[med-svn] [Git][med-team/picard-tools][master] 10 commits: New upstream version 3.3.0+dfsg

[Pierre Gruet (@pgt)]

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


Commits:
0601fb2b by Pierre Gruet at 2024-12-05T12:35:41+01:00
New upstream version 3.3.0+dfsg
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8d8f9306 by Pierre Gruet at 2024-12-05T12:36:16+01:00
Update upstream source from tag 'upstream/3.3.0+dfsg'

Update to upstream version '3.3.0+dfsg'
with Debian dir dae19386c50aae90706cc1d86f2e992413997f29
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207253ab by Pierre Gruet at 2024-12-05T12:36:56+01:00
Raising Standards version to 4.7.0, no change

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23bc363a by Pierre Gruet at 2024-12-05T12:38:46+01:00
Refreshing dates in d/copyright

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e83113cc by Pierre Gruet at 2024-12-26T21:47:55+01:00
Updating the list of build-dependencies

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80dd9b79 by Pierre Gruet at 2024-12-26T22:00:49+01:00
Refreshing patches

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74ce0b45 by Pierre Gruet at 2024-12-26T22:05:58+01:00
Fixing test accuracy issue

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b10872f5 by Pierre Gruet at 2024-12-26T22:06:24+01:00
Patching out code related to Google cloud services

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d5010dbd by Pierre Gruet at 2024-12-26T22:07:35+01:00
Updating changelog

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e589e5ba by Pierre Gruet at 2024-12-26T22:14:09+01:00
Upload to unstable

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30 changed files:

- .github/workflows/cloud_tests.yml
- .gitignore
- Dockerfile
- build.gradle
- build_push_docker.sh
- debian/changelog
- debian/control
- debian/copyright
- debian/patches/10-build.patch
- debian/patches/20-shadowjar.patch
- debian/patches/40-tests-fix-testng.patch
- − debian/patches/60-tests-exclude-network.patch
- debian/patches/com_sun_javadoc_removal_in_openjdk17.patch
- debian/patches/correct_dataprovider_TestDontMergeAbuttingData.patch
- debian/patches/fix_unreadabletests.patch
- debian/patches/omit_BamToBfq.patch
- debian/patches/remove_google_nio.patch
- debian/patches/series
- + debian/patches/test_accuracy.patch
- gradle/wrapper/gradle-wrapper.properties
- gradlew
- src/main/java/picard/analysis/CollectQualityYieldMetrics.java
- + src/main/java/picard/analysis/CollectQualityYieldMetricsFlow.java
- + src/main/java/picard/analysis/CollectQualityYieldMetricsSNVQ.java
- src/main/java/picard/analysis/directed/PanelMetricsBase.java
- src/main/java/picard/analysis/directed/TargetMetricsCollector.java
- src/main/java/picard/cmdline/CommandLineProgram.java
- src/main/java/picard/cmdline/StandardOptionDefinitions.java
- src/main/java/picard/cmdline/argumentcollections/OptionalReferenceArgumentCollection.java
- src/main/java/picard/cmdline/argumentcollections/ReferenceArgumentCollection.java


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/compare/9aa2e0e10df007b08d50193739a5a7c526d17825...e589e5ba0a6efc817aa6e9d3351ea8ff95ddda9b

-- 
View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/compare/9aa2e0e10df007b08d50193739a5a7c526d17825...e589e5ba0a6efc817aa6e9d3351ea8ff95ddda9b
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