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Three usage modes
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MphfLayer — autonomous kmer → slot mapping
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Layer\< D: LayerData> — MPHF + payload
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Three usage modes
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MphfLayer — autonomous kmer → slot mapping
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Layer\< D: LayerData> — MPHF + payload
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Evidence encoding
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< h1 id = "obilayeredmap-layered-kmer-index-crate" > obilayeredmap — layered kmer index crate< / h1 >
< h2 id = "purpose" > Purpose< / h2 >
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< p > < code > obilayeredmap< / code > implements a persistent, incrementally extensible kmer index. The index is organised in three levels: < strong > index root → partition → layer< / strong > . Each layer covers a disjoint kmer set and wraps a < code > ptr_hash< / code > MPHF with associated per-slot data. Adding a new dataset never rebuilds existing layers.< / p >
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< hr / >
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< h2 id = "three-usage-modes" > Three usage modes< / h2 >
< p > The MPHF + evidence infrastructure is the same for all modes. The < strong > payload< / strong > varies.< / p >
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< table >
< thead >
< tr >
< th > Mode< / th >
< th > Description< / th >
< th > Payload type< / th >
< th > Storage< / th >
< / tr >
< / thead >
< tbody >
< tr >
< td > 1. Set< / td >
< td > membership test only< / td >
< td > < code > ()< / code > < / td >
< td > —< / td >
< / tr >
< tr >
< td > 2. Count< / td >
< td > occurrences per kmer per sample< / td >
< td > < code > PersistentCompactIntMatrix< / code > < / td >
< td > < code > counts/< / code > directory< / td >
< / tr >
< tr >
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< td > 3. Presence/absence< / td >
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< td > which genomes contain each kmer< / td >
< td > < code > PersistentBitMatrix< / code > < / td >
< td > < code > presence/< / code > directory< / td >
< / tr >
< / tbody >
< / table >
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< p > Both < code > PersistentCompactIntMatrix< / code > and < code > PersistentBitMatrix< / code > come from the < code > obicompactvec< / code > crate.< / p >
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< hr / >
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< h2 id = "mphflayer-autonomous-kmer-slot-mapping" > MphfLayer — autonomous kmer → slot mapping< / h2 >
< p > < code > MphfLayer< / code > encapsulates the MPHF + evidence + unitig spine for one layer. It is independent of any payload data.< / 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" > MphfLayer< / span > < span class = "w" > < / span > < span class = "p" > {< / span >
< span class = "w" > < / span > < span class = "n" > mphf< / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "nc" > Mphf< / span > < span class = "p" > ,< / span >
< span class = "w" > < / span > < span class = "n" > evidence< / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "nc" > Evidence< / span > < span class = "p" > ,< / span >
< span class = "w" > < / span > < span class = "n" > unitigs< / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "nc" > UnitigFileReader< / 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 = "w" > < / span > < span class = "c1" > // number of indexed kmers = number of MPHF slots< / span >
< span class = "p" > }< / span >
< / code > < / pre > < / div >
< p > Public API:< / p >
< div class = "highlight" > < pre > < span > < / span > < code > < span class = "k" > impl< / span > < span class = "w" > < / span > < span class = "n" > MphfLayer< / 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" > open< / span > < span class = "p" > (< / span > < span class = "n" > dir< / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "kp" > & < / span > < span class = "nc" > Path< / span > < span class = "p" > )< / span > < span class = "w" > < / span > < span class = "p" > -> < / span > < span class = "w" > < / span > < span class = "nc" > OLMResult< / span > < span class = "o" > < < / span > < span class = "bp" > Self< / span > < span class = "o" > > < / 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" > find< / span > < span class = "p" > (< / span > < span class = "o" > & < / span > < span class = "bp" > self< / span > < span class = "p" > ,< / span > < span class = "w" > < / span > < span class = "n" > kmer< / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "nc" > CanonicalKmer< / span > < span class = "p" > )< / span > < span class = "w" > < / span > < span class = "p" > -> < / span > < span class = "w" > < / span > < span class = "nb" > Option< / span > < span class = "o" > < < / span > < span class = "kt" > usize< / span > < span class = "o" > > < / span > < span class = "w" > < / span > < span class = "c1" > // Some(slot) or None< / 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" > n< / span > < span class = "p" > (< / span > < span class = "o" > & < / span > < span class = "bp" > self< / span > < span class = "p" > )< / span > < span class = "w" > < / span > < span class = "p" > -> < / span > < span class = "w" > < / span > < span class = "kt" > usize< / span >
< span class = "w" > < / span > < span class = "nc" > pub< / span > < span class = "w" > < / span > < span class = "k" > fn< / span > < span class = "w" > < / span > < span class = "nf" > unitig_writer< / span > < span class = "p" > (< / span > < span class = "n" > dir< / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "kp" > & < / span > < span class = "nc" > Path< / span > < span class = "p" > )< / span > < span class = "w" > < / span > < span class = "p" > -> < / span > < span class = "w" > < / span > < span class = "nc" > OLMResult< / span > < span class = "o" > < < / span > < span class = "n" > UnitigFileWriter< / span > < span class = "o" > > < / 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 = "k" > fn< / span > < span class = "w" > < / span > < span class = "nf" > build< / span > < span class = "p" > (< / span >
< span class = "w" > < / span > < span class = "n" > dir< / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "kp" > & < / span > < span class = "nc" > Path< / span > < span class = "p" > ,< / span >
< span class = "w" > < / span > < span class = "n" > fill_slot< / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "kp" > & < / span > < span class = "nc" > mut< / span > < span class = "w" > < / span > < span class = "k" > impl< / 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" > CanonicalKmer< / span > < span class = "p" > )< / span > < span class = "w" > < / span > < span class = "p" > -> < / span > < span class = "w" > < / span > < span class = "nc" > OLMResult< / span > < span class = "o" > < < / span > < span class = "p" > ()< / span > < span class = "o" > > < / 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 = "nc" > OLMResult< / span > < span class = "o" > < < / span > < span class = "kt" > usize< / span > < span class = "o" > > < / span >
< span class = "p" > }< / span >
< / code > < / pre > < / div >
< p > < code > find< / code > returns < code > Some(slot)< / code > only after verifying via evidence that the kmer is actually indexed. It returns < code > None< / code > for absent keys (ptr_hash maps any input to a valid slot; evidence verification is the only correct-membership test).< / p >
< p > < code > build< / code > runs two sequential passes over < code > unitigs.bin< / code > :< / p >
< ol >
< li > < strong > Pass 1< / strong > : iterate all canonical kmers in parallel via rayon, construct and store < code > mphf.bin< / code > . < code > new_from_par_iter< / code > avoids materialising a full key < code > Vec< / code > .< / li >
< li > < strong > Pass 2< / strong > : iterate again sequentially, fill < code > evidence.bin< / code > , call < code > fill_slot(slot, kmer)< / code > once per kmer for payload population. A compact < code > n/8< / code > -byte seen-bitset verifies MPHF injectivity inline.< / li >
< / ol >
< p > For empty layers (n = 0), < code > build< / code > returns < code > Ok(0)< / code > immediately after creating empty < code > mphf.bin< / code > and < code > evidence.bin< / code > .< / p >
< hr / >
< h2 id = "layerd-layerdata-mphf-payload" > Layer\< D: LayerData> — MPHF + payload< / h2 >
< p > < code > Layer< D> < / code > pairs an < code > MphfLayer< / code > with one payload store.< / p >
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< 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" > LayerData< / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "nb" > Sized< / span > < span class = "w" > < / span > < span class = "p" > {< / span >
< span class = "w" > < / span > < span class = "k" > type< / span > < span class = "w" > < / span > < span class = "nc" > Item< / span > < span class = "p" > ;< / span >
< span class = "w" > < / span > < span class = "k" > fn< / span > < span class = "w" > < / span > < span class = "nf" > open< / span > < span class = "p" > (< / span > < span class = "n" > layer_dir< / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "kp" > & < / span > < span class = "nc" > Path< / span > < span class = "p" > )< / span > < span class = "w" > < / span > < span class = "p" > -> < / span > < span class = "w" > < / span > < span class = "nc" > OLMResult< / span > < span class = "o" > < < / span > < span class = "bp" > Self< / span > < span class = "o" > > < / span > < span class = "p" > ;< / span >
< span class = "w" > < / span > < span class = "k" > fn< / span > < span class = "w" > < / span > < span class = "nf" > read< / span > < span class = "p" > (< / span > < span class = "o" > & < / span > < span class = "bp" > self< / 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 = "p" > -> < / span > < span class = "w" > < / span > < span class = "nc" > Self< / span > < span class = "p" > ::< / span > < span class = "n" > Item< / span > < span class = "p" > ;< / span >
< span class = "p" > }< / span >
< span class = "k" > pub< / span > < span class = "w" > < / span > < span class = "k" > struct< / span > < span class = "w" > < / span > < span class = "nc" > Layer< / span > < span class = "o" > < < / span > < span class = "n" > D< / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "nc" > LayerData< / span > < span class = "w" > < / span > < span class = "o" > =< / span > < span class = "w" > < / span > < span class = "p" > ()< / span > < span class = "o" > > < / span > < span class = "w" > < / span > < span class = "p" > {< / span >
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< span class = "w" > < / span > < span class = "n" > mphf< / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "nc" > MphfLayer< / span > < span class = "p" > ,< / span >
< span class = "w" > < / span > < span class = "n" > data< / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "nc" > D< / span > < span class = "p" > ,< / span >
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< span class = "p" > }< / span >
< span class = "k" > pub< / span > < span class = "w" > < / span > < span class = "k" > struct< / span > < span class = "w" > < / span > < span class = "nc" > Hit< / span > < span class = "o" > < < / span > < span class = "n" > T< / span > < span class = "w" > < / span > < span class = "o" > =< / span > < span class = "w" > < / span > < span class = "p" > ()< / span > < span class = "o" > > < / 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" > 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 = "w" > < / span > < span class = "n" > data< / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "nc" > T< / span > < span class = "p" > ,< / span >
< span class = "p" > }< / span >
< / code > < / pre > < / div >
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< p > < code > LayerData< / code > covers the < strong > read path only< / strong > (< code > open< / code > + < code > read< / code > ). Build signatures differ between modes and are not in the trait.< / p >
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< table >
< thead >
< tr >
< th > Type< / th >
< th > < code > Item< / code > < / th >
< th > Description< / th >
< / tr >
< / thead >
< tbody >
< tr >
< td > < code > ()< / code > < / td >
< td > < code > ()< / code > < / td >
< td > mode 1 — membership only< / td >
< / tr >
< tr >
< td > < code > PersistentCompactIntMatrix< / code > < / td >
< td > < code > Box< [u32]> < / code > < / td >
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< td > mode 2 — count matrix (one u32 per column per slot)< / td >
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< / tr >
< tr >
< td > < code > PersistentBitMatrix< / code > < / td >
< td > < code > Box< [bool]> < / code > < / td >
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< td > mode 3 — presence matrix (one bit per genome per slot)< / td >
< / tr >
< / tbody >
< / table >
< p > < strong > Build signatures:< / strong > < / p >
< div class = "highlight" > < pre > < span > < / span > < code > < span class = "c1" > // mode 1< / span >
< span class = "k" > impl< / span > < span class = "w" > < / span > < span class = "n" > Layer< / span > < span class = "o" > < < / span > < span class = "p" > ()< / span > < span class = "o" > > < / 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" > build< / span > < span class = "p" > (< / span > < span class = "n" > out_dir< / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "kp" > & < / span > < span class = "nc" > Path< / span > < span class = "p" > )< / span > < span class = "w" > < / span > < span class = "p" > -> < / span > < span class = "w" > < / span > < span class = "nc" > OLMResult< / span > < span class = "o" > < < / span > < span class = "kt" > usize< / span > < span class = "o" > > < / span >
< span class = "p" > }< / span >
< span class = "c1" > // mode 2< / span >
< span class = "k" > impl< / span > < span class = "w" > < / span > < span class = "n" > Layer< / span > < span class = "o" > < < / span > < span class = "n" > PersistentCompactIntMatrix< / span > < span class = "o" > > < / 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" > build< / span > < span class = "p" > (< / span > < span class = "n" > out_dir< / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "kp" > & < / span > < span class = "nc" > Path< / span > < span class = "p" > ,< / span > < span class = "w" > < / span > < span class = "n" > count_of< / 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 = "n" > CanonicalKmer< / span > < span class = "p" > )< / span > < span class = "w" > < / 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" > -> < / span > < span class = "w" > < / span > < span class = "nc" > OLMResult< / span > < span class = "o" > < < / span > < span class = "kt" > usize< / span > < span class = "o" > > < / 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" > build_from_map< / span > < span class = "p" > (< / span > < span class = "n" > out_dir< / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "kp" > & < / span > < span class = "nc" > Path< / span > < span class = "p" > ,< / span > < span class = "w" > < / span > < span class = "n" > counts< / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "kp" > & < / span > < span class = "nc" > HashMap< / span > < span class = "o" > < < / span > < span class = "n" > CanonicalKmer< / span > < span class = "p" > ,< / span > < span class = "w" > < / span > < span class = "kt" > u32< / span > < span class = "o" > > < / span > < span class = "p" > )< / span > < span class = "w" > < / span > < span class = "p" > -> < / span > < span class = "w" > < / span > < span class = "nc" > OLMResult< / span > < span class = "o" > < < / span > < span class = "kt" > usize< / span > < span class = "o" > > < / span >
< span class = "p" > }< / span >
< span class = "c1" > // mode 3< / span >
< span class = "k" > impl< / span > < span class = "w" > < / span > < span class = "n" > Layer< / span > < span class = "o" > < < / span > < span class = "n" > PersistentBitMatrix< / span > < span class = "o" > > < / 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" > build_presence< / span > < span class = "p" > (< / span >
< span class = "w" > < / span > < span class = "n" > out_dir< / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "kp" > & < / span > < span class = "nc" > Path< / 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 = "w" > < / span > < span class = "n" > present_in< / 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 = "n" > CanonicalKmer< / 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" > -> < / span > < span class = "w" > < / span > < span class = "kt" > bool< / 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 = "nc" > OLMResult< / span > < span class = "o" > < < / span > < span class = "kt" > usize< / span > < span class = "o" > > < / span >
< span class = "p" > }< / span >
< / code > < / pre > < / div >
< p > All build impls delegate MPHF + evidence construction to < code > MphfLayer::build< / code > via a mode-specific < code > fill_slot< / code > callback. Mode 2 pre-reads < code > n_kmers< / code > from < code > unitigs.bin< / code > to size the < code > PersistentCompactIntMatrixBuilder< / code > before calling < code > MphfLayer::build< / code > . Mode 3 does the same for < code > PersistentBitMatrixBuilder< / code > .< / p >
< hr / >
< h2 id = "layeredstores-and-aggregation-traits" > LayeredStore\< S> and aggregation traits< / h2 >
< p > < code > LayeredStore< S> < / code > is a generic aggregation wrapper over < code > Vec< S> < / code > . It propagates three traits from < code > obicompactvec::traits< / code > up the hierarchy via blanket impls:< / 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" > LayeredStore< / span > < span class = "o" > < < / span > < span class = "n" > S< / span > < span class = "o" > > < / span > < span class = "p" > (< / span > < span class = "k" > pub< / span > < span class = "w" > < / span > < span class = "nb" > Vec< / span > < span class = "o" > < < / span > < span class = "n" > S< / span > < span class = "o" > > < / span > < span class = "p" > );< / span >
< span class = "k" > impl< / span > < span class = "o" > < < / span > < span class = "n" > S< / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "nc" > ColumnWeights< / span > < span class = "o" > > < / span > < span class = "w" > < / span > < span class = "n" > ColumnWeights< / span > < span class = "w" > < / span > < span class = "k" > for< / span > < span class = "w" > < / span > < span class = "n" > LayeredStore< / span > < span class = "o" > < < / span > < span class = "n" > S< / span > < span class = "o" > > < / 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 = "w" > < / span > < span class = "c1" > // Σ col_weights across inner stores< / span >
< span class = "k" > impl< / span > < span class = "o" > < < / span > < span class = "n" > S< / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "nc" > CountPartials< / span > < span class = "o" > > < / span > < span class = "w" > < / span > < span class = "n" > CountPartials< / span > < span class = "w" > < / span > < span class = "k" > for< / span > < span class = "w" > < / span > < span class = "n" > LayeredStore< / span > < span class = "o" > < < / span > < span class = "n" > S< / span > < span class = "o" > > < / 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 = "w" > < / span > < span class = "c1" > // element-wise Σ partials< / span >
< span class = "k" > impl< / span > < span class = "o" > < < / span > < span class = "n" > S< / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "nc" > BitPartials< / span > < span class = "o" > > < / span > < span class = "w" > < / span > < span class = "n" > BitPartials< / span > < span class = "w" > < / span > < span class = "k" > for< / span > < span class = "w" > < / span > < span class = "n" > LayeredStore< / span > < span class = "o" > < < / span > < span class = "n" > S< / span > < span class = "o" > > < / 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 = "w" > < / span > < span class = "c1" > // element-wise Σ partials< / span >
< / code > < / pre > < / div >
< p > Because blanket impls compose, < code > LayeredStore< LayeredStore< S> > < / code > automatically inherits all three traits when < code > S< / code > does — providing the partitioned level without a separate type.< / p >
< p > < strong > Aggregation hierarchy:< / strong > < / p >
< div class = "highlight" > < pre > < span > < / span > < code > PersistentCompactIntMatrix implements CountPartials
LayeredStore< PersistentCompactIntMatrix> via blanket impl (one partition)
LayeredStore< LayeredStore< …> > via blanket impl (partitioned index)
< / code > < / pre > < / div >
< p > < strong > Leaf implementors< / strong > (in < code > obicompactvec< / code > ):< / p >
< table >
< thead >
< tr >
< th > Type< / th >
< th > Traits< / th >
< / tr >
< / thead >
< tbody >
< tr >
< td > < code > PersistentCompactIntMatrix< / code > < / td >
< td > < code > ColumnWeights< / code > (via < code > sum()< / code > ) + < code > CountPartials< / code > < / td >
< / tr >
< tr >
< td > < code > PersistentBitMatrix< / code > < / td >
< td > < code > ColumnWeights< / code > (via < code > count_ones()< / code > ) + < code > BitPartials< / code > < / td >
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< / tr >
< / tbody >
< / table >
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< p > < code > PersistentCompactIntVec< / code > and < code > PersistentBitVec< / code > do not implement these traits — they are single-column primitives, not matrix-level aggregators.< / p >
< p > See < a href = "../../architecture/index_architecture/" > Kmer index architecture< / a > for the full trait API and the two-pass normalised-metric pattern.< / p >
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< hr / >
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< h2 id = "on-disk-structure" > On-disk structure< / h2 >
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< div class = "highlight" > < pre > < span > < / span > < code > index_root/ ← LayeredMap (collection)
meta.json
part_00000/ ← Partition
layer_0/ ← Layer
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mphf.bin — ptr_hash MPHF (epserde format)
unitigs.bin — packed 2-bit nucleotide sequences
unitigs.bin.idx — UIDX index: n_unitigs, n_kmers, seqls[], packed_offsets[]
evidence.bin — n ×
counts/ [mode 2] PersistentCompactIntMatrix
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meta.json {" n" : N, " n_cols" : 1}
col_000000.pciv
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presence/ [mode 3] PersistentBitMatrix
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meta.json {" n" : N, " n_cols" : G}
col_000000.pbiv
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…
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layer_1/
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…
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part_00001/
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…
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< / code > < / pre > < / div >
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< p > < strong > Partition< / strong > (< code > part_XXXXX/< / code > ): all kmers whose canonical minimiser hashes to this bucket. Partitions are independent and can be processed in parallel.< / p >
< p > < strong > Layer< / strong > (< code > layer_N/< / code > ): one < code > MphfLayer< / code > plus optional payload. Layer 0 covers dataset A; layer 1 covers kmers in B absent from A; etc. Layers within a partition are always disjoint.< / p >
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< hr / >
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< h2 id = "evidence-encoding" > Evidence encoding< / h2 >
< p > < code > evidence.bin< / code > is a flat < code > [u32; n]< / code > array with no header. Each u32 encodes one slot:< / p >
< div class = "highlight" > < pre > < span > < / span > < code > 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)
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< / code > < / pre > < / div >
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< p > Decoding: < code > chunk_id = raw > > 7< / code > , < code > rank = raw & 0x7F< / code > . Reconstructing the kmer: read k nucleotides at position < code > rank< / code > within unitig < code > chunk_id< / code > .< / p >
< p > For k=31, m=11, the observed maximum is ~46 kmers per chunk — well within the 127-kmer u7 capacity. The structural maximum from superkmer construction is k − < / p >
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< hr / >
< h2 id = "ptr_hash-configuration" > ptr_hash configuration< / h2 >
< div class = "highlight" > < pre > < span > < / span > < code > < span class = "k" > type< / span > < span class = "w" > < / span > < span class = "nc" > Mphf< / span > < span class = "w" > < / span > < span class = "o" > =< / span > < span class = "w" > < / span > < span class = "n" > PtrHash< / span > < span class = "o" > < < / span >
< span class = "w" > < / span > < span class = "kt" > u64< / span > < span class = "p" > ,< / span > < span class = "w" > < / span > < span class = "c1" > // key type: canonical kmer raw encoding< / span >
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< span class = "w" > < / span > < span class = "n" > CubicEps< / span > < span class = "p" > ,< / span > < span class = "w" > < / span > < span class = "c1" > // bucket fn: 2.4 bits/key, λ=3.5, α < / span >
< span class = "w" > < / span > < span class = "n" > CachelineEfVec< / span > < span class = "o" > < < / span > < span class = "nb" > Vec< / span > < span class = "o" > < < / span > < span class = "n" > CachelineEf< / span > < span class = "o" > > > < / span > < span class = "p" > ,< / span > < span class = "w" > < / span > < span class = "c1" > // remap: 11.6 bits/entry (Elias-Fano)< / span >
< span class = "w" > < / span > < span class = "n" > Xx64< / span > < span class = "p" > ,< / span > < span class = "w" > < / span > < span class = "c1" > // hasher: XXH3-64 with seed< / span >
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< span class = "w" > < / span > < span class = "nb" > Vec< / span > < span class = "o" > < < / span > < span class = "kt" > u8< / span > < span class = "o" > > < / span > < span class = "p" > ,< / span > < span class = "w" > < / span > < span class = "c1" > // pilots< / span >
< span class = "o" > > < / span > < span class = "p" > ;< / span >
< / code > < / pre > < / div >
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< p > < code > Xx64< / code > is chosen over < code > FxHash< / code > 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.< / p >
< p > < code > CubicEps< / code > with < code > PtrHashParams::< CubicEps> ::default()< / code > (λ=3.5) is a balanced tradeoff: 2× < code > Linear/λ=3.0< / code > , 20% less space.< / p >
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< hr / >
< h2 id = "query-path" > Query path< / h2 >
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< 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" > query< / span > < span class = "p" > (< / span > < span class = "o" > & < / span > < span class = "bp" > self< / span > < span class = "p" > ,< / span > < span class = "w" > < / span > < span class = "n" > kmer< / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "nc" > CanonicalKmer< / span > < span class = "p" > )< / span > < span class = "w" > < / span > < span class = "p" > -> < / span > < span class = "w" > < / span > < span class = "nb" > Option< / span > < span class = "o" > < < / span > < span class = "n" > Hit< / span > < span class = "o" > < < / span > < span class = "n" > D< / span > < span class = "p" > ::< / span > < span class = "n" > Item< / span > < span class = "o" > > > < / 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" > mphf< / span > < span class = "p" > .< / span > < span class = "n" > find< / span > < span class = "p" > (< / span > < span class = "n" > kmer< / span > < span class = "p" > ).< / span > < span class = "n" > map< / span > < span class = "p" > (< / span > < span class = "o" > |< / span > < span class = "n" > slot< / span > < span class = "o" > |< / span > < span class = "w" > < / span > < span class = "n" > Hit< / span > < span class = "w" > < / span > < span class = "p" > {< / span > < span class = "w" > < / span > < span class = "n" > slot< / span > < span class = "p" > ,< / span > < span class = "w" > < / span > < span class = "n" > data< / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "nc" > self< / span > < span class = "p" > .< / span > < span class = "n" > data< / span > < span class = "p" > .< / span > < span class = "n" > read< / span > < span class = "p" > (< / span > < span class = "n" > slot< / span > < span class = "p" > )< / span > < span class = "w" > < / span > < span class = "p" > })< / span >
< span class = "p" > }< / span >
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< / code > < / pre > < / div >
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< p > < code > MphfLayer::find< / code > probes the MPHF, decodes evidence, and verifies the kmer — returning < code > Some(slot)< / code > on match, < code > None< / code > otherwise. < code > data.read(slot)< / code > is called only on a confirmed hit.< / p >
< p > In < code > LayeredMap< / code > , layers are probed in order; the first match wins. Expected probe depth: 1 for kmers in layer 0.< / p >
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< hr / >
< h2 id = "add-layer-algorithm" > Add-layer algorithm< / h2 >
< p > When adding dataset B to an existing index:< / p >
< ol >
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< li > For each partition, probe existing layers for kmers of B routed to that partition.< / li >
< li > Collect kmers absent from all layers → < code > B \ index< / code > .< / li >
< li > Write < code > B \ index< / code > to a new < code > unitigs.bin< / code > via < code > MphfLayer::unitig_writer< / code > .< / li >
< li > Call < code > Layer< D> ::build< / code > on the new directory.< / li >
< li > Update < code > meta.json< / code > .< / li >
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< / ol >
< p > Each partition's new layer is built independently; the operation is fully parallel across partitions.< / p >
< hr / >
< h2 id = "dependencies" > Dependencies< / h2 >
< table >
< thead >
< tr >
< th > crate< / th >
< th > role< / th >
< / tr >
< / thead >
< tbody >
< tr >
< td > < code > ptr_hash 1.1< / code > < / td >
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< td > MPHF per layer< / td >
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< / tr >
< tr >
< td > < code > cacheline-ef 1.1< / code > < / td >
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< td > compact remap inside ptr_hash< / td >
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< / tr >
< tr >
< td > < code > epserde 0.8< / code > < / td >
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< td > zero-copy MPHF serialisation< / td >
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< / tr >
< tr >
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< td > < code > memmap2 0.9< / code > < / td >
< td > mmap of evidence and payload files< / td >
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< / tr >
< tr >
< td > < code > obiskio< / code > < / td >
< td > unitig file writer/reader< / td >
< / tr >
< tr >
< td > < code > obicompactvec< / code > < / td >
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< td > payload types + aggregation traits< / td >
< / tr >
< tr >
< td > < code > rayon 1< / code > < / td >
< td > parallel MPHF construction pass< / td >
< / tr >
< tr >
< td > < code > ndarray 0.16< / code > < / td >
< td > aggregation output arrays< / td >
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< / tr >
< / tbody >
< / table >
< / article >
< / div >
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