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GitLab

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<h3>

Steffen Möller pushed to branch upstream

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/7fef8d996fc172611f17a915e8a19efaa420978e">7fef8d99</a></strong>

<div>

<span>by Steffen Moeller</span>

<i>at 2020-04-08T12:16:18+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.4.2</pre>

</li>

</ul>

<h4>12 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#7ceee5d954a74b8640cc2bfd6c27b8fdf07d7045">

.github/workflows/test.yml

</a>

</li>

<li class="file-stats">

<a href="#3251d7a8143ce2e789f0468513df8f285f842c3a">

CHANGES.txt

</a>

</li>

<li class="file-stats">

<a href="#40ebc6823f24f296c0cd3fddd6ccda69b74ff2e4">

azure-pipelines.yml

</a>

</li>

<li class="file-stats">

<a href="#3ec39721c34812eb70f07264b96298182b24bca7">

deeptools/_version.py

</a>

</li>

<li class="file-stats">

<a href="#6535c71146ed29c18429c39896921c2ac0405ecf">

deeptools/bamPEFragmentSize.py

</a>

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<li class="file-stats">

<a href="#7abbfd754c96a0b533b2bcc3a0f5aac1f2d6de25">

deeptools/correlation.py

</a>

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<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="#3b1b774550da48a0e92eb6e50749aee4b11a1cc8">

deeptools/writeBedGraph_bam_and_bw.py

</a>

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<li class="file-stats">

<a href="#d2de9c6869fd65911899bace5f34a175e96efb2a">

galaxy/wrapper/deepTools_macros.xml

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<li class="file-stats">

<a href="#4b09717b50a322a8efb600457155a8276deca7af">

galaxy/wrapper/plotCoverage.xml

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<li class="file-stats">

<a href="#84b200ead4096f88da1811d06b79ecc1b09fcadd">

galaxy/wrapper/plotHeatmap.xml

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="7ceee5d954a74b8640cc2bfd6c27b8fdf07d7045">

<a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/7fef8d996fc172611f17a915e8a19efaa420978e#7ceee5d954a74b8640cc2bfd6c27b8fdf07d7045"><strong>.github/workflows/test.yml</strong></a>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -32,6 +32,7 @@ jobs:</td>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="yaml">    <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">dpryan79/github-actions/@master"</span></span>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="yaml">    <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Test deepTools</span></span>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="yaml">      <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>

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

</pre>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="yaml">        <span class="s" style="color: #d14;">source activate foo</span></span>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="yaml">        <span class="s" style="color: #d14;">nosetests --with-doctest -sv deeptools</span></span>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="yaml">  <span class="na" style="color: #008080;">planemo</span><span class="pi">:</span></span>

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<li id="3251d7a8143ce2e789f0468513df8f285f842c3a">

<a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/7fef8d996fc172611f17a915e8a19efaa420978e#3251d7a8143ce2e789f0468513df8f285f842c3a"><strong>CHANGES.txt</strong></a>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">3.4.2</span>

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

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Programmed around a bug in matplotlib that prevented the plotCorrelation scatter plot from working. See https://bioinformatics.stackexchange.com/questions/12830/plot-correlation-between-several-bam-files/12831</span>

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

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">3.4.1</span>

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

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Prevented temporary bedGraph files from being written to (possibly small) shared-memory drives even when TMPDIR is set to somewhere else. Now shared memory is only used if requested by setting TMPDIR (or other appropriate environment variables) to `/dev/shm`.</span>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Fixed a bug in bamPEFragmentSize that caused incompatibility with newer matplotlib releases. (issue #928)</span>

</pre>

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9

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

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">3.4.0</span>

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

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * Fixed a bug in one of the Galaxy wrappers.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> * Added the `--lineAtTickMarks` option to `plotHeatmap` so that there are dashed vertical lines for each tick mark in the plot. (issue #924)</span>

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

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">3.3.2</span>

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

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> * Fixed --yAxisLabel in plotProfile (issue #889)</span>

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<br>

</li>

<li id="40ebc6823f24f296c0cd3fddd6ccda69b74ff2e4">

<a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/7fef8d996fc172611f17a915e8a19efaa420978e#40ebc6823f24f296c0cd3fddd6ccda69b74ff2e4"><strong>azure-pipelines.yml</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,19 +17,20 @@ jobs:</td>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="yaml">    <span class="na" style="color: #008080;">displayName</span><span class="pi">:</span> <span class="s" style="color: #d14;">Add conda to PATH</span></span>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="yaml">  <span class="pi">-</span> <span class="na" style="color: #008080;">template</span><span class="pi">:</span> <span class="s" style="color: #d14;">.azure-pipelines/test-template.yml</span></span>

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

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="yaml"><span class="pi">-</span> <span class="na" style="color: #008080;">job</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">OSX'</span></span>

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="yaml">  <span class="na" style="color: #008080;">pool</span><span class="pi">:</span></span>

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="yaml">    <span class="na" style="color: #008080;">vmImage</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">macOS-10.13'</span></span>

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="yaml">  <span class="na" style="color: #008080;">strategy</span><span class="pi">:</span></span>

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="yaml">    <span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="yaml">      <span class="na" style="color: #008080;">Python37</span><span class="pi">:</span></span>

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="yaml">        <span class="s" style="color: #d14;">python.version</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">3.7'</span></span>

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="yaml">    <span class="na" style="color: #008080;">maxParallel</span><span class="pi">:</span> <span class="m" style="color: #099;">1</span></span>

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

</pre>

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="yaml">  <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="yaml">  <span class="pi">-</span> <span class="na" style="color: #008080;">bash</span><span class="pi">:</span> <span class="s" style="color: #d14;">echo "##vso[task.prependpath]$CONDA/bin"</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="yaml">    <span class="na" style="color: #008080;">displayName</span><span class="pi">:</span> <span class="s" style="color: #d14;">Add conda to PATH</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="yaml">  <span class="pi">-</span> <span class="na" style="color: #008080;">template</span><span class="pi">:</span> <span class="s" style="color: #d14;">.azure-pipelines/test-template.yml</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#Fails frequently due to CI issues</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#- job: 'OSX'</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  pool:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#    vmImage: 'macOS-10.14'</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  strategy:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#    matrix:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#      Python37:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#        python.version: '3.7'</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#    maxParallel: 1</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  steps:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - bash: echo "##vso[task.prependpath]$CONDA/bin"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#    displayName: Add conda to PATH</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - template: .azure-pipelines/test-template.yml</span></span>

</pre>

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

</pre>

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="yaml"><span class="pi">-</span> <span class="na" style="color: #008080;">job</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">galaxy'</span></span>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="yaml">  <span class="na" style="color: #008080;">dependsOn</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">Linux'</span></span>

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<li id="3ec39721c34812eb70f07264b96298182b24bca7">

<a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/7fef8d996fc172611f17a915e8a19efaa420978e#3ec39721c34812eb70f07264b96298182b24bca7"><strong>deeptools/_version.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">@@ -2,4 +2,4 @@</td>

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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>

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<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>

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

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"><span class="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">3</span>.2'</span></span></pre>

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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</span>.2'</span></span></pre>

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<li id="6535c71146ed29c18429c39896921c2ac0405ecf">

<a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/7fef8d996fc172611f17a915e8a19efaa420978e#6535c71146ed29c18429c39896921c2ac0405ecf"><strong>deeptools/bamPEFragmentSize.py</strong></a>

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python"><span class="s" style="color: #d14;">    This is essentially computing what hist() in matplotlib is doing and returning the results.</span></span>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python"><span class="s" style="color: #d14;">    This then allows us to free up the memory consumed by each sample rather than returning it all back to main() for plotting.</span></span>

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

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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python">    <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">bins</span><span class="p">,</span> <span class="n" style="color: #333;">patches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">plt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">hist</span><span class="p">(</span><span class="n" style="color: #333;">lengths</span><span class="p">,</span> <span class="n" style="color: #333;">bins</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">100</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">range</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">minVal</span><span class="p">,</span> <span class="n" style="color: #333;">maxVal</span><span class="p">),</span> <span class="n" style="color: #333;"><span class="idiff left right">normed</span></span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python">    <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">bins</span><span class="p">,</span> <span class="n" style="color: #333;">patches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">plt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">hist</span><span class="p">(</span><span class="n" style="color: #333;">lengths</span><span class="p">,</span> <span class="n" style="color: #333;">bins</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">100</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">range</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">minVal</span><span class="p">,</span> <span class="n" style="color: #333;">maxVal</span><span class="p">),</span> <span class="n" style="color: #333;"><span class="idiff left right">density</span></span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python">    <span class="n" style="color: #333;">plt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">clf</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">bins</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python"></span>

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<li id="7abbfd754c96a0b533b2bcc3a0f5aac1f2d6de25">

<a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/7fef8d996fc172611f17a915e8a19efaa420978e#7abbfd754c96a0b533b2bcc3a0f5aac1f2d6de25"><strong>deeptools/correlation.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">@@ -527,9 +527,9 @@ class Correlation:</td>

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<pre style="margin: 0;"> <span id="LC527" 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="LC528" class="line" lang="python">                <span class="n" style="color: #333;">ax</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_xticklabels</span><span class="p">([])</span></span>

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<pre style="margin: 0;"> <span id="LC529" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC530" class="line" lang="python">            <span class="n" style="color: #333;">ax</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">hist2d</span><span class="p">(</span><span class="n" style="color: #333;">vector2</span><span class="p">,</span> <span class="n" style="color: #333;">vector1</span><span class="p">,</span> <span class="n" style="color: #333;">bins</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">200</span><span class="p">,</span> <span class="n" style="color: #333;">cmin</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.1</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC530" class="line" lang="python">            <span class="n" style="color: #333;">ax</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_xlim</span><span class="p">(</span><span class="n" style="color: #333;">min_xvalue</span><span class="p">,</span> <span class="n" style="color: #333;">max_xvalue</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC531" class="line" lang="python">            <span class="n" style="color: #333;">ax</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_ylim</span><span class="p">(</span><span class="n" style="color: #333;">min_yvalue</span><span class="p">,</span> <span class="n" style="color: #333;">max_yvalue</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC532" class="line" lang="python">            <span class="n" style="color: #333;">ax</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">hist2d</span><span class="p">(</span><span class="n" style="color: #333;">vector2</span><span class="p">,</span> <span class="n" style="color: #333;">vector1</span><span class="p">,</span> <span class="n" style="color: #333;">bins</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">200</span><span class="p">,</span> <span class="n" style="color: #333;">cmin</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.1</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC533" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC534" class="line" lang="python">        <span class="n" style="color: #333;">plt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">savefig</span><span class="p">(</span><span class="n" style="color: #333;">plot_filename</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">format</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">image_format</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;">plt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>

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<li id="d92843efb3711927a1683755b7c9df524fc9274d">

<a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/7fef8d996fc172611f17a915e8a19efaa420978e#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">@@ -611,6 +611,12 @@ def heatmapperOptionalArgs(mode=['heatmap', 'profile'][0]):</td>

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<pre style="margin: 0;"> <span id="LC611" class="line" lang="python">                              <span class="s" style="color: #d14;">'example: --sortUsingSamples 1 3'</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC612" 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>

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

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<td class="diff-line-num new new_line" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC614" class="line" lang="python">        <span class="n" style="color: #333;">optional</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--linesAtTickMarks'</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;">'Draw dashed lines from all tick marks through the heatmap. '</span></span>

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<pre style="margin: 0;">+<span id="LC616" class="line" lang="python">                              <span class="s" style="color: #d14;">'This is then similar to the dashed line draw at region bounds '</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); 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">

617

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<pre style="margin: 0;">+<span id="LC617" class="line" lang="python">                              <span class="s" style="color: #d14;">'when using a reference point and --sortUsing region_length'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); 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">

618

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<pre style="margin: 0;">+<span id="LC618" class="line" lang="python">                              <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); 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="619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

619

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<pre style="margin: 0;">+<span id="LC619" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num 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">

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<td class="diff-line-num new_line" data-linenumber="620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

620

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<pre style="margin: 0;"> <span id="LC620" class="line" lang="python">        <span class="n" style="color: #333;">optional</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--clusterUsingSamples'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

615

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<td class="diff-line-num new_line" data-linenumber="621" style="width: 35px; color: rgba(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="LC621" 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 '</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="616" style="width: 35px; color: rgba(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="622" style="width: 35px; color: rgba(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="LC622" class="line" lang="python">                              <span class="s" style="color: #d14;">'matrix), that are used for clustering by '</span></span>

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<br>

</li>

<li id="e6f336c84329d2021242809e76ed32e6ed05fecc">

<a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/7fef8d996fc172611f17a915e8a19efaa420978e#e6f336c84329d2021242809e76ed32e6ed05fecc"><strong>deeptools/plotHeatmap.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -389,6 +389,7 @@ def plotMatrix(hm, outFileName,</td>

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<td class="diff-line-num old_line" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

389

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<td class="diff-line-num new_line" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC389" class="line" lang="python">               <span class="n" style="color: #333;">heatmapWidth</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">7.5</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC390" class="line" lang="python">               <span class="n" style="color: #333;">perGroup</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">whatToShow</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'plot, heatmap and colorbar'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

391

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<td class="diff-line-num new_line" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC391" class="line" lang="python">               <span class="n" style="color: #333;">plot_type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'lines'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC392" class="line" lang="python">               <span class="n" style="color: #333;">linesAtTickMarks</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC393" class="line" lang="python">               <span class="n" style="color: #333;">image_format</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="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC394" class="line" lang="python">               <span class="n" style="color: #333;">legend_location</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'upper-left'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

395

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<pre style="margin: 0;"> <span id="LC395" class="line" lang="python">               <span class="n" style="color: #333;">box_around_heatmaps</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="539" style="width: 35px; color: rgba(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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -539,7 +540,7 @@ def plotMatrix(hm, outFileName,</td>

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<td class="diff-line-num old_line" data-linenumber="539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

539

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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">

540

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<pre style="margin: 0;"> <span id="LC540" class="line" lang="python">                        <span class="n" style="color: #333;">_len</span> <span class="o" style="font-weight: 600;">*=</span> <span class="mf" style="color: #099;">0.5</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

541

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<pre style="margin: 0;"> <span id="LC541" class="line" lang="python">                        <span class="n" style="color: #333;">_reg_len</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">hm</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameters</span><span class="p">[</span><span class="s" style="color: #d14;">'upstream'</span><span class="p">][</span><span class="n" style="color: #333;">idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_len</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">hm</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameters</span><span class="p">[</span><span class="s" style="color: #d14;">'bin size'</span><span class="p">][</span><span class="n" style="color: #333;">idx</span><span class="p">])</span></span>

</pre>

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541

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<pre style="margin: 0;"> <span id="LC542" class="line" lang="python">                    <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">hm</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameters</span><span class="p">[</span><span class="s" style="color: #d14;">'ref point'</span><span class="p">][</span><span class="n" style="color: #333;">idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'TES'</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC542" class="line" lang="python">                        <span class="n" style="color: #333;">_reg_len</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">hm</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameters</span><span class="p">[</span><span class="s" style="color: #d14;">'<span class="idiff left right">down</span>stream'</span><span class="p">][</span><span class="n" style="color: #333;">idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">_len</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">hm</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameters</span><span class="p">[</span><span class="s" style="color: #d14;">'bin size'</span><span class="p">][</span><span class="n" style="color: #333;">idx</span><span class="p">])</span></span>

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<pre style="margin: 0;">+<span id="LC543" class="line" lang="python">                        <span class="n" style="color: #333;">_reg_len</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">hm</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameters</span><span class="p">[</span><span class="s" style="color: #d14;">'<span class="idiff left right">up</span>stream'</span><span class="p">][</span><span class="n" style="color: #333;">idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">_len</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">hm</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameters</span><span class="p">[</span><span class="s" style="color: #d14;">'bin size'</span><span class="p">][</span><span class="n" style="color: #333;">idx</span><span class="p">])</span></span>

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<pre style="margin: 0;"> <span id="LC544" class="line" lang="python">                <span class="n" style="color: #333;">foo</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">_reg_len</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC545" class="line" lang="python">            <span class="n" style="color: #333;">regions_length_in_bins</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">foo</span></span>

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<pre style="margin: 0;"> <span id="LC546" class="line" lang="python"></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -659,6 +660,18 @@ def plotMatrix(hm, outFileName,</td>

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<pre style="margin: 0;"> <span id="LC660" class="line" lang="python">            <span class="k" style="font-weight: 600;">elif</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">perGroup</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">sample</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC661" class="line" lang="python">                <span class="n" style="color: #333;">ax</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">axes</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_ylabel</span><span class="p">(</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="LC662" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC663" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># Plot vertical lines at tick marks if desired</span></span>

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<pre style="margin: 0;">+<span id="LC664" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">linesAtTickMarks</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC665" class="line" lang="python">                <span class="n" style="color: #333;">xticks_heat</span><span class="p">,</span> <span class="n" style="color: #333;">xtickslabel_heat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hm</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getTicks</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="LC666" class="line" lang="python">                <span class="n" style="color: #333;">xticks_heat</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="mf" style="color: #099;">0.5</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_heat</span><span class="p">]</span>  <span class="c1" style="color: #998; font-style: italic;"># There's an offset of 0.5 compared to the profile plot</span></span>

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<pre style="margin: 0;">+<span id="LC667" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</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_heat</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;">sub_matrix</span><span class="p">[</span><span class="s" style="color: #d14;">'matrix'</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">shape</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]):</span></span>

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<pre style="margin: 0;">+<span id="LC668" 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;">sub_matrix</span><span class="p">[</span><span class="s" style="color: #d14;">'matrix'</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">shape</span><span class="p">[</span><span class="mi" style="color: #099;">1</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_heat</span><span class="p">)</span></span>

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<td class="diff-line-num new new_line" data-linenumber="669" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC669" class="line" lang="python">                    <span class="n" style="color: #333;">xticks_heat_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_heat</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="670" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC670" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); 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="671" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC671" class="line" lang="python">                    <span class="n" style="color: #333;">xticks_heat_use</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xticks_heat</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="672" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC672" class="line" lang="python">                <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_heat_use</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="673" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC673" class="line" lang="python">                    <span class="n" style="color: #333;">ax</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">axvline</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;">x</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;">linewidth</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.5</span><span class="p">,</span> <span class="n" style="color: #333;">dashes</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">))</span></span>

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<td class="diff-line-num new new_line" data-linenumber="674" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC674" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC675" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># add labels to last block in a column</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="676" style="width: 35px; color: rgba(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="LC676" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">perGroup</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">sample</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">numsamples</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> \</span>

</pre>

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<pre style="margin: 0;"> <span id="LC677" class="line" lang="python">               <span class="p">(</span><span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">perGroup</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">group_idx</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">numgroups</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 unfold js-unfold old_line" data-linenumber="845" style="width: 35px; color: rgba(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="858" style="width: 35px; color: rgba(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">@@ -845,6 +858,7 @@ def main(args=None):</td>

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<td class="diff-line-num new_line" data-linenumber="858" style="width: 35px; color: rgba(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="LC858" class="line" lang="python">               <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">heatmapWidth</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="846" style="width: 35px; color: rgba(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="859" style="width: 35px; color: rgba(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="LC859" class="line" lang="python">               <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">perGroup</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

847

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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">

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<pre style="margin: 0;"> <span id="LC860" class="line" lang="python">               <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">whatToShow</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="848" style="width: 35px; color: rgba(0,0,0,0.3); 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="861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

861

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<pre style="margin: 0;">+<span id="LC861" class="line" lang="python">               <span class="n" style="color: #333;">linesAtTickMarks</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">linesAtTickMarks</span><span class="p">,</span></span>

</pre>

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<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">

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

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<td class="diff-line-num new_line" data-linenumber="863" style="width: 35px; color: rgba(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="LC863" class="line" lang="python">               <span class="n" style="color: #333;">image_format</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">plotFileFormat</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="850" style="width: 35px; color: rgba(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="LC864" class="line" lang="python">               <span class="n" style="color: #333;">legend_location</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">legendLocation</span><span class="p">,</span></span>

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</li>

<li id="3b1b774550da48a0e92eb6e50749aee4b11a1cc8">

<a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/7fef8d996fc172611f17a915e8a19efaa420978e#3b1b774550da48a0e92eb6e50749aee4b11a1cc8"><strong>deeptools/writeBedGraph_bam_and_bw.py</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -76,12 +76,7 @@ def writeBedGraph_worker(</td>

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

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python">            <span class="n" style="color: #333;">bigwigHandle</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>

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

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<td class="diff-line-num new_line old" 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="c1" style="color: #998; font-style: italic;"># is /dev/shm available?</span></span>

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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># working in this directory speeds the process</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python">    <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="82" 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="LC82" class="line" lang="python">        <span class="n" style="color: #333;">_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tempfile</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">NamedTemporaryFile</span><span class="p">(</span><span class="nb" style="color: #0086b3;">dir</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"/dev/shm"</span><span class="p">,</span> <span class="n" style="color: #333;">delete</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python">    <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">OSError</span><span class="p">:</span></span>

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

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<pre style="margin: 0;">-<span id="LC84" class="line" lang="python">        <span class="n" style="color: #333;">_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tempfile</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">NamedTemporaryFile</span><span class="p">(</span><span class="n" style="color: #333;">delete</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python">    <span class="n" style="color: #333;">_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tempfile</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">NamedTemporaryFile</span><span class="p">(</span><span class="n" style="color: #333;">delete</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python">    <span class="n" style="color: #333;">previousValue</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python">    <span class="n" style="color: #333;">lengthCoverage</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;">coverage</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>

</pre>

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<br>

</li>

<li id="d2de9c6869fd65911899bace5f34a175e96efb2a">

<a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/7fef8d996fc172611f17a915e8a19efaa420978e#d2de9c6869fd65911899bace5f34a175e96efb2a"><strong>galaxy/wrapper/deepTools_macros.xml</strong></a>

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1

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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>

</pre>

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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">

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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>

</pre>

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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">3</span>.2.0<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">4</span>.2.0<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">3</span>.2"</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">4</span>.2"</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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<br>

</li>

<li id="4b09717b50a322a8efb600457155a8276deca7af">

<a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/7fef8d996fc172611f17a915e8a19efaa420978e#4b09717b50a322a8efb600457155a8276deca7af"><strong>galaxy/wrapper/plotCoverage.xml</strong></a>

<hr>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">            #end if</span></span>

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

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">            #if ' '.join(map(str, $BED)) != 'None':</span></span>

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                #set bedFileL<span class="idiff left right">L</span>ist=[]</span></span>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                #set bedFileList=[]</span></span>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                #for $f in $BED:</span></span>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                    #silent $bedFileList.append("'%s'" % $f)</span></span>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                #end for</span></span>

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<pre style="margin: 0;"> <span id="LC101" 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;">"blacklist"</span> <span class="nt" style="color: #000080;">/></span></span>

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="xml">            <span class="nt" style="color: #000080;"></when></span></span>

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="xml">        <span class="nt" style="color: #000080;"></conditional></span></span>

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<pre style="margin: 0;">-<span id="LC104" class="line" lang="xml"></span>

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<pre style="margin: 0;"> <span id="LC104" 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;">"input_image_file_format"</span> <span class="nt" style="color: #000080;">/></span></span>

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<pre style="margin: 0;"> <span id="LC105" 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;">"--outRawCounts"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"boolean"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Save raw counts (coverages) to a file"</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="LC107" class="line" lang="xml"></span>

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<pre style="margin: 0;">-<span id="LC108" class="line" lang="xml"></span>

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="xml">    <span class="nt" style="color: #000080;"></inputs></span></span>

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="xml">    <span class="nt" style="color: #000080;"><outputs></span></span>

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<pre style="margin: 0;"> <span id="LC108" 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;">"output_image_file_format_not_nested"</span> <span class="nt" style="color: #000080;">/></span></span>

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<br>

</li>

<li id="84b200ead4096f88da1811d06b79ecc1b09fcadd">

<a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/7fef8d996fc172611f17a915e8a19efaa420978e#84b200ead4096f88da1811d06b79ecc1b09fcadd"><strong>galaxy/wrapper/plotHeatmap.xml</strong></a>

<hr>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                    --sortRegions '$advancedOpt.sortRegions'</span></span>

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                #end if</span></span>

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

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<td class="diff-line-num new old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC37" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                #if $advancedOpt.linesAtTickMarks:</span></span>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                    --linesAtTickMarks</span></span>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                #end if</span></span>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="xml"></span>

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41

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                #if $advancedOpt.sortUsing:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

38

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<td class="diff-line-num new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

42

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                    --sortUsing '$advancedOpt.sortUsing'</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

39

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<td class="diff-line-num new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

43

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                #end if</span></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -130,6 +134,8 @@</td>

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

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

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

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<td class="diff-line-num old_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC135" 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="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC136" 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="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); 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="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC138" class="line" lang="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>

</pre>

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<td class="diff-line-num new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

139

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<pre style="margin: 0;"> <span id="LC139" 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>

</pre>

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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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<td class="diff-line-num 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">

140

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="xml">                    <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Type of statistic that should be plotted in the summary image above the heatmap"</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="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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