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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/e0310ee7a46a2b404eb25ab8b859b4fd64758a5c">e0310ee7</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-06-13T22:25:49+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 3.0.5+dfsg</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/htsjdk/-/commit/52fec29243aab2b2004e3b31e554401a842b6ffa">52fec292</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-06-13T22:26:35+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/3.0.5+dfsg'
Update to upstream version '3.0.5+dfsg'
with Debian dir 58426d7777d6b4d15c639d7e64eeac553979d751</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/htsjdk/-/commit/8bd01c597c7c32d65f2a82ab0de0e9af96bdd50c">8bd01c59</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-06-13T23:46:51+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;'>Refreshing patches, grouping some of them
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/htsjdk/-/commit/c3a8d6989f2f421b35846017e95eae6c537bae7d">c3a8d698</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-06-13T23:47:22+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;'>Refreshing patches
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/htsjdk/-/commit/78623283149b01b10a1c833a43e892a0be0d2559">78623283</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-06-14T23:45:10+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;'>Skipping more tests needing the network
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/htsjdk/-/commit/db0cbd429b834528ce931f09fd0bc4e84f96a85f">db0cbd42</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-06-14T23:45:36+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/htsjdk/-/commit/1a276af47f19c0746d67e7c29fe27187a5f50171">1a276af4</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-06-20T14:46:20+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:
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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="#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="#1e654adf99a8c857b5731b0e3de199d955a3d7ca">
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debian/patches/110-debian-lib-version.patch
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<a href="#b4e355e83bca00202a902361a030a5e71f4c49ce">
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debian/patches/120-fix-build.patch
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<li class="file-stats">
<a href="#7f1911728fcb942b06eae783e11a5c11d91de2b6">
debian/patches/13-skip_network_tests
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<li class="file-stats">
<a href="#5daf38df6227a383ec0f82723188a8e8d4592172">
debian/patches/150-use-rhino-as-JS-engine.patch
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<li class="file-stats">
<a href="#332134ca0ea8ce03ab7b9306e9ab516ad5c70bb6">
debian/patches/20-fix-version.patch
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<li class="file-stats">
<a href="#7e10b3631d1a294f02feb67ba029333d859573e3">
debian/patches/30-disable-scalatest.patch
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<a href="#0e145a9888f04e5bcc1b32e5ba78679670498477">
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debian/patches/40-fix-java9
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<li class="file-stats">
<a href="#52b48dcfaeb86a97b0a2e932ab203797ce0ef59c">
debian/patches/60-enable-tests
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<li class="file-stats">
<a href="#1829ef4ce68fdf0343d52cba28050f16f50ac5d0">
debian/patches/70-removesometests-testng.patch
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<li class="file-stats">
<a href="#a69d7a92eb7bbb495ef85fc6c78e5166c47386b3">
debian/patches/90-disable-testftp.patch
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<a href="#45a5d5d6fee92c99102cebc37efea96fcbbb35b8">
debian/patches/92-disable-testhttp.patch
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debian/patches/disable-network-tests.diff
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#025493272b19a1b07b82496d32512c2235facc82">
gradle/spotbugs-exclude.xml
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<a href="#fbe448ebfc3eb2d4e308f6b8b043666f5b57235e">
gradle/wrapper/gradle-wrapper.properties
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<a href="#5bbfa66edb4db3c7c33c5181f43510990d3307f9">
gradlew
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scripts/checkScalaAndJavaFiles.sh
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<a href="#452733ba72791377698e3050bf3e011a31a3e572">
src/main/java/htsjdk/samtools/Cigar.java
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<a href="#f42ce2ab14a06d901049af2d71a3de7f4dfe6a1e">
src/main/java/htsjdk/samtools/cram/structure/CRAMRecordReadFeatures.java
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<a href="#84be1d470f0acfae9aa444a2fa8d39a1b5b3a001">
src/main/java/htsjdk/variant/vcf/VCFEncoder.java
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<a href="#b078c10e0361435a18c0c0c717d92a613a21e4dd">
src/test/java/htsjdk/HtsjdkTest.java
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<li class="file-stats">
<a href="#ec60297a4cd6ef87ea0587b8f46c752670429fbc">
src/test/java/htsjdk/samtools/CRAMReferencelessTest.java
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<li class="file-stats">
<a href="#481d56cee0ef733934004046b2857944b748f03c">
src/test/java/htsjdk/samtools/CigarTest.java
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<a href="#2d491efa8deb3082426ebaa63b81853d62106a80">
src/test/java/htsjdk/samtools/cram/structure/CRAMRecordTestHelper.java
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<li class="file-stats">
<a href="#294dbcb6fe6bd69cb228c970e4e5d5a5a47502f1">
src/test/java/htsjdk/variant/vcf/VCFEncoderTest.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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