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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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