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Canonical form and CanonicalKmerOf
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Kmer filtering (rebuild/dump/unitig)
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Types and layout
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Canonical form and CanonicalKmerOf
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Hashing
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< h1 id = "kmer-implementation" > Kmer — implementation< / h1 >
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< h2 id = "types-and-layout" > Types and layout< / h2 >
< p > < code > KmerOf< L> < / code > is a < code > #[repr(transparent)]< / code > newtype over < code > u64< / code > parameterized by a < code > KmerLength< / code > marker:< / p >
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< div class = "highlight" > < pre > < span > < / span > < code > < span class = "cp" > #[repr(transparent)]< / span >
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< span class = "k" > pub< / span > < span class = "w" > < / span > < span class = "k" > struct< / span > < span class = "w" > < / span > < span class = "nc" > KmerOf< / span > < span class = "o" > < < / span > < span class = "n" > L< / span > < span class = "p" > :< / span > < span class = "w" > < / span > < span class = "nc" > KmerLength< / span > < span class = "o" > > < / span > < span class = "p" > (< / span > < span class = "kt" > u64< / span > < span class = "p" > ,< / span > < span class = "w" > < / span > < span class = "n" > PhantomData< / span > < span class = "o" > < < / span > < span class = "n" > L< / span > < span class = "o" > > < / span > < span class = "p" > );< / span >
< / code > < / pre > < / div >
< p > Three marker types implement < code > KmerLength< / code > :< / p >
< table >
< thead >
< tr >
< th > Marker< / th >
< th > < code > len()< / code > source< / th >
< th > Used for< / th >
< / tr >
< / thead >
< tbody >
< tr >
< td > < code > KLen< / code > < / td >
< td > < code > params::k()< / code > < / td >
< td > k-mers< / td >
< / tr >
< tr >
< td > < code > MLen< / code > < / td >
< td > < code > params::m()< / code > < / td >
< td > minimizers< / td >
< / tr >
< tr >
< td > < code > ConstLen< N> < / code > < / td >
< td > const generic < code > N< / code > < / td >
< td > tests< / td >
< / tr >
< / tbody >
< / table >
< p > Public aliases:< / p >
< div class = "highlight" > < pre > < span > < / span > < code > < span class = "k" > pub< / span > < span class = "w" > < / span > < span class = "k" > type< / span > < span class = "w" > < / span > < span class = "nc" > Kmer< / span > < span class = "w" > < / span > < span class = "o" > =< / span > < span class = "w" > < / span > < span class = "n" > KmerOf< / span > < span class = "o" > < < / span > < span class = "n" > KLen< / span > < span class = "o" > > < / span > < span class = "p" > ;< / span > < span class = "w" > < / span > < span class = "c1" > // k-mer, global k< / span >
< span class = "k" > pub< / span > < span class = "w" > < / span > < span class = "k" > type< / span > < span class = "w" > < / span > < span class = "nc" > Minimizer< / span > < span class = "w" > < / span > < span class = "o" > =< / span > < span class = "w" > < / span > < span class = "n" > CanonicalKmerOf< / span > < span class = "o" > < < / span > < span class = "n" > MLen< / span > < span class = "o" > > < / span > < span class = "p" > ;< / span > < span class = "w" > < / span > < span class = "c1" > // canonical m-mer, global m< / span >
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< / code > < / pre > < / div >
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< p > Nucleotides are packed 2 bits each, < strong > left-aligned< / strong > , MSB-first. Nucleotide 0 occupies bits 63– − − − < strong > not stored< / strong > — every operation reads it from < code > L::len()< / code > .< / p >
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< table >
< thead >
< tr >
< th > 63– < / th >
< th > 61– < / th >
< th > …< / th >
< th > 63− − − − − < / th >
< th > 63− < / th >
< / tr >
< / thead >
< tbody >
< tr >
< td > nt 0< / td >
< td > nt 1< / td >
< td > …< / td >
< td > nt k− < / td >
< td > zero padding< / td >
< / tr >
< / tbody >
< / table >
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< h2 id = "global-parameters" > Global parameters< / h2 >
< p > < code > params::set_k(k)< / code > / < code > params::k()< / code > and < code > params::set_m(m)< / code > / < code > params::m()< / code > are backed by < code > OnceLock< usize> < / code > in production (write-once, panic on conflict) and by < code > thread_local! { Cell< usize> }< / code > in test builds (per-thread, freely writable). < code > params::init(k, m)< / code > sets both in one call.< / p >
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< h2 id = "encoding" > Encoding< / h2 >
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< p > < code > KmerOf::< L> ::from_ascii(ascii)< / code > encodes the first < code > L::len()< / code > bytes using the shared < code > ENC< / code > table (see < a href = "../superkmer/#ascii-encoding-and-decoding" > SuperKmer — ASCII encoding< / a > ):< / p >
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< div class = "highlight" > < pre > < span > < / span > < code > < span class = "k" > for< / span > < span class = "w" > < / span > < span class = "n" > i< / span > < span class = "w" > < / span > < span class = "k" > in< / span > < span class = "w" > < / span > < span class = "mi" > 0< / span > < span class = "o" > ..< / span > < span class = "n" > k< / span > < span class = "w" > < / span > < span class = "p" > {< / span >
< span class = "w" > < / span > < span class = "n" > val< / span > < span class = "w" > < / span > < span class = "o" > =< / span > < span class = "w" > < / span > < span class = "p" > (< / span > < span class = "n" > val< / span > < span class = "w" > < / span > < span class = "o" > < < < / span > < span class = "w" > < / span > < span class = "mi" > 2< / span > < span class = "p" > )< / span > < span class = "w" > < / span > < span class = "o" > |< / span > < span class = "w" > < / span > < span class = "n" > encode_base< / span > < span class = "p" > (< / span > < span class = "n" > ascii< / span > < span class = "p" > [< / span > < span class = "n" > i< / span > < span class = "p" > ])< / span > < span class = "w" > < / span > < span class = "k" > as< / span > < span class = "w" > < / span > < span class = "kt" > u64< / span > < span class = "p" > ;< / span >
< span class = "p" > }< / span >
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< span class = "n" > KmerOf< / span > < span class = "p" > (< / span > < span class = "n" > val< / span > < span class = "w" > < / span > < span class = "o" > < < < / span > < span class = "w" > < / span > < span class = "p" > (< / span > < span class = "mi" > 64< / span > < span class = "w" > < / span > < span class = "o" > -< / span > < span class = "w" > < / span > < span class = "mi" > 2< / span > < span class = "w" > < / span > < span class = "o" > *< / span > < span class = "w" > < / span > < span class = "n" > k< / span > < span class = "p" > ),< / span > < span class = "w" > < / span > < span class = "n" > PhantomData< / span > < span class = "p" > )< / span >
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< / code > < / pre > < / div >
< p > Zero allocation — result lives on the stack.< / p >
< h2 id = "decoding" > Decoding< / h2 >
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< p > < code > write_ascii(writer)< / code > writes k ASCII characters to any < code > W: Write< / code > using the shared < code > DEC4< / code > table: one lookup per 4 nucleotides, one partial lookup for the remainder. No allocation in the hot path.< / p >
< p > < code > to_ascii()< / code > is a convenience wrapper that allocates and returns a < code > Vec< u8> < / code > ; intended for tests and display only.< / p >
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< h2 id = "reverse-complement" > Reverse complement< / h2 >
< p > Computed as pure arithmetic — no lookup table, no memory access:< / p >
< div class = "highlight" > < pre > < span > < / span > < code > < span class = "kd" > let< / span > < span class = "w" > < / span > < span class = "n" > x< / span > < span class = "w" > < / span > < span class = "o" > =< / span > < span class = "w" > < / span > < span class = "o" > !< / span > < span class = "bp" > self< / span > < span class = "p" > .< / span > < span class = "mi" > 0< / span > < span class = "p" > ;< / span > < span class = "w" > < / span > < span class = "c1" > // complement< / span >
< span class = "kd" > let< / span > < span class = "w" > < / span > < span class = "n" > x< / span > < span class = "w" > < / span > < span class = "o" > =< / span > < span class = "w" > < / span > < span class = "n" > x< / span > < span class = "p" > .< / span > < span class = "n" > swap_bytes< / span > < span class = "p" > ();< / span > < span class = "w" > < / span > < span class = "c1" > // reverse bytes< / span >
< span class = "kd" > let< / span > < span class = "w" > < / span > < span class = "n" > x< / span > < span class = "w" > < / span > < span class = "o" > =< / span > < span class = "w" > < / span > < span class = "p" > ((< / span > < span class = "n" > x< / span > < span class = "w" > < / span > < span class = "o" > > > < / span > < span class = "w" > < / span > < span class = "mi" > 4< / span > < span class = "p" > )< / span > < span class = "w" > < / span > < span class = "o" > & < / span > < span class = "w" > < / span > < span class = "mh" > 0x0F0F0F0F0F0F0F0F< / span > < span class = "p" > )< / span > < span class = "w" > < / span > < span class = "o" > |< / span > < span class = "w" > < / span > < span class = "p" > ((< / span > < span class = "n" > x< / span > < span class = "w" > < / span > < span class = "o" > & < / span > < span class = "w" > < / span > < span class = "mh" > 0x0F0F0F0F0F0F0F0F< / span > < span class = "p" > )< / span > < span class = "w" > < / span > < span class = "o" > < < < / span > < span class = "w" > < / span > < span class = "mi" > 4< / span > < span class = "p" > );< / span > < span class = "w" > < / span > < span class = "c1" > // swap nibbles< / span >
< span class = "kd" > let< / span > < span class = "w" > < / span > < span class = "n" > x< / span > < span class = "w" > < / span > < span class = "o" > =< / span > < span class = "w" > < / span > < span class = "p" > ((< / span > < span class = "n" > x< / span > < span class = "w" > < / span > < span class = "o" > > > < / span > < span class = "w" > < / span > < span class = "mi" > 2< / span > < span class = "p" > )< / span > < span class = "w" > < / span > < span class = "o" > & < / span > < span class = "w" > < / span > < span class = "mh" > 0x3333333333333333< / span > < span class = "p" > )< / span > < span class = "w" > < / span > < span class = "o" > |< / span > < span class = "w" > < / span > < span class = "p" > ((< / span > < span class = "n" > x< / span > < span class = "w" > < / span > < span class = "o" > & < / span > < span class = "w" > < / span > < span class = "mh" > 0x3333333333333333< / span > < span class = "p" > )< / span > < span class = "w" > < / span > < span class = "o" > < < < / span > < span class = "w" > < / span > < span class = "mi" > 2< / span > < span class = "p" > );< / span > < span class = "w" > < / span > < span class = "c1" > // swap 2-bit groups< / span >
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< span class = "n" > KmerOf< / span > < span class = "p" > (< / span > < span class = "n" > x< / span > < span class = "w" > < / span > < span class = "o" > < < < / span > < span class = "w" > < / span > < span class = "p" > (< / span > < span class = "mi" > 64< / span > < span class = "w" > < / span > < span class = "o" > -< / span > < span class = "w" > < / span > < span class = "mi" > 2< / span > < span class = "w" > < / span > < span class = "o" > *< / span > < span class = "w" > < / span > < span class = "n" > k< / span > < span class = "p" > ),< / span > < span class = "w" > < / span > < span class = "n" > PhantomData< / span > < span class = "p" > )< / span >
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< / code > < / pre > < / div >
< p > After complementing, bytes are reversed (< code > swap_bytes< / code > ), then nibbles, then 2-bit groups — restoring 2-bit nucleotides to their correct positions in reverse order. A final left-shift realigns to MSB. Zero allocation — result lives on the stack.< / p >
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< h2 id = "canonical-form-and-canonicalkmerof" > Canonical form and < code > CanonicalKmerOf< / code > < / h2 >
< p > < code > canonical()< / code > returns a < code > CanonicalKmerOf< L> < / code > — a distinct newtype that carries the same < code > u64< / code > layout but enforces the invariant that the stored value equals < code > min(kmer, revcomp)< / code > :< / 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" > canonical< / 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 = "nc" > CanonicalKmerOf< / span > < span class = "o" > < < / span > < span class = "n" > L< / 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" > rc< / 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" > revcomp< / span > < span class = "p" > ();< / span >
< span class = "w" > < / span > < span class = "n" > CanonicalKmerOf< / span > < span class = "p" > (< / span > < span class = "k" > if< / span > < span class = "w" > < / span > < span class = "bp" > self< / span > < span class = "p" > .< / span > < span class = "mi" > 0< / span > < span class = "w" > < / span > < span class = "o" > < =< / span > < span class = "w" > < / span > < span class = "n" > rc< / span > < span class = "p" > .< / span > < span class = "mi" > 0< / span > < span class = "w" > < / span > < span class = "p" > {< / span > < span class = "w" > < / span > < span class = "bp" > self< / span > < span class = "p" > .< / span > < span class = "mi" > 0< / 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 = "n" > rc< / span > < span class = "p" > .< / span > < span class = "mi" > 0< / span > < span class = "w" > < / span > < span class = "p" > },< / span > < span class = "w" > < / span > < span class = "n" > PhantomData< / span > < span class = "p" > )< / span >
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< span class = "p" > }< / span >
< / code > < / pre > < / div >
< p > Lexicographic minimum of forward and reverse-complement, comparing the raw < code > u64< / code > values directly (left-aligned encoding makes this equivalent to nucleotide-wise comparison). Zero allocation — result lives on the stack.< / p >
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< p > < code > CanonicalKmerOf::from_raw_unchecked(raw)< / code > is the only other public constructor, for trusted paths such as deserialisation.< / p >
< h2 id = "sliding-window-helpers" > Sliding window helpers< / h2 >
< p > < code > push_right(nuc)< / code > / < code > push_left(nuc)< / code > shift the window by one base in O(1). < code > is_overlapping(other)< / code > checks whether the last k− < code > self< / code > equal the first k− < code > other< / code > .< / p >
< h2 id = "hashing" > Hashing< / h2 >
< p > < code > hash_kmer(raw: u64) -> u64< / code > computes < code > mix64(raw ^ 0x9e3779b97f4a7c15)< / code > , the seeded splitmix64 finalizer. < code > CanonicalKmerOf::seq_hash()< / code > delegates to < code > hash_kmer< / code > .< / p >
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< script > var target = document . getElementById ( location . hash . slice ( 1 ) ) ; target && target . name && ( target . checked = target . name . startsWith ( "__tabbed_" ) ) < / script >
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