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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-deeptools">Debian Med / python-deeptools</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/80bc61c7c9f328852df7b0000d1bf869ead7e260">80bc61c7</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-05-05T17:35:07+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/90f6c61587f11e6a4a3e5956286cc48300b34078">90f6c615</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-05-05T17:35:08+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.4.3</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/daefa66b308593f9be1ad9d30e13bd750cda3776">daefa66b</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-05-05T17:35:24+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/3.4.3'
Update to upstream version '3.4.3'
with Debian dir 3d39b53ee0d65031e66a76342cbae421cc9f6c32</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/911dd5dc4fa12b9ee76878808b70bb1cd946aecc">911dd5dc</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-05-05T17:36:07+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
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<h4>7 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#3251d7a8143ce2e789f0468513df8f285f842c3a">
CHANGES.txt
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<li class="file-stats">
<a href="#880d3b3151dcf6927855c6e6df99ad314392de18">
bin/estimateScaleFactor
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#3ec39721c34812eb70f07264b96298182b24bca7">
deeptools/_version.py
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<li class="file-stats">
<a href="#d92843efb3711927a1683755b7c9df524fc9274d">
deeptools/parserCommon.py
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<li class="file-stats">
<a href="#933931be8d4eb6bef5ca9c328d98370ed0c3370a">
deeptools/plotProfile.py
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<li class="file-stats">
<a href="#d2de9c6869fd65911899bace5f34a175e96efb2a">
galaxy/wrapper/deepTools_macros.xml
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<h4>Changes:</h4>
<li id="3251d7a8143ce2e789f0468513df8f285f842c3a">
<a href="https://salsa.debian.org/med-team/python-deeptools/-/compare/064166562018c795f7d3e73b498588729cae03ac...911dd5dc4fa12b9ee76878808b70bb1cd946aecc#3251d7a8143ce2e789f0468513df8f285f842c3a"><strong>CHANGES.txt</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">3.4.3</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Changed iteritems() in estimateEscaleFactor to its python3 compatible items().</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Added the missing argument (--clusterUsingSamples) to plotProfile.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">3.4.2</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="325" style="width: 35px; color: rgba(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="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -325,7 +330,7 @@</td>
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="plaintext"> * bamPEFragmentSize now has -bs and -n options to allow adjusting the number of alignments sampled. Note that the default value is auto-adjusted if the sampling is too sparse.</span>
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<td class="diff-line-num new_line" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="plaintext"> * bamPEFragmentSize now accepts single-end files.</span>
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<td class="diff-line-num new_line" data-linenumber="332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="plaintext"> * The --hclust option to plotProfile and plotHeatmap continues even if one of the groups is too small for plotting (matplotlib will produce a warning that you can ignore). This was issue #280.</span>
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="plaintext"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="plaintext">2.0.1</span>
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="plaintext"> * A critical bug that prevented plotPCA from running was fixed.</span>
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<li id="880d3b3151dcf6927855c6e6df99ad314392de18">
<a href="https://salsa.debian.org/med-team/python-deeptools/-/compare/064166562018c795f7d3e73b498588729cae03ac...911dd5dc4fa12b9ee76878808b70bb1cd946aecc#880d3b3151dcf6927855c6e6df99ad314392de18"><strong>bin/estimateScaleFactor</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -89,9 +89,9 @@ def parseArguments(args=None):</td>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python"><span class="s" style="color: #d14;"> The algorithm samples the genome a number of times as specified<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"><span class="s" style="color: #d14;"> The algorithm samples the genome a number of times as specified</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"><span class="s" style="color: #d14;"> by the --numberOfSamples parameter to estimate scaling factors of</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python"><span class="s" style="color: #d14;"> betweeen to samples<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"><span class="s" style="color: #d14;"> betweeen to samples</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bamfiles</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">2</span><span class="p">:</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -99,14 +99,14 @@ def main(args):</td>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"> <span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"{:,} number of samples will be computed.</span><span class="si" style="color: #d14;">\</span><span class="se" style="color: #d14;">n</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">numberOfSamples</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">sizeFactorsDict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">estimateScaleFactor</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bamfiles</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">sampleWindowLength</span><span class="p">,</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">sizeFactorsDict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">estimateScaleFactor</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bamfiles</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">sampleWindowLength</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">numberOfSamples</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">normalizationLength</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">numberOfProcessors</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">numberOfProcessors</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">chrsToSkip</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">ignoreForNormalization</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">verbose</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">verbose</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sizeFactorsDict</span><span class="p">.</span><span class="n" style="color: #333;">ite<span class="idiff left right">rite</span>ms</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sizeFactorsDict</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"{}: {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/python-deeptools/-/compare/064166562018c795f7d3e73b498588729cae03ac...911dd5dc4fa12b9ee76878808b70bb1cd946aecc#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python-deeptools (3.4.3-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Tue, 05 May 2020 17:35:30 +0200</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">python-deeptools (3.4.2-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * New upstream version</span>
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<a href="https://salsa.debian.org/med-team/python-deeptools/-/compare/064166562018c795f7d3e73b498588729cae03ac...911dd5dc4fa12b9ee76878808b70bb1cd946aecc#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;">'3.4.<span class="idiff left right">2</span>'</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;">'3.4.<span class="idiff left right">3</span>'</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-deeptools/-/compare/064166562018c795f7d3e73b498588729cae03ac...911dd5dc4fa12b9ee76878808b70bb1cd946aecc#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">@@ -573,6 +573,14 @@ def heatmapperOptionalArgs(mode=['heatmap', 'profile'][0]):</td>
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<pre style="margin: 0;"> <span id="LC573" 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>
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<pre style="margin: 0;"> <span id="LC574" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">8</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC575" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="python"> <span class="n" style="color: #333;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--clusterUsingSamples'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC577" 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>
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="python"> <span class="s" style="color: #d14;">'matrix), that are used for clustering by '</span></span>
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="python"> <span class="s" style="color: #d14;">'--kmeans or --hclust if not given, all samples '</span></span>
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="python"> <span class="s" style="color: #d14;">'are taken into account for clustering. '</span></span>
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="python"> <span class="s" style="color: #d14;">'Example: --ClusterUsingSamples 1 3'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC582" 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="LC583" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC584" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'heatmap'</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC585" class="line" lang="python"> <span class="n" style="color: #333;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC586" class="line" lang="python"> <span class="s" style="color: #d14;">'--plotType'</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/python-deeptools/-/compare/064166562018c795f7d3e73b498588729cae03ac...911dd5dc4fa12b9ee76878808b70bb1cd946aecc#933931be8d4eb6bef5ca9c328d98370ed0c3370a"><strong>deeptools/plotProfile.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -909,12 +909,12 @@ def main(args=None):</td>
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<pre style="margin: 0;"> <span id="LC909" class="line" lang="python"> <span class="n" style="color: #333;">filterHeatmapValues</span><span class="p">(</span><span class="n" style="color: #333;">hm</span><span class="p">,</span> <span class="n" style="color: #333;">hm</span><span class="p">.</span><span class="n" style="color: #333;">parameters</span><span class="p">[</span><span class="s" style="color: #d14;">'min threshold'</span><span class="p">],</span> <span class="n" style="color: #333;">hm</span><span class="p">.</span><span class="n" style="color: #333;">parameters</span><span class="p">[</span><span class="s" style="color: #d14;">'max threshold'</span><span class="p">])</span></span>
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910
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<pre style="margin: 0;"> <span id="LC910" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC911" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">kmeans</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC912" class="line" lang="python"> <span class="n" style="color: #333;">hm</span><span class="p">.</span><span class="n" style="color: #333;">matrix</span><span class="p">.</span><span class="n" style="color: #333;">hmcluster</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">kmeans</span><span class="p">,</span> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'kmeans'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC912" class="line" lang="python"> <span class="n" style="color: #333;">hm</span><span class="p">.</span><span class="n" style="color: #333;">matrix</span><span class="p">.</span><span class="n" style="color: #333;">hmcluster</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">kmeans</span><span class="p">,</span> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'kmeans'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">clustering_samples</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">clusterUsingSamples</span></span><span class="p">)</span></span>
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913
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<pre style="margin: 0;"> <span id="LC913" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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914
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<pre style="margin: 0;"> <span id="LC914" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">hclust</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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915
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915
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<pre style="margin: 0;"> <span id="LC915" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Performing hierarchical clustering."</span></span>
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916
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<pre style="margin: 0;"> <span id="LC916" class="line" lang="python"> <span class="s" style="color: #d14;">"Please note that it might be very slow for large datasets.</span><span class="si" style="color: #d14;">\</span><span class="se" style="color: #d14;">n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC917" class="line" lang="python"> <span class="n" style="color: #333;">hm</span><span class="p">.</span><span class="n" style="color: #333;">matrix</span><span class="p">.</span><span class="n" style="color: #333;">hmcluster</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">hclust</span><span class="p">,</span> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'hierarchical'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC917" class="line" lang="python"> <span class="n" style="color: #333;">hm</span><span class="p">.</span><span class="n" style="color: #333;">matrix</span><span class="p">.</span><span class="n" style="color: #333;">hmcluster</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">hclust</span><span class="p">,</span> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'hierarchical'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">clustering_samples</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">clusterUsingSamples</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC918" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC919" class="line" lang="python"> <span class="n" style="color: #333;">group_len_ratio</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">diff</span><span class="p">(</span><span class="n" style="color: #333;">hm</span><span class="p">.</span><span class="n" style="color: #333;">matrix</span><span class="p">.</span><span class="n" style="color: #333;">group_boundaries</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="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">hm</span><span class="p">.</span><span class="n" style="color: #333;">matrix</span><span class="p">.</span><span class="n" style="color: #333;">regions</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC920" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;">any</span><span class="p">(</span><span class="n" style="color: #333;">group_len_ratio</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">5.0</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">1000</span><span class="p">):</span></span>
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<a href="https://salsa.debian.org/med-team/python-deeptools/-/compare/064166562018c795f7d3e73b498588729cae03ac...911dd5dc4fa12b9ee76878808b70bb1cd946aecc#d2de9c6869fd65911899bace5f34a175e96efb2a"><strong>galaxy/wrapper/deepTools_macros.xml</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="xml"><span class="nt" style="color: #000080;"><macros></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="xml"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="xml"> <span class="nt" style="color: #000080;"><token</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"@THREADS@"</span><span class="nt" style="color: #000080;">></span>--numberOfProcessors "\${GALAXY_SLOTS:-4}"<span class="nt" style="color: #000080;"></token></span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="xml"> <span class="nt" style="color: #000080;"><token</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"@WRAPPER_VERSION@"</span><span class="nt" style="color: #000080;">></span>3.4.<span class="idiff left right">2</span>.0<span class="nt" style="color: #000080;"></token></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="xml"> <span class="nt" style="color: #000080;"><token</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"@WRAPPER_VERSION@"</span><span class="nt" style="color: #000080;">></span>3.4.<span class="idiff left right">3</span>.0<span class="nt" style="color: #000080;"></token></span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="xml"> <span class="nt" style="color: #000080;"><xml</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"requirements"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="xml"> <span class="nt" style="color: #000080;"><requirements></span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="xml"> <span class="nt" style="color: #000080;"><requirement</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"package"</span> <span class="na" style="color: #008080;">version=</span><span class="s" style="color: #d14;">"3.4.<span class="idiff left right">2</span>"</span><span class="nt" style="color: #000080;">></span>deeptools<span class="nt" style="color: #000080;"></requirement></span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="xml"> <span class="nt" style="color: #000080;"><requirement</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"package"</span> <span class="na" style="color: #008080;">version=</span><span class="s" style="color: #d14;">"3.4.<span class="idiff left right">3</span>"</span><span class="nt" style="color: #000080;">></span>deeptools<span class="nt" style="color: #000080;"></requirement></span></span>
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8
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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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