1571 lines
34 KiB
HTML
1571 lines
34 KiB
HTML
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<!doctype html>
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<html lang="en" class="no-js">
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<head>
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<meta charset="utf-8">
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<meta name="viewport" content="width=device-width,initial-scale=1">
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<link rel="prev" href="../superkmer/">
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<link rel="next" href="../chunkreader/">
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<link rel="icon" href="../../assets/images/favicon.png">
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<meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.7.6">
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<title>Kmer - obikmer</title>
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<link rel="stylesheet" href="../../assets/stylesheets/main.484c7ddc.min.css">
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<link rel="preconnect" href="https://fonts.gstatic.com" crossorigin>
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<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">
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<style>:root{--md-text-font:"Roboto";--md-code-font:"Roboto Mono"}</style>
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<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>
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</head>
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<body dir="ltr">
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<input class="md-toggle" data-md-toggle="drawer" type="checkbox" id="__drawer" autocomplete="off">
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<input class="md-toggle" data-md-toggle="search" type="checkbox" id="__search" autocomplete="off">
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<label class="md-overlay" for="__drawer"></label>
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<div data-md-component="skip">
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<a href="#kmer-implementation" class="md-skip">
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Skip to content
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</a>
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</div>
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<div data-md-component="announce">
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</div>
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<header class="md-header md-header--shadow" data-md-component="header">
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<nav class="md-header__inner md-grid" aria-label="Header">
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<a href="../.." title="obikmer" class="md-header__button md-logo" aria-label="obikmer" data-md-component="logo">
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<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>
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</a>
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<label class="md-header__button md-icon" for="__drawer">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M3 6h18v2H3zm0 5h18v2H3zm0 5h18v2H3z"/></svg>
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</label>
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<div class="md-header__title" data-md-component="header-title">
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<div class="md-header__ellipsis">
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<div class="md-header__topic">
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<span class="md-ellipsis">
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obikmer
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</span>
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</div>
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<div class="md-header__topic" data-md-component="header-topic">
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<span class="md-ellipsis">
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Kmer
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</span>
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</div>
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</div>
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</div>
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<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>
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</nav>
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</header>
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<div class="md-container" data-md-component="container">
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<main class="md-main" data-md-component="main">
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<div class="md-main__inner md-grid">
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<div class="md-sidebar md-sidebar--primary" data-md-component="sidebar" data-md-type="navigation" >
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<div class="md-sidebar__scrollwrap">
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<div class="md-sidebar__inner">
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<nav class="md-nav md-nav--primary" aria-label="Navigation" data-md-level="0">
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<label class="md-nav__title" for="__drawer">
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<a href="../.." title="obikmer" class="md-nav__button md-logo" aria-label="obikmer" data-md-component="logo">
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<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>
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</a>
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obikmer
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</label>
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<ul class="md-nav__list" data-md-scrollfix>
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<li class="md-nav__item">
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<a href="../.." class="md-nav__link">
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<span class="md-ellipsis">
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Home
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</span>
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../installation/" class="md-nav__link">
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<span class="md-ellipsis">
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Installation
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</span>
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</a>
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</li>
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<li class="md-nav__item md-nav__item--nested">
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<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
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<label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
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<span class="md-ellipsis">
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Theory
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</span>
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<span class="md-nav__icon md-icon"></span>
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</label>
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<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
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<label class="md-nav__title" for="__nav_3">
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<span class="md-nav__icon md-icon"></span>
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Theory
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</label>
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<ul class="md-nav__list" data-md-scrollfix>
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<li class="md-nav__item">
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<a href="../../kmers/" class="md-nav__link">
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<span class="md-ellipsis">
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Kmers and super-kmers
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</span>
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../theory/encoding/" class="md-nav__link">
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<span class="md-ellipsis">
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DNA encoding
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</span>
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../theory/entropy/" class="md-nav__link">
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<span class="md-ellipsis">
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Entropy filter
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</span>
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../theory/minimizer/" class="md-nav__link">
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<span class="md-ellipsis">
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Minimizer selection
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</span>
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../theory/indexing/" class="md-nav__link">
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<span class="md-ellipsis">
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Partitioning architecture
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</span>
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../theory/evolutionary_distances/" class="md-nav__link">
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<span class="md-ellipsis">
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Central-position SNP distance (discussion)
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||
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||
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||
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||
</span>
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||
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||
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||
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</a>
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</li>
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|
||
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||
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||
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</ul>
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</nav>
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</li>
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||
<li class="md-nav__item md-nav__item--active md-nav__item--nested">
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||
|
||
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||
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<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
|
||
|
||
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||
<label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
|
||
|
||
|
||
|
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<span class="md-ellipsis">
|
||
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||
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Implementation
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||
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||
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||
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||
</span>
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||
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||
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<span class="md-nav__icon md-icon"></span>
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||
</label>
|
||
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||
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
|
||
<label class="md-nav__title" for="__nav_4">
|
||
<span class="md-nav__icon md-icon"></span>
|
||
|
||
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Implementation
|
||
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</label>
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<ul class="md-nav__list" data-md-scrollfix>
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||
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<li class="md-nav__item">
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||
<a href="../superkmer/" class="md-nav__link">
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||
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||
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||
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||
<span class="md-ellipsis">
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||
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||
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||
SuperKmer
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||
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||
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||
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</span>
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||
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||
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</a>
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||
</li>
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||
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<li class="md-nav__item md-nav__item--active">
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||
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<input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
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||
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||
|
||
|
||
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<label class="md-nav__link md-nav__link--active" for="__toc">
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||
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||
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||
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<span class="md-ellipsis">
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||
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||
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||
Kmer
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||
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||
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||
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||
</span>
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||
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||
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||
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||
<span class="md-nav__icon md-icon"></span>
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</label>
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||
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<a href="./" class="md-nav__link md-nav__link--active">
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||
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||
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<span class="md-ellipsis">
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||
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||
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||
Kmer
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||
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||
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||
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</span>
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||
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||
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||
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</a>
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||
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||
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||
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<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
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||
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||
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||
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||
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<label class="md-nav__title" for="__toc">
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||
<span class="md-nav__icon md-icon"></span>
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||
Table of contents
|
||
</label>
|
||
<ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
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||
|
||
<li class="md-nav__item">
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||
<a href="#types-and-layout" class="md-nav__link">
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||
<span class="md-ellipsis">
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||
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Types and layout
|
||
|
||
</span>
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||
</a>
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||
|
||
</li>
|
||
|
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<li class="md-nav__item">
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||
<a href="#global-parameters" class="md-nav__link">
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||
<span class="md-ellipsis">
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||
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||
Global parameters
|
||
|
||
</span>
|
||
</a>
|
||
|
||
</li>
|
||
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<li class="md-nav__item">
|
||
<a href="#encoding" class="md-nav__link">
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||
<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">
|
||
<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">
|
||
<span class="md-ellipsis">
|
||
|
||
Hashing
|
||
|
||
</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>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<li class="md-nav__item">
|
||
<a href="../obipipeline/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
obipipeline library
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
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||
|
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|
||
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|
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|
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||
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|
||
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|
||
|
||
|
||
On-disk storage
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
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|
||
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|
||
|
||
MPHF selection
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
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|
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|
||
Unitig evidence encoding
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
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|
||
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|
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|
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Evidence elimination (discussion)
|
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|
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|
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|
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|
||
|
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|
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|
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|
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obilayeredmap crate
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
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||
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||
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|
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|
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|
||
|
||
|
||
PersistentCompactIntVec
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
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|
||
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||
|
||
|
||
PersistentBitVec
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
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Merge command
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||
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|
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|
||
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||
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</span>
|
||
|
||
|
||
|
||
</a>
|
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Kmer filtering
|
||
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||
|
||
|
||
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Select command
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||
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obitaxonomy crate
|
||
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||
|
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|
||
</span>
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||
|
||
|
||
|
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Encoding
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Canonical form and CanonicalKmerOf
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Hashing
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<article class="md-content__inner md-typeset">
|
||
|
||
|
||
|
||
|
||
|
||
<h1 id="kmer-implementation">Kmer — implementation</h1>
|
||
<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>
|
||
<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">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>
|
||
</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 64−2·len bits are always zero. The length is <strong>not stored</strong> — every operation reads it from <code>L::len()</code>.</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="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>
|
||
<h2 id="encoding">Encoding</h2>
|
||
<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>
|
||
<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">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>
|
||
</code></pre></div>
|
||
<p>Zero allocation — result lives on the stack.</p>
|
||
<h2 id="decoding">Decoding</h2>
|
||
<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>
|
||
<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">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>
|
||
</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-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>
|
||
<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>
|
||
<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−1 nucleotides of <code>self</code> equal the first k−1 of <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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