query: bammarkduplicates2 - are QCfail included

[keiranmraine]

If a read-pair has one end marked as qc-fail (512 / 0x200) how would bammarkduplicates2 interpret this if another pair has the same r1/r2 mapping data but doesn't have 0x200 set?

[gt1]

bammarkduplicates2 excludes QCfail entries from processing, so if one end is marked and the other is not that will effectively turn the pair into a single end read. If there is a pair mapping to the same coordinates, then a single end at the same position should be marked as a duplicate.

[keiranmraine]

thanks