[med-svn] [Git][med-team/picard-tools][upstream] New upstream version 3.5.0+dfsg

[Pierre Gruet (@pgt)]

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


Commits:
b2ac037b by Pierre Gruet at 2026-08-03T21:02:42+02:00
New upstream version 3.5.0+dfsg
- - - - -


56 changed files:

- build.gradle
- src/main/java/picard/analysis/AlignmentSummaryMetrics.java
- src/main/java/picard/analysis/CollectAlignmentSummaryMetrics.java
- src/main/java/picard/analysis/CollectBaseDistributionByCycle.java
- src/main/java/picard/analysis/CollectGcBiasMetrics.java
- src/main/java/picard/analysis/CollectInsertSizeMetrics.java
- src/main/java/picard/analysis/CollectMultipleMetrics.java
- src/main/java/picard/analysis/CollectRnaSeqMetrics.java
- src/main/java/picard/analysis/CollectRrbsMetrics.java
- src/main/java/picard/analysis/CollectWgsMetricsWithNonZeroCoverage.java
- src/main/java/picard/analysis/MeanQualityByCycle.java
- src/main/java/picard/analysis/QualityScoreDistribution.java
- src/main/java/picard/analysis/directed/InsertSizeMetricsCollector.java
- src/main/java/picard/analysis/directed/RnaSeqMetricsCollector.java
- src/main/java/picard/cmdline/CommandLineProgram.java
- src/main/java/picard/fingerprint/CrosscheckFingerprints.java
- src/main/java/picard/fingerprint/FingerprintChecker.java
- src/main/java/picard/sam/AbstractAlignmentMerger.java
- src/main/java/picard/sam/RevertSam.java
- src/main/java/picard/sam/SamAlignmentMerger.java
- src/main/java/picard/sam/ViewSam.java
- src/main/java/picard/sam/markduplicates/EstimateLibraryComplexity.java
- src/main/java/picard/sam/markduplicates/MarkDuplicates.java
- src/main/java/picard/sam/markduplicates/MarkDuplicatesForFlowHelper.java
- src/main/java/picard/sam/markduplicates/util/PhysicalLocationForMateCigar.java
- src/main/java/picard/sam/markduplicates/util/ReadEnds.java
- src/main/java/picard/sam/markduplicates/util/ReadEndsForMarkDuplicates.java
- src/main/java/picard/sam/markduplicates/util/ReadEndsForMarkDuplicatesCodec.java
- src/main/java/picard/util/RExecutor.java
- src/main/java/picard/vcf/filter/FilterVcf.java
- src/test/java/picard/IntelInflaterDeflaterLoadTest.java
- src/test/java/picard/analysis/CollectAlignmentSummaryMetricsTest.java
- + src/test/java/picard/analysis/CollectBaseDistributionByCycleTest.java
- src/test/java/picard/analysis/CollectGcBiasMetricsTest.java
- src/test/java/picard/analysis/CollectInsertSizeMetricsTest.java
- src/test/java/picard/analysis/CollectMultipleMetricsTest.java
- src/test/java/picard/analysis/CollectRnaSeqMetricsTest.java
- + src/test/java/picard/analysis/CollectRrbsMetricsTest.java
- src/test/java/picard/analysis/CollectWgsMetricsWithNonZeroCoverageTest.java
- + src/test/java/picard/analysis/MeanQualityByCycleTest.java
- + src/test/java/picard/analysis/QualityScoreDistributionTest.java
- src/test/java/picard/fingerprint/CrosscheckFingerprintsTest.java
- src/test/java/picard/fingerprint/FingerprintCheckerTest.java
- src/test/java/picard/sam/RevertSamTest.java
- src/test/java/picard/sam/markduplicates/MarkDuplicatesTest.java
- src/test/java/picard/sam/util/ReadNameParserTests.java
- src/test/java/picard/vcf/filter/TestFilterVcf.java
- + testdata/picard/fingerprint/NA12891.multiple_per_site.vcf
- + testdata/picard/fingerprint/NA12891.multiple_per_site.vcf.idx
- + testdata/picard/sam/BaseDistributionByCycle/input.sam
- + testdata/picard/sam/CollectRrbsMetrics/input.sam
- + testdata/picard/sam/InsertSizeMetrics/test_chimeras.sam
- + testdata/picard/sam/MeanQualityByCycle/input.sam
- + testdata/picard/sam/QualityScoreDistribution/input.sam
- + testdata/picard/sam/RevertSam/revert_sam_corrupt_XQ_tag.sam
- + testdata/picard/sam/RnaSeqMetrics/test_chimeras.sam


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/commit/b2ac037bd6dc6a26e4653d283bf4da65dbe9c5cd

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View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/commit/b2ac037bd6dc6a26e4653d283bf4da65dbe9c5cd
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