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<h3>

Steffen Möller pushed to branch upstream

at <a href="https://salsa.debian.org/med-team/python-bx">Debian Med / python-bx</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/python-bx/commit/9974c2d898e4358167e9fa956f30799e8ec7d16c">9974c2d8</a></strong>

<div>

<span>by Steffen Moeller</span>

<i>at 2018-10-17T10:16:22Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.8.2</pre>

</li>

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<h4>5 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">

.travis.yml

</a>

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<li class="file-stats">

<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

README.md

</a>

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<li class="file-stats">

<a href="#243cb4e08da80e92e253a4d0c60bb836981899ec">

lib/bx/intervals/io.py

</a>

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<a href="#1d6b8c4ef31f8875bd83481aae3a1f9122dfd25f">

scripts/bnMapper.py

</a>

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<li class="file-stats">

<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">

setup.py

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</li>

</ul>

<h4>Changes:</h4>

<li id="dea01dd89a3b602828e630677fde5d77c06441c8">

<a href="https://salsa.debian.org/med-team/python-bx/commit/9974c2d898e4358167e9fa956f30799e8ec7d16c#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</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">@@ -20,6 +20,7 @@ before_install:</td>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="yaml"><span class="na" style="color: teal;">install</span><span class="pi">:</span> </span>

</pre>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="yaml">    <span class="pi">-</span> <span class="s" style="color: #d14;">conda create --yes -n testenv python=$TRAVIS_PYTHON_VERSION Cython numpy nose</span></span>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="yaml">    <span class="pi">-</span> <span class="s" style="color: #d14;">source activate testenv</span></span>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml">    <span class="pi">-</span> <span class="s" style="color: #d14;">pip install python-lzo</span></span>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="yaml">    <span class="pi">-</span> <span class="s" style="color: #d14;">python setup.py build_ext --inplace</span></span>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="yaml">    <span class="pi">-</span> <span class="s" style="color: #d14;">python setup.py install</span></span>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="yaml"><span class="na" style="color: teal;">script</span><span class="pi">:</span> </span>

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<br>

</li>

<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

<a href="https://salsa.debian.org/med-team/python-bx/commit/9974c2d898e4358167e9fa956f30799e8ec7d16c#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.org/bxlab/bx-python.svg?branch=master</span><span class="p">)</span>](https://travis-ci.org/bxlab/bx-python)</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="p">[</span><span class="nv" style="color: teal;">![Read the Docs</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/readthedocs/bx-python.svg</span><span class="p">)</span>](https://bx-python.readthedocs.io/)</span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"><span class="gh" style="color: #999;"># bx-python</span></span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown">The bx-python project is a python library and associated set of scripts to allow for rapid implementation of genome scale analyses. The library contains a variety of useful modules, but the particular strengths are:</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">@@ -10,6 +12,10 @@ The bx-python project is a python library and associated set of scripts to allow</td>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown"><span class="p">    *</span> "Binned bitsets" which act just like chromosome sized bit arrays, but lazily allocate regions and allow large blocks of all set or all unset bits to be stored compactly</span>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown"><span class="p">    *</span> "Intersecter" for performing fast intersection tests that preserve both query and target intervals and associated annotation</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="12" 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">

12

</td>

<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

15

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Requirements</span></span>

</pre>

</td>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="17" 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">

17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown">Build currently requires liblzo, e.g. sudo apt-get install liblzo2-dev on debian/ubuntu).</span>

</pre>

</td>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="18" 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">

18

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

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<td class="diff-line-num new_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">

19

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Installing</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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<td class="diff-line-num new_line" data-linenumber="20" 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">

20

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="15" 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">

15

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<td class="diff-line-num new_line" data-linenumber="21" 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">

21

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="markdown">The package can be installed with pip:</span>

</pre>

</td>

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</table>

<br>

</li>

<li id="243cb4e08da80e92e253a4d0c60bb836981899ec">

<a href="https://salsa.debian.org/med-team/python-bx/commit/9974c2d898e4358167e9fa956f30799e8ec7d16c#243cb4e08da80e92e253a4d0c60bb836981899ec"><strong>lib/bx/intervals/io.py</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="99" 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="99" 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">@@ -99,7 +99,9 @@ class GenomicIntervalReader( TableReader ):</td>

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<td class="diff-line-num old_line" data-linenumber="99" 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">

99

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<td class="diff-line-num new_line" data-linenumber="99" 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">

99

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"><span class="s" style="color: #d14;">    ...               "chr2</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">tbar</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">t20</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">t300</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">txxx",</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="100" 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">

100

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<td class="diff-line-num new_line" data-linenumber="100" 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">

100

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"><span class="s" style="color: #d14;">    ...               "#I am a comment",</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="101" 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">

101

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<td class="diff-line-num new_line" data-linenumber="101" 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">

101

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"><span class="s" style="color: #d14;">    ...               "chr2</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">tbar</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">t20</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">t300</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">txxx" ], start_col=2, end_col=3 )</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="102" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="102" 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">

102

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"><span class="s" style="color: #d14;">    >>> header = next(r)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="102" 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">

102

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<td class="diff-line-num new_line" data-linenumber="103" 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">

103

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"><span class="s" style="color: #d14;">    >>> elements = list( r )</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="103" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="104" 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">

104

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"><span class="s" style="color: #d14;">    >>> elements.insert(0, header)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="103" 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">

103

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<td class="diff-line-num new_line" data-linenumber="105" 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">

105

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"><span class="s" style="color: #d14;">    >>> assert type( elements[0] ) is Header</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="104" 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">

104

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<td class="diff-line-num new_line" data-linenumber="106" 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">

106

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"><span class="s" style="color: #d14;">    >>> str( elements[0] )</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="105" 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">

105

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<td class="diff-line-num new_line" data-linenumber="107" 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">

107

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"><span class="s" style="color: #d14;">    '#chrom</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">tname</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">tstart</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">tend</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">textra'</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="174" 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="176" 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">@@ -174,6 +176,15 @@ class GenomicIntervalReader( TableReader ):</td>

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<pre style="margin: 0;"> <span id="LC176" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bitsets</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC177" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC178" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">NiceReaderWrapper</span><span class="p">(</span> <span class="n" style="color: #333;">GenomicIntervalReader</span> <span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"><span class="s" style="color: #d14;">    >>> r = NiceReaderWrapper( [ "#chrom</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">tname</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">tstart</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">tend</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">textra",</span></span>

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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"><span class="s" style="color: #d14;">    ...                          "chr1</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">tfoo</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">t1</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">t100</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">txxx",</span></span>

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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"><span class="s" style="color: #d14;">    ...                          "chr2</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">tbar</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">t20</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">t300</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">txxx",</span></span>

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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"><span class="s" style="color: #d14;">    ...                          "#I am a comment",</span></span>

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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"><span class="s" style="color: #d14;">    ...                          "chr2</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">tbar</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">t20</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">t300</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">txxx" ], start_col=2, end_col=3 )</span></span>

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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"><span class="s" style="color: #d14;">    >>> assert type(next(r)) == Header</span></span>

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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC188" 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;">reader</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span> <span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC189" class="line" lang="python">        <span class="n" style="color: #333;">GenomicIntervalReader</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">reader</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC190" 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;">outstream</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"outstream"</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="187" 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="198" 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">@@ -187,7 +198,7 @@ class NiceReaderWrapper( GenomicIntervalReader ):</td>

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<pre style="margin: 0;"> <span id="LC198" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__next__</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span> <span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC199" class="line" lang="python">        <span class="k" style="font-weight: 600;">while</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC200" 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="LC190" class="line" lang="python">                <span class="n" style="color: #333;">nextitem</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">GenomicIntervalReader</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">next</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="idiff right"> </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;">nextitem</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">super</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">NiceReaderWrapper</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">__next__</span></span><span class="p"><span class="idiff right">(</span>)</span></span>

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<pre style="margin: 0;"> <span id="LC202" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">nextitem</span></span>

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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python">            <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">ParseError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">outstream</span><span class="p">:</span></span>

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<br>

</li>

<li id="1d6b8c4ef31f8875bd83481aae3a1f9122dfd25f">

<a href="https://salsa.debian.org/med-team/python-bx/commit/9974c2d898e4358167e9fa956f30799e8ec7d16c#1d6b8c4ef31f8875bd83481aae3a1f9122dfd25f"><strong>scripts/bnMapper.py</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="21" 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="21" 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">@@ -21,6 +21,9 @@ from bx.cookbook import argparse</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;">bx.intervals.intersection</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">IntervalTree</span><span class="p">,</span> <span class="n" style="color: #333;">Interval</span></span>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"><span class="n" style="color: #333;">elem_t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dtype</span><span class="p">([(</span><span class="s" style="color: #d14;">'chrom'</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">str_</span><span class="p">,</span> <span class="mi" style="color: #099;">30</span><span class="p">),</span> <span class="p">(</span><span class="s" style="color: #d14;">'start'</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">int64</span><span class="p">),</span> <span class="p">(</span><span class="s" style="color: #d14;">'end'</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">int64</span><span class="p">),</span> <span class="p">(</span><span class="s" style="color: #d14;">'id'</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">str_</span><span class="p">,</span> <span class="mi" style="color: #099;">100</span><span class="p">)])</span></span>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"><span class="n" style="color: #333;">narrowPeak_t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dtype</span><span class="p">([(</span><span class="s" style="color: #d14;">'chrom'</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">str_</span><span class="p">,</span> <span class="mi" style="color: #099;">30</span><span class="p">),</span> <span class="p">(</span><span class="s" style="color: #d14;">'start'</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">int64</span><span class="p">),</span> <span class="p">(</span><span class="s" style="color: #d14;">'end'</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">int64</span><span class="p">),</span> <span class="p">(</span><span class="s" style="color: #d14;">'id'</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">str_</span><span class="p">,</span> <span class="mi" style="color: #099;">100</span><span class="p">),</span></span>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python">                         <span class="p">(</span><span class="s" style="color: #d14;">'score'</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">int64</span><span class="p">),</span> <span class="p">(</span><span class="s" style="color: #d14;">'strand'</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">str_</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">),</span> <span class="p">(</span><span class="s" style="color: #d14;">'signalValue'</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">float</span><span class="p">),</span></span>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python">                         <span class="p">(</span><span class="s" style="color: #d14;">'pValue'</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">float</span><span class="p">),</span> <span class="p">(</span><span class="s" style="color: #d14;">'qValue'</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">float</span><span class="p">),</span> <span class="p">(</span><span class="s" style="color: #d14;">'peak'</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">int64</span><span class="p">)])</span></span>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"><span class="n" style="color: #333;">LOG_LEVELS</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"info"</span> <span class="p">:</span> <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">INFO</span><span class="p">,</span> <span class="s" style="color: #d14;">"debug"</span> <span class="p">:</span> <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">DEBUG</span><span class="p">,</span> <span class="s" style="color: #d14;">"silent"</span> <span class="p">:</span> <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ERROR</span><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"><span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">basicConfig</span><span class="p">()</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="116" 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">@@ -116,18 +119,43 @@ def union_elements(elements):</td>

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">transform_by_chrom</span><span class="p">(</span><span class="n" style="color: #333;">all_epo</span><span class="p">,</span> <span class="n" style="color: #333;">from_elem_list</span><span class="p">,</span> <span class="n" style="color: #333;">tree</span><span class="p">,</span> <span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">,</span> <span class="n" style="color: #333;">out_fd</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python">    <span class="n" style="color: #333;">BED4_FRM</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="python">    <span class="n" style="color: #333;">BED12_FRM</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">1000</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0,0,0</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python">    <span class="n" style="color: #333;">NPEAK_FRM</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">f</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">f</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">f</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">from_elem_list</span><span class="p">[</span><span class="s" style="color: #d14;">'chrom'</span><span class="p">])</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="LC124" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python">    <span class="n" style="color: #333;">mapped_elem_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

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<td class="diff-line-num new new_line" data-linenumber="126" 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="LC126" class="line" lang="python">    <span class="n" style="color: #333;">mapped_summit_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

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<pre style="margin: 0;"> <span id="LC127" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">from_elem</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">from_elem_list</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;">matching_block_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">attrgetter</span><span class="p">(</span><span class="s" style="color: #d14;">"value"</span><span class="p">)(</span><span class="n" style="color: #333;">_</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">_</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">from_elem</span><span class="p">[</span><span class="s" style="color: #d14;">'start'</span><span class="p">],</span> <span class="n" style="color: #333;">from_elem</span><span class="p">[</span><span class="s" style="color: #d14;">'end'</span><span class="p">])]</span></span>

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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python">        <span class="c" style="color: #998; font-style: italic;"># do the actual mapping</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python">        <span class="n" style="color: #333;">to_elem_slices</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">_</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">_</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="n" style="color: #333;">transform</span><span class="p">(</span><span class="n" style="color: #333;">from_elem</span><span class="p">,</span> <span class="n" style="color: #333;">all_epo</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">gap</span><span class="p">)</span> <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="n" style="color: #333;">matching_block_ids</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">_</span><span class="p">]</span></span>

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python">        <span class="s" style="color: #d14;">""" # Original version: silently discard split alignments</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"><span class="s" style="color: #d14;">        if len(to_elem_slices) > 1 or len(to_elem_slices) == 0:</span></span>

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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python"><span class="s" style="color: #d14;">            log.debug("</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s no match or in different chain/chromosomes" </span><span class="si" style="color: #d14;">% </span><span class="s" style="color: #d14;">(str(from_elem)))</span></span>

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"><span class="s" style="color: #d14;">            continue</span></span>

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python"><span class="s" style="color: #d14;">        to_elem_slices = to_elem_slices[0]</span></span>

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python">        <span class="s" style="color: #d14;">""" Modified version below allows liftOver-like behavior of</span></span>

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"><span class="s" style="color: #d14;">        keeping the longest alignment when alignments are split across</span></span>

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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"><span class="s" style="color: #d14;">        multiple chains. Added by Adam Diehl (adadiehl@umich.edu)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python">        <span class="n" style="color: #333;">max_elem_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">to_elem_slices</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python">            <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s: no match in target: discarding."</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">from_elem</span><span class="p">)))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python">            <span class="k" style="font-weight: 600;">continue</span></span>

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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">to_elem_slices</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keep_split</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="147" 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="LC147" class="line" lang="python">            <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s spans multiple chains/chromosomes. Using longest alignment."</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">from_elem</span><span class="p">)))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="131" 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="148" 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="LC148" class="line" lang="python">            <span class="n" style="color: #333;">max_elem_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="131" 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="149" 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="LC149" 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="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">to_elem_slices</span><span class="p">)):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="131" 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="150" 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="LC150" class="line" lang="python">                <span class="n" style="color: #333;">elem_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">to_elem_slices</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</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;">to_elem_slices</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="mi" style="color: #099;">2</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="131" 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="151" 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="LC151" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">elem_len</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">max_elem_len</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="131" 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="152" 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="LC152" class="line" lang="python">                    <span class="n" style="color: #333;">max_elem_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">elem_len</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="131" 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="153" 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="LC153" class="line" lang="python">                    <span class="n" style="color: #333;">max_elem_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="154" 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="LC154" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">to_elem_slices</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="131" 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="155" 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="LC155" class="line" lang="python">            <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s spans multiple chains/chromosomes: discarding."</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">from_elem</span><span class="p">)))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="131" 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="156" 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">

156

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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python">            <span class="k" style="font-weight: 600;">continue</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="131" 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="157" 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="LC157" class="line" lang="python">        <span class="n" style="color: #333;">to_elem_slices</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">to_elem_slices</span><span class="p">[</span><span class="n" style="color: #333;">max_elem_idx</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="131" 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="158" 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="LC158" class="line" lang="python">        <span class="s" style="color: #d14;">""" End AGD modifications """</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="159" 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="LC159" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="160" 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="LC160" class="line" lang="python">        <span class="c" style="color: #998; font-style: italic;"># apply threshold</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="161" 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="LC161" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">from_elem</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;">from_elem</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;">opt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">threshold</span> <span class="o" style="font-weight: 600;">></span> <span class="nb" style="color: #0086b3;">reduce</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">b</span><span class="p">,</span><span class="n" style="color: #333;">a</span><span class="p">:</span> <span class="n" style="color: #333;">a</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;">a</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;">b</span><span class="p">,</span> <span class="n" style="color: #333;">to_elem_slices</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">):</span></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">@@ -139,19 +167,45 @@ def transform_by_chrom(all_epo, from_elem_list, tree, chrom, opt, out_fd):</td>

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">to_elem_list</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="python">            <span class="n" style="color: #333;">mapped_elem_count</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

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<td class="diff-line-num old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="169" 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="LC169" class="line" lang="python">            <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">joined to </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d elements"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">to_elem_list</span><span class="p">)))</span></span>

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<td class="diff-line-num new new_line" data-linenumber="170" 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="LC170" class="line" lang="python">            <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">to_elem_list</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

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<td class="diff-line-num new new_line" data-linenumber="171" 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="LC171" class="line" lang="python">            <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">to_elem_list</span><span class="p">[</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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<td class="diff-line-num new_line" data-linenumber="172" 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="LC172" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"BED4"</span><span class="p">:</span></span>

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<td class="diff-line-num old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="173" 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="LC173" class="line" lang="python">                <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">tel</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">to_elem_list</span><span class="p">:</span></span>

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<td class="diff-line-num old_line" data-linenumber="144" 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="LC174" class="line" lang="python">                    <span class="n" style="color: #333;">out_fd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">BED4_FRM</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">tel</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC145" 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="LC146" class="line" lang="python">                <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">to_elem_list</span><span class="p">[</span><span class="mi" style="color: #099;">0</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="LC147" class="line" lang="python">                <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">to_elem_list</span><span class="p">[</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="LC175" class="line" lang="python">            <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"BED12"</span><span class="p">:</span></span>

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<td class="diff-line-num new_line" data-linenumber="176" 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="LC176" class="line" lang="python">                <span class="n" style="color: #333;">out_fd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">BED12_FRM</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">to_elem_list</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">from_elem</span><span class="p">[</span><span class="s" style="color: #d14;">'id'</span><span class="p">],</span></span>

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<pre style="margin: 0;"> <span id="LC177" class="line" lang="python">                        <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">to_elem_list</span><span class="p">),</span></span>

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<pre style="margin: 0;"> <span id="LC178" class="line" lang="python">                        <span class="s" style="color: #d14;">","</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">e</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;">e</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">e</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">to_elem_list</span> <span class="p">),</span></span>

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<pre style="margin: 0;"> <span id="LC179" class="line" lang="python">                        <span class="s" style="color: #d14;">","</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">e</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;">start</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">e</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">to_elem_list</span> <span class="p">)</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC180" class="line" lang="python">                        <span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC153" class="line" lang="python">    <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d of </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d elements mapped"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">mapped_elem_count</span><span class="p">,</span> <span class="n" style="color: #333;">from_elem_list</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">shape</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="LC154" class="line" lang="python"></span>

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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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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python">                <span class="c" style="color: #998; font-style: italic;"># narrowPeak convention is to report the peak location relative to start</span></span>

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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python">                <span class="n" style="color: #333;">peak</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;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">end</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</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;">start</span></span>

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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">in_format</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"narrowPeak"</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python">                    <span class="c" style="color: #998; font-style: italic;"># Map the peak location</span></span>

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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python">                    <span class="c" style="color: #998; font-style: italic;">#sys.stderr.write("{}\n".format(from_elem))</span></span>

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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python">                    <span class="n" style="color: #333;">matching_block_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">attrgetter</span><span class="p">(</span><span class="s" style="color: #d14;">"value"</span><span class="p">)(</span><span class="n" style="color: #333;">_</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">_</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">from_elem</span><span class="p">[</span><span class="s" style="color: #d14;">'peak'</span><span class="p">],</span> <span class="n" style="color: #333;">from_elem</span><span class="p">[</span><span class="s" style="color: #d14;">'peak'</span><span class="p">])]</span></span>

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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python">                    <span class="n" style="color: #333;">p_elem_slices</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">_</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">_</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="n" style="color: #333;">transform</span><span class="p">(</span> <span class="n" style="color: #333;">np</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;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">from_elem</span><span class="p">[</span><span class="s" style="color: #d14;">'peak'</span><span class="p">],</span> <span class="n" style="color: #333;">from_elem</span><span class="p">[</span><span class="s" style="color: #d14;">'peak'</span><span class="p">],</span> <span class="s" style="color: #d14;">'.'</span><span class="p">),</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">elem_t</span><span class="p">),</span> <span class="n" style="color: #333;">all_epo</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">gap</span><span class="p">)</span> <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="n" style="color: #333;">matching_block_ids</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">_</span><span class="p">]</span></span>

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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">p_elem_slices</span><span class="p">)</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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<td class="diff-line-num new new_line" data-linenumber="190" 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">

190

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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python">                        <span class="n" style="color: #333;">mapped_summit_count</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="191" 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">

191

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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python">                        <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"{}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">format</span><span class="p">(</span><span class="n" style="color: #333;">p_elem_slices</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="192" 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">

192

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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python">                        <span class="c" style="color: #998; font-style: italic;"># Make sure the peak is between the start and end positions</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="193" 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">

193

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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python">                        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">p_elem_slices</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">0</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;">start</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">p_elem_slices</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">0</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;">end</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="194" 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">

194

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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python">                            <span class="n" style="color: #333;">peak</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p_elem_slices</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">0</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;">start</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="195" 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">

195

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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python">                        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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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;">mapped_summit_count</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="197" 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">

197

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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python">                            <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span><span class="s" style="color: #d14;">"Warning: elem {} summit mapped location falls outside the mapped element start and end. Using the mapped elem midpoint instead."</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">format</span><span class="p">(</span><span class="n" style="color: #333;">from_elem</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="198" 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">

198

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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python">                        </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="199" 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="LC199" class="line" lang="python">                    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="200" 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="LC200" class="line" lang="python">                        <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span><span class="s" style="color: #d14;">"Warning: elem {} summit maps to a gap region in the target alignment. Using the mapped elem midpoint instead."</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">format</span><span class="p">(</span><span class="n" style="color: #333;">from_elem</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="201" 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">

201

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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python">                <span class="n" style="color: #333;">out_fd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">NPEAK_FRM</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">to_elem_list</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">from_elem</span><span class="p">[</span><span class="s" style="color: #d14;">'id'</span><span class="p">],</span></span>

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<td class="diff-line-num new new_line" data-linenumber="202" 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="LC202" class="line" lang="python">                                          <span class="n" style="color: #333;">from_elem</span><span class="p">[</span><span class="s" style="color: #d14;">'score'</span><span class="p">],</span> <span class="n" style="color: #333;">from_elem</span><span class="p">[</span><span class="s" style="color: #d14;">'strand'</span><span class="p">],</span> <span class="n" style="color: #333;">from_elem</span><span class="p">[</span><span class="s" style="color: #d14;">'signalValue'</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="203" 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="LC203" class="line" lang="python">                                          <span class="n" style="color: #333;">from_elem</span><span class="p">[</span><span class="s" style="color: #d14;">'pValue'</span><span class="p">],</span> <span class="n" style="color: #333;">from_elem</span><span class="p">[</span><span class="s" style="color: #d14;">'qValue'</span><span class="p">],</span> <span class="n" style="color: #333;">peak</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="204" 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="LC204" class="line" lang="python">    <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d of </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d elements mapped"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">mapped_elem_count</span><span class="p">,</span> <span class="n" style="color: #333;">from_elem_list</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">shape</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"narrowPeak"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">in_format</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"narrowPeak"</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python">        <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d peak summits from </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d mapped elements mapped"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">mapped_summit_count</span><span class="p">,</span> <span class="n" style="color: #333;">mapped_elem_count</span><span class="p">))</span></span>

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<td class="diff-line-num new new_line" data-linenumber="207" 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="LC207" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python">    </span>

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<pre style="margin: 0;"> <span id="LC209" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">transform_file</span><span class="p">(</span><span class="n" style="color: #333;">ELEMS</span><span class="p">,</span> <span class="n" style="color: #333;">ofname</span><span class="p">,</span> <span class="n" style="color: #333;">EPO</span><span class="p">,</span> <span class="n" style="color: #333;">TREE</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC210" class="line" lang="python">    <span class="s" style="color: #d14;">"transform/map the elements of this file and dump the output on 'ofname'"</span></span>

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<pre style="margin: 0;"> <span id="LC211" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="193" 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="247" 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">@@ -193,16 +247,29 @@ def loadChains(path):</td>

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<pre style="margin: 0;"> <span id="LC247" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span> <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;">tStrand</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'+'</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">t</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">EPO</span> <span class="p">),</span> <span class="s" style="color: #d14;">"all target strands should be +"</span></span>

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<pre style="margin: 0;"> <span id="LC248" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">EPO</span></span>

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<pre style="margin: 0;"> <span id="LC249" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC196" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">loadFeatures</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC197" class="line" lang="python">    <span class="s" style="color: #d14;">"load BED4 features (all other columns are ignored)"</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">loadFeatures</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="251" 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="LC251" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="252" 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="LC252" class="line" lang="python"><span class="s" style="color: #d14;">    Load features. For BED, only BED4 columns are loaded.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC253" class="line" lang="python"><span class="s" style="color: #d14;">    For narrowPeak, all columns are loaded.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC254" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC255" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="256" 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="LC256" class="line" lang="python">    <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"loading from </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s ..."</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">path</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="257" 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="LC257" class="line" lang="python">    <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="201" 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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<td class="diff-line-num new_line old" data-linenumber="258" 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="LC201" class="line" lang="python">    <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fd</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="202" 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">

202

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<td class="diff-line-num new_line old" data-linenumber="258" 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="LC202" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fd</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="203" 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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<td class="diff-line-num new_line old" data-linenumber="258" 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="LC203" class="line" lang="python">            <span class="n" style="color: #333;">cols</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="204" 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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<td class="diff-line-num new_line old" data-linenumber="258" 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="LC204" class="line" lang="python">            <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span> <span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]),</span> <span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">])</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="205" 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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<td class="diff-line-num new_line old" data-linenumber="258" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC205" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">np</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;">data</span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">elem_t</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="206" 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="258" 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="LC258" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">in_format</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"BED"</span><span class="p">:</span>        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="206" 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="259" 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="LC259" class="line" lang="python">        <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fd</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="206" 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="260" 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="LC260" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fd</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="206" 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="261" 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="LC261" class="line" lang="python">                <span class="n" style="color: #333;">cols</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="206" 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="262" 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="LC262" class="line" lang="python">                <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span> <span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]),</span> <span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">])</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="206" 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="263" 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="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC263" class="line" lang="python">        <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</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;">data</span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">elem_t</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="206" 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="264" 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="LC264" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="206" 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="265" 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="LC265" class="line" lang="python">        <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fd</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC266" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fd</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="267" 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="LC267" class="line" lang="python">                <span class="n" style="color: #333;">cols</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="268" 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="LC268" class="line" lang="python">                <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span> <span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]),</span> <span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]),</span></span>

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<td class="diff-line-num new new_line" data-linenumber="269" 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="LC269" class="line" lang="python">                              <span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]),</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]),</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]),</span></span>

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<pre style="margin: 0;">+<span id="LC270" class="line" lang="python">                              <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">[</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="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]))</span> <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC271" class="line" lang="python">        <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</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;">data</span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">narrowPeak_t</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="272" 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="LC272" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">data</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC273" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC274" 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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<td class="diff-line-num new_line" data-linenumber="275" 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="LC275" class="line" lang="python">    <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argparse</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ArgumentParser</span><span class="p">(</span><span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">__doc__</span><span class="p">,</span> <span class="n" style="color: #333;">epilog</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Olgert Denas (Taylor Lab)"</span><span class="p">,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="212" 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">@@ -212,8 +279,8 @@ if __name__ == "__main__":</td>

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<pre style="margin: 0;"> <span id="LC279" class="line" lang="python">            <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Input to process. If more than a file is specified, all files will be mapped and placed on --output, which should be a directory."</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC280" class="line" lang="python">    <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"alignment"</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Alignment file (.chain or .pkl)"</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC281" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC215" class="line" lang="python">    <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-f"</span><span class="p">,</span> <span class="s" style="color: #d14;">'--format'</span><span class="p">,</span> <span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">"BED4"</span><span class="p">,</span> <span class="s" style="color: #d14;">"BED12"</span><span class="p">),</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"BED4"</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC216" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left">help</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff right">"Output format</span>."</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;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-f"</span><span class="p">,</span> <span class="s" style="color: #d14;">'--format'</span><span class="p">,</span> <span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">"BED4"</span><span class="p">,</span> <span class="s" style="color: #d14;">"BED12"</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"narrowPeak"</span></span><span class="p">),</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"BED4"</span><span class="p">,</span></span>

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<td class="diff-line-num new new_line" data-linenumber="283" 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="LC283" class="line" lang="python">            <span class="idiff left">            </span><span class="n" style="color: #333;"><span class="idiff">help</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff right">"Output format. BED4 output reports all aligned blocks as separate BED records. BED12 reports a single BED record for each mapped element, with individual blocks given in the BED12 fields. NarrowPeak reports a single narrowPeak record for each mapped element, in which the chromosome, start, end, and peak positions are mapped to the target species and all other columns are passed through unchanged</span>."</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;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="s" style="color: #d14;">'--output'</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"FILE"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'stdout'</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC285" class="line" lang="python">            <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">s</span><span class="p">:</span> <span class="p">((</span><span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">'stdout'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-'</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">"/dev/stdout"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">s</span><span class="p">),</span></span>

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<pre style="margin: 0;"> <span id="LC286" class="line" lang="python">            <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Output file. Mandatory if more than on file in input."</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC292" class="line" lang="python">            <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Ignore elements with an insertion/deletion of this or bigger size."</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC293" class="line" lang="python">    <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-v'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--verbose'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">LOG_LEVELS</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span><span class="p">()),</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'info'</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC294" class="line" lang="python">            <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Verbosity level'</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC228" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC295" class="line" lang="python">    <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-k"</span><span class="p">,</span> <span class="s" style="color: #d14;">'--keep_split'</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC296" class="line" lang="python">            <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"If elements span multiple chains, report the segment with the longest overlap instead of silently dropping them. (This is the default behavior for liftOver.)"</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC297" class="line" lang="python">    <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-i"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--in_format"</span><span class="p">,</span> <span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"BED"</span><span class="p">,</span> <span class="s" style="color: #d14;">"narrowPeak"</span><span class="p">],</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"BED"</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC298" class="line" lang="python">            <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Input file format."</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC299" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC300" class="line" lang="python">    <span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC301" class="line" lang="python">    <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">setLevel</span><span class="p">(</span><span class="n" style="color: #333;">LOG_LEVELS</span><span class="p">[</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">verbose</span><span class="p">])</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="257" 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="327" 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">@@ -257,4 +327,4 @@ if __name__ == "__main__":</td>

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<pre style="margin: 0;"> <span id="LC327" class="line" lang="python">                <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"overwriting </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s ..."</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">outpath</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC328" class="line" lang="python">            <span class="n" style="color: #333;">transform_file</span><span class="p">(</span><span class="n" style="color: #333;">loadFeatures</span><span class="p">(</span><span class="n" style="color: #333;">inpath</span><span class="p">),</span> <span class="n" style="color: #333;">outpath</span><span class="p">,</span> <span class="n" style="color: #333;">EPO</span><span class="p">,</span> <span class="n" style="color: #333;">TREE</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC329" 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="LC260" class="line" lang="python">        <span class="n" style="color: #333;">transform_file</span><span class="p">(</span><span class="n" style="color: #333;">loadFeatures</span><span class="p">(</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">input</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="p">),</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="n" style="color: #333;">EPO</span><span class="p">,</span> <span class="n" style="color: #333;">TREE</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">)</span></span></pre>

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<pre style="margin: 0;">+<span id="LC330" class="line" lang="python">        <span class="n" style="color: #333;">transform_file</span><span class="p">(</span><span class="n" style="color: #333;">loadFeatures</span><span class="p">(</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">input</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]<span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">opt</span></span> <span class="p">),</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="n" style="color: #333;">EPO</span><span class="p">,</span> <span class="n" style="color: #333;">TREE</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">)</span></span></pre>

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<br>

</li>

<li id="8e2edce0d507e1297474f25c00cae94258db38d8">

<a href="https://salsa.debian.org/med-team/python-bx/commit/9974c2d898e4358167e9fa956f30799e8ec7d16c#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>

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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>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,22 +17,21 @@ from glob import glob</td>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC18" 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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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python">    <span class="n" style="color: #333;">build_requires</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span> <span class="s" style="color: #d14;">'python-lzo'</span><span class="p">,</span> <span class="s" style="color: #d14;">'numpy'</span> <span class="p">]</span></span>

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<td class="diff-line-num new_line old" data-linenumber="20" 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="LC21" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python">    <span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> \</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="21" 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="LC21" class="line" lang="python">      <span class="nb" style="color: #0086b3;">dict</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;">"bx-python"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="24" 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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<td class="diff-line-num new_line old" data-linenumber="22" 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="LC24" 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;">"0.8.1"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="25" 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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<td class="diff-line-num new_line old" data-linenumber="22" 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="LC25" class="line" lang="python">            <span class="n" style="color: #333;">install_requires</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">build_requires</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span><span class="s" style="color: #d14;">'six'</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="26" 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="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python">            <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.8.2"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="26" 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="23" 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="LC23" class="line" lang="python">            <span class="n" style="color: #333;">setup_requires</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'numpy'</span><span class="p">,</span> <span class="s" style="color: #d14;">'cython'</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="26" 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="24" 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="LC24" 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 class="s" style="color: #d14;">'numpy'</span><span class="p">,</span> <span class="s" style="color: #d14;">'six'</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="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">

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python">            <span class="n" style="color: #333;">py_modules</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span> <span class="s" style="color: #d14;">'psyco_full'</span> <span class="p">],</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="26" 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="LC26" 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;">''</span><span class="p">:</span> <span class="s" style="color: #d14;">'lib'</span> <span class="p">},</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="27" 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="LC27" class="line" lang="python">            <span class="n" style="color: #333;">package_data</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span> <span class="s" style="color: #d14;">''</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">'*.ps'</span><span class="p">]</span> <span class="p">},</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python">            <span class="n" style="color: #333;">scripts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">glob</span><span class="p">(</span> <span class="s" style="color: #d14;">"scripts/*.py"</span> <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="29" 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="LC29" class="line" lang="python">            <span class="n" style="color: #333;">test_suite</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'nose.collector'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="31" 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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<td class="diff-line-num new_line old" data-linenumber="30" 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="LC31" class="line" lang="python">            <span class="n" style="color: #333;">tests_require</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'nose'</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" 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="30" 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="LC30" class="line" lang="python">            <span class="n" style="color: #333;">tests_require</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'nose'</span><span class="p"><span class="idiff left">,</span></span><span class="s" style="color: #d14;"><span class="idiff right">'python-lzo'</span></span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="31" 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="LC31" class="line" lang="python">            <span class="n" style="color: #333;">author</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"James Taylor, Bob Harris, David King, Brent Pedersen, Kanwei Li, and others"</span><span class="p">,</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="33" 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">

33

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<td class="diff-line-num new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python">            <span class="n" style="color: #333;">author_email</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"james@jamestaylor.org"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="33" 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="LC33" 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;">"Tools for manipulating biological data, particularly multiple sequence alignments"</span><span class="p">,</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="35" 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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<td class="diff-line-num new_line old" data-linenumber="34" 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="LC35" 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<span class="idiff left right">://bitbucket.org/james_taylor/bx-python/wiki/Home</span>"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="36" 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="34" 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="LC34" 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<span class="idiff left right">s://github.com/bxlab/bx-python</span>"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="36" 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="LC35" class="line" lang="python">            <span class="n" style="color: #333;">license</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"MIT"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="37" 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="LC36" 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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="38" 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="LC37" 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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<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 +56,8 @@ def main():</td>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python">    <span class="n" style="color: #333;">numpy</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python">    <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

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<td class="diff-line-num old_line" data-linenumber="59" 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="LC58" class="line" lang="python">        <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="60" 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="59" 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="LC59" class="line" lang="python">        <span class="c" style="color: #998; font-style: italic;"># Suppress numpy tests</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="60" 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="LC60" class="line" lang="python">        <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">test</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

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<pre style="margin: 0;"> <span id="LC61" 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="LC62" class="line" lang="python">        <span class="k" style="font-weight: 600;">pass</span></span>

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<td class="diff-line-num old_line" data-linenumber="62" 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="LC63" class="line" lang="python">    </span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="81" 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="82" 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">@@ -81,10 +82,8 @@ def main():</td>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">distutils.core</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Command</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="84" 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="LC84" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="84" 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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<td class="diff-line-num new_line old" data-linenumber="85" 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="LC84" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># Use build_ext from Cython</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="85" 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="LC85" class="line" lang="python"><span class="n" style="color: #333;">command_classes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>

</pre>

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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="LC85" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># Use build_ext from Cython if found</span></span>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"><span class="n" style="color: #333;">command_classes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>

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<pre style="margin: 0;"> <span id="LC87" 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="LC88" class="line" lang="python">    <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">Cython.Distutils</span></span>

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python">    <span class="n" style="color: #333;">command_classes</span><span class="p">[</span><span class="s" style="color: #d14;">'build_ext'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Cython</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Distutils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">build_ext</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">@@ -220,47 +219,5 @@ def get_extension_modules( numpy_include=None ):</td>

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="python">                                      <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;">"src/bunzip"</span> <span class="p">]</span> <span class="p">)</span> <span class="p">)</span>   </span>

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<pre style="margin: 0;"> <span id="LC220" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">extensions</span>     </span>

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<pre style="margin: 0;"> <span id="LC221" class="line" lang="python">     </span>

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<pre style="margin: 0;">-<span id="LC223" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># ---- Monkey patches -------------------------------------------------------</span></span>

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<pre style="margin: 0;">-<span id="LC224" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC225" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">monkey_patch_doctest</span><span class="p">():</span></span>

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<pre style="margin: 0;">-<span id="LC226" class="line" lang="python">    <span class="c" style="color: #998; font-style: italic;">#</span></span>

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<pre style="margin: 0;">-<span id="LC227" class="line" lang="python">    <span class="c" style="color: #998; font-style: italic;"># Doctest and coverage don't get along, so we need to create</span></span>

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<pre style="margin: 0;">-<span id="LC228" class="line" lang="python">    <span class="c" style="color: #998; font-style: italic;"># a monkeypatch that will replace the part of doctest that</span></span>

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<pre style="margin: 0;">-<span id="LC229" class="line" lang="python">    <span class="c" style="color: #998; font-style: italic;"># interferes with coverage reports.</span></span>

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<pre style="margin: 0;">-<span id="LC230" class="line" lang="python">    <span class="c" style="color: #998; font-style: italic;">#</span></span>

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<pre style="margin: 0;">-<span id="LC231" class="line" lang="python">    <span class="c" style="color: #998; font-style: italic;"># The monkeypatch is based on this zope patch:</span></span>

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<pre style="margin: 0;">-<span id="LC232" class="line" lang="python">    <span class="c" style="color: #998; font-style: italic;"># http://svn.zope.org/Zope3/trunk/src/zope/testing/doctest.py?rev=28679&r1=28703&r2=28705</span></span>

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<pre style="margin: 0;">-<span id="LC233" class="line" lang="python">    <span class="c" style="color: #998; font-style: italic;">#</span></span>

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<pre style="margin: 0;">-<span id="LC234" class="line" lang="python">    <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

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<td class="diff-line-num old old_line" data-linenumber="235" 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="LC235" class="line" lang="python">        <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">doctest</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="236" 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="LC236" class="line" lang="python">        <span class="n" style="color: #333;">_orp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">doctest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_OutputRedirectingPdb</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="237" 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="LC237" class="line" lang="python">        <span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">NoseOutputRedirectingPdb</span><span class="p">(</span><span class="n" style="color: #333;">_orp</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="238" 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="LC238" 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;">out</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC239" 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;">__debugger_used</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC240" class="line" lang="python">                <span class="n" style="color: #333;">_orp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC241" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC242" class="line" lang="python">            <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">set_trace</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC243" 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;">__debugger_used</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="244" 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="LC244" class="line" lang="python">                <span class="n" style="color: #333;">_orp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_trace</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="222" 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="LC245" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="246" 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="LC246" class="line" lang="python">            <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">set_continue</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="247" 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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<td class="diff-line-num new_line old" data-linenumber="222" 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="LC247" class="line" lang="python">                <span class="c" style="color: #998; font-style: italic;"># Calling set_continue unconditionally would break unit test coverage</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="248" 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="LC248" class="line" lang="python">                <span class="c" style="color: #998; font-style: italic;"># reporting, as Bdb.set_continue calls sys.settrace(None).</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="249" 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="LC249" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__debugger_used</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="250" 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="LC250" class="line" lang="python">                    <span class="n" style="color: #333;">_orp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_continue</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC251" class="line" lang="python">        <span class="n" style="color: #333;">doctest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_OutputRedirectingPdb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NoseOutputRedirectingPdb</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="252" 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="LC252" class="line" lang="python">    <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>

</pre>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="253" 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">

253

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<td class="diff-line-num new_line old" data-linenumber="222" 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="LC253" class="line" lang="python">        <span class="k" style="font-weight: 600;">pass</span></span>

</pre>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="254" 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">

254

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<td class="diff-line-num new_line old" data-linenumber="222" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC254" class="line" lang="python"></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="255" 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">

255

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<td class="diff-line-num new_line old" data-linenumber="222" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC255" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">monkey_patch_numpy</span><span class="p">():</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="256" 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">

256

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<td class="diff-line-num new_line old" data-linenumber="222" 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="LC256" class="line" lang="python">    <span class="c" style="color: #998; font-style: italic;"># Numpy pushes its tests into every importers namespace, yeccch.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="257" 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">

257

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<pre style="margin: 0;">-<span id="LC257" class="line" lang="python">    <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="258" 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">

258

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<pre style="margin: 0;">-<span id="LC258" class="line" lang="python">        <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="259" 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">

259

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<td class="diff-line-num new_line old" data-linenumber="222" 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="LC259" class="line" lang="python">        <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">test</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="260" 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">

260

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<td class="diff-line-num new_line old" data-linenumber="222" 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="LC260" class="line" lang="python">    <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="261" 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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<td class="diff-line-num new_line old" data-linenumber="222" 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="LC261" class="line" lang="python">        <span class="k" style="font-weight: 600;">pass</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="262" 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">

262

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<td class="diff-line-num new_line old" data-linenumber="222" 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="LC262" class="line" lang="python">        </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="263" 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">

263

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<td class="diff-line-num new_line" data-linenumber="222" 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">

222

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<pre style="margin: 0;"> <span id="LC222" 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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="264" 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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<td class="diff-line-num new_line old" data-linenumber="223" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC264" class="line" lang="python">    <span class="n" style="color: #333;">monkey_patch_doctest</span><span class="p">()</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="265" 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">

265

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<td class="diff-line-num new_line old" data-linenumber="223" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC265" class="line" lang="python">    <span class="n" style="color: #333;">monkey_patch_numpy</span><span class="p">()</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="266" 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">

266

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<td class="diff-line-num new_line" data-linenumber="223" 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="LC223" class="line" lang="python">    <span class="n" style="color: #333;">main</span><span class="p">()</span></span></pre>

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