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<h3>
Andreas Tille 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/5369d5af9f99aed54e7f493b32fe3bbadf602a11">5369d5af</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-01T08:49:28Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use 2to3 to port to Python3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bedtools/commit/ac2d6f645770225affacc98a18f18cf69572aa5d">ac2d6f64</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-01T09:10:26Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove unsafe links for gcc and g++
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bedtools/commit/54d75c6db177d509508106e824a8d6bc002c3cfa">54d75c6d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-01T09:10:38Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.28.0+dfsg1</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bedtools/commit/e9648312c3d6335468a289d74b652070b0f87aec">e9648312</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-01T09:11:49Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag '2.28.0+dfsg1'
Update to upstream version '2.28.0+dfsg1'
with Debian dir 46f31e170f5605cd3f01423b28ce023030406d63</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bedtools/commit/28247b1d415b256d668a438ddfa34c12d0068b84">28247b1d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-01T09:26:40Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
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<h4>7 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
<span class="new-file">
+
debian/patches/2to3.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
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<a href="#5d36d872f9395226ad251661f9a7b376da7b233d">
<span class="deleted-file">
−
g++
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<li class="file-stats">
<a href="#fce79b7fe1fee3a977fa1bd4efbd9e9a06c29c14">
<span class="deleted-file">
−
gcc
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</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bedtools/compare/2bd5eb3bc8fd6b5f9dcc597a8cee63e59f374f8b...28247b1d415b256d668a438ddfa34c12d0068b84#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bedtools (2.28.0+dfsg1-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="3" 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="LC3" class="line" lang="plaintext"> * Use 2to3 to port to Python3</span>
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<td class="diff-line-num new new_line" data-linenumber="4" 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="LC4" class="line" lang="plaintext"> Closes: #936199</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Remove unsafe links for gcc and g++</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="7" 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="LC7" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Sun, 01 Sep 2019 11:14:59 +0200</span>
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<td class="diff-line-num new new_line" data-linenumber="8" 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="LC8" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="9" 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="LC9" class="line" lang="plaintext">bedtools (2.28.0+dfsg-3) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Team upload.</span>
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<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/bedtools/compare/2bd5eb3bc8fd6b5f9dcc597a8cee63e59f374f8b...28247b1d415b256d668a438ddfa34c12d0068b84#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</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">@@ -3,6 +3,8 @@ Source: https://github.com/arq5x/bedtools2/archive/v2.25.0.tar.gz</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Comment: File barski_binding_site.png is from</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Jothi et al, 2008, doi:10.1093/nar/gkn488, licensed under no-DFSG CC-BY-NC 2.0</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Files-Excluded: */barski_binding_site.png</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> */g++</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> */gcc</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Upstream-Name: bedtools</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Files: *</span>
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<a href="https://salsa.debian.org/med-team/bedtools/compare/2bd5eb3bc8fd6b5f9dcc597a8cee63e59f374f8b...28247b1d415b256d668a438ddfa34c12d0068b84#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Use 2to3 to port to Python3</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/936199</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: Sun, 01 Sep 2019 10:31:52 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- a/docs/conf.py</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/docs/conf.py</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -43,8 +43,8 @@</span> source_suffix = '.rst'</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> master_doc = 'index'</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> # General information about the project.</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-project = u'bedtools'</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-copyright = u'2009 - 2017, Aaron R. Quinlan and Neil Kindlon'</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+project = 'bedtools'</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;">+copyright = '2009 - 2017, Aaron R. Quinlan and Neil Kindlon'</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> # The version info for the project you're documenting, acts as replacement for</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> # |version| and |release|, also used in various other places throughout the</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="p">@@ -186,8 +186,8 @@</span> htmlhelp_basename = 'bedtools-docs'</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> # Grouping the document tree into LaTeX files. List of tuples</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> # (source start file, target name, title, author, documentclass [howto/manual]).</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> latex_documents = [</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;">- ('index', 'bedtools.tex', u'Bedtools Documentation', </span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- u'Quinlan lab @ Univ. of Utah', 'manual'),</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ('index', 'bedtools.tex', 'Bedtools Documentation', </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;">+ 'Quinlan lab @ Univ. of Utah', 'manual'),</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> ]</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> # The name of an image file (relative to this directory) to place at the top of</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="p">@@ -219,7 +219,7 @@</span> latex_documents = [</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> # One entry per manual page. List of tuples</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> # (source start file, name, description, authors, manual section).</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> man_pages = [</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;">- ('index', 'bedtools', u'Bedtools Documentation', [u'UU'], 1)</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ('index', 'bedtools', 'Bedtools Documentation', ['UU'], 1)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> ]</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> # Example configuration for intersphinx: refer to the Python standard library.</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/fisher/README.md</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/fisher/README.md</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="p">@@ -2,7 +2,7 @@</span> Fisher Testing</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> ==============</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> Fisher is now based on the count of interval overlaps, subject to `-f`.</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-We can compare the output of fisher on simulated data by running `python sim.py`</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+We can compare the output of fisher on simulated data by running `python3 sim.py`</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> which will show the output from `bedtools fisher` and then running `bash shuf.sh`</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> which will repeatedly run</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/fisher/cmp.sh</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/fisher/cmp.sh</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="p">@@ -3,7 +3,7 @@</span> set -eo pipefail</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> echo "fisher,shuffled"</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> for i in $(seq 1000); do</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fisher=$(python ./sim.py | tail -1 | cut -f 2)</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fisher=$(python3 ./sim.py | tail -1 | cut -f 2)</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> shuffle=$(bash shuf.sh)</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> echo "$fisher,$shuffle"</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> done</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/fisher/sim.py</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/fisher/sim.py</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="p">@@ -25,7 +25,7 @@</span> with open('taa.bed', 'w') as fh:</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> fh.write("chr1\t%i\t%i\n" % (s, e))</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> fh.flush()</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-print >> open('tgg.genome', 'w'), ("chr1\t%i" % genome_size)</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+print(("chr1\t%i" % genome_size), file=open('tgg.genome', 'w'))</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> # NOTE: add -m here to make merged output</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-print check_output("../../bin/bedtools fisher -a taa.bed -b tbb.bed -g tgg.genome", shell=True).strip()</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+print(check_output("../../bin/bedtools fisher -a taa.bed -b tbb.bed -g tgg.genome", shell=True).strip())</span></span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/bedtools/compare/2bd5eb3bc8fd6b5f9dcc597a8cee63e59f374f8b...28247b1d415b256d668a438ddfa34c12d0068b84#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">@@ -6,3 +6,4 @@ reproducible_build.patch</td>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">#louder</span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"># not Debian-specific, upstream has worked on that, too</span>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">flag_no_overwrite</span>
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<td class="diff-line-num new old_line" data-linenumber="9" 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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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">2to3.patch</span></pre>
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<li id="68ef9f98c01c7eecd4c605cc26048a06f3304b79">
<a href="https://salsa.debian.org/med-team/bedtools/compare/2bd5eb3bc8fd6b5f9dcc597a8cee63e59f374f8b...28247b1d415b256d668a438ddfa34c12d0068b84#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">version=4</span>
</pre>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">opts="repacksuffix=+dfsg,dversionmangle=<span class="idiff left right">s/\+dfsg//g</span>,repack,compression=xz" \</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">opts="repacksuffix=+dfsg,dversionmangle=<span class="idiff left right">auto</span>,repack,compression=xz" \</span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> https://github.com/arq5x/bedtools2/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)</span></pre>
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<a href="https://salsa.debian.org/med-team/bedtools/compare/2bd5eb3bc8fd6b5f9dcc597a8cee63e59f374f8b...28247b1d415b256d668a438ddfa34c12d0068b84#5d36d872f9395226ad251661f9a7b376da7b233d"><strong>g++</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">/usr/bin/ccache</span></pre>
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<a href="https://salsa.debian.org/med-team/bedtools/compare/2bd5eb3bc8fd6b5f9dcc597a8cee63e59f374f8b...28247b1d415b256d668a438ddfa34c12d0068b84#fce79b7fe1fee3a977fa1bd4efbd9e9a06c29c14"><strong>gcc</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">/usr/bin/ccache</span></pre>
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