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<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Home · XAM.jl</title><link href="https://cdnjs.cloudflare.com/ajax/libs/normalize/4.2.0/normalize.min.css" rel="stylesheet" type="text/css"/><link href="https://fonts.googleapis.com/css?family=Lato|Roboto+Mono" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/9.12.0/styles/default.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL="."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.2.0/require.min.js" data-main="assets/documenter.js"></script><script src="siteinfo.js"></script><script src="../versions.js"></script><link href="assets/documenter.css" rel="stylesheet" type="text/css"/></head><body><nav class="toc"><h1>XAM.jl</h1><select id="version-selector" onChange="window.location.href=this.value" style="visibility: hidden"></select><form class="search" id="search-form" action="search/"><input id="search-query" name="q" type="text" placeholder="Search docs"/></form><ul><li class="current"><a class="toctext" href>Home</a><ul class="internal"><li><a class="toctext" href="#Description-1">Description</a></li><li><a class="toctext" href="#Installation-1">Installation</a></li><li><a class="toctext" href="#Testing-1">Testing</a></li><li><a class="toctext" href="#Contributing-1">Contributing</a></li><li><a class="toctext" href="#Backers-and-Sponsors-1">Backers & Sponsors</a></li><li><a class="toctext" href="#Questions?-1">Questions?</a></li></ul></li><li><a class="toctext" href="hts-files/">SAM and BAM</a></li><li><span class="toctext">API Reference</span><ul><li><a class="toctext" href="api/public/">Public</a></li></ul></li></ul></nav><article id="docs"><header><nav><ul><li><a href>Home</a></li></ul><a class="edit-page" href="https://github.com/BioJulia/XAM.jl/blob/develop/docs/src/index.md"><span class="fa"></span> Edit on GitHub</a></nav><hr/><div id="topbar"><span>Home</span><a class="fa fa-bars" href="#"></a></div></header><h1><a class="nav-anchor" id="XAM-1" href="#XAM-1">XAM</a></h1><p><a href="https://github.com/BioJulia/XAM.jl/releases/latest"><img src="https://img.shields.io/github/release/BioJulia/XAM.jl.svg" alt="Latest Release"/></a> <a href="https://github.com/BioJulia/XAM.jl/blob/master/LICENSE"><img src="https://img.shields.io/badge/license-MIT-green.svg" alt="MIT license"/></a> <a href="https://biojulia.github.io/XAM.jl/stable"><img src="https://img.shields.io/badge/docs-stable-blue.svg" alt="Stable documentation"/></a> <a href="https://biojulia.github.io/XAM.jl/latest/"><img src="https://img.shields.io/badge/docs-latest-blue.svg" alt="Latest documentation"/></a> <!– <a href="https://www.repostatus.org/#active"><img src="https://www.repostatus.org/badges/latest/active.svg" alt="Pkg Status"/></a> –> <a href="https://www.repostatus.org/#wip"><img src="https://www.repostatus.org/badges/latest/wip.svg" alt="Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public."/></a></p><p><a href="https://gitter.im/BioJulia/XAM.jl"><img src="https://img.shields.io/gitter/room/BioJulia/XAM.svg" alt="Chat"/></a></p><h2><a class="nav-anchor" id="Description-1" href="#Description-1">Description</a></h2><p>XAM provides I/O and utilities for manipulating SAM and BAM, formatted alignment map files.</p><h2><a class="nav-anchor" id="Installation-1" href="#Installation-1">Installation</a></h2><p>XAM is made available to install through BioJulia's package registry.</p><p>Julia by default only watches the "General" package registry, so before you start, you should add the BioJulia package registry.</p><p>Start a julia terminal, hit the ] key to enter pkg mode (you should see the prompt change from julia> to pkg> ), then enter the following command:</p><pre><code class="language-julia">
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