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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://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">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><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</a> branch 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 "merged" 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 & 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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