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< h1 id = "on-disk-index-layout" > On-disk index layout< / h1 >
< h2 id = "directory-tree" > Directory tree< / h2 >
< div class = "highlight" > < pre > < span > < / span > < code > < index_root> /
index.meta ← JSON: IndexMeta
scatter.done ← sentinel: scatter phase complete
count.done ← sentinel: dereplicate + count complete
index.done ← sentinel: MPHF index fully built
spectrums/
< label> .json ← kmer frequency spectrum per genome
partitions/
part_00000/ ← one dir per partition (zero-padded 5 digits, 0..2^n_bits−
index/
meta.json ← PartitionMeta { n_layers }
layer_0/
unitigs.bin ← binary unitig sequences (2-bit packed)
unitigs.bin.idx ← block-sampled offset index (exact evidence only)
mphf.bin ← serialised PtrHash MPHF
layer_meta.json ← LayerMeta { evidence: EvidenceKind }
evidence.bin ← chunk_id:rank per MPHF slot (Exact only)
fingerprint.bin ← b-bit fingerprints per MPHF slot (Approx only)
counts/ ← PersistentCompactIntMatrix (if with_counts=true)
presence/ ← PersistentBitMatrix (if presence mode, merge)
layer_1/ ← added by merge; same structure as layer_0
layer_2/ …
part_00001/ …
< / code > < / pre > < / div >
< h2 id = "state-machine-sentinels" > State machine (sentinels)< / h2 >
< p > The sentinels are touched atomically at the end of each pipeline stage.
A partial run (e.g. scatter interrupted) leaves no sentinel; the state is
detected as the lowest sentinel present.< / p >
< table >
< thead >
< tr >
< th > State< / th >
< th > Sentinel present< / th >
< th > Meaning< / th >
< / tr >
< / thead >
< tbody >
< tr >
< td > < code > Empty< / code > < / td >
< td > —< / td >
< td > < code > index.meta< / code > exists; scatter not started or interrupted< / td >
< / tr >
< tr >
< td > < code > Scattered< / code > < / td >
< td > < code > scatter.done< / code > < / td >
< td > All super-kmers routed to partition files< / td >
< / tr >
< tr >
< td > < code > Counted< / code > < / td >
< td > < code > count.done< / code > < / td >
< td > Partitions dereplicated; < code > spectrums/< / code > written< / td >
< / tr >
< tr >
< td > < code > Indexed< / code > < / td >
< td > < code > index.done< / code > < / td >
< td > All MPHF layers built; index ready for queries< / td >
< / tr >
< / tbody >
< / table >
< h2 id = "indexmeta-indexmeta" > index.meta (IndexMeta)< / h2 >
< div class = "highlight" > < pre > < span > < / span > < code > < span class = "p" > {< / span >
< span class = "w" > < / span > < span class = "nt" > " version" < / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "mi" > 1< / span > < span class = "p" > ,< / span >
< span class = "w" > < / span > < span class = "nt" > " config" < / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "p" > {< / span >
< span class = "w" > < / span > < span class = "nt" > " kmer_size" < / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "mi" > 31< / span > < span class = "p" > ,< / span >
< span class = "w" > < / span > < span class = "nt" > " minimizer_size" < / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "mi" > 11< / span > < span class = "p" > ,< / span >
< span class = "w" > < / span > < span class = "nt" > " n_bits" < / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "mi" > 8< / span > < span class = "p" > ,< / span >
< span class = "w" > < / span > < span class = "nt" > " with_counts" < / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "kc" > false< / span > < span class = "p" > ,< / span >
< span class = "w" > < / span > < span class = "nt" > " evidence" < / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "s2" > " Exact" < / span > < span class = "p" > ,< / span >
< span class = "w" > < / span > < span class = "nt" > " block_bits" < / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "mi" > 0< / span >
< span class = "w" > < / span > < span class = "p" > },< / span >
< span class = "w" > < / span > < span class = "nt" > " genomes" < / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "p" > [< / span >
< span class = "w" > < / span > < span class = "p" > {< / span > < span class = "w" > < / span > < span class = "nt" > " label" < / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "s2" > " genome_A" < / span > < span class = "p" > ,< / span > < span class = "w" > < / span > < span class = "nt" > " meta" < / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "p" > {< / span > < span class = "w" > < / span > < span class = "nt" > " species" < / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "s2" > " Homo sapiens" < / span > < span class = "w" > < / span > < span class = "p" > }< / span > < span class = "w" > < / span > < span class = "p" > }< / span >
< span class = "w" > < / span > < span class = "p" > ]< / span >
< span class = "p" > }< / span >
< / code > < / pre > < / div >
< p > < code > n_bits< / code > determines the partition count: < code > 2^n_bits< / code > directories under < code > partitions/< / code > .< / p >
< p > < code > evidence< / code > is either the string < code > "Exact"< / code > or < code > {"Approx": {"b": 8, "z": 1}}< / code > .< / p >
< p > < code > block_bits< / code > controls the < code > .idx< / code > granularity: one offset entry every < code > 2^block_bits< / code >
chunks. < code > block_bits=0< / code > stores one entry per chunk (O(1) random access, largest < code > .idx< / code > ).< / p >
< p > < code > GenomeInfo.meta< / code > is a free-form string→string map for categorical metadata (e.g.
taxonomy, sample origin). It is optional; defaults to empty.< / p >
< h2 id = "layer-files" > Layer files< / h2 >
< h3 id = "unitigsbin" > unitigs.bin< / h3 >
< p > 2-bit packed binary unitig sequences. Each record: 1 byte < code > seql_minus_k< / code >
(nucleotide length − < code > ceil((seql_minus_k + k) / 4)< / code > bytes of
packed sequence. Long unitigs are transparently split into overlapping chunks
(k− < / p >
< h3 id = "unitigsbinidx-exact-only" > unitigs.bin.idx (Exact only)< / h3 >
< p > Magic < code > UIX3< / code > , little-endian header: < code > block_bits< / code > (u32), < code > n_unitigs< / code > (u32),
< code > n_kmers< / code > (u64), then < code > ceil(n_unitigs / 2^block_bits) + 1< / code > byte-offset entries
(u32 each, last entry is a sentinel past-end offset). Absent for Approx layers.< / p >
< h3 id = "mphfbin" > mphf.bin< / h3 >
< p > PtrHash MPHF serialised with epserde. Maps canonical kmer (u64, left-aligned
2-bit) to a slot index in < code > [0, n_kmers)< / code > .< / p >
< h3 id = "layer_metajson-layermeta" > layer_meta.json (LayerMeta)< / h3 >
< p > < div class = "highlight" > < pre > < span > < / span > < code > < span class = "p" > {< / span > < span class = "w" > < / span > < span class = "nt" > " evidence" < / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "p" > {< / span > < span class = "w" > < / span > < span class = "nt" > " type" < / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "s2" > " exact" < / span > < span class = "w" > < / span > < span class = "p" > }< / span > < span class = "w" > < / span > < span class = "p" > }< / span >
< / code > < / pre > < / div >
or
< div class = "highlight" > < pre > < span > < / span > < code > < span class = "p" > {< / span > < span class = "w" > < / span > < span class = "nt" > " evidence" < / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "p" > {< / span > < span class = "w" > < / span > < span class = "nt" > " type" < / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "s2" > " approx" < / span > < span class = "p" > ,< / span > < span class = "w" > < / span > < span class = "nt" > " b" < / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "mi" > 8< / span > < span class = "p" > ,< / span > < span class = "w" > < / span > < span class = "nt" > " z" < / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "mi" > 1< / span > < span class = "w" > < / span > < span class = "p" > }< / span > < span class = "w" > < / span > < span class = "p" > }< / span >
< / code > < / pre > < / div > < / p >
< h3 id = "evidencebin-exact" > evidence.bin (Exact)< / h3 >
< p > One < code > (chunk_id: u32, rank: u8)< / code > record per MPHF slot, packed. Used to verify
that the kmer mapped to a slot is actually present: < code > unitigs.bin[chunk_id][rank]< / code >
is re-read and compared against the query.< / p >
< h3 id = "fingerprintbin-approx" > fingerprint.bin (Approx)< / h3 >
< p > < code > b< / code > -bit fingerprint per MPHF slot derived from the kmer's sequence hash.
False-positive rate per query ≈ < code > 1/2^b< / code > . With Findere parameter < code > z ≥ 2< / code > ,
< code > z< / code > consecutive k-mers must all match, reducing the effective FP rate to
approximately < code > W / 2^(b·z)< / code > per read of length < code > L< / code >
(where < code > W = L − − < / code > ).< / p >
< h3 id = "counts-persistentcompactintmatrix" > counts/ (PersistentCompactIntMatrix)< / h3 >
< p > Present when < code > with_counts=true< / code > . One column per genome; each row holds the
per-genome k-mer count for the corresponding MPHF slot. Appended column-by-column
during indexing and merge.< / p >
< h3 id = "presence-persistentbitmatrix" > presence/ (PersistentBitMatrix)< / h3 >
< p > Present when the layer was built in presence/absence mode (merge path).
One bit per genome per MPHF slot. Written during merge; never present on a
freshly indexed single-genome layer.< / p >
< h2 id = "metajson-partitionmeta" > meta.json (PartitionMeta)< / h2 >
< div class = "highlight" > < pre > < span > < / span > < code > < span class = "p" > {< / span > < span class = "w" > < / span > < span class = "nt" > " n_layers" < / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "mi" > 2< / span > < span class = "w" > < / span > < span class = "p" > }< / span >
< / code > < / pre > < / div >
< p > Records how many < code > layer_N/< / code > directories exist under < code > index/< / code > . Incremented by
each merge that adds a layer.< / p >
2026-04-16 22:38:20 +02:00
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