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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/macs">Debian Med / macs</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/macs/commit/a919eaa83caf11a5426c0e9431fa897ff7f67cb4">a919eaa8</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-10-01T00:44:00Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/macs/commit/8f6bfc8cdbdaaf13181699889f3a152e1d245001">8f6bfc8c</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-10-01T00:44:01Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.1.4</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/macs/commit/9d8a196af6ab915e7a2c84dc8cce9e69e5a80932">9d8a196a</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-10-01T01:01:00Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.1.4'
Update to upstream version '2.1.4'
with Debian dir 98e44709befa1dd027c6b1e248cfa17dad1c4207
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/macs/commit/5b2bb5b2030f7b64d102f661f724637ae32f4426">5b2bb5b2</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-10-01T10:37:21Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
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</ul>
<h4>18 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#00fe7828d56d7a3ee4030d6cea057cf13f50e70c">
ChangeLog
</a>
</li>
<li class="file-stats">
<a href="#b2270542d41297db1ee0d12698e609ea3ec25ce7">
INSTALL.md
</a>
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<li class="file-stats">
<a href="#984f107ab387553e17758fef354dbe9d80c4eaa3">
MACS2.egg-info/PKG-INFO
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<li class="file-stats">
<a href="#31291f8e6d83e2788d0b4e4676278465627c60fa">
MACS2.egg-info/SOURCES.txt
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<li class="file-stats">
<a href="#b4b38e5409758d0596f1ecc988e5dd67643d8640">
MACS2.egg-info/requires.txt
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<li class="file-stats">
<a href="#48431da50d9dc27b278c0a288c2c5eb6e1bc5db1">
MACS2/Constants.py
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<li class="file-stats">
<a href="#5b10e32bc98bb18a79345759d8d25af86740f0fc">
<span class="deleted-file">
−
MACS2/IO/BinKeeper.py
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<li class="file-stats">
<a href="#f83eb1a74dfc6efcfa02c94c20a8c871e39917f2">
MACS2/IO/CallPeakUnit.c
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<li class="file-stats">
<a href="#92d6f54eff86777dbb1d7cd341f09183f2320da8">
MACS2/IO/CallPeakUnit.pyx
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<li class="file-stats">
<a href="#8ac54c696d92e5af87f0ce070dc619f25ccf8cbf">
MACS2/IO/ScoreTrack.c
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<li class="file-stats">
<a href="#7478182f47d385af4085c8e455192f6565e8ec5b">
MACS2/IO/ScoreTrack.pyx
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<li class="file-stats">
<a href="#81c3c19aa1f3d799315ff190821707ee6fb2bf63">
MACS2/bdgdiff_cmd.py
</a>
</li>
<li class="file-stats">
<a href="#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">
PKG-INFO
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<span class="new-file">
+
debian/patches/series
</span>
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<li class="file-stats">
<a href="#e4c19aed51618bf0c7ebd03189c67e422f84d4eb">
<span class="new-file">
+
debian/patches/spelling
</span>
</a>
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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</ul>
<h4>Changes:</h4>
<li id="00fe7828d56d7a3ee4030d6cea057cf13f50e70c">
<a href="https://salsa.debian.org/med-team/macs/compare/80c600ce7b134f707ca923396ac8a671bffa1cb4...5b2bb5b2030f7b64d102f661f724637ae32f4426#00fe7828d56d7a3ee4030d6cea057cf13f50e70c"><strong>ChangeLog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="mosel"><span class="m" style="color: #099;">2019</span><span class="p">-</span><span class="m" style="color: #099;">09</span><span class="p">-</span><span class="m" style="color: #099;">30</span> <span class="n" style="color: #333;">Tao</span> <span class="n" style="color: #333;">Liu</span> <span class="p"><</span><span class="n" style="color: #333;">vladimir</span><span class="p">.</span><span class="n" style="color: #333;">liu</span><span class="p">@</span><span class="n" style="color: #333;">gmail</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="2" 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="LC2" class="line" lang="mosel"> <span class="n" style="color: #333;">MACS</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">2.1.4</span></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">
3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="mosel"></span>
</pre>
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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="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Features</span> <span class="n" style="color: #333;">added</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="5" 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">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="mosel"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="6" 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="LC6" class="line" lang="mosel"> <span class="n" style="color: #333;">Github</span> <span class="n" style="color: #333;">Actions</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">used</span> <span class="n" style="color: #333;">together</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">Travis</span> <span class="n" style="color: #333;">CI</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">testing</span> <span class="k" style="font-weight: 600;">and</span></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">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="mosel"> <span class="n" style="color: #333;">deployment</span><span class="p">.</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="mosel"></span>
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<td class="diff-line-num new new_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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<pre style="margin: 0;">+<span id="LC9" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Bugs</span> <span class="n" style="color: #333;">fixed</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="mosel"></span>
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<td class="diff-line-num new new_line" data-linenumber="11" 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="LC11" class="line" lang="mosel"> <span class="n" style="color: #333;">PR</span> <span class="p">#</span><span class="m" style="color: #099;">322</span><span class="p">:</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="mosel"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="13" 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="LC13" class="line" lang="mosel"> <span class="m" style="color: #099;">1</span><span class="p">)</span> <span class="p">#</span><span class="m" style="color: #099;">318</span> <span class="n" style="color: #333;">Random</span> <span class="n" style="color: #333;">score</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">bdgdiff</span> <span class="n" style="color: #333;">output</span><span class="p">.</span> <span class="n" style="color: #333;">It</span> <span class="n" style="color: #333;">turns</span> <span class="n" style="color: #333;">out</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">sum_v</span> <span class="n" style="color: #333;">is</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14" 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">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">initialized</span> <span class="k" style="font-weight: 600;">as</span> <span class="m" style="color: #099;">0</span> <span class="n" style="color: #333;">before</span> <span class="n" style="color: #333;">adding</span><span class="p">.</span> <span class="n" style="color: #333;">Potential</span> <span class="n" style="color: #333;">bugs</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">fixed</span> <span class="k" style="font-weight: 600;">in</span></span>
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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">
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="mosel"> <span class="n" style="color: #333;">other</span> <span class="n" style="color: #333;">functions</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ScoreTrack</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">CallPeakUnit</span> <span class="n" style="color: #333;">codes</span><span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="mosel"> <span class="m" style="color: #099;">2</span><span class="p">)</span> <span class="p">#</span><span class="m" style="color: #099;">321</span> <span class="n" style="color: #333;">Cython</span> <span class="n" style="color: #333;">dependency</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">setup</span><span class="p">.</span><span class="n" style="color: #333;">py</span> <span class="n" style="color: #333;">script</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">removed</span><span class="p">.</span> <span class="k" style="font-weight: 600;">And</span> <span class="n" style="color: #333;">place</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="mosel"> <span class="s1" style="color: #d14;">'cythonzie'</span> <span class="n" style="color: #333;">call</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">correct</span> <span class="n" style="color: #333;">position</span><span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="mosel"> <span class="m" style="color: #099;">3</span><span class="p">)</span> <span class="n" style="color: #333;">A</span> <span class="n" style="color: #333;">typo</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">fixed</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Github</span> <span class="n" style="color: #333;">Actions</span> <span class="n" style="color: #333;">script</span><span class="p">.</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="mosel"><span class="m" style="color: #099;">2019</span><span class="p">-</span><span class="m" style="color: #099;">09</span><span class="p">-</span><span class="m" style="color: #099;">19</span> <span class="n" style="color: #333;">Tao</span> <span class="n" style="color: #333;">Liu</span> <span class="p"><</span><span class="n" style="color: #333;">vladimir</span><span class="p">.</span><span class="n" style="color: #333;">liu</span><span class="p">@</span><span class="n" style="color: #333;">gmail</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">></span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="mosel"> <span class="n" style="color: #333;">MACS</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">2.1.3.3</span></span>
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<a href="https://salsa.debian.org/med-team/macs/compare/80c600ce7b134f707ca923396ac8a671bffa1cb4...5b2bb5b2030f7b64d102f661f724637ae32f4426#b2270542d41297db1ee0d12698e609ea3ec25ce7"><strong>INSTALL.md</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># INSTALL Guide For MACS</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="markdown">Time-stamp: <span class="nt" style="color: #000080;"><2019-09-<span class="idiff left">20</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff right">15:08:3</span>5</span> <span class="na" style="color: #008080;">taoliu</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown">Time-stamp: <span class="nt" style="color: #000080;"><2019-09-<span class="idiff left">30</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff right">14:47:4</span>5</span> <span class="na" style="color: #008080;">taoliu</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown">Please check the following instructions to complete your installation.</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Prerequisites</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="markdown">Python version must be equal to <span class="ge" style="font-style: italic;">*2.7*</span> to run MACS. I recommend</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="markdown">using the version <span class="ge" style="font-style: italic;">*2.7.15*</span>.</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown">Python version must be equal to <span class="ge" style="font-style: italic;">*2.7*</span> to run MACS.</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Numpy</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.scipy.org/Download</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">>=1.1<span class="idiff left right">5</span></span><span class="p">)</span> are required to run MACS v2. </span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Numpy</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.scipy.org/Download</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">>=1.1<span class="idiff left right">6</span></span><span class="p">)</span> are required to run MACS v2. </span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown">GCC is required to compile <span class="sb" style="color: #d14;">`.c`</span> codes in MACS v2 package, and python</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown">header files are needed. If you are using Mac OSX, I recommend you</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown">install Xcode; if you are using Linux, you need to make sure</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="markdown"><span class="sb" style="color: #d14;">`python-dev`</span> is installed.</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Cython</span><span class="p">](</span><span class="sx" style="color: #d14;">http://cython.org/</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">>=0.2<span class="idiff left right">5</span></span><span class="p">)</span> is required to generate <span class="sb" style="color: #d14;">`.c`</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Cython</span><span class="p">](</span><span class="sx" style="color: #d14;">http://cython.org/</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">>=0.2<span class="idiff left right">9</span></span><span class="p">)</span> is required to generate <span class="sb" style="color: #d14;">`.c`</span></span>
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<td class="diff-line-num old_line" data-linenumber="19" 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="markdown">files from <span class="sb" style="color: #d14;">`.pyx`</span> files using <span class="sb" style="color: #d14;">`setup.py`</span> script.</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Easy installation through PyPI</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="25" 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>
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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">@@ -25,12 +24,12 @@ it's not available in your system. *Note* if you have already</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown">installed numpy and scipy system-wide, you can use <span class="sb" style="color: #d14;">`virtualenv</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown"><span class="sb" style="color: #d14;">--system-site-packages`</span> to let your virtual Python environment have</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown">access to system-wide numpy and scipy libraries so that you don't need</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="markdown">to install them again.<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown">to install them again.</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="markdown">Then under command line, type <span class="sb" style="color: #d14;">`pip install MACS2`</span>. PyPI will</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="markdown">install Numpy and Cython automatically if they are absent. </span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="markdown">To upgrade MACS2, type <span class="sb" style="color: #d14;">`pip install -<span class="idiff left right">U</span> MACS2`</span>. It will check</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown">To upgrade MACS2, type <span class="sb" style="color: #d14;">`pip install -<span class="idiff left right">-upgrade</span> MACS2`</span>. It will check</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="markdown">currently installed MACS2, compare the version with the one on PyPI</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="markdown">repository, download and install newer version while necessary.</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="markdown"></span>
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<li id="984f107ab387553e17758fef354dbe9d80c4eaa3">
<a href="https://salsa.debian.org/med-team/macs/compare/80c600ce7b134f707ca923396ac8a671bffa1cb4...5b2bb5b2030f7b64d102f661f724637ae32f4426#984f107ab387553e17758fef354dbe9d80c4eaa3"><strong>MACS2.egg-info/PKG-INFO</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Metadata-Version: 2.1</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Name: MACS2</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Version: 2.1.<span class="idiff left right">3.3</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Version: 2.1.<span class="idiff left right">4</span></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Summary: Model Based Analysis for ChIP-Seq data</span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Home-page: http://github.com/taoliu/MACS/</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Author: Tao Liu</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Author-email: vladimir.liu@gmail.com</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">License: UNKNOWN</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">Description: # Recent Changes for MACS (2.1.<span class="idiff left right">3.3</span>)</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Description: # Recent Changes for MACS (2.1.<span class="idiff left right">4</span>)</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"> ### 2.1.3.3</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> ### 2.1.4</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * Features added</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> Github Actions is used together with Travis CI for testing and</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> deployment.</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> * Bugs fixed (PR #322)</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> 1) #318 Random score in `bdgdiff` output. It turns out the sum_v</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> is not initialized as 0 before adding. Potential bugs are fixed in</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> other functions in ScoreTrack and CallPeakUnit codes.</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> 2) #321 Cython dependency in `setup.py` script is removed. And</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> place 'cythonzie' call to the correct position.</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> 3) A typo is fixed in Github Actions script. </span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> ### 2.1.3</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> * Features added</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> 1) Support Docker auto-deploy. PR #309</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">@@ -43,44 +61,7 @@ Description: # Recent Changes for MACS (2.1.3.3)</td>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext"> 3) Rename COPYING to LICENSE.</span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext"> ### 2.1.2</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext"> * New features</span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext"> 1) Added missing BEDPE support. And enable the support for BAMPE</span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext"> and BEDPE formats in 'pileup', 'filterdup' and 'randsample'</span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext"> subcommands. When format is BAMPE or BEDPE, The 'pileup' command</span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext"> will pile up the whole fragment defined by mapping locations of</span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext"> the left end and right end of each read pair. Thank @purcaro</span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext"> </span>
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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext"> 2) Added options to callpeak command for tweaking max-gap and</span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext"> min-len during peak calling. Thank @jsh58!</span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext"> </span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext"> 3) The callpeak option "--to-large" option is replaced with</span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext"> "--scale-to large".</span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext"> </span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext"> 4) The randsample option "-t" has been replaced with "-i".</span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext"> </span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext"> * Bug fixes</span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="plaintext"> </span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="plaintext"> 1) Fixed memory issue related to #122 and #146</span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="plaintext"> </span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="plaintext"> 2) Fixed a bug caused by a typo. Related to #249, Thank @shengqh</span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="plaintext"> </span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="plaintext"> 3) Fixed a bug while setting commandline qvalue cutoff.</span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="plaintext"> </span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="plaintext"> 4) Better describe the 5th column of narrowPeak. Thank @alexbarrera</span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="plaintext"> </span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="plaintext"> 5) Fixed the calculation of average fragment length for paired-end</span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="plaintext"> data. Thank @jsh58</span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="plaintext"> </span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="plaintext"> 6) Fixed bugs caused by khash while computing p/q-value and log</span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="plaintext"> likelihood ratios. Thank @jsh58</span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="plaintext"> </span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="plaintext"> 7) More spelling tweaks in source code. Thank @mr-c</span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="plaintext"> # README for MACS2 (2.1.3.3)</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> # README for MACS2 (2.1.4)</span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext"> ## Introduction</span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext"> </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">@@ -268,8 +249,19 @@ Description: # Recent Changes for MACS (2.1.3.3)</td>
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="plaintext"> ##### `--min-length`, `--max-gap`</span>
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="plaintext"> These two options can be used to fine-tune the peak calling behavior by specifying the minimum length of a called peak and the maximum allowed gap between two nearby regions to be merged. In another word, a called peak has to be longer than *min-length*, and if the distance between two nearby peaks is smaller than *max-gap* then they will be merged as one. If they are not set, MACS2 will set the DEFAULT value for *min-length* as the predicted fragment size d, and the DEFAULT value for *max-gap* as the detected read length. Note, if you set a *min-length* value smaller than the fragment size, it may have NO effect on the result. For BROAD peak calling, try to set a</span>
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="plaintext"> large value such as 500bps. You can also use '--cutoff-analysis' option with default setting, and check the column 'avelpeak' under different cutoff values to decide a reasonable *min-length* value.</span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="plaintext"> These two options can be used to fine-tune the peak calling behavior</span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="plaintext"> by specifying the minimum length of a called peak and the maximum</span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="plaintext"> allowed gap between two nearby regions to be merged. In another word,</span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="plaintext"> a called peak has to be longer than *min-length*, and if the distance</span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="plaintext"> between two nearby peaks is smaller than *max-gap* then they will be</span>
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="plaintext"> merged as one. If they are not set, MACS2 will set the DEFAULT value</span>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="plaintext"> for *min-length* as the predicted fragment size d, and the DEFAULT</span>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="plaintext"> value for *max-gap* as the detected read length. Note, if you set a</span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="plaintext"> *min-length* value smaller than the fragment size, it may have NO</span>
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="plaintext"> effect on the result. For BROAD peak calling, try to set a large value</span>
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="plaintext"> such as 500bps. You can also use '--cutoff-analysis' option with</span>
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="plaintext"> default setting, and check the column 'avelpeak' under different</span>
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="plaintext"> cutoff values to decide a reasonable *min-length* value.</span>
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="plaintext"> ##### `--nolambda`</span>
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="plaintext"> </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">@@ -405,21 +397,33 @@ Description: # Recent Changes for MACS (2.1.3.3)</td>
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="plaintext"> - fold enrichment for this peak summit against random Poisson distribution with local lambda, </span>
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="plaintext"> - -log10(qvalue) at peak summit</span>
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC408" class="line" lang="plaintext"> Coordinates in XLS is 1-based which is different with BED format. When `--broad` is enabled for broad peak calling, the pileup, pvalue, qvalue, and fold change in the XLS file will be the mean value across the entire peak region, since peak summit won't be called in broad peak calling mode. </span>
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="plaintext"> Coordinates in XLS is 1-based which is different with BED</span>
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="plaintext"> format. When `--broad` is enabled for broad peak calling, the</span>
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="plaintext"> pileup, pvalue, qvalue, and fold change in the XLS file will be the</span>
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="plaintext"> mean value across the entire peak region, since peak summit won't</span>
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="plaintext"> be called in broad peak calling mode.</span>
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="plaintext"> 2. `NAME_peaks.narrowPeak` is BED6+4 format file which contains the</span>
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="plaintext"> peak locations together with peak summit, pvalue and qvalue. You</span>
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="plaintext"> can load it to UCSC genome browser. Definition of some specific</span>
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<pre style="margin: 0;"> <span id="LC409" class="line" lang="plaintext"> columns are: </span>
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="plaintext"> - 5th: integer score for display. It's calculated as `int(-10*log10pvalue)` or `int(-10*log10qvalue)` depending on whether `-p` (pvalue) or `-q` (qvalue) is used as score cutoff. Please note that currently this value might be out of the [0-1000] range defined in [UCSC Encode narrowPeak format](https://genome.ucsc.edu/FAQ/FAQformat.html#format12). You can let the value saturated at 1000 (i.e. p/q-value = 10^-100) by using the following 1-liner awk: `awk -v OFS="\t" '{$5=$5>1000?1000:$5} {print}' NAME_peaks.narrowPeak`</span>
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="plaintext"> - 5th: integer score for display. It's calculated as</span>
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="plaintext"> `int(-10*log10pvalue)` or `int(-10*log10qvalue)` depending on</span>
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="plaintext"> whether `-p` (pvalue) or `-q` (qvalue) is used as score</span>
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="plaintext"> cutoff. Please note that currently this value might be out of the</span>
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="plaintext"> [0-1000] range defined in [UCSC Encode narrowPeak</span>
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="plaintext"> format](https://genome.ucsc.edu/FAQ/FAQformat.html#format12). You</span>
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="plaintext"> can let the value saturated at 1000 (i.e. p/q-value = 10^-100) by</span>
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="plaintext"> using the following 1-liner awk: `awk -v OFS="\t"</span>
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="plaintext"> '{$5=$5>1000?1000:$5} {print}' NAME_peaks.narrowPeak`</span>
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="plaintext"> - 7th: fold-change at peak summit</span>
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="plaintext"> - 8th: -log10pvalue at peak summit</span>
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="plaintext"> - 9th: -log10qvalue at peak summit</span>
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="plaintext"> - 10th: relative summit position to peak start</span>
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC421" class="line" lang="plaintext"> The file can be loaded directly to UCSC genome browser. Remove the<span class="idiff left right"> beginning track line if you want to</span></span>
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<pre style="margin: 0;">-<span id="LC422" class="line" lang="plaintext"> analyze it by other tools.</span>
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="plaintext"> The file can be loaded directly to UCSC genome browser. Remove the</span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="plaintext"> <span class="idiff left right">beginning track line if you want to </span>analyze it by other tools.</span>
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC428" class="line" lang="plaintext"> 3. `NAME_summits.bed` is in BED format, which contains the peak</span>
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="plaintext"> summits locations for every peaks. The 5th column in this file is</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">@@ -474,7 +478,8 @@ Description: # Recent Changes for MACS (2.1.3.3)</td>
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<pre style="margin: 0;"> <span id="LC478" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC479" class="line" lang="plaintext"> ## Tips of fine-tuning peak calling</span>
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<pre style="margin: 0;"> <span id="LC480" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC477" class="line" lang="plaintext"> There are several subcommands within MACSv2 package to fine-tune or customize your analysis:</span>
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="plaintext"> There are several subcommands within MACSv2 package to fine-tune or</span>
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="plaintext"> customize your analysis:</span>
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<pre style="margin: 0;"> <span id="LC483" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC484" class="line" lang="plaintext"> 1. `bdgcmp` can be used on `*_treat_pileup.bdg` and</span>
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<pre style="margin: 0;"> <span id="LC485" class="line" lang="plaintext"> `*_control_lambda.bdg` or bedGraph files from other resources</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">@@ -494,8 +499,9 @@ Description: # Recent Changes for MACS (2.1.3.3)</td>
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<pre style="margin: 0;"> <span id="LC499" class="line" lang="plaintext"> according to parameter settings for minimum length, maximum gap</span>
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<pre style="margin: 0;"> <span id="LC500" class="line" lang="plaintext"> and cutoff.</span>
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<pre style="margin: 0;"> <span id="LC501" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC497" class="line" lang="plaintext"> 4. You can combine subcommands to do a step-by-step peak</span>
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<pre style="margin: 0;">-<span id="LC498" class="line" lang="plaintext"> calling. Read detail at [MACS2 wikipage](https://github.com/taoliu/MACS/wiki/Advanced%3A-Call-peaks-using-MACS2-subcommands)</span>
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="plaintext"> 4. You can combine subcommands to do a step-by-step peak calling. Read</span>
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="plaintext"> detail at [MACS2</span>
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="plaintext"> wikipage](https://github.com/taoliu/MACS/wiki/Advanced%3A-Call-peaks-using-MACS2-subcommands)</span>
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<pre style="margin: 0;"> <span id="LC505" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC506" class="line" lang="plaintext">Platform: UNKNOWN</span>
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<pre style="margin: 0;"> <span id="LC507" class="line" lang="plaintext">Classifier: Development Status :: 5 - Production/Stable</span>
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<li id="31291f8e6d83e2788d0b4e4676278465627c60fa">
<a href="https://salsa.debian.org/med-team/macs/compare/80c600ce7b134f707ca923396ac8a671bffa1cb4...5b2bb5b2030f7b64d102f661f724637ae32f4426#31291f8e6d83e2788d0b4e4676278465627c60fa"><strong>MACS2.egg-info/SOURCES.txt</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">@@ -2,7 +2,9 @@ ChangeLog</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">INSTALL.md</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">LICENSE</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">MANIFEST.in</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">PKG-INFO</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">README.md</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">setup.cfg</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">setup.py</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">MACS2/Constants.py</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">MACS2/OptValidator.py</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">@@ -51,7 +53,6 @@ MACS2/IO/BedGraph.c</td>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext">MACS2/IO/BedGraph.pyx</span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext">MACS2/IO/BedGraphIO.c</span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext">MACS2/IO/BedGraphIO.pyx</span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext">MACS2/IO/BinKeeper.py</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext">MACS2/IO/CallPeakUnit.c</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext">MACS2/IO/CallPeakUnit.pyx</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext">MACS2/IO/FixWidthTrack.c</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">@@ -66,4 +67,24 @@ MACS2/IO/ScoreTrack.c</td>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext">MACS2/IO/ScoreTrack.pyx</span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext">MACS2/IO/__init__.py</span>
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext">MACS2/data/__init__.py</span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="plaintext">bin/macs2</span></pre>
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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">\ No newline at end of file</td>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">bin/macs2</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">debian/README.test</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">debian/changelog</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">debian/control</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">debian/copyright</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">debian/docs</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">debian/lintian-overrides</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">debian/macs.examples</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">debian/manpages</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">debian/rules</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">debian/watch</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">debian/examples/aluY.chr1.bed.gz</span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">debian/examples/gerp.chr1.bed.gz</span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">debian/patches/series</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">debian/patches/spelling</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">debian/source/format</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">debian/source/include-binaries</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">debian/source/options</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">debian/tests/control</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">debian/tests/run-unit-test</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">debian/upstream/metadata</span></pre>
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<a href="https://salsa.debian.org/med-team/macs/compare/80c600ce7b134f707ca923396ac8a671bffa1cb4...5b2bb5b2030f7b64d102f661f724637ae32f4426#b4b38e5409758d0596f1ecc988e5dd67643d8640"><strong>MACS2.egg-info/requires.txt</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">numpy>=1.15</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">cython>=0.25</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">numpy>=1.16</span></pre>
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<a href="https://salsa.debian.org/med-team/macs/compare/80c600ce7b134f707ca923396ac8a671bffa1cb4...5b2bb5b2030f7b64d102f661f724637ae32f4426#48431da50d9dc27b278c0a288c2c5eb6e1bc5db1"><strong>MACS2/Constants.py</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="n" style="color: #333;">MACS_VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2.1.<span class="idiff left right">3.3</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="n" style="color: #333;">MACS_VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2.1.<span class="idiff left right">4</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#MACSDIFF_VERSION = "1.0.4 20110212 (tag:alpha)"</span></span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="n" style="color: #333;">FILTERDUP_VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1.0.0 20140616"</span></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="n" style="color: #333;">RANDSAMPLE_VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1.0.0 20120703"</span></span>
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<a href="https://salsa.debian.org/med-team/macs/compare/80c600ce7b134f707ca923396ac8a671bffa1cb4...5b2bb5b2030f7b64d102f661f724637ae32f4426#5b10e32bc98bb18a79345759d8d25af86740f0fc"><strong>MACS2/IO/BinKeeper.py</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Time-stamp: <2019-09-20 11:38:14 taoliu></span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">"""Module Description: BinKeeper for Wiggle-like tracks. (obsolete)</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"><span class="s" style="color: #d14;">This code is free software; you can redistribute it and/or modify it</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="python"><span class="s" style="color: #d14;">under the terms of the BSD License (see the file LICENSE included with</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="python"><span class="s" style="color: #d14;">the distribution).</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># python modules</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">re</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bisect</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">insort</span><span class="p">,</span><span class="n" style="color: #333;">bisect_left</span><span class="p">,</span><span class="n" style="color: #333;">bisect_right</span><span class="p">,</span><span class="n" style="color: #333;">insort_right</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">array</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">array</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># constants</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># to determine the byte size</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">array</span><span class="p">(</span><span class="s" style="color: #d14;">'H'</span><span class="p">,[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">itemsize</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">BYTE2</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'H'</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"><span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">(</span><span class="s" style="color: #d14;">"BYTE2 type cannot be determined!"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"></span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">array</span><span class="p">(</span><span class="s" style="color: #d14;">'I'</span><span class="p">,[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">itemsize</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">4</span><span class="p">:</span></span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">BYTE4</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'I'</span></span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"><span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">array</span><span class="p">(</span><span class="s" style="color: #d14;">'L'</span><span class="p">,[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">itemsize</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">4</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">BYTE4</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'L'</span></span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"><span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">(</span><span class="s" style="color: #d14;">"BYTE4 type cannot be determined!"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">array</span><span class="p">(</span><span class="s" style="color: #d14;">'f'</span><span class="p">,[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">itemsize</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">4</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">FBYTE4</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'f'</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"><span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">array</span><span class="p">(</span><span class="s" style="color: #d14;">'d'</span><span class="p">,[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">itemsize</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">4</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">FBYTE4</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'d'</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"><span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">(</span><span class="s" style="color: #d14;">"BYTE4 type cannot be determined!"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Misc functions</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Classes</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BinKeeperI</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"> <span class="s" style="color: #d14;">"""BinKeeper keeps point data from a chromosome in a bin list.</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"><span class="s" style="color: #d14;"> Example:</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"><span class="s" style="color: #d14;"> >>> from taolib.CoreLib.Parser import WiggleIO</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"><span class="s" style="color: #d14;"> >>> w = WiggleIO('sample.wig')</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"><span class="s" style="color: #d14;"> >>> bk = w.build_binKeeper()</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"><span class="s" style="color: #d14;"> >>> bk['chrI'].pp2v(1000,2000) # to extract values in chrI:1000..2000</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span><span class="n" style="color: #333;">binsize</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">8000</span><span class="p">,</span><span class="n" style="color: #333;">chromosomesize</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1e9</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"> <span class="s" style="color: #d14;">"""Initializer.</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"><span class="s" style="color: #d14;"> Parameters:</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"><span class="s" style="color: #d14;"> binsize : size of bin in Basepair</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"><span class="s" style="color: #d14;"> chromosomesize : size of chromosome, default is 1G</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">binsize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">binsize</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">binnumber</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">chromosomesize</span><span class="o" style="font-weight: 600;">/</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">binsize</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">xrange</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">binnumber</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">a</span><span class="p">([</span><span class="n" style="color: #333;">array</span><span class="p">(</span><span class="n" style="color: #333;">BYTE4</span><span class="p">,[]),</span><span class="n" style="color: #333;">array</span><span class="p">(</span><span class="n" style="color: #333;">FBYTE4</span><span class="p">,[])])</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add</span> <span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">value</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python"> <span class="s" style="color: #d14;">"""Add a position into BinKeeper.</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"><span class="s" style="color: #d14;"> Note: position must be sorted before adding. Otherwise, pp2v</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"><span class="s" style="color: #d14;"> and pp2p will not work.</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"> <span class="nb" style="color: #0086b3;">bin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">/</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">binsize</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span><span class="p">[</span><span class="nb" style="color: #0086b3;">bin</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span><span class="p">[</span><span class="nb" style="color: #0086b3;">bin</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)</span> </span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">p2bin</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">p</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="python"> <span class="s" style="color: #d14;">"""Return the bin index for a position.</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"><span class="s" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">/</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">binsize</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">p2cage</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python"> <span class="s" style="color: #d14;">"""Return the bin containing the position.</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python"><span class="s" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">/</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">binsize</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__pp2cages</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">p1</span><span class="p">,</span> <span class="n" style="color: #333;">p2</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">p1</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">p2</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">bin1</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">p2bin</span><span class="p">(</span><span class="n" style="color: #333;">p1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python"> <span class="n" style="color: #333;">bin2</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">p2bin</span><span class="p">(</span><span class="n" style="color: #333;">p2</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python"> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">array</span><span class="p">(</span><span class="n" style="color: #333;">BYTE4</span><span class="p">,[]),</span><span class="n" style="color: #333;">array</span><span class="p">(</span><span class="n" style="color: #333;">FBYTE4</span><span class="p">,[])]</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">xrange</span><span class="p">(</span><span class="n" style="color: #333;">bin1</span><span class="p">,</span><span class="n" style="color: #333;">bin2</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">t</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extend</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">t</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extend</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> </span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">t</span></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">pp2p</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">p1</span><span class="p">,</span> <span class="n" style="color: #333;">p2</span><span class="p">):</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python"> <span class="s" style="color: #d14;">"""Give the position list between two given positions.</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="python"></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="python"><span class="s" style="color: #d14;"> Parameters:</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python"><span class="s" style="color: #d14;"> p1 : start position</span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python"><span class="s" style="color: #d14;"> p2 : end position</span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python"><span class="s" style="color: #d14;"> Return Value:</span></span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python"><span class="s" style="color: #d14;"> list of positions between p1 and p2.</span></span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">ps</span><span class="p">,</span><span class="n" style="color: #333;">vs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__pp2cages</span><span class="p">(</span><span class="n" style="color: #333;">p1</span><span class="p">,</span><span class="n" style="color: #333;">p2</span><span class="p">)</span></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="python"> <span class="n" style="color: #333;">p1_in_cages</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bisect_left</span><span class="p">(</span><span class="n" style="color: #333;">ps</span><span class="p">,</span><span class="n" style="color: #333;">p1</span><span class="p">)</span></span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">p2_in_cages</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bisect_right</span><span class="p">(</span><span class="n" style="color: #333;">ps</span><span class="p">,</span><span class="n" style="color: #333;">p2</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ps</span><span class="p">[</span><span class="n" style="color: #333;">p1_in_cages</span><span class="p">:</span><span class="n" style="color: #333;">p2_in_cages</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">pp2v</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">p1</span><span class="p">,</span> <span class="n" style="color: #333;">p2</span><span class="p">):</span></span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python"> <span class="s" style="color: #d14;">"""Give the value list between two given positions.</span></span>
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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python"></span>
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120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="python"><span class="s" style="color: #d14;"> Parameters:</span></span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="python"><span class="s" style="color: #d14;"> p1 : start position</span></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"><span class="s" style="color: #d14;"> p2 : end position</span></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="python"><span class="s" style="color: #d14;"> Return Value:</span></span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python"><span class="s" style="color: #d14;"> list of values whose positions are between p1 and p2.</span></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">ps</span><span class="p">,</span><span class="n" style="color: #333;">vs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__pp2cages</span><span class="p">(</span><span class="n" style="color: #333;">p1</span><span class="p">,</span><span class="n" style="color: #333;">p2</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="python"> <span class="n" style="color: #333;">p1_in_cages</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bisect_left</span><span class="p">(</span><span class="n" style="color: #333;">ps</span><span class="p">,</span><span class="n" style="color: #333;">p1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="python"> <span class="n" style="color: #333;">p2_in_cages</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bisect_right</span><span class="p">(</span><span class="n" style="color: #333;">ps</span><span class="p">,</span><span class="n" style="color: #333;">p2</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">vs</span><span class="p">[</span><span class="n" style="color: #333;">p1_in_cages</span><span class="p">:</span><span class="n" style="color: #333;">p2_in_cages</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">pp2pv</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">p1</span><span class="p">,</span> <span class="n" style="color: #333;">p2</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="python"> <span class="s" style="color: #d14;">"""Give the (position,value) list between two given positions.</span></span>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="python"><span class="s" style="color: #d14;"> Parameters:</span></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="python"><span class="s" style="color: #d14;"> p1 : start position</span></span>
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="python"><span class="s" style="color: #d14;"> p2 : end position</span></span>
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="python"><span class="s" style="color: #d14;"> Return Value:</span></span>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="python"><span class="s" style="color: #d14;"> list of (position,value) between p1 and p2.</span></span>
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">ps</span><span class="p">,</span><span class="n" style="color: #333;">vs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__pp2cages</span><span class="p">(</span><span class="n" style="color: #333;">p1</span><span class="p">,</span><span class="n" style="color: #333;">p2</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="python"> <span class="n" style="color: #333;">p1_in_cages</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bisect_left</span><span class="p">(</span><span class="n" style="color: #333;">ps</span><span class="p">,</span><span class="n" style="color: #333;">p1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">p2_in_cages</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bisect_right</span><span class="p">(</span><span class="n" style="color: #333;">ps</span><span class="p">,</span><span class="n" style="color: #333;">p2</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">ps</span><span class="p">[</span><span class="n" style="color: #333;">p1_in_cages</span><span class="p">:</span><span class="n" style="color: #333;">p2_in_cages</span><span class="p">],</span><span class="n" style="color: #333;">vs</span><span class="p">[</span><span class="n" style="color: #333;">p1_in_cages</span><span class="p">:</span><span class="n" style="color: #333;">p2_in_cages</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BinKeeperII</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="python"> <span class="s" style="color: #d14;">"""BinKeeperII keeps non-overlapping interval data from a chromosome in a bin list.</span></span>
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="python"><span class="s" style="color: #d14;"> This is especially designed for bedGraph type data.</span></span>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span><span class="n" style="color: #333;">binsize</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">8000</span><span class="p">,</span><span class="n" style="color: #333;">chromosomesize</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1e9</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="python"> <span class="s" style="color: #d14;">"""Initializer.</span></span>
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="python"><span class="s" style="color: #d14;"> Parameters:</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="python"><span class="s" style="color: #d14;"> binsize : size of bin in Basepair</span></span>
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="python"><span class="s" style="color: #d14;"> chromosomesize : size of chromosome, default is 1G</span></span>
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">binsize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">binsize</span></span>
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">binnumber</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">chromosomesize</span><span class="o" style="font-weight: 600;">/</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">binsize</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="python"> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span></span>
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">xrange</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">binnumber</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="python"> <span class="n" style="color: #333;">a</span><span class="p">([</span><span class="n" style="color: #333;">array</span><span class="p">(</span><span class="n" style="color: #333;">BYTE4</span><span class="p">,[]),</span><span class="n" style="color: #333;">array</span><span class="p">(</span><span class="n" style="color: #333;">BYTE4</span><span class="p">,[]),</span><span class="n" style="color: #333;">array</span><span class="p">(</span><span class="n" style="color: #333;">FBYTE4</span><span class="p">,[])])</span></span>
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add</span> <span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">startp</span><span class="p">,</span> <span class="n" style="color: #333;">endp</span><span class="p">,</span> <span class="n" style="color: #333;">value</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="python"> <span class="s" style="color: #d14;">"""Add an interval data into BinKeeper.</span></span>
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="python"><span class="s" style="color: #d14;"> Note: position must be sorted before adding. Otherwise, pp2v</span></span>
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="python"><span class="s" style="color: #d14;"> and pp2p will not work.</span></span>
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="python"> <span class="n" style="color: #333;">startbin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">startp</span><span class="o" style="font-weight: 600;">/</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">binsize</span></span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="python"> <span class="n" style="color: #333;">endbin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">endp</span><span class="o" style="font-weight: 600;">/</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">binsize</span></span>
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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">startbin</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">endbin</span><span class="p">:</span></span>
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176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># some intervals may only be within a bin</span></span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="python"> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bisect</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bisect_left</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span><span class="p">[</span><span class="n" style="color: #333;">startbin</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">startp</span><span class="p">)</span></span>
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178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span><span class="p">[</span><span class="n" style="color: #333;">startbin</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">,</span><span class="n" style="color: #333;">startp</span><span class="p">)</span></span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span><span class="p">[</span><span class="n" style="color: #333;">startbin</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">,</span><span class="n" style="color: #333;">endp</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span><span class="p">[</span><span class="n" style="color: #333;">startbin</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">,</span><span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># some intervals may cover the end of bins</span></span>
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183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># first bin</span></span>
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184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="python"> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bisect</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bisect_left</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span><span class="p">[</span><span class="n" style="color: #333;">startbin</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">startp</span><span class="p">)</span></span>
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185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span><span class="p">[</span><span class="n" style="color: #333;">startbin</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">,</span><span class="n" style="color: #333;">startp</span><span class="p">)</span></span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span><span class="p">[</span><span class="n" style="color: #333;">startbin</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">,(</span><span class="n" style="color: #333;">startbin</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">binsize</span><span class="p">)</span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span><span class="p">[</span><span class="n" style="color: #333;">startbin</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">,</span><span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># other bins fully covered</span></span>
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">xrange</span><span class="p">(</span><span class="n" style="color: #333;">startbin</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">endbin</span><span class="p">):</span></span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">*</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">binsize</span></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="python"> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bisect</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bisect_left</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span><span class="p">[</span><span class="n" style="color: #333;">startbin</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">p</span><span class="p">)</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span><span class="p">[</span><span class="n" style="color: #333;">startbin</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">,</span><span class="n" style="color: #333;">p</span><span class="p">)</span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span><span class="p">[</span><span class="n" style="color: #333;">startbin</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">,(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">binsize</span><span class="p">)</span></span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span><span class="p">[</span><span class="n" style="color: #333;">startbin</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">,</span><span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="python"></span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="python"> <span class="n" style="color: #333;">insort_right</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">*</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">binsize</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="python"> <span class="n" style="color: #333;">insort_right</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">],(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">binsize</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">insort_right</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">],</span><span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># last bin -- the start of this bin should be covered</span></span>
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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="python"> <span class="n" style="color: #333;">insort_right</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span><span class="p">[</span><span class="n" style="color: #333;">endbin</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">endbin</span><span class="o" style="font-weight: 600;">*</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">binsize</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">insort_right</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span><span class="p">[</span><span class="n" style="color: #333;">endbin</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">],</span><span class="n" style="color: #333;">endp</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">insort_right</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span><span class="p">[</span><span class="n" style="color: #333;">endbin</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">],</span><span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">p2bin</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">p</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="python"> <span class="s" style="color: #d14;">"""Given a position, return the bin index for a position.</span></span>
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="python"><span class="s" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">/</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">binsize</span></span>
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">p2cage</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="python"> <span class="s" style="color: #d14;">"""Given a position, return the bin containing the position.</span></span>
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="python"><span class="s" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">/</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">binsize</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">pp2cages</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">p1</span><span class="p">,</span> <span class="n" style="color: #333;">p2</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="python"> <span class="s" style="color: #d14;">"""Given an interval, return the bins containing this interval.</span></span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="python"><span class="s" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">p1</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">p2</span></span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="python"> <span class="n" style="color: #333;">bin1</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">p2bin</span><span class="p">(</span><span class="n" style="color: #333;">p1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="python"> <span class="n" style="color: #333;">bin2</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">p2bin</span><span class="p">(</span><span class="n" style="color: #333;">p2</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="python"> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">array</span><span class="p">(</span><span class="n" style="color: #333;">BYTE4</span><span class="p">,[]),</span><span class="n" style="color: #333;">array</span><span class="p">(</span><span class="n" style="color: #333;">BYTE4</span><span class="p">,[]),</span><span class="n" style="color: #333;">array</span><span class="p">(</span><span class="n" style="color: #333;">FBYTE4</span><span class="p">,[])]</span></span>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">xrange</span><span class="p">(</span><span class="n" style="color: #333;">bin1</span><span class="p">,</span><span class="n" style="color: #333;">bin2</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="python"> <span class="n" style="color: #333;">t</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extend</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="python"> <span class="n" style="color: #333;">t</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extend</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="python"> <span class="n" style="color: #333;">t</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extend</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">])</span> </span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">t</span></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">pp2intervals</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">p1</span><span class="p">,</span> <span class="n" style="color: #333;">p2</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="python"> <span class="s" style="color: #d14;">"""Given an interval, return the intervals list between two given positions.</span></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="python"><span class="s" style="color: #d14;"> Parameters:</span></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="python"><span class="s" style="color: #d14;"> p1 : start position</span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="python"><span class="s" style="color: #d14;"> p2 : end position</span></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="python"><span class="s" style="color: #d14;"> Return Value:</span></span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="python"><span class="s" style="color: #d14;"> A list of intervals start and end positions (tuple) between p1 and p2.</span></span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="python"><span class="s" style="color: #d14;"> * Remember, I assume all intervals saved in this BinKeeperII</span></span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="python"><span class="s" style="color: #d14;"> are not overlapping, so if there is some overlap, this</span></span>
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="python"><span class="s" style="color: #d14;"> function will not work as expected.</span></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">startposs</span><span class="p">,</span><span class="n" style="color: #333;">endposs</span><span class="p">,</span><span class="n" style="color: #333;">vs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pp2cages</span><span class="p">(</span><span class="n" style="color: #333;">p1</span><span class="p">,</span><span class="n" style="color: #333;">p2</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="python"> <span class="n" style="color: #333;">p1_in_cages</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bisect_left</span><span class="p">(</span><span class="n" style="color: #333;">startposs</span><span class="p">,</span><span class="n" style="color: #333;">p1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="python"> <span class="n" style="color: #333;">p2_in_cages</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bisect_right</span><span class="p">(</span><span class="n" style="color: #333;">endposs</span><span class="p">,</span><span class="n" style="color: #333;">p2</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="python"> <span class="n" style="color: #333;">output_startpos_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">startposs</span><span class="p">[</span><span class="n" style="color: #333;">p1_in_cages</span><span class="p">:</span><span class="n" style="color: #333;">p2_in_cages</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="python"> <span class="n" style="color: #333;">output_endpos_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">endposs</span><span class="p">[</span><span class="n" style="color: #333;">p1_in_cages</span><span class="p">:</span><span class="n" style="color: #333;">p2_in_cages</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># check if the bin (p1_in_cages-1) covers p1</span></span>
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">p1</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">endposs</span><span class="p">[</span><span class="n" style="color: #333;">p1_in_cages</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]:</span></span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># add this interval</span></span>
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="python"> <span class="n" style="color: #333;">output_startpos_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">array</span><span class="p">(</span><span class="n" style="color: #333;">BYTE4</span><span class="p">,[</span><span class="n" style="color: #333;">p1</span><span class="p">,])</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">output_startpos_list</span></span>
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="python"> <span class="n" style="color: #333;">output_endpos_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">array</span><span class="p">(</span><span class="n" style="color: #333;">BYTE4</span><span class="p">,[</span><span class="n" style="color: #333;">endposs</span><span class="p">[</span><span class="n" style="color: #333;">p1_in_cages</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">],])</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">output_endpos_list</span></span>
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># check if the bin (p2_in_cages+1) covers p2</span></span>
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">p2</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">startposs</span><span class="p">[</span><span class="n" style="color: #333;">p2_in_cages</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]:</span></span>
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># add this interval</span></span>
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="python"> <span class="n" style="color: #333;">output_startpos_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">array</span><span class="p">(</span><span class="n" style="color: #333;">BYTE4</span><span class="p">,[</span><span class="n" style="color: #333;">startposs</span><span class="p">[</span><span class="n" style="color: #333;">p2_in_cages</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">],])</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">output_startpos_list</span></span>
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="python"> <span class="n" style="color: #333;">output_endpos_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">array</span><span class="p">(</span><span class="n" style="color: #333;">BYTE4</span><span class="p">,[</span><span class="n" style="color: #333;">p2</span><span class="p">,])</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">output_endpos_list</span></span>
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">output_startpos_list</span><span class="p">,</span><span class="n" style="color: #333;">output_endpos_list</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">pp2pvs</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">p1</span><span class="p">,</span> <span class="n" style="color: #333;">p2</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="python"> <span class="s" style="color: #d14;">"""Given an interval, return the values list between two given positions.</span></span>
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="python"><span class="s" style="color: #d14;"> Parameters:</span></span>
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="python"><span class="s" style="color: #d14;"> p1 : start position</span></span>
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="python"><span class="s" style="color: #d14;"> p2 : end position</span></span>
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="python"><span class="s" style="color: #d14;"> Return Value:</span></span>
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="python"><span class="s" style="color: #d14;"> A list of start, end positions, values (tuple) between p1 and</span></span>
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="python"><span class="s" style="color: #d14;"> p2. Each value represents the value in an interval. Remember</span></span>
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="python"><span class="s" style="color: #d14;"> the interval length and positions are lost in the output.</span></span>
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="python"><span class="s" style="color: #d14;"> * Remember, I assume all intervals saved in this BinKeeperII</span></span>
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="python"><span class="s" style="color: #d14;"> are not overlapping, so if there is some overlap, this</span></span>
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="python"><span class="s" style="color: #d14;"> function will not work as expected.</span></span>
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">startposs</span><span class="p">,</span><span class="n" style="color: #333;">endposs</span><span class="p">,</span><span class="n" style="color: #333;">vs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pp2cages</span><span class="p">(</span><span class="n" style="color: #333;">p1</span><span class="p">,</span><span class="n" style="color: #333;">p2</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="python"> <span class="n" style="color: #333;">p1_in_cages</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bisect_left</span><span class="p">(</span><span class="n" style="color: #333;">startposs</span><span class="p">,</span><span class="n" style="color: #333;">p1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="python"> <span class="n" style="color: #333;">p2_in_cages</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bisect_right</span><span class="p">(</span><span class="n" style="color: #333;">endposs</span><span class="p">,</span><span class="n" style="color: #333;">p2</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="python"> <span class="n" style="color: #333;">output_startpos_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">startposs</span><span class="p">[</span><span class="n" style="color: #333;">p1_in_cages</span><span class="p">:</span><span class="n" style="color: #333;">p2_in_cages</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="python"> <span class="n" style="color: #333;">output_endpos_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">endposs</span><span class="p">[</span><span class="n" style="color: #333;">p1_in_cages</span><span class="p">:</span><span class="n" style="color: #333;">p2_in_cages</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="python"> <span class="n" style="color: #333;">output_value_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vs</span><span class="p">[</span><span class="n" style="color: #333;">p1_in_cages</span><span class="p">:</span><span class="n" style="color: #333;">p2_in_cages</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># print p1_in_cages,p2_in_cages</span></span>
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># print vs</span></span>
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="n" style="color: #333;">output_startpos_list</span></span>
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="n" style="color: #333;">output_endpos_list</span></span>
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="n" style="color: #333;">output_value_list</span></span>
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># check if the bin (p1_in_cages-1) covers p1</span></span>
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">p1_in_cages</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">p1</span> <span class="o" style="font-weight: 600;"><</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span><span class="p">[</span><span class="n" style="color: #333;">p1_in_cages</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]:</span></span>
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># add this interval</span></span>
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="python"> <span class="n" style="color: #333;">output_startpos_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">array</span><span class="p">(</span><span class="n" style="color: #333;">BYTE4</span><span class="p">,[</span><span class="n" style="color: #333;">p1</span><span class="p">,])</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">output_startpos_list</span></span>
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298
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<pre style="margin: 0;">-<span id="LC298" class="line" lang="python"> <span class="n" style="color: #333;">output_endpos_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">array</span><span class="p">(</span><span class="n" style="color: #333;">BYTE4</span><span class="p">,[</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span><span class="p">[</span><span class="n" style="color: #333;">p1_in_cages</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">],])</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">output_endpos_list</span></span>
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="python"> <span class="n" style="color: #333;">output_value_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">array</span><span class="p">(</span><span class="n" style="color: #333;">BYTE4</span><span class="p">,[</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span><span class="p">[</span><span class="n" style="color: #333;">p1_in_cages</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">],])</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">output_value_list</span></span>
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># check if the bin (p2_in_cages+1) covers p2</span></span>
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print p2_in_cages+1,len(self.cage)</span></span>
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print p2, self.cage[p2_in_cages+1][0]</span></span>
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305
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">p2_in_cages</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">p2</span> <span class="o" style="font-weight: 600;">></span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span><span class="p">[</span><span class="n" style="color: #333;">p2_in_cages</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]:</span></span>
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># add this interval</span></span>
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="python"> <span class="n" style="color: #333;">output_startpos_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">output_startpos_list</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">array</span><span class="p">(</span><span class="n" style="color: #333;">BYTE4</span><span class="p">,[</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span><span class="p">[</span><span class="n" style="color: #333;">p2_in_cages</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">],])</span></span>
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="python"> <span class="n" style="color: #333;">output_endpos_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">output_endpos_list</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">array</span><span class="p">(</span><span class="n" style="color: #333;">BYTE4</span><span class="p">,[</span><span class="n" style="color: #333;">p2</span><span class="p">,])</span></span>
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309
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="python"> <span class="n" style="color: #333;">output_value_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">output_value_list</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">array</span><span class="p">(</span><span class="n" style="color: #333;">BYTE4</span><span class="p">,[</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cage</span><span class="p">[</span><span class="n" style="color: #333;">p2_in_cages</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">],])</span></span>
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="n" style="color: #333;">output_startpos_list</span></span>
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="n" style="color: #333;">output_endpos_list</span></span>
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="n" style="color: #333;">output_value_list</span></span>
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">output_startpos_list</span><span class="p">,</span><span class="n" style="color: #333;">output_endpos_list</span><span class="p">,</span><span class="n" style="color: #333;">output_value_list</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="python"></span></pre>
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<a href="https://salsa.debian.org/med-team/macs/compare/80c600ce7b134f707ca923396ac8a671bffa1cb4...5b2bb5b2030f7b64d102f661f724637ae32f4426#f83eb1a74dfc6efcfa02c94c20a8c871e39917f2"><strong>MACS2/IO/CallPeakUnit.c</strong></a>
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<a href="https://salsa.debian.org/med-team/macs/compare/80c600ce7b134f707ca923396ac8a671bffa1cb4...5b2bb5b2030f7b64d102f661f724637ae32f4426#92d6f54eff86777dbb1d7cd341f09183f2320da8"><strong>MACS2/IO/CallPeakUnit.pyx</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"># Time-stamp: <2019-09-<span class="idiff left right">20 11:38:30</span> taoliu></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># Time-stamp: <2019-09-<span class="idiff left right">30 13:05:38</span> taoliu></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">"""Module for Calculate Scores.</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></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">@@ -201,12 +201,13 @@ cdef float median_from_value_length ( np.ndarray value, list length ):</td>
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="plaintext"> list tmp</span>
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="plaintext"> int32_t l_half, c, tmp_l</span>
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="plaintext"> float tmp_v</span>
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="plaintext"> c = 0</span>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="plaintext"> tmp = sorted(zip( value, length ))</span>
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="plaintext"> l = sum( length )/2</span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="plaintext"> l<span class="idiff left right">_half</span> = sum( length )/2</span>
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="plaintext"> for (tmp_v, tmp_l) in tmp:</span>
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="plaintext"> c += tmp_l</span>
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="plaintext"> if c > l:</span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext"> if c > l<span class="idiff left right">_half</span>:</span>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="plaintext"> return tmp_v</span>
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="plaintext">cdef float mean_from_value_length ( np.ndarray value, list length ):</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">@@ -215,7 +216,7 @@ cdef float mean_from_value_length ( np.ndarray value, list length ):</td>
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="plaintext"> """</span>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="plaintext"> cdef:</span>
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="plaintext"> list tmp</span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="plaintext"> int32_t tmp_l</span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="plaintext"> int32_t tmp_l<span class="idiff left right">, l</span></span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="plaintext"> float tmp_v, sum_v</span>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="plaintext"> sum_v = 0</span>
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<li id="8ac54c696d92e5af87f0ce070dc619f25ccf8cbf">
<a href="https://salsa.debian.org/med-team/macs/compare/80c600ce7b134f707ca923396ac8a671bffa1cb4...5b2bb5b2030f7b64d102f661f724637ae32f4426#8ac54c696d92e5af87f0ce070dc619f25ccf8cbf"><strong>MACS2/IO/ScoreTrack.c</strong></a>
The diff for this file was not included because it is too large.
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<a href="https://salsa.debian.org/med-team/macs/compare/80c600ce7b134f707ca923396ac8a671bffa1cb4...5b2bb5b2030f7b64d102f661f724637ae32f4426#7478182f47d385af4085c8e455192f6565e8ec5b"><strong>MACS2/IO/ScoreTrack.pyx</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"># Time-stamp: <2019-09-<span class="idiff left right">20 11:40:07</span> taoliu></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># Time-stamp: <2019-09-<span class="idiff left right">30 13:02:11</span> taoliu></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">"""Module for Feature IO classes.</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
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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">@@ -17,8 +17,6 @@ from copy import copy</td>
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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">from cpython cimport bool</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">#from scipy.stats import chi2 </span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">from MACS2.Signal import maxima, enforce_valleys, enforce_peakyness</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">cimport cython</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">@@ -49,7 +47,7 @@ LOG10_E = 0.43429448190325176</td>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext">pscore_dict = dict()</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext">cdef <span class="idiff left right">inline </span>double get_pscore ( int observed, double expectation ):</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">cdef double get_pscore ( int observed, double expectation ):</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"> """Get p-value score from Poisson test. First check existing</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext"> table, if failed, call poisson_cdf function, then store the result</span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext"> in table.</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">@@ -67,7 +65,7 @@ cdef inline double get_pscore ( int observed, double expectation ):</td>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext">asym_logLR_dict = dict()</span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="plaintext">cdef <span class="idiff left right">inline </span>double logLR_asym ( double x, double y ):</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">cdef double logLR_asym ( double x, double y ):</span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext"> """Calculate log10 Likelihood between H1 ( enriched ) and H0 (</span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="plaintext"> chromatin bias ). Set minus sign for depletion.</span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="plaintext"> </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">@@ -91,7 +89,7 @@ cdef inline double logLR_asym ( double x, double y ):</td>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext">sym_logLR_dict = dict()</span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="plaintext">cdef <span class="idiff left right">inline </span>double logLR_sym ( double x, double y ):</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">cdef double logLR_sym ( double x, double y ):</span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="plaintext"> """Calculate log10 Likelihood between H1 ( enriched ) and H0 (</span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="plaintext"> another enriched ). Set minus sign for H0>H1.</span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext"> </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">@@ -113,12 +111,12 @@ cdef inline double logLR_sym ( double x, double y ):</td>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="plaintext"> sym_logLR_dict[ ( x, y ) ] = s</span>
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="plaintext"> return s</span>
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115
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="plaintext"> </span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="plaintext">cdef <span class="idiff left right">inline </span>double get_logFE ( float x, float y ):</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">cdef double get_logFE ( float x, float y ):</span>
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117
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="plaintext"> """ return 100* log10 fold enrichment with +1 pseudocount.</span>
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118
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="plaintext"> """</span>
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119
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="plaintext"> return log10( x/y )</span>
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120
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="plaintext"></span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="plaintext">cdef <span class="idiff left right">inline </span>float get_subtraction ( float x, float y):</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">cdef float get_subtraction ( float x, float y):</span>
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122
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="plaintext"> """ return subtraction.</span>
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123
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="plaintext"> """</span>
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124
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="plaintext"> return x - y</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="130" 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>
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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">@@ -130,12 +128,13 @@ cdef float median_from_value_length ( np.ndarray value, list length ):</td>
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130
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="plaintext"> list tmp</span>
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131
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="plaintext"> int32_t l_half, c, tmp_l</span>
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132
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="plaintext"> float tmp_v</span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="plaintext"> </span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext"></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext"> c = 0</span>
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134
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="plaintext"> tmp = sorted(zip( value, length ))</span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="plaintext"> l = sum( length )/2</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext"> l<span class="idiff left right">_half</span> = sum( length )/2</span>
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136
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="plaintext"> for (tmp_v, tmp_l) in tmp:</span>
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137
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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="plaintext"> c += tmp_l</span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="plaintext"> if c > l:</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext"> if c > l<span class="idiff left right">_half</span>:</span>
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139
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="plaintext"> return tmp_v</span>
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140
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="plaintext"></span>
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141
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="plaintext">cdef float mean_from_value_length ( np.ndarray value, list length ):</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="142" 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">@@ -143,9 +142,10 @@ cdef float mean_from_value_length ( np.ndarray value, list length ):</td>
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143
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="plaintext"> """</span>
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144
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="plaintext"> cdef:</span>
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145
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="plaintext"> list tmp</span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="plaintext"> int32_t tmp_l</span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext"> int32_t tmp_l<span class="idiff left right">, l</span></span>
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147
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="plaintext"> float tmp_v, sum_v</span>
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148
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext"> sum_v = 0</span>
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149
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="plaintext"> tmp = zip( value, length )</span>
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150
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="plaintext"> l = sum( length )</span>
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151
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="154" 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">@@ -154,7 +154,6 @@ cdef float mean_from_value_length ( np.ndarray value, list length ):</td>
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154
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="plaintext"></span>
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155
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="plaintext"> return sum_v / l</span>
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156
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="plaintext"></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="plaintext"></span>
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158
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="plaintext"># ------------------------------------</span>
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159
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="plaintext"># Classes</span>
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160
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="plaintext"># ------------------------------------</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1705" 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">@@ -1706,6 +1705,8 @@ cdef class TwoConditionScores:</td>
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1706
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1705
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<pre style="margin: 0;"> <span id="LC1705" class="line" lang="plaintext"> """This function try to find regions within which, scores</span>
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1707
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1706
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<pre style="margin: 0;"> <span id="LC1706" class="line" lang="plaintext"> are continuously higher than a given cutoff.</span>
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1708
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1707
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<pre style="margin: 0;"> <span id="LC1707" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC1708" class="line" lang="plaintext"> For bdgdiff.</span>
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<pre style="margin: 0;">+<span id="LC1709" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC1710" class="line" lang="plaintext"> This function is NOT using sliding-windows. Instead, any</span>
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<pre style="margin: 0;"> <span id="LC1711" class="line" lang="plaintext"> regions in bedGraph above certain cutoff will be detected,</span>
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<pre style="margin: 0;"> <span id="LC1712" class="line" lang="plaintext"> then merged if the gap between nearby two regions are below</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">@@ -1815,9 +1816,11 @@ cdef class TwoConditionScores:</td>
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<pre style="margin: 0;"> <span id="LC1816" class="line" lang="plaintext"> """</span>
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1817
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<pre style="margin: 0;"> <span id="LC1817" class="line" lang="plaintext"> cdef:</span>
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1818
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<pre style="margin: 0;"> <span id="LC1818" class="line" lang="plaintext"> int32_t tmp_s, tmp_e</span>
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<pre style="margin: 0;">-<span id="LC1818" class="line" lang="plaintext"> int32_t l<span class="idiff left right"> = 0</span></span>
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<pre style="margin: 0;">+<span id="LC1819" class="line" lang="plaintext"> int32_t l</span>
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1820
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<pre style="margin: 0;"> <span id="LC1820" class="line" lang="plaintext"> float tmp_v, sum_v</span>
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1821
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<pre style="margin: 0;"> <span id="LC1821" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC1822" class="line" lang="plaintext"> sum_v = 0</span>
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<pre style="margin: 0;">+<span id="LC1823" class="line" lang="plaintext"> l = 0</span>
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<pre style="margin: 0;"> <span id="LC1824" class="line" lang="plaintext"> for (tmp_s, tmp_e, tmp_v) in peakcontent:</span>
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1825
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<pre style="margin: 0;"> <span id="LC1825" class="line" lang="plaintext"> sum_v += tmp_v * ( tmp_e - tmp_s )</span>
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<pre style="margin: 0;"> <span id="LC1826" class="line" lang="plaintext"> l += tmp_e - tmp_s</span>
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<a href="https://salsa.debian.org/med-team/macs/compare/80c600ce7b134f707ca923396ac8a671bffa1cb4...5b2bb5b2030f7b64d102f661f724637ae32f4426#81c3c19aa1f3d799315ff190821707ee6fb2bf63"><strong>MACS2/bdgdiff_cmd.py</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Time-stamp: <2019-09-2<span class="idiff left right">0 11:30:12</span> taoliu></span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Time-stamp: <2019-09-2<span class="idiff left right">5 14:40:58</span> taoliu></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">"""Description: Naive call differential peaks from 4 bedGraph tracks for scores.</span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"></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">@@ -89,8 +89,6 @@ def run( options ):</td>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Write peaks..."</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">ofiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="python"> <span class="n" style="color: #333;">name_prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ofile</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"> <span class="n" style="color: #333;">ofiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">map</span><span class="p">(</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">outdir</span><span class="p">,</span> <span class="n" style="color: #333;">x</span> <span class="p">),</span> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ofile</span> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">name_prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ofile</span></span>
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<a href="https://salsa.debian.org/med-team/macs/compare/80c600ce7b134f707ca923396ac8a671bffa1cb4...5b2bb5b2030f7b64d102f661f724637ae32f4426#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf"><strong>PKG-INFO</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Metadata-Version: 2.1</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Name: MACS2</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Version: 2.1.<span class="idiff left right">3.3</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Version: 2.1.<span class="idiff left right">4</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Summary: Model Based Analysis for ChIP-Seq data</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Home-page: http://github.com/taoliu/MACS/</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Author: Tao Liu</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Author-email: vladimir.liu@gmail.com</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">License: UNKNOWN</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">Description: # Recent Changes for MACS (2.1.<span class="idiff left right">3.3</span>)</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Description: # Recent Changes for MACS (2.1.<span class="idiff left right">4</span>)</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"> ### 2.1.3.3</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> ### 2.1.4</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * Features added</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> Github Actions is used together with Travis CI for testing and</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> deployment.</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> * Bugs fixed (PR #322)</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> 1) #318 Random score in `bdgdiff` output. It turns out the sum_v</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> is not initialized as 0 before adding. Potential bugs are fixed in</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> other functions in ScoreTrack and CallPeakUnit codes.</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> 2) #321 Cython dependency in `setup.py` script is removed. And</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> place 'cythonzie' call to the correct position.</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> 3) A typo is fixed in Github Actions script. </span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> ### 2.1.3</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> * Features added</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> 1) Support Docker auto-deploy. PR #309</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">@@ -43,44 +61,7 @@ Description: # Recent Changes for MACS (2.1.3.3)</td>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext"> 3) Rename COPYING to LICENSE.</span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext"> ### 2.1.2</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext"> * New features</span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext"> </span>
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51
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext"> 1) Added missing BEDPE support. And enable the support for BAMPE</span>
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52
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext"> and BEDPE formats in 'pileup', 'filterdup' and 'randsample'</span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext"> subcommands. When format is BAMPE or BEDPE, The 'pileup' command</span>
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54
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext"> will pile up the whole fragment defined by mapping locations of</span>
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55
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext"> the left end and right end of each read pair. Thank @purcaro</span>
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56
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext"> </span>
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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext"> 2) Added options to callpeak command for tweaking max-gap and</span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext"> min-len during peak calling. Thank @jsh58!</span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext"> </span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext"> 3) The callpeak option "--to-large" option is replaced with</span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext"> "--scale-to large".</span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext"> </span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext"> 4) The randsample option "-t" has been replaced with "-i".</span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext"> </span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext"> * Bug fixes</span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="plaintext"> </span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="plaintext"> 1) Fixed memory issue related to #122 and #146</span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="plaintext"> </span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="plaintext"> 2) Fixed a bug caused by a typo. Related to #249, Thank @shengqh</span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="plaintext"> </span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="plaintext"> 3) Fixed a bug while setting commandline qvalue cutoff.</span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="plaintext"> </span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="plaintext"> 4) Better describe the 5th column of narrowPeak. Thank @alexbarrera</span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="plaintext"> </span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="plaintext"> 5) Fixed the calculation of average fragment length for paired-end</span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="plaintext"> data. Thank @jsh58</span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="plaintext"> 6) Fixed bugs caused by khash while computing p/q-value and log</span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="plaintext"> likelihood ratios. Thank @jsh58</span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="plaintext"> 7) More spelling tweaks in source code. Thank @mr-c</span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="plaintext"> # README for MACS2 (2.1.3.3)</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> # README for MACS2 (2.1.4)</span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext"> ## Introduction</span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext"> </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">@@ -268,8 +249,19 @@ Description: # Recent Changes for MACS (2.1.3.3)</td>
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="plaintext"> ##### `--min-length`, `--max-gap`</span>
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="plaintext"> These two options can be used to fine-tune the peak calling behavior by specifying the minimum length of a called peak and the maximum allowed gap between two nearby regions to be merged. In another word, a called peak has to be longer than *min-length*, and if the distance between two nearby peaks is smaller than *max-gap* then they will be merged as one. If they are not set, MACS2 will set the DEFAULT value for *min-length* as the predicted fragment size d, and the DEFAULT value for *max-gap* as the detected read length. Note, if you set a *min-length* value smaller than the fragment size, it may have NO effect on the result. For BROAD peak calling, try to set a</span>
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="plaintext"> large value such as 500bps. You can also use '--cutoff-analysis' option with default setting, and check the column 'avelpeak' under different cutoff values to decide a reasonable *min-length* value.</span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="plaintext"> These two options can be used to fine-tune the peak calling behavior</span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="plaintext"> by specifying the minimum length of a called peak and the maximum</span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="plaintext"> allowed gap between two nearby regions to be merged. In another word,</span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="plaintext"> a called peak has to be longer than *min-length*, and if the distance</span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="plaintext"> between two nearby peaks is smaller than *max-gap* then they will be</span>
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="plaintext"> merged as one. If they are not set, MACS2 will set the DEFAULT value</span>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="plaintext"> for *min-length* as the predicted fragment size d, and the DEFAULT</span>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="plaintext"> value for *max-gap* as the detected read length. Note, if you set a</span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="plaintext"> *min-length* value smaller than the fragment size, it may have NO</span>
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="plaintext"> effect on the result. For BROAD peak calling, try to set a large value</span>
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="plaintext"> such as 500bps. You can also use '--cutoff-analysis' option with</span>
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="plaintext"> default setting, and check the column 'avelpeak' under different</span>
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="plaintext"> cutoff values to decide a reasonable *min-length* value.</span>
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="plaintext"> ##### `--nolambda`</span>
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="plaintext"> </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">@@ -405,21 +397,33 @@ Description: # Recent Changes for MACS (2.1.3.3)</td>
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="plaintext"> - fold enrichment for this peak summit against random Poisson distribution with local lambda, </span>
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="plaintext"> - -log10(qvalue) at peak summit</span>
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC408" class="line" lang="plaintext"> Coordinates in XLS is 1-based which is different with BED format. When `--broad` is enabled for broad peak calling, the pileup, pvalue, qvalue, and fold change in the XLS file will be the mean value across the entire peak region, since peak summit won't be called in broad peak calling mode. </span>
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="plaintext"> Coordinates in XLS is 1-based which is different with BED</span>
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="plaintext"> format. When `--broad` is enabled for broad peak calling, the</span>
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="plaintext"> pileup, pvalue, qvalue, and fold change in the XLS file will be the</span>
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="plaintext"> mean value across the entire peak region, since peak summit won't</span>
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="plaintext"> be called in broad peak calling mode.</span>
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="plaintext"> 2. `NAME_peaks.narrowPeak` is BED6+4 format file which contains the</span>
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="plaintext"> peak locations together with peak summit, pvalue and qvalue. You</span>
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="plaintext"> can load it to UCSC genome browser. Definition of some specific</span>
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<pre style="margin: 0;"> <span id="LC409" class="line" lang="plaintext"> columns are: </span>
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="plaintext"> - 5th: integer score for display. It's calculated as `int(-10*log10pvalue)` or `int(-10*log10qvalue)` depending on whether `-p` (pvalue) or `-q` (qvalue) is used as score cutoff. Please note that currently this value might be out of the [0-1000] range defined in [UCSC Encode narrowPeak format](https://genome.ucsc.edu/FAQ/FAQformat.html#format12). You can let the value saturated at 1000 (i.e. p/q-value = 10^-100) by using the following 1-liner awk: `awk -v OFS="\t" '{$5=$5>1000?1000:$5} {print}' NAME_peaks.narrowPeak`</span>
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="plaintext"> - 5th: integer score for display. It's calculated as</span>
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="plaintext"> `int(-10*log10pvalue)` or `int(-10*log10qvalue)` depending on</span>
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="plaintext"> whether `-p` (pvalue) or `-q` (qvalue) is used as score</span>
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="plaintext"> cutoff. Please note that currently this value might be out of the</span>
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="plaintext"> [0-1000] range defined in [UCSC Encode narrowPeak</span>
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="plaintext"> format](https://genome.ucsc.edu/FAQ/FAQformat.html#format12). You</span>
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="plaintext"> can let the value saturated at 1000 (i.e. p/q-value = 10^-100) by</span>
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="plaintext"> using the following 1-liner awk: `awk -v OFS="\t"</span>
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="plaintext"> '{$5=$5>1000?1000:$5} {print}' NAME_peaks.narrowPeak`</span>
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="plaintext"> - 7th: fold-change at peak summit</span>
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="plaintext"> - 8th: -log10pvalue at peak summit</span>
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="plaintext"> - 9th: -log10qvalue at peak summit</span>
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="plaintext"> - 10th: relative summit position to peak start</span>
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC421" class="line" lang="plaintext"> The file can be loaded directly to UCSC genome browser. Remove the<span class="idiff left right"> beginning track line if you want to</span></span>
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<pre style="margin: 0;">-<span id="LC422" class="line" lang="plaintext"> analyze it by other tools.</span>
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="plaintext"> The file can be loaded directly to UCSC genome browser. Remove the</span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="plaintext"> <span class="idiff left right">beginning track line if you want to </span>analyze it by other tools.</span>
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC428" class="line" lang="plaintext"> 3. `NAME_summits.bed` is in BED format, which contains the peak</span>
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="plaintext"> summits locations for every peaks. The 5th column in this file is</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">@@ -474,7 +478,8 @@ Description: # Recent Changes for MACS (2.1.3.3)</td>
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<pre style="margin: 0;"> <span id="LC478" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC479" class="line" lang="plaintext"> ## Tips of fine-tuning peak calling</span>
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<pre style="margin: 0;"> <span id="LC480" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC477" class="line" lang="plaintext"> There are several subcommands within MACSv2 package to fine-tune or customize your analysis:</span>
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="plaintext"> There are several subcommands within MACSv2 package to fine-tune or</span>
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="plaintext"> customize your analysis:</span>
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<pre style="margin: 0;"> <span id="LC483" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC484" class="line" lang="plaintext"> 1. `bdgcmp` can be used on `*_treat_pileup.bdg` and</span>
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<pre style="margin: 0;"> <span id="LC485" class="line" lang="plaintext"> `*_control_lambda.bdg` or bedGraph files from other resources</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">@@ -494,8 +499,9 @@ Description: # Recent Changes for MACS (2.1.3.3)</td>
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<pre style="margin: 0;"> <span id="LC499" class="line" lang="plaintext"> according to parameter settings for minimum length, maximum gap</span>
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<pre style="margin: 0;"> <span id="LC500" class="line" lang="plaintext"> and cutoff.</span>
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<pre style="margin: 0;"> <span id="LC501" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC497" class="line" lang="plaintext"> 4. You can combine subcommands to do a step-by-step peak</span>
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<pre style="margin: 0;">-<span id="LC498" class="line" lang="plaintext"> calling. Read detail at [MACS2 wikipage](https://github.com/taoliu/MACS/wiki/Advanced%3A-Call-peaks-using-MACS2-subcommands)</span>
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="plaintext"> 4. You can combine subcommands to do a step-by-step peak calling. Read</span>
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="plaintext"> detail at [MACS2</span>
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="plaintext"> wikipage](https://github.com/taoliu/MACS/wiki/Advanced%3A-Call-peaks-using-MACS2-subcommands)</span>
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<pre style="margin: 0;"> <span id="LC505" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC506" class="line" lang="plaintext">Platform: UNKNOWN</span>
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<pre style="margin: 0;"> <span id="LC507" class="line" lang="plaintext">Classifier: Development Status :: 5 - Production/Stable</span>
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<a href="https://salsa.debian.org/med-team/macs/compare/80c600ce7b134f707ca923396ac8a671bffa1cb4...5b2bb5b2030f7b64d102f661f724637ae32f4426#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Recent Changes for MACS (2.1.<span class="idiff left right">3.3</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Recent Changes for MACS (2.1.<span class="idiff left right">4</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### 2.1.3.3</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### 2.1.4</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="p"> *</span> Features added</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"> </span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"> Github Actions is used together with Travis CI for testing and</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"> deployment.</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="p"> </span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="p"> *</span> Bugs fixed (PR #322)</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"> 1) #318 Random score in <span class="sb" style="color: #d14;">`bdgdiff`</span> output. It turns out the sum_v</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"> is not initialized as 0 before adding. Potential bugs are fixed in</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"> other functions in ScoreTrack and CallPeakUnit codes.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"> 2) #321 Cython dependency in <span class="sb" style="color: #d14;">`setup.py`</span> script is removed. And</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"> place 'cythonzie' call to the correct position.</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"> 3) A typo is fixed in Github Actions script. </span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### 2.1.3</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="markdown"><span class="p"> *</span> Features added</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 1) Support Docker auto-deploy. PR #309</span></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">@@ -35,44 +53,7 @@</td>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 3) Rename COPYING to LICENSE.</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### 2.1.2</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="markdown"><span class="sb" style="color: #d14;"> * New features</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 1) Added missing BEDPE support. And enable the support for BAMPE</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="markdown"><span class="sb" style="color: #d14;"> and BEDPE formats in 'pileup', 'filterdup' and 'randsample'</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="markdown"><span class="sb" style="color: #d14;"> subcommands. When format is BAMPE or BEDPE, The 'pileup' command</span></span>
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46
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="markdown"><span class="sb" style="color: #d14;"> will pile up the whole fragment defined by mapping locations of</span></span>
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47
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="markdown"><span class="sb" style="color: #d14;"> the left end and right end of each read pair. Thank @purcaro</span></span>
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48
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="markdown"></span>
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49
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 2) Added options to callpeak command for tweaking max-gap and</span></span>
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50
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="markdown"><span class="sb" style="color: #d14;"> min-len during peak calling. Thank @jsh58!</span></span>
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51
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="markdown"></span>
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52
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 3) The callpeak option "--to-large" option is replaced with</span></span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="markdown"><span class="sb" style="color: #d14;"> "--scale-to large".</span></span>
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54
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="markdown"></span>
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55
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 4) The randsample option "-t" has been replaced with "-i".</span></span>
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56
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="markdown"></span>
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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="markdown"><span class="sb" style="color: #d14;"> * Bug fixes</span></span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="markdown"></span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 1) Fixed memory issue related to #122 and #146</span></span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="markdown"></span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 2) Fixed a bug caused by a typo. Related to #249, Thank @shengqh</span></span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="markdown"></span>
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<td class="diff-line-num old old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 3) Fixed a bug while setting commandline qvalue cutoff.</span></span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="markdown"></span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 4) Better describe the 5th column of narrowPeak. Thank @alexbarrera</span></span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 5) Fixed the calculation of average fragment length for paired-end</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="markdown"><span class="sb" style="color: #d14;"> data. Thank @jsh58</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 6) Fixed bugs caused by khash while computing p/q-value and log</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="markdown"><span class="sb" style="color: #d14;"> likelihood ratios. Thank @jsh58</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 7) More spelling tweaks in source code. Thank @mr-c</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="markdown"><span class="gh" style="color: #999;"># README for MACS2 (2.1.3.3)</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="markdown"><span class="gh" style="color: #999;"># README for MACS2 (2.1.4)</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Introduction</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="markdown"></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">@@ -260,8 +241,19 @@ of qvalue.</td>
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">##### `--min-length`, `--max-gap`</span></span>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="markdown">These two options can be used to fine-tune the peak calling behavior by specifying the minimum length of a called peak and the maximum allowed gap between two nearby regions to be merged. In another word, a called peak has to be longer than <span class="ge" style="font-style: italic;">*min-length*</span>, and if the distance between two nearby peaks is smaller than <span class="ge" style="font-style: italic;">*max-gap*</span> then they will be merged as one. If they are not set, MACS2 will set the DEFAULT value for <span class="ge" style="font-style: italic;">*min-length*</span> as the predicted fragment size d, and the DEFAULT value for <span class="ge" style="font-style: italic;">*max-gap*</span> as the detected read length. Note, if you set a <span class="ge" style="font-style: italic;">*min-length*</span> value smaller than the fragment size, it may have NO effect on the result. For BROAD peak calling, try to set a</span>
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="markdown">large value such as 500bps. You can also use '--cutoff-analysis' option with default setting, and check the column 'avelpeak' under different cutoff values to decide a reasonable <span class="ge" style="font-style: italic;">*min-length*</span> value.</span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="markdown">These two options can be used to fine-tune the peak calling behavior</span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="markdown">by specifying the minimum length of a called peak and the maximum</span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="markdown">allowed gap between two nearby regions to be merged. In another word,</span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="markdown">a called peak has to be longer than <span class="ge" style="font-style: italic;">*min-length*</span>, and if the distance</span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="markdown">between two nearby peaks is smaller than <span class="ge" style="font-style: italic;">*max-gap*</span> then they will be</span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="markdown">merged as one. If they are not set, MACS2 will set the DEFAULT value</span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="markdown">for <span class="ge" style="font-style: italic;">*min-length*</span> as the predicted fragment size d, and the DEFAULT</span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="markdown">value for <span class="ge" style="font-style: italic;">*max-gap*</span> as the detected read length. Note, if you set a</span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="markdown"><span class="ge" style="font-style: italic;">*min-length*</span> value smaller than the fragment size, it may have NO</span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="markdown">effect on the result. For BROAD peak calling, try to set a large value</span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="markdown">such as 500bps. You can also use '--cutoff-analysis' option with</span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="markdown">default setting, and check the column 'avelpeak' under different</span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="markdown">cutoff values to decide a reasonable <span class="ge" style="font-style: italic;">*min-length*</span> value.</span>
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">##### `--nolambda`</span></span>
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="markdown"></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">@@ -397,21 +389,33 @@ for reading an alignment file is about # of CHROMOSOME * BUFFER_SIZE *</td>
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<pre style="margin: 0;"> <span id="LC389" class="line" lang="markdown"><span class="p"> -</span> fold enrichment for this peak summit against random Poisson distribution with local lambda, </span>
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<pre style="margin: 0;"> <span id="LC390" class="line" lang="markdown"><span class="p"> -</span> -log10(qvalue) at peak summit</span>
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<pre style="margin: 0;"> <span id="LC391" class="line" lang="markdown"> </span>
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<pre style="margin: 0;">-<span id="LC400" class="line" lang="markdown"> Coordinates in XLS is 1-based which is different with BED format. When <span class="sb" style="color: #d14;">`--broad`</span> is enabled for broad peak calling, the pileup, pvalue, qvalue, and fold change in the XLS file will be the mean value across the entire peak region, since peak summit won't be called in broad peak calling mode. </span>
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="markdown"> Coordinates in XLS is 1-based which is different with BED</span>
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="markdown"> format. When <span class="sb" style="color: #d14;">`--broad`</span> is enabled for broad peak calling, the</span>
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="markdown"> pileup, pvalue, qvalue, and fold change in the XLS file will be the</span>
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="markdown"> mean value across the entire peak region, since peak summit won't</span>
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="markdown"> be called in broad peak calling mode.</span>
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="markdown"><span class="p">2.</span> <span class="sb" style="color: #d14;">`NAME_peaks.narrowPeak`</span> is BED6+4 format file which contains the</span>
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="markdown"> peak locations together with peak summit, pvalue and qvalue. You</span>
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="markdown"> can load it to UCSC genome browser. Definition of some specific</span>
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="markdown"> columns are: </span>
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="markdown"><span class="p"> </span></span>
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<pre style="margin: 0;">-<span id="LC407" class="line" lang="markdown"><span class="p"> -</span> 5th: integer score for display. It's calculated as <span class="sb" style="color: #d14;">`int(-10*log10pvalue)`</span> or <span class="sb" style="color: #d14;">`int(-10*log10qvalue)`</span> depending on whether <span class="sb" style="color: #d14;">`-p`</span> (pvalue) or <span class="sb" style="color: #d14;">`-q`</span> (qvalue) is used as score cutoff. Please note that currently this value might be out of the <span class="p">[</span><span class="nv" style="color: #008080;">0-1000</span><span class="p">]</span> range defined in <span class="p">[</span><span class="nv" style="color: #008080;">UCSC Encode narrowPeak format</span><span class="p">](</span><span class="sx" style="color: #d14;">https://genome.ucsc.edu/FAQ/FAQformat.html#format12</span><span class="p">)</span>. You can let the value saturated at 1000 (i.e. p/q-value = 10^-100) by using the following 1-liner awk: <span class="sb" style="color: #d14;">`awk -v OFS="\t" '{$5=$5>1000?1000:$5} {print}' NAME_peaks.narrowPeak`</span></span>
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="markdown"><span class="p"> -</span> 5th: integer score for display. It's calculated as</span>
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="markdown"> <span class="sb" style="color: #d14;">`int(-10*log10pvalue)`</span> or <span class="sb" style="color: #d14;">`int(-10*log10qvalue)`</span> depending on</span>
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="markdown"> whether <span class="sb" style="color: #d14;">`-p`</span> (pvalue) or <span class="sb" style="color: #d14;">`-q`</span> (qvalue) is used as score</span>
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="markdown"> cutoff. Please note that currently this value might be out of the</span>
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="markdown"> <span class="p">[</span><span class="nv" style="color: #008080;">0-1000</span><span class="p">]</span> range defined in <span class="err" style="color: #a61717; background-color: #e3d2d2;">[</span>UCSC Encode narrowPeak</span>
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="markdown"> format](https://genome.ucsc.edu/FAQ/FAQformat.html#format12). You</span>
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="markdown"> can let the value saturated at 1000 (i.e. p/q-value = 10^-100) by</span>
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="markdown"> using the following 1-liner awk: <span class="sb" style="color: #d14;">`awk -v OFS="\t"</span></span>
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="markdown"><span class="sb" style="color: #d14;"> '{$5=$5>1000?1000:$5} {print}' NAME_peaks.narrowPeak`</span></span>
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="markdown"><span class="p"> -</span> 7th: fold-change at peak summit</span>
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<pre style="margin: 0;"> <span id="LC413" class="line" lang="markdown"><span class="p"> -</span> 8th: -log10pvalue at peak summit</span>
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="markdown"><span class="p"> -</span> 9th: -log10qvalue at peak summit</span>
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="markdown"><span class="p"> -</span> 10th: relative summit position to peak start</span>
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<pre style="margin: 0;"> <span id="LC416" class="line" lang="markdown"> </span>
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<pre style="margin: 0;">-<span id="LC413" class="line" lang="markdown"> The file can be loaded directly to UCSC genome browser. Remove the<span class="idiff left right"> beginning track line if you want to</span></span>
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<pre style="margin: 0;">-<span id="LC414" class="line" lang="markdown"> analyze it by other tools.</span>
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="markdown"> The file can be loaded directly to UCSC genome browser. Remove the</span>
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="markdown"> <span class="idiff left right">beginning track line if you want to </span>analyze it by other tools.</span>
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="markdown"><span class="p">3.</span> <span class="sb" style="color: #d14;">`NAME_summits.bed`</span> is in BED format, which contains the peak</span>
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="markdown"> summits locations for every peaks. The 5th column in this file is</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">@@ -466,7 +470,8 @@ for reading an alignment file is about # of CHROMOSOME * BUFFER_SIZE *</td>
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<pre style="margin: 0;"> <span id="LC471" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Tips of fine-tuning peak calling</span></span>
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<pre style="margin: 0;">-<span id="LC469" class="line" lang="markdown">There are several subcommands within MACSv2 package to fine-tune or customize your analysis:</span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="markdown">There are several subcommands within MACSv2 package to fine-tune or</span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="markdown">customize your analysis:</span>
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<pre style="margin: 0;"> <span id="LC475" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC476" class="line" lang="markdown"><span class="p">1.</span> <span class="sb" style="color: #d14;">`bdgcmp`</span> can be used on <span class="sb" style="color: #d14;">`*_treat_pileup.bdg`</span> and</span>
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<pre style="margin: 0;"> <span id="LC477" class="line" lang="markdown"> <span class="sb" style="color: #d14;">`*_control_lambda.bdg`</span> or bedGraph files from other resources</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">@@ -486,5 +491,6 @@ There are several subcommands within MACSv2 package to fine-tune or customize yo</td>
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<pre style="margin: 0;"> <span id="LC491" class="line" lang="markdown"> according to parameter settings for minimum length, maximum gap</span>
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<pre style="margin: 0;"> <span id="LC492" class="line" lang="markdown"> and cutoff.</span>
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<pre style="margin: 0;"> <span id="LC493" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC489" class="line" lang="markdown"><span class="p">4.</span> You can combine subcommands to do a step-by-step peak</span>
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<pre style="margin: 0;">-<span id="LC490" class="line" lang="markdown"> calling. Read detail at <span class="p">[</span><span class="nv" style="color: #008080;">MACS2 wikipage</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/taoliu/MACS/wiki/Advanced%3A-Call-peaks-using-MACS2-subcommands</span><span class="p">)</span></span></pre>
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="markdown"><span class="p">4.</span> You can combine subcommands to do a step-by-step peak calling. Read</span>
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="markdown"> detail at <span class="err" style="color: #a61717; background-color: #e3d2d2;">[</span>MACS2</span>
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="markdown"> wikipage](https://github.com/taoliu/MACS/wiki/Advanced%3A-Call-peaks-using-MACS2-subcommands)</span></pre>
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<a href="https://salsa.debian.org/med-team/macs/compare/80c600ce7b134f707ca923396ac8a671bffa1cb4...5b2bb5b2030f7b64d102f661f724637ae32f4426#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">macs (2.1.4-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Add patch to fix spelling typo</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Tue, 01 Oct 2019 12:35:55 +0200</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">macs (2.1.3.3-1) unstable; urgency=medium</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"> [ Jelmer Vernooij ]</span>
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<a href="https://salsa.debian.org/med-team/macs/compare/80c600ce7b134f707ca923396ac8a671bffa1cb4...5b2bb5b2030f7b64d102f661f724637ae32f4426#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">spelling</span></pre>
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<a href="https://salsa.debian.org/med-team/macs/compare/80c600ce7b134f707ca923396ac8a671bffa1cb4...5b2bb5b2030f7b64d102f661f724637ae32f4426#e4c19aed51618bf0c7ebd03189c67e422f84d4eb"><strong>debian/patches/spelling</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Subject: typo fix</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- macs.orig/MACS2/IO/CallPeakUnit.pyx</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ macs/MACS2/IO/CallPeakUnit.pyx</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -419,7 +419,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> self.cutoff_analysis_filename = cutoff_analysis_filename</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"> cpdef destroy ( self ):</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- """Remove temparary files for pileup values of each chromosome.</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ """Remove temporary files for pileup values of each chromosome.</span></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"> Note: This function MUST be called if the class object won't</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> be used anymore.</span></pre>
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<a href="https://salsa.debian.org/med-team/macs/compare/80c600ce7b134f707ca923396ac8a671bffa1cb4...5b2bb5b2030f7b64d102f661f724637ae32f4426#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Time-stamp: <2019-09-<span class="idiff left right">20 15:08:11</span> taoliu></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Time-stamp: <2019-09-<span class="idiff left right">30 17:27:35</span> taoliu></span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="s" style="color: #d14;">"""Description: </span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"></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">@@ -10,7 +10,6 @@ under the terms of the BSD License (see the file LICENSE included with</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="s" style="color: #d14;">the distribution).</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">setuptools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">setup</span><span class="p">,</span> <span class="n" style="color: #333;">Extension</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"></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">@@ -22,14 +21,14 @@ try:</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Cython.Build</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">cythonize</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">has_cython</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Note: if this script is run under pip, cython should be installed already due to requirements.txt setting.</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">ImportError</span></span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">has_cython</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span> </span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">numpy</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">get_include</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">numpy_get_include</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">numpy_include_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">numpy_get_include</span><span class="p">()]</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span><span class="p"><span class="idiff left">:</span></span><span class="idiff right"> </span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">numpy_include_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">numpy</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">get_include</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">numpy_get_include</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">numpy_include_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">numpy_get_include</span><span class="p">()]</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">ImportError</span></span><span class="p"><span class="idiff right">:</span></span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">numpy_include_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">():</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="47" 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">@@ -48,7 +47,7 @@ def main():</td>
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48
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<td class="diff-line-num new_line" data-linenumber="47" 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="LC47" class="line" lang="python"> <span class="n" style="color: #333;">Extension</span><span class="p">(</span><span class="s" style="color: #d14;">"MACS2.PeakDetect"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"MACS2/PeakDetect.pyx"</span><span class="p">],</span> <span class="n" style="color: #333;">extra_compile_args</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">extra_c_args</span><span class="p">),</span></span>
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49
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<td class="diff-line-num new_line" data-linenumber="48" 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">
48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">Extension</span><span class="p">(</span><span class="s" style="color: #d14;">"MACS2.Signal"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"MACS2/Signal.pyx"</span><span class="p">],</span> <span class="n" style="color: #333;">include_dirs</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">numpy_include_dir</span><span class="p">,</span> <span class="n" style="color: #333;">extra_compile_args</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">extra_c_args</span><span class="p">),</span></span>
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50
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<td class="diff-line-num new_line" data-linenumber="49" 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">
49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">Extension</span><span class="p">(</span><span class="s" style="color: #d14;">"MACS2.IO.PeakIO"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"MACS2/IO/PeakIO.pyx"</span><span class="p">],</span> <span class="n" style="color: #333;">extra_compile_args</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">extra_c_args</span><span class="p">),</span></span>
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51
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">Extension</span><span class="p">(</span><span class="s" style="color: #d14;">"MACS2.IO.BedGraphIO"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"MACS2/IO/BedGraphIO.pyx"</span><span class="p">],</span> <span class="n" style="color: #333;">extra_compile_args</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">extra_c_args</span><span class="p">),</span><span class="idiff left right"> </span></span>
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<td class="diff-line-num new new_line" data-linenumber="50" 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="LC50" class="line" lang="python"> <span class="n" style="color: #333;">Extension</span><span class="p">(</span><span class="s" style="color: #d14;">"MACS2.IO.BedGraphIO"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"MACS2/IO/BedGraphIO.pyx"</span><span class="p">],</span> <span class="n" style="color: #333;">extra_compile_args</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">extra_c_args</span><span class="p">),</span></span>
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52
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<td class="diff-line-num new_line" data-linenumber="51" 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">
51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">Extension</span><span class="p">(</span><span class="s" style="color: #d14;">"MACS2.IO.FixWidthTrack"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"MACS2/IO/FixWidthTrack.pyx"</span><span class="p">],</span> <span class="n" style="color: #333;">include_dirs</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">numpy_include_dir</span><span class="p">,</span> <span class="n" style="color: #333;">extra_compile_args</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">extra_c_args</span><span class="p">),</span></span>
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53
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<td class="diff-line-num new_line" data-linenumber="52" 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">
52
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">Extension</span><span class="p">(</span><span class="s" style="color: #d14;">"MACS2.IO.PairedEndTrack"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"MACS2/IO/PairedEndTrack.pyx"</span><span class="p">],</span> <span class="n" style="color: #333;">include_dirs</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">numpy_include_dir</span><span class="p">,</span> <span class="n" style="color: #333;">extra_compile_args</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">extra_c_args</span><span class="p">),</span></span>
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54
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<td class="diff-line-num new_line" data-linenumber="53" 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">
53
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">Extension</span><span class="p">(</span><span class="s" style="color: #d14;">"MACS2.IO.BedGraph"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"MACS2/IO/BedGraph.pyx"</span><span class="p">],</span> <span class="n" style="color: #333;">libraries</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"m"</span><span class="p">],</span> <span class="n" style="color: #333;">extra_compile_args</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">extra_c_args</span><span class="p">),</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="57" 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="56" 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">@@ -57,6 +56,7 @@ def main():</td>
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57
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<td class="diff-line-num new_line" data-linenumber="56" 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="LC56" class="line" lang="python"> <span class="n" style="color: #333;">Extension</span><span class="p">(</span><span class="s" style="color: #d14;">"MACS2.hashtable"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"MACS2/hashtable.pyx"</span><span class="p">],</span> <span class="n" style="color: #333;">include_dirs</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"MACS2/"</span><span class="p">,</span><span class="n" style="color: #333;">numpy_get_include</span><span class="p">()],</span> <span class="n" style="color: #333;">extra_compile_args</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">extra_c_args</span><span class="p">),</span></span>
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58
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">Extension</span><span class="p">(</span><span class="s" style="color: #d14;">"MACS2.Statistics"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"MACS2/Statistics.pyx"</span><span class="p">],</span> <span class="n" style="color: #333;">libraries</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"m"</span><span class="p">],</span> <span class="n" style="color: #333;">include_dirs</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"MACS2/"</span><span class="p">,</span><span class="n" style="color: #333;">numpy_get_include</span><span class="p">()],</span> <span class="n" style="color: #333;">extra_compile_args</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">extra_c_args</span><span class="p">),</span></span>
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59
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"> <span class="p">]</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">ext_modules</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cythonize</span><span class="p">(</span><span class="n" style="color: #333;">ext_modules</span><span class="p">,</span> <span class="n" style="color: #333;">language_level</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">ext_modules</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">Extension</span><span class="p">(</span><span class="s" style="color: #d14;">"MACS2.Prob"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"MACS2/Prob.c"</span><span class="p">],</span> <span class="n" style="color: #333;">libraries</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"m"</span><span class="p">],</span> <span class="n" style="color: #333;">include_dirs</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">numpy_include_dir</span><span class="p">,</span> <span class="n" style="color: #333;">extra_compile_args</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">extra_c_args</span> <span class="p">),</span></span>
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62
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">Extension</span><span class="p">(</span><span class="s" style="color: #d14;">"MACS2.IO.Parser"</span><span class="p">,[</span><span class="s" style="color: #d14;">"MACS2/IO/Parser.c"</span><span class="p">],</span> <span class="n" style="color: #333;">include_dirs</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">numpy_include_dir</span><span class="p">,</span> <span class="n" style="color: #333;">extra_compile_args</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">extra_c_args</span><span class="p">),</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="65" 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="65" 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">@@ -65,7 +65,7 @@ def main():</td>
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65
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">Extension</span><span class="p">(</span><span class="s" style="color: #d14;">"MACS2.PeakDetect"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"MACS2/PeakDetect.c"</span><span class="p">],</span> <span class="n" style="color: #333;">extra_compile_args</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">extra_c_args</span><span class="p">),</span></span>
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<td class="diff-line-num old_line" data-linenumber="66" 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">
66
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">Extension</span><span class="p">(</span><span class="s" style="color: #d14;">"MACS2.Signal"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"MACS2/Signal.c"</span><span class="p">],</span> <span class="n" style="color: #333;">include_dirs</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">numpy_include_dir</span><span class="p">,</span> <span class="n" style="color: #333;">extra_compile_args</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">extra_c_args</span><span class="p">),</span></span>
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67
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<td class="diff-line-num new_line" data-linenumber="67" 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">
67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">Extension</span><span class="p">(</span><span class="s" style="color: #d14;">"MACS2.IO.PeakIO"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"MACS2/IO/PeakIO.c"</span><span class="p">],</span> <span class="n" style="color: #333;">extra_compile_args</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">extra_c_args</span><span class="p">),</span></span>
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<td class="diff-line-num old old_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
68
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<td class="diff-line-num new_line old" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">Extension</span><span class="p">(</span><span class="s" style="color: #d14;">"MACS2.IO.BedGraphIO"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"MACS2/IO/BedGraphIO.c"</span><span class="p">],</span> <span class="n" style="color: #333;">extra_compile_args</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">extra_c_args</span><span class="p">),</span><span class="idiff left right"> </span></span>
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<td class="diff-line-num new old_line" data-linenumber="69" 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="68" 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">
68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">Extension</span><span class="p">(</span><span class="s" style="color: #d14;">"MACS2.IO.BedGraphIO"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"MACS2/IO/BedGraphIO.c"</span><span class="p">],</span> <span class="n" style="color: #333;">extra_compile_args</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">extra_c_args</span><span class="p">),</span></span>
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<td class="diff-line-num old_line" data-linenumber="69" 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">
69
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">Extension</span><span class="p">(</span><span class="s" style="color: #d14;">"MACS2.IO.FixWidthTrack"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"MACS2/IO/FixWidthTrack.c"</span><span class="p">],</span> <span class="n" style="color: #333;">include_dirs</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">numpy_include_dir</span><span class="p">,</span> <span class="n" style="color: #333;">extra_compile_args</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">extra_c_args</span><span class="p">),</span></span>
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70
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">Extension</span><span class="p">(</span><span class="s" style="color: #d14;">"MACS2.IO.PairedEndTrack"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"MACS2/IO/PairedEndTrack.c"</span><span class="p">],</span> <span class="n" style="color: #333;">include_dirs</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">numpy_include_dir</span><span class="p">,</span> <span class="n" style="color: #333;">extra_compile_args</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">extra_c_args</span><span class="p">),</span></span>
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71
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">Extension</span><span class="p">(</span><span class="s" style="color: #d14;">"MACS2.IO.BedGraph"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"MACS2/IO/BedGraph.c"</span><span class="p">],</span> <span class="n" style="color: #333;">libraries</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"m"</span><span class="p">],</span> <span class="n" style="color: #333;">extra_compile_args</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">extra_c_args</span><span class="p">),</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="79" 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="79" 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">@@ -79,7 +79,7 @@ def main():</td>
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">long_description</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fh</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">()</span></span>
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python"> </span>
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">setup</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"MACS2"</span><span class="p">,</span></span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"2.1.<span class="idiff left right">3.3</span>"</span><span class="p">,</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"2.1.<span class="idiff left right">4</span>"</span><span class="p">,</span></span>
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83
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<td class="diff-line-num new_line" data-linenumber="83" 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">
83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Model Based Analysis for ChIP-Seq data"</span><span class="p">,</span></span>
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84
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">long_description</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">long_description</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python"> <span class="n" style="color: #333;">long_description_content_type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"text/markdown"</span><span class="p">,</span></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">@@ -88,9 +88,7 @@ def main():</td>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">url</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'http://github.com/taoliu/MACS/'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">package_dir</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'MACS2'</span> <span class="p">:</span> <span class="s" style="color: #d14;">'MACS2'</span><span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">packages</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'MACS2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'MACS2.IO'</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#package_data={'MACS2': ['data/*.dat']}, </span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">scripts</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'bin/macs2'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="python"> <span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">scripts</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'bin/macs2'</span><span class="p">,</span> <span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">classifiers</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"> <span class="s" style="color: #d14;">'Development Status :: 5 - Production/Stable'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="python"> <span class="s" style="color: #d14;">'Environment :: Console'</span><span class="p">,</span></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">@@ -104,11 +102,10 @@ def main():</td>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"> <span class="s" style="color: #d14;">'Programming Language :: Cython'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"> <span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">install_requires</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python"> <span class="s" style="color: #d14;">'numpy>=1.15'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python"> <span class="s" style="color: #d14;">'cython>=0.25'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="s" style="color: #d14;">'numpy>=1.16'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"> <span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">cmdclass</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">command_classes</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">ext_modules</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">cythonize</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ext_modules</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">language_level</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff">"2"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">ext_modules</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">ext_modules</span></span></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'__main__'</span><span class="p">:</span></span>
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