build based on 592195b

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.5","generation_timestamp":"2024-10-17T19:13:15","documenter_version":"1.7.0"}}
+{"documenter":{"julia_version":"1.11.0","generation_timestamp":"2024-10-22T16:45:23","documenter_version":"1.7.0"}}

dev/fasta/index.html

@@ -14,7 +14,7 @@
 "TAqACC"
 
 julia> typeof(description(rec)) == typeof(sequence(rec)) <: AbstractString
-true</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/FASTX.jl/blob/93d74781f9dd8061dbc6a2cbda81a09467960e87/src/fasta/record.jl#L4-L31">source</a></section></article><h2 id="FASTAReader-and-FASTAWriter"><a class="docs-heading-anchor" href="#FASTAReader-and-FASTAWriter"><code>FASTAReader</code> and <code>FASTAWriter</code></a><a id="FASTAReader-and-FASTAWriter-1"></a><a class="docs-heading-anchor-permalink" href="#FASTAReader-and-FASTAWriter" title="Permalink"></a></h2><p><code>FASTAWriter</code> can optionally be passed the keyword <code>width</code> to control the line width. If this is zero or negative, it will write all record sequences on a single line. Else, it will wrap lines to the given maximal width.</p><h3 id="Reference:"><a class="docs-heading-anchor" href="#Reference:">Reference:</a><a id="Reference:-1"></a><a class="docs-heading-anchor-permalink" href="#Reference:" title="Permalink"></a></h3><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="FASTX.FASTA" href="#FASTX.FASTA"><code>FASTX.FASTA</code></a> — <span class="docstring-category">Module</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">FASTA</code></pre><p>Module under FASTX with code related to FASTA files.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/FASTX.jl/blob/93d74781f9dd8061dbc6a2cbda81a09467960e87/src/fasta/fasta.jl#L4-L8">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="FASTX.FASTA.Reader" href="#FASTX.FASTA.Reader"><code>FASTX.FASTA.Reader</code></a> — <span class="docstring-category">Type</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">FASTA.Reader(input::IO; index=nothing, copy::Bool=true)</code></pre><p>Create a buffered data reader of the FASTA file format. The reader is a <code>BioGenerics.IO.AbstractReader</code>, a stateful iterator of <code>FASTA.Record</code>. Readers take ownership of the underlying IO. Mutating or closing the underlying IO not using the reader is undefined behaviour. Closing the Reader also closes the underlying IO.</p><p>See more examples in the FASTX documentation.</p><p>See also: <a href="#FASTX.FASTA.Record"><code>FASTA.Record</code></a>, <a href="#FASTX.FASTA.Writer"><code>FASTA.Writer</code></a></p><p><strong>Arguments</strong></p><ul><li><code>input</code>: data source</li><li><code>index</code>: Optional random access index (currently <em>fai</em> is supported). <code>index</code> can be <code>nothing</code>, a <code>FASTA.Index</code>, or an <code>IO</code> in which case an index will be parsed from the IO, or <code>AbstractString</code>, in which case it will be treated as a path to a fai file.</li><li><code>copy::Bool</code>: iterating returns fresh copies instead of the same Record. Set to <code>false</code> for improved performance, but be wary that iterating mutates records.</li></ul><p><strong>Examples</strong></p><pre><code class="language-julia-repl hljs">julia&gt; rdr = FASTAReader(IOBuffer(&quot;&gt;header\nTAG\n&gt;another\nAGA&quot;));
+true</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/FASTX.jl/blob/592195bd275777d32c897aa5b22a492d2aad6d59/src/fasta/record.jl#L4-L31">source</a></section></article><h2 id="FASTAReader-and-FASTAWriter"><a class="docs-heading-anchor" href="#FASTAReader-and-FASTAWriter"><code>FASTAReader</code> and <code>FASTAWriter</code></a><a id="FASTAReader-and-FASTAWriter-1"></a><a class="docs-heading-anchor-permalink" href="#FASTAReader-and-FASTAWriter" title="Permalink"></a></h2><p><code>FASTAWriter</code> can optionally be passed the keyword <code>width</code> to control the line width. If this is zero or negative, it will write all record sequences on a single line. Else, it will wrap lines to the given maximal width.</p><h3 id="Reference:"><a class="docs-heading-anchor" href="#Reference:">Reference:</a><a id="Reference:-1"></a><a class="docs-heading-anchor-permalink" href="#Reference:" title="Permalink"></a></h3><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="FASTX.FASTA" href="#FASTX.FASTA"><code>FASTX.FASTA</code></a> — <span class="docstring-category">Module</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">FASTA</code></pre><p>Module under FASTX with code related to FASTA files.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/FASTX.jl/blob/592195bd275777d32c897aa5b22a492d2aad6d59/src/fasta/fasta.jl#L4-L8">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="FASTX.FASTA.Reader" href="#FASTX.FASTA.Reader"><code>FASTX.FASTA.Reader</code></a> — <span class="docstring-category">Type</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">FASTA.Reader(input::IO; index=nothing, copy::Bool=true)</code></pre><p>Create a buffered data reader of the FASTA file format. The reader is a <code>BioGenerics.IO.AbstractReader</code>, a stateful iterator of <code>FASTA.Record</code>. Readers take ownership of the underlying IO. Mutating or closing the underlying IO not using the reader is undefined behaviour. Closing the Reader also closes the underlying IO.</p><p>See more examples in the FASTX documentation.</p><p>See also: <a href="#FASTX.FASTA.Record"><code>FASTA.Record</code></a>, <a href="#FASTX.FASTA.Writer"><code>FASTA.Writer</code></a></p><p><strong>Arguments</strong></p><ul><li><code>input</code>: data source</li><li><code>index</code>: Optional random access index (currently <em>fai</em> is supported). <code>index</code> can be <code>nothing</code>, a <code>FASTA.Index</code>, or an <code>IO</code> in which case an index will be parsed from the IO, or <code>AbstractString</code>, in which case it will be treated as a path to a fai file.</li><li><code>copy::Bool</code>: iterating returns fresh copies instead of the same Record. Set to <code>false</code> for improved performance, but be wary that iterating mutates records.</li></ul><p><strong>Examples</strong></p><pre><code class="language-julia-repl hljs">julia&gt; rdr = FASTAReader(IOBuffer(&quot;&gt;header\nTAG\n&gt;another\nAGA&quot;));
 
 julia&gt; records = collect(rdr); close(rdr);
 
@@ -24,10 +24,10 @@
 
 julia&gt; foreach(println, map(sequence, records))
 TAG
-AGA</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/FASTX.jl/blob/93d74781f9dd8061dbc6a2cbda81a09467960e87/src/fasta/reader.jl#L4-L40">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="FASTX.FASTA.Writer" href="#FASTX.FASTA.Writer"><code>FASTX.FASTA.Writer</code></a> — <span class="docstring-category">Type</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">FASTA.Writer(output::IO; width=70)</code></pre><p>Create a data writer of the FASTA file format. The writer is a <code>BioGenerics.IO.AbstractWriter</code>. Writers take ownership of the underlying IO. Mutating or closing the underlying IO not using the writer is undefined behaviour. Closing the writer also closes the underlying IO.</p><p>See more examples in the FASTX documentation.</p><p>See also: <a href="#FASTX.FASTA.Record"><code>FASTA.Record</code></a>, <a href="#FASTX.FASTA.Reader"><code>FASTA.Reader</code></a></p><p><strong>Arguments</strong></p><ul><li><code>output</code>: Data sink to write to</li><li><code>width</code>: Wrapping width of sequence characters. If &lt; 1, no wrapping.</li></ul><p><strong>Examples</strong></p><pre><code class="nohighlight hljs">julia&gt; FASTA.Writer(open(&quot;some_file.fna&quot;, &quot;w&quot;)) do writer
+AGA</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/FASTX.jl/blob/592195bd275777d32c897aa5b22a492d2aad6d59/src/fasta/reader.jl#L4-L40">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="FASTX.FASTA.Writer" href="#FASTX.FASTA.Writer"><code>FASTX.FASTA.Writer</code></a> — <span class="docstring-category">Type</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">FASTA.Writer(output::IO; width=70)</code></pre><p>Create a data writer of the FASTA file format. The writer is a <code>BioGenerics.IO.AbstractWriter</code>. Writers take ownership of the underlying IO. Mutating or closing the underlying IO not using the writer is undefined behaviour. Closing the writer also closes the underlying IO.</p><p>See more examples in the FASTX documentation.</p><p>See also: <a href="#FASTX.FASTA.Record"><code>FASTA.Record</code></a>, <a href="#FASTX.FASTA.Reader"><code>FASTA.Reader</code></a></p><p><strong>Arguments</strong></p><ul><li><code>output</code>: Data sink to write to</li><li><code>width</code>: Wrapping width of sequence characters. If &lt; 1, no wrapping.</li></ul><p><strong>Examples</strong></p><pre><code class="nohighlight hljs">julia&gt; FASTA.Writer(open(&quot;some_file.fna&quot;, &quot;w&quot;)) do writer
     write(writer, record) # a FASTA.Record
-end</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/FASTX.jl/blob/93d74781f9dd8061dbc6a2cbda81a09467960e87/src/fasta/writer.jl#L4-L27">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="FASTX.FASTA.validate_fasta" href="#FASTX.FASTA.validate_fasta"><code>FASTX.FASTA.validate_fasta</code></a> — <span class="docstring-category">Function</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">validate_fasta(io::IO) &gt;: Nothing</code></pre><p>Check if <code>io</code> is a valid FASTA file. Return <code>nothing</code> if it is, and an instance of another type if not.</p><p><strong>Examples</strong></p><pre><code class="language-julia-repl hljs">julia&gt; validate_fasta(IOBuffer(&quot;&gt;a bc\nTAG\nTA&quot;)) === nothing
+end</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/FASTX.jl/blob/592195bd275777d32c897aa5b22a492d2aad6d59/src/fasta/writer.jl#L4-L27">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="FASTX.FASTA.validate_fasta" href="#FASTX.FASTA.validate_fasta"><code>FASTX.FASTA.validate_fasta</code></a> — <span class="docstring-category">Function</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">validate_fasta(io::IO) &gt;: Nothing</code></pre><p>Check if <code>io</code> is a valid FASTA file. Return <code>nothing</code> if it is, and an instance of another type if not.</p><p><strong>Examples</strong></p><pre><code class="language-julia-repl hljs">julia&gt; validate_fasta(IOBuffer(&quot;&gt;a bc\nTAG\nTA&quot;)) === nothing
 true
 
 julia&gt; validate_fasta(IOBuffer(&quot;&gt;a bc\nT&gt;G\nTA&quot;)) === nothing
-false</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/FASTX.jl/blob/93d74781f9dd8061dbc6a2cbda81a09467960e87/src/fasta/readrecord.jl#L122-L136">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../files/">« File I/O</a><a class="docs-footer-nextpage" href="../fastq/">FASTQ »</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><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.7.0 on <span class="colophon-date" title="Thursday 17 October 2024 19:13">Thursday 17 October 2024</span>. Using Julia version 1.10.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+false</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/FASTX.jl/blob/592195bd275777d32c897aa5b22a492d2aad6d59/src/fasta/readrecord.jl#L122-L136">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../files/">« File I/O</a><a class="docs-footer-nextpage" href="../fastq/">FASTQ »</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><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.7.0 on <span class="colophon-date" title="Tuesday 22 October 2024 16:45">Tuesday 22 October 2024</span>. Using Julia version 1.11.0.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>