[med-svn] [Git][med-team/picard-tools][master] 5 commits: New upstream version 2.18.23+dfsg

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / picard-tools


Commits:
2d8023c3 by Andreas Tille at 2019-01-11T21:51:59Z
New upstream version 2.18.23+dfsg
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9bb0c423 by Andreas Tille at 2019-01-11T21:52:32Z
Update upstream source from tag 'upstream/2.18.23+dfsg'

Update to upstream version '2.18.23+dfsg'
with Debian dir 218ff8637311139efd72d5fa3f9d0e2d9b27a551
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e5ffe697 by Andreas Tille at 2019-01-11T21:52:33Z
New upstream version

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e402cfd0 by Andreas Tille at 2019-01-11T21:52:33Z
debhelper 12

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fcb37a10 by Andreas Tille at 2019-01-11T21:52:35Z
Standards-Version: 4.3.0

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30 changed files:

- debian/changelog
- debian/compat
- debian/control
- src/main/java/picard/analysis/directed/RnaSeqMetricsCollector.java
- src/main/java/picard/illumina/IlluminaBasecallsToFastq.java
- src/main/java/picard/illumina/IlluminaBasecallsToSam.java
- src/main/java/picard/illumina/NewIlluminaBasecallsConverter.java
- src/main/java/picard/illumina/parser/BaseIlluminaDataProvider.java
- src/main/java/picard/illumina/parser/CbclData.java
- src/main/java/picard/illumina/parser/FilterParser.java
- src/main/java/picard/illumina/parser/IlluminaData.java
- src/main/java/picard/illumina/parser/MultiTileFilterParser.java
- src/main/java/picard/illumina/parser/readers/CbclReader.java
- src/main/java/picard/sam/markduplicates/UmiUtil.java
- src/main/java/picard/sam/markduplicates/util/OpticalDuplicateFinder.java
- src/main/java/picard/sam/util/ReadNameParser.java
- src/main/java/picard/util/ThreadPoolExecutorWithExceptions.java
- src/test/java/picard/analysis/CollectRnaSeqMetricsTest.java
- src/test/java/picard/illumina/CollectIlluminaBasecallingMetricsTest.java
- src/test/java/picard/illumina/ExtractIlluminaBarcodesTest.java
- src/test/java/picard/illumina/parser/FilterParserTest.java
- src/test/java/picard/sam/markduplicates/AbstractMarkDuplicatesCommandLineProgramTest.java
- src/test/java/picard/sam/markduplicates/UmiUtilTest.java
- testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/s_1_1101_barcode.txt.gz
- testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/s_1_1102_barcode.txt.gz
- testdata/picard/illumina/151T8B8B151T_cbcl/fastq/NN.1.fastq
- testdata/picard/illumina/151T8B8B151T_cbcl/fastq/NN.2.fastq
- testdata/picard/illumina/151T8B8B151T_cbcl/fastq/NN.barcode_1.fastq
- testdata/picard/illumina/151T8B8B151T_cbcl/fastq/NN.barcode_2.fastq
- testdata/picard/illumina/151T8B8B151T_cbcl/sams/1102.NN.sam


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/picard-tools/compare/5c2de50991138588ab4e36be161bdcf528a47d0a...fcb37a1022688e8223336003b4a73c2e00ef0a25

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View it on GitLab: https://salsa.debian.org/med-team/picard-tools/compare/5c2de50991138588ab4e36be161bdcf528a47d0a...fcb37a1022688e8223336003b4a73c2e00ef0a25
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