2026-04-16 22:38:20 +02:00
<!doctype html>
< html lang = "en" class = "no-js" >
< head >
< meta charset = "utf-8" >
< meta name = "viewport" content = "width=device-width,initial-scale=1" >
< link rel = "prev" href = "../superkmer/" >
< link rel = "next" href = "../chunkreader/" >
< link rel = "icon" href = "../../assets/images/favicon.png" >
< meta name = "generator" content = "mkdocs-1.6.1, mkdocs-material-9.7.6" >
< title > Kmer - obikmer</ title >
< link rel = "stylesheet" href = "../../assets/stylesheets/main.484c7ddc.min.css" >
< link rel = "preconnect" href = "https://fonts.gstatic.com" crossorigin >
< link rel = "stylesheet" href = "https://fonts.googleapis.com/css?family=Roboto:300,300i,400,400i,700,700i%7CRoboto+Mono:400,400i,700,700i&display=fallback" >
< style >: root { --md-text-font : "Roboto" ; --md-code-font : "Roboto Mono" }</ style >
< script > __md_scope = new URL ( "../.." , location ), __md_hash = e =>[... e ]. reduce ((( e , _ )=>( e << 5 ) - e + _ . charCodeAt ( 0 )), 0 ), __md_get = ( e , _ = localStorage , t = __md_scope )=> JSON . parse ( _ . getItem ( t . pathname + "." + e )), __md_set = ( e , _ , t = localStorage , a = __md_scope )=>{ try { t . setItem ( a . pathname + "." + e , JSON . stringify ( _ ))} catch ( e ){}}</ script >
</ head >
< body dir = "ltr" >
< input class = "md-toggle" data-md-toggle = "drawer" type = "checkbox" id = "__drawer" autocomplete = "off" >
< input class = "md-toggle" data-md-toggle = "search" type = "checkbox" id = "__search" autocomplete = "off" >
< label class = "md-overlay" for = "__drawer" ></ label >
< div data-md-component = "skip" >
< a href = "#kmer-implementation" class = "md-skip" >
Skip to content
</ a >
</ div >
< div data-md-component = "announce" >
</ div >
< header class = "md-header md-header--shadow" data-md-component = "header" >
< nav class = "md-header__inner md-grid" aria-label = "Header" >
< a href = "../.." title = "obikmer" class = "md-header__button md-logo" aria-label = "obikmer" data-md-component = "logo" >
< svg xmlns = "http://www.w3.org/2000/svg" viewBox = "0 0 24 24" >< path d = "M12 8a3 3 0 0 0 3-3 3 3 0 0 0-3-3 3 3 0 0 0-3 3 3 3 0 0 0 3 3m0 3.54C9.64 9.35 6.5 8 3 8v11c3.5 0 6.64 1.35 9 3.54 2.36-2.19 5.5-3.54 9-3.54V8c-3.5 0-6.64 1.35-9 3.54" /></ svg >
</ a >
< label class = "md-header__button md-icon" for = "__drawer" >
< svg xmlns = "http://www.w3.org/2000/svg" viewBox = "0 0 24 24" >< path d = "M3 6h18v2H3zm0 5h18v2H3zm0 5h18v2H3z" /></ svg >
</ label >
< div class = "md-header__title" data-md-component = "header-title" >
< div class = "md-header__ellipsis" >
< div class = "md-header__topic" >
< span class = "md-ellipsis" >
obikmer
</ span >
</ div >
< div class = "md-header__topic" data-md-component = "header-topic" >
< span class = "md-ellipsis" >
Kmer
</ span >
</ div >
</ div >
</ div >
< script > var palette = __md_get ( "__palette" ); if ( palette && palette . color ){ if ( "(prefers-color-scheme)" === palette . color . media ){ var media = matchMedia ( "(prefers-color-scheme: light)" ), input = document . querySelector ( media . matches ? "[data-md-color-media='(prefers-color-scheme: light)']" : "[data-md-color-media='(prefers-color-scheme: dark)']" ); palette . color . media = input . getAttribute ( "data-md-color-media" ), palette . color . scheme = input . getAttribute ( "data-md-color-scheme" ), palette . color . primary = input . getAttribute ( "data-md-color-primary" ), palette . color . accent = input . getAttribute ( "data-md-color-accent" )} for ( var [ key , value ] of Object . entries ( palette . color )) document . body . setAttribute ( "data-md-color-" + key , value )}</ script >
</ nav >
</ header >
< div class = "md-container" data-md-component = "container" >
< main class = "md-main" data-md-component = "main" >
< div class = "md-main__inner md-grid" >
< div class = "md-sidebar md-sidebar--primary" data-md-component = "sidebar" data-md-type = "navigation" >
< div class = "md-sidebar__scrollwrap" >
< div class = "md-sidebar__inner" >
< nav class = "md-nav md-nav--primary" aria-label = "Navigation" data-md-level = "0" >
< label class = "md-nav__title" for = "__drawer" >
< a href = "../.." title = "obikmer" class = "md-nav__button md-logo" aria-label = "obikmer" data-md-component = "logo" >
< svg xmlns = "http://www.w3.org/2000/svg" viewBox = "0 0 24 24" >< path d = "M12 8a3 3 0 0 0 3-3 3 3 0 0 0-3-3 3 3 0 0 0-3 3 3 3 0 0 0 3 3m0 3.54C9.64 9.35 6.5 8 3 8v11c3.5 0 6.64 1.35 9 3.54 2.36-2.19 5.5-3.54 9-3.54V8c-3.5 0-6.64 1.35-9 3.54" /></ svg >
</ a >
obikmer
</ label >
< ul class = "md-nav__list" data-md-scrollfix >
< li class = "md-nav__item" >
< a href = "../.." class = "md-nav__link" >
< span class = "md-ellipsis" >
Home
</ span >
</ a >
</ li >
< li class = "md-nav__item md-nav__item--nested" >
< input class = "md-nav__toggle md-toggle " type = "checkbox" id = "__nav_2" >
< label class = "md-nav__link" for = "__nav_2" id = "__nav_2_label" tabindex = "0" >
< span class = "md-ellipsis" >
Theory
</ span >
< span class = "md-nav__icon md-icon" ></ span >
</ label >
< nav class = "md-nav" data-md-level = "1" aria-labelledby = "__nav_2_label" aria-expanded = "false" >
< label class = "md-nav__title" for = "__nav_2" >
< span class = "md-nav__icon md-icon" ></ span >
Theory
</ label >
< ul class = "md-nav__list" data-md-scrollfix >
< li class = "md-nav__item" >
2026-04-29 22:52:42 +02:00
< a href = "../../kmers/" class = "md-nav__link" >
2026-04-16 22:38:20 +02:00
< span class = "md-ellipsis" >
Kmers and super-kmers
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "../../theory/encoding/" class = "md-nav__link" >
< span class = "md-ellipsis" >
DNA encoding
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "../../theory/entropy/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Entropy filter
</ span >
</ a >
</ li >
2026-04-29 22:52:42 +02:00
< li class = "md-nav__item" >
< a href = "../../theory/minimizer/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Minimizer selection
</ span >
</ a >
</ li >
2026-04-16 22:38:20 +02:00
< li class = "md-nav__item" >
< a href = "../../theory/indexing/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Partitioning architecture
</ span >
</ a >
</ li >
</ ul >
</ nav >
</ li >
< li class = "md-nav__item md-nav__item--active md-nav__item--nested" >
< input class = "md-nav__toggle md-toggle " type = "checkbox" id = "__nav_3" checked >
< label class = "md-nav__link" for = "__nav_3" id = "__nav_3_label" tabindex = "0" >
< span class = "md-ellipsis" >
Implementation
</ span >
< span class = "md-nav__icon md-icon" ></ span >
</ label >
< nav class = "md-nav" data-md-level = "1" aria-labelledby = "__nav_3_label" aria-expanded = "true" >
< label class = "md-nav__title" for = "__nav_3" >
< span class = "md-nav__icon md-icon" ></ span >
Implementation
</ label >
< ul class = "md-nav__list" data-md-scrollfix >
< li class = "md-nav__item" >
< a href = "../superkmer/" class = "md-nav__link" >
< span class = "md-ellipsis" >
SuperKmer
</ span >
</ a >
</ li >
< li class = "md-nav__item md-nav__item--active" >
< input class = "md-nav__toggle md-toggle" type = "checkbox" id = "__toc" >
< label class = "md-nav__link md-nav__link--active" for = "__toc" >
< span class = "md-ellipsis" >
Kmer
</ span >
< span class = "md-nav__icon md-icon" ></ span >
</ label >
< a href = "./" class = "md-nav__link md-nav__link--active" >
< span class = "md-ellipsis" >
Kmer
</ span >
</ a >
< nav class = "md-nav md-nav--secondary" aria-label = "Table of contents" >
< label class = "md-nav__title" for = "__toc" >
< span class = "md-nav__icon md-icon" ></ span >
Table of contents
</ label >
< ul class = "md-nav__list" data-md-component = "toc" data-md-scrollfix >
< li class = "md-nav__item" >
2026-06-04 21:27:01 +02:00
< a href = "#types-and-layout" class = "md-nav__link" >
2026-04-16 22:38:20 +02:00
< span class = "md-ellipsis" >
2026-06-04 21:27:01 +02:00
Types and layout
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "#global-parameters" class = "md-nav__link" >
< span class = "md-ellipsis" >
Global parameters
2026-04-16 22:38:20 +02:00
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "#encoding" class = "md-nav__link" >
< span class = "md-ellipsis" >
Encoding
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "#decoding" class = "md-nav__link" >
< span class = "md-ellipsis" >
Decoding
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "#reverse-complement" class = "md-nav__link" >
< span class = "md-ellipsis" >
Reverse complement
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
2026-06-04 21:27:01 +02:00
< a href = "#canonical-form-and-canonicalkmerof" class = "md-nav__link" >
2026-04-16 22:38:20 +02:00
< span class = "md-ellipsis" >
2026-06-04 21:27:01 +02:00
Canonical form and CanonicalKmerOf
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "#sliding-window-helpers" class = "md-nav__link" >
< span class = "md-ellipsis" >
Sliding window helpers
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "#hashing" class = "md-nav__link" >
< span class = "md-ellipsis" >
Hashing
2026-04-16 22:38:20 +02:00
</ span >
</ a >
</ li >
</ ul >
</ nav >
</ li >
< li class = "md-nav__item" >
< a href = "../chunkreader/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Chunk reader
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "../pipeline/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Construction pipeline
</ span >
</ a >
</ li >
2026-04-29 22:52:42 +02:00
< li class = "md-nav__item" >
< a href = "../obipipeline/" class = "md-nav__link" >
< span class = "md-ellipsis" >
obipipeline library
</ span >
</ a >
</ li >
2026-04-16 22:38:20 +02:00
< li class = "md-nav__item" >
< a href = "../storage/" class = "md-nav__link" >
< span class = "md-ellipsis" >
On-disk storage
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "../mphf/" class = "md-nav__link" >
< span class = "md-ellipsis" >
MPHF selection
</ span >
</ a >
</ li >
2026-04-29 22:52:42 +02:00
< li class = "md-nav__item" >
< a href = "../unitig_evidence/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Unitig evidence encoding
</ span >
</ a >
</ li >
2026-05-15 21:07:23 +08:00
2026-06-04 21:27:01 +02:00
< li class = "md-nav__item" >
< a href = "../evidence_elimination/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Evidence elimination (discussion)
</ span >
</ a >
</ li >
2026-05-15 21:07:23 +08:00
< li class = "md-nav__item" >
< a href = "../obilayeredmap/" class = "md-nav__link" >
< span class = "md-ellipsis" >
obilayeredmap crate
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "../persistent_compact_int_vec/" class = "md-nav__link" >
< span class = "md-ellipsis" >
PersistentCompactIntVec
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "../persistent_bit_vec/" class = "md-nav__link" >
< span class = "md-ellipsis" >
PersistentBitVec
</ span >
</ a >
</ li >
2026-06-04 21:27:01 +02:00
< li class = "md-nav__item" >
< a href = "../merge/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Merge command
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "../rebuild_filter/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Kmer filtering (rebuild/dump/unitig)
</ span >
</ a >
</ li >
2026-04-16 22:38:20 +02:00
</ ul >
</ nav >
</ li >
< li class = "md-nav__item md-nav__item--nested" >
< input class = "md-nav__toggle md-toggle " type = "checkbox" id = "__nav_4" >
< label class = "md-nav__link" for = "__nav_4" id = "__nav_4_label" tabindex = "0" >
< span class = "md-ellipsis" >
Architecture
</ span >
< span class = "md-nav__icon md-icon" ></ span >
</ label >
< nav class = "md-nav" data-md-level = "1" aria-labelledby = "__nav_4_label" aria-expanded = "false" >
< label class = "md-nav__title" for = "__nav_4" >
< span class = "md-nav__icon md-icon" ></ span >
Architecture
</ label >
< ul class = "md-nav__list" data-md-scrollfix >
< li class = "md-nav__item" >
< a href = "../../architecture/sequences/invariant/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Sequences
</ span >
</ a >
</ li >
2026-05-15 21:07:23 +08:00
< li class = "md-nav__item" >
< a href = "../../architecture/index_architecture/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Kmer index
</ span >
</ a >
</ li >
2026-04-16 22:38:20 +02:00
</ ul >
</ nav >
</ li >
</ ul >
</ nav >
</ div >
</ div >
</ div >
< div class = "md-sidebar md-sidebar--secondary" data-md-component = "sidebar" data-md-type = "toc" >
< div class = "md-sidebar__scrollwrap" >
< div class = "md-sidebar__inner" >
< nav class = "md-nav md-nav--secondary" aria-label = "Table of contents" >
< label class = "md-nav__title" for = "__toc" >
< span class = "md-nav__icon md-icon" ></ span >
Table of contents
</ label >
< ul class = "md-nav__list" data-md-component = "toc" data-md-scrollfix >
< li class = "md-nav__item" >
2026-06-04 21:27:01 +02:00
< a href = "#types-and-layout" class = "md-nav__link" >
2026-04-16 22:38:20 +02:00
< span class = "md-ellipsis" >
2026-06-04 21:27:01 +02:00
Types and layout
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "#global-parameters" class = "md-nav__link" >
< span class = "md-ellipsis" >
Global parameters
2026-04-16 22:38:20 +02:00
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "#encoding" class = "md-nav__link" >
< span class = "md-ellipsis" >
Encoding
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "#decoding" class = "md-nav__link" >
< span class = "md-ellipsis" >
Decoding
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "#reverse-complement" class = "md-nav__link" >
< span class = "md-ellipsis" >
Reverse complement
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
2026-06-04 21:27:01 +02:00
< a href = "#canonical-form-and-canonicalkmerof" class = "md-nav__link" >
< span class = "md-ellipsis" >
Canonical form and CanonicalKmerOf
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "#sliding-window-helpers" class = "md-nav__link" >
< span class = "md-ellipsis" >
Sliding window helpers
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "#hashing" class = "md-nav__link" >
2026-04-16 22:38:20 +02:00
< span class = "md-ellipsis" >
2026-06-04 21:27:01 +02:00
Hashing
2026-04-16 22:38:20 +02:00
</ span >
</ a >
</ li >
</ ul >
</ nav >
</ div >
</ div >
</ div >
< div class = "md-content" data-md-component = "content" >
< article class = "md-content__inner md-typeset" >
< h1 id = "kmer-implementation" > Kmer — implementation</ h1 >
2026-06-04 21:27:01 +02:00
< 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 >
2026-04-16 22:38:20 +02:00
< div class = "highlight" >< pre >< span ></ span >< code >< span class = "cp" > #[repr(transparent)]</ span >
2026-06-04 21:27:01 +02:00
< 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 >
2026-04-16 22:38:20 +02:00
</ code ></ pre ></ div >
2026-06-04 21:27:01 +02:00
< 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 >
2026-04-16 22:38:20 +02:00
< 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 >
2026-06-04 21:27:01 +02:00
< 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 >
2026-04-16 22:38:20 +02:00
< h2 id = "encoding" > Encoding</ h2 >
2026-06-04 21:27:01 +02:00
< 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 >
2026-04-16 22:38:20 +02:00
< 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 >
2026-06-04 21:27:01 +02:00
< 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 >
2026-04-16 22:38:20 +02:00
</ code ></ pre ></ div >
< p > Zero allocation — result lives on the stack.</ p >
< h2 id = "decoding" > Decoding</ h2 >
2026-06-04 21:27:01 +02:00
< 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 >
2026-04-16 22:38:20 +02:00
< 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 >
2026-06-04 21:27:01 +02:00
< 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 >
2026-04-16 22:38:20 +02:00
</ 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 >
2026-06-04 21:27:01 +02:00
< 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 >
2026-04-16 22:38:20 +02:00
< 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 >
2026-06-04 21:27:01 +02:00
< 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 >
2026-04-16 22:38:20 +02:00
</ article >
</ div >
< script > var target = document . getElementById ( location . hash . slice ( 1 )); target && target . name && ( target . checked = target . name . startsWith ( "__tabbed_" ))</ script >
</ div >
</ main >
< footer class = "md-footer" >
< div class = "md-footer-meta md-typeset" >
< div class = "md-footer-meta__inner md-grid" >
< div class = "md-copyright" >
Made with
< a href = "https://squidfunk.github.io/mkdocs-material/" target = "_blank" rel = "noopener" >
Material for MkDocs
</ a >
</ div >
</ div >
</ div >
</ footer >
</ div >
< div class = "md-dialog" data-md-component = "dialog" >
< div class = "md-dialog__inner md-typeset" ></ div >
</ div >
< script id = "__config" type = "application/json" >{ "annotate" : null , "base" : "../.." , "features" : [], "search" : "../../assets/javascripts/workers/search.2c215733.min.js" , "tags" : null , "translations" : { "clipboard.copied" : "Copied to clipboard" , "clipboard.copy" : "Copy to clipboard" , "search.result.more.one" : "1 more on this page" , "search.result.more.other" : "# more on this page" , "search.result.none" : "No matching documents" , "search.result.one" : "1 matching document" , "search.result.other" : "# matching documents" , "search.result.placeholder" : "Type to start searching" , "search.result.term.missing" : "Missing" , "select.version" : "Select version" }, "version" : null }</ script >
< script src = "../../assets/javascripts/bundle.79ae519e.min.js" ></ script >
< script src = "https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js" ></ script >
</ body >
</ html >
