<!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, "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, -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, -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/1c5e7dd6f007673eaa76c8e13d795332acd01ced">1c5e7dd6</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-06-20T16:15:45+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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 3.0.0+dfsg</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/f920cde4e14ea549ef225eaea734a2d36581ff16">f920cde4</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-06-20T16:16:51+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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/3.0.0+dfsg'

Update to upstream version '3.0.0+dfsg'
with Debian dir 15cec942ed23736450ea7b52aa7bebe5b14816a9</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/8a5af847874565f315a813ec951bfa971a67b434">8a5af847</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-06-20T16:41:33+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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/253eb10e0e118097bbfeaf439dc616621945171b">253eb10e</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-06-20T16:41:51+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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 4.6.2 (no change)
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/729299b44ab15851b8e31f163a471ec9d2210ef8">729299b4</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-06-20T16:42:22+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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/6d167d5261589f48dc9f70c2646498cfb8a12824">6d167d52</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-06-20T16:46:34+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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;'>Removing unnecessary versioned B-D
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/57a122af660ef6d18f042cc6c49361bafcd71b89">57a122af</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-07-04T14:10:09+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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/75684d98a116d196e838966532e7dcfb21e6f45c">75684d98</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-07-04T14:10:37+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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;'>Adding nashorn to d/maven.ignoreRules
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/4861fb753d6cd41482275479351fa62433eee45f">4861fb75</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-07-04T14:14:50+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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;'>Running the build-time tests from a directory with no '+' in its path
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/0f4ef03dbfa3617e42521d0436daebedc045f322">0f4ef03d</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-07-04T15:16:51+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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/6caa6eae0f72904a519ecb4f1ab609b12e89fcdc">6caa6eae</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-07-04T15:23:33+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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;'>Omitting the long-failing jar invocation in the build-time tests
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/393338cdd2a9ba4badf29d42229f44dea10e4e4b">393338cd</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-07-04T15:23:41+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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="#e92266778ac0ab35c5df350376a55fe504bb38b8">
.github/ISSUE_TEMPLATE.md
</a>
</li>
<li class="file-stats">
<a href="#b8baf23d7ed7f2b79b86aeb041867428fb196428">
.github/PULL_REQUEST_TEMPLATE.md
</a>
</li>
<li class="file-stats">
<a href="#6b8eb1151e11abd72b31ffb764de06790e5bda1e">
<span class="new-file">
+
.github/workflows/tests.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
<span class="deleted-file">

.travis.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#6651ddff6eb82c840ced7c1dddee15c6e1913dd4">
Dockerfile
</a>
</li>
<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="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#26121dc92cd4cd9822d2e9e2b619b799bf9a51f4">
<span class="new-file">
+
debian/maven.ignoreRules
</span>
</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="#2112a29d6b2dc089fd18634ad82cb140e99b56c6">
debian/patches/40-tests-fix-testng.patch
</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="#fc59194b64ff6e3314b8876b2d65744728f49562">
debian/patches/gradle_openjdk17_incompatibility.patch
</a>
</li>
<li class="file-stats">
<a href="#e56a62236fb9214df6dc57c88905f4cf21035bf2">
debian/patches/omit_BamToBfq.patch
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</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="#3a02115cc24686ccecd94ec7f340c5890a553d38">
src/main/java/picard/analysis/CollectAlignmentSummaryMetrics.java
</a>
</li>
<li class="file-stats">
<a href="#2269f0b41b877093e5ef84c96198be511137ddbc">
src/main/java/picard/analysis/CollectMultipleMetrics.java
</a>
</li>
<li class="file-stats">
<a href="#3886cebb61bb01eca0eabf743de7b60d86c8969e">
src/main/java/picard/analysis/CompareMetrics.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="#f91c189fd4550d2b3a19984cf8214fc36e993efb">
src/main/java/picard/arrays/GtcToVcf.java
</a>
</li>
<li class="file-stats">
<a href="#37d4abc808658a932ef049d97eff748f1ba6ffb5">
src/main/java/picard/arrays/VcfToAdpc.java
</a>
</li>
<li class="file-stats">
<a href="#65ca7381ecdc5f294bb518577dad4ccd55bebdc2">
src/main/java/picard/arrays/illumina/Build37ExtendedIlluminaManifest.java
</a>
</li>
<li class="file-stats">
<a href="#fa1b92087c9f0f1caff3fa041191e691130ff1c1">
src/main/java/picard/arrays/illumina/Build37ExtendedIlluminaManifestRecord.java
</a>
</li>
<li class="file-stats">
<a href="#b9a2854b3037c45e96911e479f3ac0fb27549398">
src/main/java/picard/arrays/illumina/Build37ExtendedIlluminaManifestRecordCreator.java
</a>
</li>
<li class="file-stats">
<a href="#17b48db1f9ff4b3588d1ef7d494b620b6cb3c72c">
src/main/java/picard/arrays/illumina/CreateExtendedIlluminaManifest.java
</a>
</li>
<li class="file-stats">
<a href="#7c6753d813e5b8a29e94a32405b4b2ab3c8a2c15">
src/main/java/picard/arrays/illumina/IlluminaManifest.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/463a37af2b5cb68db61363460c852d6346992163...393338cdd2a9ba4badf29d42229f44dea10e4e4b">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>