rong> [<em>string</em>]
</dt>
<dd>
<p>
Index file (generated by the gt encseq tool) for reference genome. (default: undefined)
</p>
</dd>
<dt class="hdlist1">
<strong>-bam</strong> [<em>string</em>]
</dt>
<dd>
<p>
File containing alignment of reads to genome (sorted ".bam" file). (default: undefined)
</p>
</dd>
<dt class="hdlist1">
<strong>-name</strong> [<em>string</em>]
</dt>
<dd>
<p>
specify base name for RCR to be generated. If not set, base name will be set to base name of value giv