3.3.0

What's Changed

Argument changes for FLOW based MarkDuplicates

The arguments in MarkDuplicates ) which are specific to flow based reads have been renamed. (by @dror27 #1974)
They're now prefixed with FLOW_ to make it clear when they are relevant. This requires flow read users to update their scripts.

Old	New
USE_END_IN_UNPAIRED_READ	FLOW_USE_END_IN_UNPAIRED_READS
USE_UNPAIRED_CLIPPED_END	FLOW_USE_UNPAIRED_CLIPPED_END.
UNPAIRED_START_UNCERTAINTY	FLOW_UNPAIRED_START_UNCERTAINTY
UNPAIRED_END_UNCERTAINTY	FLOW_UNPAIRED_END_UNCERTAINTY

New Feature:

RevertSam is now cloud enabled (by @takutosato in #1949)

Bug Fixes

• Update htsjdk to 4.1.3 (samtools/htsjdk@4.1.1...4.1.3) which fixes several active bugs by @lbergelson in #1979
• Fix documentation for AT_DROPOUT and GC_DROPOUT in PanelMetricsBase.java by @kockan in
  #1977

Maintenance

• Add piped input tests for RevertSam, MergeBamAlignment by @takutosato in #1974
• Fix duplicate publishing issue by @lbergelson in #1969

Full Changelog: 3.2.0...3.3.0