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GitLab

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<h3>

Andreas Tille pushed to branch upstream

at <a href="https://salsa.debian.org/med-team/drop-seq">Debian Med / drop-seq</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/drop-seq/-/commit/763ed8c0f4837f541a449cc06c564738b22b0225">763ed8c0</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2021-10-12T09:38:35+02:00</i>

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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.4.1+dfsg</pre>

</li>

</ul>

<h4>30 changed files:</h4>

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<li class="file-stats">

<a href="#bdc348bf75801c527f51cdeddc8edf027f7ef35a">

build.xml

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</li>

<li class="file-stats">

<a href="#126e844ff98b3c8e9ce07e5602abeea640905d7e">

public.iml

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<li class="file-stats">

<a href="#e417d87785a703d5c8bb1cc5e82cddfae8efe265">

src/ant/defs.xml

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</li>

<li class="file-stats">

<a href="#032778c8c38290444d9623154ed3953430fa3519">

src/java/org/broadinstitute/dropseqrna/annotation/EnhanceGTFRecords.java

</a>

</li>

<li class="file-stats">

<a href="#bf66897dbc44295e35876f589c838511ac83323b">

src/java/org/broadinstitute/dropseqrna/annotation/GTFReader.java

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<li class="file-stats">

<a href="#fe1030726e5488d620ac0704e82f64e568a5bbaf">

src/java/org/broadinstitute/dropseqrna/annotation/GeneFromGTFBuilder.java

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<li class="file-stats">

<a href="#a833f2b2e4bd626dbe653dd371caa5fc369aaec9">

src/java/org/broadinstitute/dropseqrna/annotation/ValidateReference.java

</a>

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<li class="file-stats">

<a href="#091256f5e03f4a474aaacca323c45a3f064f9c38">

src/java/org/broadinstitute/dropseqrna/barnyard/BarcodeListRetrieval.java

</a>

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<li class="file-stats">

<a href="#3fc29742029b59ebe687374cc84905308eef17b0">

src/java/org/broadinstitute/dropseqrna/barnyard/DGECommandLineBase.java

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<li class="file-stats">

<a href="#2b9909c5b5a360e211167af9b686a599ea5d6681">

src/java/org/broadinstitute/dropseqrna/barnyard/DigitalExpression.java

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<li class="file-stats">

<a href="#b7ea49725999e61f0bdf16c415245903969406ca">

src/java/org/broadinstitute/dropseqrna/barnyard/GatherMolecularBarcodeDistributionByGene.java

</a>

</li>

<li class="file-stats">

<a href="#fd3a5e40a45d2f4b41997710d2d546c6eb0197ef">

src/java/org/broadinstitute/dropseqrna/barnyard/SelectCellsByNumTranscripts.java

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<li class="file-stats">

<a href="#0c6697ef52f14a2739123f0abddc573b0efce8bb">

src/java/org/broadinstitute/dropseqrna/barnyard/SingleCellRnaSeqMetricsCollector.java

</a>

</li>

<li class="file-stats">

<a href="#4d9eed73071d00f066f1fb8debfc896aefed6bae">

src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/DigitalAlleleCounts.java

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</li>

<li class="file-stats">

<a href="#aa743a24790013f9b239f7da44936fa5f998077f">

<span class="new-file">

+

src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/DigitalAlleleCountsBestGeneIterator.java

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</a>

</li>

<li class="file-stats">

<a href="#0d81bb6818097b48bbe062000c81d8afc7704d5c">

<span class="new-file">

+

src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/DigitalAlleleCountsGeneIteratorI.java

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</a>

</li>

<li class="file-stats">

<a href="#f2826e10c6a8820995bac0a6ee723ff847696e78">

src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/DigitalAlleleCountsIterator.java

</a>

</li>

<li class="file-stats">

<a href="#5eb1e45250b8c5b84727a387522f0f44ecc64cf6">

src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/LikelihoodUtils.java

</a>

</li>

<li class="file-stats">

<a href="#6b999f80356a68baf45823ffe07e622b4d63b198">

src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/MultiCellDigitalAlleleCounts.java

</a>

</li>

<li class="file-stats">

<a href="#4715f9c62db4691599b82c890fa92f0a970c173d">

src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/MultiCellDigitalAlleleCountsIterator.java

</a>

</li>

<li class="file-stats">

<a href="#64537137acc59da98550ca639376b0079e672ea1">

src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/SNPBasePileUp.java

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</li>

<li class="file-stats">

<a href="#b39c23214908b9c503de5a341b56523b626eb888">

<span class="new-file">

+

src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/SNPInfoCollection.java

</span>

</a>

</li>

<li class="file-stats">

<a href="#1c332b8e01efb0944cfcd35871330813c7fdb5bd">

<span class="new-file">

+

src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/SNPIntervalRecordI.java

</span>

</a>

</li>

<li class="file-stats">

<a href="#22be0e5d11f0892e33514d6ad2959c67e55a3f3f">

src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/SNPUMIBasePileup.java

</a>

</li>

<li class="file-stats">

<a href="#ddf94b485d7475537602705ff0dea2a8ea08cb35">

src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/SNPUMIBasePileupIterator.java

</a>

</li>

<li class="file-stats">

<a href="#3396c79204dc2e2cc915320af5a1542ce653aba2">

src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/SNPUMICellReadIteratorWrapper.java

</a>

</li>

<li class="file-stats">

<a href="#845b0d7c549b3f9a1ba70abaa321e2a3e548eb33">

src/java/org/broadinstitute/dropseqrna/beadsynthesis/DetectBeadSynthesisErrors.java

</a>

</li>

<li class="file-stats">

<a href="#c1d64d06453d67b5a3a769eded322b152657e044">

src/java/org/broadinstitute/dropseqrna/censusseq/CensusSeq.java

</a>

</li>

<li class="file-stats">

<a href="#98780a1228bbe3f11a6e3cbac2abfac64c09c6cd">

src/java/org/broadinstitute/dropseqrna/censusseq/CsiAnalysis.java

</a>

</li>

<li class="file-stats">

<a href="#0d5efb8415038faa07e28357d176b4935c13e88e">

src/java/org/broadinstitute/dropseqrna/censusseq/CsiMetrics.java

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</li>

</ul>

<h5>The diff was not included because it is too large.</h5>

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