[med-svn] [Git][med-team/picard-tools][master] 7 commits: routine-update: New upstream version

[Michael R. Crusoe]

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


Commits:
50f29de7 by Michael R. Crusoe at 2021-01-07T13:41:40+01:00
routine-update: New upstream version

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a51591b3 by Michael R. Crusoe at 2021-01-07T13:41:43+01:00
New upstream version 2.24.0+dfsg
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97da6645 by Michael R. Crusoe at 2021-01-07T13:42:17+01:00
Update upstream source from tag 'upstream/2.24.0+dfsg'

Update to upstream version '2.24.0+dfsg'
with Debian dir da8fff9effd15134064ac13e5134774472066705
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af65fbfa by Michael R. Crusoe at 2021-01-07T13:42:17+01:00
routine-update: Standards-Version: 4.5.1

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0096e3a0 by Michael R. Crusoe at 2021-01-07T13:43:45+01:00
refresh patches.

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940f6032 by Michael R. Crusoe at 2021-01-07T13:43:53+01:00
routine-update: Ready to upload to unstable

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15cff312 by Michael R. Crusoe at 2021-01-07T13:59:56+01:00
  TODO: test failures

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30 changed files:

- debian/changelog
- debian/control
- debian/patches/30-tests-fix-dataprovider.patch
- debian/patches/40-tests-fix-testng.patch
- src/main/java/picard/analysis/AlignmentSummaryMetrics.java
- src/main/java/picard/analysis/AlignmentSummaryMetricsCollector.java
- src/main/java/picard/analysis/CollectAlignmentSummaryMetrics.java
- src/main/java/picard/analysis/CollectBaseDistributionByCycle.java
- src/main/java/picard/analysis/CollectGcBiasMetrics.java
- src/main/java/picard/analysis/CollectInsertSizeMetrics.java
- src/main/java/picard/analysis/CollectMultipleMetrics.java
- src/main/java/picard/analysis/CollectRnaSeqMetrics.java
- src/main/java/picard/analysis/CollectRrbsMetrics.java
- src/main/java/picard/analysis/CollectWgsMetrics.java
- src/main/java/picard/analysis/CollectWgsMetricsWithNonZeroCoverage.java
- src/main/java/picard/analysis/MeanQualityByCycle.java
- src/main/java/picard/analysis/QualityScoreDistribution.java
- src/main/java/picard/analysis/directed/PanelMetricsBase.java
- src/main/java/picard/analysis/directed/TargetMetricsCollector.java
- src/main/java/picard/analysis/replicates/CollectIndependentReplicateMetrics.java
- src/main/java/picard/arrays/GtcToVcf.java
- src/main/java/picard/cmdline/CommandLineProgram.java
- − src/main/java/picard/illumina/parser/ClusterIntensityFileReader.java
- − src/main/java/picard/illumina/parser/FourChannelIntensityData.java
- src/main/java/picard/illumina/parser/IlluminaData.java
- src/main/java/picard/illumina/parser/ReadData.java
- src/main/java/picard/sam/BuildBamIndex.java
- src/main/java/picard/sam/SamErrorMetric/CollectSamErrorMetrics.java
- src/main/java/picard/sam/SamErrorMetric/ReadBaseStratification.java
- src/main/java/picard/sam/ValidateSamFile.java


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/compare/fb26f35d620951878468e3f8ae811d1985840fbf...15cff3129061670ba13b4f46baea41df1a5cd13e

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View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/compare/fb26f35d620951878468e3f8ae811d1985840fbf...15cff3129061670ba13b4f46baea41df1a5cd13e
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