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<h3>
Étienne Mollier pushed to branch master
at <a href="https://salsa.debian.org/med-team/bioperl-run">Debian Med / bioperl-run</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bioperl-run/-/commit/ac21737cd72657c8064c050381c04ddf753cc80a">ac21737c</a></strong>
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<span>by Étienne Mollier</span>
<i>at 2020-12-04T23:19:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add get-overlap.patch
It maps "betools overlap" to "getOverlap".
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bioperl-run/-/commit/8dc23c6ffb4a9d9a73a1eb732bf11915bbd5c4ea">8dc23c6f</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-12-04T23:21:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">build depend on bedtools datasets
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bioperl-run/-/commit/61b1a5aed7046d17ede7f01d5f9ffab82b5ad1ea">61b1a5ae</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-12-04T23:28:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add alternate-data.patch
</pre>
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<h4>5 changed files:</h4>
<ul>
<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="#b472300eb19c309e0f4225559c8920ccf1f28829">
<span class="new-file">
+
debian/patches/alternate-data.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#e89cbd5f49fe9ae0dd57b1bf26b85f87bd0cba12">
<span class="new-file">
+
debian/patches/get-overlap.patch
</span>
</a>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bioperl-run/-/compare/7d8c9a8542ae51ea7e538a327da35a675227b933...61b1a5aed7046d17ede7f01d5f9ffab82b5ad1ea#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,6 +16,12 @@ bioperl-run (1.7.3-5) UNRELEASED; urgency=medium</td>
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<td class="diff-line-num old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
16
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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> * debhelper-compat 13 (routine-update)</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> * Remove trailing whitespace in debian/control (routine-update)</span>
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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> [ Étienne Mollier ]</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> * Add get-overlap.patch to map to the proper "getOverlap" wrapper.</span>
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<td class="diff-line-num new old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> * Add build time test dependencies to get BEDtools test data sets.</span>
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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> * Add alternate-data.patch to use a dataset available in the Debian</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> archive during build time testings.</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Thu, 03 Dec 2020 21:57:37 +0100</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">bioperl-run (1.7.3-4) unstable; urgency=medium</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/bioperl-run/-/compare/7d8c9a8542ae51ea7e538a327da35a675227b933...61b1a5aed7046d17ede7f01d5f9ffab82b5ad1ea#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,6 +28,7 @@ Build-Depends-Indep: perl,</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"># Needed for the regression tests: all Recommends of bioperl-run except embassy, that needs interactive setup.</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> amap-align,</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> bedtools,</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> bedtools-test,</span>
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31
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<td class="diff-line-num new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> ncbi-blast+-legacy,</span>
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32
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33
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> clustalw,</span>
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33
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> emboss,</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">@@ -43,6 +44,7 @@ Build-Depends-Indep: perl,</td>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> phyml,</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"> primer3,</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"> probcons,</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> python3-pybedtools,</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"> raxml,</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"> samtools,</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"> sim4,</span>
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<a href="https://salsa.debian.org/med-team/bioperl-run/-/compare/7d8c9a8542ae51ea7e538a327da35a675227b933...61b1a5aed7046d17ede7f01d5f9ffab82b5ad1ea#b472300eb19c309e0f4225559c8920ccf1f28829"><strong>debian/patches/alternate-data.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: use alternate rmsk dataset</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> This patch solves the following test suite error, occurring even though BED</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> tools are made available at build time testing:</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> .</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> ------------- EXCEPTION: Bio::Root::Exception -------------</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> MSG: File '' not BED/GFF/VCF format.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> STACK: Error::throw</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:449</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> STACK: Bio::Tools::Run::BEDTools::run /<<PKGBUILDDIR>>/blib/lib/Bio/Tools/Run/BEDTools.pm:477</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> STACK: t/BEDTools.t:252</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> -----------------------------------------------------------</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> .</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> Instead of using the default rmsk.hg18.chr21.bed file which is unavailable in</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> the archive, let's use rmsk.hg18.chr21.small.bed, provided by the package</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> python3-pybedtools, which seemingly does the job almost as well apparently.</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="p">Author: Étienne Mollier <etienne.mollier@mailoo.org></span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=974168</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="p">Forwarded: no</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="p">Last-Update: 2020-12-04</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="p">This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bioperl-run.orig/t/BEDTools.t</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bioperl-run/t/BEDTools.t</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="p">@@ -182,7 +182,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> chdir $dir; # Go back to $dir;</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> else {</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ($rmsk_bed) = `find /usr -name 'rmsk.hg18.chr21.bed' 2>/dev/null`;</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ($rmsk_bed) = `find /usr -name 'rmsk.hg18.chr21.small.bed' 2>/dev/null`;</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> ($gene_bed) = `find /usr -name 'knownGene.hg18.chr21.bed' 2>/dev/null`;</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> ($mm8_genome) = `find /usr -name 'mouse.mm8.genome' 2>/dev/null`;</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> ($mm9_genome) = `find /usr -name 'mouse.mm9.genome' 2>/dev/null`;</span></pre>
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<li id="e89cbd5f49fe9ae0dd57b1bf26b85f87bd0cba12">
<a href="https://salsa.debian.org/med-team/bioperl-run/-/compare/7d8c9a8542ae51ea7e538a327da35a675227b933...61b1a5aed7046d17ede7f01d5f9ffab82b5ad1ea#e89cbd5f49fe9ae0dd57b1bf26b85f87bd0cba12"><strong>debian/patches/get-overlap.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: change mapping of bedtools subcommand overlap</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> This patch addresses the following test error:</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> .</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> # Failed test 'get version for 'overlap''</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> # at t/BEDTools.t line 212.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> . </span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> ------------- EXCEPTION: Bio::Root::Exception -------------</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> MSG: No executable!</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> STACK: Error::throw</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:449</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> STACK: Bio::Tools::Run::BEDTools::run /<<PKGBUILDDIR>>/blib/lib/Bio/Tools/Run/BEDTools.pm:278</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> STACK: t/BEDTools.t:275</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> -----------------------------------------------------------</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> .</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> Config.pm assumes the subcommand of bedtools "overlap" is called "overlap", but</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> it is actually "getOverlap".</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">Author: Étienne Mollier <etienne.mollier@mailoo.org></span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=974168</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="p">Forwarded: no</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="p">Last-Update: 2020-12-04</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="p">This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bioperl-run.orig/lib/Bio/Tools/Run/BEDTools/Config.pm</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bioperl-run/lib/Bio/Tools/Run/BEDTools/Config.pm</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="p">@@ -134,7 +134,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> 'links' => 'linksBed',</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> 'pair_to_pair' => 'pairToPair',</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> 'subtract' => 'subtractBed',</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 'overlap' => 'overlap',</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 'overlap' => 'getOverlap',</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> 'group_by' => 'groupBy',</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> 'graph_union' => 'unionBedGraphs'</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> );</span></pre>
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<a href="https://salsa.debian.org/med-team/bioperl-run/-/compare/7d8c9a8542ae51ea7e538a327da35a675227b933...61b1a5aed7046d17ede7f01d5f9ffab82b5ad1ea#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">@@ -12,3 +12,5 @@ skip_tests_for_ncbi-blast+.patch</td>
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12
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">hyphy.patch</span>
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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
13
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">remove_tests_for_ensembl.patch</span>
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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
14
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">skip_tests_for_soap.patch</span>
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<td class="diff-line-num new old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">get-overlap.patch</span>
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<td class="diff-line-num new old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">alternate-data.patch</span></pre>
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