Pierre Gruet pushed to branch upstream at Debian Med / picard-tools
Commits: 9e6fceda by Pierre Gruet at 2025-12-23T15:28:49+01:00 New upstream version 3.4.0+dfsg - - - - - 31 changed files: - .github/workflows/cloud_tests.yml - .github/workflows/tests.yml - build.gradle - + 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/-/commit/9e6fceda1939d1e7f0065577e787e70639d13591 -- View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/commit/9e6fceda1939d1e7f0065577e787e70639d13591 You're receiving this email because of your account on salsa.debian.org.
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