Eric Coissac
caf59b5658
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.
1237 lines
21 KiB
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1237 lines
21 KiB
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obikmer — User Guide
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DNA encoding
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Low-complexity kmer filter
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Partitioning and indexing architecture
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Usage
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superkmer
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index
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merge
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filter
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select
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query
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dump
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annotate
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phylo
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unitig
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estimate
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convert
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<h1 id="convert">convert</h1>
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<p>Convert an existing index's evidence representation in place, between exact, approximate, and hybrid.</p>
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<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>convert<span class="w"> </span>INDEX<span class="w"> </span><span class="o">(</span>--exact-evidence<span class="w"> </span><span class="p">|</span><span class="w"> </span>--approx-evidence<span class="w"> </span>BITS<span class="w"> </span><span class="p">|</span><span class="w"> </span>--hybrid-evidence<span class="o">)</span><span class="w"> </span><span class="o">[</span>OPTIONS<span class="o">]</span>
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</code></pre></div>
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<h2 id="arguments">Arguments</h2>
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<table>
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<thead>
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<tr>
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<th>Argument</th>
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<th>Description</th>
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</tr>
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</thead>
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<tbody>
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<td><code>INDEX</code></td>
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<td>Index directory to convert (modified in place)</td>
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</tr>
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</tbody>
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</table>
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<h2 id="options">Options</h2>
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<p>Exactly one of the first three is required:</p>
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<table>
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<thead>
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<tr>
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<th>Option</th>
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<th>Description</th>
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<tbody>
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<td><code>--exact-evidence</code></td>
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<td>Convert to exact evidence (zero false positives)</td>
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</tr>
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<tr>
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<td><code>--approx-evidence BITS</code></td>
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<td>Convert to approximate (fingerprint-only) evidence; <code>BITS</code> = fingerprint bits per slot (b)</td>
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</tr>
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<tr>
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<td><code>--hybrid-evidence</code></td>
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<td>Convert to hybrid evidence (both exact and approximate bundles kept)</td>
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</tr>
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<tr>
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<td><code>--evidence-bits BITS</code></td>
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<td>Fingerprint bits per slot (b) — required with <code>--hybrid-evidence</code> when the source index is currently exact; rejected otherwise (the source already fixes <code>b</code>)</td>
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<tr>
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<td><code>-z, --findere-z Z</code></td>
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<td>Findere z parameter: number of consecutive stored kmers that must all match to confirm a hit. This does not shorten the indexed kmer length (fixed forever at <code>index</code> build time) — it extends the effective match window: on a k=31 index, <code>z=2</code> requires 32 consecutive matching bases, not 30</td>
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<td><code>--fp FP</code></td>
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<td>Target false-positive rate per z-window (e.g. <code>0.01</code>); derives <code>b</code> or <code>z</code> when one of them isn't given directly</td>
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<tr>
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<td><code>--block-size N</code></td>
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<td>Block size for exact evidence's on-disk index (unitigs per block). Ignored when converting to pure approximate evidence. Default <code>1</code></td>
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<p>See <a href="../index_command/#exact-vs-approximate-evidence"><code>index</code></a> for the exact/approximate trade-off and the underlying false-positive model, and <a href="../estimate/"><code>estimate</code></a> to explore parameters beforehand. The index directory is locked for exclusive access during conversion.</p>
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