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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/estimate/index.html
+4 -32
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@@ -12,7 +12,7 @@
<link rel="prev" href="../unitig/">
<link rel="next" href="../reindex/">
<link rel="next" href="../convert/">
@@ -704,34 +704,6 @@
<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">
@@ -847,14 +819,14 @@
<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
@@ -1158,7 +1130,7 @@
</tr>
</tbody>
</table>
<p>Any two of <code>-z</code>, <code>--evidence-bits</code>, <code>--fp</code> may be given; the third is derived using the same model as <code>index --approx</code> and <code>reindex --approx</code> (<span class="arithmatex">\(FP = 1 / 2^{b \cdot z}\)</span>). The report printed to stdout includes: query <span class="arithmatex">\(k\)</span>, effective indexed <span class="arithmatex">\(k\)</span> (<span class="arithmatex">\(k-z+1\)</span>), <span class="arithmatex">\(z\)</span>, evidence bits, per-kmer false-positive rate, and per-z-window false-positive rate.</p>
<p>Any two of <code>-z</code>, <code>--evidence-bits</code>, <code>--fp</code> may be given; the third is derived using the same model as <code>index --approx</code> and <code>convert --approx-evidence</code> (<span class="arithmatex">\(FP = 1 / 2^{b \cdot z}\)</span>). The report printed to stdout includes: query <span class="arithmatex">\(k\)</span>, effective indexed <span class="arithmatex">\(k\)</span> (<span class="arithmatex">\(k-z+1\)</span>), <span class="arithmatex">\(z\)</span>, evidence bits, per-kmer false-positive rate, and per-z-window false-positive rate.</p>