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

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch upstream 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
- - - - -


28 changed files:

- build.xml
- 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
- + src/java/org/broadinstitute/dropseqrna/eqtl/MetaCellMetrics.java


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/drop-seq/-/commit/4f6bae3860dbc6794ebaba7dd37b7cb7515975c0

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View it on GitLab: https://salsa.debian.org/med-team/drop-seq/-/commit/4f6bae3860dbc6794ebaba7dd37b7cb7515975c0
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