Picard 3.5.0 upgrades to HTSJDK 5.0.0 (full CRAM 3.1 write support + faster BAM/CRAM I/O).
Upgrade notes (HTSJDK 5.0.0 behavior changes)
- CRAM output now defaults to CRAM 3.1 (was 3.0); CRAM-3.0-only readers can't read it unless you pin the version.
- SRA (.sra) input support was removed upstream — convert with NCBI tooling first.
- Requires Java 17 (unchanged).
What's Changed
- Added some extra handling for when R is not available, specifically when running in a GATK docker that does not have it by @KevinCLydon in #2010
- AlignmentSummaryMetrics - Improve and harmonize PCT_CHIMERAS description by @pontushojer in #2012
- Fix a critical bug in flow base duplicate marking by @ilyasoifer in #2006
- DDO-4138 read from gar by @ungwudik in #2016
- Update htsjdk to 4.3.0 by @lbergelson in #2017
- A few fixes to crosscheckfingerprints by @kachulis in #2018
- Yf make revert sam robust to errant XQ and XB tags by @yfarjoun in #2021
- Properly plumbs the CREATE_INDEX logic in FilterVcf. by @yfarjoun in #2025
- protect collect rnaseqmetrics from pair orientation assert by @yfarjoun in #2027
- Prevent MBA from re-sorting input on error if the input is a pipe by @yfarjoun in #2024
- Address CVE by @bbimber in #2022
- switches from short to int for physical locations (avoiding overflow and inaccurate markdups) by @bwlang in #2034
- Fix tests broken under i) upcoming htsjdk 5, and ii) on non-x86 architectures. by @tfenne in #2043
- Update HTSJDK to 5.0.0; fix javadoc to use utf-8 by @jonn-smith in #2055
New Contributors
- @KevinCLydon made their first contribution in #2010
- @pontushojer made their first contribution in #2012
- @ungwudik made their first contribution in #2016
Full Changelog: 3.4.0...3.5.0