Releases: broadinstitute/picard
Releases · broadinstitute/picard
2.25.0
- Update htsjdk 2.23.0 -> 2.24.0 (#1641)
- Include common (engine-level) args in help output. (#1580)
- [refactor] Large refactor of IlluminaBaseCallsConverter (#1626)
- Refactor the IlluminaBasecallsConverter and IlluminaDataFactory to normalize creation when dealing with cbcls vs bcls
- Include a BasecallsConverter that doesn't do read name sorting by default
- Performance enhancements
2.24.2
2.24.1
2.24.0
- Adds support for reading CSI indexes. (#998)
- Fix default PAR values for hg37 for FindMendelianViolations (#1600)
- using guava instead of rolling my own CollectionsUtils... (#1619)
- Added a metric to CollectAlignmentSummaryMetrics for the mean length of 3' softclips (#1586)
- Add functionality to not combine abutting intervals (#1608)
2.23.9
- Fast fail if R is not installed in tools that use R (#1613)
-
- enable CollectIndependentReplicateMetrics to read a cram file (#1599)
- Remove cluster intensity data.
- Check Sequence Dictionaries Match in CollectWgsMetrics (#1610)
- Add flowcell location stratifier for CollectSamErrorMetrics (#1603)
- GtcToVcf should not fail if AS tag is missing (#1445)
- Increase fraction of target coverage for panel metrics (#1542)
2.23.8
2.23.7
2.23.6
2.23.5
2.23.4
- Adjust MBA read overhang clipping to be consistent with past behavior (#1571)
-
- add support for CRAM reading in IdentifyContaminant and ExtractFingerprint (#1572)
- Yf fix typo in histogram column name asm (#1568)
- Use new IntervalMergingIterator to merge intervals on the fly (#1456)
- Several changes to metrics collections (AlignmentSummaryMetrics and WgsMetrics) + some fluff (#1555)
- Make Fingerprint checking fail when run on a truly unsorted file (currently it returns a non-informative fingerprint) (#1556)
- Added a simple test for LiftoverHaplotypeMap (#1550)