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Improved handling of BAM tags to prevent unintended type changes.
Fixed 'rmdup_collapsed' underreporting the number of duplicate reads (in
the 'XP' tag), when duplicates with different CIGAR strings were processed.
Changed
PCR duplicates detected for collapsed reads using 'rmdup_collapsed' are
now identified based on alignments that include clipped bases. This
matches the behavior of the Picard 'MarkDuplicates' command.
Depending on work-load, 'rmdup_collapsed' may now run up to twice as fast.
