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<h3>
Michael R. Crusoe 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/ec128e29edd413ab652dcaf87ce97cfd333d523d">ec128e29</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-10-28T12:28:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Include patch from Bernhard Übelacker to fix 32-bit builds (Closes: #955403)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bedtools/-/commit/0723ef8b6d3658f40260d5b2b9be234755c08599">0723ef8b</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-10-28T12:28:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 13
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bedtools/-/commit/15c67124d82ce72167ba3a69b904017659a886b0">15c67124</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-10-28T12:28:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Add salsa-ci file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bedtools/-/commit/5892a8e360b5d5f4731e1ecd53b7d8f238aef7de">5892a8e3</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-10-28T12:28:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Rules-Requires-Root: no
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bedtools/-/commit/cd290726b43e23b6efc331d6f45ae44fc600a163">cd290726</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-10-28T12:28:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Bug-Database, Bug-Submit.
Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/bedtools/-/commit/9889a387f292fabdb790f306a905cf805a56e55b">9889a387</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-10-28T12:28:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">adjust bin source location
</pre>
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<h4>7 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f7e7ac4bf284040b64c84f1e5c53bd685b88398d">
debian/bedtools.install
</a>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#f32ee8ab6f890b8dabbf8e757ec6a73c9cae6249">
<span class="new-file">
+
debian/patches/32-bit-fixes.patch
</span>
</a>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#b1dbf22e88351ec0d5d1d1a7f53295504b480e61">
<span class="new-file">
+
debian/salsa-ci.yml
</span>
</a>
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<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
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</ul>
<h4>Changes:</h4>
<li id="f7e7ac4bf284040b64c84f1e5c53bd685b88398d">
<a href="https://salsa.debian.org/med-team/bedtools/-/compare/fdd468037455494cf27f2f0b6b8cdecb6f31441c...9889a387f292fabdb790f306a905cf805a56e55b#f7e7ac4bf284040b64c84f1e5c53bd685b88398d"><strong>debian/bedtools.install</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="php"><span class="n" style="color: #333;">bin</span><span class="o" style="font-weight: 600;">/*</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">bin</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="n" style="color: #333;"><span class="idiff left">usr</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">local</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">/</span></span><span class="n" style="color: #333;">bin</span><span class="o" style="font-weight: 600;">/*</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">bin</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="php"><span class="n" style="color: #333;">genomes</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">share</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">bedtools</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="php"><span class="n" style="color: #333;">debian</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">bash_completion</span><span class="o" style="font-weight: 600;">/*</span> <span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">share</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">bash</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">completion</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">completions</span></span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bedtools/-/compare/fdd468037455494cf27f2f0b6b8cdecb6f31441c...9889a387f292fabdb790f306a905cf805a56e55b#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,6 +2,12 @@ bedtools (2.29.2+dfsg-4) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Remove the need for samtools via patch from upstream.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Include patch from Bernhard Übelacker to fix 32-bit builds. TODO: the</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> autopkgtests do not yet pass on i386 (and likely neither on other 32-bit</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> archs).</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * debhelper-compat 13 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * Add salsa-ci file (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Rules-Requires-Root: no (routine-update)</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Fri, 14 Feb 2020 16:50:58 +0100</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/bedtools/-/compare/fdd468037455494cf27f2f0b6b8cdecb6f31441c...9889a387f292fabdb790f306a905cf805a56e55b#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,7 +4,7 @@ Uploaders: Charles Plessy <plessy@debian.org>,</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">2</span>),</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">3</span>),</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> python3,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> zlib1g-dev,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libbz2-dev,</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,6 +13,7 @@ Standards-Version: 4.5.0</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/bedtools</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/bedtools.git</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Homepage: https://github.com/arq5x/bedtools2</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Rules-Requires-Root: no</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Package: bedtools</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Architecture: any</span>
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<li id="f32ee8ab6f890b8dabbf8e757ec6a73c9cae6249">
<a href="https://salsa.debian.org/med-team/bedtools/-/compare/fdd468037455494cf27f2f0b6b8cdecb6f31441c...9889a387f292fabdb790f306a905cf805a56e55b#f32ee8ab6f890b8dabbf8e757ec6a73c9cae6249"><strong>debian/patches/32-bit-fixes.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Use a variable type that is 8 bytes in size on 32 bit systems too.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Author: Bernhard Übelacker <bernhardu@mailbox.org></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/955403</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Forwarded: no</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">Last-Update: 2020-10-27</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bedtools.orig/src/randomBed/randomBed.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bedtools/src/randomBed/randomBed.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">@@ -58,7 +58,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> // we need to combine two consective calls to rand()</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> // because RAND_MAX is 2^31 (2147483648), whereas</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> // mammalian genomes are obviously much larger.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CHRPOS randStart = ((((long) rand()) << 31) | rand()) % genomeSize;</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CHRPOS randStart = ((((CHRPOS) rand()) << 31) | ((CHRPOS) rand())) % genomeSize;</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> // use the above randomStart (e.g., for human 0..3.1billion) </span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> // to identify the chrom and start on that chrom.</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> pair<string, CHRPOS> location = _genome->projectOnGenome(randStart);</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bedtools.orig/src/slopBed/slopBed.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bedtools/src/slopBed/slopBed.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="p">@@ -67,7 +67,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> _bed->Close();</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-static inline long _normalize_coord(long size, long pos) {</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+static inline CHRPOS _normalize_coord(CHRPOS size, CHRPOS pos) {</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> if(pos < 0) return 0;</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> if(size >= 0 && pos > size) return size;</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> return pos;</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="p">@@ -84,8 +84,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> bool should_swap = _forceStrand && bed.strand == "-";</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- long left_slop = should_swap ? (long)_rightSlop : (long)_leftSlop;</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- long right_slop = should_swap ? (long)_leftSlop : (long)_rightSlop;</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CHRPOS left_slop = should_swap ? (CHRPOS)_rightSlop : (CHRPOS)_leftSlop;</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CHRPOS right_slop = should_swap ? (CHRPOS)_leftSlop : (CHRPOS)_rightSlop;</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> bed.start -= left_slop;</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> bed.end += right_slop;</span></pre>
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<a href="https://salsa.debian.org/med-team/bedtools/-/compare/fdd468037455494cf27f2f0b6b8cdecb6f31441c...9889a387f292fabdb790f306a905cf805a56e55b#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,3 +10,4 @@ fix_intersect_test.patch</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">spelling</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">hardening</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">no-samtools</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">32-bit-fixes.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/bedtools/-/compare/fdd468037455494cf27f2f0b6b8cdecb6f31441c...9889a387f292fabdb790f306a905cf805a56e55b#b1dbf22e88351ec0d5d1d1a7f53295504b480e61"><strong>debian/salsa-ci.yml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="nn" style="color: #555;">---</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bedtools/-/compare/fdd468037455494cf27f2f0b6b8cdecb6f31441c...9889a387f292fabdb790f306a905cf805a56e55b#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Archive: GitHub</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Bug-Database: https://github.com/arq5x/bedtools2/issues</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Bug-Submit: https://github.com/arq5x/bedtools2/issues/new</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Reference:</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> Author: Quinlan, Aaron R. and Hall, Ira M.</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> Title: ></span>
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