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<h3 style="margin-top: 20px; margin-bottom: 10px;">
Pierre Gruet pushed to branch upstream at <a href="https://salsa.debian.org/med-team/drop-seq">Debian Med / drop-seq</a>
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Commits:
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<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/drop-seq/-/commit/fe62a626a0e1bdddf5fd0d94bb8d90442510fdb3">fe62a626</a></strong>
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<span> by Pierre Gruet </span> <i> at 2023-08-21T15:01:36+02:00 </i>
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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 2.5.4+dfsg</pre>
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30 changed files:
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public.iml
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src/ant/defs.xml
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<a href="#bf66897dbc44295e35876f589c838511ac83323b">
src/java/org/broadinstitute/dropseqrna/annotation/GTFReader.java
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<a href="#fe1030726e5488d620ac0704e82f64e568a5bbaf">
src/java/org/broadinstitute/dropseqrna/annotation/GeneFromGTFBuilder.java
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<a href="#3dfd83b9458dbd8e0506d390375ab0d1d27c99f1">
src/java/org/broadinstitute/dropseqrna/annotation/ReduceGtf.java
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<a href="#a833f2b2e4bd626dbe653dd371caa5fc369aaec9">
src/java/org/broadinstitute/dropseqrna/annotation/ValidateReference.java
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<a href="#0c6697ef52f14a2739123f0abddc573b0efce8bb">
src/java/org/broadinstitute/dropseqrna/barnyard/SingleCellRnaSeqMetricsCollector.java
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src/java/org/broadinstitute/dropseqrna/barnyard/Utils.java
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<a href="#323e4cb6e661503dc739e07a38c217e186fdeb2d">
src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/GatherDigitalAlleleCounts.java
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src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/SNPInfoCollection.java
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<a href="#22be0e5d11f0892e33514d6ad2959c67e55a3f3f">
src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/SNPUMIBasePileup.java
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src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/SNPUMIBasePileupIterator.java
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<a href="#3396c79204dc2e2cc915320af5a1542ce653aba2">
src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/SNPUMICellReadIteratorWrapper.java
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src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/SNPUMICellReadIteratorWrapper2.java
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<a href="#9e64c2ba6f7c42d523a96f90dc144a508aa53475">
src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/sampleassignment/AssignCellsToSamples.java
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src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/sampleassignment/SampleGenotypeProbabilitiesIterator.java
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src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/sampleassignment/multisample/DetectDoublets.java
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src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/sampleassignment/multisample/GenotypeMatrix.java
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src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/sampleassignment/multisample/VariantDataFactory.java
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<a href="#c1d64d06453d67b5a3a769eded322b152657e044">
src/java/org/broadinstitute/dropseqrna/censusseq/CensusSeq.java
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<a href="#f6df8aeb62de4bb45e27608148a1a20db9afa6b1">
src/java/org/broadinstitute/dropseqrna/censusseq/CensusSeqUtils.java
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<a href="#98780a1228bbe3f11a6e3cbac2abfac64c09c6cd">
src/java/org/broadinstitute/dropseqrna/censusseq/CsiAnalysis.java
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<a href="#d014845c4e9252926dc8bf0c851c6ff623e01a38">
src/java/org/broadinstitute/dropseqrna/censusseq/RollCall.java
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<a href="#ef1812ea91d0420f8818e9183cc07953f6f44604">
src/java/org/broadinstitute/dropseqrna/censusseq/SNPGenomicBasePileupIterator.java
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<a href="#92fdc6c6e1d272ed216e58b0779263469147425e">
src/java/org/broadinstitute/dropseqrna/metrics/BamTagHistogram.java
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<a href="#f7662e60a22e69bc9ee1d71e2839d54c83770ea2">
src/java/org/broadinstitute/dropseqrna/metrics/CountUnmatchedSampleIndices.java
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src/java/org/broadinstitute/dropseqrna/metrics/MetricsUtil.java
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src/java/org/broadinstitute/dropseqrna/sbarro/BipartiteRabiesVirusCollapse.java
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<a href="#c68a9adebb21cc8904312fa7dd904a49718a5e4f">
src/java/org/broadinstitute/dropseqrna/spermseq/metrics/duplicates/SpermSeqMarkDuplicates.java
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<a href="#296c253c2c2a72d1dad024b48623d62d1846cdb6">
src/java/org/broadinstitute/dropseqrna/utils/AbstractSplitBamClp.java
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The diff was not included because it is too large.
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<p style="font-size: small; color: #737278;">
—
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<a href="https://salsa.debian.org/med-team/drop-seq/-/commit/fe62a626a0e1bdddf5fd0d94bb8d90442510fdb3">View it on GitLab</a>.
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