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GitLab

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<h3>

Andreas Tille pushed to branch upstream

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/python-cooler/-/commit/a2344c24d429cd4599d95cf78c3d6ac12033527b">a2344c24</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2021-09-30T11:58:24+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.8.11</pre>

</li>

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<h4>16 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">

.travis.yml

</a>

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<li class="file-stats">

<a href="#7facec255884dc55d3818e4dfbea89b1bdd7f49e">

CHANGES.md

</a>

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<li class="file-stats">

<a href="#3f454a98e586d1aa0d322e19afd5e67e08f2d3c8">

CONTRIBUTING.md

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<li class="file-stats">

<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

README.md

</a>

</li>

<li class="file-stats">

<a href="#d9252d1630264e35e18e708f44178eb887c90877">

cooler/_version.py

</a>

</li>

<li class="file-stats">

<a href="#9cc5184a33a85c4fd4a16147f4514d69b317c36e">

cooler/cli/cload.py

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<li class="file-stats">

<a href="#f05ea5db033e4268fb5e4037c337ce8a1e2cbdd5">

cooler/cli/zoomify.py

</a>

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<li class="file-stats">

<a href="#1d9095383846c54cd7065e43ebaa45b9d7b1a27d">

cooler/create/__init__.py

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<li class="file-stats">

<a href="#28e81f983d7f413af336348d329dc18e41725ea8">

cooler/create/_ingest.py

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<li class="file-stats">

<a href="#0a2c9b1333d679f975845fd110c2ffb59930996e">

docs/cli.rst

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<a href="#081652eafbed4cb98ffd30a1a25bedda4a5bdab5">

docs/datamodel.rst

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<a href="#d0153cac95479af9bfb99b746b633bc8255bb53a">

docs/index.rst

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<li class="file-stats">

<a href="#7212297a4768843c37d64be965c66153e2586c2c">

docs/make_cli_rst.py

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<li class="file-stats">

<a href="#45c312bd35bef86601c73bf3e04cfdf85f904c6c">

docs/quickstart.rst

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<li class="file-stats">

<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">

setup.py

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<li class="file-stats">

<a href="#5d4a75be2ccc16e0c3ae308d893ff01dde3679d4">

tests/test_create_sanitize.py

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<h4>Changes:</h4>

<li id="dea01dd89a3b602828e630677fde5d77c06441c8">

<a href="https://salsa.debian.org/med-team/python-cooler/-/commit/a2344c24d429cd4599d95cf78c3d6ac12033527b#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,6 +5,7 @@ python:</td>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="yaml">  <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.6"</span></span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="yaml">  <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.7"</span></span>

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<td class="old_line diff-line-num" 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">

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="yaml">  <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.8"</span></span>

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

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

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml">  <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.9"</span></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="yaml"><span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">sudo apt-get update</span></span>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">sudo apt-get install -y pigz tabix</span></span>

</pre>

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<li id="7facec255884dc55d3818e4dfbea89b1bdd7f49e">

<a href="https://salsa.debian.org/med-team/python-cooler/-/commit/a2344c24d429cd4599d95cf78c3d6ac12033527b#7facec255884dc55d3818e4dfbea89b1bdd7f49e"><strong>CHANGES.md</strong></a>

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># Release notes #</span></span>

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

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.8.10](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.8.9...v0.8.10)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.8.10](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.8.9...v0.8.10)</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown">Date : 2020-09-25</span>

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

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Bug fixes</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"><span class="p">*</span> Fixed the new header parsing in <span class="sb" style="color: #d14;">`cooler cload pairs`</span> to handle esoteric file stream implementations. Specifically <span class="sb" style="color: #d14;">`GzipFile`</span> had stopped working. By @golobor</span>

</pre>

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

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

</pre>

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<td class="old_line diff-line-num old" data-linenumber="10" 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="new_line diff-line-num old" data-linenumber="10" 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="LC10" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.8.9](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.8.8...v0.8.9)</span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.8.9](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.8.8...v0.8.9)</span></span>

</pre>

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<td class="old_line diff-line-num" 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">

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<td class="new_line diff-line-num" 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">

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

</pre>

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<td class="old_line diff-line-num" 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">

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown">Date : 2020-07-17</span>

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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" 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="markdown"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,7 +15,7 @@ Date : 2020-07-17</td>

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<td class="new_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="markdown"><span class="p">*</span> Added single-cell cooler file flavor (.scool) (#201)</span>

</pre>

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

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

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

</pre>

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<td class="old_line diff-line-num old" data-linenumber="18" 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="new_line diff-line-num old" data-linenumber="18" 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="LC18" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.8.8](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.8.7...v0.8.8)</span></span>

</pre>

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

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

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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="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.8.8](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.8.7...v0.8.8)</span></span>

</pre>

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

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

</pre>

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<td class="old_line diff-line-num" 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">

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown">Date : 2020-06-23</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -32,7 +32,7 @@ Date : 2020-06-23</td>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="markdown"><span class="p">*</span> Allow hashes in read IDs in cload pairs (#193)</span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="markdown"></span>

</pre>

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

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

</pre>

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<td class="old_line diff-line-num old" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC35" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.8.7](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.8.6...v0.8.7)</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.8.7](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.8.6...v0.8.7)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="markdown">Date: 2020-01-12</span>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="markdown"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="44" style="width: 35px; color: rgba(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="44" style="width: 35px; color: rgba(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">@@ -44,7 +44,7 @@ Date: 2020-01-12</td>

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="markdown"><span class="p">*</span> Replace <span class="sb" style="color: #d14;">`json`</span> with <span class="sb" style="color: #d14;">`simplejson`</span> to deal with attrs stored as bytes</span>

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="markdown"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="47" 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="new_line diff-line-num old" data-linenumber="47" 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="LC47" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.8.6](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.8.5...v0.8.6)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="48" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="47" style="width: 35px; color: rgba(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="LC47" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.8.6](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.8.5...v0.8.6)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="markdown"></span>

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<td class="old_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="markdown">Date: 2019-08-12</span>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="markdown"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -57,7 +57,7 @@ Date: 2019-08-12</td>

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<td class="new_line diff-line-num" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="markdown">Post-release <span class="sb" style="color: #d14;">`v0.8.6.post0`</span>: requirements files added to MANIFEST.in</span>

</pre>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="markdown"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="60" 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="new_line diff-line-num old" data-linenumber="60" 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="LC60" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.8.5](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.8.4...v0.8.5)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.8.5](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.8.4...v0.8.5)</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="61" style="width: 35px; color: rgba(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="LC61" class="line" lang="markdown"></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="markdown">Date: 2019-04-08</span>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="markdown"></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -65,7 +65,7 @@ Date: 2019-04-08</td>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="markdown"><span class="p">*</span> Fixed a regression that prevented selection of bins excluding the <span class="sb" style="color: #d14;">`chrom`</span> column.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="markdown"></span>

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.8.4](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.8.3...v0.8.4)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.8.4](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.8.3...v0.8.4)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="markdown">Date: 2019-04-04</span>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="markdown"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="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 @@ Date: 2019-04-04</td>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`Cooler.bins()`</span> selector will always properly convert bins/chrom integer IDs to categorical chromosome names when the number of contigs is very large and therefore the HDF5 ENUM header is missing. Before this would only happen when explicitly requesting <span class="sb" style="color: #d14;">`convert_enum=True`</span>.</span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="markdown"></span>

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<td class="old_line diff-line-num old" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC84" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.8.3](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.8.2...v0.8.3)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(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="LC84" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.8.3](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.8.2...v0.8.3)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="markdown">Date: 2019-02-11</span>

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="90" style="width: 35px; color: rgba(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="90" style="width: 35px; color: rgba(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">@@ -90,7 +90,7 @@ Date: 2019-02-11</td>

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`create_cooler`</span> no longer requires a "count" column when specifying custom value columns</span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="markdown"></span>

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<pre style="margin: 0;">-<span id="LC93" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.8.2](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.8.1...v0.8.2)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.8.2](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.8.1...v0.8.2)</span></span>

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="markdown">Date: 2019-01-20</span>

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="markdown"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -105,7 +105,7 @@ New options for `cooler dump` pixel output:</td>

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="markdown"><span class="p">*</span> A bug was introduced into the matrix-as-pixels selector in 0.8.0 that also affected <span class="sb" style="color: #d14;">`cooler dump`</span>. The behavior has been restored to that in 0.7.</span>

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="markdown"></span>

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

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<pre style="margin: 0;">-<span id="LC108" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.8.1](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.8.0...v0.8.1)</span></span>

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.8.1](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.8.0...v0.8.1)</span></span>

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

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="markdown">Date: 2019-01-02</span>

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="120" style="width: 35px; color: rgba(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="120" style="width: 35px; color: rgba(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">@@ -120,7 +120,7 @@ Date: 2019-01-02</td>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="markdown"><span class="p">*</span> Restore but deprecate <span class="sb" style="color: #d14;">`cooler.io.ls`</span> for backwards compatibility.</span>

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="markdown"></span>

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<pre style="margin: 0;">-<span id="LC123" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.8.0](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.7.11...v0.8.0)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.8.0](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.7.11...v0.8.0)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="markdown">Date: 2018-12-31</span>

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

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -168,7 +168,7 @@ This is a major release from 0.7 and includes an updated format version, and sev</td>

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="markdown"><span class="p">*</span> Unit tests refactored and re-written for pytest.</span>

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<pre style="margin: 0;"> <span id="LC169" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC170" class="line" lang="markdown"></span>

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<td class="old_line diff-line-num old" data-linenumber="171" 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="LC171" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.7.11](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.7.10...v0.7.11)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC171" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.7.11](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.7.10...v0.7.11)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC172" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC173" class="line" lang="markdown">Date: 2018-08-17</span>

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

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -181,7 +181,7 @@ Bug fixes</td>

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<pre style="margin: 0;"> <span id="LC181" class="line" lang="markdown"><span class="p">*</span> Fix <span class="sb" style="color: #d14;">`--count-as-float`</span> regression in load/cload.</span>

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<pre style="margin: 0;"> <span id="LC182" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC183" class="line" lang="markdown"></span>

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<td class="new_line diff-line-num old" data-linenumber="184" 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="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.7.10](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.7.9...v0.7.10)</span></span>

</pre>

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<td class="new_line diff-line-num new" 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="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.7.10](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.7.9...v0.7.10)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC185" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC186" class="line" lang="markdown">Date: 2018-05-07</span>

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<td class="old_line diff-line-num" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="190" style="width: 35px; color: rgba(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="190" style="width: 35px; color: rgba(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">@@ -190,7 +190,7 @@ Date: 2018-05-07</td>

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190

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<pre style="margin: 0;"> <span id="LC190" class="line" lang="markdown"><span class="p">*</span> Start using shuffle filter by default</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

191

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<pre style="margin: 0;"> <span id="LC191" class="line" lang="markdown"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

192

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<pre style="margin: 0;"> <span id="LC192" class="line" lang="markdown"></span>

</pre>

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

193

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<td class="new_line diff-line-num old" 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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<pre style="margin: 0;">-<span id="LC193" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.7.9](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.7.8...v0.7.9)</span></span>

</pre>

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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" 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="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.7.9](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.7.8...v0.7.9)</span></span>

</pre>

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194

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194

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

</pre>

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<td class="old_line diff-line-num" data-linenumber="195" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="195" style="width: 35px; color: rgba(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="LC195" class="line" lang="markdown">Date: 2018-03-30</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="196" style="width: 35px; color: rgba(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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196

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -198,7 +198,7 @@ Date: 2018-03-30</td>

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198

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<td class="new_line diff-line-num" 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="markdown"><span class="p">*</span> Fixed error introduced into cload pairix in last release.</span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC199" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC200" class="line" lang="markdown"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

201

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<td class="new_line diff-line-num old" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC201" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.7.8](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.7.7...v0.7.8)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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="LC201" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.7.8](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.7.7...v0.7.8)</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="202" style="width: 35px; color: rgba(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="LC202" class="line" lang="markdown"></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="203" style="width: 35px; color: rgba(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="LC203" class="line" lang="markdown">Date: 2018-03-18</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="204" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="204" style="width: 35px; color: rgba(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="LC204" class="line" lang="markdown"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="214" style="width: 35px; color: rgba(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="214" style="width: 35px; color: rgba(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">@@ -214,7 +214,7 @@ Date: 2018-03-18</td>

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<td class="new_line diff-line-num" data-linenumber="214" style="width: 35px; color: rgba(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="LC214" class="line" lang="markdown"><span class="p">*</span> Added extra checks in <span class="sb" style="color: #d14;">`cload pairix`</span> and <span class="sb" style="color: #d14;">`cload tabix`</span>. #62, #75</span>

</pre>

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<pre style="margin: 0;"> <span id="LC215" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC216" class="line" lang="markdown"></span>

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<pre style="margin: 0;">-<span id="LC217" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.7.7](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.7.6...v0.7.7)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="217" style="width: 35px; color: rgba(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="LC217" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.7.7](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.7.6...v0.7.7)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC218" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="markdown">Date: 2018-03-16</span>

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<pre style="margin: 0;"> <span id="LC220" class="line" lang="markdown"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="233" style="width: 35px; color: rgba(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="233" style="width: 35px; color: rgba(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">@@ -233,7 +233,7 @@ Date: 2018-03-16</td>

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="markdown"><span class="p">*</span> Fix argmax deprecation. #99</span>

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<pre style="margin: 0;"> <span id="LC234" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC235" class="line" lang="markdown"></span>

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<td class="new_line diff-line-num old" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC236" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.7.6](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.7.5...v0.7.6)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="236" style="width: 35px; color: rgba(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="LC236" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.7.6](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.7.5...v0.7.6)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC237" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC238" class="line" lang="markdown">Date: 2017-10-31</span>

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="252" style="width: 35px; color: rgba(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="252" style="width: 35px; color: rgba(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">@@ -252,7 +252,7 @@ Date: 2017-10-31</td>

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<td class="new_line diff-line-num" data-linenumber="252" style="width: 35px; color: rgba(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="LC252" class="line" lang="markdown">Happy Halloween!</span>

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<pre style="margin: 0;"> <span id="LC253" class="line" lang="markdown"></span>

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

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<pre style="margin: 0;">-<span id="LC255" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.7.5](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.7.4...v0.7.5)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="255" style="width: 35px; color: rgba(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="LC255" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.7.5](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.7.4...v0.7.5)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC256" class="line" lang="markdown"></span>

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<td class="old_line diff-line-num" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC257" class="line" lang="markdown">Date: 2017-07-13</span>

</pre>

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<pre style="margin: 0;"> <span id="LC258" class="line" lang="markdown"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="260" style="width: 35px; color: rgba(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="260" style="width: 35px; color: rgba(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">@@ -260,7 +260,7 @@ Date: 2017-07-13</td>

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<pre style="margin: 0;"> <span id="LC260" class="line" lang="markdown"><span class="p">*</span> Add transform options to higlass API</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="261" style="width: 35px; color: rgba(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="LC261" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC262" class="line" lang="markdown"></span>

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<td class="old_line diff-line-num old" data-linenumber="263" 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="new_line diff-line-num old" data-linenumber="263" 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="LC263" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.7.4](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.7.3...v0.7.4)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC263" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.7.4](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.7.3...v0.7.4)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC264" class="line" lang="markdown"></span>

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<td class="old_line diff-line-num" data-linenumber="265" style="width: 35px; color: rgba(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="LC265" class="line" lang="markdown">Date: 2017-05-25</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC266" class="line" lang="markdown"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="268" style="width: 35px; color: rgba(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="268" style="width: 35px; color: rgba(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">@@ -268,14 +268,14 @@ Date: 2017-05-25</td>

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<td class="new_line diff-line-num" data-linenumber="268" style="width: 35px; color: rgba(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="LC268" class="line" lang="markdown"><span class="p">*</span> Fix special cases where cooler.io.create and append would not work with certain inputs</span>

</pre>

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<pre style="margin: 0;"> <span id="LC269" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC270" class="line" lang="markdown"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="271" 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="new_line diff-line-num old" data-linenumber="271" 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="LC271" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.7.3](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.7.2...v0.7.3)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="271" style="width: 35px; color: rgba(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="LC271" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.7.3](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.7.2...v0.7.3)</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="272" style="width: 35px; color: rgba(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="LC272" class="line" lang="markdown"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="273" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="273" style="width: 35px; color: rgba(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="LC273" class="line" lang="markdown">Date: 2017-05-22</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="274" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="274" style="width: 35px; color: rgba(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="LC274" class="line" lang="markdown"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC275" class="line" lang="markdown"><span class="p">*</span> Added function to print higlass zoom resolutions for a given genome and base resolution.</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="276" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="276" style="width: 35px; color: rgba(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="LC276" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC277" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC278" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.7.2](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.7.1...v0.7.2)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC278" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.7.2](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.7.1...v0.7.2)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC279" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC280" class="line" lang="markdown">Date: 2017-05-09</span>

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

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<pre style="margin: 0;"> <span id="LC283" class="line" lang="markdown"><span class="p">*</span> Restore zoom binsize metadata to higlass files</span>

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<pre style="margin: 0;"> <span id="LC284" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC285" class="line" lang="markdown"></span>

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<pre style="margin: 0;">-<span id="LC286" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.7.1](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.7.0...v0.7.1)</span></span>

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<pre style="margin: 0;">+<span id="LC286" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.7.1](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.7.0...v0.7.1)</span></span>

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<pre style="margin: 0;"> <span id="LC287" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC288" class="line" lang="markdown">Date: 2017-04-29</span>

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<pre style="margin: 0;"> <span id="LC289" class="line" lang="markdown"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="292" style="width: 35px; color: rgba(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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<pre style="margin: 0;"> <span id="LC292" class="line" lang="markdown"><span class="p">*</span> Eliminate hard dependence on dask to make pip installs simpler. Conda package will retain dask as a run time requirement.</span>

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<pre style="margin: 0;"> <span id="LC293" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC294" class="line" lang="markdown"></span>

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<pre style="margin: 0;">-<span id="LC295" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.7.0](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.6.6...v0.7.0)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="295" style="width: 35px; color: rgba(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="LC295" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.7.0](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.6.6...v0.7.0)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC296" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC297" class="line" lang="markdown">Date: 2017-04-27</span>

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<pre style="margin: 0;"> <span id="LC298" class="line" lang="markdown"></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="324" style="width: 35px; color: rgba(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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<pre style="margin: 0;"> <span id="LC324" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`Cooler.open`</span> function now correctly opens the specific root group of the Cooler and behaves like a proper context manager in all cases</span>

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<pre style="margin: 0;"> <span id="LC325" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC326" class="line" lang="markdown"></span>

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<pre style="margin: 0;">-<span id="LC327" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.6.6](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.6.5...v0.6.6)</span></span>

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<pre style="margin: 0;">+<span id="LC327" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.6.6](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.6.5...v0.6.6)</span></span>

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<pre style="margin: 0;"> <span id="LC328" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC329" class="line" lang="markdown">Date: 2017-03-21</span>

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<pre style="margin: 0;"> <span id="LC330" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC332" class="line" lang="markdown"><span class="p">*</span> Improved pairix and tabix iterators, dropped need for slow first pass over contacts</span>

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<pre style="margin: 0;"> <span id="LC333" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC334" class="line" lang="markdown"></span>

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<td class="new_line diff-line-num old" data-linenumber="335" 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="LC335" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.6.5](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.6.4...v0.6.5)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="335" style="width: 35px; color: rgba(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="LC335" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.6.5](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.6.4...v0.6.5)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC336" class="line" lang="markdown"></span>

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<td class="new_line diff-line-num" data-linenumber="337" style="width: 35px; color: rgba(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="LC337" class="line" lang="markdown">Date: 2017-03-18</span>

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<td class="new_line diff-line-num" data-linenumber="338" style="width: 35px; color: rgba(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="LC338" class="line" lang="markdown"></span>

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<td class="old_line diff-line-num" data-linenumber="339" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="339" style="width: 35px; color: rgba(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="LC339" class="line" lang="markdown"><span class="p">*</span> Fixed pairix aggregator to properly deal with autoflipping of pairs</span>

</pre>

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<pre style="margin: 0;"> <span id="LC340" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC341" class="line" lang="markdown"></span>

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<pre style="margin: 0;">-<span id="LC342" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.6.4](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.6.3...v0.6.4)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC342" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.6.4](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.6.3...v0.6.4)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC343" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC344" class="line" lang="markdown">Date: 2017-03-17</span>

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<pre style="margin: 0;"> <span id="LC345" class="line" lang="markdown"></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -347,7 +347,7 @@ Date: 2017-03-17</td>

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<pre style="margin: 0;"> <span id="LC347" class="line" lang="markdown"><span class="p">*</span> Fixed pairix aggregator to properly deal with autoflipping of pairs</span>

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<pre style="margin: 0;"> <span id="LC348" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC349" class="line" lang="markdown"></span>

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<pre style="margin: 0;">-<span id="LC350" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.6.3](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.6.2...v0.6.3)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC350" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.6.3](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.6.2...v0.6.3)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC351" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC352" class="line" lang="markdown">Date: 2017-02-22</span>

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="356" style="width: 35px; color: rgba(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="356" style="width: 35px; color: rgba(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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<pre style="margin: 0;"> <span id="LC356" class="line" lang="markdown"><span class="p">*</span> Return matrix scale factor in balance stats rather than the bias scale factor: #35.</span>

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<pre style="margin: 0;"> <span id="LC357" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC358" class="line" lang="markdown"></span>

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<pre style="margin: 0;">-<span id="LC359" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.6.2](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.6.1...v0.6.2)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC359" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.6.2](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.6.1...v0.6.2)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC360" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC361" class="line" lang="markdown">Date: 2017-02-12</span>

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<pre style="margin: 0;"> <span id="LC362" class="line" lang="markdown"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="366" style="width: 35px; color: rgba(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="366" style="width: 35px; color: rgba(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">@@ -366,14 +366,14 @@ Fixed regressions in</td>

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<pre style="margin: 0;"> <span id="LC366" class="line" lang="markdown"><span class="p">*</span> cooler show</span>

</pre>

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<pre style="margin: 0;"> <span id="LC367" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC368" class="line" lang="markdown"></span>

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<td class="new_line diff-line-num old" data-linenumber="369" 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="LC369" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.6.1](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.6.0...v0.6.1)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC369" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.6.1](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.6.0...v0.6.1)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC370" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC371" class="line" lang="markdown">Date: 2017-02-06</span>

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<pre style="margin: 0;"> <span id="LC372" class="line" lang="markdown"></span>

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<td class="old_line diff-line-num" data-linenumber="373" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="373" style="width: 35px; color: rgba(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="LC373" class="line" lang="markdown"><span class="p">*</span> This fixes stale build used in bdist_wheel packaging that broke 0.6.0. #29</span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC375" class="line" lang="markdown"></span>

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<td class="new_line diff-line-num old" data-linenumber="376" 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="LC376" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.6.0](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.5.3...v0.6.0)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="376" style="width: 35px; color: rgba(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="LC376" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.6.0](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.5.3...v0.6.0)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC377" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC378" class="line" lang="markdown">Date: 2017-02-03</span>

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<pre style="margin: 0;"> <span id="LC379" class="line" lang="markdown"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="403" style="width: 35px; color: rgba(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="403" style="width: 35px; color: rgba(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">@@ -403,7 +403,7 @@ Date: 2017-02-03</td>

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<td class="new_line diff-line-num" data-linenumber="403" style="width: 35px; color: rgba(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="LC403" class="line" lang="markdown"><span class="p">*</span> Fixed bug in <span class="sb" style="color: #d14;">`csort`</span> that led to incorrect triangularity of trans read pairs.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC404" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC405" class="line" lang="markdown"></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="406" 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="LC406" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.5.3](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.5.2...v0.5.3)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC406" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.5.3](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.5.2...v0.5.3)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC407" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC408" class="line" lang="markdown">Date: 2016-09-10</span>

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<pre style="margin: 0;"> <span id="LC409" class="line" lang="markdown"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="414" style="width: 35px; color: rgba(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="414" style="width: 35px; color: rgba(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">@@ -414,7 +414,7 @@ Date: 2016-09-10</td>

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<pre style="margin: 0;"> <span id="LC414" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`cooler cload`</span> raises a warning when bin file lists a contig missing from the contact list</span>

</pre>

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<pre style="margin: 0;"> <span id="LC415" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC416" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC417" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.5.2](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.5.1...v0.5.2)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC417" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.5.2](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.5.1...v0.5.2)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC418" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC419" class="line" lang="markdown">Date: 2016-08-26</span>

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<pre style="margin: 0;"> <span id="LC420" class="line" lang="markdown"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="423" style="width: 35px; color: rgba(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="423" style="width: 35px; color: rgba(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">@@ -423,7 +423,7 @@ Date: 2016-08-26</td>

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<pre style="margin: 0;"> <span id="LC423" class="line" lang="markdown"><span class="p">*</span> Fix typo in setup.py and add pysam to dependencies.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC424" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC425" class="line" lang="markdown"></span>

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<td class="new_line diff-line-num old" data-linenumber="426" 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="LC426" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.5.1](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.5.0...v0.5.1)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC426" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.5.1](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.5.0...v0.5.1)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC427" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC428" class="line" lang="markdown">Date: 2016-08-24</span>

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<pre style="margin: 0;"> <span id="LC429" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="432" style="width: 35px; color: rgba(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="432" style="width: 35px; color: rgba(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">@@ -432,7 +432,7 @@ Date: 2016-08-24</td>

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432

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<td class="new_line diff-line-num" data-linenumber="432" style="width: 35px; color: rgba(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="LC432" class="line" lang="markdown"><span class="p">*</span> Rename <span class="sb" style="color: #d14;">`cooler binnify`</span> to <span class="sb" style="color: #d14;">`cooler makebins`</span>. Binnify sounds like "aggregate" which is what <span class="sb" style="color: #d14;">`cload`</span> does.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC433" class="line" lang="markdown"></span>

</pre>

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434

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<pre style="margin: 0;"> <span id="LC434" class="line" lang="markdown"></span>

</pre>

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435

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<pre style="margin: 0;">-<span id="LC435" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.5.0](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.4.0...v0.5.0)</span></span>

</pre>

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435

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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="LC435" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.5.0](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.4.0...v0.5.0)</span></span>

</pre>

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436

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436

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

<pre style="margin: 0;"> <span id="LC436" class="line" lang="markdown"></span>

</pre>

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437

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437

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<pre style="margin: 0;"> <span id="LC437" class="line" lang="markdown">Date: 2016-08-24</span>

</pre>

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438

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438

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

<pre style="margin: 0;"> <span id="LC438" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="442" style="width: 35px; color: rgba(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="442" style="width: 35px; color: rgba(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">@@ -442,7 +442,7 @@ Date: 2016-08-24</td>

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<td class="old_line diff-line-num" data-linenumber="442" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

442

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<td class="new_line diff-line-num" data-linenumber="442" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

442

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<pre style="margin: 0;"> <span id="LC442" class="line" lang="markdown"><span class="p">*</span> Minor bug fixes.</span>

</pre>

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443

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443

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<pre style="margin: 0;"> <span id="LC443" class="line" lang="markdown"></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

444

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

<pre style="margin: 0;"> <span id="LC444" class="line" lang="markdown"></span>

</pre>

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445

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<td class="new_line diff-line-num old" data-linenumber="445" 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="LC445" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.4.0](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.3.0...v0.4.0)</span></span>

</pre>

</td>

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<td class="new_line diff-line-num new" data-linenumber="445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

445

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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="LC445" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.4.0](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.3.0...v0.4.0)</span></span>

</pre>

</td>

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446

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<td class="new_line diff-line-num" data-linenumber="446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

446

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

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

</pre>

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447

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<td class="new_line diff-line-num" data-linenumber="447" style="width: 35px; color: rgba(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="LC447" class="line" lang="markdown">Date: 2016-08-18</span>

</pre>

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448

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448

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

<pre style="margin: 0;"> <span id="LC448" class="line" lang="markdown"></span>

</pre>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -463,7 +463,7 @@ Date: 2016-08-18</td>

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<pre style="margin: 0;"> <span id="LC463" class="line" lang="markdown"><span class="p">*</span> Added new scripts for contact aggregation, loading, dumping and balancing</span>

</pre>

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<pre style="margin: 0;"> <span id="LC464" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC465" class="line" lang="markdown"></span>

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<pre style="margin: 0;">-<span id="LC466" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.3.0](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.2.1...v0.3.0)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC466" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.3.0](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.2.1...v0.3.0)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC467" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC468" class="line" lang="markdown">Date: 2016-02-18</span>

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<pre style="margin: 0;"> <span id="LC469" class="line" lang="markdown"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="473" style="width: 35px; color: rgba(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="473" style="width: 35px; color: rgba(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">@@ -473,21 +473,21 @@ Date: 2016-02-18</td>

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<td class="new_line diff-line-num" data-linenumber="473" style="width: 35px; color: rgba(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="LC473" class="line" lang="markdown"><span class="p">*</span> Genomic locus string parser now accepts ENSEMBL-style number-only chromosome names and FASTA-style sequence names containing pipes.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC474" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC475" class="line" lang="markdown"></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="476" 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="LC476" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.2.1](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.2...v0.2.1)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="476" style="width: 35px; color: rgba(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="LC476" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.2.1](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.2...v0.2.1)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC477" class="line" lang="markdown"></span>

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478

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<td class="new_line diff-line-num" data-linenumber="478" style="width: 35px; color: rgba(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="LC478" class="line" lang="markdown">Date: 2016-02-07</span>

</pre>

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479

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<pre style="margin: 0;"> <span id="LC479" class="line" lang="markdown"></span>

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<td class="old_line diff-line-num" data-linenumber="480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

480

</td>

<td class="new_line diff-line-num" data-linenumber="480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

480

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<pre style="margin: 0;"> <span id="LC480" class="line" lang="markdown"><span class="p">*</span> Fixed bintable region fetcher</span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

481

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<pre style="margin: 0;"> <span id="LC481" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC482" class="line" lang="markdown"></span>

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<pre style="margin: 0;">-<span id="LC483" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.2](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/compare/v0.1...v0.2)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="484" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

483

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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="LC483" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.2](https://github.com/<span class="idiff left right">open2c</span>/cooler/compare/v0.1...v0.2)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

484

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<td class="new_line diff-line-num" data-linenumber="484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

484

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<pre style="margin: 0;"> <span id="LC484" class="line" lang="markdown"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

485

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<td class="new_line diff-line-num" data-linenumber="485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

485

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<pre style="margin: 0;"> <span id="LC485" class="line" lang="markdown">Date: 2016-01-17</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

486

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<td class="new_line diff-line-num" data-linenumber="486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

486

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

<pre style="margin: 0;"> <span id="LC486" class="line" lang="markdown"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

487

</td>

<td class="new_line diff-line-num" data-linenumber="487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

487

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

<pre style="margin: 0;"> <span id="LC487" class="line" lang="markdown"><span class="p">*</span> First beta release</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

488

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<td class="new_line diff-line-num" data-linenumber="488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

488

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

<pre style="margin: 0;"> <span id="LC488" class="line" lang="markdown"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

489

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<td class="new_line diff-line-num" data-linenumber="489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

489

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

<pre style="margin: 0;"> <span id="LC489" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="490" 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">

490

</td>

<td class="new_line diff-line-num old" data-linenumber="490" 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="LC490" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.1](https://github.com/<span class="idiff left right">mirnylab</span>/cooler/releases/tag/v0.1)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="491" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

490

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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="LC490" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.1](https://github.com/<span class="idiff left right">open2c</span>/cooler/releases/tag/v0.1)</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num" data-linenumber="491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

491

</td>

<td class="new_line diff-line-num" data-linenumber="491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

491

</td>

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

<pre style="margin: 0;"> <span id="LC491" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

492

</td>

<td class="new_line diff-line-num" data-linenumber="492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

492

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

<pre style="margin: 0;"> <span id="LC492" class="line" lang="markdown">Date: 2015-11-22</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

493

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<td class="new_line diff-line-num" data-linenumber="493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

493

</td>

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

<pre style="margin: 0;"> <span id="LC493" class="line" lang="markdown"></span>

</pre>

</td>

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</table>

<br>

</li>

<li id="3f454a98e586d1aa0d322e19afd5e67e08f2d3c8">

<a href="https://salsa.debian.org/med-team/python-cooler/-/commit/a2344c24d429cd4599d95cf78c3d6ac12033527b#3f454a98e586d1aa0d322e19afd5e67e08f2d3c8"><strong>CONTRIBUTING.md</strong></a>

<hr>

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

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,7 +21,7 @@ This project has a number of requirements for all code contributed.</td>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC21" class="line" lang="markdown">After forking and cloning the repository, install in "editable" (i.e. development) mode using the <span class="sb" style="color: #d14;">`-e`</span> option:</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

22

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<td class="new_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

22

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

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

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

23

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<td class="new_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

23

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

<pre style="margin: 0;"> <span id="LC23" class="line" lang="markdown"><span class="p">```</span><span class="nl">sh</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

24

</td>

<td class="new_line diff-line-num old" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC24" class="line" lang="markdown">git clone https://github.com/<span class="idiff left right">mirnylab</span>/cooler.git</span>

</pre>

</td>

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

</td>

<td class="new_line diff-line-num new" 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="markdown">git clone https://github.com/<span class="idiff left right">open2c</span>/cooler.git</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

25

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<td class="new_line diff-line-num" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

25

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

<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">cd </span>cooler</span>

</pre>

</td>

</tr>

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

26

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

26

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

<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown">pip <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-e</span> .[all]</span>

</pre>

</td>

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

27

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

27

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="markdown"><span class="p">```</span></span>

</pre>

</td>

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</table>

<br>

</li>

<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

<a href="https://salsa.debian.org/med-team/python-cooler/-/commit/a2344c24d429cd4599d95cf78c3d6ac12033527b#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>

<hr>

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1

</td>

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

<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># Cooler</span></span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

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

</pre>

</td>

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

<td class="old_line diff-line-num 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">

3

</td>

<td class="new_line diff-line-num 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>

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

<pre style="margin: 0;">-<span id="LC3" class="line" lang="markdown"><span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://<span class="idiff left">mirnylab</span>.github.io/cooler"</span><span class="nt" style="color: #000080;">><img</span> <span class="na" style="color: #008080;">width=</span><span class="s" style="color: #d14;">"25%"</span> <span class="na" style="color: #008080;">src=</span><span class="s" style="color: #d14;">"https://github.com/<span class="idiff right">mirnylab</span>/cooler/raw/master/docs/cooler_logo.png"</span> <span class="na" style="color: #008080;">alt=</span><span class="s" style="color: #d14;">"Cooler"</span><span class="nt" style="color: #000080;">></a></span></span>

</pre>

</td>

</tr>

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

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

</td>

<td class="new_line diff-line-num new" 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

</td>

<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="markdown"><span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://<span class="idiff left">open2c</span>.github.io/cooler"</span><span class="nt" style="color: #000080;">><img</span> <span class="na" style="color: #008080;">width=</span><span class="s" style="color: #d14;">"25%"</span> <span class="na" style="color: #008080;">src=</span><span class="s" style="color: #d14;">"https://github.com/<span class="idiff right">open2c</span>/cooler/raw/master/docs/cooler_logo.png"</span> <span class="na" style="color: #008080;">alt=</span><span class="s" style="color: #d14;">"Cooler"</span><span class="nt" style="color: #000080;">></a></span></span>

</pre>

</td>

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

<td class="old_line diff-line-num" 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

</td>

<td class="new_line diff-line-num" 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

</td>

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

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

</pre>

</td>

</tr>

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

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

5

</td>

<td class="new_line diff-line-num old" data-linenumber="5" 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="LC5" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.org/<span class="idiff left">mirnylab</span>/cooler.svg?branch=master</span><span class="p">)</span>](https://travis-ci.org/<span class="idiff right">mirnylab</span>/cooler)</span>

</pre>

</td>

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

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

</td>

<td class="new_line diff-line-num old" data-linenumber="5" 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="LC6" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![CodeCov</span><span class="p">](</span><span class="sx" style="color: #d14;">https://codecov.io/gh/<span class="idiff left">mirnylab</span>/cooler/branch/master/graph/badge.svg</span><span class="p">)</span>](https://codecov.io/gh/<span class="idiff right">mirnylab</span>/cooler)</span>

</pre>

</td>

</tr>

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

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

</td>

<td class="new_line diff-line-num new" 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

</td>

<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="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.org/<span class="idiff left">open2c</span>/cooler.svg?branch=master</span><span class="p">)</span>](https://travis-ci.org/<span class="idiff right">open2c</span>/cooler)</span>

</pre>

</td>

</tr>

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

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

</td>

<td class="new_line diff-line-num new" 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

</td>

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

<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![CodeCov</span><span class="p">](</span><span class="sx" style="color: #d14;">https://codecov.io/gh/<span class="idiff left">open2c</span>/cooler/branch/master/graph/badge.svg</span><span class="p">)</span>](https://codecov.io/gh/<span class="idiff right">open2c</span>/cooler)</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" 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

</td>

<td class="new_line diff-line-num" 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

</td>

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

<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Documentation Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://readthedocs.org/projects/cooler/badge/?version=latest</span><span class="p">)</span>](http://cooler.readthedocs.org/en/latest/)</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" 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

</td>

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

<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![install with bioconda</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square</span><span class="p">)</span>](http://bioconda.github.io/recipes/cooler/README.html)</span>

</pre>

</td>

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

<td class="old_line diff-line-num old" data-linenumber="9" 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">

9

</td>

<td class="new_line diff-line-num old" data-linenumber="9" 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="LC9" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Binder</span><span class="p">](</span><span class="sx" style="color: #d14;">https://mybinder.org/badge_logo.svg</span><span class="p">)</span>](https://mybinder.org/v2/gh/<span class="idiff left right">mirnylab</span>/cooler-binder/master)</span>

</pre>

</td>

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

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

10

</td>

<td class="new_line diff-line-num old" data-linenumber="9" 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="LC10" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Join the chat <span class="idiff left">at https://gitter.im/mirnylab/cooler</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://badges.gitter.im/mirnylab/cooler.svg</span></span><span class="p">)</span>](https://<span class="idiff">g</span>it<span class="idiff right">ter.im/mirnylab/cooler?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badg</span>e)</span>

</pre>

</td>

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

</td>

<td class="new_line diff-line-num new" 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

</td>

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

<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Binder</span><span class="p">](</span><span class="sx" style="color: #d14;">https://mybinder.org/badge_logo.svg</span><span class="p">)</span>](https://mybinder.org/v2/gh/<span class="idiff left right">open2c</span>/cooler-binder/master)</span>

</pre>

</td>

</tr>

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

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

</td>

<td class="new_line diff-line-num new" 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

</td>

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

<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Join the chat <span class="idiff left">on Slack</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://img.shields.io/badge/chat-slack-%233F0F3F?logo=slack</span></span><span class="p">)</span>](https://<span class="idiff">b</span>it<span class="idiff right">.ly/2UaOpA</span>e)</span>

</pre>

</td>

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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![DOI</span><span class="p">](</span><span class="sx" style="color: #d14;">https://zenodo.org/badge/49553222.svg</span><span class="p">)</span>](https://zenodo.org/badge/latestdoi/49553222)</span>

</pre>

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

</pre>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## A cool place to store your Hi-C</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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,7 +19,7 @@ The cooler file format is an implementation of a genomic matrix data model using</td>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown">To get started:</span>

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

</pre>

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<td class="old_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: #008080;">Install</span><span class="p">](</span><span class="sx" style="color: #d14;">#Installation</span><span class="p">)</span> cooler</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="markdown"><span class="p">-</span> Read the <span class="p">[</span><span class="nv" style="color: #008080;">documentation</span><span class="p">](</span><span class="sx" style="color: #d14;">http://cooler.readthedocs.org/en/latest/</span><span class="p">)</span> and see the Jupyter Notebook <span class="p">[</span><span class="nv" style="color: #008080;">walkthrough</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/<span class="idiff left right">mirnylab</span>/cooler-binder</span><span class="p">)</span>.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"><span class="p">-</span> Read the <span class="p">[</span><span class="nv" style="color: #008080;">documentation</span><span class="p">](</span><span class="sx" style="color: #d14;">http://cooler.readthedocs.org/en/latest/</span><span class="p">)</span> and see the Jupyter Notebook <span class="p">[</span><span class="nv" style="color: #008080;">walkthrough</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/<span class="idiff left right">open2c</span>/cooler-binder</span><span class="p">)</span>.</span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(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="LC23" class="line" lang="markdown"><span class="p">-</span> _cool_ files from published Hi-C data sets are available at <span class="sb" style="color: #d14;">`ftp://cooler.csail.mit.edu/coolers`</span>.</span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(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="LC24" class="line" lang="markdown"><span class="p">-</span> Many more multires (_mcool_) files are available on the <span class="p">[</span><span class="nv" style="color: #008080;">4DN data portal</span><span class="p">](</span><span class="sx" style="color: #d14;">https://data.4dnucleome.org/visualization/index</span><span class="p">)</span>.</span>

</pre>

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

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -47,7 +47,7 @@ See the [docs](http://cooler.readthedocs.org/en/latest/) for more information.</td>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Contributing</span></span>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="markdown"></span>

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<td class="new_line diff-line-num old" data-linenumber="50" 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="LC50" class="line" lang="markdown">Interested in contributing to cooler? That's great! To get started, check out the <span class="p">[</span><span class="nv" style="color: #008080;">contributing guide</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/<span class="idiff left right">mirnylab</span>/cooler/blob/master/CONTRIBUTING.md</span><span class="p">)</span>.</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="51" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="markdown">Interested in contributing to cooler? That's great! To get started, check out the <span class="p">[</span><span class="nv" style="color: #008080;">contributing guide</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/<span class="idiff left right">open2c</span>/cooler/blob/master/CONTRIBUTING.md</span><span class="p">)</span>.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="markdown"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Citing</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="72" style="width: 35px; color: rgba(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="72" style="width: 35px; color: rgba(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">@@ -72,7 +72,7 @@ BSD (3 Clause)</td>

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="markdown"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="73" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="73" style="width: 35px; color: rgba(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="LC73" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Related projects</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="74" style="width: 35px; color: rgba(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="LC74" class="line" lang="markdown"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="75" 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="new_line diff-line-num old" data-linenumber="75" 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="LC75" class="line" lang="markdown"><span class="p">-</span> Process Hi-C data with <span class="p">[</span><span class="nv" style="color: #008080;">distiller</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/<span class="idiff left right">mirnylab</span>/distiller</span><span class="p">)</span>!</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="76" 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="new_line diff-line-num old" data-linenumber="75" 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="LC76" class="line" lang="markdown"><span class="p">-</span> Downstream analysis with <span class="p">[</span><span class="nv" style="color: #008080;">cooltools</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/<span class="idiff left right">mirnylab</span>/cooltools</span><span class="p">)</span>!</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="77" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(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="LC75" class="line" lang="markdown"><span class="p">-</span> Process Hi-C data with <span class="p">[</span><span class="nv" style="color: #008080;">distiller</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/<span class="idiff left right">open2c</span>/distiller</span><span class="p">)</span>!</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="77" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="76" style="width: 35px; color: rgba(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="LC76" class="line" lang="markdown"><span class="p">-</span> Downstream analysis with <span class="p">[</span><span class="nv" style="color: #008080;">cooltools</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/<span class="idiff left right">open2c</span>/cooltools</span><span class="p">)</span>!</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="77" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="77" style="width: 35px; color: rgba(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="LC77" class="line" lang="markdown"><span class="p">-</span> Visualize your cooler data with <span class="p">[</span><span class="nv" style="color: #008080;">HiGlass</span><span class="p">](</span><span class="sx" style="color: #d14;">http://higlass.io</span><span class="p">)</span>!</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="78" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="78" style="width: 35px; color: rgba(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="LC78" class="line" lang="markdown"></span></pre>

</td>

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<br>

</li>

<li id="d9252d1630264e35e18e708f44178eb887c90877">

<a href="https://salsa.debian.org/med-team/python-cooler/-/commit/a2344c24d429cd4599d95cf78c3d6ac12033527b#d9252d1630264e35e18e708f44178eb887c90877"><strong>cooler/_version.py</strong></a>

<hr>

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1

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<td class="new_line diff-line-num old" data-linenumber="1" 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="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;">"0.8.1<span class="idiff left right">0</span>"</span></span>

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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;">"0.8.1<span class="idiff left right">1</span>"</span></span>

</pre>

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<td class="old_line diff-line-num" 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">

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="n" style="color: #333;">__format_version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span></span>

</pre>

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<td class="old_line diff-line-num" 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">

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="n" style="color: #333;">__format_version_mcool__</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span></span>

</pre>

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<td class="old_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="n" style="color: #333;">__format_version_scool__</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span></pre>

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<br>

</li>

<li id="9cc5184a33a85c4fd4a16147f4514d69b317c36e">

<a href="https://salsa.debian.org/med-team/python-cooler/-/commit/a2344c24d429cd4599d95cf78c3d6ac12033527b#9cc5184a33a85c4fd4a16147f4514d69b317c36e"><strong>cooler/cli/cload.py</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -20,8 +20,8 @@ from ..create import (</td>

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python">    <span class="n" style="color: #333;">TabixAggregator</span><span class="p">,</span> <span class="n" style="color: #333;">HDF5Aggregator</span><span class="p">,</span> <span class="n" style="color: #333;">PairixAggregator</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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

</pre>

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<td class="new_line diff-line-num old" data-linenumber="23" 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="LC23" class="line" lang="python"><span class="n" style="color: #333;">_pandas_<span class="idiff left">major_</span>version</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff">int</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">__version__</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 class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">])</span></span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">_pandas_<span class="idiff left right">major_</span>version</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"><span class="n" style="color: #333;">_pandas_version</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;">__version__</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="new_line diff-line-num new" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">int</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">_pandas_version</span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">])</span></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="LC25" class="line" lang="python">    <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pandas.io.common</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">get_handle</span></span>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"></span>

</pre>

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

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

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="140" style="width: 35px; color: rgba(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="140" style="width: 35px; color: rgba(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">@@ -140,7 +140,7 @@ def hiclib(bins, pairs_path, cool_path, metadata, assembly, chunksize):</td>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python"></span>

</pre>

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

</pre>

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="143" 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="new_line diff-line-num old" data-linenumber="143" 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="LC143" class="line" lang="python"><span class="s" style="color: #d14;">    hiclib on BitBucket: <https://<span class="idiff left">b</span>it<span class="idiff right">bucket.org</span>/mirnylab/hiclib>.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"><span class="s" style="color: #d14;">    hiclib on BitBucket: <https://<span class="idiff left">g</span>it<span class="idiff">hub.com</span>/mirnylab/hiclib<span class="idiff right">-legacy</span>>.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="python"></span>

</pre>

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

</pre>

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<td class="old_line diff-line-num" data-linenumber="146" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="146" style="width: 35px; color: rgba(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="LC146" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="542" style="width: 35px; color: rgba(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="542" style="width: 35px; color: rgba(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">@@ -542,13 +542,18 @@ def pairs(bins, pairs_path, cool_path, metadata, assembly, chunksize,</td>

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<pre style="margin: 0;"> <span id="LC542" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pairs_path</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'-'</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC543" class="line" lang="python">        <span class="n" style="color: #333;">f_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stdin</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC544" class="line" lang="python">        <span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">f_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_header</span><span class="p">(</span><span class="n" style="color: #333;">f_in</span><span class="p">)</span></span>

</pre>

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545

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<pre style="margin: 0;">-<span id="LC545" class="line" lang="python">    <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">_pandas_major_version</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre>

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546

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<td class="new_line diff-line-num old" data-linenumber="545" 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="LC546" class="line" lang="python">        <span class="n" style="color: #333;">f_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_handle</span><span class="p">(</span><span class="n" style="color: #333;">pairs_path</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'r'</span><span class="p">,</span> <span class="n" style="color: #333;">compression</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'infer'</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="new_line diff-line-num new" data-linenumber="545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

545

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<pre style="margin: 0;">+<span id="LC545" class="line" lang="python">    <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">_pandas_version</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

546

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<pre style="margin: 0;">+<span id="LC546" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">_pandas_version</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

547

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<pre style="margin: 0;">+<span id="LC547" class="line" lang="python">            <span class="n" style="color: #333;">f_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_handle</span><span class="p">(</span><span class="n" style="color: #333;">pairs_path</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'r'</span><span class="p">,</span> <span class="n" style="color: #333;">compression</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'infer'</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

</pre>

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548

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<pre style="margin: 0;">+<span id="LC548" 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="new_line diff-line-num new" data-linenumber="549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

549

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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="LC549" class="line" lang="python">            <span class="n" style="color: #333;">f_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_handle</span><span class="p">(</span><span class="n" style="color: #333;">pairs_path</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'r'</span><span class="p">,</span> <span class="n" style="color: #333;">compression</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'infer'</span><span class="p">).</span><span class="n" style="color: #333;">handle</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

550

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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="LC550" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

551

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<pre style="margin: 0;"> <span id="LC551" class="line" lang="python">        <span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">f_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_header</span><span class="p">(</span><span class="n" style="color: #333;">f_in</span><span class="p">)</span></span>

</pre>

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548

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<td class="new_line diff-line-num" data-linenumber="552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

552

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

<pre style="margin: 0;"> <span id="LC552" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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549

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<td class="new_line diff-line-num" data-linenumber="553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

553

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

<pre style="margin: 0;"> <span id="LC553" class="line" lang="python">        <span class="n" style="color: #333;">f_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pairs_path</span></span>

</pre>

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550

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<td class="new_line diff-line-num" data-linenumber="554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

554

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

<pre style="margin: 0;"> <span id="LC554" class="line" lang="python">        <span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">'comment'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'#'</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

551

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<td class="new_line diff-line-num" data-linenumber="555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

555

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

<pre style="margin: 0;"> <span id="LC555" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="552" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

556

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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="LC556" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

552

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<td class="new_line diff-line-num" data-linenumber="557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

557

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

<pre style="margin: 0;"> <span id="LC557" class="line" lang="python">    <span class="n" style="color: #333;">reader</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>

</pre>

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553

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<td class="new_line diff-line-num" data-linenumber="558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

558

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

<pre style="margin: 0;"> <span id="LC558" class="line" lang="python">        <span class="n" style="color: #333;">f_in</span><span class="p">,</span></span>

</pre>

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554

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<pre style="margin: 0;"> <span id="LC559" 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>

</pre>

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<br>

</li>

<li id="f05ea5db033e4268fb5e4037c337ce8a1e2cbdd5">

<a href="https://salsa.debian.org/med-team/python-cooler/-/commit/a2344c24d429cd4599d95cf78c3d6ac12033527b#f05ea5db033e4268fb5e4037c337ce8a1e2cbdd5"><strong>cooler/cli/zoomify.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="88" style="width: 35px; color: rgba(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="88" style="width: 35px; color: rgba(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">@@ -88,7 +88,9 @@ def invoke_balance(args, resolutions, outfile):</td>

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<td class="new_line diff-line-num" data-linenumber="88" style="width: 35px; color: rgba(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="LC88" class="line" lang="python"><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="89" style="width: 35px; color: rgba(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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89

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">click</span><span class="p">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="90" style="width: 35px; color: rgba(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="LC90" class="line" lang="python">    <span class="s" style="color: #d14;">"--balance-args"</span><span class="p">,</span></span>

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<td class="old_line diff-line-num old" data-linenumber="91" 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="new_line diff-line-num old" data-linenumber="91" 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="LC91" class="line" lang="python">    <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Additional arguments to pass to cooler balance"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="91" style="width: 35px; color: rgba(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="LC91" class="line" lang="python">    <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Additional arguments to pass to cooler balance. To deal with space ambiguity, "</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(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="LC92" class="line" lang="python">    <span class="s" style="color: #d14;">"use quotes to pass multiple arguments, e.g. --balance-args '--nproc 8 --ignore-diags 3' "</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="93" style="width: 35px; color: rgba(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="LC93" class="line" lang="python">    <span class="s" style="color: #d14;">"Note that nproc for balancing must be specified independently of zoomify arguments."</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

94

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="python">    <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="93" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

95

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

</pre>

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<td class="old_line diff-line-num" data-linenumber="94" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="96" style="width: 35px; color: rgba(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="LC96" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">click</span><span class="p">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span></span>

</pre>

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<br>

</li>

<li id="1d9095383846c54cd7065e43ebaa45b9d7b1a27d">

<a href="https://salsa.debian.org/med-team/python-cooler/-/commit/a2344c24d429cd4599d95cf78c3d6ac12033527b#1d9095383846c54cd7065e43ebaa45b9d7b1a27d"><strong>cooler/create/__init__.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="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">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,7 +5,7 @@ MAGIC = u"HDF5::Cooler"</td>

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5

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">MAGIC_SCOOL</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">u</span><span class="s" style="color: #d14;">"HDF5::SCOOL"</span></span>

</pre>

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<td class="old_line diff-line-num" 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">

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

<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="n" style="color: #333;">MAGIC_MCOOL</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">u</span><span class="s" style="color: #d14;">"HDF5::MCOOL"</span></span>

</pre>

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<td class="old_line diff-line-num" 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">

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<td class="new_line diff-line-num" 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">

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

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

</pre>

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<td class="old_line diff-line-num old" data-linenumber="8" 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="new_line diff-line-num old" data-linenumber="8" 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="LC8" class="line" lang="python"><span class="n" style="color: #333;">URL</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">u</span><span class="s" style="color: #d14;">"https://github.com/<span class="idiff left right">mirnylab</span>/cooler"</span></span>

</pre>

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

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<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;">URL</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">u</span><span class="s" style="color: #d14;">"https://github.com/<span class="idiff left right">open2c</span>/cooler"</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="n" style="color: #333;">CHROM_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;">dtype</span><span class="p">(</span><span class="s" style="color: #d14;">"S"</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="n" style="color: #333;">CHROMID_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;">int32</span></span>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="n" style="color: #333;">CHROMSIZE_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;">int32</span></span>

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<br>

</li>

<li id="28e81f983d7f413af336348d329dc18e41725ea8">

<a href="https://salsa.debian.org/med-team/python-cooler/-/commit/a2344c24d429cd4599d95cf78c3d6ac12033527b#28e81f983d7f413af336348d329dc18e41725ea8"><strong>cooler/create/_ingest.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">@@ -127,7 +127,7 @@ def _sanitize_records(</td>

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<pre style="margin: 0;"> <span id="LC127" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;">any</span><span class="p">(</span><span class="n" style="color: #333;">is_neg</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python">            <span class="n" style="color: #333;">err</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chunk</span><span class="p">[</span><span class="n" style="color: #333;">is_neg</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">BadInputError</span><span class="p">(</span></span>

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<pre style="margin: 0;">-<span id="LC130" class="line" lang="python">                <span class="s" style="color: #d14;">"Found an anchor position with negative value<span class="idiff left right">:</span></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">{}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python">                <span class="s" style="color: #d14;">"Found an anchor position with negative value<span class="idiff left right">. Make sure your coordinates are 1-based or use the --zero-based option when loading. </span></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">{}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python">                    <span class="n" style="color: #333;">err</span><span class="p">.</span><span class="n" style="color: #333;">head</span><span class="p">().</span><span class="n" style="color: #333;">to_csv</span><span class="p">(</span><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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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python">                <span class="p">)</span></span>

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -144,21 +144,27 @@ def _sanitize_records(</td>

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="python">            <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="python"></span>

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<td class="old_line diff-line-num" data-linenumber="146" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="146" style="width: 35px; color: rgba(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="LC146" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Handle lower triangle records</span></span>

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<td class="old_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Note: Swap assignment works as desired because boolean masks create copies</span></span>

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<td class="old_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># See https://github.com/open2c/cooler/pull/229</span></span>

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">tril_action</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="python">        <span class="n" style="color: #333;">is_tril</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">chrom1_ids</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">chrom2_ids</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="python">            <span class="p">(</span><span class="n" style="color: #333;">chrom1_ids</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">chrom2_ids</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">anchor1</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">anchor2</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC152" class="line" lang="python">        <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;">any</span><span class="p">(</span><span class="n" style="color: #333;">is_tril</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">tril_action</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"reflect"</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC153" class="line" lang="python">                <span class="n" style="color: #333;">chrom1_ids</span><span class="p">[</span><span class="n" style="color: #333;">is_tril</span><span class="p">],</span> <span class="n" style="color: #333;">chrom2_ids</span><span class="p">[</span><span class="n" style="color: #333;">is_tril</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>

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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python">                <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;">chrom1_ids</span><span class="p">[</span><span class="n" style="color: #333;">is_tril</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;">chrom2_ids</span><span class="p">[</span><span class="n" style="color: #333;">is_tril</span><span class="p">]</span></span>

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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python">                <span class="p">)</span> <span class="o" style="font-weight: 600;">=</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;">chrom2_ids</span><span class="p">[</span><span class="n" style="color: #333;">is_tril</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;">chrom1_ids</span><span class="p">[</span><span class="n" style="color: #333;">is_tril</span><span class="p">],</span></span>

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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python">                <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python">                <span class="n" style="color: #333;">anchor1</span><span class="p">[</span><span class="n" style="color: #333;">is_tril</span><span class="p">],</span> <span class="n" style="color: #333;">anchor2</span><span class="p">[</span><span class="n" style="color: #333;">is_tril</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">anchor2</span><span class="p">[</span><span class="n" style="color: #333;">is_tril</span><span class="p">],</span> <span class="n" style="color: #333;">anchor1</span><span class="p">[</span><span class="n" style="color: #333;">is_tril</span><span class="p">]</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="163" style="width: 35px; color: rgba(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="LC163" class="line" lang="python">                <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">field</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sided_fields</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="159" 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="new_line diff-line-num old" data-linenumber="164" 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="LC159" class="line" lang="python">                    <span class="n" style="color: #333;">chunk</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">is_tril</span><span class="p">,</span> <span class="n" style="color: #333;">field</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffixes</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]],</span> <span class="n" style="color: #333;">chunk</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC160" class="line" lang="python">                        <span class="n" style="color: #333;">is_tril</span><span class="p">,</span> <span class="n" style="color: #333;">field</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffixes</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="LC161" class="line" lang="python">                    <span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>

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

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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python">                        <span class="n" style="color: #333;">chunk</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">is_tril</span><span class="p">,</span> <span class="n" style="color: #333;">field</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffixes</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="LC166" class="line" lang="python">                        <span class="n" style="color: #333;">chunk</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">is_tril</span><span class="p">,</span> <span class="n" style="color: #333;">field</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffixes</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="LC167" class="line" lang="python">                    <span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="python">                        <span class="n" style="color: #333;">chunk</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">is_tril</span><span class="p">,</span> <span class="n" style="color: #333;">field</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffixes</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="LC169" class="line" lang="python">                        <span class="n" style="color: #333;">chunk</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">is_tril</span><span class="p">,</span> <span class="n" style="color: #333;">field</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffixes</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="LC170" class="line" lang="python">                    <span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="304" style="width: 35px; color: rgba(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">@@ -304,18 +310,24 @@ def _sanitize_pixels(</td>

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<pre style="margin: 0;"> <span id="LC310" class="line" lang="python">        <span class="n" style="color: #333;">chunk</span><span class="p">[</span><span class="n" style="color: #333;">bin1_field</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">1</span></span>

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<pre style="margin: 0;"> <span id="LC311" class="line" lang="python">        <span class="n" style="color: #333;">chunk</span><span class="p">[</span><span class="n" style="color: #333;">bin2_field</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">1</span></span>

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<pre style="margin: 0;"> <span id="LC312" class="line" lang="python"></span>

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<td class="new_line diff-line-num new" data-linenumber="313" style="width: 35px; color: rgba(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="LC313" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Note: Swap assignment works as desired because boolean masks create copies</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC314" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># See https://github.com/open2c/cooler/pull/229</span></span>

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<pre style="margin: 0;"> <span id="LC315" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">tril_action</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC316" class="line" lang="python">        <span class="n" style="color: #333;">is_tril</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chunk</span><span class="p">[</span><span class="n" style="color: #333;">bin1_field</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">chunk</span><span class="p">[</span><span class="n" style="color: #333;">bin2_field</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC317" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;">any</span><span class="p">(</span><span class="n" style="color: #333;">is_tril</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC318" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">tril_action</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"reflect"</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC311" class="line" lang="python">                <span class="n" style="color: #333;">chunk</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">is_tril</span><span class="p">,</span> <span class="n" style="color: #333;">bin1_field</span><span class="p">],</span> <span class="n" style="color: #333;">chunk</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">is_tril</span><span class="p">,</span> <span class="n" style="color: #333;">bin2_field</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>

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<pre style="margin: 0;">+<span id="LC319" class="line" lang="python">                <span class="p">(</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC320" class="line" lang="python">                    <span class="n" style="color: #333;">chunk</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">is_tril</span><span class="p">,</span> <span class="n" style="color: #333;">bin1_field</span><span class="p">],</span></span>

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<pre style="margin: 0;">+<span id="LC321" class="line" lang="python">                    <span class="n" style="color: #333;">chunk</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">is_tril</span><span class="p">,</span> <span class="n" style="color: #333;">bin2_field</span><span class="p">]</span></span>

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<pre style="margin: 0;">+<span id="LC322" class="line" lang="python">                <span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC323" class="line" lang="python">                    <span class="n" style="color: #333;">chunk</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">is_tril</span><span class="p">,</span> <span class="n" style="color: #333;">bin2_field</span><span class="p">],</span></span>

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<pre style="margin: 0;"> <span id="LC324" class="line" lang="python">                    <span class="n" style="color: #333;">chunk</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">is_tril</span><span class="p">,</span> <span class="n" style="color: #333;">bin1_field</span><span class="p">],</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC325" class="line" lang="python">                <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC326" class="line" lang="python">                <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">field</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sided_fields</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC316" class="line" lang="python">                    <span class="n" style="color: #333;">chunk</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">is_tril</span><span class="p">,</span> <span class="n" style="color: #333;">field</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffixes</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]],</span> <span class="n" style="color: #333;">chunk</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span></span>

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<pre style="margin: 0;">-<span id="LC317" class="line" lang="python">                        <span class="n" style="color: #333;">is_tril</span><span class="p">,</span> <span class="n" style="color: #333;">field</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffixes</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="LC318" class="line" lang="python">                    <span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC327" class="line" lang="python">                    <span class="p">(</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="328" style="width: 35px; color: rgba(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="LC328" class="line" lang="python">                        <span class="n" style="color: #333;">chunk</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">is_tril</span><span class="p">,</span> <span class="n" style="color: #333;">field</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffixes</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]],</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC329" class="line" lang="python">                        <span class="n" style="color: #333;">chunk</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">is_tril</span><span class="p">,</span> <span class="n" style="color: #333;">field</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffixes</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="new_line diff-line-num new" data-linenumber="330" style="width: 35px; color: rgba(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="LC330" class="line" lang="python">                    <span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC331" class="line" lang="python">                        <span class="n" style="color: #333;">chunk</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">is_tril</span><span class="p">,</span> <span class="n" style="color: #333;">field</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffixes</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="LC332" class="line" lang="python">                        <span class="n" style="color: #333;">chunk</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">is_tril</span><span class="p">,</span> <span class="n" style="color: #333;">field</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffixes</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="LC333" class="line" lang="python">                    <span class="p">)</span></span>

</pre>

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</li>

<li id="0a2c9b1333d679f975845fd110c2ffb59930996e">

<a href="https://salsa.debian.org/med-team/python-cooler/-/commit/a2344c24d429cd4599d95cf78c3d6ac12033527b#0a2c9b1333d679f975845fd110c2ffb59930996e"><strong>docs/cli.rst</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="115" style="width: 35px; color: rgba(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="115" style="width: 35px; color: rgba(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">@@ -115,7 +115,7 @@ Quick reference</td>

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="plaintext">    Show the version and exit.</span>

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<td class="old_line diff-line-num" data-linenumber="117" style="width: 35px; color: rgba(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="LC117" class="line" lang="plaintext"></span>

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<td class="old_line diff-line-num old" data-linenumber="118" 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="LC118" class="line" lang="plaintext">See the cooler_cli.ipynb Jupyter Notebook for specific examples on usage: (https://github.com/<span class="idiff left right">mirnylab</span>/cooler-binder).</span>

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">See the cooler_cli.ipynb Jupyter Notebook for specific examples on usage: (https://github.com/<span class="idiff left right">open2c</span>/cooler-binder).</span>

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="plaintext"></span>

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

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="plaintext"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="403" style="width: 35px; color: rgba(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="403" style="width: 35px; color: rgba(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">@@ -403,7 +403,7 @@ PAIRS_PATH : Path to contacts (i.e. read pairs) file.</td>

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<pre style="margin: 0;"> <span id="LC403" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC404" class="line" lang="plaintext">COOL_PATH : Output COOL file path or URI.</span>

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<pre style="margin: 0;"> <span id="LC405" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC406" class="line" lang="plaintext">hiclib on BitBucket: <https://<span class="idiff left">b</span>it<span class="idiff right">bucket.org</span>/mirnylab/hiclib>.</span>

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<pre style="margin: 0;">+<span id="LC406" class="line" lang="plaintext">hiclib on BitBucket: <https://<span class="idiff left">g</span>it<span class="idiff">hub.com</span>/mirnylab/hiclib<span class="idiff right">-legacy</span>>.</span>

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<pre style="margin: 0;"> <span id="LC407" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC408" class="line" lang="plaintext">.. program:: cooler cload hiclib</span>

</pre>

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<pre style="margin: 0;"> <span id="LC409" class="line" lang="plaintext">.. code-block:: shell</span>

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<br>

</li>

<li id="081652eafbed4cb98ffd30a1a25bedda4a5bdab5">

<a href="https://salsa.debian.org/med-team/python-cooler/-/commit/a2344c24d429cd4599d95cf78c3d6ac12033527b#081652eafbed4cb98ffd30a1a25bedda4a5bdab5"><strong>docs/datamodel.rst</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">@@ -4,7 +4,7 @@</td>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">What is cooler?</span>

</pre>

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<td class="old_line diff-line-num" 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">

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

</pre>

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<td class="old_line diff-line-num" 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">

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<td class="new_line diff-line-num" 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">

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

</pre>

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<td class="old_line diff-line-num 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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<td class="new_line diff-line-num 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="LC7" class="line" lang="plaintext">Cooler is the :ref:`implementation <schema>` of a data model for genomically-labeled sparse 2D arrays (matrices) with identical axes in HDF5. It is also the name of the `Python package <https://github.com/<span class="idiff left right">mirnylab</span>/cooler>`_ that supports the format.</span>

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

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

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Cooler is the :ref:`implementation <schema>` of a data model for genomically-labeled sparse 2D arrays (matrices) with identical axes in HDF5. It is also the name of the `Python package <https://github.com/<span class="idiff left right">open2c</span>/cooler>`_ that supports the format.</span>

</pre>

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<td class="old_line diff-line-num" 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">

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<td class="new_line diff-line-num" 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">

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

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">We use the term genomically-labeled array to refer to a data structure that assigns unique quantitative values to tuples of *genomic bins* obtained from an interval partition of a reference genome assembly. The tuples of bins make up the coordinates of the array’s elements. By omitting elements possessing zero or no value, the representation becomes sparse.</span>

</pre>

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<td class="new_line diff-line-num" 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="plaintext"></span>

</pre>

</td>

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<br>

</li>

<li id="d0153cac95479af9bfb99b746b633bc8255bb53a">

<a href="https://salsa.debian.org/med-team/python-cooler/-/commit/a2344c24d429cd4599d95cf78c3d6ac12033527b#d0153cac95479af9bfb99b746b633bc8255bb53a"><strong>docs/index.rst</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,7 +16,7 @@ The cooler package aims to facilitate:</td>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">* Scalable out-of-core operations on the data.</span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">* Data export and visualization.</span>

</pre>

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

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

</pre>

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<td class="old_line diff-line-num 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="LC19" class="line" lang="plaintext">Follow cooler development on `GitHub <https://github.com/<span class="idiff left right">mirnylab</span>/cooler>`_.</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">Follow cooler development on `GitHub <https://github.com/<span class="idiff left right">open2c</span>/cooler>`_.</span>

</pre>

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

</pre>

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<td class="old_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<td class="old_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(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="LC22" class="line" lang="plaintext">Contents:</span>

</pre>

</td>

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</table>

<br>

</li>

<li id="7212297a4768843c37d64be965c66153e2586c2c">

<a href="https://salsa.debian.org/med-team/python-cooler/-/commit/a2344c24d429cd4599d95cf78c3d6ac12033527b#7212297a4768843c37d64be965c66153e2586c2c"><strong>docs/make_cli_rst.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="426" style="width: 35px; color: rgba(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="426" style="width: 35px; color: rgba(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">@@ -426,7 +426,7 @@ Quick reference</td>

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<pre style="margin: 0;"> <span id="LC426" class="line" lang="python"></span>

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427

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

<pre style="margin: 0;"> <span id="LC427" class="line" lang="python"><span class="s" style="color: #d14;">    Show the version and exit.</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

428

</td>

<td class="new_line diff-line-num" data-linenumber="428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

428

</td>

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

<pre style="margin: 0;"> <span id="LC428" class="line" lang="python"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="429" 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">

429

</td>

<td class="new_line diff-line-num old" data-linenumber="429" 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="LC429" class="line" lang="python"><span class="s" style="color: #d14;">See the cooler_cli.ipynb Jupyter Notebook for specific examples on usage: (https://github.com/<span class="idiff left right">mirnylab</span>/cooler-binder).</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="430" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

429

</td>

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

<pre style="margin: 0;">+<span id="LC429" class="line" lang="python"><span class="s" style="color: #d14;">See the cooler_cli.ipynb Jupyter Notebook for specific examples on usage: (https://github.com/<span class="idiff left right">open2c</span>/cooler-binder).</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

430

</td>

<td class="new_line diff-line-num" data-linenumber="430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

430

</td>

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

<pre style="margin: 0;"> <span id="LC430" class="line" lang="python"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

431

</td>

<td class="new_line diff-line-num" data-linenumber="431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

431

</td>

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

<pre style="margin: 0;"> <span id="LC431" class="line" lang="python"><span class="s" style="color: #d14;">----</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

432

</td>

<td class="new_line diff-line-num" data-linenumber="432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

432

</td>

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

<pre style="margin: 0;"> <span id="LC432" class="line" lang="python"></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="45c312bd35bef86601c73bf3e04cfdf85f904c6c">

<a href="https://salsa.debian.org/med-team/python-cooler/-/commit/a2344c24d429cd4599d95cf78c3d6ac12033527b#45c312bd35bef86601c73bf3e04cfdf85f904c6c"><strong>docs/quickstart.rst</strong></a>

<hr>

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

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="35" style="width: 35px; color: rgba(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="35" style="width: 35px; color: rgba(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">@@ -35,7 +35,7 @@ Command line interface</td>

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

35

</td>

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

35

</td>

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

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

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

36

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<td class="new_line diff-line-num" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

36

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

<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">See:</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

37

</td>

<td class="new_line diff-line-num" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

37

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

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

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="38" 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">

38

</td>

<td class="new_line diff-line-num old" data-linenumber="38" 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="LC38" class="line" lang="plaintext">- Jupyter Notebook `CLI walkthrough <https://github.com/<span class="idiff left right">mirnylab</span>/cooler-binder/blob/master/cooler_cli.ipynb>`_.</span>

</pre>

</td>

</tr>

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

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

</td>

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

38

</td>

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

<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">- Jupyter Notebook `CLI walkthrough <https://github.com/<span class="idiff left right">open2c</span>/cooler-binder/blob/master/cooler_cli.ipynb>`_.</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

39

</td>

<td class="new_line diff-line-num" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

39

</td>

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

<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">- The `CLI Reference <http://cooler.readthedocs.io/en/latest/cli.html>`_ for more information.</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

40

</td>

<td class="new_line diff-line-num" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

40

</td>

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

<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

41

</td>

<td class="new_line diff-line-num" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

41

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

<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"></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="68" style="width: 35px; color: rgba(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="68" style="width: 35px; color: rgba(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">@@ -68,7 +68,7 @@ Python API</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

68

</td>

<td class="new_line diff-line-num" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

68

</td>

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

<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

69

</td>

<td class="new_line diff-line-num" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

69

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

<pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext">See: </span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

70

</td>

<td class="new_line diff-line-num" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

70

</td>

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

<pre style="margin: 0;"> <span id="LC70" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="71" 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">

71

</td>

<td class="new_line diff-line-num old" data-linenumber="71" 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="LC71" class="line" lang="plaintext">- Jupyter Notebook `API walkthrough <https://github.com/<span class="idiff left right">mirnylab</span>/cooler-binder/blob/master/cooler_api.ipynb>`_.</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="72" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="71" style="width: 35px; color: rgba(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="LC71" class="line" lang="plaintext">- Jupyter Notebook `API walkthrough <https://github.com/<span class="idiff left right">open2c</span>/cooler-binder/blob/master/cooler_api.ipynb>`_.</span>

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="plaintext">- The :ref:`api-reference` for more information.</span>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="plaintext">The :py:mod:`cooler` library provides a thin wrapper over the excellent NumPy-aware `h5py <http://docs.h5py.org/en/latest/>`_ Python interface to HDF5. It supports creation of cooler files and the following types of **range queries** on the data:</span>

</pre>

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<br>

</li>

<li id="8e2edce0d507e1297474f25c00cae94258db38d8">

<a href="https://salsa.debian.org/med-team/python-cooler/-/commit/a2344c24d429cd4599d95cf78c3d6ac12033527b#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>

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

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="s" style="color: #d14;">    Programming Language :: Python :: 3.6</span></span>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="s" style="color: #d14;">    Programming Language :: Python :: 3.7</span></span>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"><span class="s" style="color: #d14;">    Programming Language :: Python :: 3.8</span></span>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="s" style="color: #d14;">    Programming Language :: Python :: 3.9</span></span>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>

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

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

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="76" style="width: 35px; color: rgba(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">@@ -75,7 +76,7 @@ setup(</td>

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python">    <span class="n" style="color: #333;">long_description</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">get_long_description</span><span class="p">(),</span></span>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python">    <span class="n" style="color: #333;">long_description_content_type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'text/markdown'</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python">    <span class="n" style="color: #333;">keywords</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'genomics'</span><span class="p">,</span> <span class="s" style="color: #d14;">'bioinformatics'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Hi-C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'contact'</span><span class="p">,</span> <span class="s" style="color: #d14;">'matrix'</span><span class="p">,</span> <span class="s" style="color: #d14;">'format'</span><span class="p">,</span> <span class="s" style="color: #d14;">'hdf5'</span><span class="p">],</span></span>

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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python">    <span class="n" style="color: #333;">url</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'https://github.com/<span class="idiff left right">mirnylab</span>/cooler'</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="79" style="width: 35px; color: rgba(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="LC79" class="line" lang="python">    <span class="n" style="color: #333;">url</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'https://github.com/<span class="idiff left right">open2c</span>/cooler'</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python">    <span class="n" style="color: #333;">packages</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">find_packages</span><span class="p">(),</span></span>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python">    <span class="n" style="color: #333;">zip_safe</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python">    <span class="n" style="color: #333;">classifiers</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">strip</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="n" style="color: #333;">classifiers</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="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">s</span><span class="p">],</span></span>

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<br>

</li>

<li id="5d4a75be2ccc16e0c3ae308d893ff01dde3679d4">

<a href="https://salsa.debian.org/med-team/python-cooler/-/commit/a2344c24d429cd4599d95cf78c3d6ac12033527b#5d4a75be2ccc16e0c3ae308d893ff01dde3679d4"><strong>tests/test_create_sanitize.py</strong></a>

<hr>

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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">@@ -222,13 +222,15 @@ def test_sanitize_pixels():</td>

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<pre style="margin: 0;"> <span id="LC222" class="line" lang="python">    <span class="n" style="color: #333;">sanitize_pixels</span><span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC223" class="line" lang="python">        <span class="n" style="color: #333;">bins</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC224" class="line" lang="python">    <span class="p">)(</span><span class="n" style="color: #333;">chunk</span><span class="p">.</span><span class="n" style="color: #333;">copy</span><span class="p">())</span></span>

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<td class="old_line diff-line-num new" data-linenumber="225" style="width: 35px; color: rgba(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="LC225" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="226" style="width: 35px; color: rgba(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="LC226" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># one-based bin IDs</span></span>

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<pre style="margin: 0;"> <span id="LC227" class="line" lang="python">    <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sanitize_pixels</span><span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC228" class="line" lang="python">        <span class="n" style="color: #333;">bins</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="227" style="width: 35px; color: rgba(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="LC229" class="line" lang="python">        <span class="n" style="color: #333;">is_one_based</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC230" class="line" lang="python">    <span class="p">)(</span><span class="n" style="color: #333;">chunk</span><span class="p">.</span><span class="n" style="color: #333;">copy</span><span class="p">())</span></span>

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<pre style="margin: 0;"> <span id="LC231" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">[</span><span class="s" style="color: #d14;">'bin1_id'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">chunk</span><span class="p">[</span><span class="s" style="color: #d14;">'bin1_id'</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="nb" style="color: #0086b3;">all</span><span class="p">()</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="232" style="width: 35px; color: rgba(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="LC232" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="231" 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="new_line diff-line-num old" data-linenumber="233" 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="LC231" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># tril action</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="232" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="233" style="width: 35px; color: rgba(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="LC233" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># tril action<span class="idiff left right">: reflect (after swapping bin1, bin2)</span></span></span>

</pre>

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC234" class="line" lang="python">    <span class="n" style="color: #333;">tril_chunk</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chunk</span><span class="p">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span></span>

</pre>

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<td class="new_line diff-line-num" 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;">tril_chunk</span><span class="p">[</span><span class="s" style="color: #d14;">'bin2_id'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chunk</span><span class="p">[</span><span class="s" style="color: #d14;">'bin1_id'</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC236" class="line" lang="python">    <span class="n" style="color: #333;">tril_chunk</span><span class="p">[</span><span class="s" style="color: #d14;">'bin1_id'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chunk</span><span class="p">[</span><span class="s" style="color: #d14;">'bin2_id'</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC242" 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;">out</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">chunk</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC243" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">[</span><span class="s" style="color: #d14;">'foo2'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">chunk</span><span class="p">[</span><span class="s" style="color: #d14;">'foo1'</span><span class="p">]).</span><span class="nb" style="color: #0086b3;">all</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC244" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">[</span><span class="s" style="color: #d14;">'foo1'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">chunk</span><span class="p">[</span><span class="s" style="color: #d14;">'foo2'</span><span class="p">]).</span><span class="nb" style="color: #0086b3;">all</span><span class="p">()</span></span>

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<td class="new_line diff-line-num new" data-linenumber="245" style="width: 35px; color: rgba(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="LC245" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">[</span><span class="s" style="color: #d14;">'bin1_id'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">chunk</span><span class="p">[</span><span class="s" style="color: #d14;">'bin1_id'</span><span class="p">]).</span><span class="nb" style="color: #0086b3;">all</span><span class="p">()</span></span>

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<pre style="margin: 0;">+<span id="LC246" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">[</span><span class="s" style="color: #d14;">'bin2_id'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">chunk</span><span class="p">[</span><span class="s" style="color: #d14;">'bin2_id'</span><span class="p">]).</span><span class="nb" style="color: #0086b3;">all</span><span class="p">()</span></span>

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<td class="new_line diff-line-num new" data-linenumber="247" style="width: 35px; color: rgba(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="LC247" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># tril action: drop</span></span>

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<pre style="margin: 0;"> <span id="LC249" class="line" lang="python">    <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sanitize_pixels</span><span class="p">(</span></span>

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<td class="old_line diff-line-num" data-linenumber="244" style="width: 35px; color: rgba(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="LC250" class="line" lang="python">        <span class="n" style="color: #333;">bins</span><span class="p">,</span></span>

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<td class="new_line diff-line-num" data-linenumber="251" style="width: 35px; color: rgba(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="LC251" class="line" lang="python">        <span class="n" style="color: #333;">tril_action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"drop"</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC252" class="line" lang="python">    <span class="p">)(</span><span class="n" style="color: #333;">tril_chunk</span><span class="p">.</span><span class="n" style="color: #333;">copy</span><span class="p">())</span></span>

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<pre style="margin: 0;"> <span id="LC253" 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;">out</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span></span>

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<td class="new_line diff-line-num new" data-linenumber="254" style="width: 35px; color: rgba(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="LC254" class="line" lang="python"></span>

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<td class="new_line diff-line-num new" data-linenumber="255" style="width: 35px; color: rgba(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="LC255" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># tril action: raise</span></span>

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<pre style="margin: 0;"> <span id="LC256" class="line" lang="python">    <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">BadInputError</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC257" class="line" lang="python">        <span class="n" style="color: #333;">sanitize_pixels</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC258" class="line" lang="python">            <span class="n" style="color: #333;">bins</span><span class="p">,</span></span>

</pre>

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