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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/cfc2c703ab904b6cdca5e2b2e5b91e3a0a55ccf5">cfc2c703</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-01-24T16:31:37Z</i>

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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.18.2+dfsg</pre>

</li>

</ul>

<h4>30 changed files:</h4>

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<li class="file-stats">

<a href="#c6a6e96e6adb310d71c0adc7c198275c9add065b">

src/main/java/htsjdk/samtools/BAMFileReader.java

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<li class="file-stats">

<a href="#52658dc1fe8935b31913c89a0fd28df56adcb045">

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+

src/main/java/htsjdk/samtools/BAMSBIIndexer.java

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<li class="file-stats">

<a href="#cdef170568e651ffa7f71ffc2c681e1c9c913ee3">

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

</a>

</li>

<li class="file-stats">

<a href="#274cc5830fbf0d43cde49c2b3c5f07e2ebca70ca">

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

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<li class="file-stats">

<a href="#d4460f31fc299d131ced2a583813743b1cab9afd">

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

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<li class="file-stats">

<a href="#952de2edd1c341f6c8faa6bf6de1d49c7f5cd1f4">

<span class="new-file">

+

src/main/java/htsjdk/samtools/SBIIndex.java

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<li class="file-stats">

<a href="#c5bbd1940d807e90acff5bb3a979cf3d3e25233c">

<span class="new-file">

+

src/main/java/htsjdk/samtools/SBIIndexWriter.java

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<li class="file-stats">

<a href="#8ade29bf41936dfa97ffd3ffa00afe3a2942f4fd">

src/main/java/htsjdk/samtools/SamReaderFactory.java

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<li class="file-stats">

<a href="#681506786445d5d500b64e5b8d120fd249435de1">

src/main/java/htsjdk/samtools/SamStreams.java

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<li class="file-stats">

<a href="#b5bb85781a9a428e5ebf74bf2207f0ad4982a059">

src/main/java/htsjdk/samtools/apps/TimeChannel.java

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<li class="file-stats">

<a href="#8005a59bfefb98e66c60f5e41a4b16fdb5b7f992">

src/main/java/htsjdk/samtools/apps/TimeRandomAccessFile.java

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</li>

<li class="file-stats">

<a href="#57733d6a48c6ee322919218194d767d9581ab4bc">

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

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</li>

<li class="file-stats">

<a href="#861c3d2da3ce79af545341928d9face6ebfab914">

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

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</li>

<li class="file-stats">

<a href="#2932975514d721579122d0ce89b4d94b031a7ac7">

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

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<li class="file-stats">

<a href="#6b662e10e7662f52097ddb086186821fc0d897a7">

src/main/java/htsjdk/samtools/cram/io/ExternalCompression.java

→

src/main/java/htsjdk/samtools/cram/compression/ExternalCompression.java

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<li class="file-stats">

<a href="#2b29961138fab93123ff8cbf519791a0b80021d9">

src/main/java/htsjdk/samtools/cram/encoding/ExternalCompressor.java

→

src/main/java/htsjdk/samtools/cram/compression/ExternalCompressor.java

</a>

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<li class="file-stats">

<a href="#78a28d077007182249dee1bf72274440d3f8c513">

src/main/java/htsjdk/samtools/cram/encoding/rans/Constants.java

→

src/main/java/htsjdk/samtools/cram/compression/rans/Constants.java

</a>

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<li class="file-stats">

<a href="#12be68ec2ada0534a5e2c781b0fd81cad1425e39">

src/main/java/htsjdk/samtools/cram/encoding/rans/D04.java

→

src/main/java/htsjdk/samtools/cram/compression/rans/D04.java

</a>

</li>

<li class="file-stats">

<a href="#ba78578f349e5e977d9b614eb8ec4201fdcb5b34">

src/main/java/htsjdk/samtools/cram/encoding/rans/D14.java

→

src/main/java/htsjdk/samtools/cram/compression/rans/D14.java

</a>

</li>

<li class="file-stats">

<a href="#ff6b1582f1b4b4738a37bbc5fe34acfc6eb96814">

src/main/java/htsjdk/samtools/cram/encoding/rans/Decoding.java

→

src/main/java/htsjdk/samtools/cram/compression/rans/Decoding.java

</a>

</li>

<li class="file-stats">

<a href="#1a043f6c84275301b2bd12da79f7f5a98ac3928b">

src/main/java/htsjdk/samtools/cram/encoding/rans/E04.java

→

src/main/java/htsjdk/samtools/cram/compression/rans/E04.java

</a>

</li>

<li class="file-stats">

<a href="#1bd0431f09f4b48baaedfefaa917a833b556c486">

src/main/java/htsjdk/samtools/cram/encoding/rans/E14.java

→

src/main/java/htsjdk/samtools/cram/compression/rans/E14.java

</a>

</li>

<li class="file-stats">

<a href="#291020c4692a6ab1b466bb763d7bfb6babaa87d6">

src/main/java/htsjdk/samtools/cram/encoding/rans/Encoding.java

→

src/main/java/htsjdk/samtools/cram/compression/rans/Encoding.java

</a>

</li>

<li class="file-stats">

<a href="#94e42f190cba52e1525f30f31e16f98c5dfe89c6">

src/main/java/htsjdk/samtools/cram/encoding/rans/Frequencies.java

→

src/main/java/htsjdk/samtools/cram/compression/rans/Frequencies.java

</a>

</li>

<li class="file-stats">

<a href="#fe568f64f5a3cf2f796e77a210c1ebe52a525d22">

src/main/java/htsjdk/samtools/cram/encoding/rans/RANS.java

→

src/main/java/htsjdk/samtools/cram/compression/rans/RANS.java

</a>

</li>

<li class="file-stats">

<a href="#3753368e60ed0cc0805d025388170fc169516a76">

src/main/java/htsjdk/samtools/cram/encoding/rans/Utils.java

→

src/main/java/htsjdk/samtools/cram/compression/rans/Utils.java

</a>

</li>

<li class="file-stats">

<a href="#aaf4b4c831a2043a4c0de14807606f6fdcc20493">

<span class="deleted-file">

−

src/main/java/htsjdk/samtools/cram/encoding/BitCodec.java

</span>

</a>

</li>

<li class="file-stats">

<a href="#732e8b114710a470aae4f25c52d9909bded7ec4e">

<span class="new-file">

+

src/main/java/htsjdk/samtools/cram/encoding/ByteArrayLenCodec.java

</span>

</a>

</li>

<li class="file-stats">

<a href="#cc50ce9566ac04892b70a864cd3062e4a2c370ec">

src/main/java/htsjdk/samtools/cram/encoding/ByteArrayLenEncoding.java

</a>

</li>

<li class="file-stats">

<a href="#a5458d74b45e22d36cf36ae1152b36554c0024f6">

<span class="new-file">

+

src/main/java/htsjdk/samtools/cram/encoding/CRAMCodec.java

</span>

</a>

</li>

</ul>

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

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