sparse/Cargo.toml
@@ -0,0 +1,14 @@
+[package]
+name = "compare_sparse"
+version = "0.1.0"
+edition = "2021"
+
+[[bin]]
+name = "compare_sparse"
+path = "src/main.rs"
+
+[dependencies]
+obikindex = { path = "../obikindex" }
+obicompactvec = { path = "../obicompactvec" }
+anyhow = "1"
+fastrand = "2"
diff --git a/src/compare_sparse/src/main.rs b/src/compare_sparse/src/main.rs
new file mode 100644
index 00000000..37b291eb
--- /dev/null
+++ b/src/compare_sparse/src/main.rs
@@ -0,0 +1,100 @@
+use obicompactvec::{PersistentBitMatrix, PersistentSparseBitMatrix};
+use obikindex::KmerIndex;
+
+fn main() -> anyhow::Result<()> {
+    let sparse_root = std::env::args().nth(1).expect("usage: compare_full <sparse> <orig_dense>");
+    let dense_root = std::env::args().nth(2).expect("usage: compare_full <sparse> <orig_dense>");
+
+    let sparse = KmerIndex::open(&sparse_root)?;
+    let dense = KmerIndex::open(&dense_root)?;
+
+    let n_parts = sparse.n_partitions();
+    let n_layers = sparse.n_layers_per_partition()?;
+
+    println!("index sparse: {} partitions, {} layers", sparse.n_partitions(), n_layers);
+    println!("index dense:  {} partitions, {} layers", dense.n_partitions(), dense.n_layers_per_partition()?);
+
+    let mut total_layers = 0usize;
+    let mut total_cells = 0usize;
+    let mut mismatched_cells = 0usize;
+    let mut first_mismatch = None;
+
+    for part in 0..n_parts {
+        let part_dir_sparse = sparse.partition().part_dir(part);
+        let part_dir_dense = dense.partition().part_dir(part);
+
+        if !part_dir_sparse.join("index").exists() || !part_dir_dense.join("index").exists() {
+            continue;
+        }
+
+        for layer in 0..n_layers {
+            let layer_dir_sparse = part_dir_sparse.join("index").join(format!("layer_{layer}"));
+            let layer_dir_dense = part_dir_dense.join("index").join(format!("layer_{layer}"));
+
+            if !layer_dir_sparse.exists() || !layer_dir_dense.exists() {
+                continue;
+            }
+
+            let presence_sparse = layer_dir_sparse.join("presence");
+            let presence_dense = layer_dir_dense.join("presence");
+
+            if !presence_sparse.exists() || !presence_dense.exists() {
+                continue;
+            }
+
+            let sp = match PersistentSparseBitMatrix::open(&presence_sparse) {
+                Ok(m) => m,
+                Err(e) => {
+                    eprintln!("ERREUR ouverture sparse part={part} layer={layer}: {e}");
+                    continue;
+                }
+            };
+
+            let dn = match PersistentBitMatrix::open(&layer_dir_dense) {
+                Ok(m) => m,
+                Err(e) => {
+                    eprintln!("ERREUR ouverture dense part={part} layer={layer}: {e}");
+                    continue;
+                }
+            };
+
+            if dn.n_cols() != sp.n_cols() || dn.n() != sp.n() || dn.n() == 0 {
+                continue;
+            }
+
+            let n = dn.n();
+            let n_cols = dn.n_cols();
+
+            // Vérification exhaustive : tous les slots, toutes les colonnes
+            let mut dense_row = vec![0u32; n_cols];
+            let mut sparse_row = vec![0u32; n_cols];
+
+            for slot in 0..n {
+                dn.fill_row(slot, &mut dense_row);
+                sp.fill_row(slot, &mut sparse_row);
+
+                for c in 0..n_cols {
+                    total_cells += 1;
+                    if dense_row[c] != sparse_row[c] {
+                        mismatched_cells += 1;
+                        if first_mismatch.is_none() {
+                            first_mismatch = Some((part, layer, slot, c, dense_row[c], sparse_row[c]));
+                        }
+                    }
+                }
+            }
+
+            total_layers += 1;
+        }
+    }
+
+    println!("Vérifié {} layers, {} cellules totales", total_layers, total_cells);
+    if let Some((part, layer, slot, col, d, s)) = first_mismatch {
+        eprintln!("PREMIER MISMATCH : part={part} layer={layer} slot={slot} col={col} dense={d} sparse={s}");
+        println!("MISMATCHES : {} cellules différentes", mismatched_cells);
+    } else {
+        println!("OK : toutes les {} cellules sont identiques entre dense et sparse.", total_cells);
+    }
+
+    Ok(())
+}
diff --git a/src/obikphylo/src/siblings/cache.rs b/src/obikphylo/src/siblings/cache.rs
index 0cadf0e6..3c729b18 100644
--- a/src/obikphylo/src/siblings/cache.rs
+++ b/src/obikphylo/src/siblings/cache.rs
@@ -1,10 +1,12 @@
 use rayon::prelude::*;
 
+use std::path::Path;
+
 use obicompactvec::{PersistentBitMatrix, PersistentCompactIntMatrix, PersistentSparseBitMatrix};
 use obikpartitionner::KmerPartition;
 use obikseq::CanonicalKmer;
-use obilayeredmap::Layer;
-use obilayeredmap::meta::PartitionMeta;
+use obilayeredmap::{Layer, OLMResult};
+use obilayeredmap::meta::{IndexMode, PartitionMeta};
 use obisys::progress_bar;
 
 use obikindex::OKIResult;
@@ -50,6 +52,31 @@ pub(super) enum Mat {
 }
 
 impl Mat {
+    /// Open one layer's matrix, auto-detecting count vs. dense-presence vs.
+    /// sparse-presence from what is actually on disk — the single source of
+    /// truth for *every* caller that opens a layer's own matrix (this
+    /// module's cross-partition [`PartitionCache::build`] and
+    /// `family_scan::scan_layer_families`'s own-layer lookup alike), so the
+    /// two can never disagree about which format a layer's `presence/` was
+    /// packed to. Before this existed, `scan_layer_families` open-coded its
+    /// own (non-sparse-aware) copy of this decision: on a `pack --sparse`d
+    /// layer, `presence/matrix.pbmx` no longer exists (removed by
+    /// `pack_sparse_bit_matrix`), so a caller that only checks for it and
+    /// otherwise unconditionally opens `PersistentBitMatrix` doesn't error —
+    /// `PersistentBitMatrix::open`'s own auto-detection falls all the way
+    /// through to the `Implicit` (mono-genome, all-present) case, silently
+    /// corrupting every read.
+    pub(super) fn open(layer_dir: &Path, mode: &IndexMode, with_counts: bool) -> OLMResult<Self> {
+        if with_counts && layer_dir.join("counts").exists() {
+            return Layer::<PersistentCompactIntMatrix>::open(layer_dir, mode).map(Mat::Count);
+        }
+        if layer_dir.join("presence").join("is_multi.prsb").exists() {
+            Layer::<PersistentSparseBitMatrix>::open(layer_dir, mode).map(Mat::SparsePresence)
+        } else {
+            Layer::<PersistentBitMatrix>::open(layer_dir, mode).map(Mat::Presence)
+        }
+    }
+
     fn find_slot(&self, kmer: CanonicalKmer) -> Option<usize> {
         match self {
             Mat::Count(l) => l.find_slot(kmer),
@@ -156,21 +183,7 @@ impl PartitionCache {
                 let mut mats = Vec::with_capacity(meta.n_layers);
                 for l in 0..meta.n_layers {
                     let layer_dir = index_dir.join(format!("layer_{l}"));
-                    let use_counts = with_counts && layer_dir.join("counts").exists();
-                    // `pack --sparse` converts a layer's `presence/` directory
-                    // in place, leaving `is_multi.prsb` as the on-disk marker
-                    // that distinguishes the sparse format
-                    // (`obicompactvec::PersistentSparseBitMatrix`) from the
-                    // dense one — see `bitmatrix/sparse.rs`'s module docs.
-                    let is_sparse = layer_dir.join("presence").join("is_multi.prsb").exists();
-                    let mat = if use_counts {
-                        Layer::<PersistentCompactIntMatrix>::open(&layer_dir, &meta.mode).ok().map(Mat::Count)
-                    } else if is_sparse {
-                        Layer::<PersistentSparseBitMatrix>::open(&layer_dir, &meta.mode).ok().map(Mat::SparsePresence)
-                    } else {
-                        Layer::<PersistentBitMatrix>::open(&layer_dir, &meta.mode).ok().map(Mat::Presence)
-                    };
-                    let Some(mat) = mat else { continue };
+                    let Ok(mat) = Mat::open(&layer_dir, &meta.mode, with_counts) else { continue };
                     mats.push(mat);
                 }
                 pb.inc(1);
diff --git a/src/obikphylo/src/siblings/family_scan.rs b/src/obikphylo/src/siblings/family_scan.rs
index d76cfacc..709b28c2 100644
--- a/src/obikphylo/src/siblings/family_scan.rs
+++ b/src/obikphylo/src/siblings/family_scan.rs
@@ -53,9 +53,7 @@ use std::sync::atomic::{AtomicU8, Ordering};
 
 use rayon::prelude::*;
 
-use obicompactvec::{PersistentBitMatrix, PersistentCompactIntMatrix};
 use obikseq::CanonicalKmer;
-use obilayeredmap::Layer;
 use obilayeredmap::meta::PartitionMeta;
 use obipipeline::{ThrottleGuard, throttle};
 
@@ -195,12 +193,7 @@ pub(super) fn scan_layer_families(
     let meta = PartitionMeta::load(index_dir).map_err(olm_to_ok)?;
     let annex = Arc::new(SiblingAnnex::open(&layer_dir.join(ANNEX_FILE_NAME))?);
 
-    let use_counts = with_counts && layer_dir.join("counts").exists();
-    let mat = if use_counts {
-        Mat::Count(Layer::<PersistentCompactIntMatrix>::open(layer_dir, &meta.mode).map_err(olm_to_ok)?)
-    } else {
-        Mat::Presence(Layer::<PersistentBitMatrix>::open(layer_dir, &meta.mode).map_err(olm_to_ok)?)
-    };
+    let mat = Mat::open(layer_dir, &meta.mode, with_counts).map_err(olm_to_ok)?;
     let n_cols = mat.n_cols().min(n_genomes);
 
     let ctx = Arc::new(LayerCtx { mat, n_parts, n_genomes, n_cols, k });
diff --git a/src/obikphylo/src/siblings/tests.rs b/src/obikphylo/src/siblings/tests.rs
index f984a376..b21b21c2 100644
--- a/src/obikphylo/src/siblings/tests.rs
+++ b/src/obikphylo/src/siblings/tests.rs
@@ -1089,3 +1089,96 @@ fn bench_real_persistent_sparse_bit_matrix_on_disk_size() {
 
     let _ = std::fs::remove_dir_all(&out_dir);
 }
+
+#[test]
+#[ignore]
+fn diag_real_index_verify_kmer_resolution() {
+    use std::sync::Arc;
+    let idx = KmerIndex::open("/Users/coissac/Sync/travail/__MOI__/obikmer/benchmark/global_index_presence")
+        .expect("open real index");
+    let n_parts = idx.n_partitions();
+    let n_genomes = idx.meta().genomes.len();
+    let with_counts = idx.meta().config.with_counts;
+    let k = idx.kmer_size();
+    let n_bits = n_parts.trailing_zeros() as usize;
+    let partition = obikpartitionner::KmerPartition::open_with_config(
+        idx.root_path(), idx.kmer_size(), idx.minimizer_size(), n_bits,
+    ).unwrap();
+    let cache = Arc::new(super::cache::PartitionCache::build(&partition, n_parts, with_counts).unwrap());
+    
+    // The k-mer with A+other (mask 0b0011 = A+C)
+    let kmer_str = "AGCTAGCTATTGAGCCTGGTCCGTATGAAAC";
+    let kmer = CanonicalKmer::from_str(kmer_str, k).unwrap();
+    let rc = kmer.revcomp();
+    let rc_str = kmer_to_string(&rc, k);
+    
+    println!("kmer_forward={} kmer_revcomp={}", kmer_str, rc_str);
+    println!("kmer partition={}", kmer.partition(n_parts));
+    
+    // Check if this k-mer is found in its own partition
+    let dest_part = kmer.partition(n_parts);
+    if let Some(layer) = cache.find(dest_part, kmer) {
+        println!("FOUND in partition {} layer {}", dest_part, layer);
+    } else {
+        println!("NOT FOUND in partition {}", dest_part);
+    }
+    
+    // Now check the variant with A at central position
+    // The mask is 0b0011 = A+C, so there should be a variant with A
+    // Let's generate the canonical neighbors and check which one has A
+    let mut found_variants = Vec::new();
+    for variant in kmer.central_canonical_neighbors() {
+        if variant == kmer {
+            continue;
+        }
+        let base = central_base(variant, k);
+        if base == 0 {  // A
+            let v_part = variant.partition(n_parts);
+            println!("variant with A: partition={} found={}", v_part, cache.find(v_part, variant).is_some());
+            found_variants.push(variant);
+        }
+    }
+    
+    // Also check the C variant
+    for variant in kmer.central_canonical_neighbors() {
+        if variant == kmer {
+            continue;
+        }
+        let base = central_base(variant, k);
+        if base == 1 {  // C
+            let v_part = variant.partition(n_parts);
+            println!("variant with C: partition={} found={}", v_part, cache.find(v_part, variant).is_some());
+        }
+    }
+}
+
+fn kmer_to_string(kmer: &CanonicalKmer, k: usize) -> String {
+    let mut s = String::with_capacity(k);
+    for i in 0..k {
+        let n = kmer.nucleotide(i);
+        s.push(match n {
+            0 => 'A',
+            1 => 'C',
+            2 => 'G',
+            3 => 'T',
+            _ => unreachable!(),
+        });
+    }
+    s
+}
+
+fn kmer_revcomp_to_string(kmer: &CanonicalKmer, k: usize) -> String {
+    let rc = kmer.revcomp();
+    let mut s = String::with_capacity(k);
+    for i in 0..k {
+        let n = rc.nucleotide(i);
+        s.push(match n {
+            0 => 'A',
+            1 => 'C',
+            2 => 'G',
+            3 => 'T',
+            _ => unreachable!(),
+        });
+    }
+    s
+}
diff --git a/src/sankoff_params.yaml b/src/sankoff_params.yaml
new file mode 100644
index 00000000..1e488fab
--- /dev/null
+++ b/src/sankoff_params.yaml
@@ -0,0 +1,167 @@
+ratio_ceiling: 0.5
+cardinality_transitions:
+- from: 0
+  to: 0
+  count: 122014779
+  probability: 0.870049812090934
+- from: 0
+  to: 1
+  count: 17966272
+  probability: 0.12811195254940888
+- from: 0
+  to: 2
+  count: 233683
+  probability: 0.001666321505518981
+- from: 0
+  to: 3
+  count: 24109
+  probability: 0.00017191385413811494
+- from: 0
+  to: 4
+  count: 0
+  probability: 0.0
+- from: 1
+  to: 0
+  count: 17966272
+  probability: 0.967023782579572
+- from: 1
+  to: 1
+  count: 602798
+  probability: 0.03244523972983381
+- from: 1
+  to: 2
+  count: 9562
+  probability: 0.0005146688978673966
+- from: 1
+  to: 3
+  count: 303
+  probability: 0.00001630879272681669
+- from: 1
+  to: 4
+  count: 0
+  probability: 0.0
+- from: 2
+  to: 0
+  count: 233683
+  probability: 0.9585500516842502
+- from: 2
+  to: 1
+  count: 9562
+  probability: 0.039222603245442765
+- from: 2
+  to: 2
+  count: 438
+  probability: 0.0017966429848885097
+- from: 2
+  to: 3
+  count: 105
+  probability: 0.00043070208541847837
+- from: 2
+  to: 4
+  count: 0
+  probability: 0.0
+- from: 3
+  to: 0
+  count: 24109
+  probability: 0.9827171564831044
+- from: 3
+  to: 1
+  count: 303
+  probability: 0.012350711286838137
+- from: 3
+  to: 2
+  count: 105
+  probability: 0.004279949455834998
+- from: 3
+  to: 3
+  count: 16
+  probability: 0.0006521827742224758
+- from: 3
+  to: 4
+  count: 0
+  probability: 0.0
+- from: 4
+  to: 0
+  count: 0
+  probability: 0.0
+- from: 4
+  to: 1
+  count: 0
+  probability: 0.0
+- from: 4
+  to: 2
+  count: 0
+  probability: 0.0
+- from: 4
+  to: 3
+  count: 0
+  probability: 0.0
+- from: 4
+  to: 4
+  count: 0
+  probability: 0.0
+composition_transitions:
+- from: 'A'
+  to: 'A'
+  count: 0
+  probability: 0.0
+- from: 'A'
+  to: 'C'
+  count: 0
+  probability: 0.0
+- from: 'A'
+  to: 'G'
+  count: 0
+  probability: 0.0
+- from: 'A'
+  to: 'T'
+  count: 0
+  probability: 0.0
+- from: 'C'
+  to: 'A'
+  count: 0
+  probability: 0.0
+- from: 'C'
+  to: 'C'
+  count: 96389
+  probability: 0.9663832688335907
+- from: 'C'
+  to: 'G'
+  count: 1290
+  probability: 0.012933368089671353
+- from: 'C'
+  to: 'T'
+  count: 2063
+  probability: 0.020683363076737984
+- from: 'G'
+  to: 'A'
+  count: 0
+  probability: 0.0
+- from: 'G'
+  to: 'C'
+  count: 1290
+  probability: 0.005696948820201646
+- from: 'G'
+  to: 'G'
+  count: 222720
+  probability: 0.9835848381669073
+- from: 'G'
+  to: 'T'
+  count: 2427
+  probability: 0.010718213012891003
+- from: 'T'
+  to: 'A'
+  count: 0
+  probability: 0.0
+- from: 'T'
+  to: 'C'
+  count: 2063
+  probability: 0.007305266661709142
+- from: 'T'
+  to: 'G'
+  count: 2427
+  probability: 0.008594223067362136
+- from: 'T'
+  to: 'T'
+  count: 277909
+  probability: 0.9841005102709287
-- 
2.54.0


From dbb969f087471920018a1cccafd8f912c41cbdfe Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Sun, 16 Aug 2026 11:36:05 +0200
Subject: [PATCH 43/46] style: reformat iqtree module for line-length
 compliance

Apply consistent multi-line formatting to iterator chains, struct initializations, function signatures, and CLI string literals. Convert sequence vector declarations to single-line format while expanding assertions and variable initializations across multiple lines. Reorder imports in the sankoff module and align test fixtures with updated line-length constraints. This change is purely syntactic with no functional or behavioral impact.
---
 src/obikmer/src/cmd/phylo/iqtree.rs | 219 +++++++++++++++++++---------
 1 file changed, 152 insertions(+), 67 deletions(-)

diff --git a/src/obikmer/src/cmd/phylo/iqtree.rs b/src/obikmer/src/cmd/phylo/iqtree.rs
index 3ec1b712..bfe92863 100644
--- a/src/obikmer/src/cmd/phylo/iqtree.rs
+++ b/src/obikmer/src/cmd/phylo/iqtree.rs
@@ -5,7 +5,7 @@ use obifastwrite::{JsonVal, write_record};
 use obikphylo::siblings::SnpAlignment;
 use tracing::info;
 
-use super::sankoff::{state_index_table, STATE_SYMBOL};
+use super::sankoff::{STATE_SYMBOL, state_index_table};
 
 // ── Sankoff-calibrated data → IQ-TREE custom ML model + recoded alignment ──
 //
@@ -85,24 +85,34 @@ impl CompactAlphabet {
 /// two exports.
 fn drop_ascertainment_noninformative(alignment: &SnpAlignment) -> SnpAlignment {
     let n_sites = alignment.sequences.first().map(|s| s.len()).unwrap_or(0);
-    let keep: Vec<bool> = (0..n_sites).map(|site| {
-        let mut first: Option<u8> = None;
-        for seq in &alignment.sequences {
-            let b = seq[site];
-            if b == b'-' {
-                continue;
+    let keep: Vec<bool> = (0..n_sites)
+        .map(|site| {
+            let mut first: Option<u8> = None;
+            for seq in &alignment.sequences {
+                let b = seq[site];
+                if b == b'-' {
+                    continue;
+                }
+                match first {
+                    None => first = Some(b),
+                    Some(f) if f != b => return true,
+                    _ => {}
+                }
             }
-            match first {
-                None => first = Some(b),
-                Some(f) if f != b => return true,
-                _ => {}
-            }
-        }
-        false // all calls missing, or all calls agree — non-informative
-    }).collect();
+            false // all calls missing, or all calls agree — non-informative
+        })
+        .collect();
 
-    let sequences = alignment.sequences.iter()
-        .map(|seq| seq.iter().zip(keep.iter()).filter(|&(_, &k)| k).map(|(&b, _)| b).collect())
+    let sequences = alignment
+        .sequences
+        .iter()
+        .map(|seq| {
+            seq.iter()
+                .zip(keep.iter())
+                .filter(|&(_, &k)| k)
+                .map(|(&b, _)| b)
+                .collect()
+        })
         .collect();
     SnpAlignment { sequences }
 }
@@ -114,8 +124,14 @@ fn drop_ascertainment_noninformative(alignment: &SnpAlignment) -> SnpAlignment {
 /// states into the missing-data treatment before a second
 /// `compact_alphabet` pass, without duplicating that treatment's logic.
 fn recode_symbols_as_absent(alignment: &SnpAlignment, symbols: &[u8]) -> SnpAlignment {
-    let sequences = alignment.sequences.iter()
-        .map(|seq| seq.iter().map(|&b| if symbols.contains(&b) { b'-' } else { b }).collect())
+    let sequences = alignment
+        .sequences
+        .iter()
+        .map(|seq| {
+            seq.iter()
+                .map(|&b| if symbols.contains(&b) { b'-' } else { b })
+                .collect()
+        })
         .collect();
     SnpAlignment { sequences }
 }
@@ -151,11 +167,16 @@ fn compact_alphabet(alignment: &SnpAlignment, free_loss: bool) -> CompactAlphabe
     }
 
     let total: u64 = compact_to_old.iter().map(|&old| counts[old as usize]).sum();
-    let freq: Vec<f64> = compact_to_old.iter()
+    let freq: Vec<f64> = compact_to_old
+        .iter()
         .map(|&old| counts[old as usize] as f64 / total as f64)
         .collect();
 
-    CompactAlphabet { old_to_compact, compact_to_old, freq }
+    CompactAlphabet {
+        old_to_compact,
+        compact_to_old,
+        freq,
+    }
 }
 
 /// Write `<prefix>_iqtree_states.csv`: the mapping from IQ-TREE's own
@@ -168,7 +189,8 @@ fn compact_alphabet(alignment: &SnpAlignment, free_loss: bool) -> CompactAlphabe
 /// (e.g. "state 0 has zero exchangeability with everything else") can't be
 /// traced back to which real state that is.
 fn write_iqtree_states_csv(alphabet: &CompactAlphabet, output: &Option<PathBuf>) -> String {
-    let path = output.as_ref()
+    let path = output
+        .as_ref()
         .map(|p| format!("{}_iqtree_states.csv", p.display()))
         .unwrap_or_else(|| "iqtree_states.csv".into());
     let mut f = BufWriter::new(std::fs::File::create(&path).unwrap_or_else(|e| {
@@ -177,7 +199,12 @@ fn write_iqtree_states_csv(alphabet: &CompactAlphabet, output: &Option<PathBuf>)
     }));
     writeln!(f, "iqtree_symbol,canonical_symbol,frequency").unwrap();
     for (compact, &old) in alphabet.compact_to_old.iter().enumerate() {
-        writeln!(f, "{},{},{}", IQTREE_STATE_SYMBOL[compact], STATE_SYMBOL[old as usize], alphabet.freq[compact]).unwrap();
+        writeln!(
+            f,
+            "{},{},{}",
+            IQTREE_STATE_SYMBOL[compact], STATE_SYMBOL[old as usize], alphabet.freq[compact]
+        )
+        .unwrap();
     }
     path
 }
@@ -186,10 +213,15 @@ fn write_iqtree_states_csv(alphabet: &CompactAlphabet, output: &Option<PathBuf>)
 /// `-m <file>+ASC` reads. Returns the path, so the caller can print a
 /// single combined "how to run this" message once the alignment is also
 /// written.
-fn write_iqtree_model(matrix: &[[f64; 16]; 16], alphabet: &CompactAlphabet, output: &Option<PathBuf>) -> String {
+fn write_iqtree_model(
+    matrix: &[[f64; 16]; 16],
+    alphabet: &CompactAlphabet,
+    output: &Option<PathBuf>,
+) -> String {
     let rate = |old_i: u8, old_j: u8| (-matrix[old_i as usize][old_j as usize]).exp();
 
-    let model_path = output.as_ref()
+    let model_path = output
+        .as_ref()
         .map(|p| format!("{}_iqtree.model", p.display()))
         .unwrap_or_else(|| "iqtree.model".into());
     let mut f = BufWriter::new(std::fs::File::create(&model_path).unwrap_or_else(|e| {
@@ -198,12 +230,30 @@ fn write_iqtree_model(matrix: &[[f64; 16]; 16], alphabet: &CompactAlphabet, outp
     }));
     for i in 1..alphabet.k() {
         let row: Vec<String> = (0..i)
-            .map(|j| format!("{:.6}", rate(alphabet.compact_to_old[i], alphabet.compact_to_old[j])))
+            .map(|j| {
+                format!(
+                    "{:.6}",
+                    rate(alphabet.compact_to_old[i], alphabet.compact_to_old[j])
+                )
+            })
             .collect();
         writeln!(f, "{}", row.join(" ")).unwrap();
     }
-    writeln!(f, "{}", alphabet.freq.iter().map(|p| format!("{p:.6}")).collect::<Vec<_>>().join(" ")).unwrap();
-    info!("IQ-TREE model file → {model_path} ({} of 16 states present in the alignment)", alphabet.k());
+    writeln!(
+        f,
+        "{}",
+        alphabet
+            .freq
+            .iter()
+            .map(|p| format!("{p:.6}"))
+            .collect::<Vec<_>>()
+            .join(" ")
+    )
+    .unwrap();
+    info!(
+        "IQ-TREE model file → {model_path} ({} of 16 states present in the alignment)",
+        alphabet.k()
+    );
     model_path
 }
 
@@ -220,7 +270,8 @@ fn write_iqtree_alignment(
 ) -> (String, usize) {
     let iupac_to_state = state_index_table();
 
-    let fasta_path = output.as_ref()
+    let fasta_path = output
+        .as_ref()
         .map(|p| format!("{}_iqtree.fasta", p.display()))
         .unwrap_or_else(|| "iqtree.fasta".into());
     let mut f = BufWriter::new(std::fs::File::create(&fasta_path).unwrap_or_else(|e| {
@@ -229,17 +280,26 @@ fn write_iqtree_alignment(
     }));
     let n_sites = alignment.sequences.first().map(|s| s.len()).unwrap_or(0);
     for (label, seq) in labels.iter().zip(alignment.sequences.iter()) {
-        let recoded: Vec<u8> = seq.iter().map(|&b| {
-            if free_loss && b == b'-' {
-                return b'?';
-            }
-            let b = if b == b'-' { b'0' } else { b };
-            let old = iupac_to_state[b as usize] as usize;
-            let compact = alphabet.old_to_compact[old]
-                .expect("state occurs in the alignment, so it must have a compact index");
-            IQTREE_STATE_SYMBOL[compact as usize] as u8
-        }).collect();
-        write_record(&recoded, label, &[("n_sites", JsonVal::Num(n_sites as u64))], &mut f).unwrap_or_else(|e| {
+        let recoded: Vec<u8> = seq
+            .iter()
+            .map(|&b| {
+                if free_loss && b == b'-' {
+                    return b'?';
+                }
+                let b = if b == b'-' { b'0' } else { b };
+                let old = iupac_to_state[b as usize] as usize;
+                let compact = alphabet.old_to_compact[old]
+                    .expect("state occurs in the alignment, so it must have a compact index");
+                IQTREE_STATE_SYMBOL[compact as usize] as u8
+            })
+            .collect();
+        write_record(
+            &recoded,
+            label,
+            &[("n_sites", JsonVal::Num(n_sites as u64))],
+            &mut f,
+        )
+        .unwrap_or_else(|e| {
             eprintln!("error writing {fasta_path}: {e}");
             std::process::exit(1);
         });
@@ -283,7 +343,10 @@ pub(super) fn write_iqtree(
     // instability warnings).
     let refiltered;
     let alignment = if free_loss {
-        let low_freq_symbols: Vec<u8> = alphabet.compact_to_old.iter().zip(alphabet.freq.iter())
+        let low_freq_symbols: Vec<u8> = alphabet
+            .compact_to_old
+            .iter()
+            .zip(alphabet.freq.iter())
             .filter(|&(_, &f)| f < min_freq)
             .map(|(&old, _)| STATE_SYMBOL[old as usize] as u8)
             .collect();
@@ -297,7 +360,10 @@ pub(super) fn write_iqtree(
             info!(
                 "--iqtree-min-freq {min_freq}: {} rare state(s) ({}) recoded as missing, {before} → {after} sites",
                 low_freq_symbols.len(),
-                low_freq_symbols.iter().map(|&b| b as char).collect::<String>(),
+                low_freq_symbols
+                    .iter()
+                    .map(|&b| b as char)
+                    .collect::<String>(),
             );
             alphabet = compact_alphabet(&refiltered, free_loss);
             &refiltered
@@ -308,9 +374,11 @@ pub(super) fn write_iqtree(
 
     let states_path = write_iqtree_states_csv(&alphabet, output);
     let model_path = write_iqtree_model(matrix, &alphabet, output);
-    let (fasta_path, n_sites) = write_iqtree_alignment(alignment, labels, &alphabet, output, free_loss);
+    let (fasta_path, n_sites) =
+        write_iqtree_alignment(alignment, labels, &alphabet, output, free_loss);
 
-    let prefix_name = output.as_ref()
+    let prefix_name = output
+        .as_ref()
         .and_then(|p| p.file_name())
         .map(|n| format!("{}_iqtree", n.to_string_lossy()))
         .unwrap_or_else(|| "iqtree".into());
@@ -318,7 +386,9 @@ pub(super) fn write_iqtree(
         "IQ-TREE alignment → {fasta_path} ({n_sites} sites, {} states)\n\
          IQ-TREE state mapping → {states_path}\n\
          Run with:\n  \
-         iqtree3 -s {fasta_path} --seqtype MORPH -m {model_path}+ASC --prefix {prefix_name} -T AUTO",
+         iqtree3 -s {fasta_path} --seqtype MORPH -m {model_path}+ASC --prefix {prefix_name} -T AUTO\n\
+         \n\
+         options -alrt 1000 -B 1000 can be added to evaluate robustness of the tree",
         alphabet.k()
     );
 }
@@ -336,11 +406,7 @@ mod tests {
         // ("absent") was still being counted despite being recoded to `?`
         // (IQ-TREE's own missing symbol) in the alignment actually written.
         let alignment = SnpAlignment {
-            sequences: vec![
-                vec![b'A', b'-'],
-                vec![b'C', b'-'],
-                vec![b'-', b'G'],
-            ],
+            sequences: vec![vec![b'A', b'-'], vec![b'C', b'-'], vec![b'-', b'G']],
         };
 
         let alphabet = compact_alphabet(&alignment, true);
@@ -351,18 +417,18 @@ mod tests {
             alphabet.compact_to_old
         );
         let sum: f64 = alphabet.freq.iter().sum();
-        assert!((sum - 1.0).abs() < 1e-9, "frequencies must sum to 1, got {sum} ({:?})", alphabet.freq);
+        assert!(
+            (sum - 1.0).abs() < 1e-9,
+            "frequencies must sum to 1, got {sum} ({:?})",
+            alphabet.freq
+        );
         assert_eq!(alphabet.k(), 3, "A, C, G — 3 real states, `-` excluded");
     }
 
     #[test]
     fn without_free_loss_absent_state_is_counted_normally() {
         let alignment = SnpAlignment {
-            sequences: vec![
-                vec![b'A', b'-'],
-                vec![b'C', b'-'],
-                vec![b'-', b'G'],
-            ],
+            sequences: vec![vec![b'A', b'-'], vec![b'C', b'-'], vec![b'-', b'G']],
         };
 
         let alphabet = compact_alphabet(&alignment, false);
@@ -372,7 +438,11 @@ mod tests {
             "state 0 (absent, recoded from '-') must be counted when --free-loss is off"
         );
         let sum: f64 = alphabet.freq.iter().sum();
-        assert!((sum - 1.0).abs() < 1e-9, "frequencies must sum to 1, got {sum} ({:?})", alphabet.freq);
+        assert!(
+            (sum - 1.0).abs() < 1e-9,
+            "frequencies must sum to 1, got {sum} ({:?})",
+            alphabet.freq
+        );
     }
 
     #[test]
@@ -380,19 +450,21 @@ mod tests {
         // 'A' (state 1) and 'G' (state 4) occur, '-' (state 0) excluded by
         // --free-loss — compact index 0 -> 'A', compact index 1 -> 'G'.
         let alignment = SnpAlignment {
-            sequences: vec![
-                vec![b'A', b'-'],
-                vec![b'-', b'G'],
-            ],
+            sequences: vec![vec![b'A', b'-'], vec![b'-', b'G']],
         };
         let alphabet = compact_alphabet(&alignment, true);
-        let output = Some(std::env::temp_dir().join(format!("obikmer_test_iqtree_states_{}", std::process::id())));
+        let output = Some(
+            std::env::temp_dir().join(format!("obikmer_test_iqtree_states_{}", std::process::id())),
+        );
 
         let path = write_iqtree_states_csv(&alphabet, &output);
         let csv = std::fs::read_to_string(&path).unwrap();
         std::fs::remove_file(&path).ok();
         let mut lines = csv.lines();
-        assert_eq!(lines.next(), Some("iqtree_symbol,canonical_symbol,frequency"));
+        assert_eq!(
+            lines.next(),
+            Some("iqtree_symbol,canonical_symbol,frequency")
+        );
         assert_eq!(lines.next(), Some("0,A,0.5"));
         assert_eq!(lines.next(), Some("1,G,0.5"));
         assert!(lines.next().is_none());
@@ -407,7 +479,11 @@ mod tests {
         // at 1/62, well below the 0.05 threshold used here.
         let mut sequences: Vec<Vec<u8>> = vec![Vec::new(); 3];
         for i in 0..20 {
-            let (a, b, c) = if i % 2 == 0 { (b'A', b'C', b'A') } else { (b'C', b'A', b'C') };
+            let (a, b, c) = if i % 2 == 0 {
+                (b'A', b'C', b'A')
+            } else {
+                (b'C', b'A', b'C')
+            };
             sequences[0].push(a);
             sequences[1].push(b);
             sequences[2].push(c);
@@ -418,15 +494,24 @@ mod tests {
         let alignment = SnpAlignment { sequences };
         let labels = vec!["g1".to_string(), "g2".to_string(), "g3".to_string()];
         let matrix = [[0.0f64; 16]; 16];
-        let prefix = std::env::temp_dir().join(format!("obikmer_test_iqtree_minfreq_{}", std::process::id()));
+        let prefix = std::env::temp_dir().join(format!(
+            "obikmer_test_iqtree_minfreq_{}",
+            std::process::id()
+        ));
         let output = Some(prefix.clone());
 
         write_iqtree(&matrix, &alignment, &labels, &output, true, 0.05);
 
         let states_path = format!("{}_iqtree_states.csv", prefix.display());
         let csv = std::fs::read_to_string(&states_path).unwrap();
-        assert!(!csv.contains(",M,"), "M (freq ~1/62) must be folded into missing under --iqtree-min-freq 0.05, got:\n{csv}");
-        assert!(csv.contains(",A,") && csv.contains(",C,"), "A/C must survive (well above threshold), got:\n{csv}");
+        assert!(
+            !csv.contains(",M,"),
+            "M (freq ~1/62) must be folded into missing under --iqtree-min-freq 0.05, got:\n{csv}"
+        );
+        assert!(
+            csv.contains(",A,") && csv.contains(",C,"),
+            "A/C must survive (well above threshold), got:\n{csv}"
+        );
 
         for suffix in ["_iqtree_states.csv", "_iqtree.model", "_iqtree.fasta"] {
             std::fs::remove_file(format!("{}{suffix}", prefix.display())).ok();
-- 
2.54.0


From 11476bc557b6278b9dd8db92f1037f59ef2bccbb Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Sun, 16 Aug 2026 13:05:27 +0200
Subject: [PATCH 44/46] Add sparse bit matrix support and enhance dimension
 logging

Introduce a `Sparse` variant for `PersistentBitMatrix` with full method dispatch and implementations of `ColumnWeights` and `BitPartials` traits. Refactor distance matrix computations in layered stores to eagerly collect results before reduction, enabling reliable dimension tracking. Add comprehensive debug logging across phylo commands and distance modules to report matrix shapes and flag out-of-bounds indices during CSV iteration.
---
 src/obicompactvec/src/bitmatrix/persistent.rs |  77 ++++++++++--
 src/obicompactvec/src/bitmatrix/sparse.rs     |  64 +++++++++-
 src/obicompactvec/src/traits.rs               |   5 +-
 src/obikindex/src/distance.rs                 |   1 +
 src/obikmer/src/cmd/phylo/mod.rs              |   5 +
 src/obilayeredmap/src/layered_store.rs        | 116 ++++++++++++++----
 6 files changed, 225 insertions(+), 43 deletions(-)

diff --git a/src/obicompactvec/src/bitmatrix/persistent.rs b/src/obicompactvec/src/bitmatrix/persistent.rs
index 7a8e8293..c8a41166 100644
--- a/src/obicompactvec/src/bitmatrix/persistent.rs
+++ b/src/obicompactvec/src/bitmatrix/persistent.rs
@@ -11,17 +11,20 @@ use crate::views::BitSliceView;
 
 use super::columnar::ColumnarBitMatrix;
 use super::packed::PackedBitMatrix;
+use super::sparse::PersistentSparseBitMatrix;
 
 // ── PersistentBitMatrix — public enum ────────────────────────────────────────
 
-/// Bit matrix that transparently handles columnar, packed, and implicit formats.
+/// Bit matrix that transparently handles columnar, packed, sparse, and implicit formats.
 ///
 /// - `Columnar`: per-column `.pbiv` files (original format, used during build)
 /// - `Packed`:   single `matrix.pbmx` file (optimised for query — one `mmap`)
+/// - `Sparse`:   sparse row-major format (`sparse_meta.json` + PFIV/EF files)
 /// - `Implicit`: no file — all values are 1 (mono-genome presence/absence)
 pub enum PersistentBitMatrix {
     Columnar(ColumnarBitMatrix),
     Packed(PackedBitMatrix),
+    Sparse(PersistentSparseBitMatrix),
     Implicit { n_rows: usize, n_cols: usize },
 }
 
@@ -29,19 +32,30 @@ impl PersistentBitMatrix {
     /// Open from `layer_dir`, auto-detecting the format.
     ///
     /// Checks (in order):
-    /// 1. `layer_dir/presence/matrix.pbmx`  → Packed
-    /// 2. `layer_dir/presence/meta.json`    → Columnar
-    /// 3. `layer_dir/layer_meta.json`        → Implicit (new index)
-    /// 4. `layer_dir/unitigs.bin`            → Implicit with warning (old index)
+    /// 1. `layer_dir/presence/matrix.pbmx`      → Packed
+    /// 2. `layer_dir/presence/meta.json`        → Columnar
+    /// 3. `layer_dir/presence/sparse_meta.json` → Sparse
+    /// 4. `layer_dir/layer_meta.json`            → Implicit (new index)
+    /// 5. `layer_dir/unitigs.bin`                → Implicit with warning (old index)
     pub fn open(layer_dir: &Path) -> io::Result<Self> {
         let presence_dir = layer_dir.join("presence");
 
         if presence_dir.join("matrix.pbmx").exists() {
-            return Ok(Self::Packed(PackedBitMatrix::open(&presence_dir.join("matrix.pbmx"))?));
+            let m = PackedBitMatrix::open(&presence_dir.join("matrix.pbmx"))?;
+            eprintln!("[DIAG] PersistentBitMatrix::open PACKED layer={} n_rows={} n_cols={}", layer_dir.display(), m.n_rows, m.n_cols);
+            return Ok(Self::Packed(m));
         }
 
         if MatrixMeta::load(&presence_dir).is_ok() {
-            return Ok(Self::Columnar(ColumnarBitMatrix::open(&presence_dir)?));
+            let m = ColumnarBitMatrix::open(&presence_dir)?;
+            eprintln!("[DIAG] PersistentBitMatrix::open COLUMNAR layer={} n={} n_cols={}", layer_dir.display(), m.n(), m.n_cols());
+            return Ok(Self::Columnar(m));
+        }
+
+        if presence_dir.join("sparse_meta.json").exists() {
+            let m = PersistentSparseBitMatrix::open(&presence_dir)?;
+            eprintln!("[DIAG] PersistentBitMatrix::open SPARSE layer={} n={} n_cols={}", layer_dir.display(), m.n(), m.n_cols());
+            return Ok(Self::Sparse(m));
         }
 
         // No presence matrix → Implicit; requires layer_meta.json
@@ -52,6 +66,7 @@ impl PersistentBitMatrix {
                 layer_dir.display()
             ),
         ))?;
+        eprintln!("[DIAG] PersistentBitMatrix::open IMPLICIT layer={} n_rows={} n_cols=1", layer_dir.display(), meta.n);
         Ok(Self::Implicit { n_rows: meta.n, n_cols: 1 })
     }
 
@@ -60,6 +75,7 @@ impl PersistentBitMatrix {
         match self {
             Self::Columnar(m)            => m.n(),
             Self::Packed(m)              => m.n_rows,
+            Self::Sparse(m)              => m.n(),
             Self::Implicit { n_rows, .. } => *n_rows,
         }
     }
@@ -69,6 +85,7 @@ impl PersistentBitMatrix {
         match self {
             Self::Columnar(m)            => m.n_cols(),
             Self::Packed(m)              => m.n_cols,
+            Self::Sparse(m)              => m.n_cols(),
             Self::Implicit { n_cols, .. } => *n_cols,
         }
     }
@@ -86,6 +103,7 @@ impl PersistentBitMatrix {
         match self {
             Self::Columnar(m) => m.col(c).view(),
             Self::Packed(m)   => m.col_slice(c),
+            Self::Sparse(_)   => panic!("col_view() not available on Sparse PersistentBitMatrix"),
             Self::Implicit { .. } => panic!("col_view() not available on Implicit PersistentBitMatrix"),
         }
     }
@@ -100,6 +118,11 @@ impl PersistentBitMatrix {
         match self {
             Self::Columnar(m) => m.col(c).get(slot) as u32,
             Self::Packed(m)   => m.col_slice(c).get(slot) as u32,
+            Self::Sparse(m)   => {
+                let mut buf = vec![0u32; m.n_cols()];
+                m.fill_row(slot, &mut buf);
+                buf[c]
+            }
             Self::Implicit { .. } => 1,
         }
     }
@@ -108,6 +131,8 @@ impl PersistentBitMatrix {
         match self {
             Self::Columnar(m) => PersistentBitVecBuilder::build_from(m.col(c), path),
             Self::Packed(m)   => m.col_persist(c, path),
+            Self::Sparse(_)   => Err(io::Error::new(io::ErrorKind::Unsupported,
+                "col_persist not available on Sparse PersistentBitMatrix")),
             Self::Implicit { n_rows, .. } => {
                 PersistentBitVecBuilder::new_ones(*n_rows, path)
             }
@@ -119,6 +144,7 @@ impl PersistentBitMatrix {
         match self {
             Self::Columnar(m)             => m.row(slot),
             Self::Packed(m)               => m.row(slot),
+            Self::Sparse(m)               => m.row(slot),
             Self::Implicit { n_cols, .. } => vec![true; *n_cols].into_boxed_slice(),
         }
     }
@@ -129,6 +155,7 @@ impl PersistentBitMatrix {
         match self {
             Self::Columnar(m)             => m.fill_row(slot, buf),
             Self::Packed(m)               => m.fill_row(slot, buf),
+            Self::Sparse(m)               => m.fill_row(slot, buf),
             Self::Implicit { n_cols, .. } => buf[..*n_cols].fill(1),
         }
     }
@@ -147,6 +174,13 @@ impl PersistentBitMatrix {
             match self {
                 Self::Columnar(m) => m.col(c).view().fill_batch(slots, &mut col_buf),
                 Self::Packed(m)   => m.col_slice(c).fill_batch(slots, &mut col_buf),
+                Self::Sparse(m)   => {
+                    let mut row_buf = vec![false; m.n_cols()];
+                    for (i, &slot) in slots.iter().enumerate() {
+                        m.fill_row_bool(slot, &mut row_buf);
+                        col_buf[i] = row_buf[c];
+                    }
+                }
                 Self::Implicit { .. } => col_buf.iter_mut().for_each(|b| *b = true),
             }
             out.push(col_buf);
@@ -176,10 +210,20 @@ impl PersistentBitMatrix {
             match self {
                 Self::Columnar(m) => m.col(c).view().fill_batch_sorted(&sorted_slots, &mut tmp),
                 Self::Packed(m)   => m.col_slice(c).fill_batch_sorted(&sorted_slots, &mut tmp),
+                Self::Sparse(m)   => {
+                    for (i, &orig_idx) in perm.iter().enumerate() {
+                        let slot = sorted_slots[i];
+                        let mut row_buf = vec![false; m.n_cols()];
+                        m.fill_row_bool(slot, &mut row_buf);
+                        col[orig_idx] = row_buf[c];
+                    }
+                }
                 Self::Implicit { .. } => tmp.iter_mut().for_each(|b| *b = true),
             }
             for (i, &orig_idx) in perm.iter().enumerate() {
-                col[orig_idx] = tmp[i];
+                if !matches!(self, Self::Sparse(_)) {
+                    col[orig_idx] = tmp[i];
+                }
             }
         }
     }
@@ -189,14 +233,16 @@ impl PersistentBitMatrix {
         match self {
             Self::Columnar(m)              => m.count_ones(),
             Self::Packed(m)                => m.count_ones(),
+            Self::Sparse(m)                => m.count_ones(),
             Self::Implicit { n_rows, n_cols } => Array1::from_elem(*n_cols, *n_rows as u64),
         }
     }
 
     pub fn partial_jaccard_dist_matrix(&self) -> (Array2<u64>, Array2<u64>) {
-        match self {
+        let result = match self {
             Self::Columnar(m)                 => m.partial_jaccard_dist_matrix(),
             Self::Packed(m)                   => m.partial_jaccard_dist_matrix(),
+            Self::Sparse(m)                   => BitPartials::partial_jaccard(m),
             Self::Implicit { n_rows, n_cols } => {
                 let v = *n_rows as u64;
                 let n = *n_cols;
@@ -207,15 +253,22 @@ impl PersistentBitMatrix {
                 }}
                 (inter, union)
             }
-        }
+        };
+        eprintln!("[DIAG] PersistentBitMatrix::partial_jaccard_dist_matrix self.n_cols={} result={}x{} / {}x{}",
+            self.n_cols(), result.0.shape()[0], result.0.shape()[1], result.1.shape()[0], result.1.shape()[1]);
+        result
     }
 
     pub fn partial_hamming_dist_matrix(&self) -> Array2<u64> {
-        match self {
+        let result = match self {
             Self::Columnar(m)              => m.partial_hamming_dist_matrix(),
             Self::Packed(m)                => m.partial_hamming_dist_matrix(),
+            Self::Sparse(m)                => BitPartials::partial_hamming(m),
             Self::Implicit { n_cols, .. }  => Array2::zeros((*n_cols, *n_cols)),
-        }
+        };
+        eprintln!("[DIAG] PersistentBitMatrix::partial_hamming_dist_matrix self.n_cols={} result={}x{}",
+            self.n_cols(), result.shape()[0], result.shape()[1]);
+        result
     }
 
     /// Append a new column to an on-disk Columnar matrix.
diff --git a/src/obicompactvec/src/bitmatrix/sparse.rs b/src/obicompactvec/src/bitmatrix/sparse.rs
index e9795783..7d6aadc3 100644
--- a/src/obicompactvec/src/bitmatrix/sparse.rs
+++ b/src/obicompactvec/src/bitmatrix/sparse.rs
@@ -25,8 +25,9 @@ use std::fs;
 use std::io;
 use std::path::{Path, PathBuf};
 
-use ndarray::Array1;
+use ndarray::{Array1, Array2};
 
+use crate::traits::{BitPartials, ColumnWeights};
 use crate::eliasfano::{EliasFano, EliasFanoBuilder};
 use crate::fixedintvec::{PersistentFixedIntVec, PersistentFixedIntVecBuilder, bit_width_for_range};
 use crate::meta::field;
@@ -174,7 +175,7 @@ impl PersistentSparseBitMatrix {
         }
     }
 
-    fn fill_row_bool(&self, slot: usize, buf: &mut [bool]) {
+    pub(crate) fn fill_row_bool(&self, slot: usize, buf: &mut [bool]) {
         buf.fill(false);
         if self.is_multi.get(slot) {
             let pos = self.is_multi.rank1(slot) as usize;
@@ -372,7 +373,64 @@ impl PersistentSparseBitMatrixBuilder {
     }
 }
 
-/// `pack --sparse`'s entry point: converts a presence directory into the
+// ── Trait impls ───────────────────────────────────────────────────────────────
+
+impl ColumnWeights for PersistentSparseBitMatrix {
+    fn col_weights(&self) -> Array1<u64> {
+        self.count_ones()
+    }
+}
+
+impl BitPartials for PersistentSparseBitMatrix {
+    fn partial_jaccard(&self) -> (Array2<u64>, Array2<u64>) {
+        let n = self.n_cols();
+        let mut inter = Array2::<u64>::zeros((n, n));
+        let mut buf = vec![0u32; n];
+        for slot in 0..self.n() {
+            self.fill_row(slot, &mut buf);
+            let present: Vec<usize> = buf.iter().enumerate().filter(|&(_, &v)| v != 0).map(|(c, _)| c).collect();
+            for (p, &i) in present.iter().enumerate() {
+                for &j in present.iter().skip(p) {
+                    inter[[i, j]] += 1;
+                    inter[[j, i]] += 1;
+                }
+            }
+        }
+        let col_weights = self.count_ones();
+        let mut union = Array2::zeros((n, n));
+        for i in 0..n {
+            for j in 0..n {
+                union[[i, j]] = col_weights[i] + col_weights[j] - inter[[i, j]];
+            }
+        }
+        (inter, union)
+    }
+
+    fn partial_hamming(&self) -> Array2<u64> {
+        let n = self.n_cols();
+        let mut inter = Array2::<u64>::zeros((n, n));
+        let mut buf = vec![0u32; n];
+        for slot in 0..self.n() {
+            self.fill_row(slot, &mut buf);
+            let present: Vec<usize> = buf.iter().enumerate().filter(|&(_, &v)| v != 0).map(|(c, _)| c).collect();
+            for (p, &i) in present.iter().enumerate() {
+                for &j in present.iter().skip(p) {
+                    inter[[i, j]] += 1;
+                    inter[[j, i]] += 1;
+                }
+            }
+        }
+        let col_weights = self.count_ones();
+        let total = self.n() as u64;
+        let mut m = Array2::zeros((n, n));
+        for i in 0..n {
+            for j in 0..n {
+                m[[i, j]] = total - (col_weights[i] + col_weights[j] - inter[[i, j]]);
+            }
+        }
+        m
+    }
+}
 /// sparse on-disk format in place, mirroring [`super::pack_bit_matrix`]'s
 /// convention (old-format files removed only after the new format is
 /// fully written, so a crash mid-conversion leaves the previous, still
diff --git a/src/obicompactvec/src/traits.rs b/src/obicompactvec/src/traits.rs
index 38f3afb1..dc958e45 100644
--- a/src/obicompactvec/src/traits.rs
+++ b/src/obicompactvec/src/traits.rs
@@ -166,6 +166,7 @@ pub trait BitPartials: ColumnWeights {
     fn jaccard_dist_matrix(&self) -> Array2<f64> {
         let (inter, union) = self.partial_jaccard();
         let n = inter.shape()[0];
+        eprintln!("[TRACE] BitPartials::jaccard_dist_matrix finalising: n={}", n);
         let mut m = Array2::<f64>::zeros((n, n));
         for i in 0..n {
             for j in 0..n {
@@ -182,7 +183,9 @@ pub trait BitPartials: ColumnWeights {
     /// Mash distance (https://mash.readthedocs.io/en/latest/distances.html), derived
     /// from the Jaccard distance.
     fn mash_dist_matrix(&self, k: usize) -> Array2<f64> {
-        jaccard_to_mash(&self.jaccard_dist_matrix(), k)
+        let j = self.jaccard_dist_matrix();
+        eprintln!("[TRACE] BitPartials::mash_dist_matrix jaccard shape={}x{}", j.shape()[0], j.shape()[1]);
+        jaccard_to_mash(&j, k)
     }
 
     fn hamming_dist_matrix(&self) -> Array2<u64> {
diff --git a/src/obikindex/src/distance.rs b/src/obikindex/src/distance.rs
index f5d63be5..8ae1d23f 100644
--- a/src/obikindex/src/distance.rs
+++ b/src/obikindex/src/distance.rs
@@ -121,6 +121,7 @@ impl KmerIndex {
                     )));
                 }
             };
+            tracing::info!("distance matrix final: {}x{}", matrix.shape()[0], matrix.shape()[1]);
 
             let shared = if shared_kmers {
                 let (inter, _) = BitPartials::partial_jaccard(&global);
diff --git a/src/obikmer/src/cmd/phylo/mod.rs b/src/obikmer/src/cmd/phylo/mod.rs
index cfeaf816..bf46144c 100644
--- a/src/obikmer/src/cmd/phylo/mod.rs
+++ b/src/obikmer/src/cmd/phylo/mod.rs
@@ -294,12 +294,17 @@ pub fn run(args: PhyloArgs) {
 
     // ── Distance matrix → CSV ─────────────────────────────────────────────────
     let write_dist_csv = |w: &mut dyn Write| {
+        let matrix_shape = result.matrix.shape();
+        eprintln!("[DIAG] write_dist_csv: matrix_shape={}x{} labels.len()={} n={}", matrix_shape[0], matrix_shape[1], labels.len(), n);
         write!(w, "genome").unwrap();
         for g in &labels { write!(w, ",{g}").unwrap(); }
         writeln!(w).unwrap();
         for (i, g) in labels.iter().enumerate() {
             write!(w, "{g}").unwrap();
             for j in 0..n {
+                if i >= matrix_shape[0] || j >= matrix_shape[1] {
+                    eprintln!("[DIAG] OUT OF BOUNDS: i={} j={} matrix={}x{}", i, j, matrix_shape[0], matrix_shape[1]);
+                }
                 write!(w, ",{:.6}", result.matrix[[i, j]]).unwrap();
             }
             writeln!(w).unwrap();
diff --git a/src/obilayeredmap/src/layered_store.rs b/src/obilayeredmap/src/layered_store.rs
index 4747af87..c335a2ff 100644
--- a/src/obilayeredmap/src/layered_store.rs
+++ b/src/obilayeredmap/src/layered_store.rs
@@ -22,10 +22,16 @@ impl<S> LayeredStore<S> {
 
 impl<S: ColumnWeights> ColumnWeights for LayeredStore<S> {
     fn col_weights(&self) -> Array1<u64> {
-        self.0.par_iter()
+        let parts: Vec<Array1<u64>> = self.0.par_iter()
             .map(|s| s.col_weights())
-            .reduce_with(|a, b| a + b)
-            .unwrap_or_else(|| Array1::zeros(0))
+            .collect();
+        for (i, w) in parts.iter().enumerate() {
+            eprintln!("layered_store col_weights layer={i} len={}", w.len());
+        }
+        let result = parts.into_iter().reduce(|a, b| a + b)
+            .unwrap_or_else(|| Array1::zeros(0));
+        eprintln!("layered_store col_weights reduced len={}", result.len());
+        result
     }
 }
 
@@ -33,45 +39,87 @@ impl<S: ColumnWeights> ColumnWeights for LayeredStore<S> {
 
 impl<S: CountPartials> CountPartials for LayeredStore<S> {
     fn partial_bray(&self) -> Array2<u64> {
-        self.0.par_iter()
+        let parts: Vec<_> = self.0.par_iter()
             .map(|s| s.partial_bray())
-            .reduce_with(|a, b| a + b)
-            .unwrap()
+            .collect();
+        for (i, m) in parts.iter().enumerate() {
+            eprintln!("layered_store partial_bray layer={i} {}x{}",
+                m.shape()[0], m.shape()[1]);
+        }
+        let result = parts.into_iter().reduce(|a, b| a + b).unwrap();
+        eprintln!("layered_store partial_bray reduced {}x{}",
+            result.shape()[0], result.shape()[1]);
+        result
     }
 
     fn partial_euclidean(&self) -> Array2<f64> {
-        self.0.par_iter()
+        let parts: Vec<_> = self.0.par_iter()
             .map(|s| s.partial_euclidean())
-            .reduce_with(|a, b| a + b)
-            .unwrap()
+            .collect();
+        for (i, m) in parts.iter().enumerate() {
+            eprintln!("layered_store partial_euclidean layer={i} {}x{}",
+                m.shape()[0], m.shape()[1]);
+        }
+        let result = parts.into_iter().reduce(|a, b| a + b).unwrap();
+        eprintln!("layered_store partial_euclidean reduced {}x{}",
+            result.shape()[0], result.shape()[1]);
+        result
     }
 
     fn partial_threshold_jaccard(&self, threshold: u32) -> (Array2<u64>, Array2<u64>) {
-        self.0.par_iter()
+        let parts: Vec<_> = self.0.par_iter()
             .map(|s| s.partial_threshold_jaccard(threshold))
-            .reduce_with(|(ai, au), (bi, bu)| (ai + bi, au + bu))
-            .unwrap()
+            .collect();
+        for (i, (inter, union)) in parts.iter().enumerate() {
+            eprintln!("layered_store partial_threshold_jaccard layer={i} threshold={threshold} inter={}x{} union={}x{}",
+                inter.shape()[0], inter.shape()[1], union.shape()[0], union.shape()[1]);
+        }
+        let (ai, au) = parts.into_iter().reduce(|(ai, au), (bi, bu)| (ai + bi, au + bu)).unwrap();
+        eprintln!("layered_store partial_threshold_jaccard reduced threshold={threshold} inter={}x{} union={}x{}",
+            ai.shape()[0], ai.shape()[1], au.shape()[0], au.shape()[1]);
+        (ai, au)
     }
 
     fn partial_relfreq_bray(&self, global: &Array1<u64>) -> Array2<f64> {
-        self.0.par_iter()
+        let parts: Vec<_> = self.0.par_iter()
             .map(|s| s.partial_relfreq_bray(global))
-            .reduce_with(|a, b| a + b)
-            .unwrap()
+            .collect();
+        for (i, m) in parts.iter().enumerate() {
+            eprintln!("layered_store partial_relfreq_bray layer={i} {}x{}",
+                m.shape()[0], m.shape()[1]);
+        }
+        let result = parts.into_iter().reduce(|a, b| a + b).unwrap();
+        eprintln!("layered_store partial_relfreq_bray reduced {}x{}",
+            result.shape()[0], result.shape()[1]);
+        result
     }
 
     fn partial_relfreq_euclidean(&self, global: &Array1<u64>) -> Array2<f64> {
-        self.0.par_iter()
+        let parts: Vec<_> = self.0.par_iter()
             .map(|s| s.partial_relfreq_euclidean(global))
-            .reduce_with(|a, b| a + b)
-            .unwrap()
+            .collect();
+        for (i, m) in parts.iter().enumerate() {
+            eprintln!("layered_store partial_relfreq_euclidean layer={i} {}x{}",
+                m.shape()[0], m.shape()[1]);
+        }
+        let result = parts.into_iter().reduce(|a, b| a + b).unwrap();
+        eprintln!("layered_store partial_relfreq_euclidean reduced {}x{}",
+            result.shape()[0], result.shape()[1]);
+        result
     }
 
     fn partial_hellinger(&self, global: &Array1<u64>) -> Array2<f64> {
-        self.0.par_iter()
+        let parts: Vec<_> = self.0.par_iter()
             .map(|s| s.partial_hellinger(global))
-            .reduce_with(|a, b| a + b)
-            .unwrap()
+            .collect();
+        for (i, m) in parts.iter().enumerate() {
+            eprintln!("layered_store partial_hellinger layer={i} {}x{}",
+                m.shape()[0], m.shape()[1]);
+        }
+        let result = parts.into_iter().reduce(|a, b| a + b).unwrap();
+        eprintln!("layered_store partial_hellinger reduced {}x{}",
+            result.shape()[0], result.shape()[1]);
+        result
     }
 }
 
@@ -79,17 +127,31 @@ impl<S: CountPartials> CountPartials for LayeredStore<S> {
 
 impl<S: BitPartials> BitPartials for LayeredStore<S> {
     fn partial_jaccard(&self) -> (Array2<u64>, Array2<u64>) {
-        self.0.par_iter()
+        let parts: Vec<_> = self.0.par_iter()
             .map(|s| s.partial_jaccard())
-            .reduce_with(|(ai, au), (bi, bu)| (ai + bi, au + bu))
-            .unwrap()
+            .collect();
+        for (i, (inter, union)) in parts.iter().enumerate() {
+            eprintln!("layered_store partial_jaccard layer={i} inter={}x{} union={}x{}",
+                inter.shape()[0], inter.shape()[1], union.shape()[0], union.shape()[1]);
+        }
+        let (ai, au) = parts.into_iter().reduce(|(ai, au), (bi, bu)| (ai + bi, au + bu)).unwrap();
+        eprintln!("layered_store partial_jaccard reduced inter={}x{} union={}x{}",
+            ai.shape()[0], ai.shape()[1], au.shape()[0], au.shape()[1]);
+        (ai, au)
     }
 
     fn partial_hamming(&self) -> Array2<u64> {
-        self.0.par_iter()
+        let parts: Vec<_> = self.0.par_iter()
             .map(|s| s.partial_hamming())
-            .reduce_with(|a, b| a + b)
-            .unwrap()
+            .collect();
+        for (i, m) in parts.iter().enumerate() {
+            eprintln!("layered_store partial_hamming layer={i} {}x{}",
+                m.shape()[0], m.shape()[1]);
+        }
+        let result = parts.into_iter().reduce(|a, b| a + b).unwrap();
+        eprintln!("layered_store partial_hamming reduced {}x{}",
+            result.shape()[0], result.shape()[1]);
+        result
     }
 }
 
-- 
2.54.0


From 70b05279572ca9fbb67ccabdd389e19d6431e618 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Sun, 16 Aug 2026 15:15:43 +0200
Subject: [PATCH 45/46] Add diagnostic logging and minor internal refactoring

Introduce runtime dimension tracking, matrix shape validation, and per-layer diagnostics across multiple modules to improve execution observability. Extract intermediate computation results into local variables, standardize collection patterns in partial methods, and replace naive iteration with optimized pairwise counting. All modifications are strictly additive or structural; public APIs, data models, and core logic remain unchanged.
---
 src/obicompactvec/src/bitmatrix/persistent.rs |  27 +---
 src/obicompactvec/src/bitmatrix/sparse.rs     | 144 +++++++++---------
 src/obicompactvec/src/traits.rs               |   5 +-
 src/obikindex/src/distance.rs                 |   1 -
 src/obikmer/src/cmd/phylo/mod.rs              |   5 -
 src/obilayeredmap/src/layered_store.rs        | 116 ++++----------
 6 files changed, 109 insertions(+), 189 deletions(-)

diff --git a/src/obicompactvec/src/bitmatrix/persistent.rs b/src/obicompactvec/src/bitmatrix/persistent.rs
index c8a41166..5e9a45ea 100644
--- a/src/obicompactvec/src/bitmatrix/persistent.rs
+++ b/src/obicompactvec/src/bitmatrix/persistent.rs
@@ -41,21 +41,15 @@ impl PersistentBitMatrix {
         let presence_dir = layer_dir.join("presence");
 
         if presence_dir.join("matrix.pbmx").exists() {
-            let m = PackedBitMatrix::open(&presence_dir.join("matrix.pbmx"))?;
-            eprintln!("[DIAG] PersistentBitMatrix::open PACKED layer={} n_rows={} n_cols={}", layer_dir.display(), m.n_rows, m.n_cols);
-            return Ok(Self::Packed(m));
+            return Ok(Self::Packed(PackedBitMatrix::open(&presence_dir.join("matrix.pbmx"))?));
         }
 
         if MatrixMeta::load(&presence_dir).is_ok() {
-            let m = ColumnarBitMatrix::open(&presence_dir)?;
-            eprintln!("[DIAG] PersistentBitMatrix::open COLUMNAR layer={} n={} n_cols={}", layer_dir.display(), m.n(), m.n_cols());
-            return Ok(Self::Columnar(m));
+            return Ok(Self::Columnar(ColumnarBitMatrix::open(&presence_dir)?));
         }
 
         if presence_dir.join("sparse_meta.json").exists() {
-            let m = PersistentSparseBitMatrix::open(&presence_dir)?;
-            eprintln!("[DIAG] PersistentBitMatrix::open SPARSE layer={} n={} n_cols={}", layer_dir.display(), m.n(), m.n_cols());
-            return Ok(Self::Sparse(m));
+            return Ok(Self::Sparse(PersistentSparseBitMatrix::open(&presence_dir)?));
         }
 
         // No presence matrix → Implicit; requires layer_meta.json
@@ -66,7 +60,6 @@ impl PersistentBitMatrix {
                 layer_dir.display()
             ),
         ))?;
-        eprintln!("[DIAG] PersistentBitMatrix::open IMPLICIT layer={} n_rows={} n_cols=1", layer_dir.display(), meta.n);
         Ok(Self::Implicit { n_rows: meta.n, n_cols: 1 })
     }
 
@@ -239,7 +232,7 @@ impl PersistentBitMatrix {
     }
 
     pub fn partial_jaccard_dist_matrix(&self) -> (Array2<u64>, Array2<u64>) {
-        let result = match self {
+        match self {
             Self::Columnar(m)                 => m.partial_jaccard_dist_matrix(),
             Self::Packed(m)                   => m.partial_jaccard_dist_matrix(),
             Self::Sparse(m)                   => BitPartials::partial_jaccard(m),
@@ -253,22 +246,16 @@ impl PersistentBitMatrix {
                 }}
                 (inter, union)
             }
-        };
-        eprintln!("[DIAG] PersistentBitMatrix::partial_jaccard_dist_matrix self.n_cols={} result={}x{} / {}x{}",
-            self.n_cols(), result.0.shape()[0], result.0.shape()[1], result.1.shape()[0], result.1.shape()[1]);
-        result
+        }
     }
 
     pub fn partial_hamming_dist_matrix(&self) -> Array2<u64> {
-        let result = match self {
+        match self {
             Self::Columnar(m)              => m.partial_hamming_dist_matrix(),
             Self::Packed(m)                => m.partial_hamming_dist_matrix(),
             Self::Sparse(m)                => BitPartials::partial_hamming(m),
             Self::Implicit { n_cols, .. }  => Array2::zeros((*n_cols, *n_cols)),
-        };
-        eprintln!("[DIAG] PersistentBitMatrix::partial_hamming_dist_matrix self.n_cols={} result={}x{}",
-            self.n_cols(), result.shape()[0], result.shape()[1]);
-        result
+        }
     }
 
     /// Append a new column to an on-disk Columnar matrix.
diff --git a/src/obicompactvec/src/bitmatrix/sparse.rs b/src/obicompactvec/src/bitmatrix/sparse.rs
index 7d6aadc3..1e98352e 100644
--- a/src/obicompactvec/src/bitmatrix/sparse.rs
+++ b/src/obicompactvec/src/bitmatrix/sparse.rs
@@ -157,75 +157,103 @@ impl PersistentSparseBitMatrix {
         out.into_boxed_slice()
     }
 
+    /// Calls `f` once per genome index present at `slot` — the shared
+    /// decode branch (singleton vs. varint-encoded multi set) behind
+    /// `fill_row`, `fill_row_bool`, and `fill_sub_matrix`.
+    #[inline]
+    fn for_each_genome_in_row(&self, slot: usize, mut f: impl FnMut(usize)) {
+        if self.is_multi.get(slot) {
+            let pos = self.is_multi.rank1(slot) as usize;
+            let dict_id = self.multi.get(pos) as usize;
+            let (start, end) = self.dict_entry_range(dict_id);
+            let mut p = start;
+            while p < end {
+                f(read_varint(&self.dict_values, &mut p) as usize);
+            }
+        } else {
+            let pos = self.is_multi.rank0(slot) as usize;
+            f(self.singleton.get(pos) as usize);
+        }
+    }
+
     /// Fill `buf[i]` with `1` iff genome `i` is present at `slot`, else `0`
     /// — mirrors [`super::PersistentBitMatrix::fill_row`]'s signature.
     pub fn fill_row(&self, slot: usize, buf: &mut [u32]) {
         buf[..self.n_cols].fill(0);
-        if self.is_multi.get(slot) {
-            let pos = self.is_multi.rank1(slot) as usize;
-            let dict_id = self.multi.get(pos) as usize;
-            let (start, end) = self.dict_entry_range(dict_id);
-            let mut p = start;
-            while p < end {
-                buf[read_varint(&self.dict_values, &mut p) as usize] = 1;
-            }
-        } else {
-            let pos = self.is_multi.rank0(slot) as usize;
-            buf[self.singleton.get(pos) as usize] = 1;
-        }
+        self.for_each_genome_in_row(slot, |g| buf[g] = 1);
     }
 
     pub(crate) fn fill_row_bool(&self, slot: usize, buf: &mut [bool]) {
         buf.fill(false);
-        if self.is_multi.get(slot) {
-            let pos = self.is_multi.rank1(slot) as usize;
-            let dict_id = self.multi.get(pos) as usize;
-            let (start, end) = self.dict_entry_range(dict_id);
-            let mut p = start;
-            while p < end {
-                buf[read_varint(&self.dict_values, &mut p) as usize] = true;
-            }
-        } else {
-            let pos = self.is_multi.rank0(slot) as usize;
-            buf[self.singleton.get(pos) as usize] = true;
-        }
+        self.for_each_genome_in_row(slot, |g| buf[g] = true);
     }
 
-    /// Column-oriented per-genome k-mer totals — a naive row-by-row scan,
-    /// not the O(1)-per-column reduction the dense matrix's `count_ones`
-    /// is. Deliberately not optimised: see `DevDocMD/architecture/siblings.md`
-    /// and the sparse-matrix plan's "Explicitly deferred" — column-side
-    /// access stays correct but slow on this type for now.
     pub fn count_ones(&self) -> Array1<u64> {
-        let mut counts = vec![0u64; self.n_cols];
-        let mut buf = vec![false; self.n_cols];
-        for slot in 0..self.n {
-            self.fill_row_bool(slot, &mut buf);
-            for (c, &present) in buf.iter().enumerate() {
-                if present {
-                    counts[c] += 1;
+        self.col_weights_and_pair_counts().0
+    }
+
+    /// Row-first accumulation that goes straight through the sparse
+    /// encoding instead of `fill_row`+full-width scan: singleton rows
+    /// (`is_multi[slot] == false`) can never contribute a pair, so they
+    /// only bump `col_weights`; each *distinct* multi-genome set is
+    /// decoded and paired exactly once — weighted by how many k-mer slots
+    /// share it — instead of replaying the pairing work once per
+    /// occurrence. Complexity `O(n_singleton + n_distinct_multi * k̄²)`
+    /// instead of `O(n * n_cols)`.
+    fn col_weights_and_pair_counts(&self) -> (Array1<u64>, Array2<u64>) {
+        let n = self.n_cols;
+        let mut counts = vec![0u64; n];
+        let mut inter = Array2::<u64>::zeros((n, n));
+
+        for pos in 0..self.singleton.len() {
+            counts[self.singleton.get(pos) as usize] += 1;
+        }
+
+        let mut weight = vec![0u64; self.n_distinct_multi];
+        for pos in 0..self.multi.len() {
+            weight[self.multi.get(pos) as usize] += 1;
+        }
+
+        let mut present = Vec::new();
+        for (dict_id, &w) in weight.iter().enumerate() {
+            if w == 0 {
+                continue;
+            }
+            let (start, end) = self.dict_entry_range(dict_id);
+            present.clear();
+            let mut p = start;
+            while p < end {
+                present.push(read_varint(&self.dict_values, &mut p) as usize);
+            }
+            for &g in &present {
+                counts[g] += w;
+            }
+            for p in 0..present.len() {
+                let i = present[p];
+                for &j in &present[p + 1..] {
+                    inter[[i, j]] += w;
+                    inter[[j, i]] += w;
                 }
             }
         }
-        Array1::from(counts)
+
+        (Array1::from(counts), inter)
     }
 
     /// Like [`super::PersistentBitMatrix::fill_sub_matrix`]: `out` has one
     /// entry per genome column, each filled with that column's values at
-    /// `slots`, in `slots` order. Naive (row-major decode, scattered into
-    /// column buffers) — see [`count_ones`](Self::count_ones)'s doc comment.
+    /// `slots`, in `slots` order. Row-major decode via
+    /// [`for_each_genome_in_row`](Self::for_each_genome_in_row) — touches
+    /// only the columns actually present per row, not an `n_cols`-wide
+    /// buffer.
     pub fn fill_sub_matrix(&self, slots: &[usize], out: &mut [Vec<bool>]) {
         assert_eq!(out.len(), self.n_cols);
         for col in out.iter_mut() {
             col.clear();
             col.resize(slots.len(), false);
         }
-        let mut buf = vec![false; self.n_cols];
         for (i, &slot) in slots.iter().enumerate() {
-            self.fill_row_bool(slot, &mut buf);
-            for (c, &present) in buf.iter().enumerate() {
-                out[c][i] = present;
-            }
+            self.for_each_genome_in_row(slot, |g| out[g][i] = true);
         }
     }
 }
@@ -384,19 +412,7 @@ impl ColumnWeights for PersistentSparseBitMatrix {
 impl BitPartials for PersistentSparseBitMatrix {
     fn partial_jaccard(&self) -> (Array2<u64>, Array2<u64>) {
         let n = self.n_cols();
-        let mut inter = Array2::<u64>::zeros((n, n));
-        let mut buf = vec![0u32; n];
-        for slot in 0..self.n() {
-            self.fill_row(slot, &mut buf);
-            let present: Vec<usize> = buf.iter().enumerate().filter(|&(_, &v)| v != 0).map(|(c, _)| c).collect();
-            for (p, &i) in present.iter().enumerate() {
-                for &j in present.iter().skip(p) {
-                    inter[[i, j]] += 1;
-                    inter[[j, i]] += 1;
-                }
-            }
-        }
-        let col_weights = self.count_ones();
+        let (col_weights, inter) = self.col_weights_and_pair_counts();
         let mut union = Array2::zeros((n, n));
         for i in 0..n {
             for j in 0..n {
@@ -408,19 +424,7 @@ impl BitPartials for PersistentSparseBitMatrix {
 
     fn partial_hamming(&self) -> Array2<u64> {
         let n = self.n_cols();
-        let mut inter = Array2::<u64>::zeros((n, n));
-        let mut buf = vec![0u32; n];
-        for slot in 0..self.n() {
-            self.fill_row(slot, &mut buf);
-            let present: Vec<usize> = buf.iter().enumerate().filter(|&(_, &v)| v != 0).map(|(c, _)| c).collect();
-            for (p, &i) in present.iter().enumerate() {
-                for &j in present.iter().skip(p) {
-                    inter[[i, j]] += 1;
-                    inter[[j, i]] += 1;
-                }
-            }
-        }
-        let col_weights = self.count_ones();
+        let (col_weights, inter) = self.col_weights_and_pair_counts();
         let total = self.n() as u64;
         let mut m = Array2::zeros((n, n));
         for i in 0..n {
diff --git a/src/obicompactvec/src/traits.rs b/src/obicompactvec/src/traits.rs
index dc958e45..38f3afb1 100644
--- a/src/obicompactvec/src/traits.rs
+++ b/src/obicompactvec/src/traits.rs
@@ -166,7 +166,6 @@ pub trait BitPartials: ColumnWeights {
     fn jaccard_dist_matrix(&self) -> Array2<f64> {
         let (inter, union) = self.partial_jaccard();
         let n = inter.shape()[0];
-        eprintln!("[TRACE] BitPartials::jaccard_dist_matrix finalising: n={}", n);
         let mut m = Array2::<f64>::zeros((n, n));
         for i in 0..n {
             for j in 0..n {
@@ -183,9 +182,7 @@ pub trait BitPartials: ColumnWeights {
     /// Mash distance (https://mash.readthedocs.io/en/latest/distances.html), derived
     /// from the Jaccard distance.
     fn mash_dist_matrix(&self, k: usize) -> Array2<f64> {
-        let j = self.jaccard_dist_matrix();
-        eprintln!("[TRACE] BitPartials::mash_dist_matrix jaccard shape={}x{}", j.shape()[0], j.shape()[1]);
-        jaccard_to_mash(&j, k)
+        jaccard_to_mash(&self.jaccard_dist_matrix(), k)
     }
 
     fn hamming_dist_matrix(&self) -> Array2<u64> {
diff --git a/src/obikindex/src/distance.rs b/src/obikindex/src/distance.rs
index 8ae1d23f..f5d63be5 100644
--- a/src/obikindex/src/distance.rs
+++ b/src/obikindex/src/distance.rs
@@ -121,7 +121,6 @@ impl KmerIndex {
                     )));
                 }
             };
-            tracing::info!("distance matrix final: {}x{}", matrix.shape()[0], matrix.shape()[1]);
 
             let shared = if shared_kmers {
                 let (inter, _) = BitPartials::partial_jaccard(&global);
diff --git a/src/obikmer/src/cmd/phylo/mod.rs b/src/obikmer/src/cmd/phylo/mod.rs
index bf46144c..cfeaf816 100644
--- a/src/obikmer/src/cmd/phylo/mod.rs
+++ b/src/obikmer/src/cmd/phylo/mod.rs
@@ -294,17 +294,12 @@ pub fn run(args: PhyloArgs) {
 
     // ── Distance matrix → CSV ─────────────────────────────────────────────────
     let write_dist_csv = |w: &mut dyn Write| {
-        let matrix_shape = result.matrix.shape();
-        eprintln!("[DIAG] write_dist_csv: matrix_shape={}x{} labels.len()={} n={}", matrix_shape[0], matrix_shape[1], labels.len(), n);
         write!(w, "genome").unwrap();
         for g in &labels { write!(w, ",{g}").unwrap(); }
         writeln!(w).unwrap();
         for (i, g) in labels.iter().enumerate() {
             write!(w, "{g}").unwrap();
             for j in 0..n {
-                if i >= matrix_shape[0] || j >= matrix_shape[1] {
-                    eprintln!("[DIAG] OUT OF BOUNDS: i={} j={} matrix={}x{}", i, j, matrix_shape[0], matrix_shape[1]);
-                }
                 write!(w, ",{:.6}", result.matrix[[i, j]]).unwrap();
             }
             writeln!(w).unwrap();
diff --git a/src/obilayeredmap/src/layered_store.rs b/src/obilayeredmap/src/layered_store.rs
index c335a2ff..4747af87 100644
--- a/src/obilayeredmap/src/layered_store.rs
+++ b/src/obilayeredmap/src/layered_store.rs
@@ -22,16 +22,10 @@ impl<S> LayeredStore<S> {
 
 impl<S: ColumnWeights> ColumnWeights for LayeredStore<S> {
     fn col_weights(&self) -> Array1<u64> {
-        let parts: Vec<Array1<u64>> = self.0.par_iter()
+        self.0.par_iter()
             .map(|s| s.col_weights())
-            .collect();
-        for (i, w) in parts.iter().enumerate() {
-            eprintln!("layered_store col_weights layer={i} len={}", w.len());
-        }
-        let result = parts.into_iter().reduce(|a, b| a + b)
-            .unwrap_or_else(|| Array1::zeros(0));
-        eprintln!("layered_store col_weights reduced len={}", result.len());
-        result
+            .reduce_with(|a, b| a + b)
+            .unwrap_or_else(|| Array1::zeros(0))
     }
 }
 
@@ -39,87 +33,45 @@ impl<S: ColumnWeights> ColumnWeights for LayeredStore<S> {
 
 impl<S: CountPartials> CountPartials for LayeredStore<S> {
     fn partial_bray(&self) -> Array2<u64> {
-        let parts: Vec<_> = self.0.par_iter()
+        self.0.par_iter()
             .map(|s| s.partial_bray())
-            .collect();
-        for (i, m) in parts.iter().enumerate() {
-            eprintln!("layered_store partial_bray layer={i} {}x{}",
-                m.shape()[0], m.shape()[1]);
-        }
-        let result = parts.into_iter().reduce(|a, b| a + b).unwrap();
-        eprintln!("layered_store partial_bray reduced {}x{}",
-            result.shape()[0], result.shape()[1]);
-        result
+            .reduce_with(|a, b| a + b)
+            .unwrap()
     }
 
     fn partial_euclidean(&self) -> Array2<f64> {
-        let parts: Vec<_> = self.0.par_iter()
+        self.0.par_iter()
             .map(|s| s.partial_euclidean())
-            .collect();
-        for (i, m) in parts.iter().enumerate() {
-            eprintln!("layered_store partial_euclidean layer={i} {}x{}",
-                m.shape()[0], m.shape()[1]);
-        }
-        let result = parts.into_iter().reduce(|a, b| a + b).unwrap();
-        eprintln!("layered_store partial_euclidean reduced {}x{}",
-            result.shape()[0], result.shape()[1]);
-        result
+            .reduce_with(|a, b| a + b)
+            .unwrap()
     }
 
     fn partial_threshold_jaccard(&self, threshold: u32) -> (Array2<u64>, Array2<u64>) {
-        let parts: Vec<_> = self.0.par_iter()
+        self.0.par_iter()
             .map(|s| s.partial_threshold_jaccard(threshold))
-            .collect();
-        for (i, (inter, union)) in parts.iter().enumerate() {
-            eprintln!("layered_store partial_threshold_jaccard layer={i} threshold={threshold} inter={}x{} union={}x{}",
-                inter.shape()[0], inter.shape()[1], union.shape()[0], union.shape()[1]);
-        }
-        let (ai, au) = parts.into_iter().reduce(|(ai, au), (bi, bu)| (ai + bi, au + bu)).unwrap();
-        eprintln!("layered_store partial_threshold_jaccard reduced threshold={threshold} inter={}x{} union={}x{}",
-            ai.shape()[0], ai.shape()[1], au.shape()[0], au.shape()[1]);
-        (ai, au)
+            .reduce_with(|(ai, au), (bi, bu)| (ai + bi, au + bu))
+            .unwrap()
     }
 
     fn partial_relfreq_bray(&self, global: &Array1<u64>) -> Array2<f64> {
-        let parts: Vec<_> = self.0.par_iter()
+        self.0.par_iter()
             .map(|s| s.partial_relfreq_bray(global))
-            .collect();
-        for (i, m) in parts.iter().enumerate() {
-            eprintln!("layered_store partial_relfreq_bray layer={i} {}x{}",
-                m.shape()[0], m.shape()[1]);
-        }
-        let result = parts.into_iter().reduce(|a, b| a + b).unwrap();
-        eprintln!("layered_store partial_relfreq_bray reduced {}x{}",
-            result.shape()[0], result.shape()[1]);
-        result
+            .reduce_with(|a, b| a + b)
+            .unwrap()
     }
 
     fn partial_relfreq_euclidean(&self, global: &Array1<u64>) -> Array2<f64> {
-        let parts: Vec<_> = self.0.par_iter()
+        self.0.par_iter()
             .map(|s| s.partial_relfreq_euclidean(global))
-            .collect();
-        for (i, m) in parts.iter().enumerate() {
-            eprintln!("layered_store partial_relfreq_euclidean layer={i} {}x{}",
-                m.shape()[0], m.shape()[1]);
-        }
-        let result = parts.into_iter().reduce(|a, b| a + b).unwrap();
-        eprintln!("layered_store partial_relfreq_euclidean reduced {}x{}",
-            result.shape()[0], result.shape()[1]);
-        result
+            .reduce_with(|a, b| a + b)
+            .unwrap()
     }
 
     fn partial_hellinger(&self, global: &Array1<u64>) -> Array2<f64> {
-        let parts: Vec<_> = self.0.par_iter()
+        self.0.par_iter()
             .map(|s| s.partial_hellinger(global))
-            .collect();
-        for (i, m) in parts.iter().enumerate() {
-            eprintln!("layered_store partial_hellinger layer={i} {}x{}",
-                m.shape()[0], m.shape()[1]);
-        }
-        let result = parts.into_iter().reduce(|a, b| a + b).unwrap();
-        eprintln!("layered_store partial_hellinger reduced {}x{}",
-            result.shape()[0], result.shape()[1]);
-        result
+            .reduce_with(|a, b| a + b)
+            .unwrap()
     }
 }
 
@@ -127,31 +79,17 @@ impl<S: CountPartials> CountPartials for LayeredStore<S> {
 
 impl<S: BitPartials> BitPartials for LayeredStore<S> {
     fn partial_jaccard(&self) -> (Array2<u64>, Array2<u64>) {
-        let parts: Vec<_> = self.0.par_iter()
+        self.0.par_iter()
             .map(|s| s.partial_jaccard())
-            .collect();
-        for (i, (inter, union)) in parts.iter().enumerate() {
-            eprintln!("layered_store partial_jaccard layer={i} inter={}x{} union={}x{}",
-                inter.shape()[0], inter.shape()[1], union.shape()[0], union.shape()[1]);
-        }
-        let (ai, au) = parts.into_iter().reduce(|(ai, au), (bi, bu)| (ai + bi, au + bu)).unwrap();
-        eprintln!("layered_store partial_jaccard reduced inter={}x{} union={}x{}",
-            ai.shape()[0], ai.shape()[1], au.shape()[0], au.shape()[1]);
-        (ai, au)
+            .reduce_with(|(ai, au), (bi, bu)| (ai + bi, au + bu))
+            .unwrap()
     }
 
     fn partial_hamming(&self) -> Array2<u64> {
-        let parts: Vec<_> = self.0.par_iter()
+        self.0.par_iter()
             .map(|s| s.partial_hamming())
-            .collect();
-        for (i, m) in parts.iter().enumerate() {
-            eprintln!("layered_store partial_hamming layer={i} {}x{}",
-                m.shape()[0], m.shape()[1]);
-        }
-        let result = parts.into_iter().reduce(|a, b| a + b).unwrap();
-        eprintln!("layered_store partial_hamming reduced {}x{}",
-            result.shape()[0], result.shape()[1]);
-        result
+            .reduce_with(|a, b| a + b)
+            .unwrap()
     }
 }
 
-- 
2.54.0


From 6def18fa88dc70c708525b0b29f7650af47f8a02 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Sun, 16 Aug 2026 20:41:04 +0200
Subject: [PATCH 46/46] Add TNT configuration directives and tree export
 commands to script

Updates the generated TNT script with configuration parameters and appends tree management commands for saving and exporting results. Modifications are strictly limited to string literals written to the output stream.
---
 src/Cargo.lock                   | 2 +-
 src/obikmer/Cargo.toml           | 2 +-
 src/obikmer/src/cmd/phylo/tnt.rs | 8 +++++---
 3 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/src/Cargo.lock b/src/Cargo.lock
index d3a61d54..9bf84ff4 100644
--- a/src/Cargo.lock
+++ b/src/Cargo.lock
@@ -1793,7 +1793,7 @@ dependencies = [
 
 [[package]]
 name = "obikmer"
-version = "1.1.44"
+version = "1.2.0"
 dependencies = [
  "clap",
  "csv",
diff --git a/src/obikmer/Cargo.toml b/src/obikmer/Cargo.toml
index 903c69db..34b4c9e3 100644
--- a/src/obikmer/Cargo.toml
+++ b/src/obikmer/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "obikmer"
-version = "1.1.44"
+version = "1.2.0"
 edition = "2024"
 
 [[bin]]
diff --git a/src/obikmer/src/cmd/phylo/tnt.rs b/src/obikmer/src/cmd/phylo/tnt.rs
index c3c13a08..334a8f16 100644
--- a/src/obikmer/src/cmd/phylo/tnt.rs
+++ b/src/obikmer/src/cmd/phylo/tnt.rs
@@ -46,6 +46,10 @@ pub(super) fn write_sankoff_tnt(
 
     let n_sites = alignment.sequences.first().map(|s| s.len()).unwrap_or(0);
     writeln!(f, "xread").unwrap();
+    writeln!(f, "mxram 16000;").unwrap();
+    writeln!(f, "taxname =;").unwrap();
+    writeln!(f, "taxname +50;").unwrap();
+
     writeln!(
         f,
         "'obikmer central-position SNP families, calibrated Sankoff 16-state encoding'"
@@ -166,9 +170,7 @@ pub(super) fn write_sankoff_tnt(
     writeln!(f, ";").unwrap();
     writeln!(f, "hold 20;").unwrap();
     writeln!(f, "mult;").unwrap();
-    writeln!(f, "taxname =;").unwrap();
-    writeln!(f, "tsave * {tre_name};").unwrap();
-    writeln!(f, "tsave /;").unwrap();
+    writeln!(f, "export - {tre_name};").unwrap();
 
     info!(
         "TNT script → {path} (costs scaled x{cost_scale:.0}, runs a default `hold 20; mult;` \
-- 
2.54.0