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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
The text was updated successfully, but these errors were encountered:
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
The text was updated successfully, but these errors were encountered: