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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/picard-tools">Debian Med / picard-tools</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/picard-tools/-/commit/0601fb2b9891fdbcabec88cd48b338fdb88a805d">0601fb2b</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2024-12-05T12:35:41+01:00 </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 3.3.0+dfsg</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/8d8f93064b33564303cb3f2744045ca535e28b77">8d8f9306</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2024-12-05T12:36:16+01:00 </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/3.3.0+dfsg'
Update to upstream version '3.3.0+dfsg'
with Debian dir dae19386c50aae90706cc1d86f2e992413997f29</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/207253ab0594b070da13d276669820e6bb87d1b5">207253ab</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2024-12-05T12:36:56+01:00 </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;'>Raising Standards version to 4.7.0, no change
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/23bc363a40c5c543f7bc8db04591a69cff28e04d">23bc363a</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2024-12-05T12:38:46+01:00 </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 dates in d/copyright
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/e83113cc474cc7df59263fde176054b530660b72">e83113cc</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2024-12-26T21:47:55+01:00 </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 the list of build-dependencies
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/80dd9b79acbc2dfd398077cc88c2e9c8a9b6c77a">80dd9b79</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2024-12-26T22:00:49+01:00 </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/picard-tools/-/commit/74ce0b450551116e628191be9de90c02be2b2efc">74ce0b45</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2024-12-26T22:05:58+01:00 </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;'>Fixing test accuracy issue
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/b10872f52f79a76d46922aea30c400a7893ca91d">b10872f5</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2024-12-26T22:06:24+01:00 </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;'>Patching out code related to Google cloud services
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/d5010dbdf263de25fc439bfff6b3a7e89e0e3f54">d5010dbd</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2024-12-26T22:07:35+01:00 </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/picard-tools/-/commit/e589e5ba0a6efc817aa6e9d3351ea8ff95ddda9b">e589e5ba</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2024-12-26T22:14:09+01:00 </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>
</ul>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
30 changed files:
</h4>
<ul>
<li class="file-stats">
<a href="#da79ec0a668f7046c8dcfb73c8e1670a3426c431">
.github/workflows/cloud_tests.yml
</a>
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<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
.gitignore
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<a href="#6651ddff6eb82c840ced7c1dddee15c6e1913dd4">
Dockerfile
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<a href="#f07866736216be0ee2aba49e392191aeae700a35">
build.gradle
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<a href="#6909ff640be7be2de90d276c91938e5bcd21a003">
build_push_docker.sh
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
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<li class="file-stats">
<a href="#577d10c98de0506495e06f99a24267fade0dfe9c">
debian/patches/10-build.patch
</a>
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<li class="file-stats">
<a href="#4851dcaa1d5c2005435e71f102230da1daac1df0">
debian/patches/20-shadowjar.patch
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<a href="#2112a29d6b2dc089fd18634ad82cb140e99b56c6">
debian/patches/40-tests-fix-testng.patch
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<a href="#267b223587f808a65b35e2693e029c59fb4476cf">
<span class="deleted-file">
−
debian/patches/60-tests-exclude-network.patch
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<a href="#5f0c7ec1c36479f44cc0dc154b0c940f52fe9467">
debian/patches/com_sun_javadoc_removal_in_openjdk17.patch
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<li class="file-stats">
<a href="#cd0856bacc408b153d6e692efa65918b90c31069">
debian/patches/correct_dataprovider_TestDontMergeAbuttingData.patch
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<li class="file-stats">
<a href="#2338e60d4382624824f4ac493301417b621e0a9d">
debian/patches/fix_unreadabletests.patch
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<a href="#e56a62236fb9214df6dc57c88905f4cf21035bf2">
debian/patches/omit_BamToBfq.patch
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<a href="#a19ab181f42f2952911fb425a841f9a77adf945f">
debian/patches/remove_google_nio.patch
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<a href="#ead65e9902f936eb91826241ba2bc58332f60f0e">
<span class="new-file">
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debian/patches/test_accuracy.patch
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<li class="file-stats">
<a href="#fbe448ebfc3eb2d4e308f6b8b043666f5b57235e">
gradle/wrapper/gradle-wrapper.properties
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<a href="#5bbfa66edb4db3c7c33c5181f43510990d3307f9">
gradlew
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<a href="#b2834490f63ed514ea04878a07bfeb9a3745de6c">
src/main/java/picard/analysis/CollectQualityYieldMetrics.java
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src/main/java/picard/analysis/CollectQualityYieldMetricsFlow.java
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src/main/java/picard/analysis/CollectQualityYieldMetricsSNVQ.java
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src/main/java/picard/analysis/directed/PanelMetricsBase.java
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<a href="#7dc078e8a631cb6833fea5fe97f4d605fadaef7f">
src/main/java/picard/analysis/directed/TargetMetricsCollector.java
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<a href="#1fa2570ced8b3c33e4b3bd1f563ab3786ec64e29">
src/main/java/picard/cmdline/CommandLineProgram.java
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src/main/java/picard/cmdline/StandardOptionDefinitions.java
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src/main/java/picard/cmdline/argumentcollections/OptionalReferenceArgumentCollection.java
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<a href="#64b06edd6c9e122bd332f42f569ea625fcb0c8e2">
src/main/java/picard/cmdline/argumentcollections/ReferenceArgumentCollection.java
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<h5 style="margin-top: 10px; margin-bottom: 10px; font-size: .875rem;">
The diff was not included because it is too large.
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