[med-svn] [Git][med-team/picard-tools][master] 15 commits: Rewriting d/watch with version 5

[Pierre Gruet (@pgt)]

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

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9e6fceda by Pierre Gruet at 2025-12-23T15:28:49+01:00
New upstream version 3.4.0+dfsg
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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
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bad60450 by Pierre Gruet at 2025-12-23T15:31:44+01:00
Refreshing patches

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9c95d9ba by Pierre Gruet at 2025-12-23T15:32:17+01:00
Removing Priority: optional, which is now default

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443bdbff by Pierre Gruet at 2025-12-23T15:32:47+01:00
Removing R-R-R: no, which is now default

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66bf32fb by Pierre Gruet at 2025-12-23T15:32:59+01:00
Raising Standards version to 4.7.3

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a3e2bc80 by Pierre Gruet at 2025-12-23T15:34:02+01:00
Removing unneeded versioned B-D on htsjdk

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7c75efb5 by Pierre Gruet at 2025-12-23T15:34:35+01:00
Updating changelog

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2e9a049e by Pierre Gruet at 2025-12-23T23:31:24+01:00
Refreshing patches

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a5535f21 by Pierre Gruet at 2025-12-25T22:46:04+01:00
Relying on javahelper to populate control files

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d0278540 by Pierre Gruet at 2025-12-25T22:46:18+01:00
Fixing more int/double comparisons in tests

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8232eb9a by Pierre Gruet at 2025-12-25T22:46:33+01:00
Fixing more inaccurate data providers for the tests

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357b2a76 by Pierre Gruet at 2025-12-25T22:46:52+01:00
Updating changelog

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ec27bed7 by Pierre Gruet at 2025-12-25T22:47:06+01:00
Upload to unstable

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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

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View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/compare/9710f8d449eb175adbd8582065ab6c2036c4e393...ec27bed73dfee7997eee634b508cfa4a994fd237
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