1311 lines
21 KiB
HTML
1311 lines
21 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="../select/">
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<link rel="next" href="../dump/">
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<meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.7.6">
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<title>query - obikmer — User Guide</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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<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="#query" 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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<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 — User Guide" class="md-header__button md-logo" aria-label="obikmer — User Guide" 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 — User Guide
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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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query
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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 — User Guide" class="md-nav__button md-logo" aria-label="obikmer — User Guide" 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 — User Guide
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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="../../theory/kmers_and_superkmers/" 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_filter/" class="md-nav__link">
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<span class="md-ellipsis">
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Low-complexity kmer 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_selection/" 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_architecture/" class="md-nav__link">
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<span class="md-ellipsis">
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Partitioning and indexing 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_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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Usage
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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_4_label" aria-expanded="true">
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<label class="md-nav__title" for="__nav_4">
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<span class="md-nav__icon md-icon"></span>
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Usage
|
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||
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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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||
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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="../index_command/" class="md-nav__link">
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||
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||
<span class="md-ellipsis">
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index
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||
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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="../merge/" class="md-nav__link">
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<span class="md-ellipsis">
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merge
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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="../filter/" class="md-nav__link">
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<span class="md-ellipsis">
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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="../select/" class="md-nav__link">
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<span class="md-ellipsis">
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select
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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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||
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||
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||
<span class="md-ellipsis">
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||
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||
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query
|
||
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||
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||
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||
</span>
|
||
|
||
|
||
|
||
<span class="md-nav__icon md-icon"></span>
|
||
</label>
|
||
|
||
<a href="./" class="md-nav__link md-nav__link--active">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
query
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
|
||
|
||
|
||
<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
|
||
|
||
|
||
|
||
|
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|
||
<label class="md-nav__title" for="__toc">
|
||
<span class="md-nav__icon md-icon"></span>
|
||
Table of contents
|
||
</label>
|
||
<ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
|
||
|
||
<li class="md-nav__item">
|
||
<a href="#arguments" class="md-nav__link">
|
||
<span class="md-ellipsis">
|
||
|
||
Arguments
|
||
|
||
</span>
|
||
</a>
|
||
|
||
</li>
|
||
|
||
<li class="md-nav__item">
|
||
<a href="#options" class="md-nav__link">
|
||
<span class="md-ellipsis">
|
||
|
||
Options
|
||
|
||
</span>
|
||
</a>
|
||
|
||
</li>
|
||
|
||
<li class="md-nav__item">
|
||
<a href="#output" class="md-nav__link">
|
||
<span class="md-ellipsis">
|
||
|
||
Output
|
||
|
||
</span>
|
||
</a>
|
||
|
||
</li>
|
||
|
||
</ul>
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</nav>
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</li>
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|
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|
||
|
||
|
||
<li class="md-nav__item">
|
||
<a href="../dump/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
dump
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
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||
|
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|
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|
||
|
||
|
||
|
||
<li class="md-nav__item">
|
||
<a href="../annotate/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
annotate
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
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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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|
||
|
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|
||
<li class="md-nav__item">
|
||
<a href="../phylo/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
phylo
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
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</li>
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|
||
<h1 id="query">query</h1>
|
||
<p>Query an index with sequences and annotate each query with the kmer matches found.</p>
|
||
<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>query<span class="w"> </span>INDEX<span class="w"> </span>INPUTS...<span class="w"> </span><span class="o">[</span>OPTIONS<span class="o">]</span>
|
||
</code></pre></div>
|
||
<h2 id="arguments">Arguments</h2>
|
||
<table>
|
||
<thead>
|
||
<tr>
|
||
<th>Argument</th>
|
||
<th>Description</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr>
|
||
<td><code>INDEX</code></td>
|
||
<td>Index directory to query against</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>INPUTS...</code></td>
|
||
<td>Input sequence files (FASTA/FASTQ, gzip optional); at least one required</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<h2 id="options">Options</h2>
|
||
<table>
|
||
<thead>
|
||
<tr>
|
||
<th>Option</th>
|
||
<th>Default</th>
|
||
<th>Description</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr>
|
||
<td><code>--detail</code></td>
|
||
<td>off</td>
|
||
<td>Report per-position, per-genome coverage vectors in the output</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>--count-missing</code></td>
|
||
<td>off</td>
|
||
<td>Also count query kmers absent from the index</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>--force-presence</code></td>
|
||
<td>off</td>
|
||
<td>Report presence (0/1) per genome instead of raw counts</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>--presence-threshold</code></td>
|
||
<td><code>1</code></td>
|
||
<td>Minimum accumulated count to declare a genome present (implies <code>--force-presence</code>)</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>-z, --findere-z</code></td>
|
||
<td>derived from the index metadata</td>
|
||
<td>Override the Findere z parameter</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>-T, --threads</code></td>
|
||
<td>detected core count</td>
|
||
<td>Number of worker threads</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>--chunk-size</code></td>
|
||
<td>auto-sized (available RAM ÷ threads, clamped to 4–256 MiB)</td>
|
||
<td>I/O chunk size, in MiB</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>--max-open-files</code></td>
|
||
<td><code>threads / 4</code> (min 1)</td>
|
||
<td>Maximum number of input files open simultaneously</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<h2 id="output">Output</h2>
|
||
<p>FASTA on stdout, one record per query, annotated in the OBITools-style header format <code>>id {"key":value,...}</code>:</p>
|
||
<ul>
|
||
<li><code>kmer_count</code>: total number of kmers matched</li>
|
||
<li><code>kmer_missing</code>: number of query kmers absent from the index (only with <code>--count-missing</code>)</li>
|
||
<li><code>kmer_strict_matches</code>: per-genome match counts</li>
|
||
<li><code>coverage</code>: per-position, per-genome coverage vectors (only with <code>--detail</code>)</li>
|
||
</ul>
|
||
<p><code>--mismatch</code> is accepted by the CLI but not currently functional; using it produces a warning and is ignored.</p>
|
||
|
||
|
||
|
||
|
||
|
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