I would like to know what formulas are being used in the most common genome aligners to determine the MAPQ of reads that fall inside repeats in their entirety? By falling inside repeats in their entirety, I mean that the whole read length is inside the repeat. Also that both read pairs of a PE fall inside the repeat. My definition of repeats here, just as a simplification, is "stretches of DNA sequences in a genome that are identically found in multiple locations".
Is there a consensus on which scoring formula to use for reads falling on repetitive regions of the genome?
EDITED: As an example, does
bowtie score the same as
bwa aln score the same as
Highlighted below is the relevant code snippet for
bwamem_pair.c that makes things different between
bwa aln and