build based on c605145

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.9.4","generation_timestamp":"2023-12-22T01:47:55","documenter_version":"1.2.1"}}
+{"documenter":{"julia_version":"1.9.4","generation_timestamp":"2023-12-22T02:00:53","documenter_version":"1.2.1"}}

dev/api/consensus/index.html

@@ -3,9 +3,9 @@
     reference::NucleotideSeq,
     variants::Union{AbstractString,AbstractPath};
     frequency::Float64=0.5,
-)</code></pre><p>Get the consensus <code>Haplotype</code>from <code>variants</code> applied to <code>reference</code>.</p><p><strong>Arguments</strong></p><ul><li><code>reference::NucleotideSeq</code>: Sequence of the reference genome that variants were called from</li><li><code>variants::Union{AbstractString,AbstractPath}</code>: Path to variant call file that mutations will be applied from</li></ul><p><strong>Keywords</strong></p><ul><li><code>frequency::Float64=0.5</code>: Fraction of total reads that must have supported the alternate position in order to be included as part of the consensus. In other words, only VCF records that have a <code>AF</code> (allele/alternate frequency) higher than this will be considered to contribute to the consensus.</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/ksumngs/HapLink.jl/blob/0490ccd6d190918fbd2f3bb0138576e0b3392fd2/src/consensus.jl#L45-L65">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="HapLink.consensus_record-Tuple{Union{AbstractString, FilePathsBase.AbstractPath}, Union{AbstractString, FilePathsBase.AbstractPath}}" href="#HapLink.consensus_record-Tuple{Union{AbstractString, FilePathsBase.AbstractPath}, Union{AbstractString, FilePathsBase.AbstractPath}}"><code>HapLink.consensus_record</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">consensus_record(
+)</code></pre><p>Get the consensus <code>Haplotype</code>from <code>variants</code> applied to <code>reference</code>.</p><p><strong>Arguments</strong></p><ul><li><code>reference::NucleotideSeq</code>: Sequence of the reference genome that variants were called from</li><li><code>variants::Union{AbstractString,AbstractPath}</code>: Path to variant call file that mutations will be applied from</li></ul><p><strong>Keywords</strong></p><ul><li><code>frequency::Float64=0.5</code>: Fraction of total reads that must have supported the alternate position in order to be included as part of the consensus. In other words, only VCF records that have a <code>AF</code> (allele/alternate frequency) higher than this will be considered to contribute to the consensus.</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/ksumngs/HapLink.jl/blob/c60514550d066bd695942bde25c3cee64a1e590d/src/consensus.jl#L45-L65">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="HapLink.consensus_record-Tuple{Union{AbstractString, FilePathsBase.AbstractPath}, Union{AbstractString, FilePathsBase.AbstractPath}}" href="#HapLink.consensus_record-Tuple{Union{AbstractString, FilePathsBase.AbstractPath}, Union{AbstractString, FilePathsBase.AbstractPath}}"><code>HapLink.consensus_record</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">consensus_record(
     reference::Union{AbstractString,AbstractPath},
     variants::Union{AbstractString,AbstractPath};
     frequency::Float64=0.5,
     prefix::Union{AbstractString,Nothing}=nothing,
-)</code></pre><p>Get the consensus <code>FASTA.Record</code>from <code>variants</code> applied to the first sequence in <code>reference</code>.</p><p><strong>Arguments</strong></p><ul><li><code>reference::Union{AbstractString,AbstractPath}</code>: Path to the reference genome that variants were called from. Only the first sequence will be used.</li><li><code>variants::Union{AbstractString,AbstractPath}</code>: Path to variant call file that mutations will be applied from</li></ul><p><strong>Keywords</strong></p><ul><li><code>frequency::Float64=0.5</code>: Fraction of total reads that must have supported the alternate position in order to be included as part of the consensus. In other words, only VCF records that have a <code>AF</code> (allele/alternate frequency) higher than this will be considered to contribute to the consensus.</li><li><code>prefix::Union{AbstractString,Nothing}=nothing</code>: Name to give to the output record. By default, the name of the output record will be the same as the name of the input record with <code>_CONSENSUS</code> appended. If <code>prefix</code> is supplied, then the name of the output record will be <code>$(prefix)_CONSENSUS</code>.</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/ksumngs/HapLink.jl/blob/0490ccd6d190918fbd2f3bb0138576e0b3392fd2/src/consensus.jl#L1-L27">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../variationcall/">« VariationCall</a><a class="docs-footer-nextpage" href="../psuedoread/">Pseudoread »</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="Friday 22 December 2023 01:47">Friday 22 December 2023</span>. Using Julia version 1.9.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+)</code></pre><p>Get the consensus <code>FASTA.Record</code>from <code>variants</code> applied to the first sequence in <code>reference</code>.</p><p><strong>Arguments</strong></p><ul><li><code>reference::Union{AbstractString,AbstractPath}</code>: Path to the reference genome that variants were called from. Only the first sequence will be used.</li><li><code>variants::Union{AbstractString,AbstractPath}</code>: Path to variant call file that mutations will be applied from</li></ul><p><strong>Keywords</strong></p><ul><li><code>frequency::Float64=0.5</code>: Fraction of total reads that must have supported the alternate position in order to be included as part of the consensus. In other words, only VCF records that have a <code>AF</code> (allele/alternate frequency) higher than this will be considered to contribute to the consensus.</li><li><code>prefix::Union{AbstractString,Nothing}=nothing</code>: Name to give to the output record. By default, the name of the output record will be the same as the name of the input record with <code>_CONSENSUS</code> appended. If <code>prefix</code> is supplied, then the name of the output record will be <code>$(prefix)_CONSENSUS</code>.</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/ksumngs/HapLink.jl/blob/c60514550d066bd695942bde25c3cee64a1e590d/src/consensus.jl#L1-L27">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../variationcall/">« VariationCall</a><a class="docs-footer-nextpage" href="../psuedoread/">Pseudoread »</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="Friday 22 December 2023 02:00">Friday 22 December 2023</span>. Using Julia version 1.9.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>