[med-svn] [Git][med-team/drop-seq][master] 6 commits: New upstream version 2.5.2+dfsg

[Pierre Gruet (@pgt)]

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


Commits:
4f6bae38 by Pierre Gruet at 2023-01-22T09:10:13+01:00
New upstream version 2.5.2+dfsg
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08090daf by Pierre Gruet at 2023-01-22T09:12:21+01:00
Update upstream source from tag 'upstream/2.5.2+dfsg'

Update to upstream version '2.5.2+dfsg'
with Debian dir bda00e1ad06cf0f899b8fccdad61f2524bf7682b
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53805441 by Pierre Gruet at 2023-01-22T09:14:57+01:00
Dropping unexisting java-runtime package from the list of runtime dependencies

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d63162a8 by Pierre Gruet at 2023-01-22T09:18:25+01:00
Refreshing d/copyright

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8cbbd4a3 by Pierre Gruet at 2023-01-22T09:19:06+01:00
Updating changelog

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a1aaded5 by Pierre Gruet at 2023-01-22T09:19:15+01:00
Upload to unstable

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30 changed files:

- build.xml
- debian/changelog
- debian/control
- debian/copyright
- src/ant/defs.xml
- src/java/org/broadinstitute/dropseqrna/annotation/CompareAnnotationFlags.java
- src/java/org/broadinstitute/dropseqrna/annotation/FunctionalDataProcessor.java
- src/java/org/broadinstitute/dropseqrna/barnyard/DGECommandLineBase.java
- src/java/org/broadinstitute/dropseqrna/barnyard/DigitalExpression.java
- + src/java/org/broadinstitute/dropseqrna/barnyard/DownsampleTranscriptsAndQuantiles.java
- src/java/org/broadinstitute/dropseqrna/barnyard/GatherMolecularBarcodeDistributionByGene.java
- + src/java/org/broadinstitute/dropseqrna/barnyard/UMICollectionByCellParser.java
- + src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/GatherDigitalAlleleCounts.java
- src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/LikelihoodUtils.java
- src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/sampleassignment/AssignCellsToSamples.java
- src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/sampleassignment/CellCollectionSampleLikelihoodCollection.java
- src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/sampleassignment/multisample/DetectDoublets.java
- src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/sampleassignment/multisample/SamplePairAssignmentForCell.java
- + src/java/org/broadinstitute/dropseqrna/barnyard/digitalexpression/FilterDge.java
- src/java/org/broadinstitute/dropseqrna/barnyard/digitalexpression/UMICollection.java
- src/java/org/broadinstitute/dropseqrna/beadsynthesis/DetectBeadSynthesisErrors.java
- src/java/org/broadinstitute/dropseqrna/censusseq/CensusSeq.java
- src/java/org/broadinstitute/dropseqrna/censusseq/CommonSNPsData.java
- src/java/org/broadinstitute/dropseqrna/censusseq/OptimizeGradientAdjustment.java
- src/java/org/broadinstitute/dropseqrna/censusseq/OptimizeSampleRatiosCommonSNPs.java
- src/java/org/broadinstitute/dropseqrna/censusseq/OptimizeSampleRatiosCommonSNPsResult.java
- src/java/org/broadinstitute/dropseqrna/censusseq/OptimizeSampleRatiosGradientFunction.java
- src/java/org/broadinstitute/dropseqrna/censusseq/OptimizeSampleRatiosLikelihoodFunctionCommonSNPs.java
- + src/java/org/broadinstitute/dropseqrna/eqtl/CreateMetaCells.java
- + src/java/org/broadinstitute/dropseqrna/eqtl/DonorMergeStrategy.java


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/drop-seq/-/compare/e51614e57593c3243fccc2506dfdd6a644767805...a1aaded58271ad0f43a0f76fc67a04382ffd1992

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View it on GitLab: https://salsa.debian.org/med-team/drop-seq/-/compare/e51614e57593c3243fccc2506dfdd6a644767805...a1aaded58271ad0f43a0f76fc67a04382ffd1992
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