[med-svn] [Git][med-team/picard-tools][master] 11 commits: routine-update: New upstream version

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch master at Debian Med / picard-tools


Commits:
42c77037 by Michael R. Crusoe at 2020-08-27T17:05:54+02:00
routine-update: New upstream version

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beb54d3c by Michael R. Crusoe at 2020-08-27T17:06:02+02:00
New upstream version 2.23.3+dfsg
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51530a86 by Michael R. Crusoe at 2020-08-27T17:07:27+02:00
Update upstream source from tag 'upstream/2.23.3+dfsg'

Update to upstream version '2.23.3+dfsg'
with Debian dir 84a4a3e4035253c12dc713d2546e05437d626ddf
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df7f0fab by Michael R. Crusoe at 2020-08-27T17:07:28+02:00
routine-update: Standards-Version: 4.5.0

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f4282594 by Michael R. Crusoe at 2020-08-27T17:07:30+02:00
routine-update: debhelper-compat 13

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8f809bf9 by Michael R. Crusoe at 2020-08-27T17:11:08+02:00
Refresh patches

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3194c16e by Michael R. Crusoe at 2020-08-27T17:11:34+02:00
routine-update: Remove trailing whitespace in debian/changelog

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4bd0b94c by Michael R. Crusoe at 2020-08-27T17:11:35+02:00
routine-update: Add salsa-ci file

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df9591cf by Michael R. Crusoe at 2020-08-27T17:11:36+02:00
routine-update: Rules-Requires-Root: no

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0872901c by Michael R. Crusoe at 2020-08-27T17:11:39+02:00
Trim trailing whitespace.

Changes-By: lintian-brush
Fixes: lintian: trailing-whitespace
See-also: https://lintian.debian.org/tags/trailing-whitespace.html

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d339c2a8 by Michael R. Crusoe at 2020-08-27T17:11:46+02:00
Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.

Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html

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30 changed files:

- README.md
- build.gradle
- debian/changelog
- − debian/compat
- debian/control
- debian/patches/10-build.xml.patch
- debian/patches/20-shadowjar.patch
- debian/patches/30-tests-fix-dataprovider.patch
- debian/patches/40-tests-fix-testng.patch
- debian/patches/remove_google_nio.patch
- debian/rules
- + debian/salsa-ci.yml
- debian/upstream/metadata
- src/main/java/picard/analysis/CollectMultipleMetrics.java
- src/main/java/picard/arrays/ArraysCallingMetricAccumulator.java
- src/main/java/picard/arrays/CollectArraysVariantCallingMetrics.java
- src/main/java/picard/arrays/CombineGenotypingArrayVcfs.java
- src/main/java/picard/arrays/GtcToVcf.java
- + src/main/java/picard/arrays/illumina/BpmToNormalizationManifestCsv.java
- src/main/java/picard/arrays/illumina/CompareGtcFiles.java
- + src/main/java/picard/arrays/illumina/IlluminaBPMFile.java
- + src/main/java/picard/arrays/illumina/IlluminaBPMLocusEntry.java
- src/main/java/picard/arrays/illumina/InfiniumDataFile.java
- src/main/java/picard/arrays/illumina/InfiniumEGTFile.java
- src/main/java/picard/arrays/illumina/InfiniumGTCFile.java
- src/main/java/picard/arrays/illumina/InfiniumVcfFields.java
- src/main/java/picard/cmdline/CommandLineProgram.java
- + src/main/java/picard/fingerprint/CappedHaplotypeProbabilities.java
- src/main/java/picard/fingerprint/CrosscheckFingerprints.java
- + src/main/java/picard/fingerprint/ExtractFingerprint.java


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/compare/7e6e04739bba5aa27566e9f888b0a04becb75021...d339c2a82aeaf7a857a8b77acdddbbbf3dbe224d

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View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/compare/7e6e04739bba5aa27566e9f888b0a04becb75021...d339c2a82aeaf7a857a8b77acdddbbbf3dbe224d
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