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GitLab

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<h3>

Steffen Möller pushed to branch master

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/b86c3499dc65bb4cc5ac4e87e6beb3511b97baac">b86c3499</a></strong>

<div>

<span>by Steffen Moeller</span>

<i>at 2020-09-15T11:10:31+02:00</i>

</div>

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

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/f7cc8edb1d0f104eee8eb51ec049cb93dd8a5fc8">f7cc8edb</a></strong>

<div>

<span>by Steffen Moeller</span>

<i>at 2020-09-15T11:10:32+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.5.0</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/8d099abf84c77da89fb5ea28e671a9ce4d6dec22">8d099abf</a></strong>

<div>

<span>by Steffen Moeller</span>

<i>at 2020-09-15T11:10:52+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/3.5.0'

Update to upstream version '3.5.0'

with Debian dir 5b1b93377ff3690cbd53b8b10625fb219e9c16eb</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/5e04108a89c779961862b4f766793634c4125b39">5e04108a</a></strong>

<div>

<span>by Steffen Moeller</span>

<i>at 2020-09-15T11:10:52+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 13

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/778b045cad10a9ffb96c37157678a6b7126f69dc">778b045c</a></strong>

<div>

<span>by Steffen Moeller</span>

<i>at 2020-09-17T15:51:19+02:00</i>

</div>

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

</pre>

</li>

</ul>

<h4>17 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#3251d7a8143ce2e789f0468513df8f285f842c3a">

CHANGES.txt

</a>

</li>

<li class="file-stats">

<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

README.md

</a>

</li>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

debian/control

</a>

</li>

<li class="file-stats">

<a href="#5671f49ae181d5b005cecd24d93508d05a1ef49a">

debian/patches/tmp_inhibit_test_readFiltering.patch

</a>

</li>

<li class="file-stats">

<a href="#3ec39721c34812eb70f07264b96298182b24bca7">

deeptools/_version.py

</a>

</li>

<li class="file-stats">

<a href="#4c55801e0a0513d8510000d92ca993e58142fc7b">

deeptools/bamCompare.py

</a>

</li>

<li class="file-stats">

<a href="#f5d86efbc2efe8a8f8bf80196dde3a5a19f11fdf">

deeptools/computeGCBias.py

</a>

</li>

<li class="file-stats">

<a href="#419cb713bac82fae39f1b6238833e4b93c9a75fc">

deeptools/computeMatrixOperations.py

</a>

</li>

<li class="file-stats">

<a href="#d4edcba76f67fc7a4bdbed79f5fe9206b4a88652">

deeptools/correctGCBias.py

</a>

</li>

<li class="file-stats">

<a href="#d92843efb3711927a1683755b7c9df524fc9274d">

deeptools/parserCommon.py

</a>

</li>

<li class="file-stats">

<a href="#e6f336c84329d2021242809e76ed32e6ed05fecc">

deeptools/plotHeatmap.py

</a>

</li>

<li class="file-stats">

<a href="#933931be8d4eb6bef5ca9c328d98370ed0c3370a">

deeptools/plotProfile.py

</a>

</li>

<li class="file-stats">

<a href="#b509e8bc4a8e48a682d63505a1080b6033a0803f">

deeptools/test/test_readFiltering.py

</a>

</li>

<li class="file-stats">

<a href="#abc059e39dfccf4038fabfb18bfb7b5121e4e2e4">

galaxy/wrapper/computeMatrixOperations.xml

</a>

</li>

<li class="file-stats">

<a href="#d2de9c6869fd65911899bace5f34a175e96efb2a">

galaxy/wrapper/deepTools_macros.xml

</a>

</li>

<li class="file-stats">

<a href="#84b200ead4096f88da1811d06b79ecc1b09fcadd">

galaxy/wrapper/plotHeatmap.xml

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="3251d7a8143ce2e789f0468513df8f285f842c3a">

<a href="https://salsa.debian.org/med-team/python-deeptools/-/compare/911dd5dc4fa12b9ee76878808b70bb1cd946aecc...778b045cad10a9ffb96c37157678a6b7126f69dc#3251d7a8143ce2e789f0468513df8f285f842c3a"><strong>CHANGES.txt</strong></a>

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

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

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">3.5.0</span>

</pre>

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

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

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

2

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

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

</pre>

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

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

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

3

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

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Fixed a small issue in computeGCBias (issue #969)</span>

</pre>

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</tr>

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

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

</td>

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

4

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

<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Added dataRange to computeMatricOperation to return min,max,median and 10th and 90th percentile.</span>

</pre>

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

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

</td>

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

5

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

<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Fixed a small typo in bamCompare. (issue #966)</span>

</pre>

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

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

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

6

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<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="plaintext"> * Save the output matrix of the plotheatmap in a format to be compatible with running plotheatmap on it again.(issue #953)</span>

</pre>

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

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

</td>

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

7

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

<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Different colors can now be set by user for plotProfile --plotType heatmap (issue #956)</span>

</pre>

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

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

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

8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Added the `auto` option to the zMin and zMax of plotHeatmap. (issue #908)</span>

</pre>

</td>

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

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

</td>

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

9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * Added `--sortUsingSamples` and `--clusterUsingSamples` to the plotHeatmap galaxy wrapper. (issue #976)</span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

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<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="plaintext"></span>

</pre>

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

1

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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">3.4.3</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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

13

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

<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> * Changed iteritems() in estimateEscaleFactor to its python3 compatible items().</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

<a href="https://salsa.debian.org/med-team/python-deeptools/-/compare/911dd5dc4fa12b9ee76878808b70bb1cd946aecc...778b045cad10a9ffb96c37157678a6b7126f69dc#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>

<hr>

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1

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

1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># deepTools</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC2" 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/deeptools/deepTools.svg?branch=master</span><span class="p">)</span>](https://travis-ci.org/deeptools/deepTools) <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/deeptools/badge/</span><span class="p">)</span>](http://deeptools.readthedocs.org/) <span class="p">[</span><span class="nv" style="color: #008080;">![PyPI Version</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/pypi/v/deeptools.svg?style=plastic</span><span class="p">)</span>](https://pypi.org/project/deepTools/) </span>

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" 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://dev.azure.com/dpryan79/dpryan79/_apis/build/status/deeptools.deepTools?branchName=master</span><span class="p">)</span>](https://dev.azure.com/dpryan79/dpryan79/_build/latest?definitionId=1&branchName=master)</span>

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" 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/deeptools/badge/</span><span class="p">)</span>](http://deeptools.readthedocs.org/) <span class="p">[</span><span class="nv" style="color: #008080;">![PyPI Version</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/pypi/v/deeptools.svg?style=plastic</span><span class="p">)</span>](https://pypi.org/project/deepTools/) </span>

</pre>

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4

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<pre style="margin: 0;"> <span id="LC4" 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</span><span class="p">)</span>](http://bioconda.github.io/recipes/deeptools/README.html)</span>

</pre>

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4

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

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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## User-friendly tools for exploring deep-sequencing data</span></span>

</pre>

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</table>

<br>

</li>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/python-deeptools/-/compare/911dd5dc4fa12b9ee76878808b70bb1cd946aecc...778b045cad10a9ffb96c37157678a6b7126f69dc#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

<hr>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python-deeptools (3.5.0-1) unstable; urgency=medium</span>

</pre>

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

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2

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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="LC2" class="line" lang="plaintext"></span>

</pre>

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

</pre>

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

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">  * debhelper-compat 13 (routine-update)</span>

</pre>

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

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5

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

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org>  Tue, 15 Sep 2020 11:10:31 +0200</span>

</pre>

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

</pre>

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1

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8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">python-deeptools (3.4.3-1) unstable; urgency=medium</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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9

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

</pre>

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3

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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">  * New upstream version</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/python-deeptools/-/compare/911dd5dc4fa12b9ee76878808b70bb1cd946aecc...778b045cad10a9ffb96c37157678a6b7126f69dc#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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="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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>

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3

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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Steffen Moeller <moeller@debian.org></span>

</pre>

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4

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4

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

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5

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5

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

</pre>

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6

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">2</span>),</span>

</pre>

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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">3</span>),</span>

</pre>

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7

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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<td class="diff-line-num new_line" data-linenumber="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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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">               python3-all,</span>

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9

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

9

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">               python3-setuptools,</span>

</pre>

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<br>

</li>

<li id="5671f49ae181d5b005cecd24d93508d05a1ef49a">

<a href="https://salsa.debian.org/med-team/python-deeptools/-/compare/911dd5dc4fa12b9ee76878808b70bb1cd946aecc...778b045cad10a9ffb96c37157678a6b7126f69dc#5671f49ae181d5b005cecd24d93508d05a1ef49a"><strong>debian/patches/tmp_inhibit_test_readFiltering.patch</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,17 +3,19 @@ Last-Update: 2020-01-15 00:46:37 +0100</td>

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3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Description: Not running one test that complains about a file not having</span></span>

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4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"> been closed: https://github.com/deeptools/deepTools/issues/903</span>

</pre>

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5

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

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff">--- a/deeptools/test/test_readFiltering.py</span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/deeptools/test/test_readFiltering.py</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">Index: python-deeptools/deeptools/test/test_readFiltering.py</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-deeptools.orig/deeptools/test/test_readFiltering.py</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-deeptools/deeptools/test/test_readFiltering.py</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<td class="diff-line-num new_line" data-linenumber="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="diff"><span class="p">@@ -4,6 +4,7 @@</span> import deeptools.alignmentSieve as sieve</span>

</pre>

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9

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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> import os.path</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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<td class="diff-line-num new_line" data-linenumber="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="diff"> from os import unlink</span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> import hashlib</span>

</pre>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import unittest</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

15

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

</pre>

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

13

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

16

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

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

</pre>

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<td class="diff-line-num old old_line" data-linenumber="14" 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">

14

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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC14" class="line" lang="diff"> ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"</span>

</pre>

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

15

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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC15" class="line" lang="diff"> BAMFILE_FILTER = ROOT + "test_filtering.bam"</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="16" 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">

16

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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC16" class="line" lang="diff"><span class="p">@@ -52,7 +53,7 @@</span> def test_estimate_read_filtering_params(</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

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

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

18

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<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="diff"><span class="p">@@ -54,7 +55,7 @@</span> def test_estimate_read_filtering_params(</span>

</pre>

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

17

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

19

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff">     assert_equal(resp, expected)</span>

</pre>

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

18

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<td class="diff-line-num new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff">     unlink(outfile)</span>

</pre>

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

19

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

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="3ec39721c34812eb70f07264b96298182b24bca7">

<a href="https://salsa.debian.org/med-team/python-deeptools/-/compare/911dd5dc4fa12b9ee76878808b70bb1cd946aecc...778b045cad10a9ffb96c37157678a6b7126f69dc#3ec39721c34812eb70f07264b96298182b24bca7"><strong>deeptools/_version.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="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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,4 +2,4 @@</td>

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2

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2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># This file is originally generated from Git information by running 'setup.py</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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

<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># version'. Distribution tarballs contain a pre-generated copy of this file.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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

</pre>

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

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<pre style="margin: 0;">-<span id="LC5" 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;">'3.<span class="idiff left right">4.3</span>'</span></span></pre>

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

</td>

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

5

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

<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'3.<span class="idiff left right">5.0</span>'</span></span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="4c55801e0a0513d8510000d92ca993e58142fc7b">

<a href="https://salsa.debian.org/med-team/python-deeptools/-/compare/911dd5dc4fa12b9ee76878808b70bb1cd946aecc...778b045cad10a9ffb96c37157678a6b7126f69dc#4c55801e0a0513d8510000d92ca993e58142fc7b"><strong>deeptools/bamCompare.py</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="254" style="width: 35px; color: rgba(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="254" style="width: 35px; color: rgba(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">@@ -254,7 +254,7 @@ def main(args=None):</td>

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254

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<pre style="margin: 0;"> <span id="LC254" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">normalizeUsing</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'None'</span><span class="p">:</span></span>

</pre>

</td>

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

255

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255

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<pre style="margin: 0;"> <span id="LC255" class="line" lang="python">        <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">normalizeUsing</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span>  <span class="c1" style="color: #998; font-style: italic;"># For the sake of sanity</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC256" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">scaleFactorsMethod</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'None'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">normalizeUsing</span><span class="p">:</span></span>

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<td class="diff-line-num new_line old" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC257" class="line" lang="python">        <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="s" style="color: #d14;">"`--normalizeUsing {}` is only valid if you also use `--scaleFactorMethod None`! To prevent erroneous output, I will quit now.</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 class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">normalizeUsing</span><span class="p">))</span></span>

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<td class="diff-line-num new old_line" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="257" style="width: 35px; color: rgba(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="LC257" class="line" lang="python">        <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="s" style="color: #d14;">"`--normalizeUsing {}` is only valid if you also use `--scaleFactor<span class="idiff left right">s</span>Method None`! To prevent erroneous output, I will quit now.</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 class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">normalizeUsing</span><span class="p">))</span></span>

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

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<pre style="margin: 0;"> <span id="LC259" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Get mapping statistics</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC260" class="line" lang="python">    <span class="n" style="color: #333;">bam1</span><span class="p">,</span> <span class="n" style="color: #333;">mapped1</span><span class="p">,</span> <span class="n" style="color: #333;">unmapped1</span><span class="p">,</span> <span class="n" style="color: #333;">stats1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bamHandler</span><span class="p">.</span><span class="n" style="color: #333;">openBam</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bamfile1</span><span class="p">,</span> <span class="n" style="color: #333;">returnStats</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">nThreads</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">numberOfProcessors</span><span class="p">)</span></span>

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<br>

</li>

<li id="f5d86efbc2efe8a8f8bf80196dde3a5a19f11fdf">

<a href="https://salsa.debian.org/med-team/python-deeptools/-/compare/911dd5dc4fa12b9ee76878808b70bb1cd946aecc...778b045cad10a9ffb96c37157678a6b7126f69dc#f5d86efbc2efe8a8f8bf80196dde3a5a19f11fdf"><strong>deeptools/computeGCBias.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="604" style="width: 35px; color: rgba(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="604" style="width: 35px; color: rgba(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">@@ -604,7 +604,7 @@ def plotGCbias(file_name, frequencies, reads_per_gc, region_size, image_format=N</td>

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<pre style="margin: 0;"> <span id="LC604" class="line" lang="python">    <span class="n" style="color: #333;">plt</span><span class="p">.</span><span class="n" style="color: #333;">setp</span><span class="p">(</span><span class="n" style="color: #333;">bp</span><span class="p">[</span><span class="s" style="color: #d14;">'whiskers'</span><span class="p">],</span> <span class="n" style="color: #333;">color</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'black'</span><span class="p">,</span> <span class="n" style="color: #333;">linestyle</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'dashed'</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC605" class="line" lang="python">    <span class="n" style="color: #333;">plt</span><span class="p">.</span><span class="n" style="color: #333;">setp</span><span class="p">(</span><span class="n" style="color: #333;">bp</span><span class="p">[</span><span class="s" style="color: #d14;">'fliers'</span><span class="p">],</span> <span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'None'</span><span class="p">)</span></span>

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<td class="diff-line-num new_line" data-linenumber="606" style="width: 35px; color: rgba(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="LC606" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># get the whisker that spands the most</span></span>

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<td class="diff-line-num new_line old" data-linenumber="607" 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="LC607" class="line" lang="python">    <span class="n" style="color: #333;">y_max</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">([</span><span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">get_data</span><span class="p">()[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">bp</span><span class="p">[</span><span class="s" style="color: #d14;">'whiskers'</span><span class="p">]])</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="607" style="width: 35px; color: rgba(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="LC607" class="line" lang="python">    <span class="n" style="color: #333;">y_max</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">nan</span>max</span><span class="p">([</span><span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">get_data</span><span class="p">()[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">bp</span><span class="p">[</span><span class="s" style="color: #d14;">'whiskers'</span><span class="p">]])</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="608" style="width: 35px; color: rgba(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="LC608" class="line" lang="python">    <span class="n" style="color: #333;">ax1</span><span class="p">.</span><span class="n" style="color: #333;">set_ylim</span><span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">y_max</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">0.05</span><span class="p">),</span> <span class="n" style="color: #333;">y_max</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">1.05</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="609" style="width: 35px; color: rgba(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="LC609" class="line" lang="python">    <span class="n" style="color: #333;">ax1</span><span class="p">.</span><span class="n" style="color: #333;">set_ylabel</span><span class="p">(</span><span class="s" style="color: #d14;">'Number of reads'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC610" class="line" lang="python">    <span class="n" style="color: #333;">ax1</span><span class="p">.</span><span class="n" style="color: #333;">set_xlabel</span><span class="p">(</span><span class="s" style="color: #d14;">'GC fraction'</span><span class="p">)</span></span>

</pre>

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<br>

</li>

<li id="419cb713bac82fae39f1b6238833e4b93c9a75fc">

<a href="https://salsa.debian.org/med-team/python-deeptools/-/compare/911dd5dc4fa12b9ee76878808b70bb1cd946aecc...778b045cad10a9ffb96c37157678a6b7126f69dc#419cb713bac82fae39f1b6238833e4b93c9a75fc"><strong>deeptools/computeMatrixOperations.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">@@ -46,6 +46,9 @@ or</td>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"><span class="s" style="color: #d14;">or</span></span>

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"><span class="s" style="color: #d14;">  computeMatrixOperations sort -h</span></span>

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

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"><span class="s" style="color: #d14;">or</span></span>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"><span class="s" style="color: #d14;">  computeMatrixOperations dataRange -h</span></span>

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

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"><span class="s" style="color: #d14;">"""</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python">        <span class="n" style="color: #333;">epilog</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'example usages:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python">               <span class="s" style="color: #d14;">'computeMatrixOperations subset -m input.mat.gz -o output.mat.gz --group "group 1" "group 2" --samples "sample 3" "sample 10"</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">'</span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<pre style="margin: 0;"> <span id="LC129" 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;">'Sort a matrix file to correspond to the order of entries in the desired input file(s). The groups of regions designated by the files must be present in the order found in the output of computeMatrix (otherwise, use the subset command first). Note that this subcommand can also be used to remove unwanted regions, since regions not present in the input file(s) will be omitted from the output.'</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python">        <span class="n" style="color: #333;">usage</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Example usage:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">  computeMatrixOperations sort -m input.mat.gz -R regions1.bed regions2.bed regions3.gtf -o input.sorted.mat.gz</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># dataRange</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="129" style="width: 35px; color: rgba(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="LC133" class="line" lang="python">    <span class="n" style="color: #333;">subparsers</span><span class="p">.</span><span class="n" style="color: #333;">add_parser</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python">        <span class="s" style="color: #d14;">'dataRange'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="135" style="width: 35px; color: rgba(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="LC135" class="line" lang="python">        <span class="n" style="color: #333;">formatter_class</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">argparse</span><span class="p">.</span><span class="n" style="color: #333;">ArgumentDefaultsHelpFormatter</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python">        <span class="n" style="color: #333;">parents</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333;">infoArgs</span><span class="p">()],</span></span>

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<pre style="margin: 0;">+<span id="LC137" 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;">'Returns the min, max, median, 10th and 90th percentile of the matrix values per sample.'</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python">        <span class="n" style="color: #333;">usage</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Example usage:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">  computeMatrixOperations dataRange -m input.mat.gz</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python">    <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--version'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'version'</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC141" 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;">'%(prog)s {}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">__version__</span><span class="p">))</span></span>

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

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<pre style="margin: 0;"> <span id="LC311" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{0}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">sample</span><span class="p">))</span></span>

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

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

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<pre style="margin: 0;">+<span id="LC314" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">printDataRange</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC315" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;">+<span id="LC316" class="line" lang="python"><span class="s" style="color: #d14;">    Prints the min, max, median, 10th and 90th percentile of the matrix values per sample.</span></span>

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<pre style="margin: 0;">+<span id="LC317" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<pre style="margin: 0;">+<span id="LC318" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Samples</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Min</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Max</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Median</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">10th</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">90th"</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC319" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">sample</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">.</span><span class="n" style="color: #333;">matrix</span><span class="p">.</span><span class="n" style="color: #333;">sample_labels</span><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;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matrix</span><span class="p">.</span><span class="n" style="color: #333;">matrix</span><span class="p">.</span><span class="n" style="color: #333;">sample_boundaries</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC321" class="line" lang="python">        <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matrix</span><span class="p">.</span><span class="n" style="color: #333;">matrix</span><span class="p">.</span><span class="n" style="color: #333;">sample_boundaries</span><span class="p">[</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="322" style="width: 35px; color: rgba(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="LC322" class="line" lang="python">        <span class="n" style="color: #333;">sample_matrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matrix</span><span class="p">.</span><span class="n" style="color: #333;">matrix</span><span class="p">.</span><span class="n" style="color: #333;">matrix</span><span class="p">[...,</span> <span class="n" style="color: #333;">start</span><span class="p">:</span><span class="n" style="color: #333;">end</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="323" style="width: 35px; color: rgba(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="LC323" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{1}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{2}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{3}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{4}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{5}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">amin</span><span class="p">(</span><span class="n" style="color: #333;">sample_matrix</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

324

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<pre style="margin: 0;">+<span id="LC324" class="line" lang="python">                                                    <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">amax</span><span class="p">(</span><span class="n" style="color: #333;">sample_matrix</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

325

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<pre style="margin: 0;">+<span id="LC325" class="line" lang="python">                                                    <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">ma</span><span class="p">.</span><span class="n" style="color: #333;">median</span><span class="p">(</span><span class="n" style="color: #333;">sample_matrix</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

326

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<pre style="margin: 0;">+<span id="LC326" class="line" lang="python">                                                    <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">percentile</span><span class="p">(</span><span class="n" style="color: #333;">sample_matrix</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

327

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<pre style="margin: 0;">+<span id="LC327" class="line" lang="python">                                                    <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">percentile</span><span class="p">(</span><span class="n" style="color: #333;">sample_matrix</span><span class="p">,</span> <span class="mi" style="color: #099;">90</span><span class="p">)))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

328

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="329" style="width: 35px; color: rgba(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="LC329" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="330" style="width: 35px; color: rgba(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="LC330" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">relabelMatrix</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="331" style="width: 35px; color: rgba(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="LC331" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="332" style="width: 35px; color: rgba(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="LC332" class="line" lang="python"><span class="s" style="color: #d14;">    Relabel the samples and groups in a matrix</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="771" style="width: 35px; color: rgba(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="798" style="width: 35px; color: rgba(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">@@ -771,6 +798,8 @@ def main(args=None):</td>

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<td class="diff-line-num new_line" data-linenumber="798" style="width: 35px; color: rgba(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="LC798" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="799" style="width: 35px; color: rgba(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="LC799" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">command</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'info'</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="800" style="width: 35px; color: rgba(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="LC800" class="line" lang="python">        <span class="n" style="color: #333;">printInfo</span><span class="p">(</span><span class="n" style="color: #333;">hm</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="774" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

801

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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="LC801" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">command</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'dataRange'</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="774" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

802

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<pre style="margin: 0;">+<span id="LC802" class="line" lang="python">        <span class="n" style="color: #333;">printDataRange</span><span class="p">(</span><span class="n" style="color: #333;">hm</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC803" class="line" lang="python">    <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">command</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'subset'</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC804" class="line" lang="python">        <span class="n" style="color: #333;">sIdx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getSampleBounds</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">hm</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="805" style="width: 35px; color: rgba(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="LC805" class="line" lang="python">        <span class="n" style="color: #333;">gIdx</span><span class="p">,</span> <span class="n" style="color: #333;">gBounds</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getGroupBounds</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">hm</span><span class="p">)</span></span>

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<br>

</li>

<li id="d4edcba76f67fc7a4bdbed79f5fe9206b4a88652">

<a href="https://salsa.debian.org/med-team/python-deeptools/-/compare/911dd5dc4fa12b9ee76878808b70bb1cd946aecc...778b045cad10a9ffb96c37157678a6b7126f69dc#d4edcba76f67fc7a4bdbed79f5fe9206b4a88652"><strong>deeptools/correctGCBias.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="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -239,10 +239,10 @@ def writeCorrected_worker(chrNameBam, chrNameBit, start, end, step):</td>

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="python">    <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC240" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">debug</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC241" class="line" lang="python">            <span class="n" style="color: #333;">endTime</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">time</span><span class="p">.</span><span class="n" style="color: #333;">time</span><span class="p">()</span></span>

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<pre style="margin: 0;">-<span id="LC242" class="line" lang="python">            <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"{}, processing {} ({:.1f} per sec) "</span><span class="p"><span class="idiff left right">)</span></span></span>

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<pre style="margin: 0;">-<span id="LC243" class="line" lang="python">            <span class="s" style="color: #d14;">"reads @ {}:{}-{}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">multiprocessing</span><span class="p">.</span><span class="n" style="color: #333;">current_process</span><span class="p">().</span><span class="n" style="color: #333;">name</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC244" class="line" lang="python">                                      <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">endTime</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">startTime</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC245" class="line" lang="python">                                      <span class="n" style="color: #333;"><span class="idiff left">chrNameBit</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">start</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">end</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

242

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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python">            <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"{}, processing {} ({:.1f} per sec) "</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="243" style="width: 35px; color: rgba(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="LC243" class="line" lang="python">            <span class="idiff left right">      </span><span class="s" style="color: #d14;">"reads @ {}:{}-{}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">multiprocessing</span><span class="p">.</span><span class="n" style="color: #333;">current_process</span><span class="p">().</span><span class="n" style="color: #333;">name</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="244" style="width: 35px; color: rgba(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="LC244" class="line" lang="python">                                      <span class="idiff left right">      </span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">endTime</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">startTime</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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="idiff left">      </span><span class="n" style="color: #333;"><span class="idiff">chrNameBit</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">start</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">end</span></span><span class="p"><span class="idiff right">)</span>)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC246" class="line" lang="python">    <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">NameError</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC247" class="line" lang="python">        <span class="k" style="font-weight: 600;">pass</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC248" class="line" lang="python"></span>

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<li id="d92843efb3711927a1683755b7c9df524fc9274d">

<a href="https://salsa.debian.org/med-team/python-deeptools/-/compare/911dd5dc4fa12b9ee76878808b70bb1cd946aecc...778b045cad10a9ffb96c37157678a6b7126f69dc#d92843efb3711927a1683755b7c9df524fc9274d"><strong>deeptools/parserCommon.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">@@ -358,11 +358,10 @@ def numberOfProcessors(string):</td>

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<pre style="margin: 0;"> <span id="LC358" class="line" lang="python">                <span class="s" style="color: #d14;">"{} is not a valid number of processors"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="p">))</span></span>

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

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<pre style="margin: 0;"> <span id="LC360" class="line" lang="python">        <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC361" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">argparse</span><span class="p">.</span><span class="n" style="color: #333;">ArgumentTypeError</span><span class="p">(</span><span class="s" style="color: #d14;">"the <span class="idiff left right">value given</span> is not valid. "</span></span>

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<pre style="margin: 0;">+<span id="LC361" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">argparse</span><span class="p">.</span><span class="n" style="color: #333;">ArgumentTypeError</span><span class="p">(</span><span class="s" style="color: #d14;">"the <span class="idiff left right">given value {}</span> is not valid. "</span></span>

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<pre style="margin: 0;"> <span id="LC362" class="line" lang="python">                                             <span class="s" style="color: #d14;">"Error message: {}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">The number of "</span></span>

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<pre style="margin: 0;"> <span id="LC363" class="line" lang="python">                                             <span class="s" style="color: #d14;">"available processors in your "</span></span>

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<pre style="margin: 0;">-<span id="LC364" class="line" lang="python">                                             <span class="s" style="color: #d14;">"computer is {}."</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">e</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC365" class="line" lang="python">                                                                      <span class="n" style="color: #333;">availProc</span><span class="p">))</span></span>

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<pre style="margin: 0;">+<span id="LC364" class="line" lang="python">                                             <span class="s" style="color: #d14;">"computer is {}."</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="n" style="color: #333;">availProc</span><span class="p">))</span></span>

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

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<pre style="margin: 0;"> <span id="LC366" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">numberOfProcessors</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">availProc</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC367" class="line" lang="python">            <span class="n" style="color: #333;">numberOfProcessors</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">availProc</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -444,7 +443,7 @@ def heatmapperOutputArgs(args=None,</td>

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<pre style="margin: 0;"> <span id="LC443" class="line" lang="python">        <span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--outFileNameMatrix'</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC444" class="line" lang="python">                            <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'If this option is given, then the matrix '</span></span>

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<pre style="margin: 0;"> <span id="LC445" class="line" lang="python">                            <span class="s" style="color: #d14;">'of values underlying the heatmap will be saved '</span></span>

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<pre style="margin: 0;">-<span id="LC447" class="line" lang="python">                            <span class="s" style="color: #d14;">'using this name, e.g. MyMatrix.<span class="idiff left right">tab</span>.'</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC446" class="line" lang="python">                            <span class="s" style="color: #d14;">'using this name, e.g. MyMatrix.<span class="idiff left right">gz</span>.'</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC447" class="line" lang="python">                            <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'FILE'</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC448" class="line" lang="python">                            <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">writableFile</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC449" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="614" style="width: 35px; color: rgba(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="613" style="width: 35px; color: rgba(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">@@ -614,9 +613,9 @@ def heatmapperOptionalArgs(mode=['heatmap', 'profile'][0]):</td>

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<pre style="margin: 0;"> <span id="LC613" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC614" class="line" lang="python">        <span class="n" style="color: #333;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--sortUsingSamples'</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC615" 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;">'List of sample numbers (order as in matrix), '</span></span>

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<pre style="margin: 0;">-<span id="LC617" class="line" lang="python">                              <span class="s" style="color: #d14;">'<span class="idiff left right">that are used for sorting by --sortUsing,</span> '</span></span>

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<pre style="margin: 0;">-<span id="LC618" class="line" lang="python">                              <span class="s" style="color: #d14;">'<span class="idiff left right">no value uses all samples,</span> '</span></span>

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<pre style="margin: 0;">-<span id="LC619" class="line" lang="python">                              <span class="s" style="color: #d14;">'<span class="idiff left right">e</span>xample: --sortUsingSamples 1 3'</span><span class="p">,</span></span>

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<td class="diff-line-num new old_line" data-linenumber="620" style="width: 35px; color: rgba(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="LC616" class="line" lang="python">                              <span class="s" style="color: #d14;">'<span class="idiff left right">which are used by --sortUsing for sorting.</span> '</span></span>

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<td class="diff-line-num new old_line" data-linenumber="620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="617" style="width: 35px; color: rgba(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="LC617" class="line" lang="python">                              <span class="s" style="color: #d14;">'<span class="idiff left right">If no value is set, it uses all samples.</span> '</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="618" style="width: 35px; color: rgba(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="LC618" class="line" lang="python">                              <span class="s" style="color: #d14;">'<span class="idiff left right">E</span>xample: --sortUsingSamples 1 3'</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC619" 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;">int</span><span class="p">,</span> <span class="n" style="color: #333;">nargs</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="LC620" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC621" class="line" lang="python">        <span class="n" style="color: #333;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--linesAtTickMarks'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="704" style="width: 35px; color: rgba(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="703" style="width: 35px; color: rgba(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">@@ -704,15 +703,17 @@ def heatmapperOptionalArgs(mode=['heatmap', 'profile'][0]):</td>

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704

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703

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<pre style="margin: 0;"> <span id="LC703" class="line" lang="python">                              <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

705

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<td class="diff-line-num new_line" data-linenumber="704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

704

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<pre style="margin: 0;"> <span id="LC704" 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;">'Minimum value for the heatmap intensities. Multiple values, separated by '</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

706

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<td class="diff-line-num new_line" data-linenumber="705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

705

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<pre style="margin: 0;"> <span id="LC705" class="line" lang="python">                                   <span class="s" style="color: #d14;">'spaces can be set for each heatmap. If the number of zMin values is smaller than'</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="707" 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">

707

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<td class="diff-line-num new_line old" data-linenumber="706" 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="LC707" class="line" lang="python">                                   <span class="s" style="color: #d14;">'the number of heatmaps the values are recycled.'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="708" 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">

708

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<td class="diff-line-num new_line old" data-linenumber="706" 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="LC708" 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;">float</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

706

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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="LC706" class="line" lang="python">                                   <span class="s" style="color: #d14;">'the number of heatmaps the values are recycled. If a value is set to "auto", it will be set '</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

707

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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="LC707" class="line" lang="python">                                   <span class="s" style="color: #d14;">' to the first percentile of the matrix values.'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="709" style="width: 35px; color: rgba(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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708

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<pre style="margin: 0;">+<span id="LC708" 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 class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

709

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<td class="diff-line-num new_line" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

709

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<pre style="margin: 0;"> <span id="LC709" class="line" lang="python">                              <span class="n" style="color: #333;">nargs</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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<td class="diff-line-num old_line" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

710

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<td class="diff-line-num new_line" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

710

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<pre style="margin: 0;"> <span id="LC710" class="line" lang="python">        <span class="n" style="color: #333;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--zMax'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-max'</span><span class="p">,</span></span>

</pre>

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711

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<td class="diff-line-num new_line" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

711

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<pre style="margin: 0;"> <span id="LC711" class="line" lang="python">                              <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>

</pre>

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712

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<td class="diff-line-num new_line" data-linenumber="712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

712

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<pre style="margin: 0;"> <span id="LC712" 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;">'Maximum value for the heatmap intensities. Multiple values, separated by '</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

713

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<td class="diff-line-num new_line" data-linenumber="713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

713

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

<pre style="margin: 0;"> <span id="LC713" class="line" lang="python">                                   <span class="s" style="color: #d14;">'spaces can be set for each heatmap. If the number of zMax values is smaller than'</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="714" 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">

714

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<td class="diff-line-num new_line old" data-linenumber="714" 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="LC714" class="line" lang="python">                                   <span class="s" style="color: #d14;">'the number of heatmaps the values are recycled.'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="715" 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">

715

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<td class="diff-line-num new_line old" data-linenumber="714" 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="LC715" 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;">float</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="716" style="width: 35px; color: rgba(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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714

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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="LC714" class="line" lang="python">                                   <span class="s" style="color: #d14;">'the number of heatmaps the values are recycled. If a value is set to "auto", it will be set '</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

715

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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="LC715" class="line" lang="python">                                   <span class="s" style="color: #d14;">' to the 98th percentile of the matrix values.'</span><span class="p">,</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

716

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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="LC716" 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 class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

716

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<td class="diff-line-num new_line" data-linenumber="717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

717

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<pre style="margin: 0;"> <span id="LC717" class="line" lang="python">                              <span class="n" style="color: #333;">nargs</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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<td class="diff-line-num old_line" data-linenumber="717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

717

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<pre style="margin: 0;"> <span id="LC718" class="line" lang="python">        <span class="n" style="color: #333;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--heatmapHeight'</span><span class="p">,</span></span>

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718

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<pre style="margin: 0;"> <span id="LC719" 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;">'Plot height in cm. The default for the heatmap '</span></span>

</pre>

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<br>

</li>

<li id="e6f336c84329d2021242809e76ed32e6ed05fecc">

<a href="https://salsa.debian.org/med-team/python-deeptools/-/compare/911dd5dc4fa12b9ee76878808b70bb1cd946aecc...778b045cad10a9ffb96c37157678a6b7126f69dc#e6f336c84329d2021242809e76ed32e6ed05fecc"><strong>deeptools/plotHeatmap.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">@@ -412,6 +412,16 @@ def plotMatrix(hm, outFileName,</td>

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<pre style="margin: 0;"> <span id="LC412" class="line" lang="python">            <span class="n" style="color: #333;">zMin</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</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="LC413" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<td class="diff-line-num 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">

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC414" class="line" lang="python">            <span class="n" style="color: #333;">zMin</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">zMin</span><span class="p">]</span>  <span class="c1" style="color: #998; font-style: italic;"># convert to list to support multiple entries</span></span>

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<td class="diff-line-num new new_line" data-linenumber="415" style="width: 35px; color: rgba(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="LC415" class="line" lang="python">    <span class="k" style="font-weight: 600;">elif</span> <span class="s" style="color: #d14;">'auto'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">zMin</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC416" class="line" lang="python">        <span class="n" style="color: #333;">matrix_flatten</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hm</span><span class="p">.</span><span class="n" style="color: #333;">matrix</span><span class="p">.</span><span class="n" style="color: #333;">flatten</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

417

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<pre style="margin: 0;">+<span id="LC417" class="line" lang="python">        <span class="n" style="color: #333;">auto_min</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;">percentile</span><span class="p">(</span><span class="n" style="color: #333;">matrix_flatten</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="418" style="width: 35px; color: rgba(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="LC418" 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="n" style="color: #333;">isnan</span><span class="p">(</span><span class="n" style="color: #333;">auto_min</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

419

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<pre style="margin: 0;">+<span id="LC419" class="line" lang="python">            <span class="n" style="color: #333;">auto_min</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

420

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<pre style="margin: 0;">+<span id="LC420" class="line" lang="python">        <span class="n" style="color: #333;">new_mins</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'auto'</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">auto_min</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">zMin</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="421" style="width: 35px; color: rgba(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="LC421" class="line" lang="python">        <span class="n" style="color: #333;">zMin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_mins</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC422" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="423" style="width: 35px; color: rgba(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="LC423" class="line" lang="python">        <span class="n" style="color: #333;">new_mins</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">zMin</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="424" style="width: 35px; color: rgba(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="LC424" class="line" lang="python">        <span class="n" style="color: #333;">zMin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_mins</span></span>

</pre>

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

</pre>

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<pre style="margin: 0;"> <span id="LC426" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">zMax</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC427" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">matrix_flatten</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="422" style="width: 35px; color: rgba(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">@@ -422,6 +432,23 @@ def plotMatrix(hm, outFileName,</td>

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<pre style="margin: 0;"> <span id="LC432" class="line" lang="python">            <span class="n" style="color: #333;">zMax</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="bp" style="color: #999;">None</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC433" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC434" class="line" lang="python">            <span class="n" style="color: #333;">zMax</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">zMax</span><span class="p">]</span></span>

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<td class="diff-line-num new new_line" data-linenumber="435" style="width: 35px; color: rgba(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="LC435" class="line" lang="python">    <span class="k" style="font-weight: 600;">elif</span> <span class="s" style="color: #d14;">'auto'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">zMax</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="436" style="width: 35px; color: rgba(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="LC436" class="line" lang="python">        <span class="n" style="color: #333;">matrix_flatten</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hm</span><span class="p">.</span><span class="n" style="color: #333;">matrix</span><span class="p">.</span><span class="n" style="color: #333;">flatten</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="437" style="width: 35px; color: rgba(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="LC437" class="line" lang="python">        <span class="n" style="color: #333;">auto_max</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;">percentile</span><span class="p">(</span><span class="n" style="color: #333;">matrix_flatten</span><span class="p">,</span> <span class="mf" style="color: #099;">98.0</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="438" style="width: 35px; color: rgba(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="LC438" 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="n" style="color: #333;">isnan</span><span class="p">(</span><span class="n" style="color: #333;">auto_max</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

439

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<pre style="margin: 0;">+<span id="LC439" class="line" lang="python">            <span class="n" style="color: #333;">auto_max</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC440" class="line" lang="python">        <span class="n" style="color: #333;">new_maxs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'auto'</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">auto_max</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">zMax</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="441" style="width: 35px; color: rgba(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="LC441" class="line" lang="python">        <span class="n" style="color: #333;">zMax</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_maxs</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC442" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="443" style="width: 35px; color: rgba(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="LC443" class="line" lang="python">        <span class="n" style="color: #333;">new_maxs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">zMax</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC444" class="line" lang="python">        <span class="n" style="color: #333;">zMax</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_maxs</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC445" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">zMin</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">zMax</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

446

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<pre style="margin: 0;">+<span id="LC446" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">zMax</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

447

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<pre style="margin: 0;">+<span id="LC447" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">zMin</span><span class="p">[</span><span class="n" style="color: #333;">index</span><span class="p">]:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

448

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<pre style="margin: 0;">+<span id="LC448" class="line" lang="python">                <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"Warnirng: In bigwig {}, the given zmin ({}) is larger than "</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

449

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<pre style="margin: 0;">+<span id="LC449" class="line" lang="python">                                 <span class="s" style="color: #d14;">"or equal to the given zmax ({}). Thus, it has been set "</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="450" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

450

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<pre style="margin: 0;">+<span id="LC450" class="line" lang="python">                                 <span class="s" style="color: #d14;">"to None. </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 class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">zMin</span><span class="p">[</span><span class="n" style="color: #333;">index</span><span class="p">],</span> <span class="n" style="color: #333;">value</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="451" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

451

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<pre style="margin: 0;">+<span id="LC451" class="line" lang="python">                <span class="n" style="color: #333;">zMin</span><span class="p">[</span><span class="n" style="color: #333;">index</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

425

</td>

<td class="diff-line-num new_line" data-linenumber="452" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

452

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

</pre>

</td>

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<td class="diff-line-num 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">

426

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<td class="diff-line-num new_line" data-linenumber="453" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

453

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<pre style="margin: 0;"> <span id="LC453" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">yMin</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

427

</td>

<td class="diff-line-num new_line" data-linenumber="454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

454

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

<pre style="margin: 0;"> <span id="LC454" class="line" lang="python">        <span class="n" style="color: #333;">yMin</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="bp" style="color: #999;">None</span><span class="p">]</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="833" style="width: 35px; color: rgba(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="860" style="width: 35px; color: rgba(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">@@ -833,7 +860,7 @@ def main(args=None):</td>

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<td class="diff-line-num old_line" data-linenumber="833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

833

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<td class="diff-line-num new_line" data-linenumber="860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

860

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<pre style="margin: 0;"> <span id="LC860" class="line" lang="python">            <span class="n" style="color: #333;">hm</span><span class="p">.</span><span class="n" style="color: #333;">matrix</span><span class="p">.</span><span class="n" style="color: #333;">computeSilhouette</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">hclust</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

834

</td>

<td class="diff-line-num new_line" data-linenumber="861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

861

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

<pre style="margin: 0;"> <span id="LC861" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

835

</td>

<td class="diff-line-num new_line" data-linenumber="862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

862

</td>

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

<pre style="margin: 0;"> <span id="LC862" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">outFileNameMatrix</span><span class="p">:</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="836" 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">

836

</td>

<td class="diff-line-num new_line old" data-linenumber="863" 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="LC836" class="line" lang="python">        <span class="n" style="color: #333;">hm</span><span class="p">.</span><span class="n" style="color: #333;">save_matrix<span class="idiff left right">_values</span></span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">outFileNameMatrix</span><span class="p">)</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

863

</td>

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

<pre style="margin: 0;">+<span id="LC863" class="line" lang="python">        <span class="n" style="color: #333;">hm</span><span class="p">.</span><span class="n" style="color: #333;">save_matrix</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">outFileNameMatrix</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

837

</td>

<td class="diff-line-num new_line" data-linenumber="864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

864

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

<pre style="margin: 0;"> <span id="LC864" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

838

</td>

<td class="diff-line-num new_line" data-linenumber="865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

865

</td>

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

<pre style="margin: 0;"> <span id="LC865" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">outFileSortedRegions</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

839

</td>

<td class="diff-line-num new_line" data-linenumber="866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

866

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

<pre style="margin: 0;"> <span id="LC866" class="line" lang="python">        <span class="n" style="color: #333;">hm</span><span class="p">.</span><span class="n" style="color: #333;">save_BED</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">outFileSortedRegions</span><span class="p">)</span></span>

</pre>

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<li id="933931be8d4eb6bef5ca9c328d98370ed0c3370a">

<a href="https://salsa.debian.org/med-team/python-deeptools/-/compare/911dd5dc4fa12b9ee76878808b70bb1cd946aecc...778b045cad10a9ffb96c37157678a6b7126f69dc#933931be8d4eb6bef5ca9c328d98370ed0c3370a"><strong>deeptools/plotProfile.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">@@ -6,6 +6,7 @@ import sys</td>

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

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">argparse</span></span>

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

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">math</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ceil</span></span>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">matplotlib</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="n" style="color: #333;">matplotlib</span><span class="p">.</span><span class="n" style="color: #333;">use</span><span class="p">(</span><span class="s" style="color: #d14;">'Agg'</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="n" style="color: #333;">matplotlib</span><span class="p">.</span><span class="n" style="color: #333;">rcParams</span><span class="p">[</span><span class="s" style="color: #d14;">'pdf.fonttype'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">42</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="458" style="width: 35px; color: rgba(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="459" style="width: 35px; color: rgba(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">@@ -458,6 +459,13 @@ class Profile(object):</td>

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<td class="diff-line-num new_line" data-linenumber="459" style="width: 35px; color: rgba(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="LC459" class="line" lang="python">        <span class="n" style="color: #333;">py</span><span class="p">.</span><span class="n" style="color: #333;">plot</span><span class="p">(</span><span class="n" style="color: #333;">fig</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">out_file_name</span><span class="p">,</span> <span class="n" style="color: #333;">auto_open</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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<td class="diff-line-num new_line" data-linenumber="460" style="width: 35px; color: rgba(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="LC460" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="460" style="width: 35px; color: rgba(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="LC461" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">plot_heatmap</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<td class="diff-line-num new new_line" data-linenumber="462" style="width: 35px; color: rgba(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="LC462" class="line" lang="python">        <span class="n" style="color: #333;">cmap</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'RdYlBu_r'</span><span class="p">]</span></span>

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<td class="diff-line-num new old_line" data-linenumber="461" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="463" style="width: 35px; color: rgba(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="LC463" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">color_list</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 class="c1" style="color: #998; font-style: italic;"># check the length to be equal to the numebr of plots otherwise multiply it!</span></span>

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<td class="diff-line-num new new_line" data-linenumber="464" style="width: 35px; color: rgba(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="LC464" class="line" lang="python">            <span class="n" style="color: #333;">cmap</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">color_list</span></span>

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<td class="diff-line-num new new_line" data-linenumber="465" style="width: 35px; color: rgba(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="LC465" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">cmap</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">numplots</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC466" class="line" lang="python">            <span class="n" style="color: #333;">all_colors</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cmap</span></span>

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<pre style="margin: 0;">+<span id="LC467" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">ceil</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">numplots</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;">cmap</span><span class="p">))):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="461" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="468" style="width: 35px; color: rgba(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="LC468" class="line" lang="python">                <span class="n" style="color: #333;">cmap</span><span class="p">.</span><span class="n" style="color: #333;">extend</span><span class="p">(</span><span class="n" style="color: #333;">all_colors</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="461" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

461

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<td class="diff-line-num new_line" data-linenumber="469" style="width: 35px; color: rgba(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="LC469" class="line" lang="python">        <span class="n" style="color: #333;">matrix_flatten</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

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<td class="diff-line-num new_line" data-linenumber="470" style="width: 35px; color: rgba(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="LC470" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">y_min</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="bp" style="color: #999;">None</span><span class="p">]:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="471" style="width: 35px; color: rgba(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="LC471" class="line" lang="python">            <span class="n" style="color: #333;">matrix_flatten</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hm</span><span class="p">.</span><span class="n" style="color: #333;">matrix</span><span class="p">.</span><span class="n" style="color: #333;">flatten</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="479" style="width: 35px; color: rgba(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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -479,7 +487,6 @@ class Profile(object):</td>

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<td class="diff-line-num old_line" data-linenumber="479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<pre style="margin: 0;"> <span id="LC487" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" 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">

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<td class="diff-line-num new_line" 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">

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<pre style="margin: 0;"> <span id="LC488" class="line" lang="python">        <span class="n" style="color: #333;">ax_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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

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<td class="diff-line-num new_line" 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">

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<pre style="margin: 0;"> <span id="LC489" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># turn off y ticks</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="490" style="width: 35px; color: rgba(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="LC490" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">plot</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">numplots</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" 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">

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<td class="diff-line-num new_line" 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

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<pre style="margin: 0;"> <span id="LC491" class="line" lang="python">            <span class="n" style="color: #333;">labels</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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

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<td class="diff-line-num new_line" 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">

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<pre style="margin: 0;"> <span id="LC492" class="line" lang="python">            <span class="n" style="color: #333;">col</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">plot</span> <span class="o" style="font-weight: 600;">%</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">plots_per_row</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="503" style="width: 35px; color: rgba(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="510" style="width: 35px; color: rgba(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">@@ -503,9 +510,10 @@ class Profile(object):</td>

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<td class="diff-line-num old_line" data-linenumber="503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

510

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<pre style="margin: 0;"> <span id="LC510" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="511" style="width: 35px; color: rgba(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="LC511" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">per_group</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="512" style="width: 35px; color: rgba(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="LC512" class="line" lang="python">                <span class="n" style="color: #333;">title</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hm</span><span class="p">.</span><span class="n" style="color: #333;">matrix</span><span class="p">.</span><span class="n" style="color: #333;">group_labels</span><span class="p">[</span><span class="n" style="color: #333;">plot</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="513" style="width: 35px; color: rgba(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="LC513" class="line" lang="python">                <span class="n" style="color: #333;">tickIdx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">plot</span> <span class="o" style="font-weight: 600;">%</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hm</span><span class="p">.</span><span class="n" style="color: #333;">matrix</span><span class="p">.</span><span class="n" style="color: #333;">get_num_samples</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

506

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<td class="diff-line-num new_line" data-linenumber="514" style="width: 35px; color: rgba(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="LC514" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC515" class="line" lang="python">                <span class="n" style="color: #333;">title</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hm</span><span class="p">.</span><span class="n" style="color: #333;">matrix</span><span class="p">.</span><span class="n" style="color: #333;">sample_labels</span><span class="p">[</span><span class="n" style="color: #333;">plot</span><span class="p">]</span></span>

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<td class="diff-line-num new_line old" data-linenumber="516" 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="LC508" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC516" class="line" lang="python">                <span class="n" style="color: #333;">tickIdx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">plot</span></span>

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<pre style="margin: 0;"> <span id="LC517" class="line" lang="python">            <span class="n" style="color: #333;">ax</span><span class="p">.</span><span class="n" style="color: #333;">set_title</span><span class="p">(</span><span class="n" style="color: #333;">title</span><span class="p">)</span></span>

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<td class="diff-line-num new_line" data-linenumber="518" style="width: 35px; color: rgba(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="LC518" class="line" lang="python">            <span class="n" style="color: #333;">mat</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span>  <span class="c1" style="color: #998; font-style: italic;"># when drawing a heatmap (in contrast to drawing lines)</span></span>

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<pre style="margin: 0;"> <span id="LC519" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">data_idx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">numlines</span><span class="p">):</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="526" style="width: 35px; color: rgba(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="534" style="width: 35px; color: rgba(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">@@ -526,13 +534,12 @@ class Profile(object):</td>

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<pre style="margin: 0;"> <span id="LC534" class="line" lang="python">                    <span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sub_matrix</span><span class="p">[</span><span class="s" style="color: #d14;">'group'</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC535" class="line" lang="python">                <span class="n" style="color: #333;">labels</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">label</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC536" class="line" lang="python">                <span class="n" style="color: #333;">mat</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">ma</span><span class="p">.</span><span class="n" style="color: #333;">__getattribute__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">averagetype</span><span class="p">)(</span><span class="n" style="color: #333;">sub_matrix</span><span class="p">[</span><span class="s" style="color: #d14;">'matrix'</span><span class="p">],</span> <span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="537" 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="LC529" class="line" lang="python"></span>

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<td class="diff-line-num new_line" data-linenumber="537" style="width: 35px; color: rgba(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="LC537" class="line" lang="python">            <span class="n" style="color: #333;">img</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ax</span><span class="p">.</span><span class="n" style="color: #333;">imshow</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">vstack</span><span class="p">(</span><span class="n" style="color: #333;">mat</span><span class="p">),</span> <span class="n" style="color: #333;">interpolation</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'nearest'</span><span class="p">,</span></span>

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<td class="diff-line-num new_line old" data-linenumber="538" 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="LC531" class="line" lang="python">                            <span class="n" style="color: #333;">cmap</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;"><span class="idiff left right">'RdYlBu_r'</span></span><span class="p">,</span> <span class="n" style="color: #333;">aspect</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'auto'</span><span class="p">,</span> <span class="n" style="color: #333;">vmin</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">localYMin</span><span class="p">,</span> <span class="n" style="color: #333;">vmax</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">localYMax</span><span class="p">)</span></span>

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<td class="diff-line-num new old_line" data-linenumber="532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="538" style="width: 35px; color: rgba(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="LC538" class="line" lang="python">                            <span class="n" style="color: #333;">cmap</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;"><span class="idiff left">cmap</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">plot</span></span><span class="p"><span class="idiff right">]</span>,</span> <span class="n" style="color: #333;">aspect</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'auto'</span><span class="p">,</span> <span class="n" style="color: #333;">vmin</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">localYMin</span><span class="p">,</span> <span class="n" style="color: #333;">vmax</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">localYMax</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC539" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">fig</span><span class="p">.</span><span class="n" style="color: #333;">colorbar</span><span class="p">(</span><span class="n" style="color: #333;">img</span><span class="p">,</span> <span class="n" style="color: #333;">cax</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cax</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="540" style="width: 35px; color: rgba(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="LC540" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC541" class="line" lang="python">            <span class="n" style="color: #333;">totalWidth</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;">vstack</span><span class="p">(</span><span class="n" style="color: #333;">mat</span><span class="p">).</span><span class="n" style="color: #333;">shape</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

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535

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<td class="diff-line-num new_line old" data-linenumber="542" 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="LC535" class="line" lang="python">            <span class="n" style="color: #333;">xticks</span><span class="p">,</span> <span class="n" style="color: #333;">xtickslabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">getTicks</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">plot</span></span><span class="p">)</span></span>

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<td class="diff-line-num new old_line" data-linenumber="536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

542

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<pre style="margin: 0;">+<span id="LC542" class="line" lang="python">            <span class="n" style="color: #333;">xticks</span><span class="p">,</span> <span class="n" style="color: #333;">xtickslabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">getTicks</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">tickIdx</span></span><span class="p">)</span></span>

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<td class="diff-line-num old_line" data-linenumber="536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

536

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543

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<pre style="margin: 0;"> <span id="LC543" 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="n" style="color: #333;">ceil</span><span class="p">(</span><span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">xticks</span><span class="p">))</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">totalWidth</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">):</span></span>

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<td class="diff-line-num old_line" data-linenumber="537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

537

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<td class="diff-line-num new_line" data-linenumber="544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

544

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<pre style="margin: 0;"> <span id="LC544" class="line" lang="python">                <span class="n" style="color: #333;">tickscale</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">totalWidth</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">xticks</span><span class="p">)</span></span>

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<td class="diff-line-num old_line" data-linenumber="538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

538

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<td class="diff-line-num new_line" data-linenumber="545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

545

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<pre style="margin: 0;"> <span id="LC545" class="line" lang="python">                <span class="n" style="color: #333;">xticks_use</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tickscale</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">xticks</span><span class="p">]</span></span>

</pre>

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<br>

</li>

<li id="b509e8bc4a8e48a682d63505a1080b6033a0803f">

<a href="https://salsa.debian.org/med-team/python-deeptools/-/compare/911dd5dc4fa12b9ee76878808b70bb1cd946aecc...778b045cad10a9ffb96c37157678a6b7126f69dc#b509e8bc4a8e48a682d63505a1080b6033a0803f"><strong>deeptools/test/test_readFiltering.py</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,6 +4,8 @@ import deeptools.alignmentSieve as sieve</td>

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4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os.path</span></span>

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5

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5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">os</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">unlink</span></span>

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6

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6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">hashlib</span></span>

</pre>

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

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

7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pysam</span></span>

</pre>

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

8

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

</pre>

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7

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

9

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="n" style="color: #333;">ROOT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">abspath</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">))</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/test_data/"</span></span>

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

9

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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="n" style="color: #333;">BAMFILE_FILTER</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ROOT</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"test_filtering.bam"</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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -72,12 +74,12 @@ def test_sieve():</td>

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72

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74

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python">                <span class="s" style="color: #d14;">'test_filtering</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">5</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">193</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python">    <span class="n" style="color: #333;">assert_equal</span><span class="p">(</span><span class="n" style="color: #333;">resp</span><span class="p">,</span> <span class="n" style="color: #333;">expected</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python">    <span class="n" style="color: #333;">unlink</span><span class="p">(</span><span class="n" style="color: #333;">outlog</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python">    <span class="n" style="color: #333;">h</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hashlib</span><span class="p">.</span><span class="n" style="color: #333;">md5</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">open</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">outfile</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"rb"</span></span><span class="p"><span class="idiff">).</span></span><span class="n" style="color: #333;"><span class="idiff">read</span></span><span class="p"><span class="idiff right">(</span>)).</span><span class="n" style="color: #333;">hexdigest</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="77" 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="LC76" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">h</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"<span class="idiff left right">977bdab227a4dbfa3fc9f27c23a3e0b7</span>"</span><span class="p">)</span></span>

</pre>

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

<pre style="margin: 0;">+<span id="LC77" class="line" lang="python">    <span class="n" style="color: #333;">h</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hashlib</span><span class="p">.</span><span class="n" style="color: #333;">md5</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">pysam</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">view</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">outfile</span></span><span class="p"><span class="idiff">).</span></span><span class="n" style="color: #333;"><span class="idiff">encode</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff right">'utf-8'</span></span><span class="p">)).</span><span class="n" style="color: #333;">hexdigest</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">h</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"<span class="idiff left right">acbc4443fb0387bfd6c412af9d4fc414</span>"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" 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">

77

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<td class="diff-line-num new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC79" class="line" lang="python">    <span class="n" style="color: #333;">unlink</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" 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="diff-line-num new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

80

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

<pre style="margin: 0;"> <span id="LC80" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="79" 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="LC79" class="line" lang="python">    <span class="n" style="color: #333;">h</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">hashlib</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">md5</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">open</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">outfiltered</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"rb"</span></span><span class="p"><span class="idiff">).</span></span><span class="n" style="color: #333;"><span class="idiff">read</span></span><span class="p"><span class="idiff right">(</span>)).</span><span class="n" style="color: #333;">hexdigest</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="81" 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="LC80" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">h</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"762e79b7a2245ff6b2cea4139a1455de</span>"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

81

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python">    <span class="n" style="color: #333;">h<span class="idiff left">1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">hashlib</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">md5</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">pysam</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">view</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">outfiltered</span></span><span class="p"><span class="idiff">).</span></span><span class="n" style="color: #333;"><span class="idiff">encode</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff right">'utf-8'</span></span><span class="p">)).</span><span class="n" style="color: #333;">hexdigest</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

82

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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="LC82" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">h<span class="idiff left">1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"b90befdd5f073f14acb9a38661f301ad</span>"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num 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">

81

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<td class="diff-line-num new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

83

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

<pre style="margin: 0;"> <span id="LC83" class="line" lang="python">    <span class="n" style="color: #333;">unlink</span><span class="p">(</span><span class="n" style="color: #333;">outfiltered</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

82

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<td class="diff-line-num new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

84

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

<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

83

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<td class="diff-line-num new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

85

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

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

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="abc059e39dfccf4038fabfb18bfb7b5121e4e2e4">

<a href="https://salsa.debian.org/med-team/python-deeptools/-/compare/911dd5dc4fa12b9ee76878808b70bb1cd946aecc...778b045cad10a9ffb96c37157678a6b7126f69dc#abc059e39dfccf4038fabfb18bfb7b5121e4e2e4"><strong>galaxy/wrapper/computeMatrixOperations.xml</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="71" style="width: 35px; color: rgba(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">@@ -71,6 +71,9 @@</td>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="xml">                -m $submodule.matrixFile</span>

</pre>

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="xml">                -R '#echo "' '".join($files)#'</span>

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<td class="diff-line-num old_line" 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="xml">                -o $outFileName</span>

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<td class="diff-line-num new old_line" data-linenumber="74" style="width: 35px; color: rgba(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="LC74" class="line" lang="xml">            #else if $submodule.command == "dataRange":</span>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="xml">                dataRange</span>

</pre>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="xml">                -m $submodule.matrixFile</span>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="xml">            #end if</span>

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="xml">]]></span>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="xml">    <span class="nt" style="color: #000080;"></command></span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="85" style="width: 35px; color: rgba(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>

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="xml">                <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"rbind"</span><span class="nt" style="color: #000080;">></span>Bind matrices, top to bottom (rbind)<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<td class="diff-line-num new_line" 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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<pre style="margin: 0;"> <span id="LC89" class="line" lang="xml">                <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"cbind"</span><span class="nt" style="color: #000080;">></span>Bind matrices, left to right (cbind)<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

90

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="xml">                <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"sort"</span><span class="nt" style="color: #000080;">></span>Sort by region order in specified files (sort)<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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="xml">                <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"dataRange"</span><span class="nt" style="color: #000080;">></span>Returns the min, max, median, 10th and 90th percentile of the matrix values per sample (dataRange)<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="xml">            <span class="nt" style="color: #000080;"></param></span></span>

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="xml">            <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"info"</span><span class="nt" style="color: #000080;">></span></span>

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<td class="diff-line-num new_line" 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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<pre style="margin: 0;"> <span id="LC94" class="line" lang="xml">                <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">argument=</span><span class="s" style="color: #d14;">"matrixFile"</span> <span class="na" style="color: #008080;">format=</span><span class="s" style="color: #d14;">"deeptools_compute_matrix_archive"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"data"</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="151" style="width: 35px; color: rgba(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="155" style="width: 35px; color: rgba(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="LC155" class="line" lang="xml">                        <span class="na" style="color: #008080;">help=</span><span class="s" style="color: #d14;">"File, in BED format, containing the regions to plot."</span><span class="nt" style="color: #000080;">/></span></span>

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<pre style="margin: 0;">+<span id="LC159" class="line" lang="xml">            <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"dataRange"</span><span class="nt" style="color: #000080;">></span></span>

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<pre style="margin: 0;">+<span id="LC160" class="line" lang="xml">                <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">argument=</span><span class="s" style="color: #d14;">"matrixFile"</span> <span class="na" style="color: #008080;">format=</span><span class="s" style="color: #d14;">"deeptools_compute_matrix_archive"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"data"</span></span>

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<pre style="margin: 0;">+<span id="LC161" class="line" lang="xml">                       <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Matrix file from the computeMatrix tool"</span> <span class="na" style="color: #008080;">help=</span><span class="s" style="color: #d14;">""</span><span class="nt" style="color: #000080;">/></span></span>

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<pre style="margin: 0;">+<span id="LC162" class="line" lang="xml">                <span class="nt" style="color: #000080;"></param></span></span>

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<pre style="margin: 0;">+<span id="LC163" class="line" lang="xml">            <span class="nt" style="color: #000080;"></when></span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -205,7 +215,8 @@ What it does</td>

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<pre style="margin: 0;"> <span id="LC215" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">+----------------+--------------------------------------------------------------------------------------------------------------------------+</span></span>

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<pre style="margin: 0;"> <span id="LC216" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">+ sort           | Sorts the given file so regions are in the order of occurence in the input BED/GTF file(s).                              |</span></span>

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<pre style="margin: 0;"> <span id="LC217" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">+----------------+--------------------------------------------------------------------------------------------------------------------------+</span></span>

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

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<pre style="margin: 0;">+<span id="LC218" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">+ dataRange      | Returns the min, max, median, 10th and 90th percentile of the matrix values per sample.                                  |</span></span>

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<pre style="margin: 0;">+<span id="LC219" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">+----------------+--------------------------------------------------------------------------------------------------------------------------+</span></span>

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

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<pre style="margin: 0;"> <span id="LC221" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">These operations are useful when you want to run computeMatrix on multiple files (thereby keeping all of the values together) and later exclude regions/samples or add new ones. Another common use would be if you require the output of computeMatrix to be sorted to match the order of regions in the input file.</span></span>

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<pre style="margin: 0;"> <span id="LC222" class="line" lang="xml"></span>

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<li id="d2de9c6869fd65911899bace5f34a175e96efb2a">

<a href="https://salsa.debian.org/med-team/python-deeptools/-/compare/911dd5dc4fa12b9ee76878808b70bb1cd946aecc...778b045cad10a9ffb96c37157678a6b7126f69dc#d2de9c6869fd65911899bace5f34a175e96efb2a"><strong>galaxy/wrapper/deepTools_macros.xml</strong></a>

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="xml"><span class="nt" style="color: #000080;"><macros></span></span>

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

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="xml">    <span class="nt" style="color: #000080;"><token</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"@THREADS@"</span><span class="nt" style="color: #000080;">></span>--numberOfProcessors "\${GALAXY_SLOTS:-4}"<span class="nt" style="color: #000080;"></token></span></span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="xml">    <span class="nt" style="color: #000080;"><token</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"@WRAPPER_VERSION@"</span><span class="nt" style="color: #000080;">></span>3.<span class="idiff left right">4.3</span>.0<span class="nt" style="color: #000080;"></token></span></span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="xml">    <span class="nt" style="color: #000080;"><token</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"@WRAPPER_VERSION@"</span><span class="nt" style="color: #000080;">></span>3.<span class="idiff left right">5.0</span>.0<span class="nt" style="color: #000080;"></token></span></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="xml">    <span class="nt" style="color: #000080;"><xml</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"requirements"</span><span class="nt" style="color: #000080;">></span></span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="xml">        <span class="nt" style="color: #000080;"><requirements></span></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="xml">            <span class="nt" style="color: #000080;"><requirement</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"package"</span> <span class="na" style="color: #008080;">version=</span><span class="s" style="color: #d14;">"3.<span class="idiff left right">4.3</span>"</span><span class="nt" style="color: #000080;">></span>deeptools<span class="nt" style="color: #000080;"></requirement></span></span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="xml">            <span class="nt" style="color: #000080;"><requirement</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"package"</span> <span class="na" style="color: #008080;">version=</span><span class="s" style="color: #d14;">"3.<span class="idiff left right">5.0</span>"</span><span class="nt" style="color: #000080;">></span>deeptools<span class="nt" style="color: #000080;"></requirement></span></span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="xml">            <span class="nt" style="color: #000080;"><requirement</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"package"</span> <span class="na" style="color: #008080;">version=</span><span class="s" style="color: #d14;">"1.9"</span><span class="nt" style="color: #000080;">></span>samtools<span class="nt" style="color: #000080;"></requirement></span></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="xml">        <span class="nt" style="color: #000080;"></requirements></span></span>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="xml">        <span class="nt" style="color: #000080;"><expand</span> <span class="na" style="color: #008080;">macro=</span><span class="s" style="color: #d14;">"stdio"</span> <span class="nt" style="color: #000080;">/></span></span>

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<li id="84b200ead4096f88da1811d06b79ecc1b09fcadd">

<a href="https://salsa.debian.org/med-team/python-deeptools/-/compare/911dd5dc4fa12b9ee76878808b70bb1cd946aecc...778b045cad10a9ffb96c37157678a6b7126f69dc#84b200ead4096f88da1811d06b79ecc1b09fcadd"><strong>galaxy/wrapper/plotHeatmap.xml</strong></a>

<hr>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="xml">                #if str($advancedOpt.yMin).strip() != "":</span>

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="xml">                    --yMin $advancedOpt.yMin</span>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="xml">                #end if</span>

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<pre style="margin: 0;">-<span id="LC78" class="line" lang="xml">                #if <span class="idiff left right">$advancedOpt.yMax</span>:</span>

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<td class="diff-line-num new new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

78

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="xml">                #if <span class="idiff left right">str($advancedOpt.yMax).strip() != ""</span>:</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

79

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<td class="diff-line-num new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

79

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="xml">                    --yMax $advancedOpt.yMax</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

80

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<td class="diff-line-num new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

80

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="xml">                #end if</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

81

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="xml">                #if str($advancedOpt.sortUsingSamples).strip() != "":</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

82

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="xml">                    --sortUsingSamples $advancedOpt.sortUsingSamples</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

83

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="xml">                #end if</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

84

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="xml">                #if str($advancedOpt.clusterUsingSamples).strip() != "":</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

85

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="xml">                    --clusterUsingSamples $advancedOpt.clusterUsingSamples</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

86

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="xml">                #end if</span>

</pre>

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81

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<td class="diff-line-num new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

87

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

82

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<td class="diff-line-num 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">

88

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="xml">                --xAxisLabel '$advancedOpt.xAxisLabel'</span>

</pre>

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83

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<td class="diff-line-num new_line" 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">

89

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="xml">                --yAxisLabel '$advancedOpt.yAxisLabel'</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -134,6 +140,15 @@</td>

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<td class="diff-line-num old_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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140

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="xml">            <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"yes"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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141

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="xml">                <span class="nt" style="color: #000080;"><expand</span> <span class="na" style="color: #008080;">macro=</span><span class="s" style="color: #d14;">"sortRegions"</span> <span class="nt" style="color: #000080;">/></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC142" class="line" lang="xml">                <span class="nt" style="color: #000080;"><expand</span> <span class="na" style="color: #008080;">macro=</span><span class="s" style="color: #d14;">"sortUsing"</span> <span class="nt" style="color: #000080;">/></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="143" style="width: 35px; color: rgba(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="LC143" class="line" lang="xml">                <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">argument=</span><span class="s" style="color: #d14;">"--sortUsingSamples"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"text"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="144" style="width: 35px; color: rgba(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="LC144" class="line" lang="xml">                    <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"List of samples to be used for sorting"</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="145" style="width: 35px; color: rgba(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="LC145" class="line" lang="xml">                    <span class="na" style="color: #008080;">help=</span><span class="s" style="color: #d14;">"List of sample numbers (order as in matrix), which are used by --sortUsing for sorting.</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="146" style="width: 35px; color: rgba(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="LC146" class="line" lang="xml"><span class="s" style="color: #d14;">                    If no value is set, it uses all samples. Example: 1 3 (space separated!)"</span> <span class="nt" style="color: #000080;">/></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="xml">                    <span class="nt" style="color: #000080;"><sanitizer></span></span>

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="xml">                        <span class="nt" style="color: #000080;"><valid</span> <span class="na" style="color: #008080;">initial=</span><span class="s" style="color: #d14;">"string.printable"</span><span class="nt" style="color: #000080;">></span></span>

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<pre style="margin: 0;">+<span id="LC149" class="line" lang="xml">                            <span class="nt" style="color: #000080;"><add</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">" "</span><span class="nt" style="color: #000080;">/></span></span>

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<pre style="margin: 0;">+<span id="LC150" class="line" lang="xml">                        <span class="nt" style="color: #000080;"></valid></span></span>

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<pre style="margin: 0;">+<span id="LC151" class="line" lang="xml">                    <span class="nt" style="color: #000080;"></sanitizer></span></span>

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<pre style="margin: 0;"> <span id="LC152" class="line" lang="xml">                <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">argument=</span><span class="s" style="color: #d14;">"--linesAtTickMarks"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"boolean"</span> <span class="na" style="color: #008080;">truevalue=</span><span class="s" style="color: #d14;">"--linesAtTickMarks"</span> <span class="na" style="color: #008080;">falsevalue=</span><span class="s" style="color: #d14;">""</span></span>

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="xml">                    <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Draw dashed lines in heatmap above all tick marks?"</span> <span class="nt" style="color: #000080;">/></span></span>

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="xml">                <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">argument=</span><span class="s" style="color: #d14;">"--averageTypeSummaryPlot"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -168,19 +183,19 @@</td>

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<pre style="margin: 0;"> <span id="LC183" class="line" lang="xml">                    <span class="na" style="color: #008080;">help=</span><span class="s" style="color: #d14;">"The alpha channel (transparency) to use for the heatmaps. The default is 1.0 and values must</span></span>

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<pre style="margin: 0;"> <span id="LC184" class="line" lang="xml"><span class="s" style="color: #d14;">                    be between 0 and 1. A value of 0.0 would be fully transparent."</span> <span class="nt" style="color: #000080;">/></span></span>

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

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<pre style="margin: 0;">-<span id="LC171" class="line" lang="xml">                <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">argument=</span><span class="s" style="color: #d14;">"--colorList"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"text"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">""</span> <span class="na" style="color: #008080;"><span class="idiff left">size=</span></span><span class="s" style="color: #d14;"><span class="idiff">"50"</span></span><span class="idiff right"> </span><span class="na" style="color: #008080;">optional=</span><span class="s" style="color: #d14;">"True"</span></span>

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<pre style="margin: 0;">+<span id="LC186" class="line" lang="xml">                <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">argument=</span><span class="s" style="color: #d14;">"--colorList"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"text"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">""</span> <span class="na" style="color: #008080;">optional=</span><span class="s" style="color: #d14;">"True"</span></span>

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<pre style="margin: 0;"> <span id="LC187" class="line" lang="xml">                    <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"List of colors for each heatmap. Separate lists by spaces and the colors in the list by comas"</span></span>

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<td class="diff-line-num new_line" data-linenumber="188" style="width: 35px; color: rgba(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="LC188" class="line" lang="xml">                    <span class="na" style="color: #008080;">help=</span><span class="s" style="color: #d14;">"The color of the heatmaps can be specified as a list of colors separated by comas with</span></span>

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<td class="diff-line-num new_line" data-linenumber="189" style="width: 35px; color: rgba(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="LC189" class="line" lang="xml"><span class="s" style="color: #d14;">                    not space in between. For example: white,blue white,green will set a color map from white</span></span>

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC190" class="line" lang="xml"><span class="s" style="color: #d14;">                    to blue for the first heatmap and for white to green for the next heatmap."</span><span class="nt" style="color: #000080;">/></span></span>

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<pre style="margin: 0;"> <span id="LC191" class="line" lang="xml">                <span class="nt" style="color: #000080;"><expand</span> <span class="na" style="color: #008080;">macro=</span><span class="s" style="color: #d14;">"zMin_zMax"</span> <span class="nt" style="color: #000080;">/></span></span>

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<td class="diff-line-num old old_line" data-linenumber="177" 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">

177

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<td class="diff-line-num new_line old" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC177" class="line" lang="xml">                <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">argument=</span><span class="s" style="color: #d14;">"--yMin"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"float"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">""</span> <span class="na" style="color: #008080;"><span class="idiff left">size=</span></span><span class="s" style="color: #d14;"><span class="idiff">"3"</span></span><span class="idiff right"> </span><span class="na" style="color: #008080;">optional=</span><span class="s" style="color: #d14;">"True"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

192

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<pre style="margin: 0;">+<span id="LC192" class="line" lang="xml">                <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">argument=</span><span class="s" style="color: #d14;">"--yMin"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"float"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">""</span> <span class="na" style="color: #008080;">optional=</span><span class="s" style="color: #d14;">"True"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

178

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<td class="diff-line-num new_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

193

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<pre style="margin: 0;"> <span id="LC193" class="line" lang="xml">                    <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Minimum value for the Y-axis of the summary plot. Leave empty for automatic values"</span> <span class="na" style="color: #008080;">help=</span><span class="s" style="color: #d14;">""</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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

179

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<td class="diff-line-num new_line old" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC179" class="line" lang="xml">                <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">argument=</span><span class="s" style="color: #d14;">"--yMax"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"float"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">""</span> <span class="na" style="color: #008080;"><span class="idiff left">size=</span></span><span class="s" style="color: #d14;"><span class="idiff">"3"</span></span><span class="idiff right"> </span><span class="na" style="color: #008080;">optional=</span><span class="s" style="color: #d14;">"True"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

194

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<pre style="margin: 0;">+<span id="LC194" class="line" lang="xml">                <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">argument=</span><span class="s" style="color: #d14;">"--yMax"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"float"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">""</span> <span class="na" style="color: #008080;">optional=</span><span class="s" style="color: #d14;">"True"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

180

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<td class="diff-line-num new_line" 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">

195

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<pre style="margin: 0;"> <span id="LC195" class="line" lang="xml">                    <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Maximum value for Y-axis of the summary plot. Leave empty for automatic values"</span> <span class="na" style="color: #008080;">help=</span><span class="s" style="color: #d14;">""</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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

181

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<td class="diff-line-num new_line old" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC181" class="line" lang="xml">                <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">argument=</span><span class="s" style="color: #d14;">"--xAxisLabel"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"text"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"distance from TSS (bp)"</span><span class="idiff left"> </span><span class="na" style="color: #008080;"><span class="idiff">size=</span></span><span class="s" style="color: #d14;"><span class="idiff right">"200"</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

196

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<pre style="margin: 0;">+<span id="LC196" class="line" lang="xml">                <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">argument=</span><span class="s" style="color: #d14;">"--xAxisLabel"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"text"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"distance from TSS (bp)"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

182

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<td class="diff-line-num new_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

197

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

<pre style="margin: 0;"> <span id="LC197" class="line" lang="xml">                    <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"The x-axis label"</span> <span class="na" style="color: #008080;">help=</span><span class="s" style="color: #d14;">""</span> <span class="nt" style="color: #000080;">/></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="183" 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">

183

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<td class="diff-line-num new_line old" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC183" class="line" lang="xml">                <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">argument=</span><span class="s" style="color: #d14;">"--yAxisLabel"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"text"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"genes"</span><span class="idiff left"> </span><span class="na" style="color: #008080;"><span class="idiff">size=</span></span><span class="s" style="color: #d14;"><span class="idiff right">"30"</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

198

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<pre style="margin: 0;">+<span id="LC198" class="line" lang="xml">                <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">argument=</span><span class="s" style="color: #d14;">"--yAxisLabel"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"text"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"genes"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

184

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

199

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<pre style="margin: 0;"> <span id="LC199" class="line" lang="xml">                    <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"The y-axis label for the top panel"</span> <span class="na" style="color: #008080;">help=</span><span class="s" style="color: #d14;">""</span> <span class="nt" style="color: #000080;">/></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

185

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

200

</td>

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

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

186

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<td class="diff-line-num new_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

201

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

<pre style="margin: 0;"> <span id="LC201" class="line" lang="xml">                <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">argument=</span><span class="s" style="color: #d14;">"--heatmapWidth"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"float"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"7.5"</span> <span class="na" style="color: #008080;">min=</span><span class="s" style="color: #d14;">"1"</span> <span class="na" style="color: #008080;">max=</span><span class="s" style="color: #d14;">"100"</span></span>

</pre>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="210" style="width: 35px; color: rgba(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">@@ -195,17 +210,17 @@</td>

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<td class="diff-line-num old_line" 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">

195

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<td class="diff-line-num new_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

210

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<pre style="margin: 0;"> <span id="LC210" class="line" lang="xml">                    <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"heatmap and colorbar"</span><span class="nt" style="color: #000080;">></span>heatmap and colorbar<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<td class="diff-line-num old_line" 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">

196

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<td class="diff-line-num new_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

211

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<pre style="margin: 0;"> <span id="LC211" class="line" lang="xml">                <span class="nt" style="color: #000080;"></param></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

197

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<td class="diff-line-num new_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

212

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<pre style="margin: 0;"> <span id="LC212" class="line" lang="xml"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

198

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<td class="diff-line-num new_line old" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC198" class="line" lang="xml">                <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">argument=</span><span class="s" style="color: #d14;">"--startLabel"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"text"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"TSS"</span><span class="idiff left"> </span><span class="na" style="color: #008080;"><span class="idiff">size=</span></span><span class="s" style="color: #d14;"><span class="idiff right">"10"</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

213

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<pre style="margin: 0;">+<span id="LC213" class="line" lang="xml">                <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">argument=</span><span class="s" style="color: #d14;">"--startLabel"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"text"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"TSS"</span></span>

</pre>

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

199

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<td class="diff-line-num 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">

214

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<pre style="margin: 0;"> <span id="LC214" class="line" lang="xml">                    <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Label for the region start"</span></span>

</pre>

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

200

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<td class="diff-line-num new_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

215

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<pre style="margin: 0;"> <span id="LC215" class="line" lang="xml">                    <span class="na" style="color: #008080;">help =</span><span class="s" style="color: #d14;">"Only for scale-regions mode. Label shown in the plot for the start of the region. Default is TSS (transcription start site), but could be changed to anything, e.g. &quot;peak start&quot;."</span> <span class="nt" style="color: #000080;">/></span></span>

</pre>

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

201

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<td class="diff-line-num new_line old" data-linenumber="216" 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="xml">                <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">argument=</span><span class="s" style="color: #d14;">"--endLabel"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"text"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"TES"</span><span class="idiff left"> </span><span class="na" style="color: #008080;"><span class="idiff">size=</span></span><span class="s" style="color: #d14;"><span class="idiff right">"10"</span></span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

216

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<pre style="margin: 0;">+<span id="LC216" class="line" lang="xml">                <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">argument=</span><span class="s" style="color: #d14;">"--endLabel"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"text"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"TES"</span></span>

</pre>

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<td class="diff-line-num old_line" 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">

202

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<td class="diff-line-num new_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

217

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<pre style="margin: 0;"> <span id="LC217" class="line" lang="xml">                    <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Label for the region end"</span></span>

</pre>

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<td class="diff-line-num old_line" 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">

203

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<td class="diff-line-num new_line" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

218

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<pre style="margin: 0;"> <span id="LC218" class="line" lang="xml">                    <span class="na" style="color: #008080;">help=</span><span class="s" style="color: #d14;">"Only for scale-regions mode. Label shown in the plot for the region end. Default is TES (transcription end site)."</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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<td class="diff-line-num old_line" 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">

204

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<td class="diff-line-num new_line" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

219

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

<pre style="margin: 0;"> <span id="LC219" class="line" lang="xml"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

205

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<td class="diff-line-num new_line old" data-linenumber="220" 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="LC205" class="line" lang="xml">                <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">argument=</span><span class="s" style="color: #d14;">"--referencePointLabel"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"text"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"TSS"</span><span class="idiff left"> </span><span class="na" style="color: #008080;"><span class="idiff">size=</span></span><span class="s" style="color: #d14;"><span class="idiff right">"10"</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

220

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<pre style="margin: 0;">+<span id="LC220" class="line" lang="xml">                <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">argument=</span><span class="s" style="color: #d14;">"--referencePointLabel"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"text"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"TSS"</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

206

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<td class="diff-line-num new_line" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

221

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<pre style="margin: 0;"> <span id="LC221" class="line" lang="xml">                    <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Reference point label"</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

207

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<td class="diff-line-num new_line" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

222

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

<pre style="margin: 0;"> <span id="LC222" class="line" lang="xml">                    <span class="na" style="color: #008080;">help =</span><span class="s" style="color: #d14;">"Label shown in the plot for the reference-point. Default is the same as the reference point selected (e.g. TSS), but could be anything, e.g. &quot;peak start&quot; etc."</span> <span class="nt" style="color: #000080;">/></span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="208" 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">

208

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<td class="diff-line-num new_line old" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC208" class="line" lang="xml">                <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">argument=</span><span class="s" style="color: #d14;">"--samplesLabel"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"text"</span><span class="idiff left"> </span><span class="na" style="color: #008080;"><span class="idiff">size=</span></span><span class="s" style="color: #d14;"><span class="idiff right">"30"</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

223

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<pre style="margin: 0;">+<span id="LC223" class="line" lang="xml">                <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">argument=</span><span class="s" style="color: #d14;">"--samplesLabel"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"text"</span></span>

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<pre style="margin: 0;"> <span id="LC224" class="line" lang="xml">                    <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Labels for the samples (each bigwig) plotted"</span></span>

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<pre style="margin: 0;"> <span id="LC225" class="line" lang="xml">                    <span class="na" style="color: #008080;">help=</span><span class="s" style="color: #d14;">"The default is to use the file name of the sample. The sample labels should be separated by</span></span>

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<pre style="margin: 0;"> <span id="LC226" class="line" lang="xml"><span class="s" style="color: #d14;">                    spaces and quoted if a label itself contains a space E.g. label-1 &quot;label 2&quot;"</span><span class="nt" style="color: #000080;">></span></span>

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<pre style="margin: 0;"> <span id="LC229" class="line" lang="xml">                        <span class="nt" style="color: #000080;"></valid></span></span>

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<pre style="margin: 0;"> <span id="LC230" class="line" lang="xml">                    <span class="nt" style="color: #000080;"></sanitizer></span></span>

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<pre style="margin: 0;"> <span id="LC231" class="line" lang="xml">                <span class="nt" style="color: #000080;"></param></span></span>

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<pre style="margin: 0;">-<span id="LC217" class="line" lang="xml">                <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">argument=</span><span class="s" style="color: #d14;">"--regionsLabel"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"text"</span><span class="idiff left"> </span><span class="na" style="color: #008080;"><span class="idiff">size=</span></span><span class="s" style="color: #d14;"><span class="idiff right">"30"</span></span></span>

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<pre style="margin: 0;">+<span id="LC232" class="line" lang="xml">                <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">argument=</span><span class="s" style="color: #d14;">"--regionsLabel"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"text"</span></span>

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="xml">                    <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Labels for the regions plotted in the heatmap"</span></span>

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<pre style="margin: 0;"> <span id="LC234" class="line" lang="xml">                    <span class="na" style="color: #008080;">help=</span><span class="s" style="color: #d14;">"If more than one region is being plotted a list of labels separated by space is required.</span></span>

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<pre style="margin: 0;"> <span id="LC235" class="line" lang="xml"><span class="s" style="color: #d14;">                          If a label itself contains a space, then quotes are needed.</span></span>

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<pre style="margin: 0;"> <span id="LC243" class="line" lang="xml">                    <span class="na" style="color: #008080;">help=</span><span class="s" style="color: #d14;">"The default is to make one plot per bigWig file, i.e., all samples next to each other. Choosing this option will make one plot per group of regions."</span><span class="nt" style="color: #000080;">/></span></span>

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<pre style="margin: 0;"> <span id="LC244" class="line" lang="xml"></span>

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<pre style="margin: 0;"> <span id="LC245" class="line" lang="xml">                <span class="nt" style="color: #000080;"><expand</span> <span class="na" style="color: #008080;">macro=</span><span class="s" style="color: #d14;">"kmeans_clustering"</span> <span class="nt" style="color: #000080;">/></span></span>

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<pre style="margin: 0;">+<span id="LC246" class="line" lang="xml">                <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">argument=</span><span class="s" style="color: #d14;">"--clusterUsingSamples"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"text"</span></span>

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<pre style="margin: 0;">+<span id="LC247" class="line" lang="xml">                    <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"List of samples to be used for clustering"</span></span>

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<pre style="margin: 0;">+<span id="LC248" class="line" lang="xml">                    <span class="na" style="color: #008080;">help=</span><span class="s" style="color: #d14;">"List of sample numbers (order as in matrix), which are used by --kmeans or --hclust for clustering.</span></span>

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<pre style="margin: 0;">+<span id="LC249" class="line" lang="xml"><span class="s" style="color: #d14;">                    If no value is set, it uses all samples. Example: 1 3 (space separated!)"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC250" class="line" lang="xml">                    <span class="nt" style="color: #000080;"><sanitizer></span></span>

</pre>

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251

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<pre style="margin: 0;">+<span id="LC251" class="line" lang="xml">                        <span class="nt" style="color: #000080;"><valid</span> <span class="na" style="color: #008080;">initial=</span><span class="s" style="color: #d14;">"string.printable"</span><span class="nt" style="color: #000080;">></span></span>

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<pre style="margin: 0;">+<span id="LC252" class="line" lang="xml">                            <span class="nt" style="color: #000080;"><add</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">" "</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC253" class="line" lang="xml">                        <span class="nt" style="color: #000080;"></valid></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC254" class="line" lang="xml">                    <span class="nt" style="color: #000080;"></sanitizer></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC255" class="line" lang="xml">            <span class="nt" style="color: #000080;"></when></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC256" class="line" lang="xml">        <span class="nt" style="color: #000080;"></conditional></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC257" class="line" lang="xml">    <span class="nt" style="color: #000080;"></inputs></span></span>

</pre>

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