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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 &amp; 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://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> <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/dev/"><img src="https://img.shields.io/badge/docs-latest-blue.svg" alt="Latest documentation"/></a> <a href="https://gitter.im/BioJulia/XAM.jl?utm_source=badge&amp;utm_medium=badge&amp;utm_campaign=pr-badge&amp;utm_content=badge"><img src="https://badges.gitter.im/BioJulia/XAM.jl.svg" alt="Join the chat at https://gitter.im/BioJulia/XAM.jl"/></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&#39;s package registry.</p><p>Julia by default only watches the &quot;General&quot; package registry, so before you start, you should add the BioJulia package registry.</p><p>Start a julia terminal, hit the <code>]</code> key to enter pkg mode (you should see the prompt change from <code>julia&gt;</code> to <code>pkg&gt;</code> ), then enter the following command:</p><pre><code class="language-julia">registry add https://github.com/BioJulia/BioJuliaRegistry.git</code></pre><p>After you&#39;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><code class="language-julia">add XAM</code></pre><p>If you are interested in the cutting edge of the development, please check out the <a href="https://github.com/BioJulia/XAM.jl/tree/develop">develop branch</a> to try new features before release.</p><h2><a class="nav-anchor" id="Testing-1" href="#Testing-1">Testing</a></h2><p>XAM is tested against Julia <code>1.X</code> on Linux, OS X, and Windows.</p><p><strong>Latest build status:</strong></p><p><a href="https://travis-ci.com/BioJulia/XAM.jl"><img src="https://travis-ci.com/BioJulia/XAM.jl.svg?branch=master" alt/></a> <a href="https://ci.appveyor.com/project/BioJulia/xam-jl"><img src="https://ci.appveyor.com/api/projects/status/y2u4o589q38s6f34?svg=true" alt="Build status"/></a> <a href="https://codecov.io/gh/BioJulia/XAM.jl"><img src="https://codecov.io/gh/BioJulia/XAM.jl/branch/master/graph/badge.svg" alt="codecov"/></a></p><h2><a class="nav-anchor" id="Contributing-1" href="#Contributing-1">Contributing</a></h2><p>We appreciate contributions from users including reporting bugs, fixing issues, improving performance and adding new features.</p><p>Take a look at the <a href="https://github.com/BioJulia/Contributing">contributing files</a> detailed contributor and maintainer guidelines, and code of conduct.</p><h3><a class="nav-anchor" id="Financial-contributions-1" href="#Financial-contributions-1">Financial contributions</a></h3><p>We also welcome financial contributions in full transparency on our <a href="https://opencollective.com/biojulia">open collective</a>. Anyone can file an expense. If the expense makes sense for the development of the community, it will be &quot;merged&quot; in the ledger of our open collective by the core contributors and the person who filed the expense will be reimbursed.</p><h2><a class="nav-anchor" id="Backers-and-Sponsors-1" href="#Backers-and-Sponsors-1">Backers &amp; Sponsors</a></h2><p>Thank you to all our backers and sponsors!</p><p>Love our work and community? <a href="https://opencollective.com/biojulia#backer">Become a backer</a>.</p><p><a href="https://opencollective.com/biojulia#backers"><img src="https://opencollective.com/biojulia/backers.svg?width=890" alt="backers"/></a></p><p>Does your company use BioJulia? Help keep BioJulia feature rich and healthy by <a href="https://opencollective.com/biojulia#sponsor">sponsoring the project</a>. Your logo will show up here with a link to your website.</p><p><a href="https://opencollective.com/biojulia/sponsor/0/website"><img src="https://opencollective.com/biojulia/sponsor/0/avatar.svg" alt/></a> <a href="https://opencollective.com/biojulia/sponsor/1/website"><img src="https://opencollective.com/biojulia/sponsor/1/avatar.svg" alt/></a> <a href="https://opencollective.com/biojulia/sponsor/2/website"><img src="https://opencollective.com/biojulia/sponsor/2/avatar.svg" alt/></a> <a href="https://opencollective.com/biojulia/sponsor/3/website"><img src="https://opencollective.com/biojulia/sponsor/3/avatar.svg" alt/></a> <a href="https://opencollective.com/biojulia/sponsor/4/website"><img src="https://opencollective.com/biojulia/sponsor/4/avatar.svg" alt/></a> <a href="https://opencollective.com/biojulia/sponsor/5/website"><img src="https://opencollective.com/biojulia/sponsor/5/avatar.svg" alt/></a> <a href="https://opencollective.com/biojulia/sponsor/6/website"><img src="https://opencollective.com/biojulia/sponsor/6/avatar.svg" alt/></a> <a href="https://opencollective.com/biojulia/sponsor/7/website"><img src="https://opencollective.com/biojulia/sponsor/7/avatar.svg" alt/></a> <a href="https://opencollective.com/biojulia/sponsor/8/website"><img src="https://opencollective.com/biojulia/sponsor/8/avatar.svg" alt/></a> <a href="https://opencollective.com/biojulia/sponsor/9/website"><img src="https://opencollective.com/biojulia/sponsor/9/avatar.svg" alt/></a></p><h2><a class="nav-anchor" id="Questions?-1" href="#Questions?-1">Questions?</a></h2><p>If you have a question about contributing or using BioJulia software, come on over and chat to us on <a href="https://gitter.im/BioJulia/General">Gitter</a>, or you can try the <a href="https://discourse.julialang.org/c/domain/bio">Bio category of the Julia discourse site</a>.</p><footer><hr/><a class="next" href="hts-files/"><span class="direction">Next</span><span class="title">SAM and BAM</span></a></footer></article></body></html>
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