Fix # alignments reported for paired-end, and exiting after -u #65
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This is an attempt to fix two issues I found that manifest in some modes of Bowtie, including paired-end mode.
The first issue is that I noticed long running times even when
-uwas set to a low number. I think this is because some loops over the input reads weren't breaking as soon as the-ulimit was passed. The changes toaligner.hseem to fix this.The second is that I noticed the reported number of alignments was wrong for paired-end reads. It seemed to double count the pairs. The change to
hit.hseems to fix this.