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<h3>
Pierre Gruet 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/eb31452fa590eb7b2038b6e20639c04df785030b">eb31452f</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-11-17T21:39:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Information in d/README.source is outdated
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/02c98cce9c5d11ab5b8d83cf25facadf17c5736f">02c98cce</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-11-17T21:47:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.26.5+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/afcf32d03b409a9142189b94ff1dd648c225a17f">afcf32d0</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-11-17T21:48:03+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.26.5+dfsg'
Update to upstream version '2.26.5+dfsg'
with Debian dir c0fa7746651ca432d796ca12ed769a0c80b814da</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/6380e91c93a08766d2263285a23fcdf4d034e261">6380e91c</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-11-17T21:58:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refreshing d/copyright
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/07614d9eff24e089160a55a34fbcf98c7491f13a">07614d9e</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-11-17T22:21:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refreshing patches
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/7eb3d8e3e5ec18b26d5ea48c7ee99ce9c6b2b779">7eb3d8e3</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-11-23T22:12:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Using my debian.org email address
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/4d1423c5b78decc4d4f7fde8fb0729424743561e">4d1423c5</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-11-27T20:49:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Setting properly the classpath in the .manifest file, no jar list in PicardCommandLine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/604a2394128528a3e3bdc4229c8633ac8db8cb90">604a2394</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-11-27T20:49:56+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Updating the list of dependencies
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/8ccc72ec6251b651c79c94b9df543df4eb735498">8ccc72ec</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-11-27T20:50:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Correcting a type error in a test concerning Illumina data provider
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/f53741c061d13f9edb843fb9de1daee8350b6b6c">f53741c0</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-11-27T20:50:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adding a Lintian override for the embedded javascript
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/358bbd0693f684546b9ca45447f01f7c356aa727">358bbd06</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-11-27T20:51:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adding a dependency of the doc package in libjs-jquery
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/5d7526bda3546457039150b09c3c4a7688fbd520">5d7526bd</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-11-27T20:52:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adding myself as uploader
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/749155db83bf71ea66d8f4517b614b86a2b42264">749155db</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-11-27T20:53:44+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Updating changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/ad572e7eb372b0fd9d9db9f1d4f32fe92d5663c6">ad572e7e</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-11-27T20:55:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of salsa.debian.org:med-team/picard-tools
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/35fe7b686c72df9c0e8e46f952bc58ac82a13f97">35fe7b68</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-11-27T20:58:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.26.6+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/40348821574729ddafa1ef10e159f455aa320696">40348821</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-11-27T20:59:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.26.6+dfsg'
Update to upstream version '2.26.6+dfsg'
with Debian dir 2731bb2876fde27953f739d99c3e7a75252f5ae9</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/cd4efd32d2e2ab7edf5485dfe09340f22e49f27a">cd4efd32</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-11-27T21:02:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refreshing patches
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/bd5398251c6862c101faf7c8ea45e27598551ff5">bd539825</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-11-27T21:44:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Raising Standards version to 4.6.0 (no change)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/d2aeb3b596ddbcda65d2e349fa882d09e96f7769">d2aeb3b5</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-11-27T21:47:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Updating changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/cce55ffb44014102a84715981b8bd715d55cd4a6">cce55ffb</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-12-02T22:35:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>30 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#ed7a5e9dc0e0c0bf286ef4d767cb3b64a25240a1">
<span class="new-file">
+
.github/workflows/trivy.yml
</span>
</a>
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<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
</a>
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<li class="file-stats">
<a href="#6651ddff6eb82c840ced7c1dddee15c6e1913dd4">
Dockerfile
</a>
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<li class="file-stats">
<a href="#79b82ce9b64a924266619555502f890dd80c83b9">
LICENSE.txt
</a>
</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
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<li class="file-stats">
<a href="#f07866736216be0ee2aba49e392191aeae700a35">
build.gradle
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<li class="file-stats">
<a href="#6909ff640be7be2de90d276c91938e5bcd21a003">
build_push_docker.sh
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<li class="file-stats">
<a href="#cf9802e192b48f765b1b5c8268d550d89c933053">
<span class="deleted-file">
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debian/README.source
</span>
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</li>
<li class="file-stats">
<a href="#4ac01070feee0f0c017d8fa6afa466b49a18888f">
debian/bin/PicardCommandLine
</a>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<a href="#5bf9ae0af81df5c9327f0f91fa03f26a42b93b37">
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debian/libpicard-java-doc.lintian-overrides
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debian/libpicard-java.classpath
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<a href="#07cf65e813f1d838319cc6f62fd4cd773646e99e">
debian/libpicard-java.manifest
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<a href="#e186644cad34bbb8e38eb75706855e6cd177ad48">
debian/patches/10-build.xml.patch
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<a href="#4851dcaa1d5c2005435e71f102230da1daac1df0">
debian/patches/20-shadowjar.patch
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<a href="#4416da23ca69dd7403c07c230b77bb0c32e0abb1">
debian/patches/30-tests-fix-dataprovider.patch
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<a href="#2112a29d6b2dc089fd18634ad82cb140e99b56c6">
debian/patches/40-tests-fix-testng.patch
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<a href="#cd0856bacc408b153d6e692efa65918b90c31069">
debian/patches/correct_dataprovider_TestDontMergeAbuttingData.patch
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debian/patches/fix_unreadabletests.patch
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scripts/travis/check_for_pull_request
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src/main/java/picard/analysis/AlignmentSummaryMetrics.java
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src/main/java/picard/analysis/AlignmentSummaryMetricsCollector.java
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<a href="#3a02115cc24686ccecd94ec7f340c5890a553d38">
src/main/java/picard/analysis/CollectAlignmentSummaryMetrics.java
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<a href="#8d7507e76526876f60daef574438762bd6f57ab0">
src/main/java/picard/analysis/CollectBaseDistributionByCycle.java
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<a href="#39018791387cf476a9ea4511dd7a82d4982e3c05">
src/main/java/picard/analysis/CollectGcBiasMetrics.java
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<a href="#a8427986ca1c000c6402307f4ef77043d503630e">
src/main/java/picard/analysis/CollectInsertSizeMetrics.java
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<a href="#5a50cf7890c2934c93d21101ade49bf5551587ea">
src/main/java/picard/analysis/CollectJumpingLibraryMetrics.java
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<a href="#c224cce9721892da1834c94773de15da5dd22df4">
src/main/java/picard/analysis/CollectOxoGMetrics.java
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<h5>The diff was not included because it is too large.</h5>
</div>
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