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<h1 id="select">select</h1>
<p>Project and/or aggregate the genome columns of an index into a new (or in-place) index. Where <a href="../filter/"><code>filter</code></a> selects rows (kmers), <code>select</code> operates on columns (genomes): grouping several genomes into one aggregated column, reordering columns, or dropping some.</p>
<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span><span class="k">select</span><span class="w"> </span>SOURCE<span class="w"> </span><span class="o">(</span>--output<span class="w"> </span>OUTPUT<span class="w"> </span><span class="p">|</span><span class="w"> </span>--in-place<span class="o">)</span><span class="w"> </span><span class="o">[</span>OPTIONS<span class="o">]</span>
</code></pre></div>
<h2 id="arguments">Arguments</h2>
<table>
<thead>
<tr>
<th>Argument</th>
<th>Description</th>
</tr>
</thead>
<tbody>
<tr>
<td><code>SOURCE</code></td>
<td>Source index directory</td>
</tr>
</tbody>
</table>
<h2 id="options">Options</h2>
<table>
<thead>
<tr>
<th>Option</th>
<th>Default</th>
<th>Description</th>
</tr>
</thead>
<tbody>
<tr>
<td><code>--output</code></td>
<td>—</td>
<td>Output index directory (mutually exclusive with <code>--in-place</code>)</td>
</tr>
<tr>
<td><code>--in-place</code></td>
<td>off</td>
<td>Rewrite the source index in place (mutually exclusive with <code>--output</code>)</td>
</tr>
<tr>
<td><code>-f, --force</code></td>
<td>off</td>
<td>Overwrite an existing output directory</td>
</tr>
<tr>
<td><code>--group NAME:PRED</code></td>
<td>none</td>
<td>Define a named group of genomes by predicate (repeatable; mutually exclusive with <code>--aggregate-by</code>)</td>
</tr>
<tr>
<td><code>--group-op NAME:OP</code></td>
<td>none</td>
<td>Aggregation operator for a named group</td>
</tr>
<tr>
<td><code>--aggregate-by KEY</code></td>
<td>none</td>
<td>Automatically create one group per distinct value of a metadata key (mutually exclusive with <code>--group</code>)</td>
</tr>
<tr>
<td><code>--aggregate-op OP</code></td>
<td>none</td>
<td>Aggregation operator applied to every auto-generated group</td>
</tr>
<tr>
<td><code>--select COL,...</code></td>
<td>all columns</td>
<td>Output columns, in order (group names or genome labels)</td>
</tr>
<tr>
<td><code>--presence-threshold</code></td>
<td><code>0</code></td>
<td>Minimum count for a genome to be considered a carrier (logical operators only)</td>
</tr>
</tbody>
</table>
<h2 id="aggregation-operators">Aggregation operators</h2>
<p><code>any</code>, <code>all</code>, <code>none</code> (logical, evaluated against <code>--presence-threshold</code>), <code>sum</code>, <code>min</code>, <code>max</code> (numeric, count index only). If a group's operator is left unspecified, it defaults to <code>any</code> when the source is a presence/absence index and <code>sum</code> when it stores counts.</p>
<p>A <code>select</code> never changes the underlying kmer set — only the per-genome data (counts or presence) is rewritten, so an unaggregated pass-through column (a plain genome label in <code>--select</code>) is a cheap copy.</p>
<p>At least one of <code>--output</code>/<code>--in-place</code> is required, and at least one output column must be defined; every name listed in <code>--select</code> must resolve to either a defined group or an existing genome label. See <a href="../predicates/">Genome predicates and taxonomy paths</a> for the predicate syntax used by <code>--group</code>.</p>
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