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