- update to htsjdk 2.18.2 (#1267)
- changing ADD_PG_TAG_TO_READ to boolean (#1262)
- Liftover all indels in flipped strand (#1266)
- fixing a subtle bug with keeperOrNull
- Histogram of duplicate set sizes to be reported in the MarkDuplicates metrics file (#569)
- Tool to add
OAsam tag to reads (#1202) - optimization A
- Changed the OpticalDuplicateFinder to no longer be order dependant in its output.