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<h1 id="annotate">annotate</h1>
<p>Add or update genome metadata of an index from a CSV file, or dump the current metadata as CSV.</p>
<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>annotate<span class="w"> </span>INDEX<span class="w"> </span>--csv<span class="w"> </span>FILE<span class="w"> </span><span class="o">[</span>OPTIONS<span class="o">]</span>
obikmer<span class="w"> </span>annotate<span class="w"> </span>INDEX<span class="w"> </span>--dump
</code></pre></div>
<h2 id="arguments">Arguments</h2>
<table>
<thead>
<tr>
<th>Argument</th>
<th>Description</th>
</tr>
</thead>
<tbody>
<tr>
<td><code>INDEX</code></td>
<td>Index directory to annotate (modified in place)</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>--csv</code></td>
<td>—</td>
<td>CSV file of metadata to apply (must contain an id column); required unless <code>--dump</code> is used</td>
</tr>
<tr>
<td><code>--sep</code></td>
<td><code>,</code></td>
<td>CSV field separator</td>
</tr>
<tr>
<td><code>--id-col</code></td>
<td><code>id</code></td>
<td>Name of the column containing genome labels</td>
</tr>
<tr>
<td><code>--na-value</code></td>
<td><code>NA</code></td>
<td>Value meaning "remove this field" (deletes the existing key if present)</td>
</tr>
<tr>
<td><code>--no-overwrite</code></td>
<td>off</td>
<td>Do not overwrite existing metadata keys</td>
</tr>
<tr>
<td><code>--dump</code></td>
<td>off</td>
<td>Print all genome metadata as CSV to stdout instead of applying a file</td>
</tr>
</tbody>
</table>


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