Merge branch 'ar/chore-build-docs-060' into 'master'

ArtRand · ArtRand · commit c7611e4dfdb9 · 2025-11-30T16:37:58.000Z
chore(docs): build docs

See merge request machine-learning/modkit!311
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@@ -181,7 +181,7 @@ <h1 id="constructing-bedmethyl-tables"><a class="header" href="#constructing-bed
 <p>A primary use of <code>modkit</code> is to create summary counts of modified and unmodified bases in an extended <a href="https://www.encodeproject.org/data-standards/wgbs/">bedMethyl</a> format.
 bedMethyl files tabulate the counts of base modifications from every sequencing read over each aligned reference genomic position.
 In order to create a bedMethyl table, your modBAM must be aligned to a reference genome or transcriptome.
-Although not required, providing a reference and using the <code>--modified-bases</code> option will provide the clearest results and can greatly improve performance (details below).
+Although not required, providing a reference and using the <code>--modified-bases</code> option will provide the clearest results with the best computational performance.
 Only <strong>primary alignments</strong> are used in generating the table, it is recommended to mark duplicate alignments before running as multiple primary alignments can be double counted.</p>
 <h2 id="recommended-usage"><a class="header" href="#recommended-usage">Recommended usage</a></h2>
 <blockquote class="blockquote-tag blockquote-tag-important">
@@ -205,18 +205,18 @@ <h2 id="recommended-usage"><a class="header" href="#recommended-usage">Recommend
 <p>Passing <code>--modified-bases</code> not required, but directs Modkit to use optimized routines which will lead to better efficiency.
 This option <em>does</em> require a FASTA reference, and will only emit bedmethyl records for base modifications to the primary sequence base in the reference.
 For example, a command with the option <code>--modified-bases 5mC 5hmC 6mA</code> will <em>not</em> have 6mA records on genomic Cytosine locations where a read has a C&gt;A mismatch nor 5mC/5hmC records at genomic Adenine locations.
-For more details on how this option works see <a href="./migrating_060.html">migrating to v0.6.0</a>.</p>
+For more details on how this option changes results from previous versions see <a href="./migrating_060.html">migrating to v0.6.0</a>.</p>
 <p>A subset of the base modifications present in the modBAM can specified
 For example, passing the option <code>--modified-bases 5mC</code> when the modBAM contains 5mC and 5hmC calls will only produce 5mC records.</p>
 <blockquote class="blockquote-tag blockquote-tag-note">
 <p class="blockquote-tag-title"><svg viewbox="0 0 16 16" width="18" height="18"><path d="M0 8a8 8 0 1 1 16 0A8 8 0 0 1 0 8Zm8-6.5a6.5 6.5 0 1 0 0 13 6.5 6.5 0 0 0 0-13ZM6.5 7.75A.75.75 0 0 1 7.25 7h1a.75.75 0 0 1 .75.75v2.75h.25a.75.75 0 0 1 0 1.5h-2a.75.75 0 0 1 0-1.5h.25v-2h-.25a.75.75 0 0 1-.75-.75ZM8 6a1 1 0 1 1 0-2 1 1 0 0 1 0 2Z"></path></svg>Note</p>
 <p>If the reference FASTA does not have an index at <code>path/to/reference.fasta.fai</code> one will be created.</p>
 </blockquote>
 <h3 id="syntax-of---modified-bases"><a class="header" href="#syntax-of---modified-bases">Syntax of <code>--modified-bases</code></a></h3>
-<p>You may pass the “long-name” such as “5mC” or a primary base and the “short-name”.
-For example: <code>--modified-bases 5mC 5hmC 6mA</code> and <code>--modified-bases C:m C:h A:a</code> are equivalent.
+<p>You may pass the “long name” such as “5mC” or a primary base and the “short name” separated by a <code>:</code>.
+For example, <code>--modified-bases 5mC 5hmC 6mA</code> and <code>--modified-bases C:m C:h A:a</code> are equivalent.
 ChEBI codes can also be used.
-For example, a to make a pileup for a modBAM with a direct RNA reads you may use: <code>--modified-bases A:17596 A:69426 A:a C:m C:19228 G:19229</code>.</p>
+For example, a to make a pileup for a modBAM with direct RNA reads you may use: <code>--modified-bases A:17596 A:69426 A:a C:m C:19228 G:19229</code>.</p>
 <blockquote class="blockquote-tag blockquote-tag-tip">
 <p class="blockquote-tag-title"><svg viewbox="0 0 16 16" width="18" height="18"><path d="M8 1.5c-2.363 0-4 1.69-4 3.75 0 .984.424 1.625.984 2.304l.214.253c.223.264.47.556.673.848.284.411.537.896.621 1.49a.75.75 0 0 1-1.484.211c-.04-.282-.163-.547-.37-.847a8.456 8.456 0 0 0-.542-.68c-.084-.1-.173-.205-.268-.32C3.201 7.75 2.5 6.766 2.5 5.25 2.5 2.31 4.863 0 8 0s5.5 2.31 5.5 5.25c0 1.516-.701 2.5-1.328 3.259-.095.115-.184.22-.268.319-.207.245-.383.453-.541.681-.208.3-.33.565-.37.847a.751.751 0 0 1-1.485-.212c.084-.593.337-1.078.621-1.489.203-.292.45-.584.673-.848.075-.088.147-.173.213-.253.561-.679.985-1.32.985-2.304 0-2.06-1.637-3.75-4-3.75ZM5.75 12h4.5a.75.75 0 0 1 0 1.5h-4.5a.75.75 0 0 1 0-1.5ZM6 15.25a.75.75 0 0 1 .75-.75h2.5a.75.75 0 0 1 0 1.5h-2.5a.75.75 0 0 1-.75-.75Z"></path></svg>Tip</p>
 <p>If you don’t know which modified bases are present in your modBAM run: <code>modkit modbam check-tags $bam --head 100</code>.</p>
@@ -225,7 +225,8 @@ <h3 id="running-without-a-reference"><a class="header" href="#running-without-a-
 <p>A reference and <code>--modified-bases</code> is not required, for example:</p>
 <pre><code class="language-bash">modkit pileup path/to/reads.bam output/path/pileup.bed --log-filepath pileup.log
 </code></pre>
-<p>This invocation may be slower than using <code>--modified-bases</code> with a reference.</p>
+<p>This command will produce a bedMethyl record for every position in the reference for which there is at least one base modification call (either modified or unmodified).
+This invocation may be slower than using <code>--modified-bases</code> with a reference.</p>
 <p>In both cases, a single file (described <a href="#description-of-bedmethyl-output">below</a>) with base count summaries will be created.</p>
 <p>The program performs best-practices filtering and manipulation of the raw data stored in the input file.
 For further details see <a href="./filtering.html">filtering modified-base calls</a>.</p>
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