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<h3>

Andreas Tille pushed to branch upstream

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/pyranges/-/commit/823b99cc8d170fdb4cea05cad9dae23c6aa03791">823b99cc</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2020-11-02T08:39:35+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.0.85+ds</pre>

</li>

</ul>

<h4>13 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#277f6644ade46b30f40eac6cd851ebc571c513ca">

CHANGELOG.txt

</a>

</li>

<li class="file-stats">

<a href="#c202e0596fbfdd462c81a85a2eb86f34c79acb44">

<span class="new-file">

+

pyranges/helpers.py

</span>

</a>

</li>

<li class="file-stats">

<a href="#a003cdfd143ee210b2dcddd91eb808534179aa58">

pyranges/methods/init.py

</a>

</li>

<li class="file-stats">

<a href="#dddcd774fd1256508f8820859e8f5b92ef3b7a2d">

pyranges/methods/join.py

</a>

</li>

<li class="file-stats">

<a href="#8c48c21853b09baaaa8fccb7e8e26c6b642641e6">

pyranges/multithreaded.py

</a>

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<li class="file-stats">

<a href="#31d8d2e59f702daa2a2e649f9cad595627709282">

pyranges/pyranges.py

</a>

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<li class="file-stats">

<a href="#711da21135a3a4234ce9fcf1ce9784b260d88de9">

pyranges/readers.py

</a>

</li>

<li class="file-stats">

<a href="#566f1cb8da08788ed255cc6747654d68de96e800">

pyranges/statistics.py

</a>

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<li class="file-stats">

<a href="#f749b7da2fda3f99439b6daf60313743b04835f8">

pyranges/version.py

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<li class="file-stats">

<a href="#b3cf00cd9f3e5259a0b377665944e5eec081a0ae">

tests/test_binary.py

</a>

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<li class="file-stats">

<a href="#46bad905c253724a69380d7306cf2bffb52c654b">

<span class="new-file">

+

tests/test_change_chromosome_custom.py

</span>

</a>

</li>

<li class="file-stats">

<a href="#6b2ab2a98e32fd00ffe974c417898c8a992ce396">

tests/test_io.py

</a>

</li>

<li class="file-stats">

<a href="#5e74d0b6a3180cb25aa5c8cad46556233d6b3a21">

tests/test_unary.py

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="277f6644ade46b30f40eac6cd851ebc571c513ca">

<a href="https://salsa.debian.org/med-team/pyranges/-/commit/823b99cc8d170fdb4cea05cad9dae23c6aa03791#277f6644ade46b30f40eac6cd851ebc571c513ca"><strong>CHANGELOG.txt</strong></a>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># 0.0.85 (17.09.20)</span>

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">- fix error when parsing gtf-files with whitespace in value-tags</span>

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>

</pre>

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4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"># 0.0.84 (18.08.20)</span>

</pre>

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

5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">- add option to report overlap in join</span>

</pre>

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6

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

</pre>

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7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"># 0.0.83 (18.08.20)</span>

</pre>

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8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">- hotfix</span>

</pre>

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9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>

</pre>

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10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"># 0.0.82 (18.08.20)</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">- fix error introduced in 0.0.80</span>

</pre>

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

12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" 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="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">

13

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"># 0.0.81 (13.08.20)</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" 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="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">- fix Fisher's implementation</span>

</pre>

</td>

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

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

15

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>

</pre>

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

16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"># 0.0.80 (10.08.20)</span>

</pre>

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</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="plaintext">- fix reassigning chromosomes in apply</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1" 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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18

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

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1

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19

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"># 0.0.79 (08.06.20)</span>

</pre>

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2

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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="plaintext">- fix bug in features.introns where the gene_id column was overwritten (issue #134)</span>

</pre>

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3

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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="plaintext"></span>

</pre>

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<br>

</li>

<li id="c202e0596fbfdd462c81a85a2eb86f34c79acb44">

<a href="https://salsa.debian.org/med-team/pyranges/-/commit/823b99cc8d170fdb4cea05cad9dae23c6aa03791#c202e0596fbfdd462c81a85a2eb86f34c79acb44"><strong>pyranges/helpers.py</strong></a>

<hr>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_chromosomes_from_dict</span><span class="p">(</span><span class="n" style="color: #333;">dfs</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python">    <span class="n" style="color: #333;">keys</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;">dfs</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">())</span></span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">keys</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python">        <span class="n" style="color: #333;">chromosomes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">keys</span><span class="p">]</span></span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python">        <span class="n" style="color: #333;">chromosomes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">keys</span></span>

</pre>

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9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">chromosomes</span></span>

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11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_strands_from_dict</span><span class="p">(</span><span class="n" style="color: #333;">dfs</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python">    <span class="n" style="color: #333;">keys</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;">dfs</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">())</span></span>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">keys</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">):</span></span>

</pre>

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<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="python">        <span class="n" style="color: #333;">strands</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">k</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;">k</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">keys</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

19

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<pre style="margin: 0;">+<span id="LC19" 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="0" 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="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

20

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

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

21

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

<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

22

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">strands</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

23

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

<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

24

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

<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="25" 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">

25

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

<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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">

26

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

<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_key_from_df</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="27" 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">

27

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

<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="28" 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="LC28" class="line" lang="python">    <span class="n" style="color: #333;">chromosome</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">Chromosome</span><span class="p">.</span><span class="n" style="color: #333;">head</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">).</span><span class="n" style="color: #333;">iloc</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="diff-line-num new old_line" data-linenumber="0" 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="29" 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">

29

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

<pre style="margin: 0;">+<span id="LC29" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"Strand"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">df</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC30" class="line" lang="python">        <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">Strand</span><span class="p">.</span><span class="n" style="color: #333;">head</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">).</span><span class="n" style="color: #333;">iloc</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="diff-line-num new old_line" data-linenumber="0" 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="31" 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">

31

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

<pre style="margin: 0;">+<span id="LC31" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">chromosome</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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">

32

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

<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="33" 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">

33

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

<pre style="margin: 0;">+<span id="LC33" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">chromosome</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="0" 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">

34

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

<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="0" 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="35" 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">

35

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

<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">single_value_key</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="38" 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="LC38" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"Strand"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">df</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="39" 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="LC39" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">[[</span><span class="s" style="color: #d14;">"Chromosome"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Strand"</span><span class="p">]].</span><span class="n" style="color: #333;">drop_duplicates</span><span class="p">([</span><span class="s" style="color: #d14;">"Chromosome"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Strand"</span><span class="p">]))</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC40" 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="41" 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="LC41" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">Chromosome</span><span class="p">.</span><span class="n" style="color: #333;">drop_duplicates</span><span class="p">())</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="42" 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="LC42" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"></span></pre>

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<br>

</li>

<li id="a003cdfd143ee210b2dcddd91eb808534179aa58">

<a href="https://salsa.debian.org/med-team/pyranges/-/commit/823b99cc8d170fdb4cea05cad9dae23c6aa03791#a003cdfd143ee210b2dcddd91eb808534179aa58"><strong>pyranges/methods/init.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6" 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="6" 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">@@ -6,6 +6,7 @@ from natsort import natsorted</td>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pyranges.statistics</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">StatisticsMethods</span></span>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pyranges.genomicfeatures</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">GenomicFeaturesMethods</span></span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pyranges</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">PyRanges</span></span>

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<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pyranges.helpers</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">single_value_key</span><span class="p">,</span> <span class="n" style="color: #333;">get_key_from_df</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">set_dtypes</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">,</span> <span class="n" style="color: #333;">int64</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="166" 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="167" 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">@@ -166,40 +167,32 @@ def _init(self,</td>

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<pre style="margin: 0;"> <span id="LC167" 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="LC168" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC169" class="line" lang="python">        <span class="n" style="color: #333;">empty_removed</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">k</span><span class="p">:</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">()</span> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC169" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">empty_removed</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC170" class="line" lang="python">            <span class="n" style="color: #333;">first_key</span><span class="p">,</span> <span class="n" style="color: #333;">first_df</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;">empty_removed</span><span class="p">.</span><span class="n" style="color: #333;">items</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="LC171" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># from pydbg import dbg;</span></span>

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<pre style="margin: 0;">-<span id="LC172" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># dbg(first_df)</span></span>

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<pre style="margin: 0;">-<span id="LC173" class="line" lang="python">            <span class="n" style="color: #333;">stranded</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Strand"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">first_df</span></span>

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<pre style="margin: 0;">-<span id="LC174" class="line" lang="python"></span>

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<td class="diff-line-num old old_line" data-linenumber="175" 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="LC175" class="line" lang="python">            <span class="n" style="color: #333;">all_strands_valid</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>

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<pre style="margin: 0;">-<span id="LC176" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">stranded</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;">all_strands_valid</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">([</span></span>

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<pre style="margin: 0;">-<span id="LC178" class="line" lang="python">                    <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;">df</span><span class="p">.</span><span class="n" style="color: #333;">Strand</span><span class="p">.</span><span class="n" style="color: #333;">drop_duplicates</span><span class="p">())</span> <span class="o" style="font-weight: 600;">-</span></span>

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<pre style="margin: 0;">-<span id="LC179" class="line" lang="python">                        <span class="nb" style="color: #0086b3;">set</span><span class="p">([</span><span class="s" style="color: #d14;">"+"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-"</span><span class="p">]))</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">df</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">empty_removed</span><span class="p">.</span><span class="n" style="color: #333;">values</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="LC181" class="line" lang="python"></span>

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<td class="diff-line-num old old_line" data-linenumber="182" 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="LC182" 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;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">first_df</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="s" style="color: #d14;">"Chromosome Start End"</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span></span>

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<pre style="margin: 0;">-<span id="LC183" class="line" lang="python">            <span class="p">)),</span> <span class="s" style="color: #d14;">"Columns Chromosome, Start and End must be in the dataframe!"</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="170" 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="LC184" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="185" 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">

185

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<td class="diff-line-num new_line old" data-linenumber="170" 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="LC185" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># if not has strand key, but is stranded, need to add strand key</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="186" 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="170" 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="LC186" class="line" lang="python">            <span class="n" style="color: #333;">has_strand_key</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">first_key</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="187" 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="170" 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="LC187" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">has_strand_key</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">stranded</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">all_strands_valid</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="188" 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="170" 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="LC188" class="line" lang="python">                <span class="n" style="color: #333;">new_dfs</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="189" 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="170" 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="LC189" class="line" lang="python">                <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">empty_removed</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="190" 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="170" 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="LC190" class="line" lang="python">                    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">sdf</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">groupby</span><span class="p">(</span><span class="s" style="color: #d14;">"Strand"</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="191" 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="170" 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="LC191" class="line" lang="python">                        <span class="n" style="color: #333;">new_dfs</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sdf</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="192" 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="170" 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="LC192" class="line" lang="python">                <span class="n" style="color: #333;">empty_removed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_dfs</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="193" 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="170" 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="LC193" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="194" 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="170" 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="LC194" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># need to merge strand keys if not strands valid anymore</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="195" 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="170" 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="LC195" class="line" lang="python">            <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">has_strand_key</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">all_strands_valid</span> <span class="ow" style="font-weight: 600;">or</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">stranded</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="196" 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="170" 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="LC196" class="line" lang="python">                <span class="n" style="color: #333;">new_dfs</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="197" 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="LC197" class="line" lang="python">                <span class="n" style="color: #333;">cs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">([</span><span class="n" style="color: #333;">k</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">empty_removed</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">()])</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="198" 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="170" 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="LC198" class="line" lang="python">                <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">natsorted</span><span class="p">(</span><span class="n" style="color: #333;">cs</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="199" 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="170" 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="LC199" class="line" lang="python">                    <span class="n" style="color: #333;">dfs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">empty_removed</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">((</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">))</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="s" style="color: #d14;">"+-"</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="200" 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="LC200" class="line" lang="python">                    <span class="n" style="color: #333;">new_dfs</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">concat</span><span class="p">(</span></span>

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<td class="diff-line-num new_line old" data-linenumber="170" 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="p">[</span><span class="n" style="color: #333;">df</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">df</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">dfs</span> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">df</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">]).</span><span class="n" style="color: #333;">reset_index</span><span class="p">(</span><span class="n" style="color: #333;">drop</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

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

</pre>

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<td class="diff-line-num new old_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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<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>

</pre>

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<td class="diff-line-num new old_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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<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;">_single_value_key</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 new new_line" data-linenumber="172" 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="LC172" class="line" lang="python">        <span class="n" style="color: #333;">_key_same</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 new new_line" data-linenumber="173" 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="LC173" class="line" lang="python">        <span class="n" style="color: #333;">_strand_valid</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 new new_line" data-linenumber="174" 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="LC174" class="line" lang="python">        <span class="n" style="color: #333;">_has_strand</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 new new_line" data-linenumber="175" 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="LC175" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">df</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">empty_removed</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="176" 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="LC176" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="177" 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="LC177" class="line" lang="python">            <span class="n" style="color: #333;">_key</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_key_from_df</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="178" 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="LC178" class="line" lang="python">            <span class="n" style="color: #333;">_single_value_key</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">single_value_key</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">_single_value_key</span></span>

</pre>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="179" 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="LC179" class="line" lang="python">            <span class="n" style="color: #333;">_key_same</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">_key</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">key</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">_key_same</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="180" 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="LC180" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="181" 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="LC181" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">_key</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="182" 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="LC182" class="line" lang="python">                <span class="n" style="color: #333;">_strand_valid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_strand_valid</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="n" style="color: #333;">_key</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">"+"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-"</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="183" 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="LC183" 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="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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<td class="diff-line-num new new_line" data-linenumber="184" 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="LC184" class="line" lang="python">                <span class="n" style="color: #333;">_has_strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="185" 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="LC185" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="186" 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="LC186" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="187" 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="LC187" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">([</span><span class="n" style="color: #333;">_single_value_key</span><span class="p">,</span> <span class="n" style="color: #333;">_key_same</span><span class="p">,</span> <span class="n" style="color: #333;">_strand_valid</span><span class="p">]):</span></span>

</pre>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="188" 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="LC188" class="line" lang="python">            <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">concat</span><span class="p">(</span><span class="n" style="color: #333;">empty_removed</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">()).</span><span class="n" style="color: #333;">reset_index</span><span class="p">(</span><span class="n" style="color: #333;">drop</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="189" 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="LC189" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_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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<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">

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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">_has_strand</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">_strand_valid</span><span class="p">:</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">

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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python">                <span class="n" style="color: #333;">empty_removed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">groupby</span><span class="p">([</span><span class="s" style="color: #d14;">"Chromosome"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Strand"</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">

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<pre style="margin: 0;">+<span id="LC192" 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="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">

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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python">                <span class="n" style="color: #333;">empty_removed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">groupby</span><span class="p">(</span><span class="s" style="color: #d14;">"Chromosome"</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">

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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"></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">

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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python">            <span class="n" style="color: #333;">empty_removed</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">k</span><span class="p">:</span> <span class="n" style="color: #333;">v</span> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">empty_removed</span><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC196" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">__dict__</span><span class="p">[</span><span class="s" style="color: #d14;">"dfs"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">empty_removed</span></span>

</pre>

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<td class="diff-line-num 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">

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

</pre>

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<br>

</li>

<li id="dddcd774fd1256508f8820859e8f5b92ef3b7a2d">

<a href="https://salsa.debian.org/med-team/pyranges/-/commit/823b99cc8d170fdb4cea05cad9dae23c6aa03791#dddcd774fd1256508f8820859e8f5b92ef3b7a2d"><strong>pyranges/methods/join.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="124" 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">@@ -124,8 +124,6 @@ def _write_both(scdf, ocdf, **kwargs):</td>

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<td class="diff-line-num new_line" data-linenumber="124" 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="LC124" 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 old_line" data-linenumber="125" 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="125" 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="LC125" class="line" lang="python">        <span class="n" style="color: #333;">suffix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"suffixes"</span><span class="p">,</span> <span class="s" style="color: #d14;">"_a _b"</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">())[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC127" class="line" lang="python">    <span class="n" style="color: #333;">how</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">"how"</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="128" 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="LC128" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="129" 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="LC127" class="line" lang="python">    <span class="n" style="color: #333;">scdf</span><span class="p">,</span> <span class="n" style="color: #333;">ocdf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_both_dfs</span><span class="p">(</span><span class="n" style="color: #333;">scdf</span><span class="p">,</span> <span class="n" style="color: #333;">ocdf</span><span class="p">,</span> <span class="n" style="color: #333;">how</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">how</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python">    <span class="n" style="color: #333;">nix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">Index</span><span class="p">(</span><span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">scdf</span><span class="p">)))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="131" 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="LC129" class="line" lang="python">    <span class="n" style="color: #333;">scdf</span><span class="p">.</span><span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nix</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="135" 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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -135,4 +133,7 @@ def _write_both(scdf, ocdf, **kwargs):</td>

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="136" 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="134" 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="LC134" class="line" lang="python">    <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scdf</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">ocdf</span><span class="p">,</span> <span class="n" style="color: #333;">rsuffix</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">suffix</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="138" 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="136" 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="LC136" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"report_overlap"</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="138" 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="137" 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="LC137" class="line" lang="python">        <span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">"Overlap"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">df</span><span class="p">[[</span><span class="s" style="color: #d14;">"End"</span><span class="p">,</span> <span class="s" style="color: #d14;">"End"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">suffix</span><span class="p">]].</span><span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">df</span><span class="p">[[</span><span class="s" style="color: #d14;">"Start"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Start"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">suffix</span><span class="p">]].</span><span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">axis</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 new_line" data-linenumber="138" 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="LC138" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">df</span></span></pre>

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<br>

</li>

<li id="8c48c21853b09baaaa8fccb7e8e26c6b642641e6">

<a href="https://salsa.debian.org/med-team/pyranges/-/commit/823b99cc8d170fdb4cea05cad9dae23c6aa03791#8c48c21853b09baaaa8fccb7e8e26c6b642641e6"><strong>pyranges/multithreaded.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="8" 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="8" 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">@@ -8,6 +8,7 @@ from natsort import natsorted</td>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="10" 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="LC10" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">defaultdict</span></span>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"></span>

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_n_args</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">):</span></span>

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<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">

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

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -104,6 +105,7 @@ def process_results(results, keys):</td>

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">to_delete</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python">        <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">results_dict</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"></span>

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<td class="diff-line-num new new_line" data-linenumber="108" 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="LC108" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">results_dict</span></span>

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="286" 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="288" 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">@@ -286,9 +288,6 @@ def pyrange_apply(function, self, other, **kwargs):</td>

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<pre style="margin: 0;"> <span id="LC288" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC289" class="line" lang="python">                <span class="n" style="color: #333;">df</span><span class="p">,</span> <span class="n" style="color: #333;">odf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">make_binary_sparse</span><span class="p">(</span><span class="n" style="color: #333;">kwargs</span><span class="p">,</span> <span class="n" style="color: #333;">df</span><span class="p">,</span> <span class="n" style="color: #333;">odf</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC290" class="line" lang="python"></span>

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<td class="diff-line-num new_line old" data-linenumber="291" 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="LC289" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># dbg(df)</span></span>

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<pre style="margin: 0;">-<span id="LC290" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># dbg(odf)</span></span>

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<pre style="margin: 0;">-<span id="LC291" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC291" class="line" lang="python">                <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">call_f</span><span class="p">(</span><span class="n" style="color: #333;">function</span><span class="p">,</span> <span class="n" style="color: #333;">nparams</span><span class="p">,</span> <span class="n" style="color: #333;">df</span><span class="p">,</span> <span class="n" style="color: #333;">odf</span><span class="p">,</span> <span class="n" style="color: #333;">kwargs</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;">results</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="294" 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="293" 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="LC293" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="389" 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="388" 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">@@ -389,6 +388,7 @@ def pyrange_apply_single(function, self, **kwargs):</td>

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<td class="diff-line-num old_line" data-linenumber="389" 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">

389

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<td class="diff-line-num new_line" data-linenumber="388" 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">

388

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<pre style="margin: 0;"> <span id="LC388" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="390" 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">

390

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<pre style="margin: 0;"> <span id="LC389" class="line" lang="python">    <span class="n" style="color: #333;">results</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">process_results</span><span class="p">(</span><span class="n" style="color: #333;">results</span><span class="p">,</span> <span class="n" style="color: #333;">keys</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="391" 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">

391

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<td class="diff-line-num new_line" data-linenumber="390" 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">

390

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<pre style="margin: 0;"> <span id="LC390" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="392" 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="391" 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="LC391" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="392" 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">

392

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<td class="diff-line-num new_line" data-linenumber="392" 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">

392

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<pre style="margin: 0;"> <span id="LC392" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">results</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="393" 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">

393

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<td class="diff-line-num new_line" data-linenumber="393" 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">

393

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<pre style="margin: 0;"> <span id="LC393" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="394" 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">

394

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<td class="diff-line-num new_line" data-linenumber="394" 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">

394

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<pre style="margin: 0;"> <span id="LC394" class="line" lang="python"></span>

</pre>

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<br>

</li>

<li id="31d8d2e59f702daa2a2e649f9cad595627709282">

<a href="https://salsa.debian.org/med-team/pyranges/-/commit/823b99cc8d170fdb4cea05cad9dae23c6aa03791#31d8d2e59f702daa2a2e649f9cad595627709282"><strong>pyranges/pyranges.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_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="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">@@ -176,6 +176,7 @@ class PyRanges():</td>

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176

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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">

176

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<pre style="margin: 0;"> <span id="LC176" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="177" 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="LC177" class="line" lang="python">        <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;">df</span><span class="p">,</span> <span class="n" style="color: #333;">chromosomes</span><span class="p">,</span> <span class="n" style="color: #333;">starts</span><span class="p">,</span> <span class="n" style="color: #333;">ends</span><span class="p">,</span> <span class="n" style="color: #333;">strands</span><span class="p">,</span> <span class="n" style="color: #333;">int64</span><span class="p">,</span> <span class="n" style="color: #333;">copy_df</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="178" 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">

178

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178

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<pre style="margin: 0;"> <span id="LC178" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="179" 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="179" 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">

179

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="179" 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">

179

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<td class="diff-line-num new_line" data-linenumber="180" 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="LC180" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__array_ufunc__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="180" 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="181" 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">

181

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<pre style="margin: 0;"> <span id="LC181" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="181" 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">

181

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<td class="diff-line-num new_line" data-linenumber="182" 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">

182

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<pre style="margin: 0;"> <span id="LC182" class="line" lang="python">        <span class="s" style="color: #d14;">"""Apply unary numpy-function.</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1987" 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="1988" 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">@@ -1987,7 +1988,7 @@ class PyRanges():</td>

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<td class="diff-line-num old_line" data-linenumber="1987" 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">

1987

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<td class="diff-line-num new_line" data-linenumber="1988" 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">

1988

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

<pre style="margin: 0;"> <span id="LC1988" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1988" 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">

1988

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<td class="diff-line-num new_line" data-linenumber="1989" 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">

1989

</td>

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

<pre style="margin: 0;"> <span id="LC1989" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">natsorted</span><span class="p">([(</span><span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">df</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">df</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">dfs</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">()])</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1989" 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">

1989

</td>

<td class="diff-line-num new_line" data-linenumber="1990" 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">

1990

</td>

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

<pre style="margin: 0;"> <span id="LC1990" class="line" lang="python"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="1990" 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">

1990

</td>

<td class="diff-line-num new_line old" data-linenumber="1991" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1990" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">other</span><span class="p">,</span> <span class="n" style="color: #333;">strandedness</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">how</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">slack</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">suffix</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"_b"</span><span class="p">,</span> <span class="n" style="color: #333;">nb_cpu</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">):</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1991" 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="1991" 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">

1991

</td>

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

<pre style="margin: 0;">+<span id="LC1991" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">other</span><span class="p">,</span> <span class="n" style="color: #333;">strandedness</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">how</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">report_overlap</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff">False</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">slack</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">suffix</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"_b"</span><span class="p">,</span> <span class="n" style="color: #333;">nb_cpu</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">):</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1991" 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">

1991

</td>

<td class="diff-line-num new_line" data-linenumber="1992" 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">

1992

</td>

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

<pre style="margin: 0;"> <span id="LC1992" class="line" lang="python"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1992" 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">

1992

</td>

<td class="diff-line-num new_line" data-linenumber="1993" 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">

1993

</td>

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

<pre style="margin: 0;"> <span id="LC1993" class="line" lang="python">        <span class="s" style="color: #d14;">"""Join PyRanges on genomic location.</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1993" 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">

1993

</td>

<td class="diff-line-num new_line" data-linenumber="1994" 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">

1994

</td>

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

<pre style="margin: 0;"> <span id="LC1994" class="line" lang="python"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2008" 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="2009" 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">@@ -2008,6 +2009,10 @@ class PyRanges():</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="2008" 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">

2008

</td>

<td class="diff-line-num new_line" data-linenumber="2009" 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">

2009

</td>

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

<pre style="margin: 0;"> <span id="LC2009" class="line" lang="python"><span class="s" style="color: #d14;">            How to handle intervals without overlap. None means only keep overlapping intervals.</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="2009" 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">

2009

</td>

<td class="diff-line-num new_line" data-linenumber="2010" 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">

2010

</td>

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

<pre style="margin: 0;"> <span id="LC2010" class="line" lang="python"><span class="s" style="color: #d14;">            "left" keeps all intervals in self, "right" keeps all intervals in other.</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="2010" 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">

2010

</td>

<td class="diff-line-num new_line" data-linenumber="2011" 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">

2011

</td>

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

<pre style="margin: 0;"> <span id="LC2011" class="line" lang="python"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2011" 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="2012" 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">

2012

</td>

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

<pre style="margin: 0;">+<span id="LC2012" class="line" lang="python"><span class="s" style="color: #d14;">        report_overlap : bool, default False</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2011" 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="2013" 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">

2013

</td>

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

<pre style="margin: 0;">+<span id="LC2013" class="line" lang="python"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2011" 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="2014" 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">

2014

</td>

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

<pre style="margin: 0;">+<span id="LC2014" class="line" lang="python"><span class="s" style="color: #d14;">            Report amount of overlap in base pairs. </span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2011" 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="2015" 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">

2015

</td>

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

<pre style="margin: 0;">+<span id="LC2015" class="line" lang="python"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="2011" 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">

2011

</td>

<td class="diff-line-num new_line" data-linenumber="2016" 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">

2016

</td>

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

<pre style="margin: 0;"> <span id="LC2016" class="line" lang="python"><span class="s" style="color: #d14;">        slack : int, default 0</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="2012" 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">

2012

</td>

<td class="diff-line-num new_line" data-linenumber="2017" 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">

2017

</td>

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

<pre style="margin: 0;"> <span id="LC2017" class="line" lang="python"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="2013" 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">

2013

</td>

<td class="diff-line-num new_line" data-linenumber="2018" 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">

2018

</td>

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

<pre style="margin: 0;"> <span id="LC2018" class="line" lang="python"><span class="s" style="color: #d14;">            Lengthen intervals in self before joining.</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2108" 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="2113" 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">@@ -2108,7 +2113,7 @@ class PyRanges():</td>

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<td class="diff-line-num new_line" data-linenumber="2113" 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">

2113

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<pre style="margin: 0;"> <span id="LC2113" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2109" 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">

2109

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<td class="diff-line-num new_line" data-linenumber="2114" 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="LC2114" class="line" lang="python">        <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pyranges.methods.join</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">_write_both</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2110" 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">

2110

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<td class="diff-line-num new_line" data-linenumber="2115" 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">

2115

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

<pre style="margin: 0;"> <span id="LC2115" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2111" 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">

2111

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<td class="diff-line-num new_line old" data-linenumber="2116" 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="LC2111" class="line" lang="python">        <span class="n" style="color: #333;">kwargs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"strandedness"</span><span class="p">:</span> <span class="n" style="color: #333;">strandedness</span><span class="p">,</span> <span class="s" style="color: #d14;">"how"</span><span class="p">:</span> <span class="n" style="color: #333;">how</span><span class="p">,</span> <span class="s" style="color: #d14;">"suffix"</span><span class="p">:</span> <span class="n" style="color: #333;">suffix</span><span class="p">,</span> <span class="s" style="color: #d14;">"nb_cpu"</span><span class="p">:</span> <span class="n" style="color: #333;">nb_cpu</span><span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2112" 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="2116" 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">

2116

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<pre style="margin: 0;">+<span id="LC2116" class="line" lang="python">        <span class="n" style="color: #333;">kwargs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"strandedness"</span><span class="p">:</span> <span class="n" style="color: #333;">strandedness</span><span class="p">,</span> <span class="s" style="color: #d14;">"how"</span><span class="p">:</span> <span class="n" style="color: #333;">how</span><span class="p">,</span> <span class="s" style="color: #d14;">"<span class="idiff left">report_overlap"</span></span><span class="p"><span class="idiff">:</span></span><span class="n" style="color: #333;"><span class="idiff">report_overlap</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"</span>suffix"</span><span class="p">:</span> <span class="n" style="color: #333;">suffix</span><span class="p">,</span> <span class="s" style="color: #d14;">"nb_cpu"</span><span class="p">:</span> <span class="n" style="color: #333;">nb_cpu</span><span class="p">}</span></span>

</pre>

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2112

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<td class="diff-line-num new_line" data-linenumber="2117" 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="LC2117" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># slack = kwargs.get("slack")</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2113" 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">

2113

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<td class="diff-line-num new_line" data-linenumber="2118" 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="LC2118" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">slack</span><span class="p">:</span></span>

</pre>

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2114

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<td class="diff-line-num new_line" data-linenumber="2119" 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="LC2119" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">Start__slack</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">Start</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2137" 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="2142" 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">@@ -2137,7 +2142,6 @@ class PyRanges():</td>

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2137

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<td class="diff-line-num new_line" data-linenumber="2142" 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">

2142

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<pre style="margin: 0;"> <span id="LC2142" class="line" lang="python">            <span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">"example_header_self"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">head</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">).</span><span class="n" style="color: #333;">df</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="2143" 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">

2143

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<pre style="margin: 0;"> <span id="LC2143" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2139" 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="2144" 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="LC2144" class="line" lang="python">        <span class="n" style="color: #333;">dfs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pyrange_apply</span><span class="p">(</span><span class="n" style="color: #333;">_write_both</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">other</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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2140" 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">

2140

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<td class="diff-line-num new_line old" data-linenumber="2145" 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="LC2140" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2141" 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="2145" 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="LC2145" class="line" lang="python">        <span class="n" style="color: #333;">gr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PyRanges</span><span class="p">(</span><span class="n" style="color: #333;">dfs</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2142" 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">

2142

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<td class="diff-line-num new_line" data-linenumber="2146" 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">

2146

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<pre style="margin: 0;"> <span id="LC2146" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2143" 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">

2143

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<td class="diff-line-num new_line" data-linenumber="2147" 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">

2147

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<pre style="margin: 0;"> <span id="LC2147" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">slack</span><span class="p">:</span></span>

</pre>

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<br>

</li>

<li id="711da21135a3a4234ce9fcf1ce9784b260d88de9">

<a href="https://salsa.debian.org/med-team/pyranges/-/commit/823b99cc8d170fdb4cea05cad9dae23c6aa03791#711da21135a3a4234ce9fcf1ce9784b260d88de9"><strong>pyranges/readers.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="313" 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="313" 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">@@ -313,7 +313,7 @@ def read_gtf_full(f, as_df=False, nrows=None, skiprows=0, duplicate_attr=False):</td>

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<pre style="margin: 0;"> <span id="LC313" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC314" class="line" lang="python">    <span class="n" style="color: #333;">names</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Chromosome Source Feature Start End Score Strand Frame Attribute"</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC315" class="line" lang="python">    <span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC316" class="line" lang="python"><span class="idiff left">    </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># names = "Chromosome Start End Score Strand Source Feature Frame Attribute".split()</span></span></span>

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<pre style="margin: 0;">+<span id="LC316" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC317" class="line" lang="python">    <span class="n" style="color: #333;">df_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">read_csv</span><span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC318" class="line" lang="python">        <span class="n" style="color: #333;">f</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC319" class="line" lang="python">        <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -352,8 +352,14 @@ def to_rows(anno):</td>

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<pre style="margin: 0;"> <span id="LC352" class="line" lang="python">        <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">(</span><span class="s" style="color: #d14;">"Invalid attribute string: {l}. If the file is in GFF3 format, use pr.read_gff3 instead."</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">l</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC353" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC354" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">l</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">anno</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC355" class="line" lang="python">        <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'"'</span><span class="p">,</span> <span class="s" style="color: #d14;">''</span><span class="p">).</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">";"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">).</span><span class="n" style="color: #333;">split</span><span class="p">()</span></span>

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<pre style="margin: 0;">-<span id="LC356" class="line" lang="python">        <span class="n" style="color: #333;">rowdicts</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">({</span><span class="n" style="color: #333;">k</span><span class="p">:</span> <span class="n" style="color: #333;">v</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="p">([</span><span class="nb" style="color: #0086b3;">iter</span><span class="p">(</span><span class="n" style="color: #333;">l</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>

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<pre style="margin: 0;">+<span id="LC355" class="line" lang="python">        <span class="n" style="color: #333;">rowdicts</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">({</span><span class="n" style="color: #333;">k</span><span class="p">:</span> <span class="n" style="color: #333;">v</span></span>

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<pre style="margin: 0;">+<span id="LC356" class="line" lang="python">                         <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="n" style="color: #333;">kv</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'"'</span><span class="p">,</span> <span class="s" style="color: #d14;">''</span><span class="p">).</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="bp" style="color: #999;">None</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="LC357" class="line" lang="python">                                      <span class="c1" style="color: #998; font-style: italic;"># l[:-1] removes final ";" cheaply</span></span>

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<pre style="margin: 0;">+<span id="LC358" class="line" lang="python">                                      <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">kv</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">l</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="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"; "</span><span class="p">)]})</span></span>

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<pre style="margin: 0;">+<span id="LC359" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC360" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># for l in anno:</span></span>

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<pre style="margin: 0;">+<span id="LC361" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#     l = l.replace('"', '').replace(";", "").split()</span></span>

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<pre style="margin: 0;">+<span id="LC362" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#     rowdicts.append({k: v for k, v in zip(*([iter(l)] * 2))})</span></span>

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<pre style="margin: 0;"> <span id="LC363" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC364" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">.</span><span class="n" style="color: #333;">from_dict</span><span class="p">(</span><span class="n" style="color: #333;">rowdicts</span><span class="p">).</span><span class="n" style="color: #333;">set_index</span><span class="p">(</span><span class="n" style="color: #333;">anno</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC365" class="line" lang="python"></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -362,8 +368,10 @@ def to_rows_keep_duplicates(anno):</td>

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<pre style="margin: 0;"> <span id="LC368" class="line" lang="python">    <span class="n" style="color: #333;">rowdicts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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<pre style="margin: 0;"> <span id="LC369" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">l</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">anno</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC370" class="line" lang="python">        <span class="n" style="color: #333;">rowdict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>

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<pre style="margin: 0;">-<span id="LC365" class="line" lang="python">        <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'"'</span><span class="p">,</span> <span class="s" style="color: #d14;">''</span><span class="p">).</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">";"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">).</span><span class="n" style="color: #333;">split</span><span class="p">()</span></span>

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<pre style="margin: 0;">-<span id="LC366" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="p">([</span><span class="nb" style="color: #0086b3;">iter</span><span class="p">(</span><span class="n" style="color: #333;">l</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>

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<pre style="margin: 0;">+<span id="LC371" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC372" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># l[:-1] removes final ";" cheaply</span></span>

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<pre style="margin: 0;">+<span id="LC373" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="n" style="color: #333;">kv</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'"'</span><span class="p">,</span> <span class="s" style="color: #d14;">''</span><span class="p">).</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="bp" style="color: #999;">None</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;">kv</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">l</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="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"; "</span><span class="p">)):</span></span>

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<pre style="margin: 0;">+<span id="LC374" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC375" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">k</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rowdict</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC376" class="line" lang="python">                <span class="n" style="color: #333;">rowdict</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">v</span></span>

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<pre style="margin: 0;"> <span id="LC377" class="line" lang="python">            <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">k</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rowdict</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">rowdict</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">):</span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="450" 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">@@ -442,8 +450,6 @@ def read_gtf_restricted(f,</td>

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<pre style="margin: 0;"> <span id="LC450" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">to_rows_gff3</span><span class="p">(</span><span class="n" style="color: #333;">anno</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC451" class="line" lang="python">    <span class="n" style="color: #333;">rowdicts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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<pre style="margin: 0;"> <span id="LC452" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC445" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># anno = anno.str.replace(";$", "")</span></span>

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<pre style="margin: 0;">-<span id="LC446" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC453" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">l</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">anno</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC454" class="line" lang="python">        <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">it</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"="</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">it</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">";"</span><span class="p">))</span></span>

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<td class="diff-line-num new_line" data-linenumber="455" 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="LC455" class="line" lang="python">        <span class="n" style="color: #333;">rowdicts</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">({</span><span class="n" style="color: #333;">k</span><span class="p">:</span> <span class="n" style="color: #333;">v</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">l</span><span class="p">})</span></span>

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<br>

</li>

<li id="566f1cb8da08788ed255cc6747654d68de96e800">

<a href="https://salsa.debian.org/med-team/pyranges/-/commit/823b99cc8d170fdb4cea05cad9dae23c6aa03791#566f1cb8da08788ed255cc6747654d68de96e800"><strong>pyranges/statistics.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold new_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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -81,7 +81,7 @@ def fdr(p_vals):</td>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">fdr</span></span>

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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>

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<pre style="margin: 0;">-<span id="LC84" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fisher_exact</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">n1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">d1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">n2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">d2</span></span><span class="p">,</span> <span class="n" style="color: #333;">pseudocount</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="LC84" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fisher_exact</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">tp</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fp</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fn</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">tn</span></span><span class="p">,</span> <span class="n" style="color: #333;">pseudocount</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="LC85" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python">    <span class="s" style="color: #d14;">"""Fisher's exact for contingency tables.</span></span>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -91,21 +91,21 @@ def fisher_exact(n1, d1, n2, d2, pseudocount=0):</td>

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"><span class="s" style="color: #d14;">    Parameters</span></span>

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"><span class="s" style="color: #d14;">    ----------</span></span>

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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python"><span class="s" style="color: #d14;">    <span class="idiff left right">n1</span> : array-like of int</span></span>

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"><span class="s" style="color: #d14;">    <span class="idiff left right">tp</span> : array-like of int</span></span>

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python"><span class="s" style="color: #d14;">        Top left square of contingency table.</span></span>

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"><span class="s" style="color: #d14;">        Top left square of contingency table<span class="idiff left right"> (true positives)</span>.</span></span>

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python"><span class="s" style="color: #d14;">    <span class="idiff left right">d1</span> : array-like of int</span></span>

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"><span class="s" style="color: #d14;">    <span class="idiff left right">fp</span> : array-like of int</span></span>

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC100" class="line" lang="python"><span class="s" style="color: #d14;">        <span class="idiff left right">Bottom left square of contingency table</span>.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"><span class="s" style="color: #d14;">        <span class="idiff left right">Top right square of contingency table (false positives)</span>.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"><span class="s" style="color: #d14;">    <span class="idiff left right">n2</span> : array-like of int</span></span>

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"><span class="s" style="color: #d14;">    <span class="idiff left right">fn</span> : array-like of int</span></span>

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="104" 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="LC104" class="line" lang="python"><span class="s" style="color: #d14;">        <span class="idiff left right">Top right square of contingency table</span>.</span></span>

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"><span class="s" style="color: #d14;">        <span class="idiff left right">Bottom left square of contingency table (false negatives)</span>.</span></span>

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC106" class="line" lang="python"><span class="s" style="color: #d14;">    <span class="idiff left right">d2</span> : array-like of int</span></span>

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"><span class="s" style="color: #d14;">    <span class="idiff left right">tn</span> : array-like of int</span></span>

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"></span>

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<td class="diff-line-num old old_line" data-linenumber="108" 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="LC108" class="line" lang="python"><span class="s" style="color: #d14;">        Bottom right square of contingency table.</span></span>

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"><span class="s" style="color: #d14;">        Bottom right square of contingency table<span class="idiff left right"> (true negatives)</span>.</span></span>

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"><span class="s" style="color: #d14;">    pseudocount : float, default 0</span></span>

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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"></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">@@ -116,7 +116,7 @@ def fisher_exact(n1, d1, n2, d2, pseudocount=0):</td>

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python"><span class="s" style="color: #d14;">    The odds-ratio is computed thusly:</span></span>

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python"><span class="s" style="color: #d14;">    ``((<span class="idiff left right">n1 + pseudocount) / (d2 + pseudocount)) / ((n2 + pseudocount) / (d1</span> + pseudocount))``</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"><span class="s" style="color: #d14;">    ``((<span class="idiff left right">tp + pseudocount) / (fp + pseudocount)) / ((fn + pseudocount) / (tn</span> + pseudocount))``</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="python"><span class="s" style="color: #d14;">    Returns</span></span>

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="python"><span class="s" style="color: #d14;">    -------</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">@@ -132,19 +132,17 @@ def fisher_exact(n1, d1, n2, d2, pseudocount=0):</td>

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python"><span class="s" style="color: #d14;">    Examples</span></span>

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"><span class="s" style="color: #d14;">    --------</span></span>

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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC135" class="line" lang="python"><span class="s" style="color: #d14;">    >>> d = {"TP": [1<span class="idiff left right">, 0, 8], "FP": [11, 12, 1], "TN": [9, 10, 2], "FN": [3, 2, 5</span>]}</span></span>

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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"><span class="s" style="color: #d14;">    >>> d = {"TP": [1<span class="idiff left right">2, 0], "FP": [5, 12], "TN": [29, 10], "FN": [2, 2</span>]}</span></span>

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python"><span class="s" style="color: #d14;">    >>> df = pd.DataFrame(d)</span></span>

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

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="python"><span class="s" style="color: #d14;">       TP  FP  TN  FN</span></span>

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<pre style="margin: 0;">-<span id="LC139" class="line" lang="python"><span class="s" style="color: #d14;">    0  <span class="idiff left right"> 1  11   9   3</span></span></span>

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"><span class="s" style="color: #d14;">    0  <span class="idiff left right">12   5  29   2</span></span></span>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python"><span class="s" style="color: #d14;">    1   0  12  10   2</span></span>

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<pre style="margin: 0;">-<span id="LC141" class="line" lang="python"><span class="s" style="color: #d14;">    2   8   1   2   5</span></span>

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="python"><span class="s" style="color: #d14;">    >>> pr.stats.fisher_exact(df.TP, df.FP, df.TN, df.FN)</span></span>

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<pre style="margin: 0;"> <span id="LC143" class="line" lang="python"><span class="s" style="color: #d14;">             OR         P     PLeft    PRight</span></span>

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<pre style="margin: 0;">-<span id="LC145" class="line" lang="python"><span class="s" style="color: #d14;">    0  0.<span class="idiff left right">407407  0.002759  0.001380  0.999966</span></span></span>

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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"><span class="s" style="color: #d14;">    0  0.<span class="idiff left right">165517  0.080269  0.044555  0.994525</span></span></span>

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="python"><span class="s" style="color: #d14;">    1  0.000000  0.000067  0.000034  1.000000</span></span>

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<pre style="margin: 0;">-<span id="LC147" class="line" lang="python"><span class="s" style="color: #d14;">    2  0.800000  0.034965  0.999126  0.024476</span></span>

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python"></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -155,14 +153,14 @@ def fisher_exact(n1, d1, n2, d2, pseudocount=0):</td>

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"fisher needs to be installed to use fisher exact. pip install fisher or conda install -c bioconda fisher."</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python">        <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</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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<pre style="margin: 0;"> <span id="LC155" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC158" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left">n1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">array</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">n1</span></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;">np</span><span class="p">.</span><span class="n" style="color: #333;">uint</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC159" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left">n2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">array</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">n2</span></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;">np</span><span class="p">.</span><span class="n" style="color: #333;">uint</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC160" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left">d1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">array</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">d1</span></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;">np</span><span class="p">.</span><span class="n" style="color: #333;">uint</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC161" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left">d2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">array</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">d2</span></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;">np</span><span class="p">.</span><span class="n" style="color: #333;">uint</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left">tp</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">array</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">tp</span></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;">np</span><span class="p">.</span><span class="n" style="color: #333;">uint</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left">fp</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">array</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">fp</span></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;">np</span><span class="p">.</span><span class="n" style="color: #333;">uint</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left">fn</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">array</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">fn</span></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;">np</span><span class="p">.</span><span class="n" style="color: #333;">uint</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left">tn</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">array</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">tn</span></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;">np</span><span class="p">.</span><span class="n" style="color: #333;">uint</span><span class="p">)</span></span>

</pre>

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160

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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC163" class="line" lang="python">    <span class="n" style="color: #333;">left</span><span class="p">,</span> <span class="n" style="color: #333;">right</span><span class="p">,</span> <span class="n" style="color: #333;">twosided</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pvalue_npy</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">n1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">d1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">n2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">d2</span></span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python">    <span class="n" style="color: #333;">left</span><span class="p">,</span> <span class="n" style="color: #333;">right</span><span class="p">,</span> <span class="n" style="color: #333;">twosided</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pvalue_npy</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">tp</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fp</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fn</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">tn</span></span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC165" class="line" lang="python">    <span class="n" style="color: #333;">OR</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;"><span class="idiff left">n1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pseudocount</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">d2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pseudocount</span></span><span class="p"><span class="idiff">))</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="p"><span class="idiff">((</span></span><span class="n" style="color: #333;"><span class="idiff">n2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pseudocount</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">d1</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pseudocount</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python">    <span class="n" style="color: #333;">OR</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;"><span class="idiff left">tp</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pseudocount</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">fp</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pseudocount</span></span><span class="p"><span class="idiff">))</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="p"><span class="idiff">((</span></span><span class="n" style="color: #333;"><span class="idiff">fn</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pseudocount</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">tn</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pseudocount</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC164" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC165" class="line" lang="python">    <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">({</span><span class="s" style="color: #d14;">"OR"</span><span class="p">:</span> <span class="n" style="color: #333;">OR</span><span class="p">,</span> <span class="s" style="color: #d14;">"P"</span><span class="p">:</span> <span class="n" style="color: #333;">twosided</span><span class="p">,</span> <span class="s" style="color: #d14;">"PLeft"</span><span class="p">:</span> <span class="n" style="color: #333;">left</span><span class="p">,</span> <span class="s" style="color: #d14;">"PRight"</span><span class="p">:</span> <span class="n" style="color: #333;">right</span><span class="p">})</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC166" class="line" lang="python"></span>

</pre>

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<li id="f749b7da2fda3f99439b6daf60313743b04835f8">

<a href="https://salsa.debian.org/med-team/pyranges/-/commit/823b99cc8d170fdb4cea05cad9dae23c6aa03791#f749b7da2fda3f99439b6daf60313743b04835f8"><strong>pyranges/version.py</strong></a>

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<pre style="margin: 0;">-<span id="LC1" 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;">"0.0.<span class="idiff left right">79</span>"</span></span></pre>

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<pre style="margin: 0;">+<span id="LC1" 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;">"0.0.<span class="idiff left right">85</span>"</span></span></pre>

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<li id="b3cf00cd9f3e5259a0b377665944e5eec081a0ae">

<a href="https://salsa.debian.org/med-team/pyranges/-/commit/823b99cc8d170fdb4cea05cad9dae23c6aa03791#b3cf00cd9f3e5259a0b377665944e5eec081a0ae"><strong>tests/test_binary.py</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">@@ -162,6 +162,7 @@ def test_set_union(gr, gr2, strandedness):</td>

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python">    <span class="n" style="color: #333;">suppress_health_check</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">HealthCheck</span><span class="p">.</span><span class="nb" style="color: #0086b3;">all</span><span class="p">())</span></span>

</pre>

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163

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163

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<pre style="margin: 0;"> <span id="LC163" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">given</span><span class="p">(</span><span class="n" style="color: #333;">gr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">dfs_min</span><span class="p">(),</span> <span class="n" style="color: #333;">gr2</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">dfs_min</span><span class="p">())</span>  <span class="c1" style="color: #998; font-style: italic;"># pylint: disable=no-value-for-parameter</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="164" 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">

164

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<td class="diff-line-num new_line" data-linenumber="164" 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">

164

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<pre style="margin: 0;"> <span id="LC164" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># @reproduce_failure('4.32.2', b'AXicY2RAA4wQzIgiCAAAgAAF')</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="165" 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="165" 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">

165

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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># @reproduce_failure('5.5.4', b'AXicY2RABYyMEAqKGRgAAHMABg==')</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="165" 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">

165

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<td class="diff-line-num new_line" data-linenumber="166" 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">

166

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<pre style="margin: 0;"> <span id="LC166" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_overlap</span><span class="p">(</span><span class="n" style="color: #333;">gr</span><span class="p">,</span> <span class="n" style="color: #333;">gr2</span><span class="p">,</span> <span class="n" style="color: #333;">strandedness</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="166" 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">

166

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<td class="diff-line-num new_line" data-linenumber="167" 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">

167

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="167" 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">

167

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<td class="diff-line-num new_line" data-linenumber="168" 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="LC168" class="line" lang="python">    <span class="n" style="color: #333;">overlap_command</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"bedtools intersect -u {strand} -a {f1} -b {f2}"</span></span>

</pre>

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<br>

</li>

<li id="46bad905c253724a69380d7306cf2bffb52c654b">

<a href="https://salsa.debian.org/med-team/pyranges/-/commit/823b99cc8d170fdb4cea05cad9dae23c6aa03791#46bad905c253724a69380d7306cf2bffb52c654b"><strong>tests/test_change_chromosome_custom.py</strong></a>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pandas</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pd</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pyranges</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pr</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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

<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_change_chromosomes</span><span class="p">():</span></span>

</pre>

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

5

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

<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python">    <span class="n" style="color: #333;">df1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">({</span><span class="s" style="color: #d14;">"Chromosome"</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">"chr1"</span><span class="p">,</span> <span class="s" style="color: #d14;">"chr2"</span><span class="p">],</span> <span class="s" style="color: #d14;">"Start"</span><span class="p">:</span> <span class="p">[</span><span class="mi" style="color: #099;">100</span><span class="p">,</span> <span class="mi" style="color: #099;">200</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python">                    <span class="s" style="color: #d14;">"End"</span><span class="p">:</span> <span class="p">[</span><span class="mi" style="color: #099;">150</span><span class="p">,</span> <span class="mi" style="color: #099;">201</span><span class="p">]})</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

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

<pre style="margin: 0;">+<span id="LC8" class="line" lang="python">    <span class="n" style="color: #333;">py1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pr</span><span class="p">.</span><span class="n" style="color: #333;">PyRanges</span><span class="p">(</span><span class="n" style="color: #333;">df1</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python">    <span class="n" style="color: #333;">df2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">({</span><span class="s" style="color: #d14;">"Chromosome"</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">"1"</span><span class="p">,</span> <span class="s" style="color: #d14;">"2"</span><span class="p">],</span> <span class="s" style="color: #d14;">"Start"</span><span class="p">:</span> <span class="p">[</span><span class="mi" style="color: #099;">1000</span><span class="p">,</span> <span class="mi" style="color: #099;">2000</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="10" 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">

10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python">                    <span class="s" style="color: #d14;">"End"</span><span class="p">:</span> <span class="p">[</span><span class="mi" style="color: #099;">1500</span><span class="p">,</span> <span class="mi" style="color: #099;">20010</span><span class="p">]})</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python">    <span class="n" style="color: #333;">py2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pr</span><span class="p">.</span><span class="n" style="color: #333;">PyRanges</span><span class="p">(</span><span class="n" style="color: #333;">df2</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="12" 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">

12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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">

13

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">modify_chrom_series</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python">        <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">Chromosome</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">Chromosome</span><span class="p">.</span><span class="nb" style="color: #0086b3;">apply</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">val</span><span class="p">:</span> <span class="n" style="color: #333;">val</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"chr"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">))</span></span>

</pre>

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

15

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">df</span></span>

</pre>

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

16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fix_chrom</span><span class="p">(</span><span class="n" style="color: #333;">regions</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">regions</span><span class="p">.</span><span class="nb" style="color: #0086b3;">apply</span><span class="p">(</span><span class="n" style="color: #333;">modify_chrom_series</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

19

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

<pre style="margin: 0;">+<span id="LC19" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">py1</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

20

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

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

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

21

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python">    <span class="n" style="color: #333;">py1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fix_chrom</span><span class="p">(</span><span class="n" style="color: #333;">py1</span><span class="p">)</span></span>

</pre>

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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">

22

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

23

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

<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

24

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">py1</span><span class="p">.</span><span class="n" style="color: #333;">chromosomes</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">"1"</span><span class="p">,</span> <span class="s" style="color: #d14;">"2"</span><span class="p">]</span></span></pre>

</td>

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<br>

</li>

<li id="6b2ab2a98e32fd00ffe974c417898c8a992ce396">

<a href="https://salsa.debian.org/med-team/pyranges/-/commit/823b99cc8d170fdb4cea05cad9dae23c6aa03791#6b2ab2a98e32fd00ffe974c417898c8a992ce396"><strong>tests/test_io.py</strong></a>

<hr>

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1

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<td class="diff-line-num new_line" data-linenumber="1" 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">

1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pyranges</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pr</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2" 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">

2

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<td class="diff-line-num new_line" data-linenumber="2" 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">

2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"></span>

</pre>

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3

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<td class="diff-line-num new_line old" data-linenumber="3" 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="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># def test_read_bam():</span></span>

</pre>

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4

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<td class="diff-line-num new_line old" data-linenumber="3" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

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

</pre>

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5

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<td class="diff-line-num new_line old" data-linenumber="3" 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="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#     pr.read_bam("tests/test_data/test_sorted.bam")</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="6" 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">

6

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<td class="diff-line-num new_line old" data-linenumber="3" 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">

</td>

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="7" 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">

7

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<td class="diff-line-num new_line" data-linenumber="3" 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">

3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="8" 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">

8

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<td class="diff-line-num new_line" data-linenumber="4" 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">

4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_read_gtf</span><span class="p">():</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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<td class="diff-line-num new_line" data-linenumber="5" 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">

5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="10" 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">

10

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<td class="diff-line-num new_line" data-linenumber="6" 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">

6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python">    <span class="n" style="color: #333;">gr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pr</span><span class="p">.</span><span class="n" style="color: #333;">read_gtf</span><span class="p">(</span><span class="s" style="color: #d14;">"tests/test_data/ensembl.gtf"</span><span class="p">,</span> <span class="n" style="color: #333;">full</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="11" 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">

11

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<td class="diff-line-num new_line old" data-linenumber="7" 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="LC11" 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="n" style="color: #333;">gr</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">28</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="12" 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="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

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

<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="12" 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="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

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

<pre style="margin: 0;">+<span id="LC8" 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="n" style="color: #333;">gr</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">26</span></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

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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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

<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"></span>

</pre>

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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="10" 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">

10

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python">    <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gr</span><span class="p">.</span><span class="n" style="color: #333;">df</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="11" 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">

11

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python">    <span class="n" style="color: #333;">transcript</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">iloc</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,7 +16,8 @@ def test_read_gtf():</td>

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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

19

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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16

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

</pre>

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

17

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python">    <span class="n" style="color: #333;">gr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pr</span><span class="p">.</span><span class="n" style="color: #333;">read_gtf</span><span class="p">(</span><span class="s" style="color: #d14;">"tests/test_data/ensembl.gtf"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num 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">

21

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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

18

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python">                     <span class="n" style="color: #333;">full</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">duplicate_attr</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

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

22

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<td class="diff-line-num new_line old" data-linenumber="19" 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="LC22" 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="n" style="color: #333;">gr</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">28</span></span>

</pre>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

19

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

<pre style="margin: 0;">+<span id="LC19" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">gr</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

20

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

<pre style="margin: 0;">+<span id="LC20" 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="n" style="color: #333;">gr</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">26</span></span>

</pre>

</td>

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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="LC22" class="line" lang="python">    <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gr</span><span class="p">.</span><span class="n" style="color: #333;">df</span></span>

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25

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python">    <span class="n" style="color: #333;">transcript</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">iloc</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

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<li id="5e74d0b6a3180cb25aa5c8cad46556233d6b3a21">

<a href="https://salsa.debian.org/med-team/pyranges/-/commit/823b99cc8d170fdb4cea05cad9dae23c6aa03791#5e74d0b6a3180cb25aa5c8cad46556233d6b3a21"><strong>tests/test_unary.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="234" 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="234" 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">@@ -234,6 +234,7 @@ makewindows_command = "bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n {})"</td>

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234

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<pre style="margin: 0;"> <span id="LC234" class="line" lang="python">    <span class="n" style="color: #333;">deadline</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">deadline</span><span class="p">,</span></span>

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<td class="diff-line-num old_line" data-linenumber="235" 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="LC235" class="line" lang="python">    <span class="n" style="color: #333;">suppress_health_check</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">HealthCheck</span><span class="p">.</span><span class="nb" style="color: #0086b3;">all</span><span class="p">())</span></span>

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<td class="diff-line-num old_line" data-linenumber="236" 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="236" 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="LC236" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">given</span><span class="p">(</span><span class="n" style="color: #333;">gr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">dfs_min</span><span class="p">())</span>  <span class="c1" style="color: #998; font-style: italic;"># pylint: disable=no-value-for-parameter</span></span>

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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># @reproduce_failure('5.5.4', b'AXicY2RgYGAEIzgAsRkBAFsABg==')</span></span>

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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;">test_windows</span><span class="p">(</span><span class="n" style="color: #333;">gr</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="239" 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="240" 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="LC240" class="line" lang="python">    <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">tempfile</span><span class="p">.</span><span class="n" style="color: #333;">TemporaryDirectory</span><span class="p">()</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">temp_dir</span><span class="p">:</span></span>

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