Picard 3.0.0:
The same as before but now on Java 17
The big change is that Picard is moving from Java 8 -> 17.
Java 8 is very old and no longer available by default on most systems. Java 17 is the newest long term support release. This will enable us to take advantage of improvements in the language as well as benefiting from improvements and security fixes in the newer JVMs.
Major changes
Bug fixes and minor improvements
- Improvements to CompareMetrics by @kachulis in #1839
- Fix typo in a filter name output by LiftoverVcf by @lbergelson in #1842
- Stop removing periods from the end of output names by @tlangs in #1433
- Avoid merging fingerprints when there is only one by @yfarjoun in #1826
- Remove commons.lang dependency because it is redundant with commons lang3 by @lbergelson in #1856
- Delete the now redundant ClassFinder by @lbergelson in #1857
- Remove obsolete references to Google Genomics API by @lbergelson in #1858
- Fix Duplicate Set Index for queryname sorted input to MarkDuplicates by @kachulis in #1843
- Allow empty input files for CollectAlignmentSummaryMetrics and FastqToSam by @kachulis in #1859
Documentation and infrastructure changes
- Update CrosscheckFingerprints summary by @derekca in #1721
- Updated the issue template to link to our support forum by @droazen in #1837
- Adding a gh actions test by @lbergelson in #1853
Full Changelog: 2.27.5...3.0.0