[med-svn] [Git][med-team/picard-tools][upstream] New upstream version 3.3.0+dfsg

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch upstream at Debian Med / picard-tools


Commits:
0601fb2b by Pierre Gruet at 2024-12-05T12:35:41+01:00
New upstream version 3.3.0+dfsg
- - - - -


30 changed files:

- .github/workflows/cloud_tests.yml
- .gitignore
- Dockerfile
- build.gradle
- build_push_docker.sh
- gradle/wrapper/gradle-wrapper.properties
- gradlew
- src/main/java/picard/analysis/CollectQualityYieldMetrics.java
- + src/main/java/picard/analysis/CollectQualityYieldMetricsFlow.java
- + src/main/java/picard/analysis/CollectQualityYieldMetricsSNVQ.java
- src/main/java/picard/analysis/directed/PanelMetricsBase.java
- src/main/java/picard/analysis/directed/TargetMetricsCollector.java
- src/main/java/picard/cmdline/CommandLineProgram.java
- src/main/java/picard/cmdline/StandardOptionDefinitions.java
- src/main/java/picard/cmdline/argumentcollections/OptionalReferenceArgumentCollection.java
- src/main/java/picard/cmdline/argumentcollections/ReferenceArgumentCollection.java
- src/main/java/picard/cmdline/argumentcollections/RequiredReferenceArgumentCollection.java
- src/main/java/picard/fingerprint/FingerprintChecker.java
- + src/main/java/picard/flow/FlowBasedArgumentCollection.java
- + src/main/java/picard/flow/FlowBasedKeyCodec.java
- + src/main/java/picard/flow/FlowBasedRead.java
- + src/main/java/picard/flow/FlowReadGroupInfo.java
- src/main/java/picard/nio/DeleteRecursive.java
- src/main/java/picard/nio/GATKBucketUtils.java → src/main/java/picard/nio/PicardBucketUtils.java
- src/main/java/picard/nio/PicardHtsPath.java
- src/main/java/picard/nio/GATKIOUtils.java → src/main/java/picard/nio/PicardIOUtils.java
- src/main/java/picard/sam/AbstractAlignmentMerger.java
- src/main/java/picard/sam/CreateSequenceDictionary.java
- src/main/java/picard/sam/DownsampleSam.java
- src/main/java/picard/sam/MergeBamAlignment.java


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/commit/0601fb2b9891fdbcabec88cd48b338fdb88a805d

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View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/commit/0601fb2b9891fdbcabec88cd48b338fdb88a805d
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