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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/5c5e2f76d0fb254e387d16fffcbb898dce45badb">5c5e2f76</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-17T14:00:42Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.16.1+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htsjdk/commit/0b5eb2a62e4ae892e16d7b84f33fe7bffe9a6bb9">0b5eb2a6</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-17T14:01:03Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.16.1+dfsg'
Update to upstream version '2.16.1+dfsg'
with Debian dir 927de226c94872f2efbb8b294ffb6da754089b77</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htsjdk/commit/4cf4fba0ac3a22ac699a049d1483c6107ab39cf9">4cf4fba0</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-17T14:01:03Z</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/ab2abc916f411c2dfc5db1d523482013e3910f65">ab2abc91</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-17T14:01:03Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper 11
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htsjdk/commit/102a32b3ece6670dccd191c5e3debb9857e2c3d2">102a32b3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-17T14:01:07Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.2.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htsjdk/commit/f0bb4b0ecfb581cb58c2a3fba28e8347f77617d0">f0bb4b0e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-17T14:19:03Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refresh patches
</pre>
</li>
</ul>
<h4>30 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
</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="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
debian/compat
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#e186644cad34bbb8e38eb75706855e6cd177ad48">
debian/patches/10-build.xml.patch
</a>
</li>
<li class="file-stats">
<a href="#7f1911728fcb942b06eae783e11a5c11d91de2b6">
debian/patches/13-skip_network_tests
</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="#fbe448ebfc3eb2d4e308f6b8b043666f5b57235e">
gradle/wrapper/gradle-wrapper.properties
</a>
</li>
<li class="file-stats">
<a href="#5bbfa66edb4db3c7c33c5181f43510990d3307f9">
gradlew
</a>
</li>
<li class="file-stats">
<a href="#52776e045edefe05ccd5daccebac565b6665bab9">
src/main/java/htsjdk/samtools/BAMFileWriter.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="#61dad633b446e3eb67d2cdc43e2ebc9dd4878345">
src/main/java/htsjdk/samtools/BAMRecordCodec.java
</a>
</li>
<li class="file-stats">
<a href="#80e16130a35788d7564c430d4392321991238f9d">
src/main/java/htsjdk/samtools/BamFileIoUtils.java
</a>
</li>
<li class="file-stats">
<a href="#d5f9b57588db1d4a34f0f98dc0b8ce09e84b87fb">
src/main/java/htsjdk/samtools/BinaryBAMIndexWriter.java
</a>
</li>
<li class="file-stats">
<a href="#089d4c72e361a0f8eecae22b77155e0a07b870ed">
src/main/java/htsjdk/samtools/CRAMFileReader.java
</a>
</li>
<li class="file-stats">
<a href="#2527486a516a38ab96f541be00b269701f60d232">
src/main/java/htsjdk/samtools/CRAMFileWriter.java
</a>
</li>
<li class="file-stats">
<a href="#6137a58ff7318431b5061d64c2aec4e14880fe1e">
src/main/java/htsjdk/samtools/CachingBAMFileIndex.java
</a>
</li>
<li class="file-stats">
<a href="#0cfa6bc34a953a2fd3fc7d50e0b68753c6c67373">
src/main/java/htsjdk/samtools/Defaults.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="#bd57c0919da7536e98f056e9bf8692209ba43488">
src/main/java/htsjdk/samtools/SAMFileWriterFactory.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="#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="#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="#726c2ec7c30496bab01d5f046f0ecc650a8f7a1e">
src/main/java/htsjdk/samtools/SAMTextWriter.java
</a>
</li>
<li class="file-stats">
<a href="#d4460f31fc299d131ced2a583813743b1cab9afd">
src/main/java/htsjdk/samtools/SAMUtils.java
</a>
</li>
</ul>
<h5>The diff was not included because it is too large.</h5>
</div>
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