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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>
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<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/htsjdk/-/commit/386fe92fcd2e393e6042a9137b486ef4159c14c8">386fe92f</a></strong>
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<span> by Pierre Gruet </span> <i> at 2024-10-09T09:45:19+02:00 </i>
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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "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 4.1.3+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="#f07866736216be0ee2aba49e392191aeae700a35">
build.gradle
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<li class="file-stats">
<a href="#fbe448ebfc3eb2d4e308f6b8b043666f5b57235e">
gradle/wrapper/gradle-wrapper.properties
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<li class="file-stats">
<a href="#5bbfa66edb4db3c7c33c5181f43510990d3307f9">
gradlew
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<li class="file-stats">
<a href="#c1fd3ddfa5246209d0d5cf69c072e1b6767bfac0">
scripts/install-samtools.sh
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<li class="file-stats">
<a href="#cfb2c495b10b95bd2908683cfcbf1506ed49459c">
src/main/java/htsjdk/beta/codecs/hapref/fasta/FASTADecoderV1_0.java
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<li class="file-stats">
<a href="#9b15bf3009830362b7c62c90a03019f9f6cb8afb">
src/main/java/htsjdk/beta/codecs/reads/ReadsCodecUtils.java
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<li class="file-stats">
<a href="#0b307b7be72387907daf16b5f2be3afe43a71c53">
src/main/java/htsjdk/beta/codecs/reads/bam/BAMCodec.java
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<li class="file-stats">
<a href="#2b6d2d2ac2d6462a95f706d49a6b71a085533d98">
src/main/java/htsjdk/beta/codecs/reads/bam/BAMDecoder.java
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<li class="file-stats">
<a href="#aaa5e300b24355fd46167868f1a94d1c5299b859">
src/main/java/htsjdk/beta/codecs/reads/bam/BAMEncoder.java
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<li class="file-stats">
<a href="#862fc3ca692b773fea9bb2d73000624351a4630e">
src/main/java/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMDecoderV1_0.java
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<li class="file-stats">
<a href="#0ccbe1f01fc4b8900db0c386aa3b61b246bfeb95">
src/main/java/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMEncoderV1_0.java
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<li class="file-stats">
<a href="#ae2fd4dbde9e3b1363f952bd3b8c7d9d7dc6c9d0">
src/main/java/htsjdk/beta/codecs/reads/cram/CRAMCodec.java
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<li class="file-stats">
<a href="#4a6a2cd3189cf02bb3e39e2b5cf1f0b4c60403f6">
src/main/java/htsjdk/beta/codecs/reads/cram/CRAMDecoder.java
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<li class="file-stats">
<a href="#58442ba08783f3095d289e49e64566fef698c5c1">
src/main/java/htsjdk/beta/codecs/reads/cram/CRAMEncoder.java
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<li class="file-stats">
<a href="#163e2c819649c1678549401659ba04a5cb24061d">
src/main/java/htsjdk/beta/codecs/reads/cram/cramV2_1/CRAMDecoderV2_1.java
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<li class="file-stats">
<a href="#492bec952608db6824c76e50f4ba74bcd4452b2c">
src/main/java/htsjdk/beta/codecs/reads/cram/cramV2_1/CRAMEncoderV2_1.java
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<li class="file-stats">
<a href="#4195713a70b636bafd7f16984055e049e0ec8599">
src/main/java/htsjdk/beta/codecs/reads/cram/cramV3_0/CRAMDecoderV3_0.java
</a>
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<li class="file-stats">
<a href="#991796bb21724a4a039c1bae59e5804a477a7eec">
src/main/java/htsjdk/beta/codecs/reads/cram/cramV3_0/CRAMEncoderV3_0.java
</a>
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<li class="file-stats">
<a href="#33d370211a51bfc99fd4d289393889dbf2b24f10">
src/main/java/htsjdk/beta/codecs/reads/htsget/HtsgetBAMCodec.java
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<li class="file-stats">
<a href="#c5fe6ab7fbad5d7a3679a4323eb8c26b4b6d8d26">
src/main/java/htsjdk/beta/codecs/reads/htsget/HtsgetBAMDecoder.java
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<li class="file-stats">
<a href="#a800eb53753a37c8810c7440937d365f4d38f181">
src/main/java/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/HtsgetBAMCodecV1_2.java
</a>
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<li class="file-stats">
<a href="#08de4fc3b346746b42b426743aed9cdbcf85e4b2">
src/main/java/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/HtsgetBAMDecoderV1_2.java
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<li class="file-stats">
<a href="#076748422bcf8954f03d9c33ae34503c6a516c27">
src/main/java/htsjdk/beta/codecs/reads/sam/SAMCodec.java
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<li class="file-stats">
<a href="#5ee4392bd2cd1ed4feb05d83b60bedaa3b68a551">
src/main/java/htsjdk/beta/codecs/reads/sam/SAMDecoder.java
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<li class="file-stats">
<a href="#968c5b344f1d0cd1590b312e0d2de71266c0078e">
src/main/java/htsjdk/beta/codecs/reads/sam/SAMEncoder.java
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</li>
<li class="file-stats">
<a href="#6e9816388871367a6390b6cbff9a02d00a98fba8">
src/main/java/htsjdk/beta/codecs/reads/sam/samV1_0/SAMDecoderV1_0.java
</a>
</li>
<li class="file-stats">
<a href="#b7b74b8a129cb6cb7d2cbeb328f03d36e420a0f8">
src/main/java/htsjdk/beta/codecs/reads/sam/samV1_0/SAMEncoderV1_0.java
</a>
</li>
<li class="file-stats">
<a href="#35e77078ad64ac060f1a6e37cff4a2dbb73952a1">
src/main/java/htsjdk/beta/codecs/variants/vcf/VCFDecoder.java
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</li>
<li class="file-stats">
<a href="#da7edb2f7c04e88057af7282da43a4deb9d79078">
src/main/java/htsjdk/beta/codecs/variants/vcf/VCFEncoder.java
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</li>
<li class="file-stats">
<a href="#6114fc0c4d89c40c2caa9faf36e4c2fdf1a6ce6d">
src/main/java/htsjdk/beta/codecs/variants/vcf/VariantsCodecUtils.java
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</li>
</ul>
<h5 style="margin-top: 10px; margin-bottom: 10px; font-size: .875rem;">
The diff was not included because it is too large.
</h5>
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<p style="font-size: small; color: #737278;">
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