<htmllang="en"><head><metacharset="UTF-8"/><metaname="viewport"content="width=device-width, initial-scale=1.0"/><title>Home · XAM.jl</title><linkhref="https://cdnjs.cloudflare.com/ajax/libs/normalize/4.2.0/normalize.min.css"rel="stylesheet"type="text/css"/><linkhref="https://fonts.googleapis.com/css?family=Lato|Roboto+Mono"rel="stylesheet"type="text/css"/><linkhref="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.6.3/css/font-awesome.min.css"rel="stylesheet"type="text/css"/><linkhref="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/9.12.0/styles/default.min.css"rel="stylesheet"type="text/css"/><script>documenterBaseURL="."</script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.2.0/require.min.js"data-main="assets/documenter.js"></script><scriptsrc="siteinfo.js"></script><scriptsrc="../versions.js"></script><linkhref="assets/documenter.css"rel="stylesheet"type="text/css"/></head><body><navclass="toc"><h1>XAM.jl</h1><selectid="version-selector"onChange="window.location.href=this.value"style="visibility: hidden"></select><formclass="search"id="search-form"action="search/"><inputid="search-query"name="q"type="text"placeholder="Search docs"/></form><ul><liclass="current"><aclass="toctext"href>Home</a><ulclass="internal"><li><aclass="toctext"href="#Description-1">Description</a></li><li><aclass="toctext"href="#Installation-1">Installation</a></li><li><aclass="toctext"href="#Testing-1">Testing</a></li><li><aclass="toctext"href="#Contributing-1">Contributing</a></li><li><aclass="toctext"href="#Backers-and-Sponsors-1">Backers & Sponsors</a></li><li><aclass="toctext"href="#Questions?-1">Questions?</a></li></ul></li><li><aclass="toctext"href="hts-files/">SAM and BAM</a></li><li><spanclass="toctext">API Reference</span><ul><li><aclass="toctext"href="api/public/">Public</a></li></ul></li></ul></nav><articleid="docs"><header><nav><ul><li><ahref>Home</a></li></ul><aclass="edit-page"href="https://github.com/BioJulia/XAM.jl/blob/develop/docs/src/index.md"><spanclass="fa"></span> Edit on GitHub</a></nav><hr/><divid="topbar"><span>Home</span><aclass="fa fa-bars"href="#"></a></div></header><h1><aclass="nav-anchor"id="XAM-1"href="#XAM-1">XAM</a></h1><p><ahref="https://github.com/BioJulia/XAM.jl/releases/latest"><imgsrc="https://img.shields.io/github/release/BioJulia/XAM.jl.svg"alt="Latest Release"/></a><ahref="https://github.com/BioJulia/XAM.jl/blob/master/LICENSE"><imgsrc="https://img.shields.io/badge/license-MIT-green.svg"alt="MIT license"/></a><ahref="https://biojulia.github.io/XAM.jl/stable"><imgsrc="https://img.shields.io/badge/docs-stable-blue.svg"alt="Stable documentation"/></a><ahref="https://biojulia.github.io/XAM.jl/latest/"><imgsrc="https://img.shields.io/badge/docs-latest-blue.svg"alt="Latest documentation"/></a><ahref="https://www.repostatus.org/#active"><imgsrc="https://www.repostatus.org/badges/latest/active.svg"alt="Pkg Status"/></a><ahref="https://gitter.im/BioJulia/XAM.jl"><imgsrc="https://img.shields.io/gitter/room/BioJulia/XAM.svg"alt="Chat"/></a></p><h2><aclass="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><aclass="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><codeclass="language-julia">registry add https://github.com/BioJulia/BioJuliaRegistry.git</code></pre><p>After you've added the registry, you can install XAM from the julia REPL. Press <code>]</code> to enter pkg mode again, and enter the following:</p><pre><codeclass="language-julia">add XAM</cod
