Pierre Gruet pushed to branch master at Debian Med / picard-tools
Commits: ac518bb5 by Pierre Gruet at 2022-11-01T20:28:47+01:00 New upstream version 2.27.5+dfsg - - - - - 5cddd0f0 by Pierre Gruet at 2022-11-01T20:29:45+01:00 Update upstream source from tag 'upstream/2.27.5+dfsg' Update to upstream version '2.27.5+dfsg' with Debian dir 3ac603ec8efc74ef4cc46effe338afacc68b4e26 - - - - - fdca5f8f by Pierre Gruet at 2022-11-01T20:31:55+01:00 Refreshing patches - - - - - 62d788f3 by Pierre Gruet at 2022-11-02T17:40:53+01:00 Skipping tests which cannot run because of old Gradle not providing --add-opens - - - - - 5ea0b2a0 by Pierre Gruet at 2022-11-02T17:41:35+01:00 Skipping a test because of a byte changing when switching to OpenJDK17 - - - - - 18bda0d1 by Pierre Gruet at 2022-11-02T17:42:06+01:00 Adding a versioned B-D on libhtsjdk-java because of a change in the ABI - - - - - 8d269aa6 by Pierre Gruet at 2022-11-02T17:44:32+01:00 Updating changelog - - - - - 1837ad94 by Pierre Gruet at 2022-11-03T21:03:24+01:00 Marking the 60- patch as Forwarded: not-needed - - - - - 17b4d41e by Pierre Gruet at 2022-11-04T11:07:15+01:00 Excluding the BamToBfq class from the jar to be conservative, as its test is possibly problematic with OpenJDK17 - - - - - 90670e8b by Pierre Gruet at 2022-11-04T11:10:10+01:00 Upload to unstable - - - - - 30 changed files: - build.gradle - debian/changelog - debian/control - debian/patches/10-build.xml.patch - debian/patches/30-tests-fix-dataprovider.patch - debian/patches/60-tests-exclude-network.patch - debian/patches/fix_unreadabletests.patch - + debian/patches/gradle_openjdk17_incompatibility.patch - + debian/patches/omit_BamToBfq.patch - debian/patches/remove_google_nio.patch - debian/patches/series - 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/util/SequenceDictionaryUtils.java - src/test/java/picard/analysis/artifacts/CollectSequencingArtifactMetricsTest.java - src/test/java/picard/analysis/directed/CollectHsMetricsTest.java - src/test/java/picard/analysis/replicates/CollectIndependentReplicatesMetricTest.java - src/test/java/picard/fastq/BamToBfqTest.java - src/test/java/picard/fingerprint/CrosscheckFingerprintsTest.java - src/test/java/picard/fingerprint/FingerprintCheckerTest.java - src/test/java/picard/illumina/CheckIlluminaDirectoryTest.java - src/test/java/picard/illumina/CollectIlluminaBasecallingMetricsTest.java - src/test/java/picard/illumina/ExtractIlluminaBarcodesTest.java - src/test/java/picard/illumina/IlluminaBasecallsToFastqTest.java - src/test/java/picard/illumina/IlluminaLaneMetricsCollectorTest.java - src/test/java/picard/illumina/parser/BclParserTest.java - src/test/java/picard/illumina/parser/IlluminaFileUtilTest.java - src/test/java/picard/metrics/CollectRrbsMetricsTest.java - src/test/java/picard/sam/CramCompatibilityTest.java The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/compare/0d58d801b9ac66f55fadbbebe17c9b463b4ea05a...90670e8ba7605bee8ad05f2a77a6c49fdcbf1bf1 -- View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/compare/0d58d801b9ac66f55fadbbebe17c9b463b4ea05a...90670e8ba7605bee8ad05f2a77a6c49fdcbf1bf1 You're receiving this email because of your account on salsa.debian.org.
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