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 -- View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/commit/b2ac037bd6dc6a26e4653d283bf4da65dbe9c5cd You're receiving this email because of your account on salsa.debian.org. Manage all notifications: https://salsa.debian.org/-/profile/notifications | Help: https://salsa.debian.org/help
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