an class="keywordflow">if</span>(score_cmp(score_cutoff, align-&gt;score)){
<a name="l00373"></a>00373 <span class="comment">//      std::cout &lt;&lt; "failed score cut off of " &lt;&lt; score_cutoff </span>
<a name="l00374"></a>00374 <span class="comment">//                &lt;&lt; " with a score of " &lt;&lt; align-&gt;score &lt;&lt; "\n";</span>
<a name="l00375"></a>00375       <span class="comment">// We may need to clean up the memory for the frag file</span>
<a name="l00376"></a>00376       <span cla