<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN" "http://www.w3.org/TR/REC-html40/loose.dtd">
<html lang="en" style='--code-editor-font: var(--default-mono-font, "Menlo"), DejaVu Sans Mono, Liberation Mono, Consolas, Ubuntu Mono, Courier New, andale mono, lucida console, monospace;'>
<head>
<meta content="text/html; charset=US-ASCII" http-equiv="Content-Type">
<title>
GitLab
</title>
<style data-premailer="ignore" type="text/css">
a { color: #1068bf; }
</style>
<style>img {
max-width: 100%; height: auto;
}
body {
font-size: 0.875rem;
}
body {
-webkit-text-shadow: rgba(255,255,255,0.01) 0 0 1px;
}
body {
font-family: var(--default-regular-font, -apple-system),BlinkMacSystemFont,"Segoe UI",Roboto,"Noto Sans",Ubuntu,Cantarell,"Helvetica Neue",sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol","Noto Color Emoji"; font-size: inherit;
}
</style>
</head>
<body style='font-size: inherit; -webkit-text-shadow: rgba(255,255,255,0.01) 0 0 1px; font-family: var(--default-regular-font, -apple-system),BlinkMacSystemFont,"Segoe UI",Roboto,"Noto Sans",Ubuntu,Cantarell,"Helvetica Neue",sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol","Noto Color Emoji";'>
<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: bold;"><a href="https://salsa.debian.org/med-team/drop-seq/-/commit/2a523755bb341419b7c9aa10ac106367bbfa719c">2a523755</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-08-14T15:38:55+02:00 </i>
</div>
<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;'>Fixing the clean target
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/drop-seq/-/commit/fe62a626a0e1bdddf5fd0d94bb8d90442510fdb3">fe62a626</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-08-21T15:01:36+02:00 </i>
</div>
<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>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/drop-seq/-/commit/85691564a98169e2f7ac6190f8b8840444d25b99">85691564</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-08-21T15:03:20+02:00 </i>
</div>
<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;'>Update upstream source from tag 'upstream/2.5.4+dfsg'
Update to upstream version '2.5.4+dfsg'
with Debian dir 26f739889d94cb5625ac2daccb9e441cf248a43d</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/drop-seq/-/commit/94574002b1d861a3c07a634d39a8e3f29fab61f5">94574002</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-08-21T15:05:34+02:00 </i>
</div>
<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;'>Refreshing copyright years in d/copyright
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/drop-seq/-/commit/f938d6efb8a4bc14d5811adc1837c2de070b7796">f938d6ef</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-08-21T15:07:59+02:00 </i>
</div>
<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;'>Updating changelog
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/drop-seq/-/commit/0fe09beff8b9249df11b37b45189a0229aa99048">0fe09bef</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-08-21T16:19:35+02:00 </i>
</div>
<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;'>Upload to unstable
</pre>
</li>
</ul>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
30 changed files:
</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#126e844ff98b3c8e9ce07e5602abeea640905d7e">
public.iml
</a>
</li>
<li class="file-stats">
<a href="#e417d87785a703d5c8bb1cc5e82cddfae8efe265">
src/ant/defs.xml
</a>
</li>
<li class="file-stats">
<a href="#bf66897dbc44295e35876f589c838511ac83323b">
src/java/org/broadinstitute/dropseqrna/annotation/GTFReader.java
</a>
</li>
<li class="file-stats">
<a href="#fe1030726e5488d620ac0704e82f64e568a5bbaf">
src/java/org/broadinstitute/dropseqrna/annotation/GeneFromGTFBuilder.java
</a>
</li>
<li class="file-stats">
<a href="#3dfd83b9458dbd8e0506d390375ab0d1d27c99f1">
src/java/org/broadinstitute/dropseqrna/annotation/ReduceGtf.java
</a>
</li>
<li class="file-stats">
<a href="#a833f2b2e4bd626dbe653dd371caa5fc369aaec9">
src/java/org/broadinstitute/dropseqrna/annotation/ValidateReference.java
</a>
</li>
<li class="file-stats">
<a href="#0c6697ef52f14a2739123f0abddc573b0efce8bb">
src/java/org/broadinstitute/dropseqrna/barnyard/SingleCellRnaSeqMetricsCollector.java
</a>
</li>
<li class="file-stats">
<a href="#2cacdf5556986fdd1deb52e389f918827870f5e7">
src/java/org/broadinstitute/dropseqrna/barnyard/Utils.java
</a>
</li>
<li class="file-stats">
<a href="#323e4cb6e661503dc739e07a38c217e186fdeb2d">
src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/GatherDigitalAlleleCounts.java
</a>
</li>
<li class="file-stats">
<a href="#b39c23214908b9c503de5a341b56523b626eb888">
src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/SNPInfoCollection.java
</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="#e4d286490f1b4fbe90d750b11e879f575f854f04">
<span class="new-file">
+
src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/SNPUMICellReadIteratorWrapper2.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#9e64c2ba6f7c42d523a96f90dc144a508aa53475">
src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/sampleassignment/AssignCellsToSamples.java
</a>
</li>
<li class="file-stats">
<a href="#5ddf06ae30fb661ffc073a876c1f7662670682a3">
src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/sampleassignment/SampleGenotypeProbabilitiesIterator.java
</a>
</li>
<li class="file-stats">
<a href="#cf5480c44d646871ad1317e1b8e5a4084b56709c">
src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/sampleassignment/multisample/DetectDoublets.java
</a>
</li>
<li class="file-stats">
<a href="#963217dd39daf893efc04d2e48309724199707c9">
src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/sampleassignment/multisample/GenotypeMatrix.java
</a>
</li>
<li class="file-stats">
<a href="#221955d047c7b4dfe987e824aa220d038fe6b446">
src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/sampleassignment/multisample/VariantDataFactory.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="#f6df8aeb62de4bb45e27608148a1a20db9afa6b1">
src/java/org/broadinstitute/dropseqrna/censusseq/CensusSeqUtils.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="#d014845c4e9252926dc8bf0c851c6ff623e01a38">
src/java/org/broadinstitute/dropseqrna/censusseq/RollCall.java
</a>
</li>
<li class="file-stats">
<a href="#ef1812ea91d0420f8818e9183cc07953f6f44604">
src/java/org/broadinstitute/dropseqrna/censusseq/SNPGenomicBasePileupIterator.java
</a>
</li>
<li class="file-stats">
<a href="#92fdc6c6e1d272ed216e58b0779263469147425e">
src/java/org/broadinstitute/dropseqrna/metrics/BamTagHistogram.java
</a>
</li>
<li class="file-stats">
<a href="#f7662e60a22e69bc9ee1d71e2839d54c83770ea2">
src/java/org/broadinstitute/dropseqrna/metrics/CountUnmatchedSampleIndices.java
</a>
</li>
<li class="file-stats">
<a href="#b2d30789e67cbdf3b5cb445f8e02205b521181c9">
<span class="new-file">
+
src/java/org/broadinstitute/dropseqrna/metrics/MetricsUtil.java
</span>
</a>
</li>
</ul>
<h5 style="margin-top: 10px; margin-bottom: 10px; font-size: 0.875rem;">
The diff was not included because it is too large.
</h5>
</div>
<div class="footer" style="margin-top: 10px;">
<p style="font-size: small; color: #737278;">
—
<br>
<a href="https://salsa.debian.org/med-team/drop-seq/-/compare/8887ed0e7c42eded3e10cd109c76d320c8434fc8...0fe09beff8b9249df11b37b45189a0229aa99048">View it on GitLab</a>.
<br>
You're receiving this email because of your account on <a target="_blank" rel="noopener noreferrer" href="https://salsa.debian.org">salsa.debian.org</a>. <a href="https://salsa.debian.org/-/profile/notifications" target="_blank" rel="noopener noreferrer" class="mng-notif-link">Manage all notifications</a> · <a href="https://salsa.debian.org/help" target="_blank" rel="noopener noreferrer" class="help-link">Help</a>
</p>
</div>
</body>
</html>