[med-svn] [Git][med-team/picard-tools][master] 12 commits: New upstream version 3.0.0+dfsg

[Pierre Gruet (@pgt)]

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


Commits:
1c5e7dd6 by Pierre Gruet at 2023-06-20T16:15:45+02:00
New upstream version 3.0.0+dfsg
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f920cde4 by Pierre Gruet at 2023-06-20T16:16:51+02:00
Update upstream source from tag 'upstream/3.0.0+dfsg'

Update to upstream version '3.0.0+dfsg'
with Debian dir 15cec942ed23736450ea7b52aa7bebe5b14816a9
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8a5af847 by Pierre Gruet at 2023-06-20T16:41:33+02:00
Refreshing patches

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253eb10e by Pierre Gruet at 2023-06-20T16:41:51+02:00
Raising Standards version to 4.6.2 (no change)

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729299b4 by Pierre Gruet at 2023-06-20T16:42:22+02:00
Updating changelog

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6d167d52 by Pierre Gruet at 2023-06-20T16:46:34+02:00
Removing unnecessary versioned B-D

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57a122af by Pierre Gruet at 2023-07-04T14:10:09+02:00
Refreshing patches

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75684d98 by Pierre Gruet at 2023-07-04T14:10:37+02:00
Adding nashorn to d/maven.ignoreRules

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4861fb75 by Pierre Gruet at 2023-07-04T14:14:50+02:00
Running the build-time tests from a directory with no '+' in its path

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0f4ef03d by Pierre Gruet at 2023-07-04T15:16:51+02:00
Updating changelog

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6caa6eae by Pierre Gruet at 2023-07-04T15:23:33+02:00
Omitting the long-failing jar invocation in the build-time tests

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393338cd by Pierre Gruet at 2023-07-04T15:23:41+02:00
Upload to unstable

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30 changed files:

- .github/ISSUE_TEMPLATE.md
- .github/PULL_REQUEST_TEMPLATE.md
- + .github/workflows/tests.yml
- − .travis.yml
- Dockerfile
- README.md
- build.gradle
- debian/changelog
- debian/control
- + debian/maven.ignoreRules
- debian/patches/10-build.xml.patch
- debian/patches/20-shadowjar.patch
- debian/patches/40-tests-fix-testng.patch
- debian/patches/com_sun_javadoc_removal_in_openjdk17.patch
- debian/patches/gradle_openjdk17_incompatibility.patch
- debian/patches/omit_BamToBfq.patch
- debian/rules
- gradle/wrapper/gradle-wrapper.properties
- gradlew
- src/main/java/picard/analysis/CollectAlignmentSummaryMetrics.java
- src/main/java/picard/analysis/CollectMultipleMetrics.java
- src/main/java/picard/analysis/CompareMetrics.java
- src/main/java/picard/arrays/CollectArraysVariantCallingMetrics.java
- src/main/java/picard/arrays/GtcToVcf.java
- src/main/java/picard/arrays/VcfToAdpc.java
- src/main/java/picard/arrays/illumina/Build37ExtendedIlluminaManifest.java
- src/main/java/picard/arrays/illumina/Build37ExtendedIlluminaManifestRecord.java
- src/main/java/picard/arrays/illumina/Build37ExtendedIlluminaManifestRecordCreator.java
- src/main/java/picard/arrays/illumina/CreateExtendedIlluminaManifest.java
- src/main/java/picard/arrays/illumina/IlluminaManifest.java


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/compare/463a37af2b5cb68db61363460c852d6346992163...393338cdd2a9ba4badf29d42229f44dea10e4e4b

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View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/compare/463a37af2b5cb68db61363460c852d6346992163...393338cdd2a9ba4badf29d42229f44dea10e4e4b
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