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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/26feb9cc4a546debcbd8191529e4135e210b964a">26feb9cc</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-03-28T14:18:36+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.14.3+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htsjdk/commit/0c4c86ec4d5dc8f586cb02e6578415d547f56b85">0c4c86ec</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-03-28T14:18:54+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.14.3+dfsg'
Update to upstream version '2.14.3+dfsg'
with Debian dir f3cb3f9088d070b7bd9c7562139c0c4a17af8e82</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htsjdk/commit/afe5dc32bddaa7c972f7c05d26da2bed89706ba4">afe5dc32</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-03-28T14:22:08+02:00</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/f2dd84b2489250d75b2fd3199e8948b68b35a2ff">f2dd84b2</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-03-28T14:22:17+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update pom files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htsjdk/commit/39dd500d77a8623adc6136b2d587e8e623e4103e">39dd500d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-03-28T14:22:46+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.1.3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htsjdk/commit/7e7b3488e4559f284396e6f5667522303482dc50">7e7b3488</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-03-28T14:31:01+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adapt quilt patches
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htsjdk/commit/b29ccd1bb9ebafbd966c069af0d14730e728018b">b29ccd1b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-03-28T14:33:21+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Drop warning and upload to experimental until picard-tools will catch up
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htsjdk/commit/0fa566a17784405b9a78b7fdc1a673f2fccba59b">0fa566a1</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-03-28T14:54:02+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Make sure the package will not incidentally uploaded to unstable
</pre>
</li>
</ul>
<h4>30 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
.gitignore
</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="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#c8c726c9c45ea77bb11f9d79575dda5f2770aee3">
debian/htsjdk.pom
</a>
</li>
<li class="file-stats">
<a href="#23ace2ce5518061709dd2e261fa002cac72a9cdf">
debian/htsjdk.pom.asc
</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="#52776e045edefe05ccd5daccebac565b6665bab9">
src/main/java/htsjdk/samtools/BAMFileWriter.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="#5fab15f03c9563674b7e855b486954a324f563fd">
src/main/java/htsjdk/samtools/DownsamplingIteratorFactory.java
</a>
</li>
<li class="file-stats">
<a href="#1a21ae2c7bfd3beb03c56856147ecb6094f05630">
src/main/java/htsjdk/samtools/NotPrimarySkippingIterator.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="#bd57c0919da7536e98f056e9bf8692209ba43488">
src/main/java/htsjdk/samtools/SAMFileWriterFactory.java
</a>
</li>
<li class="file-stats">
<a href="#daaaae026d12144a23e76d8027ffdf1b04171b11">
src/main/java/htsjdk/samtools/SAMFlag.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="#f84af59dfc0d4ea4f8efa3c30ab5410d6e687016">
src/main/java/htsjdk/samtools/SAMRecordQueryNameComparator.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="#a030c6b5caf0e18156662c46b4c4e3e82cbf8c16">
<span class="deleted-file">
−
src/main/java/htsjdk/samtools/SAMRecordUtil.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#d4460f31fc299d131ced2a583813743b1cab9afd">
src/main/java/htsjdk/samtools/SAMUtils.java
</a>
</li>
<li class="file-stats">
<a href="#8dcdf1341d0110669b942d8ec543f914d8afbb7e">
src/main/java/htsjdk/samtools/SAMValidationError.java
</a>
</li>
<li class="file-stats">
<a href="#dd7e7f9ef58d444c69a7e006a153fc8e4aedd2aa">
src/main/java/htsjdk/samtools/SamFileValidator.java
</a>
</li>
<li class="file-stats">
<a href="#4202fd3bc88700a352babbc5c7341058014ec051">
src/main/java/htsjdk/samtools/SamFlagField.java
</a>
</li>
<li class="file-stats">
<a href="#ae408041267fd1eeeac55a0d326f90514b4f5dcc">
src/main/java/htsjdk/samtools/SamInputResource.java
</a>
</li>
<li class="file-stats">
<a href="#8ade29bf41936dfa97ffd3ffa00afe3a2942f4fd">
src/main/java/htsjdk/samtools/SamReaderFactory.java
</a>
</li>
<li class="file-stats">
<a href="#86796c92d536a149b844c6eb32f80220022e5d07">
<span class="new-file">
+
src/main/java/htsjdk/samtools/SecondaryAlignmentSkippingIterator.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#c895bc03ca392835aa995eb0357f2344a58ba42b">
src/main/java/htsjdk/samtools/SecondaryOrSupplementarySkippingIterator.java
</a>
</li>
<li class="file-stats">
<a href="#737ac803bf8fbb4b20614e8e4bf93db3f2f8f0db">
src/main/java/htsjdk/samtools/cram/build/Cram2SamRecordFactory.java
</a>
</li>
<li class="file-stats">
<a href="#56cfe403afc59c294679c0ab5f3fdd0dd825f549">
src/main/java/htsjdk/samtools/cram/build/Sam2CramRecordFactory.java
</a>
</li>
<li class="file-stats">
<a href="#5bcb912172743bc8e53ade4f5785946972c7df86">
src/main/java/htsjdk/samtools/cram/ref/EnaRefService.java
</a>
</li>
</ul>
<h5>The diff was not included because it is too large.</h5>
</div>
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