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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://fonts.googleapis.com/css?family=Lato|Roboto+Mono" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.2/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.2/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.2/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.11.1/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL="."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="assets/documenter.js"></script><script src="siteinfo.js"></script><script src="../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-dark.css" data-theme-name="documenter-dark"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><a class="docs-logo" href><img src="assets/logo.svg" alt="XAM.jl logo"/></a><div class="docs-package-name"><span class="docs-autofit">XAM.jl</span></div><form class="docs-search" action="search/"><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li class="is-active"><a class="tocitem" href>Home</a><ul class="internal"><li><a class="tocitem" href="#Description-1"><span>Description</span></a></li><li><a class="tocitem" href="#Installation-1"><span>Installation</span></a></li><li><a class="tocitem" href="#Testing-1"><span>Testing</span></a></li><li><a class="tocitem" href="#Contributing-1"><span>Contributing</span></a></li><li><a class="tocitem" href="#Backers-and-Sponsors-1"><span>Backers &amp; Sponsors</span></a></li><li><a class="tocitem" href="#Questions?-1"><span>Questions?</span></a></li></ul></li><li><a class="tocitem" href="man/hts-files/">SAM and BAM</a></li><li><a class="tocitem" href="man/api/">API Reference</a></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href>Home</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Home</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://github.com/BioJulia/XAM.jl/blob/develop/docs/src/index.md" title="Edit on GitHub"><span class="docs-icon fab"></span><span class="docs-label is-hidden-touch">Edit on GitHub</span></a><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article class="content" id="documenter-page"><h1 id="XAM.jl-1"><a class="docs-heading-anchor" href="#XAM.jl-1">XAM.jl</a><a class="docs-heading-anchor-permalink" href="#XAM.jl-1" title="Permalink"></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-dev-blue.svg" alt="Latest documentation"/></a> <a href="https://gitter.im/BioJulia/XAM.jl"><img src="https://badges.gitter.im/BioJulia/XAM.jl.svg" alt="Join the chat at https://gitter.im/BioJulia/XAM.jl"/></a></p><blockquote><p>This project follows the <a href="http://semver.org">semver</a> pro forma and uses the <a href="https://nvie.com/posts/a-successful-git-branching-model/">git-flow branching model</a>.</p></blockquote><h2 id="Description-1"><a class="docs-heading-anchor" href="#Description-1">Description</a><a class="docs-heading-anchor-permalink" href="#Description-1" title="Permalink"></a></h2><p>XAM provides I/O and utilities for manipulating SAM and BAM formatted alignment map files.</p><h2 id="Installation-1"><a class="docs-heading-anchor" href="#Installation-1">Installation</a><a class="docs-heading-anchor-permalink" href="#Installation-1" title="Permalink"></a></h2><p>XAM is made available to install through BioJulia&#39;s package registry. Julia&#39;s package manager only uses the &quot;General&quot; package registry by default. Your Julia configuration needs to include the BioJulia registry to be able to install the latest version of XAM.</p><p>To add the BioJulia registry from the <a href="https://docs.julialang.org/en/v1/manual/getting-started/">Julia REPL</a>, press <code>]</code> to enter <a href="https://docs.julialang.org/en/v1/stdlib/Pkg/">pkg mode</a>, then enter the following command:</p><pre><code class="language-julia">registry add https://github.com/BioJulia/BioJuliaRegistry.git</code></pre><p>Once the registry is added to your configuration, you can install XAM while in <a href="https://docs.julialang.org/en/v1/stdlib/Pkg/">pkg mode</a> with 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 id="Testing-1"><a class="docs-heading-anchor" href="#Testing-1">Testing</a><a class="docs-heading-anchor-permalink" href="#Testing-1" title="Permalink"></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://github.com/BioJulia/XAM.jl/actions?query=workflow%3A%22Unit+tests%22+branch%3Amaster"><img src="https://github.com/BioJulia/XAM.jl/workflows/Unit%20tests/badge.svg?branch=master" alt="Unit tests"/></a> <a href="https://github.com/BioJulia/XAM.jl/actions?query=workflow%3ADocumentation+branch%3Amaster"><img src="https://github.com/BioJulia/XAM.jl/workflows/Documentation/badge.svg?branch=master" alt="Documentation"/></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 id="Contributing-1"><a class="docs-heading-anchor" href="#Contributing-1">Contributing</a><a class="docs-heading-anchor-permalink" href="#Contributing-1" title="Permalink"></a></h2><p>We appreciate <a href="https://github.com/BioJulia/XAM.jl/graphs/contributors">contributions</a> 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 id="Financial-contributions-1"><a class="docs-heading-anchor" href="#Financial-contributions-1">Financial contributions</a><a class="docs-heading-anchor-permalink" href="#Financial-contributions-1" title="Permalink"></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 the core contributors and the person who filed the expense will be reimbursed.</p><h2 id="Backers-and-Sponsors-1"><a class="docs-heading-anchor" href="#Backers-and-Sponsors-1">Backers &amp; Sponsors</a><a class="docs-heading-anchor-permalink" href="#Backers-and-Sponsors-1" title="Permalink"></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 id="Questions?-1"><a class="docs-heading-anchor" href="#Questions?-1">Questions?</a><a class="docs-heading-anchor-permalink" href="#Questions?-1" title="Permalink"></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></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="man/hts-files/">SAM and BAM »</a></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> on <span class="colophon-date" title="Tuesday 25 February 2020 08:21">Tuesday 25 February 2020</span>. Using Julia version 1.3.0.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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