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-{"documenter":{"julia_version":"1.10.2","generation_timestamp":"2024-03-24T17:02:29","documenter_version":"1.3.0"}}
+{"documenter":{"julia_version":"1.10.3","generation_timestamp":"2024-05-16T08:22:43","documenter_version":"1.4.1"}}

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- 0</code></pre><h2 id="Limitations"><a class="docs-heading-anchor" href="#Limitations">Limitations</a><a id="Limitations-1"></a><a class="docs-heading-anchor-permalink" href="#Limitations" title="Permalink"></a></h2><p>The main downside of counting <span>$K$</span>-mers this way is that the arrays grow exponentially with respect to <span>$K$</span>. The 31-mer array of a DNA sequence would have a length of <span>$4^{31} = 4,611,686,018,427,387,904$</span>, which is equivalent to four exbibytes of memory, if the values are stored with 8-bit integers — which is just not feasible, really. Not only does allocating a lot of memory take up a lot of memory, but it can also take a substantial amount of time! This method of counting <span>$K$</span>-mers therefore works best for lower <span>$K$</span>-values.</p></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="kmer_int_repr/">Integer representation of k-mers »</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="auto">Automatic (OS)</option><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> version 1.3.0 on <span class="colophon-date" title="Sunday 24 March 2024 17:02">Sunday 24 March 2024</span>. Using Julia version 1.10.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+ 0</code></pre><h2 id="Limitations"><a class="docs-heading-anchor" href="#Limitations">Limitations</a><a id="Limitations-1"></a><a class="docs-heading-anchor-permalink" href="#Limitations" title="Permalink"></a></h2><p>The main downside of counting <span>$K$</span>-mers this way is that the arrays grow exponentially with respect to <span>$K$</span>. The 31-mer array of a DNA sequence would have a length of <span>$4^{31} = 4,611,686,018,427,387,904$</span>, which is equivalent to four exbibytes of memory, if the values are stored with 8-bit integers — which is just not feasible, really. Not only does allocating a lot of memory take up a lot of memory, but it can also take a substantial amount of time! This method of counting <span>$K$</span>-mers therefore works best for lower <span>$K$</span>-values.</p></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="kmer_int_repr/">Integer representation of k-mers »</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="auto">Automatic (OS)</option><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> version 1.4.1 on <span class="colophon-date" title="Thursday 16 May 2024 08:22">Thursday 16 May 2024</span>. Using Julia version 1.10.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/kmer_int_repr/index.html

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-<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Integer representation of k-mers · VectorizedKmers.jl</title><meta name="title" content="Integer representation of k-mers · VectorizedKmers.jl"/><meta property="og:title" content="Integer representation of k-mers · VectorizedKmers.jl"/><meta property="twitter:title" content="Integer representation of k-mers · VectorizedKmers.jl"/><meta name="description" content="Documentation for VectorizedKmers.jl."/><meta property="og:description" content="Documentation for VectorizedKmers.jl."/><meta property="twitter:description" content="Documentation for VectorizedKmers.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" 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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="VectorizedKmers.jl logo"/></a><div class="docs-package-name"><span class="docs-autofit"><a href="../">VectorizedKmers.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 class="is-active"><a class="tocitem" href>Integer representation of k-mers</a></li><li><a class="tocitem" href="../references/">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"><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>Integer representation of k-mers</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Integer representation of k-mers</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/anton083/VectorizedKmers.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/anton083/VectorizedKmers.jl/blob/main/docs/src/kmer_int_repr.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="Integer-representation-of-K-mers"><a class="docs-heading-anchor" href="#Integer-representation-of-K-mers">Integer representation of K-mers</a><a id="Integer-representation-of-K-mers-1"></a><a class="docs-heading-anchor-permalink" href="#Integer-representation-of-K-mers" title="Permalink"></a></h1><p>This package relies on representing K-mers as integers for indexing.</p><p>For DNA, each non-ambiguous nucleotide is assigned a number between 0 and 3:</p><table><tr><th style="text-align: right">Nucleotide</th><th style="text-align: right">Base-4</th><th style="text-align: right">Base-2</th></tr><tr><td style="text-align: right">A</td><td style="text-align: right">0</td><td style="text-align: right">00</td></tr><tr><td style="text-align: right">C</td><td style="text-align: right">1</td><td style="text-align: right">01</td></tr><tr><td style="text-align: right">G</td><td style="text-align: right">2</td><td style="text-align: right">10</td></tr><tr><td style="text-align: right">T</td><td style="text-align: right">3</td><td style="text-align: right">11</td></tr></table><p>Any ordering works, but this is the one used by <a href="https://github.com/BioJulia/BioSequences.jl">BioSequences.jl</a>. It also has some nice properties, like being in alphabetical order, and that XOR-ing a base with 3 gives you its complement.</p><p>We could theoretically convert any DNA sequence to an integer, but 64-bit unsigned integers limit us to 32-mers.</p><p>Consider the DNA sequence <code>GATTACA</code>. If we convert it to an integer using the table above, we get <span>$2033010_4 = 10001111000100_2 = 9156_{10}$</span>, so the integer value of <code>GATTACA</code> is 9156. Since Julia uses 1-based indexing, we would add 1 to this value to get the index for the value in a vector associated with <code>GATTACA</code>.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Home</a><a class="docs-footer-nextpage" href="../references/">API Reference »</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="auto">Automatic (OS)</option><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> version 1.3.0 on <span class="colophon-date" title="Sunday 24 March 2024 17:02">Sunday 24 March 2024</span>. Using Julia version 1.10.2.</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>Integer representation of k-mers · VectorizedKmers.jl</title><meta name="title" content="Integer representation of k-mers · VectorizedKmers.jl"/><meta property="og:title" content="Integer representation of k-mers · VectorizedKmers.jl"/><meta property="twitter:title" content="Integer representation of k-mers · VectorizedKmers.jl"/><meta name="description" content="Documentation for VectorizedKmers.jl."/><meta property="og:description" content="Documentation for VectorizedKmers.jl."/><meta property="twitter:description" content="Documentation for VectorizedKmers.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="VectorizedKmers.jl logo"/></a><div class="docs-package-name"><span class="docs-autofit"><a href="../">VectorizedKmers.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 class="is-active"><a class="tocitem" href>Integer representation of k-mers</a></li><li><a class="tocitem" href="../references/">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"><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>Integer representation of k-mers</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Integer representation of k-mers</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/anton083/VectorizedKmers.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/anton083/VectorizedKmers.jl/blob/main/docs/src/kmer_int_repr.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="Integer-representation-of-K-mers"><a class="docs-heading-anchor" href="#Integer-representation-of-K-mers">Integer representation of K-mers</a><a id="Integer-representation-of-K-mers-1"></a><a class="docs-heading-anchor-permalink" href="#Integer-representation-of-K-mers" title="Permalink"></a></h1><p>This package relies on representing K-mers as integers for indexing.</p><p>For DNA, each non-ambiguous nucleotide is assigned a number between 0 and 3:</p><table><tr><th style="text-align: right">Nucleotide</th><th style="text-align: right">Base-4</th><th style="text-align: right">Base-2</th></tr><tr><td style="text-align: right">A</td><td style="text-align: right">0</td><td style="text-align: right">00</td></tr><tr><td style="text-align: right">C</td><td style="text-align: right">1</td><td style="text-align: right">01</td></tr><tr><td style="text-align: right">G</td><td style="text-align: right">2</td><td style="text-align: right">10</td></tr><tr><td style="text-align: right">T</td><td style="text-align: right">3</td><td style="text-align: right">11</td></tr></table><p>Any ordering works, but this is the one used by <a href="https://github.com/BioJulia/BioSequences.jl">BioSequences.jl</a>. It also has some nice properties, like being in alphabetical order, and that XOR-ing a base with 3 gives you its complement.</p><p>We could theoretically convert any DNA sequence to an integer, but 64-bit unsigned integers limit us to 32-mers.</p><p>Consider the DNA sequence <code>GATTACA</code>. If we convert it to an integer using the table above, we get <span>$2033010_4 = 10001111000100_2 = 9156_{10}$</span>, so the integer value of <code>GATTACA</code> is 9156. Since Julia uses 1-based indexing, we would add 1 to this value to get the index for the value in a vector associated with <code>GATTACA</code>.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Home</a><a class="docs-footer-nextpage" href="../references/">API Reference »</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="auto">Automatic (OS)</option><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> version 1.4.1 on <span class="colophon-date" title="Thursday 16 May 2024 08:22">Thursday 16 May 2024</span>. Using Julia version 1.10.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>