[med-svn] [Git][med-team/drop-seq][upstream] New upstream version 2.5.4+dfsg

[Pierre Gruet (@pgt)]

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


Commits:
fe62a626 by Pierre Gruet at 2023-08-21T15:01:36+02:00
New upstream version 2.5.4+dfsg
- - - - -


30 changed files:

- public.iml
- src/ant/defs.xml
- src/java/org/broadinstitute/dropseqrna/annotation/GTFReader.java
- src/java/org/broadinstitute/dropseqrna/annotation/GeneFromGTFBuilder.java
- src/java/org/broadinstitute/dropseqrna/annotation/ReduceGtf.java
- src/java/org/broadinstitute/dropseqrna/annotation/ValidateReference.java
- src/java/org/broadinstitute/dropseqrna/barnyard/SingleCellRnaSeqMetricsCollector.java
- src/java/org/broadinstitute/dropseqrna/barnyard/Utils.java
- src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/GatherDigitalAlleleCounts.java
- src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/SNPInfoCollection.java
- src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/SNPUMIBasePileup.java
- src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/SNPUMIBasePileupIterator.java
- src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/SNPUMICellReadIteratorWrapper.java
- + src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/SNPUMICellReadIteratorWrapper2.java
- src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/sampleassignment/AssignCellsToSamples.java
- src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/sampleassignment/SampleGenotypeProbabilitiesIterator.java
- src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/sampleassignment/multisample/DetectDoublets.java
- src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/sampleassignment/multisample/GenotypeMatrix.java
- src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/sampleassignment/multisample/VariantDataFactory.java
- src/java/org/broadinstitute/dropseqrna/censusseq/CensusSeq.java
- src/java/org/broadinstitute/dropseqrna/censusseq/CensusSeqUtils.java
- src/java/org/broadinstitute/dropseqrna/censusseq/CsiAnalysis.java
- src/java/org/broadinstitute/dropseqrna/censusseq/RollCall.java
- src/java/org/broadinstitute/dropseqrna/censusseq/SNPGenomicBasePileupIterator.java
- src/java/org/broadinstitute/dropseqrna/metrics/BamTagHistogram.java
- src/java/org/broadinstitute/dropseqrna/metrics/CountUnmatchedSampleIndices.java
- + src/java/org/broadinstitute/dropseqrna/metrics/MetricsUtil.java
- src/java/org/broadinstitute/dropseqrna/sbarro/BipartiteRabiesVirusCollapse.java
- src/java/org/broadinstitute/dropseqrna/spermseq/metrics/duplicates/SpermSeqMarkDuplicates.java
- src/java/org/broadinstitute/dropseqrna/utils/AbstractSplitBamClp.java


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/drop-seq/-/commit/fe62a626a0e1bdddf5fd0d94bb8d90442510fdb3

-- 
View it on GitLab: https://salsa.debian.org/med-team/drop-seq/-/commit/fe62a626a0e1bdddf5fd0d94bb8d90442510fdb3
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20230821/1655ada5/attachment.htm>