obikmer/docmd/implementation/obilayeredmap.md

obilayeredmap — layered kmer index crate

Purpose

obilayeredmap implements a persistent, incrementally extensible kmer index. Each layer covers a disjoint kmer set and wraps a ptr_hash MPHF with associated per-slot data. Adding a new dataset never rebuilds existing layers.

---

Three usage modes

The MPHF + evidence infrastructure is the same for all modes. The payload varies.

Mode	Description	Payload type	Storage
1. Set	membership test only	()	—
2. Count	occurrences per kmer per sample	PersistentCompactIntMatrix	counts/ directory
3. Presence/absence	which genomes contain each kmer	PersistentBitMatrix	presence/ directory

Both PersistentCompactIntMatrix and PersistentBitMatrix come from the obicompactvec crate.

---

Evidence kinds

Each layer carries one of two evidence bundles, recorded in layer_meta.json at build time:

pub enum EvidenceKind {
    Exact,
    Approx { b: u8, z: u8 },
}

EvidenceKind is stored in LayerMeta (one per layer directory). open() reads it to decide which evidence files to load.

• Exact: writes evidence.bin + unitigs.bin.idx. Zero false positives. Requires random-access .idx at query time.
• Approx: writes fingerprint.bin only. False-positive rate per kmer query = 1/2^b. z is the Findere consecutive-kmer parameter: z consecutive kmers must all match, reducing the effective FP rate per read to approximately W / 2^(b·z) where W = L − k − z + 2 is the number of windows in a read of length L. No .idx written or required.

---

MphfLayer — autonomous kmer → slot mapping

MphfLayer encapsulates the MPHF and evidence store for one layer. It is independent of any payload.

pub struct MphfLayer {
    mphf: Mphf,
    ev:   LayerEvidence,   // loaded at open() time
    n:    usize,
}

LayerEvidence is an internal enum, not public:

enum LayerEvidence {
    Exact  { evidence: Evidence, unitigs: UnitigFileReader },
    Approx { fingerprint: FingerprintVec },
}

Query API

Three public query methods, all returning Option<usize> (slot index):

pub fn find(&self, kmer: CanonicalKmer) -> Option<usize>
pub fn find_exact(&self, kmer: CanonicalKmer) -> Option<usize>
pub fn find_approx(&self, kmer: CanonicalKmer) -> Option<usize>

• find dispatches transparently to find_exact or find_approx based on the evidence variant loaded at open().
• find_exact panics if the layer holds approximate evidence; zero false positives.
• find_approx panics if the layer holds exact evidence; FP rate 1/2^b per kmer.

open() requires unitigs.bin.idx (random access into unitigs). open_sequential() on UnitigFileReader does not require the .idx and is used during build passes.

Build surface

// Full MPHF + exact evidence build (two-pass, parallel)
pub(crate) fn build(dir, block_bits, fill_slot) -> OLMResult<usize>

// Evidence-only builds (MPHF already present in dir)
pub fn build_exact_evidence(dir, block_bits) -> OLMResult<usize>
pub fn build_approx_evidence(dir, b, z)      -> OLMResult<usize>
pub fn build_evidence(dir, kind, block_bits) -> OLMResult<usize>  // dispatch

MphfLayer::build runs two sequential passes over unitigs.bin:

1. Pass 1 (parallel via rayon): iterate all canonical kmers, construct and store mphf.bin. new_from_par_iter avoids materialising a full key Vec.
2. Pass 2 (sequential): iterate again, fill evidence.bin, call fill_slot(slot, kmer) once per kmer for payload population. A compact n/8-byte seen-bitset verifies MPHF injectivity inline.

build always produces exact evidence. For approximate evidence, use build_approx_evidence after MPHF construction.

For empty layers (n = 0), all build variants return Ok(0) immediately after creating empty output files.

---

Layer<D: LayerData> — MPHF + payload

Layer<D> pairs an MphfLayer with one payload store.

pub trait LayerData: Sized {
    type Item;
    fn open(layer_dir: &Path) -> OLMResult<Self>;
    fn read(&self, slot: usize) -> Self::Item;
}

pub struct Layer<D: LayerData = ()> {
    mphf: MphfLayer,
    data: D,
}

pub struct Hit<T = ()> {
    pub slot: usize,
    pub data: T,
}

LayerData covers the read path only (open + read). Build signatures differ between modes and are not part of the trait.

Type	Item	Description
()	()	mode 1 — membership only
PersistentCompactIntMatrix	Box<[u32]>	mode 2 — count matrix (one u32 per column per slot)
PersistentBitMatrix	Box<[bool]>	mode 3 — presence matrix (one bit per genome per slot)

Build signatures

// mode 1
impl Layer<()> {
    pub fn build(out_dir: &Path, block_bits: u8) -> OLMResult<usize>
}

// mode 2
impl Layer<PersistentCompactIntMatrix> {
    pub fn build(out_dir: &Path, block_bits: u8,
                 count_of: impl Fn(CanonicalKmer) -> u32) -> OLMResult<usize>
    pub fn build_from_map(out_dir: &Path, block_bits: u8,
                          counts: &HashMap<CanonicalKmer, u32>) -> OLMResult<usize>
}

// mode 3
impl Layer<PersistentBitMatrix> {
    pub fn build_presence(out_dir: &Path, block_bits: u8,
                          n_genomes: usize,
                          present_in: impl Fn(CanonicalKmer, usize) -> bool) -> OLMResult<usize>
}

All build impls delegate MPHF + evidence construction to MphfLayer::build via a mode-specific fill_slot callback. Modes 2 and 3 pre-read n_kmers from unitigs.bin via UnitigFileReader::open_sequential to size the matrix builder before calling MphfLayer::build.

Evidence build helpers on Layer

impl<D: LayerData> Layer<D> {
    pub fn build_exact_evidence(layer_dir: &Path, block_bits: u8) -> OLMResult<usize>
    pub fn build_approx_evidence(layer_dir: &Path, b: u8, z: u8)  -> OLMResult<usize>
    pub fn build_evidence(layer_dir: &Path, kind: &EvidenceKind, block_bits: u8) -> OLMResult<usize>
}

These delegate directly to the corresponding MphfLayer methods and are provided so call sites can remain typed at the Layer<D> level.

---

FingerprintVec and FingerprintVecWriter

Approximate evidence is stored as a packed b-bit array, one fingerprint per MPHF slot.

fingerprint.bin format:
  magic:   b"FPVF"  (4 bytes)
  b:       u8       (bits per fingerprint, 1..=64)
  padding: [0u8; 3]
  n:       u64 LE   (number of slots)
  data:    packed bits, ceil(n*b/8) bytes, Lsb0 order

impl FingerprintVec {
    pub fn open(path: &Path) -> OLMResult<Self>
    pub fn get(&self, slot: usize) -> u64
    pub fn matches(&self, slot: usize, fingerprint: u64) -> bool
    pub fn n(&self) -> usize
    pub fn b(&self) -> u8
}

matches(slot, hash) extracts the b-bit fingerprint stored at slot and compares it to the low b bits of hash. It is the core operation of find_approx.

---

LayeredMap<D> — collection of layers

LayeredMap<D> wraps Vec<Layer<D>> for a single partition directory.

pub struct LayeredMap<D: LayerData = ()> {
    root:   PathBuf,
    meta:   PartitionMeta,
    layers: Vec<Layer<D>>,
}

PartitionMeta (meta.json at the partition root) stores n_layers.

Common methods

pub fn open(root: &Path)   -> OLMResult<Self>
pub fn create(root: &Path) -> OLMResult<Self>
pub fn n_layers(&self)     -> usize
pub fn layer(&self, i: usize) -> &Layer<D>
pub fn query(&self, kmer: CanonicalKmer) -> Option<(usize, Hit<D::Item>)>
pub fn next_layer_writer(&self) -> OLMResult<UnitigFileWriter>

query probes layers in order and returns (layer_index, Hit) on the first match. Expected probe depth: 1 for kmers in layer 0.

push_layer

push_layer builds the next layer from a unitigs.bin already written via next_layer_writer, using DEFAULT_BLOCK_BITS:

// mode 1
impl LayeredMap<()> {
    pub fn push_layer(&mut self) -> OLMResult<usize>
}

// mode 2
impl LayeredMap<PersistentCompactIntMatrix> {
    pub fn push_layer(&mut self, count_of: impl Fn(CanonicalKmer) -> u32) -> OLMResult<usize>
    pub fn push_layer_from_map(&mut self, counts: &HashMap<CanonicalKmer, u32>) -> OLMResult<usize>
}

Mode 3 (PersistentBitMatrix) has no push_layer on LayeredMap; callers build directly via Layer<PersistentBitMatrix>::build_presence.

---

LayeredStore<S> and aggregation traits

LayeredStore<S> is a generic aggregation wrapper over Vec<S>. It propagates three traits from obicompactvec::traits up the hierarchy via blanket impls:

pub struct LayeredStore<S>(pub Vec<S>);

impl<S: ColumnWeights> ColumnWeights for LayeredStore<S> { … }  // Σ col_weights across inner stores
impl<S: CountPartials> CountPartials  for LayeredStore<S> { … }  // element-wise Σ partials
impl<S: BitPartials>   BitPartials    for LayeredStore<S> { … }  // element-wise Σ partials

Because blanket impls compose, LayeredStore<LayeredStore<S>> automatically inherits all three traits when S does — providing the partitioned level without a separate type.

Leaf implementors (in obicompactvec):

Type	Traits
PersistentCompactIntMatrix	ColumnWeights (via sum()) + CountPartials
PersistentBitMatrix	ColumnWeights (via count_ones()) + BitPartials

See Kmer index architecture for the full trait API and the two-pass normalised-metric pattern.

---

On-disk structure

partition_root/                    ← LayeredMap (one partition)
  meta.json                        — {"n_layers": N}
  layer_0/                         ← Layer
    layer_meta.json                — {"type": "exact"} or {"type": "approx", "b": B, "z": Z}
    mphf.bin                       — ptr_hash MPHF (epserde format)
    unitigs.bin                    — packed 2-bit nucleotide sequences
    unitigs.bin.idx                — UIDX index (exact evidence only)
    evidence.bin                   — [u32; n], LE  (exact evidence only)
    fingerprint.bin                — packed b-bit array  (approx evidence only)
    counts/                        [mode 2] PersistentCompactIntMatrix
      meta.json
      col_000000.pciv
    presence/                      [mode 3] PersistentBitMatrix
      meta.json
      col_000000.pbiv  …
  layer_1/
    …

unitigs.bin.idx is required by open() (random access). open_sequential() on UnitigFileReader omits it and is used during build passes and approx-evidence construction.

---

Evidence encoding (exact)

evidence.bin is a flat [u32; n] array with no header. Each u32 encodes one slot:

bits [31:7] = chunk_id (25 bits) — index of the unitig chunk
bits [6:0]  = rank     (7 bits)  — kmer index within the chunk (0-based)

chunk_id = raw >> 7, rank = raw & 0x7F. Reconstructing the kmer: read k nucleotides at position rank within unitig chunk_id (requires unitigs.bin.idx for random access).

For k=31, m=11, the observed maximum is ~46 kmers per chunk — well within the 127-kmer u7 capacity.

---

ptr_hash configuration

type Mphf = PtrHash<
    u64,                              // key type: canonical kmer raw encoding
    CubicEps,                         // bucket fn: 2.4 bits/key, λ=3.5, α=0.99
    CachelineEfVec<Vec<CachelineEf>>, // remap: Elias-Fano
    Xx64,                             // hasher: XXH3-64 with seed
    Vec<u8>,                          // pilots
>;

Xx64 is chosen over FxHash because canonical kmer raw values are left-aligned u64 with structural zeros in the low bits (42 zeros for k=11, 2 zeros for k=31), which single-multiply hashes distribute poorly.

CubicEps with PtrHashParams::<CubicEps>::default() (λ=3.5): 2× slower construction than Linear/λ=3.0, ~20% less space.

---

Column append and merge support

These methods extend existing layers with new genome columns without touching the MPHF.

Layer-level genome column append

impl Layer<PersistentBitMatrix> {
    pub fn append_genome_column(layer_dir: &Path, value_of: impl Fn(usize) -> bool) -> OLMResult<()>
}

impl Layer<PersistentCompactIntMatrix> {
    pub fn append_genome_column(layer_dir: &Path, value_of: impl Fn(usize) -> u32) -> OLMResult<()>
}

Both delegate to the corresponding PersistentBitMatrix::append_column / PersistentCompactIntMatrix::append_column. They write a new column file (col_NNNNNN.pbiv / col_NNNNNN.pciv) and update meta.json to increment n_cols. value_of is called once per slot (0..n).

Presence matrix initialisation

impl Layer<()> {
    pub fn init_presence_matrix(layer_dir: &Path, n_kmers: usize) -> OLMResult<()>
}

Called on the first merge of a Presence-mode index. Creates presence/ with meta.json {"n": n_kmers, "n_cols": 1} and col_000000.pbiv set entirely to true. This retroactively records genome 0 (the original source) as present in every slot, satisfying the column-count invariant before any new-source column is appended.

Why the MPHF is never rebuilt

The MPHF, evidence, and unitigs are built once from the kmer set of a layer and are immutable for the lifetime of that layer. Adding a genome column does not change the kmer set — it only appends a new data column indexed by the same slot numbers. The only disk writes are one new .pciv/.pbiv file and a single meta.json update.

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Add-layer algorithm

When adding dataset B to an existing index:

1. For each partition, probe existing layers for kmers of B routed to that partition.
2. Collect kmers absent from all layers → B \ index.
3. Write B \ index to a new unitigs.bin via next_layer_writer().
4. Call Layer<D>::build (or build_presence) on the new layer directory.
5. Call push_layer (or append_layer) to register the new layer in meta.json.

Each partition's new layer is built independently; the operation is fully parallel across partitions.

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Dependencies

crate	role
ptr_hash 1.1	MPHF per layer
cacheline-ef 1.1	compact remap inside ptr_hash
epserde 0.8	zero-copy MPHF serialisation
memmap2 0.9	mmap of evidence and fingerprint files
bitvec	packed b-bit fingerprint storage
obiskio	unitig file writer/reader + .idx build
obicompactvec	payload types + aggregation traits
rayon 1	parallel MPHF construction pass
serde / serde_json	LayerMeta + PartitionMeta serialisation