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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><script data-outdated-warner src="assets/warner.js"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/0.045/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/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" 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"><div class="docs-package-name"><span class="docs-autofit"><a href>VectorizedKmers.jl</a></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></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/anton083/VectorizedKmers.jl/blob/main/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="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>Documentation for <a href="https://github.com/anton083/VectorizedKmers.jl">VectorizedKmers</a>.</p><ul><li><a href="#VectorizedKmers.AbstractKmerCount"><code>VectorizedKmers.AbstractKmerCount</code></a></li><li><a href="#VectorizedKmers.AbstractKmerCountVector"><code>VectorizedKmers.AbstractKmerCountVector</code></a></li><li><a href="#VectorizedKmers.KmerCount"><code>VectorizedKmers.KmerCount</code></a></li><li><a href="#VectorizedKmers.count_kmers!-Union{Tuple{T}, Tuple{K}, Tuple{A}, Tuple{KmerCount{A, K, T}, Vector{&lt;:Integer}}} where {A, K, T}"><code>VectorizedKmers.count_kmers!</code></a></li></ul><article class="docstring"><header><a class="docstring-binding" id="VectorizedKmers.AbstractKmerCount" href="#VectorizedKmers.AbstractKmerCount"><code>VectorizedKmers.AbstractKmerCount</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">AbstractKmerCount{A, K, T &lt;: Real, V &lt;: AbstractVector{T}}</code></pre><p>Abstract type for K-mer counts. <code>A</code> is the alphabet size, <code>K</code> is the K-mer size, and <code>T</code> is the element type of the underlying <code>counts</code> field, which in turn has type <code>V{T}</code>.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/anton083/VectorizedKmers.jl/blob/832b4d0becfd2f505c2daf5bc7d2e1fe9420682b/src/kmer_count.jl#L1-L9">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="VectorizedKmers.AbstractKmerCountVector" href="#VectorizedKmers.AbstractKmerCountVector"><code>VectorizedKmers.AbstractKmerCountVector</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">AbstractKmerCountVector{A, K, T &lt;: Real, M &lt;: AbstractMatrix{T}} &lt;: AbstractVector{KmerCount{A, K, T}}</code></pre><p>A container for K-mer counts, where K-mer counts are stored together as rows or columns in a matrix. <code>A</code> is the alphabet size, <code>K</code> is the K-mer size, <code>T</code> is the element type of the counts, and <code>M</code> is the type of the matrix in which the K-mer counts are stored.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/anton083/VectorizedKmers.jl/blob/832b4d0becfd2f505c2daf5bc7d2e1fe9420682b/src/kmer_count_vec.jl#L1-L7">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="VectorizedKmers.KmerCount" href="#VectorizedKmers.KmerCount"><code>VectorizedKmers.KmerCount</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">KmerCount{A, K, T, V} &lt;: AbstractKmerCount{A, K, T, V}</code></pre><p>A concrete type for K-mer counts with vector type <code>Base.Vector{T}</code>.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/anton083/VectorizedKmers.jl/blob/832b4d0becfd2f505c2daf5bc7d2e1fe9420682b/src/kmer_count.jl#L18-L22">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="VectorizedKmers.count_kmers!-Union{Tuple{T}, Tuple{K}, Tuple{A}, Tuple{KmerCount{A, K, T}, Vector{&lt;:Integer}}} where {A, K, T}" href="#VectorizedKmers.count_kmers!-Union{Tuple{T}, Tuple{K}, Tuple{A}, Tuple{KmerCount{A, K, T}, Vector{&lt;:Integer}}} where {A, K, T}"><code>VectorizedKmers.count_kmers!</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">count_kmers!(kmer_count, kmers; reset=true)</code></pre><p>Mutate the <code>counts</code> vector in <code>kmer_count</code> by adding the counts of each kmer in <code>kmers</code>. The K-mers in <code>kmers</code> must be represented as integers between 0 and length(kmer_count) - 1.</p><p>If <code>reset</code> is <code>true</code>, the <code>counts</code> vector will be zero-ed before counting.</p><p>This is not a very efficient method, since it takes an entire vector. It is mainly used for testing. Ideally the K-mers would be procedurally calculated in constant memory.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/anton083/VectorizedKmers.jl/blob/832b4d0becfd2f505c2daf5bc7d2e1fe9420682b/src/kmer_count.jl#L35-L45">source</a></section></article></article><nav class="docs-footer"><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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Sunday 13 August 2023 11:28">Sunday 13 August 2023</span>. Using Julia version 1.9.2.</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><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/0.045/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/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" 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"><div class="docs-package-name"><span class="docs-autofit"><a href>VectorizedKmers.jl</a></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></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/anton083/VectorizedKmers.jl/blob/main/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="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>Documentation for <a href="https://github.com/anton083/VectorizedKmers.jl">VectorizedKmers</a>.</p><ul><li><a href="#VectorizedKmers.AbstractKmerCount"><code>VectorizedKmers.AbstractKmerCount</code></a></li><li><a href="#VectorizedKmers.AbstractKmerCountVector"><code>VectorizedKmers.AbstractKmerCountVector</code></a></li><li><a href="#VectorizedKmers.KmerCount"><code>VectorizedKmers.KmerCount</code></a></li><li><a href="#VectorizedKmers.count_kmers!-Union{Tuple{T}, Tuple{K}, Tuple{A}, Tuple{KmerCount{A, K, T}, Vector{&lt;:Integer}}} where {A, K, T}"><code>VectorizedKmers.count_kmers!</code></a></li></ul><article class="docstring"><header><a class="docstring-binding" id="VectorizedKmers.AbstractKmerCount" href="#VectorizedKmers.AbstractKmerCount"><code>VectorizedKmers.AbstractKmerCount</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">AbstractKmerCount{A, K, T &lt;: Real, V &lt;: AbstractVector{T}}</code></pre><p>Abstract type for K-mer counts. <code>A</code> is the alphabet size, <code>K</code> is the K-mer size, and <code>T</code> is the element type of the underlying <code>counts</code> field, which in turn has type <code>V{T}</code>.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/anton083/VectorizedKmers.jl/blob/f75dcb959d41379dda1d3278609c7512c688c9de/src/kmer_count.jl#L1-L9">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="VectorizedKmers.AbstractKmerCountVector" href="#VectorizedKmers.AbstractKmerCountVector"><code>VectorizedKmers.AbstractKmerCountVector</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">AbstractKmerCountVector{A, K, T &lt;: Real, M &lt;: AbstractMatrix{T}} &lt;: AbstractVector{KmerCount{A, K, T}}</code></pre><p>A container for K-mer counts, where K-mer counts are stored together as rows or columns in a matrix. <code>A</code> is the alphabet size, <code>K</code> is the K-mer size, <code>T</code> is the element type of the counts, and <code>M</code> is the type of the matrix in which the K-mer counts are stored.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/anton083/VectorizedKmers.jl/blob/f75dcb959d41379dda1d3278609c7512c688c9de/src/kmer_count_vec.jl#L1-L7">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="VectorizedKmers.KmerCount" href="#VectorizedKmers.KmerCount"><code>VectorizedKmers.KmerCount</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">KmerCount{A, K, T, V} &lt;: AbstractKmerCount{A, K, T, V}</code></pre><p>A concrete type for K-mer counts with vector type <code>Base.Vector{T}</code>.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/anton083/VectorizedKmers.jl/blob/f75dcb959d41379dda1d3278609c7512c688c9de/src/kmer_count.jl#L18-L22">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="VectorizedKmers.count_kmers!-Union{Tuple{T}, Tuple{K}, Tuple{A}, Tuple{KmerCount{A, K, T}, Vector{&lt;:Integer}}} where {A, K, T}" href="#VectorizedKmers.count_kmers!-Union{Tuple{T}, Tuple{K}, Tuple{A}, Tuple{KmerCount{A, K, T}, Vector{&lt;:Integer}}} where {A, K, T}"><code>VectorizedKmers.count_kmers!</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">count_kmers!(kmer_count, kmers; reset=true)</code></pre><p>Mutate the <code>counts</code> vector in <code>kmer_count</code> by adding the counts of each kmer in <code>kmers</code>. The K-mers in <code>kmers</code> must be represented as integers between 0 and length(kmer_count) - 1.</p><p>If <code>reset</code> is <code>true</code>, the <code>counts</code> vector will be zero-ed before counting.</p><p>This is not a very efficient method, since it takes an entire vector. It is mainly used for testing. Ideally the K-mers would be procedurally calculated in constant memory.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/anton083/VectorizedKmers.jl/blob/f75dcb959d41379dda1d3278609c7512c688c9de/src/kmer_count.jl#L35-L45">source</a></section></article></article><nav class="docs-footer"><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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Sunday 13 August 2023 11:42">Sunday 13 August 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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