Eric Coissac
bb7adc1154
Expands MkDocs navigation and documentation for evidence elimination, the merge command, and kmer filtering. Refactors kmer representation to a generic `KmerOf<L>` type with a bitwise reverse complement algorithm. Unifies MPHF construction, introduces approximate fingerprint-based indexing, and updates the pipeline, chunkreader, and storage layouts. Adds code coverage reports and clarifies architectural invariants for improved maintainability.
1348 lines
32 KiB
HTML
1348 lines
32 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 md-nav__item--nested">
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<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
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<label class="md-nav__link" for="__nav_2" id="__nav_2_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_2_label" aria-expanded="false">
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<label class="md-nav__title" for="__nav_2">
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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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</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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<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
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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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Implementation
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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="true">
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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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Implementation
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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="../superkmer/" class="md-nav__link">
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<span class="md-ellipsis">
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SuperKmer
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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--active">
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<input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
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<label class="md-nav__link md-nav__link--active" for="__toc">
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<span class="md-ellipsis">
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Kmer
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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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<a href="./" class="md-nav__link md-nav__link--active">
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<span class="md-ellipsis">
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Kmer
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</span>
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</a>
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<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
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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
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</label>
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<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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Types and layout
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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="#global-parameters" class="md-nav__link">
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<span class="md-ellipsis">
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Global parameters
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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="#encoding" class="md-nav__link">
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<span class="md-ellipsis">
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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="#decoding" class="md-nav__link">
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<span class="md-ellipsis">
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Decoding
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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="#reverse-complement" class="md-nav__link">
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<span class="md-ellipsis">
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Reverse complement
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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="#canonical-form-and-canonicalkmerof" class="md-nav__link">
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<span class="md-ellipsis">
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Canonical form and CanonicalKmerOf
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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="#sliding-window-helpers" class="md-nav__link">
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<span class="md-ellipsis">
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Sliding window helpers
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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="#hashing" class="md-nav__link">
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<span class="md-ellipsis">
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Hashing
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</span>
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</a>
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</li>
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</ul>
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</nav>
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</li>
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<li class="md-nav__item">
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<a href="../chunkreader/" class="md-nav__link">
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<span class="md-ellipsis">
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Chunk reader
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||
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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="../pipeline/" class="md-nav__link">
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<span class="md-ellipsis">
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Construction pipeline
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||
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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="../obipipeline/" class="md-nav__link">
|
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<span class="md-ellipsis">
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obipipeline library
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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="../storage/" class="md-nav__link">
|
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<span class="md-ellipsis">
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On-disk storage
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||
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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="../mphf/" class="md-nav__link">
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<span class="md-ellipsis">
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|
||
MPHF selection
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<li class="md-nav__item">
|
||
<a href="../unitig_evidence/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
Unitig evidence encoding
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<li class="md-nav__item">
|
||
<a href="../evidence_elimination/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
Evidence elimination (discussion)
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<li class="md-nav__item">
|
||
<a href="../obilayeredmap/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
obilayeredmap crate
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
|
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|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
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|
||
<li class="md-nav__item">
|
||
<a href="../persistent_compact_int_vec/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
PersistentCompactIntVec
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
|
||
|
||
|
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|
||
|
||
|
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|
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|
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|
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<li class="md-nav__item">
|
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<a href="../persistent_bit_vec/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
PersistentBitVec
|
||
|
||
|
||
|
||
</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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<li class="md-nav__item">
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<a href="../merge/" class="md-nav__link">
|
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|
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|
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<span class="md-ellipsis">
|
||
|
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|
||
Merge command
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
|
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<a href="../rebuild_filter/" class="md-nav__link">
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<span class="md-ellipsis">
|
||
|
||
|
||
Kmer filtering (rebuild/dump/unitig)
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
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</a>
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</li>
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Architecture
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Architecture
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Sequences
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</span>
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|
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|
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</a>
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Kmer index
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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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Types and layout
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Global parameters
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<a href="#encoding" class="md-nav__link">
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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="#decoding" class="md-nav__link">
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<span class="md-ellipsis">
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Decoding
|
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|
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</span>
|
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</a>
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|
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</li>
|
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|
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<li class="md-nav__item">
|
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<a href="#reverse-complement" class="md-nav__link">
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<span class="md-ellipsis">
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Reverse complement
|
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</span>
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|
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</li>
|
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|
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<li class="md-nav__item">
|
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<a href="#canonical-form-and-canonicalkmerof" class="md-nav__link">
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<span class="md-ellipsis">
|
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|
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Canonical form and CanonicalKmerOf
|
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|
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</span>
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</a>
|
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|
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</li>
|
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|
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<li class="md-nav__item">
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<a href="#sliding-window-helpers" class="md-nav__link">
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<span class="md-ellipsis">
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Sliding window helpers
|
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</span>
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</a>
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</li>
|
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|
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<li class="md-nav__item">
|
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<a href="#hashing" class="md-nav__link">
|
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<span class="md-ellipsis">
|
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Hashing
|
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|
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</span>
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</a>
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</li>
|
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|
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</ul>
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</div>
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</div>
|
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<div class="md-content" data-md-component="content">
|
||
|
||
<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>
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<div class="highlight"><pre><span></span><code><span class="k">pub</span><span class="w"> </span><span class="k">fn</span><span class="w"> </span><span class="nf">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>
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||
<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>
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||
<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>
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||
</code></pre></div>
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||
<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>
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||
<h2 id="sliding-window-helpers">Sliding window helpers</h2>
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||
<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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