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build based on b708539
2020-02-22 19:53:02 +00:00
<!DOCTYPE html>
build based on e8ad60b
2020-03-13 12:03:09 +00:00
<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>API Reference · 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><a class="tocitem" href="../../">Home</a></li><li><a class="tocitem" href="../hts-files/">SAM and BAM</a></li><li class="is-active"><a class="tocitem" href>API Reference</a><ul class="internal"><li><a class="tocitem" href="#SAM-API-1"><span>SAM API</span></a></li><li><a class="tocitem" href="#BAM-API-1"><span>BAM API</span></a></li></ul></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>API Reference</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>API Reference</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://github.com/BioJulia/XAM.jl/blob/develop/docs/src/man/api.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="API-Reference-1"><a class="docs-heading-anchor" href="#API-Reference-1">API Reference</a><a class="docs-heading-anchor-permalink" href="#API-Reference-1" title="Permalink"></a></h1><h2 id="SAM-API-1"><a class="docs-heading-anchor" href="#SAM-API-1">SAM API</a><a class="docs-heading-anchor-permalink" href="#SAM-API-1" title="Permalink"></a></h2><h3 id="Public-1"><a class="docs-heading-anchor" href="#Public-1">Public</a><a class="docs-heading-anchor-permalink" href="#Public-1" title="Permalink"></a></h3><article class="docstring"><header><a class="docstring-binding" id="XAM.SAM.FLAG_DUP" href="#XAM.SAM.FLAG_DUP"><code>XAM.SAM.FLAG_DUP</code></a> — <span class="docstring-category">Constant</span></header><section><div><p>0x0400: optical or PCR duplicate</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/XAM.jl/blob/e8a
build based on b708539
2020-02-22 19:53:02 +00:00
BioAlignments.SAM.MetaInfo:
tag: CO
value: some comment
julia&gt; string(ans)
&quot;@CO some comment&quot;
julia&gt; SAM.MetaInfo(&quot;SQ&quot;, [&quot;SN&quot; =&gt; &quot;chr1&quot;, &quot;LN&quot; =&gt; 12345])
BioAlignments.SAM.MetaInfo:
tag: SQ
value: SN=chr1 LN=12345
julia&gt; string(ans)
build based on e8ad60b
2020-03-13 12:03:09 +00:00
&quot;@SQ SN:chr1 LN:12345&quot;</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/XAM.jl/blob/e8ad60b086d7a355718d0f4cf6a33a3bb4fd9a19/src/sam/metainfo.jl#L45-L70">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="XAM.SAM.MetaInfo-Tuple{AbstractString}" href="#XAM.SAM.MetaInfo-Tuple{AbstractString}"><code>XAM.SAM.MetaInfo</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">MetaInfo(str::AbstractString)</code></pre><p>Create a SAM metainfo from <code>str</code>.</p><p><strong>Examples</strong></p><pre><code class="language-none">julia&gt; SAM.MetaInfo(&quot;@CO some comment&quot;)
build based on b708539
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BioAlignments.SAM.MetaInfo:
tag: CO
value: some comment
julia&gt; SAM.MetaInfo(&quot;@SQ SN:chr1 LN:12345&quot;)
BioAlignments.SAM.MetaInfo:
tag: SQ
build based on e8ad60b
2020-03-13 12:03:09 +00:00
value: SN=chr1 LN=12345</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/XAM.jl/blob/e8ad60b086d7a355718d0f4cf6a33a3bb4fd9a19/src/sam/metainfo.jl#L23-L40">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="XAM.SAM.Reader-Tuple{IO}" href="#XAM.SAM.Reader-Tuple{IO}"><code>XAM.SAM.Reader</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">SAM.Reader(input::IO)</code></pre><p>Create a data reader of the SAM file format.</p><p><strong>Arguments</strong></p><ul><li><code>input</code>: data source</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/XAM.jl/blob/e8ad60b086d7a355718d0f4cf6a33a3bb4fd9a19/src/sam/reader.jl#L16-L23">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="XAM.SAM.Record-Tuple{AbstractString}" href="#XAM.SAM.Record-Tuple{AbstractString}"><code>XAM.SAM.Record</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">SAM.Record(str::AbstractString)</code></pre><p>Create a SAM record from <code>str</code>. This function verifies the format and indexes fields for accessors.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/XAM.jl/blob/e8ad60b086d7a355718d0f4cf6a33a3bb4fd9a19/src/sam/record.jl#L63-L68">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="XAM.SAM.Record-Tuple{Array{UInt8,1}}" href="#XAM.SAM.Record-Tuple{Array{UInt8,1}}"><code>XAM.SAM.Record</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">SAM.Record(data::Vector{UInt8})</code></pre><p>Create a SAM record from <code>data</code>. This function verifies the format and indexes fields for accessors. Note that the ownership of <code>data</code> is transferred to a new record object.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/XAM.jl/blob/e8ad60b086d7a355718d0f4cf6a33a3bb4fd9a19/src/sam/record.jl#L39-L45">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="XAM.SAM.Record-Tuple{}" href="#XAM.SAM.Record-Tuple{}"><code>XAM.SAM.Record</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">SAM.Record()</code></pre><p>Create an unfilled SAM record.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/XAM.jl/blob/e8ad60b086d7a355718d0f4cf6a33a3bb4fd9a19/src/sam/record.jl#L23-L27">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="XAM.SAM.Writer" href="#XAM.SAM.Writer"><code>XAM.SAM.Writer</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia">Writer(output::IO, header::Header=Header())</code></pre><p>Create a data writer of the SAM file format.</p><p><strong>Arguments</strong></p><ul><li><code>output</code>: data sink</li><li><code>header=Header()</code>: SAM header object</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/XAM.jl/blob/e8ad60b086d7a355718d0f4cf6a33a3bb4fd9a19/src/sam/writer.jl#L4-L12">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="Base.findall-Tuple{XAM.SAM.Header,AbstractString}" href="#Base.findall-Tuple{XAM.SAM.Header,AbstractString}"><code>Base.findall</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">find(header::Header, key::AbstractString)::Vector{MetaInfo}</code></pre><p>Find metainfo objects satisfying <code>SAM.tag(metainfo) == key</code>.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/XAM.jl/blob/e8ad60b086d7a355718d0f4cf6a33a3bb4fd9a19/src/sam/header.jl#L36-L40">source</a></section></article><article
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