1286 lines
20 KiB
HTML
1286 lines
20 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 name="viewport" content="width=device-width,initial-scale=1">
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<link rel="prev" href="../index_command/">
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<link rel="next" href="../filter/">
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<meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.7.6">
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<title>merge - obikmer — User Guide</title>
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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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<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="#merge" 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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<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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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M3 6h18v2H3zm0 5h18v2H3zm0 5h18v2H3z"/></svg>
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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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merge
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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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<nav class="md-nav md-nav--primary" aria-label="Navigation" data-md-level="0">
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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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<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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</a>
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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 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 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 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 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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</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">
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<a href="../index_command/" class="md-nav__link">
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<span class="md-ellipsis">
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index
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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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merge
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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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merge
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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="#arguments" class="md-nav__link">
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<span class="md-ellipsis">
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Arguments
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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="#options" class="md-nav__link">
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<span class="md-ellipsis">
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Options
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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="#behaviour" class="md-nav__link">
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<span class="md-ellipsis">
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Behaviour
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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="../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 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 class="md-nav__item">
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<a href="../query/" class="md-nav__link">
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<span class="md-ellipsis">
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query
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</span>
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</a>
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<li class="md-nav__item">
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<a href="../dump/" class="md-nav__link">
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<span class="md-ellipsis">
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dump
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</span>
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</a>
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<li class="md-nav__item">
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<a href="../annotate/" class="md-nav__link">
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<span class="md-ellipsis">
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annotate
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</span>
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</a>
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<li class="md-nav__item">
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<a href="../phylo/" class="md-nav__link">
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<span class="md-ellipsis">
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phylo
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</span>
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</a>
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<h1 id="merge">merge</h1>
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<p>Merge multiple built indexes into a single index.</p>
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<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>merge<span class="w"> </span>-o<span class="w"> </span>OUTPUT<span class="w"> </span>SOURCE...<span class="w"> </span><span class="o">[</span>OPTIONS<span class="o">]</span>
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</code></pre></div>
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<h2 id="arguments">Arguments</h2>
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<table>
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<thead>
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<tr>
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<th>Argument</th>
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<th>Description</th>
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<tbody>
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<tr>
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<td><code>SOURCE...</code></td>
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<td>Index directories to merge (at least one required)</td>
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</tr>
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</tbody>
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</table>
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<h2 id="options">Options</h2>
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<table>
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<thead>
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<tr>
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<th>Option</th>
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<th>Default</th>
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<th>Description</th>
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<tbody>
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<tr>
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<td><code>-o, --output</code></td>
|
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<td>— (required)</td>
|
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<td>Output index directory</td>
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</tr>
|
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<tr>
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<td><code>--force</code></td>
|
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<td>off</td>
|
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<td>Overwrite an existing output directory</td>
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</tr>
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<tr>
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<td><code>--force-presence</code></td>
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<td>off</td>
|
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<td>Store the merged index as presence/absence even if all sources have counts</td>
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</tr>
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<tr>
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<td><code>--rename-duplicates</code></td>
|
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<td>off</td>
|
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<td>Disambiguate duplicate genome labels (<code>.1</code>, <code>.2</code>, …) instead of failing</td>
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</tr>
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<tr>
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<td><code>--budget-fraction</code></td>
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<td><code>0.5</code></td>
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<td>Fraction of available RAM reserved as the memory budget for parallel partition merging</td>
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</tr>
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</table>
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<h2 id="behaviour">Behaviour</h2>
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<p>The output mode is chosen automatically: if every source index stores counts, the merged index stores counts too; otherwise it is presence/absence. <code>--force-presence</code> forces presence/absence regardless of the sources.</p>
|
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<p>By default, merging two indexes that share a genome label fails with an error; <code>--rename-duplicates</code> instead appends a numeric suffix to keep both copies.</p>
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