From my understanding, the above command should output all reads that align perfectly more than 20 times to ${MANY} and output all perfect alignments for reads that align 20 or fewer times to ${OUTFILE}. I am finding multiple instances, however, where a read will have over 20 perfect alignments reported in ${OUTFILE} and not be listed in ${MANY}.
Is this a bug or is my understanding of the flags incorrect?
From my understanding, the above command should output all reads that align perfectly more than 20 times to ${MANY} and output all perfect alignments for reads that align 20 or fewer times to ${OUTFILE}. I am finding multiple instances, however, where a read will have over 20 perfect alignments reported in ${OUTFILE} and not be listed in ${MANY}.
Is this a bug or is my understanding of the flags incorrect?
Tested with both 1.2.2 and 1.2.3