[med-svn] [Git][med-team/picard-tools][master] 7 commits: Updating d/watch after a change in the Github layout

[Pierre Gruet (@pgt)]

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


Commits:
db6080a4 by Pierre Gruet at 2022-09-21T15:07:28+02:00
Updating d/watch after a change in the Github layout

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f17ae3a5 by Pierre Gruet at 2022-09-22T16:29:27+02:00
New upstream version 2.27.4+dfsg
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2ba244dd by Pierre Gruet at 2022-09-22T16:30:40+02:00
Update upstream source from tag 'upstream/2.27.4+dfsg'

Update to upstream version '2.27.4+dfsg'
with Debian dir 2192af7cc5e657c4beb6b8f2ba7ce29c3a7ebe95
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4118172d by Pierre Gruet at 2022-09-22T16:32:19+02:00
Refreshing patches

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08a3c99a by Pierre Gruet at 2022-09-22T16:33:15+02:00
Updating changelog

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94763177 by Pierre Gruet at 2022-09-22T17:22:15+02:00
Refreshing the Lintian override for embedded JS

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0d58d801 by Pierre Gruet at 2022-09-22T20:26:07+02:00
Upload to unstable

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30 changed files:

- .gitignore
- build.gradle
- debian/changelog
- debian/libpicard-java-doc.lintian-overrides
- debian/patches/10-build.xml.patch
- debian/watch
- src/main/java/picard/analysis/AlignmentSummaryMetrics.java
- src/main/java/picard/analysis/AlignmentSummaryMetricsCollector.java
- src/main/java/picard/analysis/CollectQualityYieldMetrics.java
- + src/main/java/picard/analysis/HistogramGenerator.java
- src/main/java/picard/analysis/MeanQualityByCycle.java
- src/main/java/picard/sam/DuplicationMetrics.java
- + src/main/java/picard/sam/DuplicationMetricsFactory.java
- src/main/java/picard/sam/FastqToSam.java
- + src/main/java/picard/sam/FlowBasedDuplicationMetrics.java
- src/main/java/picard/sam/RevertSam.java
- src/main/java/picard/sam/markduplicates/CollectDuplicateMetrics.java
- src/main/java/picard/sam/markduplicates/EstimateLibraryComplexity.java
- src/main/java/picard/sam/markduplicates/MarkDuplicates.java
- + src/main/java/picard/sam/markduplicates/MarkDuplicatesForFlowArgumentCollection.java
- + src/main/java/picard/sam/markduplicates/MarkDuplicatesForFlowHelper.java
- + src/main/java/picard/sam/markduplicates/MarkDuplicatesHelper.java
- src/main/java/picard/sam/markduplicates/MarkDuplicatesWithMateCigarIterator.java
- src/main/java/picard/sam/markduplicates/SimpleMarkDuplicatesWithMateCigar.java
- src/main/java/picard/sam/markduplicates/util/AbstractMarkDuplicatesCommandLineProgram.java
- src/main/java/picard/sam/markduplicates/util/LibraryIdGenerator.java
- src/main/java/picard/sam/markduplicates/util/ReadEnds.java
- src/main/java/picard/sam/markduplicates/util/ReadEndsForMarkDuplicates.java
- src/main/java/picard/util/AccumulateQualityYieldMetrics.java
- src/main/java/picard/vcf/GenotypeConcordance.java


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/compare/85ccfccc0cebe75e1f717a150575cd8d02135f22...0d58d801b9ac66f55fadbbebe17c9b463b4ea05a

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View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/compare/85ccfccc0cebe75e1f717a150575cd8d02135f22...0d58d801b9ac66f55fadbbebe17c9b463b4ea05a
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