<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN" "http://www.w3.org/TR/REC-html40/loose.dtd">
<html lang="en" style='--code-editor-font: var(--default-mono-font, "Menlo"), DejaVu Sans Mono, Liberation Mono, Consolas, Ubuntu Mono, Courier New, andale mono, lucida console, monospace;'>
<head>
<meta content="text/html; charset=US-ASCII" http-equiv="Content-Type">
<title>
GitLab
</title>

<style data-premailer="ignore" type="text/css">
a { color: #1068bf; }
</style>


<style>img {
max-width: 100%; height: auto;
}
body {
font-size: 0.875rem;
}
body {
-webkit-text-shadow: rgba(255,255,255,0.01) 0 0 1px;
}
body {
font-family: var(--default-regular-font, -apple-system),BlinkMacSystemFont,"Segoe UI",Roboto,"Noto Sans",Ubuntu,Cantarell,"Helvetica Neue",sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol","Noto Color Emoji"; font-size: inherit;
}
</style>
</head>
<body style='font-size: inherit; -webkit-text-shadow: rgba(255,255,255,0.01) 0 0 1px; font-family: var(--default-regular-font, -apple-system),BlinkMacSystemFont,"Segoe UI",Roboto,"Noto Sans",Ubuntu,Cantarell,"Helvetica Neue",sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol","Noto Color Emoji";'>
<div class="content">

<h3 style="margin-top: 20px; margin-bottom: 10px;">
Étienne Mollier pushed to branch master at <a href="https://salsa.debian.org/med-team/bedtools">Debian Med / bedtools</a>
</h3>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
Commits:
</h4>
<ul>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/bedtools/-/commit/50e76de36b46b1d7930bef2546f98230360cd505">50e76de3</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-06-23T22:12:45+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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;'>routine-update: New upstream version
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/bedtools/-/commit/de42b01261334616ce2106135fd1677386537fe5">de42b012</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-06-23T22:12:47+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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 2.31.0+dfsg</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/bedtools/-/commit/b045ade9a446040e90b3213a9ccca3093321b5dc">b045ade9</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-06-23T22:13:12+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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;'>Update upstream source from tag 'upstream/2.31.0+dfsg'

Update to upstream version '2.31.0+dfsg'
with Debian dir a5f8b71ca488edf4146df385591d9f977eb0f379</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/bedtools/-/commit/a738110746ebd67b2bc4a733a790e1043d5a1515">a7381107</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-06-23T22:13:12+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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;'>routine-update: Standards-Version: 4.6.2
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/bedtools/-/commit/821afd62cc90abdb9f48fce40671d8109421bcc6">821afd62</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-06-23T22:14:07+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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;'>remove_barski_binding_site.png.patch: unfuzz.
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/bedtools/-/commit/ca88564d3e41aba3073c86263f652f3a4e08d00d">ca88564d</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-06-23T22:17:52+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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;'>2to3.patch: refresh.
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/bedtools/-/commit/04322fad832830043e562b23ab55412aaa234c1c">04322fad</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-06-23T22:19:47+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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;'>2to3.patch: declare forwarding not-needed.

Upstream looks to assume python is python3 nowadays.
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/bedtools/-/commit/df5ad2bdeadfa5f46d4b95e7015f0634746b01b0">df5ad2bd</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-06-23T22:20:50+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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;'>hardening patch: unfuzz.
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/bedtools/-/commit/a7b07acb37ce85cee9a9f156e35bf84cb58b06bc">a7b07acb</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-06-23T22:21:08+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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;'>htsutil patch: unfuzz.
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/bedtools/-/commit/0555677f9a8f52fe9b3b5f52e6fd18649748caad">0555677f</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-06-23T22:24:46+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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;'>gcc-13.patch: add; fix ftbfs with gcc-13.

Closes: #1037588
Thanks: David Seifert
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/bedtools/-/commit/9a4d3bff97d7066addfabfa70a90768b11eaf5c8">9a4d3bff</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-06-23T22:51:57+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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;'>2to3.patch: remove my unneeded "fix".

Gbp-Dch: ignore
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/bedtools/-/commit/9411a76206cb6312afde284d3729024066af5b6d">9411a762</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-06-23T22:52:22+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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;'>d/control: bedtools-test depend on python3.
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/bedtools/-/commit/f9286654d20ab0115ddebae801333d10f7b37bd2">f9286654</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-06-23T22:56:20+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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;'>2to3.patch: remove remaining occurrences of python.

There are still some tests and some documentation referring to the
unversionned python, which in Debian is by default python2.
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/bedtools/-/commit/ad36a93f547695e9e3fd55c94cfcbfe7b081b932">ad36a93f</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-06-23T23:18:39+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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;'>ready to upload to unstable.
</pre>
</li>
</ul>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
30 changed files:
</h4>
<ul>
<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="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
debian/patches/2to3.patch
</a>
</li>
<li class="file-stats">
<a href="#6da75f7fef0ac9337ebe063db5cf63a8b5c30ff3">
<span class="new-file">
+
debian/patches/gcc-13.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#d6c09299b1f914372840e8fd6fcc850f8a11b236">
debian/patches/hardening
</a>
</li>
<li class="file-stats">
<a href="#b3f1fba1f77df75a03d5b5e1637614a1d2b4645b">
debian/patches/htsutil
</a>
</li>
<li class="file-stats">
<a href="#dfb6980319a365a70e68133891e096ba4f729dfc">
debian/patches/remove_barski_binding_site.png.patch
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#254a2da7a740675e537439eb88e32083b9ea4771">
docs/conf.py
</a>
</li>
<li class="file-stats">
<a href="#45279d673fb082724ea28f80389f732df86f12b2">
docs/content/bedtools-suite.rst
</a>
</li>
<li class="file-stats">
<a href="#96546b98f68cd24f5d4aa902aa32da8e1adf5200">
docs/content/general-usage.rst
</a>
</li>
<li class="file-stats">
<a href="#7e2c6a8f69d5f4c98b9a6c07bf681f16307a9035">
docs/content/history.rst
</a>
</li>
<li class="file-stats">
<a href="#19bd6248617da7c05d8c4973f56f6ff6212d5632">
<span class="new-file">
+
docs/content/images/tool-glyphs/multiinter-glyph.png
</span>
</a>
</li>
<li class="file-stats">
<a href="#f4c9bbf257f02b8907438fd39c4eee92829b3e75">
<span class="new-file">
+
docs/content/images/tool-glyphs/summary.png
</span>
</a>
</li>
<li class="file-stats">
<a href="#0ad0c9480aebc31dd47d0a136ec23871c6059bca">
docs/content/installation.rst
</a>
</li>
<li class="file-stats">
<a href="#bb2eeb9dff74dfd614b2d0b57b86618dbfd17ed2">
docs/content/overview.rst
</a>
</li>
<li class="file-stats">
<a href="#aa630dd5415c6570682d749debc4f9b76c6080f4">
docs/content/tools/bamtobed.rst
</a>
</li>
<li class="file-stats">
<a href="#6c750ccfbfa3d0b87bae479208a95e5649b78bec">
docs/content/tools/bamtofastq.rst
</a>
</li>
<li class="file-stats">
<a href="#6d18c433858243595a8ee50d86186975f3d290a7">
docs/content/tools/closest.rst
</a>
</li>
<li class="file-stats">
<a href="#6208d32a7c007d88e1f6d5239fdf5e3e3a537432">
docs/content/tools/genomecov.rst
</a>
</li>
<li class="file-stats">
<a href="#3e9ca6775e8b77711ecd2d4afe8eae9f2df9de9c">
docs/content/tools/groupby.rst
</a>
</li>
<li class="file-stats">
<a href="#c6ab52a857004a1f96039a80f396663df4be6363">
docs/content/tools/maskfasta.rst
</a>
</li>
<li class="file-stats">
<a href="#d10e151ca64939ef837895aa9596e987c58e31dd">
docs/content/tools/multiinter.rst
</a>
</li>
<li class="file-stats">
<a href="#109d68c230bc27bee9c109b784473bc3a7a4fff7">
docs/content/tools/overlap.rst
</a>
</li>
<li class="file-stats">
<a href="#4e2f9caa9be5af235e55cbbf5900acf884186d11">
docs/content/tools/shift.rst
</a>
</li>
<li class="file-stats">
<a href="#12273b4323e4c49f5225d63eb25721bfae841bb6">
<span class="new-file">
+
docs/content/tools/summary.rst
</span>
</a>
</li>
<li class="file-stats">
<a href="#d0153cac95479af9bfb99b746b633bc8255bb53a">
docs/index.rst
</a>
</li>
</ul>
<h5 style="margin-top: 10px; margin-bottom: 10px; font-size: 0.875rem;">
The diff was not included because it is too large.
</h5>

</div>
<div class="footer" style="margin-top: 10px;">
<p style="font-size: small; color: #737278;">

<br>
<a href="https://salsa.debian.org/med-team/bedtools/-/compare/4219183268d78af75628673989254cea91ef006b...ad36a93f547695e9e3fd55c94cfcbfe7b081b932">View it on GitLab</a>.
<br>
You're receiving this email because of your account on <a target="_blank" rel="noopener noreferrer" href="https://salsa.debian.org">salsa.debian.org</a>. <a href="https://salsa.debian.org/-/profile/notifications" target="_blank" rel="noopener noreferrer" class="mng-notif-link">Manage all notifications</a> · <a href="https://salsa.debian.org/help" target="_blank" rel="noopener noreferrer" class="help-link">Help</a>



</p>
</div>
</body>
</html>