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{"documenter":{"julia_version":"1.10.2","generation_timestamp":"2024-03-06T09:51:08","documenter_version":"1.3.0"}}
{"documenter":{"julia_version":"1.10.2","generation_timestamp":"2024-03-06T11:19:05","documenter_version":"1.3.0"}}
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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 · VectorizedKmers.jl</title><meta name="title" content="Home · VectorizedKmers.jl"/><meta property="og:title" content="Home · VectorizedKmers.jl"/><meta property="twitter:title" content="Home · 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script data-outdated-warner src="assets/warner.js"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" 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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 class="is-active"><a class="tocitem" href>Home</a><ul class="internal"><li><a class="tocitem" href="#Installation"><span>Installation</span></a></li></ul></li><li><a class="tocitem" href="kmer_int_repr/">Integer representation of k-mers</a></li><li><span class="tocitem">k-mer counting</span><ul><li><a class="tocitem" href="kmer_count_vector/">Vectors of k-mer counts</a></li><li><a class="tocitem" href="kmer_count_matrix/">Matrices of k-mers counts</a></li></ul></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>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-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/index.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="VectorizedKmers"><a class="docs-heading-anchor" href="#VectorizedKmers">VectorizedKmers</a><a id="VectorizedKmers-1"></a><a class="docs-heading-anchor-permalink" href="#VectorizedKmers" title="Permalink"></a></h1><p><a href="https://github.com/anton083/VectorizedKmers.jl/releases/latest"><img src="https://img.shields.io/github/release/anton083/VectorizedKmers.jl.svg" alt="Latest Release"/></a> <a href="https://opensource.org/license/MIT"><img src="https://img.shields.io/badge/license-MIT-green.svg" alt="MIT license"/></a> <a href="https://anton083.github.io/VectorizedKmers.jl/stable/"><img src="https://img.shields.io/badge/docs-stable-blue.svg" alt="Documentation"/></a> <a href="https://anton083.github.io/VectorizedKmers.jl/dev/"><img src="https://img.shields.io/badge/docs-latest-blue.svg" alt="Documentation"/></a> <a href="https://github.com/anton083/VectorizedKmers.jl/actions/workflows/CI.yml?query=branch%3Amain"><img src="https://github.com/anton083/VectorizedKmers.jl/actions/workflows/CI.yml/badge.svg?branch=main" alt="Status"/></a> <a href="https://codecov.io/gh/anton083/VectorizedKmers.jl"><img src="https://codecov.io/gh/anton083/VectorizedKmers.jl/branch/main/graph/badge.svg" alt="Coverage"/></a></p><p><a href="https://github.com/anton083/VectorizedKmers.jl">VectorizedKmers.jl</a> is a Julia package for fast <span>$k$</span>-mer counting of biological sequences. The core idea is that <span>$k$</span>-mers with an alphabet size <span>$S$</span> are essentially integers in base <span>$S$</span>, and can be used as indices in a vector of size <span>$S^k$</span> to count the corresponding <span>$k$</span>-mers.</p><p>The <code>KmerVector</code> type is a wrapper for <code>AbstractVector</code>, which means that these vector k-mer counts are not limited to Julia&#39;s <code>Base.Vector</code> type; other kinds of vectors can be used as well, such as <code>CUDA.CuVector</code>, <code>SparseArrays.SparseVector</code> or even matrix views.</p><p>To efficiently group k-mer counts together, the <code>AbstractKmerMatrix</code> stores them in a matrix as rows or columns. It can wrap any <code>AbstractMatrix</code>, such as <code>Matrix</code> or <code>CuMatrix</code>, and accessing its elements by index returns a <code>KmerVector</code> wrapped around a view of a row or column of the original matrix.</p><p>This data structure can be used to quickly approximate distances between sequences. Most notably, the squared Euclidean distance was used to approximate edit distance in <a href="https://doi.org/10.1093/nar/gkz657">this paper</a>. The dot product has also proven to be a useful metric for comparing correlation between sequences.</p><h2 id="Installation"><a class="docs-heading-anchor" href="#Installation">Installation</a><a id="Installation-1"></a><a class="docs-heading-anchor-permalink" href="#Installation" title="Permalink"></a></h2><p>You can install VectorizedKmers in your environment from the Julia REPL by entering pkg mode with <code>]</code> and then running:</p><pre><code class="nohighlight hljs">add VectorizedKmers</code></pre></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="Wednesday 6 March 2024 09:51">Wednesday 6 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>Home · VectorizedKmers.jl</title><meta name="title" content="Home · VectorizedKmers.jl"/><meta property="og:title" content="Home · VectorizedKmers.jl"/><meta property="twitter:title" content="Home · 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 class="is-active"><a class="tocitem" href>Home</a><ul class="internal"><li><a class="tocitem" href="#Installation"><span>Installation</span></a></li></ul></li><li><a class="tocitem" href="kmer_int_repr/">Integer representation of k-mers</a></li><li><span class="tocitem">k-mer counting</span><ul><li><a class="tocitem" href="kmer_count_vector/">Vectors of k-mer counts</a></li><li><a class="tocitem" href="kmer_count_matrix/">Matrices of k-mers counts</a></li></ul></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>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-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/index.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="VectorizedKmers"><a class="docs-heading-anchor" href="#VectorizedKmers">VectorizedKmers</a><a id="VectorizedKmers-1"></a><a class="docs-heading-anchor-permalink" href="#VectorizedKmers" title="Permalink"></a></h1><p><a href="https://github.com/anton083/VectorizedKmers.jl/releases/latest"><img src="https://img.shields.io/github/release/anton083/VectorizedKmers.jl.svg" alt="Latest Release"/></a> <a href="https://opensource.org/license/MIT"><img src="https://img.shields.io/badge/license-MIT-green.svg" alt="MIT license"/></a> <a href="https://anton083.github.io/VectorizedKmers.jl/stable/"><img src="https://img.shields.io/badge/docs-stable-blue.svg" alt="Documentation"/></a> <a href="https://anton083.github.io/VectorizedKmers.jl/dev/"><img src="https://img.shields.io/badge/docs-latest-blue.svg" alt="Documentation"/></a> <a href="https://github.com/anton083/VectorizedKmers.jl/actions/workflows/CI.yml?query=branch%3Amain"><img src="https://github.com/anton083/VectorizedKmers.jl/actions/workflows/CI.yml/badge.svg?branch=main" alt="Status"/></a> <a href="https://codecov.io/gh/anton083/VectorizedKmers.jl"><img src="https://codecov.io/gh/anton083/VectorizedKmers.jl/branch/main/graph/badge.svg" alt="Coverage"/></a></p><p><a href="https://github.com/anton083/VectorizedKmers.jl">VectorizedKmers.jl</a> is a Julia package for fast <span>$k$</span>-mer counting of biological sequences. The core idea is that <span>$k$</span>-mers with an alphabet size <span>$S$</span> are essentially integers in base <span>$S$</span>, and can be used as indices in a vector of size <span>$S^k$</span> to count the corresponding <span>$k$</span>-mers.</p><p>The <code>KmerVector</code> type is a wrapper for <code>AbstractVector</code>, which means that these vector k-mer counts are not limited to Julia&#39;s <code>Base.Vector</code> type; other kinds of vectors can be used as well, such as <code>CUDA.CuVector</code>, <code>SparseArrays.SparseVector</code> or even matrix views.</p><p>To efficiently group k-mer counts together, the <code>AbstractKmerMatrix</code> stores them in a matrix as rows or columns. It can wrap any <code>AbstractMatrix</code>, such as <code>Matrix</code> or <code>CuMatrix</code>, and accessing its elements by index returns a <code>KmerVector</code> wrapped around a view of a row or column of the original matrix.</p><p>This data structure can be used to quickly approximate distances between sequences. Most notably, the squared Euclidean distance was used to approximate edit distance in <a href="https://doi.org/10.1093/nar/gkz657">this paper</a>. The dot product has also proven to be a useful metric for comparing correlation between sequences.</p><h2 id="Installation"><a class="docs-heading-anchor" href="#Installation">Installation</a><a id="Installation-1"></a><a class="docs-heading-anchor-permalink" href="#Installation" title="Permalink"></a></h2><p>You can install VectorizedKmers in your environment from the Julia REPL by entering pkg mode with <code>]</code> and then running:</p><pre><code class="nohighlight hljs">add VectorizedKmers</code></pre></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="Wednesday 6 March 2024 11:19">Wednesday 6 March 2024</span>. Using Julia version 1.10.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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