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.
1258 lines
20 KiB
HTML
1258 lines
20 KiB
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obikmer — User Guide
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merge
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Theory
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Kmers and super-kmers
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DNA encoding
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Low-complexity kmer filter
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Minimizer selection
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Partitioning and indexing architecture
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Usage
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<span class="md-nav__icon md-icon"></span>
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Usage
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<ul class="md-nav__list" data-md-scrollfix>
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superkmer
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index
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merge
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merge
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</a>
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<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
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Table of contents
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<ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
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Arguments
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Options
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Behaviour
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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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<h1 id="merge">merge</h1>
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<p>Merge multiple built indexes into a single index.</p>
|
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<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>merge<span class="w"> </span>-o<span class="w"> </span>OUTPUT<span class="w"> </span>SOURCE...<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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<tr>
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<td><code>SOURCE...</code></td>
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<td>Index directories to merge (at least one required)</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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<table>
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<thead>
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<tr>
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<th>Option</th>
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<th>Default</th>
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<th>Description</th>
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</thead>
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<tbody>
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<tr>
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<td><code>-o, --output</code></td>
|
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<td>— (required)</td>
|
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<td>Output index directory</td>
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</tr>
|
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<tr>
|
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<td><code>--force</code></td>
|
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<td>off</td>
|
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<td>Overwrite an existing output directory</td>
|
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</tr>
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<tr>
|
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<td><code>--force-presence</code></td>
|
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<td>off</td>
|
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<td>Store the merged index as presence/absence even if all sources have counts</td>
|
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</tr>
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<tr>
|
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<td><code>--rename-duplicates</code></td>
|
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<td>off</td>
|
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<td>Disambiguate duplicate genome labels (<code>.1</code>, <code>.2</code>, …) instead of failing</td>
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</tr>
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<tr>
|
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<td><code>--budget-fraction</code></td>
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<td><code>0.5</code></td>
|
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<td>Fraction of available RAM reserved as the memory budget for parallel partition merging</td>
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</tr>
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</tbody>
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</table>
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<h2 id="behaviour">Behaviour</h2>
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<p>The output mode is chosen automatically: if every source index stores counts, the merged index stores counts too; otherwise it is presence/absence. <code>--force-presence</code> forces presence/absence regardless of the sources.</p>
|
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<p>By default, merging two indexes that share a genome label fails with an error; <code>--rename-duplicates</code> instead appends a numeric suffix to keep both copies.</p>
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