Keep anchor alignments in the complete bam
keep problematic pairs in complete bam
3% of alignments are missing for the complete bam
Keep all alignments in the complete bam
Adjust flags for complete bam
default -B --aligned-base-rate: 0.2
Having severe clipped mates as candidates
Add option, -b
Change -b to -P; the working version for poorly aligned mates
handling clipped mates is done