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GitLab

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<h3>

Andreas Tille pushed to branch upstream

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>

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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.14.3+dfsg</pre>

</li>

</ul>

<h4>30 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">

.gitignore

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<li class="file-stats">

<a href="#f07866736216be0ee2aba49e392191aeae700a35">

build.gradle

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</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

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<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

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<li class="file-stats">

<a href="#daaaae026d12144a23e76d8027ffdf1b04171b11">

src/main/java/htsjdk/samtools/SAMFlag.java

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<li class="file-stats">

<a href="#b9092567a6b258b395f6b5e3d1a66b3a0db66272">

src/main/java/htsjdk/samtools/SAMRecord.java

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<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

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<li class="file-stats">

<a href="#a030c6b5caf0e18156662c46b4c4e3e82cbf8c16">

<span class="deleted-file">

−

src/main/java/htsjdk/samtools/SAMRecordUtil.java

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</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>

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<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>

<li class="file-stats">

<a href="#389ed107ad0a321ee38c9a9217f6011bcb50b80f">

src/main/java/htsjdk/samtools/filter/NotPrimaryAlignmentFilter.java

</a>

</li>

<li class="file-stats">

<a href="#f7bfabd6a80a996093c2961cee1942fddb5f1794">

src/main/java/htsjdk/samtools/filter/ReadNameFilter.java

</a>

</li>

<li class="file-stats">

<a href="#90780b92a977050f3881323489a2555b68df3051">

src/main/java/htsjdk/samtools/filter/SecondaryAlignmentFilter.java

</a>

</li>

<li class="file-stats">

<a href="#6c81cc56b1d4a2a65d4bd9f0454fd0377607ab76">

src/main/java/htsjdk/samtools/filter/SecondaryOrSupplementaryFilter.java

</a>

</li>

<li class="file-stats">

<a href="#ee26571f0a3fd1282fa785118f840a3c8678755e">

src/main/java/htsjdk/samtools/filter/TagFilter.java

</a>

</li>

<li class="file-stats">

<a href="#d9f8b7c49325e28ca1f16f86380075c49b6a3069">

src/main/java/htsjdk/samtools/liftover/LiftOver.java

</a>

</li>

</ul>

<h5>The diff was not included because it is too large.</h5>

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