[med-svn] [Git][med-team/picard-tools][master] 8 commits: New upstream version 3.1.1+dfsg

[Pierre Gruet (@pgt)]

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


Commits:
c1ab316e by Pierre Gruet at 2023-12-14T13:16:36+01:00
New upstream version 3.1.1+dfsg
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98e0f677 by Pierre Gruet at 2023-12-14T13:17:03+01:00
Update upstream source from tag 'upstream/3.1.1+dfsg'

Update to upstream version '3.1.1+dfsg'
with Debian dir c05e4deb7ab5ed2606cbe4d8c3c01cb5d60c744a
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515d8a2c by Pierre Gruet at 2023-12-14T21:36:49+01:00
Refreshing patches

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b5953e62 by Pierre Gruet at 2023-12-16T22:37:18+01:00
Enabling the test with BarclayParser again

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40fd4cc9 by Pierre Gruet at 2023-12-16T22:37:54+01:00
Patching out more code portions using google-nio

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6e784b77 by Pierre Gruet at 2023-12-16T22:38:09+01:00
Refreshing patches

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0b1f5678 by Pierre Gruet at 2023-12-16T22:38:28+01:00
Updating changelog

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9aa2e0e1 by Pierre Gruet at 2023-12-16T22:38:37+01:00
Upload to unstable

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30 changed files:

- + .gitattributes
- + .github/workflows/cloud_tests.yml
- .gitignore
- build.gradle
- debian/changelog
- debian/maven.ignoreRules
- debian/patches/10-build.xml.patch → 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/50-tests-exclude-Barclay.patch
- debian/patches/com_sun_javadoc_removal_in_openjdk17.patch
- debian/patches/correct_dataprovider_TestDontMergeAbuttingData.patch
- − debian/patches/fix_javadoc_ascii.patch
- debian/patches/fix_unreadabletests.patch
- debian/patches/non-intel-skip-intel-tests
- debian/patches/omit_BamToBfq.patch
- debian/patches/remove_google_nio.patch
- debian/patches/series
- gradle/wrapper/gradle-wrapper.properties
- gradlew
- src/main/java/picard/analysis/AlignmentSummaryMetricsCollector.java
- src/main/java/picard/analysis/CollectOxoGMetrics.java
- src/main/java/picard/analysis/CollectWgsMetrics.java
- src/main/java/picard/analysis/SinglePassSamProgram.java
- src/main/java/picard/analysis/directed/CollectTargetedMetrics.java
- src/main/java/picard/analysis/replicates/CollectIndependentReplicateMetrics.java
- src/main/java/picard/cmdline/CommandLineProgram.java
- src/main/java/picard/cmdline/PicardCommandLine.java
- src/main/java/picard/fingerprint/CheckFingerprint.java


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/compare/393338cdd2a9ba4badf29d42229f44dea10e4e4b...9aa2e0e10df007b08d50193739a5a7c526d17825

-- 
View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/compare/393338cdd2a9ba4badf29d42229f44dea10e4e4b...9aa2e0e10df007b08d50193739a5a7c526d17825
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