Cloudy Edition
Highlights
Improving Google Cloud Support
We've done away with the picard-cloud.jar. The default picard jar now includes the necessary libraries to read from google cloud buckets. This is part of an ongoing push to cloud enable more of the important picard tools. It will reduce confusion and simplify code.
- cloud jar is now default jar #1900
- IntervalListTools is cloud enabled #1852
- updated google nio library which supports
_in bucket names #1903 - new test infrastructure for writing tests that use google cloud #1860
IntelGKL update
A new version
- A new version of the Intel GKL library fixes several major bugs. #1901
- A bug fix which enables the IntelInflater which was accidentally being ignored. #1885
Dependency and Gradle Updates
- Updated dependencies to their latest versions to incorporate security and bug fixes.
- Updated to gradle 8.2.1
Notes
- Downstream toolkits will have to make some changes if they want to continue to NOT provide the google cloud libraries.
- Updating to gradle 8.2.1 was necessitated by a packaging issue. One of the updated dependencies now includes java 19 code in it's multi-version jar and we needed to update to the newest version of the shadowJar plugin in order to handle it. See #1903 for more disussin.
Change List
- Remove unused method Fingerprint.filterSuspectSites() by @lbergelson in #1849
- Fix crash on PF_READS == 0 for AlignmentSummaryMetricsCollector by @kockan in #1871
- More informative error messages when dictionaries don't match by @kachulis in #1870
- Enable IntelInflater by @lbergelson in #1885
- Add .DS_STORE and .java-version to .gitignore by @lbergelson in #1886
- Fix deprecated uses of newInstance() by @lbergelson in #1887
- Add tests to verify sequence dictionary MD5s respect dos line endings. by @cmnbroad in #1884
- Mark GENOTYPING_ERROR_RATE as a DeprecatedFeature and remove code ref… by @cmnbroad in #1878
- Refactoring by @LadDeep in #1868
- Fix #1081. Make --USE_SEQUENTIAL_FASTQS help message more user friendly by @nrockweiler in #1891
- DbSnpBitSetUtil should verify that the VCF dict should match the inpu… by @nh13 in #1889
- Fix the dependency issue causing dsp-appsec-trivy workflow to fail. by @kockan in #1895
- Lb add cloud tests by @lbergelson in #1860
- make cloud jar mandatory by @lbergelson in #1900
- Support cloud input/output for IntervalListTools by @takutosato in #1852
- typo correction "Didn't recognized" -> "Didn't recognize" by @tomkinsc in #1902
- Update google-cloud-nio to support underscores in bucket names by @kshakir in #1903
- Fix gradle 8 publishing issue by @kshakir in #1904
- Update all our dependencies to the latest version by @lbergelson in #1901
New Contributors
- @kockan made their first contribution in #1871
- @LadDeep made their first contribution in #1868
- @nrockweiler made their first contribution in #1891
- @tomkinsc made their first contribution in #1902
- @kshakir made their first contribution in #1903
Full Changelog: 3.0.0...3.1.0