AlignmentEndTrimmer: This application can be used to trim alignments according to the density of mismatches. Each base of the alignment is compared to the reference sequence from the start of the alignment to the end. If the bases match, the score is increased by -m. If the bases don't match, the score is decreased by -n. The alignment position with the highest score is used as the new alignment end point. The cigar string, alignment position, mpos and flags are all updated to reflect trimming.
