Allowing unmapped reads in counts, bsrate, format and uniq #261
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…or incorrect chrom sorting and skipping any unmapped reads which are identified by get_tid returning -1
… mapped as indicated by a -1 for tid obtained by get_tid
…to check read names for a suffix to ignore, if the tid is found to be negative ignore the read as it is unmapped
…m the get_tid function
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This is done by simply skipping the reads for which tid is -1 and completely ignoring them