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<div class="content">
<h3 style="margin-top: 20px; margin-bottom: 10px;">
Pierre Gruet pushed to branch upstream at <a href="https://salsa.debian.org/med-team/htsjdk">Debian Med / htsjdk</a>
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<h4 style="margin-top: 10px; margin-bottom: 10px;">
Commits:
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<ul>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/htsjdk/-/commit/0c5275b15d2b8aad0dec0be9856d0761f1ef26f3">0c5275b1</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2023-12-01T11:11:26+01:00 </i>
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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 4.0.2+dfsg</pre>
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<h4 style="margin-top: 10px; margin-bottom: 10px;">
30 changed files:
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<li class="file-stats">
<a href="#6b8eb1151e11abd72b31ffb764de06790e5bda1e">
.github/workflows/tests.yml
</a>
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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="#0f4f982aa8b05c43f1b04a07a005b38194a3cef3">
src/main/java/htsjdk/beta/io/bundle/BundleJSON.java
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</li>
<li class="file-stats">
<a href="#80e16130a35788d7564c430d4392321991238f9d">
src/main/java/htsjdk/samtools/BamFileIoUtils.java
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<li class="file-stats">
<a href="#0cfa6bc34a953a2fd3fc7d50e0b68753c6c67373">
src/main/java/htsjdk/samtools/Defaults.java
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<li class="file-stats">
<a href="#0c2a3954cf743381ce8a0e1317b6e62af6a0ed8a">
src/main/java/htsjdk/samtools/SAMReadGroupRecord.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="#38f186b3b8546dc53abc703f7e967a9b026d6e2c">
src/main/java/htsjdk/samtools/SAMRecordIterator.java
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<li class="file-stats">
<a href="#8a44f49ee7d97ebcc7900c487672a832950d4de5">
src/main/java/htsjdk/samtools/SAMRecordSetBuilder.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="#dd7e7f9ef58d444c69a7e006a153fc8e4aedd2aa">
src/main/java/htsjdk/samtools/SamFileValidator.java
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<li class="file-stats">
<a href="#b3a96294be815da4b9dec3e1655f4a271638ffc3">
src/main/java/htsjdk/samtools/TextTagCodec.java
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<li class="file-stats">
<a href="#79e145fd36f7644e7c46fa6775a9d9caf2d04ff8">
src/main/java/htsjdk/samtools/cram/structure/Slice.java
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<li class="file-stats">
<a href="#fb3acecdbdaf50383b72f86b90785f1dad117e96">
src/main/java/htsjdk/samtools/util/AbstractProgressLogger.java
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<li class="file-stats">
<a href="#81125ecd7099f68597ffd6d37c0fbeb692e7b304">
src/main/java/htsjdk/samtools/util/BlockCompressedInputStream.java
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<li class="file-stats">
<a href="#08893f21c192e1983e27bd3198004ddaf362041a">
src/main/java/htsjdk/samtools/util/FileExtensions.java
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<li class="file-stats">
<a href="#3cc7f9eb81404b37ebc1bcd46e53c6ce16ab4828">
src/main/java/htsjdk/samtools/util/IOUtil.java
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<li class="file-stats">
<a href="#7d5e62b952e24cdd592dbaa34d8825581f0ad871">
src/main/java/htsjdk/samtools/util/Interval.java
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<li class="file-stats">
<a href="#143c1ca88bc3f62f0f52ce7c3d2c9a02040dd1e3">
src/main/java/htsjdk/samtools/util/htsget/HtsgetErrorResponse.java
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</li>
<li class="file-stats">
<a href="#c96e9e5bd0e7979af85e40b8407c0b1d551ab98f">
src/main/java/htsjdk/samtools/util/htsget/HtsgetPOSTRequest.java
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</li>
<li class="file-stats">
<a href="#565d0b17c01dddb3f75f7a88787fccb946f6db3a">
src/main/java/htsjdk/samtools/util/htsget/HtsgetResponse.java
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<li class="file-stats">
<a href="#f454198ccc8094987f246c8d468971a6a567abba">
<span class="new-file">
+
src/main/java/htsjdk/tribble/NamedFeature.java
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<li class="file-stats">
<a href="#23e08218c8b3b1592c7403d4f55453895363c002">
src/main/java/htsjdk/tribble/bed/BEDFeature.java
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<li class="file-stats">
<a href="#f01dca88a536b1514f7c219a0222ca471b811a64">
src/main/java/htsjdk/variant/variantcontext/Allele.java
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</li>
<li class="file-stats">
<a href="#3409118f065cd839e406e5f5f088853ec2314dd0">
src/main/java/htsjdk/variant/variantcontext/Genotype.java
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<li class="file-stats">
<a href="#bcf117b5d33941732fddc9d270b7e388f4b387dd">
src/main/java/htsjdk/variant/vcf/VCFCodec.java
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</li>
<li class="file-stats">
<a href="#83b2e79ffe78976c329c929ae81ccd8bac849e68">
src/main/java/htsjdk/variant/vcf/VCFHeaderVersion.java
</a>
</li>
<li class="file-stats">
<a href="#b56ce3202336ee2a89cde4c8d65b1a9a7f683663">
src/test/java/htsjdk/beta/io/bundle/BundleJSONTest.java
</a>
</li>
<li class="file-stats">
<a href="#8342dbd6c1f05bc52f098100a4e072e6fa351ec4">
<span class="new-file">
+
src/test/java/htsjdk/samtools/BamFileIoUtilsUnitTest.java
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</a>
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<h5 style="margin-top: 10px; margin-bottom: 10px; font-size: 0.875rem;">
The diff was not included because it is too large.
</h5>
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