Pierre Gruet pushed to branch master at Debian Med / picard-tools
Commits: 194de664 by Pierre Gruet at 2025-12-23T15:23:02+01:00 Rewriting d/watch with version 5 - - - - - 9e6fceda by Pierre Gruet at 2025-12-23T15:28:49+01:00 New upstream version 3.4.0+dfsg - - - - - e427f3fe by Pierre Gruet at 2025-12-23T15:30:02+01:00 Update upstream source from tag 'upstream/3.4.0+dfsg' Update to upstream version '3.4.0+dfsg' with Debian dir 0afb5b060a6d0157bcdecf727807e1dbbe0414f0 - - - - - bad60450 by Pierre Gruet at 2025-12-23T15:31:44+01:00 Refreshing patches - - - - - 9c95d9ba by Pierre Gruet at 2025-12-23T15:32:17+01:00 Removing Priority: optional, which is now default - - - - - 443bdbff by Pierre Gruet at 2025-12-23T15:32:47+01:00 Removing R-R-R: no, which is now default - - - - - 66bf32fb by Pierre Gruet at 2025-12-23T15:32:59+01:00 Raising Standards version to 4.7.3 - - - - - a3e2bc80 by Pierre Gruet at 2025-12-23T15:34:02+01:00 Removing unneeded versioned B-D on htsjdk - - - - - 7c75efb5 by Pierre Gruet at 2025-12-23T15:34:35+01:00 Updating changelog - - - - - 2e9a049e by Pierre Gruet at 2025-12-23T23:31:24+01:00 Refreshing patches - - - - - a5535f21 by Pierre Gruet at 2025-12-25T22:46:04+01:00 Relying on javahelper to populate control files - - - - - d0278540 by Pierre Gruet at 2025-12-25T22:46:18+01:00 Fixing more int/double comparisons in tests - - - - - 8232eb9a by Pierre Gruet at 2025-12-25T22:46:33+01:00 Fixing more inaccurate data providers for the tests - - - - - 357b2a76 by Pierre Gruet at 2025-12-25T22:46:52+01:00 Updating changelog - - - - - ec27bed7 by Pierre Gruet at 2025-12-25T22:47:06+01:00 Upload to unstable - - - - - 39 changed files: - .github/workflows/cloud_tests.yml - .github/workflows/tests.yml - build.gradle - debian/changelog - debian/control - debian/patches/10-build.patch - debian/patches/30-tests-fix-dataprovider.patch - debian/patches/correct_dataprovider_TestDontMergeAbuttingData.patch - debian/patches/test_accuracy.patch - debian/rules - debian/watch - + src/main/java/picard/analysis/CollectUmiPrevalenceMetrics.java - src/main/java/picard/analysis/directed/HsMetrics.java - src/main/java/picard/arrays/CreateVerifyIDIntensityContaminationMetricsFile.java - + src/main/java/picard/filter/CountingFilterWrapper.java - src/main/java/picard/fingerprint/CalculateFingerprintMetrics.java - src/main/java/picard/fingerprint/CheckFingerprint.java - src/main/java/picard/fingerprint/CrosscheckFingerprints.java - src/main/java/picard/fingerprint/ExtractFingerprint.java - src/main/java/picard/fingerprint/FingerprintChecker.java - src/main/java/picard/fingerprint/FingerprintUtils.java - src/main/java/picard/fingerprint/IdentifyContaminant.java - src/main/java/picard/fingerprint/Snp.java - src/main/java/picard/sam/SamComparisonMetric.java - src/main/java/picard/sam/SamErrorMetric/SimpleErrorCalculator.java - src/main/java/picard/sam/markduplicates/EstimateLibraryComplexity.java - src/main/java/picard/sam/markduplicates/MarkDuplicates.java - src/main/java/picard/sam/util/SamComparison.java - src/main/java/picard/util/SequenceDictionaryUtils.java - src/main/java/picard/vcf/MergeVcfs.java - + src/test/java/picard/analysis/CollectUmiPrevalenceMetricsTest.java - src/test/java/picard/analysis/directed/CollectHsMetricsTest.java - src/test/java/picard/fingerprint/CheckFingerprintTest.java - src/test/java/picard/fingerprint/FingerprintCheckerTest.java - src/test/java/picard/sam/SamErrorMetric/BaseErrorCalculationTest.java - src/test/java/picard/sam/SamErrorMetric/CollectSamErrorMetricsTest.java - src/test/java/picard/sam/util/SamComparisonTest.java - + testdata/picard/independent_replicates/twopairsWithManyUmis.sam - testdata/picard/reference/chrM.reference.fasta The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/compare/9710f8d449eb175adbd8582065ab6c2036c4e393...ec27bed73dfee7997eee634b508cfa4a994fd237 -- View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/compare/9710f8d449eb175adbd8582065ab6c2036c4e393...ec27bed73dfee7997eee634b508cfa4a994fd237 You're receiving this email because of your account on salsa.debian.org.
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