bam_mplp_init_overlaps() - if called, mpileup will detect overlapping
read pairs and for each base pair set the base quality of the
lower-quality base to zero, thus effectively discarding it from
calling. If the two bases are identical, the quality of the other base
is increased to the sum of their qualities (capped at 200), otherwise
it is multiplied by 0.8.
bam_mplp_init_overlaps() - if called, mpileup will detect overlapping read pairs and for each base pair set the base quality of the lower-quality base to zero, thus effectively discarding it from calling. If the two bases are identical, the quality of the other base is increased to the sum of their qualities (capped at 200), otherwise it is multiplied by 0.8.