[med-svn] [Git][med-team/picard-tools][master] 6 commits: New upstream version 2.18.25+dfsg

[Olivier Sallou]

Olivier Sallou pushed to branch master at Debian Med / picard-tools


Commits:
ebc5863a by Olivier Sallou at 2019-01-25T10:43:57Z
New upstream version 2.18.25+dfsg
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a71b8f3a by Olivier Sallou at 2019-01-25T10:44:29Z
Update upstream source from tag 'upstream/2.18.25+dfsg'

Update to upstream version '2.18.25+dfsg'
with Debian dir feee292f8bde481c7419dce2b4e49da22575b77b
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20608c86 by Olivier Sallou at 2019-01-25T10:47:14Z
new upstream release 2.18.25

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96674a54 by Olivier Sallou at 2019-01-25T10:47:57Z
refresh patches for fuzz

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13b391f5 by Olivier Sallou at 2019-01-25T10:48:34Z
upload v2.18.25

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cf962220 by Olivier Sallou at 2019-01-25T10:49:03Z
fix version

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30 changed files:

- Dockerfile
- build.gradle
- debian/changelog
- debian/control
- debian/patches/20-shadowjar.patch
- debian/patches/fix_unreadabletests.patch
- + src/main/java/picard/sam/AddOATag.java
- src/main/java/picard/sam/markduplicates/MarkDuplicates.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/OpticalDuplicateFinder.java
- src/main/java/picard/sam/util/PGTagArgumentCollection.java
- src/main/java/picard/util/LiftoverUtils.java
- src/main/java/picard/vcf/LiftoverVcf.java
- + src/test/java/picard/sam/AddOATagTest.java
- src/test/java/picard/sam/CompareSAMsTest.java
- src/test/java/picard/sam/ValidateSamFileTest.java
- src/test/java/picard/sam/markduplicates/AbstractMarkDuplicatesCommandLineProgramTester.java
- + src/test/java/picard/sam/markduplicates/MarkDuplicatesSetSizeHistogramTest.java
- + src/test/java/picard/sam/markduplicates/MarkDuplicatesSetSizeHistogramTester.java
- src/test/java/picard/sam/markduplicates/UmiAwareMarkDuplicatesWithMateCigarTester.java
- src/test/java/picard/sam/markduplicates/util/OpticalDuplicateFinderTest.java
- src/test/java/picard/sam/testers/SamFileTester.java
- src/test/java/picard/util/LiftoverVcfTest.java
- src/test/java/picard/vcf/VcfTestUtils.java
- testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list
- testdata/picard/analysis/directed/CollectHsMetrics/lowbaseq.sam
- testdata/picard/analysis/directed/CollectHsMetrics/lowmapq.sam
- testdata/picard/analysis/directed/CollectHsMetrics/overlapping.sam
- testdata/picard/analysis/directed/CollectHsMetrics/single-short-read.sam


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/picard-tools/compare/b5887cee88ee8a326fa4ce0ff35be89d661cd5bd...cf962220447ec2f4960a339f1de26a25839b3fef

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View it on GitLab: https://salsa.debian.org/med-team/picard-tools/compare/b5887cee88ee8a326fa4ce0ff35be89d661cd5bd...cf962220447ec2f4960a339f1de26a25839b3fef
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