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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/htsjdk">Debian Med / htsjdk</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/htsjdk/commit/5a9aa2104b572f75786852a15f6f723f21a396f0">5a9aa210</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-02T10:18:04Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.18.0+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htsjdk/commit/926a3c7c0b21477ebd161d2b9b7b1fccd9c41d89">926a3c7c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-02T10:18:29Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.18.0+dfsg'
Update to upstream version '2.18.0+dfsg'
with Debian dir 9d9f71ae3629b48e8c59bd9030eed4c13d6b2f5d</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htsjdk/commit/655fc0962f0c81d17b0ed19b6716e6efe62879a7">655fc096</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-02T10:18:29Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htsjdk/commit/c54ab1306ae182cd9c23203435560ac63341a568">c54ab130</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-02T10:30:54Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refresh patches
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htsjdk/commit/d98b433135cf59e0060288b4075bfa3ed55f9d13">d98b4331</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-02T10:51:20Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add TODO
</pre>
</li>
</ul>
<h4>30 changed files:</h4>
<ul>
<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="#eacc88751a9dfebcbf60538e262fa864e473a2b8">
debian/patches/100-fix-java11
</a>
</li>
<li class="file-stats">
<a href="#7f1911728fcb942b06eae783e11a5c11d91de2b6">
debian/patches/13-skip_network_tests
</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="#0e145a9888f04e5bcc1b32e5ba78679670498477">
debian/patches/40-fix-java9
</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="#3524a28c3a83250c95bbe1f9b5d0f7ba6510ca75">
src/main/java/htsjdk/samtools/AbstractSAMHeaderRecord.java
</a>
</li>
<li class="file-stats">
<a href="#993dacb3974ba8ae9df67faf7d12d33647fdb7d3">
src/main/java/htsjdk/samtools/BAMRecord.java
</a>
</li>
<li class="file-stats">
<a href="#cdef170568e651ffa7f71ffc2c681e1c9c913ee3">
src/main/java/htsjdk/samtools/CRAMIterator.java
</a>
</li>
<li class="file-stats">
<a href="#6e1a414bfc1c28b89138df50d419a663a12eb889">
<span class="deleted-file">
−
src/main/java/htsjdk/samtools/FixBAMFile.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#08635c297835f435d053c63e57fc24beef173856">
src/main/java/htsjdk/samtools/LinearIndex.java
</a>
</li>
<li class="file-stats">
<a href="#e96cfaf2afff7c5cbbed08310b317936bb42eb77">
src/main/java/htsjdk/samtools/SAMBinaryTagAndUnsignedArrayValue.java
</a>
</li>
<li class="file-stats">
<a href="#7c4164c40fb89ec9c0643b8dd378c1cf0957f5d1">
src/main/java/htsjdk/samtools/SAMBinaryTagAndValue.java
</a>
</li>
<li class="file-stats">
<a href="#93ff58778463905bd2b8bc30bb18a26b9c8adcbb">
src/main/java/htsjdk/samtools/SAMFileHeader.java
</a>
</li>
<li class="file-stats">
<a href="#e6cdc1abc0fa0f0287c09c4cf048f8deee507291">
src/main/java/htsjdk/samtools/SAMFileWriterImpl.java
</a>
</li>
<li class="file-stats">
<a href="#1e54404fdd8d643007fad6688662c2c4f0d4e93b">
src/main/java/htsjdk/samtools/SAMLineParser.java
</a>
</li>
<li class="file-stats">
<a href="#b9092567a6b258b395f6b5e3d1a66b3a0db66272">
src/main/java/htsjdk/samtools/SAMRecord.java
</a>
</li>
<li class="file-stats">
<a href="#8a44f49ee7d97ebcc7900c487672a832950d4de5">
src/main/java/htsjdk/samtools/SAMRecordSetBuilder.java
</a>
</li>
<li class="file-stats">
<a href="#8028318b55c23d368ca013b2b9d38fd4a006013a">
src/main/java/htsjdk/samtools/SAMSequenceDictionary.java
</a>
</li>
<li class="file-stats">
<a href="#274cc5830fbf0d43cde49c2b3c5f07e2ebca70ca">
src/main/java/htsjdk/samtools/SAMSequenceRecord.java
</a>
</li>
<li class="file-stats">
<a href="#e311202d3cb201fd1dd4c0abb4248adde79f2f81">
src/main/java/htsjdk/samtools/SAMSortOrderChecker.java
</a>
</li>
<li class="file-stats">
<a href="#c9ff1e32eeacbae344955f9c13d7f3ae806925c0">
src/main/java/htsjdk/samtools/SAMTag.java
</a>
</li>
<li class="file-stats">
<a href="#4d82de20676ba51df39d89929d1f2e1281388b05">
src/main/java/htsjdk/samtools/SAMTagUtil.java
</a>
</li>
<li class="file-stats">
<a href="#049094dbf13adf6c4bc0e63a8fcfd3076daa96f2">
src/main/java/htsjdk/samtools/SAMTextHeaderCodec.java
</a>
</li>
<li class="file-stats">
<a href="#726c2ec7c30496bab01d5f046f0ecc650a8f7a1e">
src/main/java/htsjdk/samtools/SAMTextWriter.java
</a>
</li>
<li class="file-stats">
<a href="#49b0c9d0482641d6e56ded5cabdd721e0ef22aea">
<span class="deleted-file">
−
src/main/java/htsjdk/samtools/SAMTools.java
</span>
</a>
</li>
</ul>
<h5>The diff was not included because it is too large.</h5>
</div>
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