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< h1 id = "kmer-implementation" > Kmer — implementation< / h1 >
< h2 id = "memory-layout" > Memory layout< / h2 >
< p > < code > Kmer< / code > is a < code > #[repr(transparent)]< / code > newtype over < code > u64< / code > :< / p >
< div class = "highlight" > < pre > < span > < / span > < code > < span class = "cp" > #[repr(transparent)]< / span >
< span class = "k" > pub< / span > < span class = "w" > < / span > < span class = "k" > struct< / span > < span class = "w" > < / span > < span class = "nc" > Kmer< / span > < span class = "p" > (< / span > < span class = "kt" > u64< / span > < span class = "p" > );< / span >
< / code > < / pre > < / div >
< p > Nucleotides are packed 2 bits each, < strong > left-aligned< / strong > , MSB-first. Nucleotide 0 occupies bits 63– 62; nucleotide i occupies bits 63− 2i and 62− 2i. The low 64− 2k bits are always zero. k is < strong > not stored< / strong > — it is a parameter of every operation that needs it, and will be owned by the future collection-level indexer.< / p >
< table >
< thead >
< tr >
< th > 63– 62< / th >
< th > 61– 60< / th >
< th > …< / th >
< th > 63− 2(k− 1)− 1 to 63− 2(k− 1)< / th >
< th > 63− 2k down to 0< / th >
< / tr >
< / thead >
< tbody >
< tr >
< td > nt 0< / td >
< td > nt 1< / td >
< td > …< / td >
< td > nt k− 1< / td >
< td > zero padding< / td >
< / tr >
< / tbody >
< / table >
< h2 id = "encoding" > Encoding< / h2 >
< p > < code > Kmer::from_ascii(ascii, k)< / code > encodes the first k bytes of an ASCII slice using the shared < code > ENC< / code > table (see < a href = "../superkmer/#ascii-encoding-and-decoding" > SuperKmer — ASCII encoding< / a > ):< / p >
< 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 >
< span class = "n" > Kmer< / 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 >
< / code > < / pre > < / div >
< p > Zero allocation — result lives on the stack.< / p >
< h2 id = "decoding" > Decoding< / h2 >
< p > < code > write_ascii(k, buf)< / code > appends k ASCII characters to a caller-supplied < code > Vec< u8> < / code > using the shared < code > DEC4< / code > table: one lookup per 4 nucleotides, two partial-byte lookups for the remainder. No allocation in the hot path.< / p >
< p > < code > to_ascii(k)< / code > is a convenience wrapper that allocates and returns a < code > Vec< u8> < / code > ; intended for tests and display only.< / p >
< 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 >
< span class = "n" > Kmer< / 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 >
< / 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 >
< h2 id = "canonical-form" > Canonical form< / h2 >
< 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 = "n" > k< / 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 = "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 = "n" > k< / span > < span class = "p" > );< / span >
< span class = "w" > < / 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 = "o" > *< / span > < span class = "bp" > self< / 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 = "w" > < / span > < span class = "p" > }< / span >
< 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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