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<div class="content">
<h3 style="margin-top: 20px; margin-bottom: 10px;">
Pierre Gruet pushed to branch master at <a href="https://salsa.debian.org/med-team/drop-seq">Debian Med / drop-seq</a>
</h3>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
Commits:
</h4>
<ul>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/drop-seq/-/commit/dfa238cdcb9df06b84d59b8f27058779d8e938dc">dfa238cd</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2024-09-29T21:41:11+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","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;'>Refreshing the list of files to remove when repacking
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/drop-seq/-/commit/fc203848b5b74713f45b9d52c7e40f902eb2488e">fc203848</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2024-09-29T21:45:09+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","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 3.0.2+dfsg</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/drop-seq/-/commit/ad52d5eede37602e71ea2124ffef23353a04a5c8">ad52d5ee</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2024-09-29T21:47:04+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","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;'>Update upstream source from tag 'upstream/3.0.2+dfsg'
Update to upstream version '3.0.2+dfsg'
with Debian dir b2f248be4ba49293287ed26f161d2ca5dc7f0fa5</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/drop-seq/-/commit/b669bc4c184b214cd7b1f635b3ca8b277f53a1bf">b669bc4c</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2024-09-29T21:58:05+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","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;'>Refreshing patches
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/drop-seq/-/commit/25d41b38fde65ddac782ac3ced4ca02a41898f5f">25d41b38</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2024-09-29T21:59:43+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","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;'>Updating changelog
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/drop-seq/-/commit/9a0df4025fb81e5d3b3ae0e17e79711359e276c5">9a0df402</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2024-09-29T23:07:26+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","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;'>Upload to unstable
</pre>
</li>
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<h4 style="margin-top: 10px; margin-bottom: 10px;">
30 changed files:
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<li class="file-stats">
<a href="#a2a0f2265fe4fea07d13f31356bde869bdcd56fd">
debian/patches/link_excluded_file.patch
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<li class="file-stats">
<a href="#e1981ba76cdf45cf038512bc7b6853a0a54d5007">
debian/patches/openjdk_21_syntax.patch
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<li class="file-stats">
<a href="#4592439063fda75ebb65ac4b6d0f48b1af2cdcbf">
debian/patches/paths_in_scripts.patch
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<a href="#e6b2b610a62d952a2e59514b812e2e911ceb2675">
debian/patches/put_defs_sh_out_of_path.patch
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<li class="file-stats">
<a href="#5b1ccb80482aeff6d2cfc6bf5c2aa0dad29cf03c">
<span class="new-file">
+
doc/Donor_Assignment_Computational_Cookbook.pdf
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<li class="file-stats">
<a href="#31d0ebf173b4f9927c3afeb2de3c47024bf13f34">
dropseq/build.gradle.kts
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<li class="file-stats">
<a href="#ec27dae6e852c099bfcae8de5204d286bb6f04ff">
<span class="deleted-file">
−
gradle/wrapper/gradle-wrapper.jar
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<a href="#fbe448ebfc3eb2d4e308f6b8b043666f5b57235e">
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gradle/wrapper/gradle-wrapper.properties
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<li class="file-stats">
<a href="#8e9221aabc1ae60d5762110adcd5fdc0677a9334">
src/R/packages/DropSeq.dropulation/DESCRIPTION
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<li class="file-stats">
<a href="#2422cd9a00089f97234a4e3fd674a0fc6b491071">
src/R/packages/DropSeq.dropulation/NAMESPACE
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<a href="#4d77f4bf999f2e0201525efdfa856abf33131874">
src/R/packages/DropSeq.dropulation/R/DonorAssignmentStandardAnalysis.R
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<li class="file-stats">
<a href="#5cb03078aa89fd985bfc9ebd779d8350ad4e9e65">
src/R/packages/DropSeq.dropulation/README.md
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<li class="file-stats">
<a href="#066a2f87256b6473d5fb1ea2444fe67f0d077e09">
src/R/packages/DropSeq.utilities/DESCRIPTION
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<a href="#f2e529f290260b65faa75e509e38c320ec9f372f">
src/build/make_wrapper_scripts.sh
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<a href="#a6419a6af38c87a6554d274a5de6e647aa36fb9a">
src/build/public_clp_template.sh
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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
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<a href="#9dffe16f517f0a960c306c96eb4b8550d42dfa69">
src/java/org/broadinstitute/dropseqrna/barnyard/MarkChimericReads.java
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<a href="#fd3a5e40a45d2f4b41997710d2d546c6eb0197ef">
src/java/org/broadinstitute/dropseqrna/barnyard/SelectCellsByNumTranscripts.java
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<a href="#a4a272c280e359b99c1a5afc399bc054933e7a47">
src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/FilterReadsByUMISupport.java
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<a href="#323e4cb6e661503dc739e07a38c217e186fdeb2d">
src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/GatherDigitalAlleleCounts.java
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<a href="#ddf94b485d7475537602705ff0dea2a8ea08cb35">
src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/SNPUMIBasePileupIterator.java
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<a href="#b33e0cc880dba359e2678a2d62011b00eaf2c4d8">
src/java/org/broadinstitute/dropseqrna/barnyard/digitalexpression/UMICollection.java
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<a href="#87ec433d730cff385cb0b0b1da655e142836d56c">
src/java/org/broadinstitute/dropseqrna/beadsynthesis/BiasedBarcodeCollectionFactory.java
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<a href="#73e4d6046b50eed4805f1001a819ef753806bb34">
src/java/org/broadinstitute/dropseqrna/beadsynthesis/CorrectAndSplitScrnaReadPairs.java
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<a href="#845b0d7c549b3f9a1ba70abaa321e2a3e548eb33">
src/java/org/broadinstitute/dropseqrna/beadsynthesis/DetectBeadSynthesisErrors.java
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<a href="#853aa628878415aefe553acef8acafbbf1aecd41">
src/java/org/broadinstitute/dropseqrna/eqtl/CreateMetaCells.java
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The diff was not included because it is too large.
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