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{"documenter":{"julia_version":"1.10.0","generation_timestamp":"2024-01-02T20:07:58","documenter_version":"1.2.1"}}
{"documenter":{"julia_version":"1.10.0","generation_timestamp":"2024-01-15T11:20:39","documenter_version":"1.2.1"}}
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<!DOCTYPE html>
<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>I/O · BioSequences.jl</title><meta name="title" content="I/O · BioSequences.jl"/><meta property="og:title" content="I/O · BioSequences.jl"/><meta property="twitter:title" content="I/O · BioSequences.jl"/><meta name="description" content="Documentation for BioSequences.jl."/><meta property="og:description" content="Documentation for BioSequences.jl."/><meta property="twitter:description" content="Documentation for BioSequences.jl."/><script data-outdated-warner src="../assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.050/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.8/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="../search_index.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" data-theme-primary-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.png" alt="BioSequences.jl logo"/></a><div class="docs-package-name"><span class="docs-autofit"><a href="../">BioSequences.jl</a></span></div><button class="docs-search-query input is-rounded is-small is-clickable my-2 mx-auto py-1 px-2" id="documenter-search-query">Search docs (Ctrl + /)</button><ul class="docs-menu"><li><a class="tocitem" href="../">Home</a></li><li><a class="tocitem" href="../symbols/">Biological Symbols</a></li><li><a class="tocitem" href="../types/">BioSequences Types</a></li><li><a class="tocitem" href="../construction/">Constructing sequences</a></li><li><a class="tocitem" href="../transforms/">Indexing &amp; modifying sequences</a></li><li><a class="tocitem" href="../predicates/">Predicates</a></li><li><a class="tocitem" href="../random/">Random sequences</a></li><li><a class="tocitem" href="../sequence_search/">Pattern matching and searching</a></li><li><a class="tocitem" href="../iteration/">Iteration</a></li><li><a class="tocitem" href="../counting/">Counting</a></li><li class="is-active"><a class="tocitem" href>I/O</a></li><li><a class="tocitem" href="../interfaces/">Implementing custom types</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"><a class="docs-sidebar-button docs-navbar-link fa-solid fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href>I/O</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>I/O</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/BioJulia/BioSequences.jl" title="View the repository on GitHub"><span class="docs-icon fa-brands"></span><span class="docs-label is-hidden-touch">GitHub</span></a><a class="docs-navbar-link" href="https://github.com/BioJulia/BioSequences.jl/blob/master/docs/src/io.md" title="Edit source on GitHub"><span class="docs-icon fa-solid"></span></a><a class="docs-settings-button docs-navbar-link fa-solid fa-gear" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-article-toggle-button fa-solid fa-chevron-up" id="documenter-article-toggle-button" href="javascript:;" title="Collapse all docstrings"></a></div></header><article class="content" id="documenter-page"><h1 id="I/O-for-sequencing-file-formats"><a class="docs-heading-anchor" href="#I/O-for-sequencing-file-formats">I/O for sequencing file formats</a><a id="I/O-for-sequencing-file-formats-1"></a><a class="docs-heading-anchor-permalink" href="#I/O-for-sequencing-file-formats" title="Permalink"></a></h1><p>Versions of BioSequences prior to v2.0 provided a FASTA, FASTQ, and 2Bit submodule for working with formatted sequence files.</p><p>After version v2.0, in order to neatly separate concerns, these submodules were removed.</p><p>Instead there will now be dedicated BioJulia packages for each format. Each of these will be compatible with BioSequences.</p><p>A list of all of the different formats and packages is provided below to help you find them quickly.</p><table><tr><th style="text-align: left">Format</th><th style="text-align: left">Package</th></tr><tr><td style="text-align: left">FASTA</td><td style="text-align: left"><a href="https://github.com/BioJulia/FASTX.jl">FASTX.jl</a></td></tr><tr><td style="text-align: left">FASTQ</td><td style="text-align: left"><a href="https://github.com/BioJulia/FASTX.jl">FASTX.jl</a></td></tr><tr><td style="text-align: left">2Bit</td><td style="text-align: left"><a href="https://github.com/BioJulia/TwoBit.jl">TwoBit.jl</a></td></tr></table></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../counting/">« Counting</a><a class="docs-footer-nextpage" href="../interfaces/">Implementing custom types »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></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><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.2.1 on <span class="colophon-date" title="Tuesday 2 January 2024 20:07">Tuesday 2 January 2024</span>. Using Julia version 1.10.0.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>I/O · BioSequences.jl</title><meta name="title" content="I/O · BioSequences.jl"/><meta property="og:title" content="I/O · BioSequences.jl"/><meta property="twitter:title" content="I/O · BioSequences.jl"/><meta name="description" content="Documentation for BioSequences.jl."/><meta property="og:description" content="Documentation for BioSequences.jl."/><meta property="twitter:description" content="Documentation for BioSequences.jl."/><script data-outdated-warner src="../assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.050/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.8/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="../search_index.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" data-theme-primary-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.png" alt="BioSequences.jl logo"/></a><div class="docs-package-name"><span class="docs-autofit"><a href="../">BioSequences.jl</a></span></div><button class="docs-search-query input is-rounded is-small is-clickable my-2 mx-auto py-1 px-2" id="documenter-search-query">Search docs (Ctrl + /)</button><ul class="docs-menu"><li><a class="tocitem" href="../">Home</a></li><li><a class="tocitem" href="../symbols/">Biological Symbols</a></li><li><a class="tocitem" href="../types/">BioSequences Types</a></li><li><a class="tocitem" href="../construction/">Constructing sequences</a></li><li><a class="tocitem" href="../transforms/">Indexing &amp; modifying sequences</a></li><li><a class="tocitem" href="../predicates/">Predicates</a></li><li><a class="tocitem" href="../random/">Random sequences</a></li><li><a class="tocitem" href="../sequence_search/">Pattern matching and searching</a></li><li><a class="tocitem" href="../counting/">Counting</a></li><li class="is-active"><a class="tocitem" href>I/O</a></li><li><a class="tocitem" href="../interfaces/">Implementing custom types</a></li><li><a class="tocitem" href="../recipes/">Recipes</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"><a class="docs-sidebar-button docs-navbar-link fa-solid fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href>I/O</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>I/O</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/BioJulia/BioSequences.jl" title="View the repository on GitHub"><span class="docs-icon fa-brands"></span><span class="docs-label is-hidden-touch">GitHub</span></a><a class="docs-navbar-link" href="https://github.com/BioJulia/BioSequences.jl/blob/master/docs/src/io.md" title="Edit source on GitHub"><span class="docs-icon fa-solid"></span></a><a class="docs-settings-button docs-navbar-link fa-solid fa-gear" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-article-toggle-button fa-solid fa-chevron-up" id="documenter-article-toggle-button" href="javascript:;" title="Collapse all docstrings"></a></div></header><article class="content" id="documenter-page"><h1 id="I/O-for-sequencing-file-formats"><a class="docs-heading-anchor" href="#I/O-for-sequencing-file-formats">I/O for sequencing file formats</a><a id="I/O-for-sequencing-file-formats-1"></a><a class="docs-heading-anchor-permalink" href="#I/O-for-sequencing-file-formats" title="Permalink"></a></h1><p>Versions of BioSequences prior to v2.0 provided a FASTA, FASTQ, and 2Bit submodule for working with formatted sequence files.</p><p>After version v2.0, in order to neatly separate concerns, these submodules were removed.</p><p>Instead there will now be dedicated BioJulia packages for each format. Each of these will be compatible with BioSequences.</p><p>A list of all of the different formats and packages is provided below to help you find them quickly.</p><table><tr><th style="text-align: left">Format</th><th style="text-align: left">Package</th></tr><tr><td style="text-align: left">FASTA</td><td style="text-align: left"><a href="https://github.com/BioJulia/FASTX.jl">FASTX.jl</a></td></tr><tr><td style="text-align: left">FASTQ</td><td style="text-align: left"><a href="https://github.com/BioJulia/FASTX.jl">FASTX.jl</a></td></tr><tr><td style="text-align: left">2Bit</td><td style="text-align: left"><a href="https://github.com/BioJulia/TwoBit.jl">TwoBit.jl</a></td></tr></table></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../counting/">« Counting</a><a class="docs-footer-nextpage" href="../interfaces/">Implementing custom types »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></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><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.2.1 on <span class="colophon-date" title="Monday 15 January 2024 11:20">Monday 15 January 2024</span>. Using Julia version 1.10.0.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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