vadimzalunin/crammer — Issue #16: Non-empty CIGAR for unmapped reads
Author: vadimzalunin
Created: 2012-03-06 11:00:06+00:00
State: open

2. cramtools usually correctly removes any alignment info (mapq, md:z:, nm:i: etc) for reads that don't align (flag &4), however I see a small number of reads where cramtools sets the cigar string to 76M. My data set is paired 76+76