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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/htsjdk">Debian Med / htsjdk</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/htsjdk/-/commit/0c5275b15d2b8aad0dec0be9856d0761f1ef26f3">0c5275b1</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-12-01T11:11:26+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 4.0.2+dfsg</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/htsjdk/-/commit/7b628377976f6311cb63f28860e8339d234b5669">7b628377</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-12-01T11:12:03+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/4.0.2+dfsg'
Update to upstream version '4.0.2+dfsg'
with Debian dir ef4fac6250e82a4d46952420f42906b7ec4351ea</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/htsjdk/-/commit/b7d9fccea75d8c3e5b12c3e9b45ab05be636265d">b7d9fcce</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-12-14T09:36:30+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;'>Adding nashorn to maven.ignoreRules
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/htsjdk/-/commit/fff4e3dc0000384ef8792e73fdc076be89f25331">fff4e3dc</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-12-14T09:38:28+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;'>Using mjson instead of unpackaged, non-DFSG-free org.json
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/htsjdk/-/commit/acdd91f9b4db5f939579e3f492df887bf0027d2f">acdd91f9</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-12-14T09:44:55+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;'>Solving ambiguous assertions in the unit tests
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/htsjdk/-/commit/ebadccd8f4b3a3bb8cc26054885aaae5dc6a1725">ebadccd8</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-12-14T09:45:17+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;'>Deactivating the tests for VCF 4.4 as this version of htsjdk does not handle them
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/htsjdk/-/commit/bdc3e0cc7f9f7fc80775aaa091355334e8571010">bdc3e0cc</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-12-14T09:45:29+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/htsjdk/-/commit/404ae6531413c611c6d043e8f979455b8d466508">404ae653</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-12-14T09:46:38+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/htsjdk/-/commit/9debcd7e387bfb465db263bde05ab1b66274c5fb">9debcd7e</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-12-14T09:50:46+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;'>Forwarding patch
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/htsjdk/-/commit/fd0670323965e2d2aa97d804d388208ec3d91459">fd067032</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-12-14T10:11:09+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;'>Adding getDebianVersion definition, deleted by mistake
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/htsjdk/-/commit/00c7f6311ea8e4fa1175eafc3c73b946fbc8541e">00c7f631</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-12-14T10:11:16+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/htsjdk/-/commit/23fb7f554be415c197b50701b6ed589aa483c672">23fb7f55</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-12-14T10:11:28+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;'>Upload to unstable
</pre>
</li>
</ul>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
30 changed files:
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<li class="file-stats">
<a href="#6b8eb1151e11abd72b31ffb764de06790e5bda1e">
.github/workflows/tests.yml
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<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<a href="#f07866736216be0ee2aba49e392191aeae700a35">
build.gradle
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#26121dc92cd4cd9822d2e9e2b619b799bf9a51f4">
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debian/maven.ignoreRules
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<a href="#58530b38acb0fa3a65612c676abaea46c4a3f2f3">
debian/maven.rules
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<a href="#e186644cad34bbb8e38eb75706855e6cd177ad48">
debian/patches/10-build.xml.patch
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<li class="file-stats">
<a href="#eacc88751a9dfebcbf60538e262fa864e473a2b8">
debian/patches/100-fix-java11
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<a href="#7f1911728fcb942b06eae783e11a5c11d91de2b6">
debian/patches/13-skip_network_tests
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<a href="#5daf38df6227a383ec0f82723188a8e8d4592172">
debian/patches/150-use-rhino-as-JS-engine.patch
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<li class="file-stats">
<a href="#0f43f601e2a1dabd2e90f15081f4f0ff617249aa">
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<a href="#582b62cc9b8b6f296011421b9a0739bccd4c13e7">
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<a href="#332134ca0ea8ce03ab7b9306e9ab516ad5c70bb6">
debian/patches/20-fix-version.patch
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<a href="#7e10b3631d1a294f02feb67ba029333d859573e3">
debian/patches/30-disable-scalatest.patch
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<a href="#52b48dcfaeb86a97b0a2e932ab203797ce0ef59c">
debian/patches/60-enable-tests
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<a href="#a69d7a92eb7bbb495ef85fc6c78e5166c47386b3">
debian/patches/90-disable-testftp.patch
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debian/patches/92-disable-testhttp.patch
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debian/patches/series
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<a href="#0f4f982aa8b05c43f1b04a07a005b38194a3cef3">
src/main/java/htsjdk/beta/io/bundle/BundleJSON.java
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<a href="#80e16130a35788d7564c430d4392321991238f9d">
src/main/java/htsjdk/samtools/BamFileIoUtils.java
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src/main/java/htsjdk/samtools/Defaults.java
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<a href="#0c2a3954cf743381ce8a0e1317b6e62af6a0ed8a">
src/main/java/htsjdk/samtools/SAMReadGroupRecord.java
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<a href="#b9092567a6b258b395f6b5e3d1a66b3a0db66272">
src/main/java/htsjdk/samtools/SAMRecord.java
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src/main/java/htsjdk/samtools/SAMRecordIterator.java
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src/main/java/htsjdk/samtools/SAMRecordSetBuilder.java
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src/main/java/htsjdk/samtools/SAMUtils.java
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<a href="#dd7e7f9ef58d444c69a7e006a153fc8e4aedd2aa">
src/main/java/htsjdk/samtools/SamFileValidator.java
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<a href="#b3a96294be815da4b9dec3e1655f4a271638ffc3">
src/main/java/htsjdk/samtools/TextTagCodec.java
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<a href="#79e145fd36f7644e7c46fa6775a9d9caf2d04ff8">
src/main/java/htsjdk/samtools/cram/structure/Slice.java
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The diff was not included because it is too large.
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</div>
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