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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: 600;"><a href="https://salsa.debian.org/med-team/htsjdk/-/commit/386fe92fcd2e393e6042a9137b486ef4159c14c8">386fe92f</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2024-10-09T09:45:19+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "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 4.1.3+dfsg</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/htsjdk/-/commit/32e940dcd719997afa1f7b96ef1dbf69029a3228">32e940dc</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2024-10-09T09:46:05+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "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/4.1.3+dfsg'
Update to upstream version '4.1.3+dfsg'
with Debian dir d28aea167091cac9ac94e4b8fe3b70eb30a72d9a</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/htsjdk/-/commit/9eb962a3659dd479a936fa17f4ec6acab0bed807">9eb962a3</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2024-12-26T21:41:58+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "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: 600;"><a href="https://salsa.debian.org/med-team/htsjdk/-/commit/05a568a1758690ade1663662a5b871c944a77b24">05a568a1</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2024-12-26T21:42:55+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "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 libjson-java instead of mjson to replace non-free org.json
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/htsjdk/-/commit/2e64792f1ee9a7ba623fe2c313dd50d7db800345">2e64792f</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2024-12-26T21:43:10+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "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 Maven rules
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/htsjdk/-/commit/8c086fbb06de9c5145db74fa684a40a24c35a87e">8c086fbb</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2024-12-26T21:44:07+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "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;'>Removing a test file that seems to be unreadable
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/htsjdk/-/commit/095c99996f2cb0d9213785dbb57cfe958270142b">095c9999</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2024-12-26T21:45:27+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "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;'>Changing date format in patch 10
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/htsjdk/-/commit/4d9a71929cea186e4e08ea43855afa6dd3d46fff">4d9a7192</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2024-12-26T21:48:42+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "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;'>Removing old mjson patch from d/p/series
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/htsjdk/-/commit/3bac8806a558dfd4432cb8e8ffe2859672fe75fb">3bac8806</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2024-12-26T21:56:40+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "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;'>Polishing header of patch 171
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/htsjdk/-/commit/2f542a56b5d96994ff53e8535ad8c60af55131b3">2f542a56</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2024-12-26T21:56:52+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "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: 600;"><a href="https://salsa.debian.org/med-team/htsjdk/-/commit/086d201474f121455dd9b17ac2172df2df8cc10b">086d2014</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2024-12-26T23:44:52+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "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;'>Cleaning test file only if it is at the root currently
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/htsjdk/-/commit/4a58db4251b844adac96f61ee2c8dd6d2767318d">4a58db42</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2024-12-26T23:45:04+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "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="#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="#58530b38acb0fa3a65612c676abaea46c4a3f2f3">
debian/maven.rules
</a>
</li>
<li class="file-stats">
<a href="#e186644cad34bbb8e38eb75706855e6cd177ad48">
debian/patches/10-build.xml.patch
</a>
</li>
<li class="file-stats">
<a href="#eacc88751a9dfebcbf60538e262fa864e473a2b8">
debian/patches/100-fix-java11
</a>
</li>
<li class="file-stats">
<a href="#5daf38df6227a383ec0f82723188a8e8d4592172">
debian/patches/150-use-rhino-as-JS-engine.patch
</a>
</li>
<li class="file-stats">
<a href="#0f43f601e2a1dabd2e90f15081f4f0ff617249aa">
<span class="deleted-file">
−
debian/patches/170-use-mjson.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#fb253f2715f90a1647e05f8031c2f09ddc541c40">
<span class="new-file">
+
debian/patches/171-use-org-kordamp-json.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#aa3b1f1fb94ebc7611288507fdf33f239a7bbde2">
<span class="deleted-file">
−
debian/patches/180-ambiguous-assertions.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#332134ca0ea8ce03ab7b9306e9ab516ad5c70bb6">
debian/patches/20-fix-version.patch
</a>
</li>
<li class="file-stats">
<a href="#7e10b3631d1a294f02feb67ba029333d859573e3">
debian/patches/30-disable-scalatest.patch
</a>
</li>
<li class="file-stats">
<a href="#52b48dcfaeb86a97b0a2e932ab203797ce0ef59c">
debian/patches/60-enable-tests
</a>
</li>
<li class="file-stats">
<a href="#a69d7a92eb7bbb495ef85fc6c78e5166c47386b3">
debian/patches/90-disable-testftp.patch
</a>
</li>
<li class="file-stats">
<a href="#45a5d5d6fee92c99102cebc37efea96fcbbb35b8">
debian/patches/92-disable-testhttp.patch
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</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="#c1fd3ddfa5246209d0d5cf69c072e1b6767bfac0">
scripts/install-samtools.sh
</a>
</li>
<li class="file-stats">
<a href="#cfb2c495b10b95bd2908683cfcbf1506ed49459c">
src/main/java/htsjdk/beta/codecs/hapref/fasta/FASTADecoderV1_0.java
</a>
</li>
<li class="file-stats">
<a href="#9b15bf3009830362b7c62c90a03019f9f6cb8afb">
src/main/java/htsjdk/beta/codecs/reads/ReadsCodecUtils.java
</a>
</li>
<li class="file-stats">
<a href="#0b307b7be72387907daf16b5f2be3afe43a71c53">
src/main/java/htsjdk/beta/codecs/reads/bam/BAMCodec.java
</a>
</li>
<li class="file-stats">
<a href="#2b6d2d2ac2d6462a95f706d49a6b71a085533d98">
src/main/java/htsjdk/beta/codecs/reads/bam/BAMDecoder.java
</a>
</li>
<li class="file-stats">
<a href="#aaa5e300b24355fd46167868f1a94d1c5299b859">
src/main/java/htsjdk/beta/codecs/reads/bam/BAMEncoder.java
</a>
</li>
<li class="file-stats">
<a href="#862fc3ca692b773fea9bb2d73000624351a4630e">
src/main/java/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMDecoderV1_0.java
</a>
</li>
<li class="file-stats">
<a href="#0ccbe1f01fc4b8900db0c386aa3b61b246bfeb95">
src/main/java/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMEncoderV1_0.java
</a>
</li>
<li class="file-stats">
<a href="#ae2fd4dbde9e3b1363f952bd3b8c7d9d7dc6c9d0">
src/main/java/htsjdk/beta/codecs/reads/cram/CRAMCodec.java
</a>
</li>
<li class="file-stats">
<a href="#4a6a2cd3189cf02bb3e39e2b5cf1f0b4c60403f6">
src/main/java/htsjdk/beta/codecs/reads/cram/CRAMDecoder.java
</a>
</li>
<li class="file-stats">
<a href="#58442ba08783f3095d289e49e64566fef698c5c1">
src/main/java/htsjdk/beta/codecs/reads/cram/CRAMEncoder.java
</a>
</li>
</ul>
<h5 style="margin-top: 10px; margin-bottom: 10px; font-size: .875rem;">
The diff was not included because it is too large.
</h5>
</div>
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—
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