[med-svn] [Git][med-team/picard-tools][master] 10 commits: New upstream version 2.27.5+dfsg

[Pierre Gruet (@pgt)]

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
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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
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fdca5f8f by Pierre Gruet at 2022-11-01T20:31:55+01:00
Refreshing patches

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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

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5ea0b2a0 by Pierre Gruet at 2022-11-02T17:41:35+01:00
Skipping a test because of a byte changing when switching to OpenJDK17

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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

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8d269aa6 by Pierre Gruet at 2022-11-02T17:44:32+01:00
Updating changelog

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1837ad94 by Pierre Gruet at 2022-11-03T21:03:24+01:00
Marking the 60- patch as Forwarded: not-needed

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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

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90670e8b by Pierre Gruet at 2022-11-04T11:10:10+01:00
Upload to unstable

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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

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View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/compare/0d58d801b9ac66f55fadbbebe17c9b463b4ea05a...90670e8ba7605bee8ad05f2a77a6c49fdcbf1bf1
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