- Adds DUPLEX_UMI argument to UmiAwareMarkDuplicatesWithMateCigar (#1235)
- Fixed bug in MarkDuplicates where it was mismarking which reads were optical duplicates when TAGGING_POLICY is set. (#1244)
- Fixed order dependance bug in graphUtils.cluster() algorithm. (#1245)
- Protection against using the wrong sample alias which produces zero L… (#1242)
- Use provided sequence dictionary with MergeVcfs. (#1234)
- As dsdegp 2574 pf percent misreported (#1231)
- Add Scatter by IntervalCount (IntervalListTools) (#1208)
- fixing mistake in documentation of RevertSam (#1232)
- Revert "Changed the OpticalDuplicateFinding code to rely on a proper clustering algorithm"
- Changed the OpticalDuplicateFinding code to rely on a proper clustering algorithm
- Made OpticalDuplicateFinder Serializable (#1230)