[med-svn] [Git][med-team/drop-seq][master] 7 commits: New upstream version 2.4.1+dfsg

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch master at Debian Med / drop-seq


Commits:
763ed8c0 by Andreas Tille at 2021-10-12T09:38:35+02:00
New upstream version 2.4.1+dfsg
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67aa1093 by Pierre Gruet at 2021-10-12T11:51:57+02:00
New upstream version 2.4.1+dfsg
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6d7c921f by Pierre Gruet at 2021-10-12T11:53:34+02:00
Update upstream source from tag 'upstream/2.4.1+dfsg'

Update to upstream version '2.4.1+dfsg'
with Debian dir 5c84278da5942361be129fbefa50c0a54ddd9cc9
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7dfeed78 by Pierre Gruet at 2021-10-12T13:58:18+02:00
Depending on biojava4, with proper paths and manifest

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4ed6ae9f by Pierre Gruet at 2021-10-12T15:17:58+02:00
Updating d/tests/ref after the PolyATrimmer class evolved

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fe27731d by Pierre Gruet at 2021-10-12T15:18:32+02:00
Updating changelog

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36456acf by Pierre Gruet at 2021-10-12T15:51:51+02:00
Upload to unstable

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30 changed files:

- build.xml
- debian/changelog
- debian/control
- debian/drop-seq-tools.manifest
- + debian/patches/biojava4_packages.patch
- debian/patches/series
- debian/rules
- debian/tests/ref/PolyATrimmer.sam
- public.iml
- src/ant/defs.xml
- src/java/org/broadinstitute/dropseqrna/annotation/EnhanceGTFRecords.java
- src/java/org/broadinstitute/dropseqrna/annotation/GTFReader.java
- src/java/org/broadinstitute/dropseqrna/annotation/GeneFromGTFBuilder.java
- src/java/org/broadinstitute/dropseqrna/annotation/ValidateReference.java
- src/java/org/broadinstitute/dropseqrna/barnyard/BarcodeListRetrieval.java
- src/java/org/broadinstitute/dropseqrna/barnyard/DGECommandLineBase.java
- src/java/org/broadinstitute/dropseqrna/barnyard/DigitalExpression.java
- src/java/org/broadinstitute/dropseqrna/barnyard/GatherMolecularBarcodeDistributionByGene.java
- src/java/org/broadinstitute/dropseqrna/barnyard/SelectCellsByNumTranscripts.java
- src/java/org/broadinstitute/dropseqrna/barnyard/SingleCellRnaSeqMetricsCollector.java
- src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/DigitalAlleleCounts.java
- + src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/DigitalAlleleCountsBestGeneIterator.java
- + src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/DigitalAlleleCountsGeneIteratorI.java
- src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/DigitalAlleleCountsIterator.java
- src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/LikelihoodUtils.java
- src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/MultiCellDigitalAlleleCounts.java
- src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/MultiCellDigitalAlleleCountsIterator.java
- src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/SNPBasePileUp.java
- + src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/SNPInfoCollection.java
- + src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/SNPIntervalRecordI.java


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/drop-seq/-/compare/d137c0382fd4e4c45b2ee098c4e68c2d1510f23e...36456acfdf120d9ba5f1fec7e61ef1407ff543ff

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View it on GitLab: https://salsa.debian.org/med-team/drop-seq/-/compare/d137c0382fd4e4c45b2ee098c4e68c2d1510f23e...36456acfdf120d9ba5f1fec7e61ef1407ff543ff
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