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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/picard-tools">Debian Med / picard-tools</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/42c77037950c92ea8c5cdd33d258df14415220b2">42c77037</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-08-27T17:05:54+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/beb54d3cf2a3541c5990e91f76b251f5545b72fc">beb54d3c</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-08-27T17:06:02+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.23.3+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/51530a868e11adeef64194c64924c45faaa9aab5">51530a86</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-08-27T17:07:27+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.23.3+dfsg'
Update to upstream version '2.23.3+dfsg'
with Debian dir 84a4a3e4035253c12dc713d2546e05437d626ddf</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/df7f0fabae93c816739e9183265b15feb016847f">df7f0fab</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-08-27T17:07:28+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.5.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/f42825941238936e34ae8b83a8e2139cec5e5591">f4282594</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-08-27T17:07:30+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 13
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/8f809bf9cfe1160a106c496739bd55b891d23828">8f809bf9</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-08-27T17:11:08+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refresh patches
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/3194c16e64e51ad24d13fa954ff687a0e38aa5bd">3194c16e</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-08-27T17:11:34+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Remove trailing whitespace in debian/changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/4bd0b94ce9b0cd665979c60c6535303cd6dc3d21">4bd0b94c</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-08-27T17:11:35+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Add salsa-ci file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/df9591cf53337bb35d9e8bd4c0f615e10c3b1ac3">df9591cf</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-08-27T17:11:36+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Rules-Requires-Root: no
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/0872901c38523d6a3aedb9813563874ad03dc0d1">0872901c</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-08-27T17:11:39+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Trim trailing whitespace.
Changes-By: lintian-brush
Fixes: lintian: trailing-whitespace
See-also: https://lintian.debian.org/tags/trailing-whitespace.html
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/d339c2a82aeaf7a857a8b77acdddbbbf3dbe224d">d339c2a8</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-08-27T17:11:46+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.
Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html
</pre>
</li>
</ul>
<h4>30 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
</li>
<li class="file-stats">
<a href="#f07866736216be0ee2aba49e392191aeae700a35">
build.gradle
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<span class="deleted-file">
−
debian/compat
</span>
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#e186644cad34bbb8e38eb75706855e6cd177ad48">
debian/patches/10-build.xml.patch
</a>
</li>
<li class="file-stats">
<a href="#4851dcaa1d5c2005435e71f102230da1daac1df0">
debian/patches/20-shadowjar.patch
</a>
</li>
<li class="file-stats">
<a href="#4416da23ca69dd7403c07c230b77bb0c32e0abb1">
debian/patches/30-tests-fix-dataprovider.patch
</a>
</li>
<li class="file-stats">
<a href="#2112a29d6b2dc089fd18634ad82cb140e99b56c6">
debian/patches/40-tests-fix-testng.patch
</a>
</li>
<li class="file-stats">
<a href="#a19ab181f42f2952911fb425a841f9a77adf945f">
debian/patches/remove_google_nio.patch
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#b1dbf22e88351ec0d5d1d1a7f53295504b480e61">
<span class="new-file">
+
debian/salsa-ci.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
</a>
</li>
<li class="file-stats">
<a href="#2269f0b41b877093e5ef84c96198be511137ddbc">
src/main/java/picard/analysis/CollectMultipleMetrics.java
</a>
</li>
<li class="file-stats">
<a href="#aeb3cb9c88748b54a0beea66707d8c4b0507be57">
src/main/java/picard/arrays/ArraysCallingMetricAccumulator.java
</a>
</li>
<li class="file-stats">
<a href="#cf132dbe9e717d8c260a4178d5b64adf408c06cc">
src/main/java/picard/arrays/CollectArraysVariantCallingMetrics.java
</a>
</li>
<li class="file-stats">
<a href="#df4dc620efcebfaf5b5242aaf6701781c854f842">
src/main/java/picard/arrays/CombineGenotypingArrayVcfs.java
</a>
</li>
<li class="file-stats">
<a href="#f91c189fd4550d2b3a19984cf8214fc36e993efb">
src/main/java/picard/arrays/GtcToVcf.java
</a>
</li>
<li class="file-stats">
<a href="#d71a309d7e87d38051648d80540afcffb9dff561">
<span class="new-file">
+
src/main/java/picard/arrays/illumina/BpmToNormalizationManifestCsv.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#14bf942877365386019fca7216d550be88788d09">
src/main/java/picard/arrays/illumina/CompareGtcFiles.java
</a>
</li>
<li class="file-stats">
<a href="#a96221eeb7972c91f16503644debfa6080aa98e9">
<span class="new-file">
+
src/main/java/picard/arrays/illumina/IlluminaBPMFile.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#2153898b667a816a34fd89fa93fa2047d3b85547">
<span class="new-file">
+
src/main/java/picard/arrays/illumina/IlluminaBPMLocusEntry.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#5cc86ec2adb7e484276793b9e78d120178ebdc9b">
src/main/java/picard/arrays/illumina/InfiniumDataFile.java
</a>
</li>
<li class="file-stats">
<a href="#63b8e622485f24ca7d415bd6b664d8945f37f285">
src/main/java/picard/arrays/illumina/InfiniumEGTFile.java
</a>
</li>
<li class="file-stats">
<a href="#ba0b62634fb0a7a59ef3fd636dc30c32065b15a7">
src/main/java/picard/arrays/illumina/InfiniumGTCFile.java
</a>
</li>
<li class="file-stats">
<a href="#b9b651583fcedc46139b545c2a6e6885e7f47f80">
src/main/java/picard/arrays/illumina/InfiniumVcfFields.java
</a>
</li>
<li class="file-stats">
<a href="#1fa2570ced8b3c33e4b3bd1f563ab3786ec64e29">
src/main/java/picard/cmdline/CommandLineProgram.java
</a>
</li>
<li class="file-stats">
<a href="#86ac663cd55856855f703ea436ae922385440eff">
<span class="new-file">
+
src/main/java/picard/fingerprint/CappedHaplotypeProbabilities.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#f7d76d352dfb807611c35d4412191ed995aa7003">
src/main/java/picard/fingerprint/CrosscheckFingerprints.java
</a>
</li>
<li class="file-stats">
<a href="#c3522ad5b834cc5c5ba705bd1f56a4c19c5c6348">
<span class="new-file">
+
src/main/java/picard/fingerprint/ExtractFingerprint.java
</span>
</a>
</li>
</ul>
<h5>The diff was not included because it is too large.</h5>
</div>
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