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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/bbmap">Debian Med / bbmap</a>
</h3>
<h4>
Commits:
</h4>
<ul>
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<strong><a href="https://salsa.debian.org/med-team/bbmap/-/commit/6847642f17dbeab49676206b558aec03591996d1">6847642f</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2021-01-28T17:09:05+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 38.88+dfsg</pre>
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<h4>30 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#e463fa97b3ad8760b49cf0b08654d96aa72d6e84">
applyvariants.sh
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</li>
<li class="file-stats">
<a href="#67d907d61087ac2bc1410f5791ecd5d94426cc74">
bbduk.sh
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</li>
<li class="file-stats">
<a href="#be7260b2e2b4ab59dbd69285dbc941c2cbcff3af">
current/align2/AbstractMapper.java
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</li>
<li class="file-stats">
<a href="#73532331acf08c8ae4be3a551111af7c8f57a3f5">
current/align2/BBIndex.java
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</li>
<li class="file-stats">
<a href="#33591d221e8ef748ff99a42d5edd3ab2bea9d41b">
current/align2/BBIndex5.java
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<li class="file-stats">
<a href="#7c71ed1174aff31ad13ce4e88ab1a0454bfcfef3">
current/align2/BBIndexAcc.java
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<li class="file-stats">
<a href="#f06e3d20f974abdac3d9af0ea69272b41dfb772f">
current/align2/BBIndexPacBio.java
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<li class="file-stats">
<a href="#c28e80621c1e24cafa4204e862d5d0bd70aaf612">
current/align2/BBIndexPacBioSkimmer.java
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<li class="file-stats">
<a href="#62b97e902920c150ab4ef1adf802e2702176e6f7">
current/align2/BBSplitter.java
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<li class="file-stats">
<a href="#32ca876b08317068631c0e33c7fe64dde4a90b72">
current/align2/BBWrap.java
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<li class="file-stats">
<a href="#779953996c11d23866051b5d448be3c1ca9b800b">
current/align2/BandedAlignerJNI.java
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<li class="file-stats">
<a href="#405a62c10ac2c3323584108d31452b3e546b868c">
current/align2/CompareSamFiles.java
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<li class="file-stats">
<a href="#7d3a65b56a85951ec983489580e35d4702f58ad6">
current/align2/GradeSamFile.java
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<li class="file-stats">
<a href="#eb38d7c4f416695d891d2f8187b2e857e82ca042">
current/align2/IndexMaker4.java
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<li class="file-stats">
<a href="#9fbbd63722522269940832afb51a1fd59ed98f8a">
current/align2/IndexMaker5.java
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<li class="file-stats">
<a href="#a7b631d8f456e525c5472ef7e78fc664d1d0f267">
current/align2/MakeRocCurve.java
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<li class="file-stats">
<a href="#275b1824ac327767f33b9f74a88d7d4a0c89491b">
current/align2/MultiStateAligner11tsJNI.java
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<li class="file-stats">
<a href="#837464c66ce56be5e75f13536ae463a06333ac05">
current/align2/PrintTime.java
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<li class="file-stats">
<a href="#f782d3f5f2a0caac382364db133ebecf2eb318b5">
current/align2/RandomReads3.java
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<li class="file-stats">
<a href="#14f30e18717d2fc09a1eba6235981a2fe1a4e216">
current/aligner/AllToAll.java
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<li class="file-stats">
<a href="#fd68fc453a9a27fdefb4c987c1beed15ab4dcc52">
current/aligner/SingleStateAlignerPacBioAdapter.java
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<li class="file-stats">
<a href="#859f33d4bc5ba51f2152e72ae7389d40c090d337">
current/assemble/AbstractBuildThread.java
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<li class="file-stats">
<a href="#c4621eca88cc44925421ee09aed79696103fbec6">
current/assemble/AbstractExploreThread.java
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<li class="file-stats">
<a href="#0178ad043dc048c47fe7a4fa7dd135e198c6ec75">
current/assemble/AbstractProcessContigThread.java
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<li class="file-stats">
<a href="#649adf1519714691cc23b2803e10bdc684e80ca6">
current/assemble/BubblePopper.java
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</li>
<li class="file-stats">
<a href="#71f0cbc97c5a6dcff4abac99b9d6e67422d8ada8">
current/assemble/KmerCompressor.java
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<li class="file-stats">
<a href="#f6f415de25e5b38af707a823e4fc39c6e3d77a95">
current/assemble/Postfilter.java
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<li class="file-stats">
<a href="#c83b8870014d3f3c36343d260d6769bfe0926238">
current/assemble/TadPipe.java
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</li>
<li class="file-stats">
<a href="#7325505e925acb2556d8e0d25d4b41776875fc57">
current/assemble/Tadpole.java
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</li>
</ul>
<h5>The diff was not included because it is too large.</h5>
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