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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" style="color: #1068bf;">Debian Med / picard-tools</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/picard-tools/-/commit/db6080a47b7eb71f9bac078e26078be39ffdd29c" style="color: #1068bf;">db6080a4</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-09-21T15:07:28+02:00</i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "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: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>Updating d/watch after a change in the Github layout
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/f17ae3a5adf9516c80a4e5d57455fa80fe172c0f" style="color: #1068bf;">f17ae3a5</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-09-22T16:29:27+02:00</i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "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: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>New upstream version 2.27.4+dfsg</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/2ba244dd670ce58ef5ccb4256deb13975ed6d118" style="color: #1068bf;">2ba244dd</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-09-22T16:30:40+02:00</i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "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: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>Update upstream source from tag 'upstream/2.27.4+dfsg'
Update to upstream version '2.27.4+dfsg'
with Debian dir 2192af7cc5e657c4beb6b8f2ba7ce29c3a7ebe95</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/4118172d81562f1b50135d182c918586c9fcbed0" style="color: #1068bf;">4118172d</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-09-22T16:32:19+02:00</i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "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: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>Refreshing patches
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/08a3c99abe3358c914d27dff582bc392ecaf7b18" style="color: #1068bf;">08a3c99a</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-09-22T16:33:15+02:00</i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "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: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>Updating changelog
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/947631774df78f1cfe5936deb2d34bca51b8fdd7" style="color: #1068bf;">94763177</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-09-22T17:22:15+02:00</i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "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: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>Refreshing the Lintian override for embedded JS
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/0d58d801b9ac66f55fadbbebe17c9b463b4ea05a" style="color: #1068bf;">0d58d801</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-09-22T20:26:07+02:00</i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "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: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>Upload to unstable
</pre>
</li>
</ul>
<h4 style="margin-top: 10px; margin-bottom: 10px;">30 changed files:</h4>
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<a href="#a5cc2925ca8258af241be7e5b0381edf30266302" style="color: #1068bf;">
.gitignore
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<a href="#f07866736216be0ee2aba49e392191aeae700a35" style="color: #1068bf;">
build.gradle
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1" style="color: #1068bf;">
debian/changelog
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<a href="#5bf9ae0af81df5c9327f0f91fa03f26a42b93b37" style="color: #1068bf;">
debian/libpicard-java-doc.lintian-overrides
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<a href="#e186644cad34bbb8e38eb75706855e6cd177ad48" style="color: #1068bf;">
debian/patches/10-build.xml.patch
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<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79" style="color: #1068bf;">
debian/watch
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<a href="#bac4c9ac8d5063b8b48c84e1a30915ee1d4b4523" style="color: #1068bf;">
src/main/java/picard/analysis/AlignmentSummaryMetrics.java
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<a href="#39ad2a42470243aa1402488d16e8309995fc1180" style="color: #1068bf;">
src/main/java/picard/analysis/AlignmentSummaryMetricsCollector.java
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<a href="#b2834490f63ed514ea04878a07bfeb9a3745de6c" style="color: #1068bf;">
src/main/java/picard/analysis/CollectQualityYieldMetrics.java
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<a href="#04f554de73499a24d9a36adee63d01f42eabc54c" style="color: #1068bf;">
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src/main/java/picard/analysis/HistogramGenerator.java
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<a href="#da9ff87ef6c58326bf722021f76a9882a5eea09c" style="color: #1068bf;">
src/main/java/picard/analysis/MeanQualityByCycle.java
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<a href="#7882db8ab241e139efe87ded3c26da9c35a5cb4e" style="color: #1068bf;">
src/main/java/picard/sam/DuplicationMetrics.java
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src/main/java/picard/sam/DuplicationMetricsFactory.java
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src/main/java/picard/sam/FastqToSam.java
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src/main/java/picard/sam/FlowBasedDuplicationMetrics.java
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src/main/java/picard/sam/RevertSam.java
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<a href="#2120d65da84b4b7a5d51519d03bd830e009237d7" style="color: #1068bf;">
src/main/java/picard/sam/markduplicates/CollectDuplicateMetrics.java
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<a href="#61a4238b24579fdfac2bacdffc5bc57b36b76d92" style="color: #1068bf;">
src/main/java/picard/sam/markduplicates/EstimateLibraryComplexity.java
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src/main/java/picard/sam/markduplicates/MarkDuplicates.java
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src/main/java/picard/sam/markduplicates/MarkDuplicatesForFlowArgumentCollection.java
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src/main/java/picard/sam/markduplicates/MarkDuplicatesForFlowHelper.java
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src/main/java/picard/sam/markduplicates/MarkDuplicatesHelper.java
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src/main/java/picard/sam/markduplicates/MarkDuplicatesWithMateCigarIterator.java
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<a href="#8ad686c82529eba8ecafc5adb5e9abf298d598cc" style="color: #1068bf;">
src/main/java/picard/sam/markduplicates/SimpleMarkDuplicatesWithMateCigar.java
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src/main/java/picard/sam/markduplicates/util/AbstractMarkDuplicatesCommandLineProgram.java
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<a href="#cf498877f67ccdc131c3b4a9aaa43351b05b4275" style="color: #1068bf;">
src/main/java/picard/sam/markduplicates/util/LibraryIdGenerator.java
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<a href="#0a053fb38482a12b21fb9d58286462f0ab7fc52a" style="color: #1068bf;">
src/main/java/picard/sam/markduplicates/util/ReadEnds.java
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src/main/java/picard/sam/markduplicates/util/ReadEndsForMarkDuplicates.java
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src/main/java/picard/util/AccumulateQualityYieldMetrics.java
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src/main/java/picard/vcf/GenotypeConcordance.java
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<h5 style="margin-top: 10px; margin-bottom: 10px; font-size: 0.875rem;">The diff was not included because it is too large.</h5>
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