Cope with unequal paired-end read lengths
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lweasel commented
hits_checker.py assumes that both reads of every pair are the same length. However this is not necessarily the case - eg. data where all first reads are 76bp and all second reads are 75b. Depending on which strand the pair maps, this may mean that the pair is considered to be of different lengths for different species, and the code for determining whether minmatch or mismatch thresholds has been violated can go haywire.