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Update documentation for CLI command renames and new commands

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Renames the reindex command to convert across all usage guides and navigation menus. Adds documentation for the newly introduced name-tree command. Updates flag references, such as replacing --metric with --distance in pack and phylo modules, and adjusts MkDocs configuration to match the revised structure. All changes are strictly limited to documentation and configuration files.
This commit is contained in:
Eric Coissac
2026-08-28 23:06:05 +02:00
parent 95fa0c93b2
commit caf59b5658
38 changed files with 666 additions and 2433 deletions
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doc/usage/index_command/index.html
+3 -31
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@@ -784,34 +784,6 @@
<li class="md-nav__item">
<a href="../name-tree/" class="md-nav__link">
<span class="md-ellipsis">
name-tree
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../unitig/" class="md-nav__link">
@@ -869,14 +841,14 @@
<li class="md-nav__item">
<a href="../reindex/" class="md-nav__link">
<a href="../convert/" class="md-nav__link">
<span class="md-ellipsis">
reindex
convert
@@ -1301,7 +1273,7 @@
<p>By default, an index stores <strong>exact</strong> evidence: a kmer is either present or absent (or has an exact count with <code>--with-counts</code>), with no false positives.</p>
<p>With <code>--approx</code>, evidence is stored as a compact <strong>fingerprint</strong> instead, trading a small, tunable false-positive rate for reduced memory/disk usage. The false-positive model is:</p>
<div class="arithmatex">\[FP = \frac{1}{2^{b \cdot z}}\]</div>
<p>where <span class="arithmatex">\(b\)</span> is <code>--evidence-bits</code> and <span class="arithmatex">\(z\)</span> is <code>--findere-z</code>. Any two of <code>-z</code>, <code>--evidence-bits</code>, <code>--fp</code> can be given and the third is derived; if none are given, defaults are <span class="arithmatex">\(b=8\)</span>, <span class="arithmatex">\(z=1\)</span> (<span class="arithmatex">\(FP \approx 1/256\)</span>). See <a href="../estimate/"><code>estimate</code></a> to explore this trade-off before building an index, and <a href="../reindex/"><code>reindex</code></a> to convert an existing index between the two representations.</p>
<p>where <span class="arithmatex">\(b\)</span> is <code>--evidence-bits</code> and <span class="arithmatex">\(z\)</span> is <code>--findere-z</code>. Any two of <code>-z</code>, <code>--evidence-bits</code>, <code>--fp</code> can be given and the third is derived; if none are given, defaults are <span class="arithmatex">\(b=8\)</span>, <span class="arithmatex">\(z=1\)</span> (<span class="arithmatex">\(FP \approx 1/256\)</span>). See <a href="../estimate/"><code>estimate</code></a> to explore this trade-off before building an index, and <a href="../convert/"><code>convert</code></a> to change an existing index's representation afterwards.</p>
<p><code>z</code> must be strictly less than k: the effective indexed kmer length under approximate evidence is k−z+1.</p>