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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-pybedtools">Debian Med / python-pybedtools</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pybedtools/commit/1ddd1ca695f38a4d9dc20c2a008c5573e7bb5dc3">1ddd1ca6</a></strong>
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<span>by Andreas Tille</span>
<i>at 2017-11-09T12:01:45+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add back test_issue_178 after upstream provided a patch
</pre>
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<strong><a href="https://salsa.debian.org/med-team/python-pybedtools/commit/57355f023cf5fb0cad5ec0fefc0334b5be8dcd2c">57355f02</a></strong>
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<span>by Andreas Tille</span>
<i>at 2017-11-09T12:11:30+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Team upload to unstable
</pre>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#e87fc8c0ee00c147dde17649d26dbf9e69bfd011">
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+
debian/patches/c8dff864dbc942bb7adb3e719b0702f7e3989d36.patch
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</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/python-pybedtools/compare/f2ad9e590dd66dd14d811c1e5c1995062d6e2278...57355f023cf5fb0cad5ec0fefc0334b5be8dcd2c#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">python-pybedtools (0.7.10-2) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python-pybedtools (0.7.10-2) <span class="idiff left right">unstable</span>; urgency=medium</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"> * Provide link to upstream issue for failed test</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Add back test_issue_178 after upstream provided a patch</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="LC5" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Wed, 08 Nov 2017 09:25:08</span> +0100</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Thu, 09 Nov 2017 12:01:51</span> +0100</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">python-pybedtools (0.7.10-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<li id="e87fc8c0ee00c147dde17649d26dbf9e69bfd011">
<a href="https://salsa.debian.org/med-team/python-pybedtools/compare/f2ad9e590dd66dd14d811c1e5c1995062d6e2278...57355f023cf5fb0cad5ec0fefc0334b5be8dcd2c#e87fc8c0ee00c147dde17649d26dbf9e69bfd011"><strong>debian/patches/c8dff864dbc942bb7adb3e719b0702f7e3989d36.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">From: Ryan Dale <dalerr@niddk.nih.gov></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Date: Wed, 8 Nov 2017 15:35:02 -0500</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Subject: [PATCH] address #227</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">---</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> pybedtools/contrib/bigwig.py | 62 +++++++++++++++++++++++++++++++++++++-------</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> pybedtools/test/test1.py | 36 ++++++++++++++-----------</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> 2 files changed, 73 insertions(+), 25 deletions(-)</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pybedtools/contrib/bigwig.py</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pybedtools/contrib/bigwig.py</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -48,8 +48,17 @@ def bedgraph_to_bigwig(bedgraph, genome,</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> bedgraph.fn,</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> genome_file,</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> output]</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- p = subprocess.Popen(cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE)</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- stdout, stderr = p.communicate()</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ try:</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ p = subprocess.Popen(cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE)</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ stdout, stderr = p.communicate()</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except FileNotFoundError:</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ raise FileNotFoundError(</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "bedGraphToBigWig was not found on the path. This is an external "</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "tool from UCSC which can be downloaded from "</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "http://hgdownload.soe.ucsc.edu/admin/exe/. Alternatatively, use "</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "`conda install ucsc-bedgraphtobigwig`"</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ )</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> if p.returncode:</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> raise ValueError("cmds: %s\nstderr:%s\nstdout:%s"</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> % (" ".join(cmds), stderr, stdout))</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -72,8 +81,16 @@ def bigwig_to_bedgraph(fn, chrom=None, s</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> outfn = pybedtools.BedTool._tmp()</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> cmds.append(outfn)</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> </span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- p = subprocess.Popen(cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE)</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- stdout, stderr = p.communicate()</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ try:</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ p = subprocess.Popen(cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE)</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ stdout, stderr = p.communicate()</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except FileNotFoundError:</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ raise FileNotFoundError(</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "bigWigToBedGraph was not found on the path. This is an external "</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "tool from UCSC which can be downloaded from "</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "http://hgdownload.soe.ucsc.edu/admin/exe/. Alternatatively, use "</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "`conda install ucsc-bedgraphtobigwig`"</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ )</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> if p.returncode:</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> raise ValueError("cmds: %s\nstderr:%s\nstdout:%s"</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> % (" ".join(cmds), stderr, stdout))</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -87,8 +104,17 @@ def wig_to_bigwig(wig, genome, output):</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> wig.fn,</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> genome_file,</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> output]</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- subprocess.Popen(cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE)</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- stdout, stderr = p.communicate()</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ try:</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ p = subprocess.Popen(cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE)</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ stdout, stderr = p.communicate()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except FileNotFoundError:</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ raise FileNotFoundError(</span></span>
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<td class="diff-line-num new new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "bigWigToBedGraph was not found on the path. This is an external "</span></span>
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<td class="diff-line-num new new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "tool from UCSC which can be downloaded from "</span></span>
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<td class="diff-line-num new new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "http://hgdownload.soe.ucsc.edu/admin/exe/. Alternatatively, use "</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "`conda install ucsc-bedgraphtobigwig`"</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ )</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> if p.returncode:</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> raise ValueError('cmds: %s\nstderr:%s\nstdout:%s'</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> % (' '.join(cmds), stderr, stdout))</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -120,15 +146,31 @@ def bam_to_bigwig(bam, genome, output, s</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> x.fn,</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> genome_file,</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> output]</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- p = subprocess.Popen(cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE, universal_newlines=True)</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- stdout, stderr = p.communicate()</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ try:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ p = subprocess.Popen(cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE, universal_newlines=True)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ stdout, stderr = p.communicate()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except FileNotFoundError:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ raise FileNotFoundError(</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "bedGraphToBigWig was not found on the path. This is an external "</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "tool from UCSC which can be downloaded from "</span></span>
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<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
84
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "http://hgdownload.soe.ucsc.edu/admin/exe/. Alternatatively, use "</span></span>
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<td class="diff-line-num new new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "`conda install ucsc-bedgraphtobigwig`"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ )</span></span>
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<td class="diff-line-num new new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> </span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> if p.returncode and 'bedSort' in stderr:</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> print('BAM header was not sorted; sorting bedGraph')</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> y = x.sort()</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> cmds[1] = y.fn</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- p = subprocess.Popen(cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE, universal_newlines=True)</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- stdout, stderr = p.communicate()</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ try:</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ p = subprocess.Popen(cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE, universal_newlines=True)</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ stdout, stderr = p.communicate()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except FileNotFoundError:</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ raise FileNotFoundError(</span></span>
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<td class="diff-line-num new new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
99
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "bedSort was not found on the path. This is an external "</span></span>
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<td class="diff-line-num new new_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
100
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "tool from UCSC which can be downloaded from "</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "http://hgdownload.soe.ucsc.edu/admin/exe/. Alternatatively, use "</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "`conda install ucsc-bedgraphtobigwig`"</span></span>
</pre>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ )</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> if p.returncode:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> raise ValueError('cmds: %s\nstderr: %s\nstdout: %s'</span>
</pre>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pybedtools/test/test1.py</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pybedtools/test/test1.py</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2104,21 +2104,27 @@ def test_issue_196():</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> </span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> </span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> def test_issue_178():</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fn = pybedtools.example_filename('gdc.othersort.bam')</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- pybedtools.contrib.bigwig.bam_to_bigwig(fn, genome='dm3', output='tmp.bw')</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- x = pybedtools.contrib.bigwig.bigwig_to_bedgraph('tmp.bw')</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- assert x == fix(</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- '''</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- chr2L 70 75 1</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- chr2L 140 145 1</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- chr2L 150 155 1</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- chr2L 160 165 1</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- chr2L 210 215 1</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- chrX 10 15 1</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- chrX 70 75 1</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- chrX 140 145 1</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ''')</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- os.unlink('tmp.bw')</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ try:</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fn = pybedtools.example_filename('gdc.othersort.bam')</span></span>
</pre>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ pybedtools.contrib.bigwig.bam_to_bigwig(fn, genome='dm3', output='tmp.bw')</span></span>
</pre>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ x = pybedtools.contrib.bigwig.bigwig_to_bedgraph('tmp.bw')</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ assert x == fix(</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ '''</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ chr2L 70 75 1</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ chr2L 140 145 1</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ chr2L 150 155 1</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ chr2L 160 165 1</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ chr2L 210 215 1</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ chrX 10 15 1</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ chrX 70 75 1</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ chrX 140 145 1</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ''')</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ os.unlink('tmp.bw')</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # If bedGraphToBigWig is not on the path, see</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # https://github.com/daler/pybedtools/issues/227</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except FileNotFoundError:</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ pass</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> </span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"> def test_issue_203():</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"> x = pybedtools.example_bedtool('x.bed')</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/python-pybedtools/compare/f2ad9e590dd66dd14d811c1e5c1995062d6e2278...57355f023cf5fb0cad5ec0fefc0334b5be8dcd2c#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -3,3 +3,4 @@ enable-package-data</td>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">disable-write-version</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">disable-test-156</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">rename-scripts</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">c8dff864dbc942bb7adb3e719b0702f7e3989d36.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/python-pybedtools/compare/f2ad9e590dd66dd14d811c1e5c1995062d6e2278...57355f023cf5fb0cad5ec0fefc0334b5be8dcd2c#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -5,9 +5,8 @@ DH_VERBOSE := 1</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">export PYBUILD_NAME=pybedtools</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">export MATPLOTLIBRC=$(CURDIR)/debian/</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"># test_issue_178 fails, issue opened at upstream</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"># https://github.com/daler/pybedtools/issues/227</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">export PYBUILD_TEST_ARGS=--attr '!url' --exclude='(test_issue_178)'</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"># Add back test_issue_178 after upstream provided a patch https://github.com/daler/pybedtools/pull/228</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">export PYBUILD_TEST_ARGS=--attr '!url' # --exclude='(test_issue_178)'</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">export PYBUILD_BEFORE_TEST=cp {dir}/debian/mpl-expected.png {build_dir}/pybedtools/test/</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">export HOME=$(shell echo $$PWD"/fakehome")</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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