millironx/XAM.jl
1
0
Fork 0
mirror of https://github.com/MillironX/XAM.jl.git synced 2024-12-25 06:08:19 +00:00
Code Issues Releases Packages Activity
XAM.jl/dev/index.html
zeptodoctor ec72c4664b build based on 81dbf41
2020-05-22 03:08:00 +00:00

2 lines
12 KiB
HTML
Raw Blame History

This file contains ambiguous Unicode characters

This file contains Unicode characters that might be confused with other characters. If you think that this is intentional, you can safely ignore this warning. Use the Escape button to reveal them.

<!DOCTYPE html>
<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/#active"><img src="https://www.repostatus.org/badges/latest/active.svg" alt="Project Status: Active – The project has reached a stable, usable state and is being actively developed."/></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>The latest version of XAM is made available to install through BioJulia&#39;s package registry. By default, Julia&#39;s package manager only includes the &quot;General&quot; package registry.</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="Friday 22 May 2020 03:07">Friday 22 May 2020</span>. Using Julia version 1.3.0.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
Reference in a new issue View git blame Copy permalink