[med-svn] [Git][med-team/picard-tools][upstream] New upstream version 3.4.0+dfsg

[Pierre Gruet (@pgt)]

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

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View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/commit/9e6fceda1939d1e7f0065577e787e70639d13591
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