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<h3>
Étienne Mollier pushed to branch master
at <a href="https://salsa.debian.org/med-team/bedtools">Debian Med / bedtools</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bedtools/-/commit/d3b073f7f315de4e849c96c776ed4e6bb56225a2">d3b073f7</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-01-27T15:11:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bedtools/-/commit/b6cb18707ce2740c61b513db00a2257da306d25b">b6cb1870</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-01-27T15:11:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.30.0+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bedtools/-/commit/8e2a0b2eeaa40c9155bf9269609a212f832c859f">8e2a0b2e</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-01-27T15:12:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.30.0+dfsg'
Update to upstream version '2.30.0+dfsg'
with Debian dir ef4d8263068b691b4523f0cc81247527235d2f63</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bedtools/-/commit/2d5ed08673bf8461ebe8779dfbf1fa2598176fc0">2d5ed086</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-01-27T15:17:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">refresh 2to3.patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bedtools/-/commit/91def4b68ff895a01a4721c9b2d56840860ae4ff">91def4b6</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-01-27T15:18:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">refresh hardening patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bedtools/-/commit/864f8856967e4669a26cda48f0ef87a5469a73ed">864f8856</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-01-27T16:32:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">remove test related patches
The test suite has been reviewed by upstream, following John
Marshall's intervention on Debian Med:
https://lists.debian.org/debian-med/2021/01/msg00189.html
Thanks John
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bedtools/-/commit/39ec1ebcdf77fdaa9b6f0dc77b11aaedd7311c44">39ec1ebc</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-01-27T16:36:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">32-bit-fixes.patch applied upstream
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bedtools/-/commit/119bc1d5ae60bc6f32da7f0c4087617c53a4d512">119bc1d5</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-01-27T16:37:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">spelling patch applied upstream
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bedtools/-/commit/21c7ab343cd6766daaee374ab6b5785f16852f91">21c7ab34</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-01-27T16:40:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">remove references to htsutil
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bedtools/-/commit/d41d79abab39f7dedf686ebe202457d92d12354a">d41d79ab</a></strong>
<div>
<span>by John Marshall</span>
<i>at 2021-01-27T17:11:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add htsutil patch
This patch inlines the htsutil test tool to reduce the memory footprint
of the bedtools package, compared to adding it as a side program.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bedtools/-/commit/8495d8188556bc4acbb7f81d35fcc448da4ebdd5">8495d818</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-01-27T17:16:14+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/rules: set htsutil to use subcommand
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bedtools/-/commit/852d8af6492451daa009dc812c7fe7b972d9fed1">852d8af6</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-01-27T17:16:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/t/run-unit-test: use htsutil subcommand
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bedtools/-/commit/d2e90e8ac9e394875c73f8cdb1c9d16d1754418a">d2e90e8a</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-01-27T17:24:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">updated changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bedtools/-/commit/e8ffe8bdde9782b2f23945a2d033f5739cff42f2">e8ffe8bd</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-01-27T17:27:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
</ul>
<h4>30 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#c778226b6c4c0fb51cf7942c8ee1f3d9fc1249d0">
.github/workflows/main.yml
</a>
</li>
<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
.gitignore
</a>
</li>
<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
</a>
</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
</li>
<li class="file-stats">
<a href="#6faa3ccfbe0e68c8aebae8c72005f82c9a824857">
<span class="deleted-file">
−
debian/bedtools-test.links
</span>
</a>
</li>
<li class="file-stats">
<a href="#f7e7ac4bf284040b64c84f1e5c53bd685b88398d">
debian/bedtools.install
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
debian/patches/2to3.patch
</a>
</li>
<li class="file-stats">
<a href="#f32ee8ab6f890b8dabbf8e757ec6a73c9cae6249">
<span class="deleted-file">
−
debian/patches/32-bit-fixes.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#49ca19704f11c8ca01105bc2a3f3cf7983aa49f0">
<span class="deleted-file">
−
debian/patches/fix_intersect_test.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#a7198a3a1ab06f44764befcbb9f5b789b4404f69">
<span class="deleted-file">
−
debian/patches/fix_test_script.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#d6c09299b1f914372840e8fd6fcc850f8a11b236">
debian/patches/hardening
</a>
</li>
<li class="file-stats">
<a href="#b3f1fba1f77df75a03d5b5e1637614a1d2b4645b">
<span class="new-file">
+
debian/patches/htsutil
</span>
</a>
</li>
<li class="file-stats">
<a href="#c01a5549a47d3878d06fe57012e999b00bc461bb">
<span class="deleted-file">
−
debian/patches/no-samtools
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#e4c19aed51618bf0c7ebd03189c67e422f84d4eb">
<span class="deleted-file">
−
debian/patches/spelling
</span>
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
</a>
</li>
<li class="file-stats">
<a href="#254a2da7a740675e537439eb88e32083b9ea4771">
docs/conf.py
</a>
</li>
<li class="file-stats">
<a href="#54af9d69704715c9e558b29bf1304552eed1c05b">
docs/content/advanced-usage.rst
</a>
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<li class="file-stats">
<a href="#96546b98f68cd24f5d4aa902aa32da8e1adf5200">
docs/content/general-usage.rst
</a>
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<li class="file-stats">
<a href="#7e2c6a8f69d5f4c98b9a6c07bf681f16307a9035">
docs/content/history.rst
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<li class="file-stats">
<a href="#0ad0c9480aebc31dd47d0a136ec23871c6059bca">
docs/content/installation.rst
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<li class="file-stats">
<a href="#ab840828f6320aae33b8591bcdd29458c19d478b">
docs/content/tools/getfasta.rst
</a>
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<li class="file-stats">
<a href="#28b2fd9a9a33cdb4eb07f96b014470014a0c1de6">
docs/content/tools/intersect.rst
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<li class="file-stats">
<a href="#3805673d31b88b6f8a1c9baa62056947b510c694">
docs/content/tools/multicov.rst
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<li class="file-stats">
<a href="#0b897f3ead3633587c6b09c9d19cdac0eb2517a5">
src/annotateBed/annotateBed.cpp
</a>
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<li class="file-stats">
<a href="#e65646782bea8c8fcf9864b7bd5c8047cc3ab82f">
src/annotateBed/annotateMain.cpp
</a>
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<li class="file-stats">
<a href="#6dd5ed69e2042b1d5a311d0f156d323d18bb1fdf">
src/bamToFastq/bamToFastq.cpp
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<li class="file-stats">
<a href="#70abd534673ef8f1c3cbd4aa1569d740e609fe29">
src/bedpeToBam/bedpeToBam.cpp
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</ul>
<h5>The diff was not included because it is too large.</h5>
</div>
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