<!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, "GitLab Mono"), JetBrains Mono, 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, "GitLab Sans"),-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, "GitLab Sans"),-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/picard-tools">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/c1ab316e8d2d59c90e9504e26b97b563315c8daf">c1ab316e</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-12-14T13:16:36+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "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 3.1.1+dfsg</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/98e0f677503b1bb80ee85489e21e701072d3bf10">98e0f677</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-12-14T13:17:03+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "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/3.1.1+dfsg'

Update to upstream version '3.1.1+dfsg'
with Debian dir c05e4deb7ab5ed2606cbe4d8c3c01cb5d60c744a</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/515d8a2c09f2412a58384fc07837bb6ded05e14b">515d8a2c</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-12-14T21:36:49+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "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: bold;"><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/b5953e62ece967748658f33bf6f9eeda36192be2">b5953e62</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-12-16T22:37:18+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "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;'>Enabling the test with BarclayParser again
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/40fd4cc94e93420c969c36de43563b9658d6d78d">40fd4cc9</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-12-16T22:37:54+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "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 more code portions using google-nio
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/6e784b77cfd5ac70b206cd5e84b26c5f50248d11">6e784b77</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-12-16T22:38:09+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "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: bold;"><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/0b1f56789d4b5105975a745a94b01ed7dbc83e63">0b1f5678</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-12-16T22:38:28+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "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: bold;"><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/9aa2e0e10df007b08d50193739a5a7c526d17825">9aa2e0e1</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-12-16T22:38:37+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "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="#24139dae656713ba861751fb2c2ac38839349a7a">
<span class="new-file">
+
.gitattributes
</span>
</a>
</li>
<li class="file-stats">
<a href="#da79ec0a668f7046c8dcfb73c8e1670a3426c431">
<span class="new-file">
+
.github/workflows/cloud_tests.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
.gitignore
</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="#26121dc92cd4cd9822d2e9e2b619b799bf9a51f4">
debian/maven.ignoreRules
</a>
</li>
<li class="file-stats">
<a href="#577d10c98de0506495e06f99a24267fade0dfe9c">
debian/patches/10-build.xml.patch

debian/patches/10-build.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="#4c28a8ec31f904862c75ca6cdb725c2cba7bae50">
<span class="deleted-file">

debian/patches/50-tests-exclude-Barclay.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#5f0c7ec1c36479f44cc0dc154b0c940f52fe9467">
debian/patches/com_sun_javadoc_removal_in_openjdk17.patch
</a>
</li>
<li class="file-stats">
<a href="#cd0856bacc408b153d6e692efa65918b90c31069">
debian/patches/correct_dataprovider_TestDontMergeAbuttingData.patch
</a>
</li>
<li class="file-stats">
<a href="#9126f334daf6ad90527cca2c80f2dc88b472204a">
<span class="deleted-file">

debian/patches/fix_javadoc_ascii.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#2338e60d4382624824f4ac493301417b621e0a9d">
debian/patches/fix_unreadabletests.patch
</a>
</li>
<li class="file-stats">
<a href="#37bb2f3c2440cc1875044024554eb64f7c32b0d2">
debian/patches/non-intel-skip-intel-tests
</a>
</li>
<li class="file-stats">
<a href="#e56a62236fb9214df6dc57c88905f4cf21035bf2">
debian/patches/omit_BamToBfq.patch
</a>
</li>
<li class="file-stats">
<a href="#a19ab181f42f2952911fb425a841f9a77adf945f">
debian/patches/remove_google_nio.patch
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#fbe448ebfc3eb2d4e308f6b8b043666f5b57235e">
gradle/wrapper/gradle-wrapper.properties
</a>
</li>
<li class="file-stats">
<a href="#5bbfa66edb4db3c7c33c5181f43510990d3307f9">
gradlew
</a>
</li>
<li class="file-stats">
<a href="#39ad2a42470243aa1402488d16e8309995fc1180">
src/main/java/picard/analysis/AlignmentSummaryMetricsCollector.java
</a>
</li>
<li class="file-stats">
<a href="#c224cce9721892da1834c94773de15da5dd22df4">
src/main/java/picard/analysis/CollectOxoGMetrics.java
</a>
</li>
<li class="file-stats">
<a href="#ef17ffbbef833877458003eb2f12fc07610dfc1e">
src/main/java/picard/analysis/CollectWgsMetrics.java
</a>
</li>
<li class="file-stats">
<a href="#a1e25612276960b201d9078bebb48c2a3c52e3fc">
src/main/java/picard/analysis/SinglePassSamProgram.java
</a>
</li>
<li class="file-stats">
<a href="#9af105d9cdd2d7f8a89fb06cade4843d35624ea0">
src/main/java/picard/analysis/directed/CollectTargetedMetrics.java
</a>
</li>
<li class="file-stats">
<a href="#ad1f1dc5e8b9664bb405dbc8386d79b194eada83">
src/main/java/picard/analysis/replicates/CollectIndependentReplicateMetrics.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="#ca0acf17531387f8a95053d24c87c9deed09c2f7">
src/main/java/picard/cmdline/PicardCommandLine.java
</a>
</li>
<li class="file-stats">
<a href="#4b494ef67355a05286058b71311a9448ce743651">
src/main/java/picard/fingerprint/CheckFingerprint.java
</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/picard-tools/-/compare/393338cdd2a9ba4badf29d42229f44dea10e4e4b...9aa2e0e10df007b08d50193739a5a7c526d17825">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>