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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/5a9aa2104b572f75786852a15f6f723f21a396f0">5a9aa210</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-12-02T10:18:04Z</i>

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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.18.0+dfsg</pre>

</li>

</ul>

<h4>30 changed files:</h4>

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<li class="file-stats">

<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

README.md

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<li class="file-stats">

<a href="#f07866736216be0ee2aba49e392191aeae700a35">

build.gradle

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<li class="file-stats">

<a href="#3524a28c3a83250c95bbe1f9b5d0f7ba6510ca75">

src/main/java/htsjdk/samtools/AbstractSAMHeaderRecord.java

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<li class="file-stats">

<a href="#993dacb3974ba8ae9df67faf7d12d33647fdb7d3">

src/main/java/htsjdk/samtools/BAMRecord.java

</a>

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<li class="file-stats">

<a href="#cdef170568e651ffa7f71ffc2c681e1c9c913ee3">

src/main/java/htsjdk/samtools/CRAMIterator.java

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<li class="file-stats">

<a href="#6e1a414bfc1c28b89138df50d419a663a12eb889">

<span class="deleted-file">

−

src/main/java/htsjdk/samtools/FixBAMFile.java

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<li class="file-stats">

<a href="#08635c297835f435d053c63e57fc24beef173856">

src/main/java/htsjdk/samtools/LinearIndex.java

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<li class="file-stats">

<a href="#e96cfaf2afff7c5cbbed08310b317936bb42eb77">

src/main/java/htsjdk/samtools/SAMBinaryTagAndUnsignedArrayValue.java

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<li class="file-stats">

<a href="#7c4164c40fb89ec9c0643b8dd378c1cf0957f5d1">

src/main/java/htsjdk/samtools/SAMBinaryTagAndValue.java

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<li class="file-stats">

<a href="#93ff58778463905bd2b8bc30bb18a26b9c8adcbb">

src/main/java/htsjdk/samtools/SAMFileHeader.java

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<li class="file-stats">

<a href="#e6cdc1abc0fa0f0287c09c4cf048f8deee507291">

src/main/java/htsjdk/samtools/SAMFileWriterImpl.java

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<li class="file-stats">

<a href="#1e54404fdd8d643007fad6688662c2c4f0d4e93b">

src/main/java/htsjdk/samtools/SAMLineParser.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="#8a44f49ee7d97ebcc7900c487672a832950d4de5">

src/main/java/htsjdk/samtools/SAMRecordSetBuilder.java

</a>

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<li class="file-stats">

<a href="#8028318b55c23d368ca013b2b9d38fd4a006013a">

src/main/java/htsjdk/samtools/SAMSequenceDictionary.java

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<li class="file-stats">

<a href="#274cc5830fbf0d43cde49c2b3c5f07e2ebca70ca">

src/main/java/htsjdk/samtools/SAMSequenceRecord.java

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<li class="file-stats">

<a href="#e311202d3cb201fd1dd4c0abb4248adde79f2f81">

src/main/java/htsjdk/samtools/SAMSortOrderChecker.java

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<li class="file-stats">

<a href="#c9ff1e32eeacbae344955f9c13d7f3ae806925c0">

src/main/java/htsjdk/samtools/SAMTag.java

</a>

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<li class="file-stats">

<a href="#4d82de20676ba51df39d89929d1f2e1281388b05">

src/main/java/htsjdk/samtools/SAMTagUtil.java

</a>

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<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>

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<li class="file-stats">

<a href="#49b0c9d0482641d6e56ded5cabdd721e0ef22aea">

<span class="deleted-file">

−

src/main/java/htsjdk/samtools/SAMTools.java

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</a>

</li>

<li class="file-stats">

<a href="#d4460f31fc299d131ced2a583813743b1cab9afd">

src/main/java/htsjdk/samtools/SAMUtils.java

</a>

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<li class="file-stats">

<a href="#f27e3e1c6beda3177bff3ef40aeb70ce92aa344f">

src/main/java/htsjdk/samtools/SQTagUtil.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="#39d4e19d290901edb25bc0ad2caaae6b68ecd66d">

src/main/java/htsjdk/samtools/SamReader.java

</a>

</li>

<li class="file-stats">

<a href="#b3a96294be815da4b9dec3e1655f4a271638ffc3">

src/main/java/htsjdk/samtools/TextTagCodec.java

</a>

</li>

<li class="file-stats">

<a href="#6f2666fb13a6b9407dbc31ebdb1606ec9f7e8c00">

src/main/java/htsjdk/samtools/cram/CRAIIndex.java

</a>

</li>

<li class="file-stats">

<a href="#57733d6a48c6ee322919218194d767d9581ab4bc">

src/main/java/htsjdk/samtools/cram/build/CompressionHeaderFactory.java

</a>

</li>

<li class="file-stats">

<a href="#861c3d2da3ce79af545341928d9face6ebfab914">

src/main/java/htsjdk/samtools/cram/build/ContainerFactory.java

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</li>

</ul>

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

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