do not require number of total alignments to equal number of alignments processed in first stage
in bammarkduplicates and bammarkduplicates2 as first stage drops secondary etc. reads
bump version after fixing assertion failure in bammarkduplicates and
bammarkduplicates2 in the presence of secondary or supplementary alignments
Merge branch 'experimental' into experimental-debian
bump version after fixing assertion failure in bammarkduplicates and
bammarkduplicates2 in the presence of secondary or supplementary alignments