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 - - - - - b2ac037b by Pierre Gruet at 2026-08-03T21:02:42+02:00 New upstream version 3.5.0+dfsg - - - - - 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 - - - - - 855c9a38 by Pierre Gruet at 2026-08-04T10:25:49+02:00 Replacing deprecated skip-non-installable autopkgtest restriction with the list of Architectures - - - - - ce740f82 by Pierre Gruet at 2026-08-04T10:26:19+02:00 Raising Standards version to 4.7.4 (no change) - - - - - 9d7d45be by Pierre Gruet at 2026-08-04T10:33:45+02:00 Refreshing patches - - - - - 58036bdd by Pierre Gruet at 2026-08-04T10:34:00+02:00 Fixing type mismatches in tests - - - - - 732f924b by Pierre Gruet at 2026-08-04T10:34:47+02:00 Updating changelog - - - - - 6b4684b0 by Pierre Gruet at 2026-08-04T10:35:50+02:00 Upload to unstable - - - - - 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 You're receiving this email because of your account on salsa.debian.org. Manage all notifications: https://salsa.debian.org/-/profile/notifications | Help: https://salsa.debian.org/help
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
