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<h3>
Pierre Gruet 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/b869680be30cad9b627cb669d899eac50d20f682">b869680b</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-11-17T22:36:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.24.1+dfsg</pre>
</li>
</ul>
<h4>30 changed files:</h4>
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<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
.gitignore
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<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
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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
</a>
</li>
<li class="file-stats">
<a href="#14edc413e9dc7f33d9dfec4ab78ab93f77183c87">
<span class="new-file">
+
scripts/htsget-scripts/README.md
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<li class="file-stats">
<a href="#ff6ac8945b7f3b83a4d42f5de34956f26949210e">
<span class="new-file">
+
scripts/htsget-scripts/htsget_config.json
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</li>
<li class="file-stats">
<a href="#4613c31cac70ad6935e3ff6cc2d3e96deff74ca5">
<span class="new-file">
+
scripts/htsget-scripts/start-htsget-test-server.sh
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<li class="file-stats">
<a href="#703fde6d8b024b2f84429199a95907848ca6ef21">
<span class="new-file">
+
src/main/java/htsjdk/io/AsyncWriterPool.java
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<li class="file-stats">
<a href="#86547273028ff0cdde55bd2142669fa8ca462819">
<span class="new-file">
+
src/main/java/htsjdk/io/HtsPath.java
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<li class="file-stats">
<a href="#4e5ec019e8bb3dbecfcdb21c06a91daf1efa5455">
<span class="new-file">
+
src/main/java/htsjdk/io/IOPath.java
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<li class="file-stats">
<a href="#b2cf977aead882ddce53327fb7dfff8680662138">
<span class="new-file">
+
src/main/java/htsjdk/io/Writer.java
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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="#c6a6e96e6adb310d71c0adc7c198275c9add065b">
src/main/java/htsjdk/samtools/BAMFileReader.java
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<li class="file-stats">
<a href="#089d4c72e361a0f8eecae22b77155e0a07b870ed">
src/main/java/htsjdk/samtools/CRAMFileReader.java
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<li class="file-stats">
<a href="#79d86210e02dab105f2012884a462db15824db05">
src/main/java/htsjdk/samtools/DuplicateSetIterator.java
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<li class="file-stats">
<a href="#d5981b282a97db867d2c5e69c783fc8a1afa894d">
<span class="new-file">
+
src/main/java/htsjdk/samtools/HtsgetBAMFileReader.java
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</a>
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<li class="file-stats">
<a href="#6a86fe922e2a95200ffbf136f560f842c48e1775">
src/main/java/htsjdk/samtools/QueryInterval.java
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<li class="file-stats">
<a href="#b9092567a6b258b395f6b5e3d1a66b3a0db66272">
src/main/java/htsjdk/samtools/SAMRecord.java
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</li>
<li class="file-stats">
<a href="#fcccf360b5a8ca4f4907e21ae813ebaa67c0acbb">
src/main/java/htsjdk/samtools/SAMRecordDuplicateComparator.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>
<li class="file-stats">
<a href="#8028318b55c23d368ca013b2b9d38fd4a006013a">
src/main/java/htsjdk/samtools/SAMSequenceDictionary.java
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</li>
<li class="file-stats">
<a href="#274cc5830fbf0d43cde49c2b3c5f07e2ebca70ca">
src/main/java/htsjdk/samtools/SAMSequenceRecord.java
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</li>
<li class="file-stats">
<a href="#d4460f31fc299d131ced2a583813743b1cab9afd">
src/main/java/htsjdk/samtools/SAMUtils.java
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</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
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</li>
<li class="file-stats">
<a href="#5a18e0c98433afb554990592498d397c7561778b">
src/main/java/htsjdk/samtools/SamPairUtil.java
</a>
</li>
<li class="file-stats">
<a href="#39d4e19d290901edb25bc0ad2caaae6b68ecd66d">
src/main/java/htsjdk/samtools/SamReader.java
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</li>
</ul>
<h5>The diff was not included because it is too large.</h5>
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