[med-svn] [Git][med-team/picard-tools][master] 9 commits: B-D on default-jdk again, to get the correct documentation files

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch master at Debian Med / picard-tools


Commits:
ad3ce090 by Pierre Gruet at 2026-07-08T11:50:06+02:00
B-D on default-jdk again, to get the correct documentation files

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b2ac037b by Pierre Gruet at 2026-08-03T21:02:42+02:00
New upstream version 3.5.0+dfsg
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89533cb8 by Pierre Gruet at 2026-08-03T21:02:54+02:00
Update upstream source from tag 'upstream/3.5.0+dfsg'

Update to upstream version '3.5.0+dfsg'
with Debian dir 553425f1dbb79a68d9667ba877878d9392d8791e
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855c9a38 by Pierre Gruet at 2026-08-04T10:25:49+02:00
Replacing deprecated skip-non-installable autopkgtest restriction with the list of Architectures

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ce740f82 by Pierre Gruet at 2026-08-04T10:26:19+02:00
Raising Standards version to 4.7.4 (no change)

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9d7d45be by Pierre Gruet at 2026-08-04T10:33:45+02:00
Refreshing patches

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58036bdd by Pierre Gruet at 2026-08-04T10:34:00+02:00
Fixing type mismatches in tests

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732f924b by Pierre Gruet at 2026-08-04T10:34:47+02:00
Updating changelog

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6b4684b0 by Pierre Gruet at 2026-08-04T10:35:50+02:00
Upload to unstable

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67 changed files:

- build.gradle
- debian/changelog
- debian/control
- debian/patches/10-build.patch
- debian/patches/20-shadowjar.patch
- debian/patches/30-tests-fix-dataprovider.patch
- debian/patches/40-tests-fix-testng.patch
- − debian/patches/non-intel-skip-intel-tests
- debian/patches/remove_google_nio.patch
- debian/patches/series
- + debian/patches/test_with_correct_type.patch
- debian/tests/control
- 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/-/compare/d9a512d43ea9ad97fa8163a74dc9f94761d85775...6b4684b0e770309ad3cdd4e07f45befd1df6ab65

-- 
View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/compare/d9a512d43ea9ad97fa8163a74dc9f94761d85775...6b4684b0e770309ad3cdd4e07f45befd1df6ab65
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