Hi, I have a question please. For soft-clipped or hard-clipped reads, for example a read with a cigar string 100M50S, does the mapping quality score of the read reflect: 1. Mapping quality of both the 100 bases, as well as the 50 clipped bases? 2. Mapping quality of the 100 bases only?
If it is the combined quality of both the 100 bases + 50 bases, how do I extract the mapping quality of only the 100 matched bases in pysam? Thanks!