45d49ed501
Add comprehensive documentation for the `obilayeredmap` crate, `PersistentCompactIntVec`, `PersistentBitVec`, and the hierarchical k-mer index architecture, including sidebar navigation updates across all documentation pages. Refactor the Bray-Curtis distance computation in `obicompactvec` to decouple numerator and denominator calculations, replacing direct pairwise calls with explicit loops over precomputed sums. Update tests to verify column sum accuracy and align with the simplified API.
912 lines
15 KiB
HTML
912 lines
15 KiB
HTML
|
|
<!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="icon" href="/assets/images/favicon.png">
|
|
<meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.7.6">
|
|
|
|
|
|
|
|
<title>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">
|
|
|
|
</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">
|
|
|
|
|
|
|
|
</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">
|
|
<a href="/kmers/" class="md-nav__link">
|
|
|
|
|
|
|
|
<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>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<li class="md-nav__item">
|
|
<a href="/theory/minimizer/" class="md-nav__link">
|
|
|
|
|
|
|
|
<span class="md-ellipsis">
|
|
|
|
|
|
Minimizer selection
|
|
|
|
|
|
|
|
</span>
|
|
|
|
|
|
|
|
</a>
|
|
</li>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<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--nested">
|
|
|
|
|
|
|
|
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
|
|
|
|
|
|
<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="false">
|
|
<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="/implementation/superkmer/" class="md-nav__link">
|
|
|
|
|
|
|
|
<span class="md-ellipsis">
|
|
|
|
|
|
SuperKmer
|
|
|
|
|
|
|
|
</span>
|
|
|
|
|
|
|
|
</a>
|
|
</li>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<li class="md-nav__item">
|
|
<a href="/implementation/kmer/" class="md-nav__link">
|
|
|
|
|
|
|
|
<span class="md-ellipsis">
|
|
|
|
|
|
Kmer
|
|
|
|
|
|
|
|
</span>
|
|
|
|
|
|
|
|
</a>
|
|
</li>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<li class="md-nav__item">
|
|
<a href="/implementation/chunkreader/" class="md-nav__link">
|
|
|
|
|
|
|
|
<span class="md-ellipsis">
|
|
|
|
|
|
Chunk reader
|
|
|
|
|
|
|
|
</span>
|
|
|
|
|
|
|
|
</a>
|
|
</li>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<li class="md-nav__item">
|
|
<a href="/implementation/pipeline/" class="md-nav__link">
|
|
|
|
|
|
|
|
<span class="md-ellipsis">
|
|
|
|
|
|
Construction pipeline
|
|
|
|
|
|
|
|
</span>
|
|
|
|
|
|
|
|
</a>
|
|
</li>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<li class="md-nav__item">
|
|
<a href="/implementation/obipipeline/" class="md-nav__link">
|
|
|
|
|
|
|
|
<span class="md-ellipsis">
|
|
|
|
|
|
obipipeline library
|
|
|
|
|
|
|
|
</span>
|
|
|
|
|
|
|
|
</a>
|
|
</li>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<li class="md-nav__item">
|
|
<a href="/implementation/storage/" class="md-nav__link">
|
|
|
|
|
|
|
|
<span class="md-ellipsis">
|
|
|
|
|
|
On-disk storage
|
|
|
|
|
|
|
|
</span>
|
|
|
|
|
|
|
|
</a>
|
|
</li>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<li class="md-nav__item">
|
|
<a href="/implementation/mphf/" class="md-nav__link">
|
|
|
|
|
|
|
|
<span class="md-ellipsis">
|
|
|
|
|
|
MPHF selection
|
|
|
|
|
|
|
|
</span>
|
|
|
|
|
|
|
|
</a>
|
|
</li>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<li class="md-nav__item">
|
|
<a href="/implementation/unitig_evidence/" class="md-nav__link">
|
|
|
|
|
|
|
|
<span class="md-ellipsis">
|
|
|
|
|
|
Unitig evidence encoding
|
|
|
|
|
|
|
|
</span>
|
|
|
|
|
|
|
|
</a>
|
|
</li>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<li class="md-nav__item">
|
|
<a href="/implementation/obilayeredmap/" class="md-nav__link">
|
|
|
|
|
|
|
|
<span class="md-ellipsis">
|
|
|
|
|
|
obilayeredmap crate
|
|
|
|
|
|
|
|
</span>
|
|
|
|
|
|
|
|
</a>
|
|
</li>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<li class="md-nav__item">
|
|
<a href="/implementation/persistent_compact_int_vec/" class="md-nav__link">
|
|
|
|
|
|
|
|
<span class="md-ellipsis">
|
|
|
|
|
|
PersistentCompactIntVec
|
|
|
|
|
|
|
|
</span>
|
|
|
|
|
|
|
|
</a>
|
|
</li>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<li class="md-nav__item">
|
|
<a href="/implementation/persistent_bit_vec/" class="md-nav__link">
|
|
|
|
|
|
|
|
<span class="md-ellipsis">
|
|
|
|
|
|
PersistentBitVec
|
|
|
|
|
|
|
|
</span>
|
|
|
|
|
|
|
|
</a>
|
|
</li>
|
|
|
|
|
|
|
|
|
|
</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>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<li class="md-nav__item">
|
|
<a href="/architecture/index_architecture/" class="md-nav__link">
|
|
|
|
|
|
|
|
<span class="md-ellipsis">
|
|
|
|
|
|
Kmer index
|
|
|
|
|
|
|
|
</span>
|
|
|
|
|
|
|
|
</a>
|
|
</li>
|
|
|
|
|
|
|
|
|
|
</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">
|
|
|
|
|
|
|
|
|
|
</nav>
|
|
</div>
|
|
</div>
|
|
</div>
|
|
|
|
|
|
|
|
<div class="md-content" data-md-component="content">
|
|
|
|
<article class="md-content__inner md-typeset">
|
|
|
|
<h1>404 - Not found</h1>
|
|
|
|
</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> |