-genome">ref.genome<a class="anchor" aria-label="anchor" href="#arg-ref-genome"></a></dt>
<dd><p>A <code>ref.genome</code> argument as described in
<code><a href="ICAMS.html">ICAMS</a></code>.</p></dd>


<dt id="arg-num-of-cores">num.of.cores<a class="anchor" aria-label="anchor" href="#arg-num-of-cores"></a></dt>
<dd><p>The number of cores to use. Not available on Windows
unless <code>num.of.cores = 1</code>.</p></dd>


<dt id="arg-trans-ranges">trans.ranges<a class="anchor" aria-label="anchor" href="#arg-t