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<h3>
Steffen Möller pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/umis">Debian Med / umis</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/umis/commit/1279f98c26934b5800b87f5e3c549d24a85660ee">1279f98c</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-01-18T22:48:39+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.0.6</pre>
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<h4>3 changed files:</h4>
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<li class="file-stats">
<a href="#d30b04166486087de34ff05cf278d3dd2ddd2360">
HISTORY.md
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<li class="file-stats">
<a href="#993a5ccc8a9a226410ec4fb8767ac9f1a99859c7">
umis/umis.py
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<h4>Changes:</h4>
<li id="d30b04166486087de34ff05cf278d3dd2ddd2360">
<a href="https://salsa.debian.org/med-team/umis/commit/1279f98c26934b5800b87f5e3c549d24a85660ee#d30b04166486087de34ff05cf278d3dd2ddd2360"><strong>HISTORY.md</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 1.0.4 (in progress)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 1.0.6</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"><span class="p">-</span> Fix for the python3 fix.</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="markdown"></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="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 1.0.5</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="p">-</span> Fix for cb_filter with python3.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 1.0.4</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="p">-</span> Enable cb_histogram to be used on samples without UMIs.</span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="p">-</span> Enable filtering of cells during <span class="sb" style="color: #d14;">`demultiplex_cells`</span>.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="p">-</span> Fix incorrect pandas.read_csv call with header=-1.</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 1.0.3 </span></span>
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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown"><span class="p">-</span> Python 3 support</span>
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<li id="8e2edce0d507e1297474f25c00cae94258db38d8">
<a href="https://salsa.debian.org/med-team/umis/commit/1279f98c26934b5800b87f5e3c549d24a85660ee#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,7 +8,7 @@ def read(fname):</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"></span>
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="n" style="color: #333;">setup</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'umis'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC11" 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;">'1.0.<span class="idiff left right">3</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC11" 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;">'1.0.<span class="idiff left right">6</span>'</span><span class="p">,</span></span>
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12
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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Package for estimating UMI counts in Transcript Tag Counting data.'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">packages</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">find_packages</span><span class="p">(),</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"> <span class="n" style="color: #333;">install_requires</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'click'</span><span class="p">,</span> <span class="s" style="color: #d14;">'pysam>=0.8.3'</span><span class="p">,</span> <span class="s" style="color: #d14;">'pandas'</span><span class="p">,</span> <span class="s" style="color: #d14;">'regex'</span><span class="p">,</span> <span class="s" style="color: #d14;">'scipy'</span><span class="p">,</span> <span class="s" style="color: #d14;">'toolz'</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">@@ -24,7 +24,7 @@ import numpy as np</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">scipy.io</span><span class="p">,</span> <span class="n" style="color: #333;">scipy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sparse</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">click</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC27" 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;">"1.0.<span class="idiff left right">3</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC27" 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;">"1.0.<span class="idiff left right">6</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"><span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">basicConfig</span><span class="p">(</span><span class="n" style="color: #333;">level</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">INFO</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"><span class="n" style="color: #333;">logger</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getLogger</span><span class="p">(</span><span class="n" style="color: #333;">__name__</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">@@ -35,7 +35,10 @@ BARCODEINFO = {"sample": BarcodeInfo(bamtag="XS", readprefix="SAMPLE"),</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"> <span class="s" style="color: #d14;">"molecular"</span><span class="p">:</span> <span class="n" style="color: #333;">BarcodeInfo</span><span class="p">(</span><span class="n" style="color: #333;">bamtag</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"RX"</span><span class="p">,</span> <span class="n" style="color: #333;">readprefix</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"UMI"</span><span class="p">)}</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">open_gzipsafe</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gzip</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".gz"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">else</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_python3</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gzip</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"rt"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".gz"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">else</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gzip</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".gz"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">else</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">safe_makedir</span><span class="p">(</span><span class="n" style="color: #333;">dname</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="s" style="color: #d14;">"""Make a directory if it doesn't exist, handling concurrent race conditions.</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">@@ -75,7 +78,7 @@ def read_fastq(filename):</td>
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">filename</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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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">filename_fh</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdin</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">filename</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">'gz'</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_python3</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_python3</span><span class="p"><span class="idiff left right">()</span>:</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">filename_fh</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gzip</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'rt'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">filename_fh</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BufferedReader</span><span class="p">(</span><span class="n" style="color: #333;">gzip</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'rt'</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">@@ -485,7 +488,7 @@ def tagcount(sam, out, genemap, output_evidence_table, positional, minevidence,</td>
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485
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488
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<pre style="margin: 0;"> <span id="LC488" class="line" lang="python"> <span class="n" style="color: #333;">cb_hist</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC489" class="line" lang="python"> <span class="n" style="color: #333;">filter_cb</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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487
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490
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<pre style="margin: 0;"> <span id="LC490" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cb_histogram</span><span class="p">:</span></span>
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488
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<pre style="margin: 0;">-<span id="LC488" class="line" lang="python"> <span class="n" style="color: #333;">cb_hist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read_csv</span><span class="p">(</span><span class="n" style="color: #333;">cb_histogram</span><span class="p">,</span> <span class="n" style="color: #333;">index_col</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">=<span class="idiff left">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">,</span> <span class="n" style="color: #333;">squeeze</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="python"> <span class="n" style="color: #333;">cb_hist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read_csv</span><span class="p">(</span><span class="n" style="color: #333;">cb_histogram</span><span class="p">,</span> <span class="n" style="color: #333;">index_col</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;"><span class="idiff left right">None</span></span><span class="p">,</span> <span class="n" style="color: #333;">squeeze</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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489
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492
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<pre style="margin: 0;"> <span id="LC492" class="line" lang="python"> <span class="n" style="color: #333;">total_num_cbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cb_hist</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">shape</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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490
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493
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<pre style="margin: 0;"> <span id="LC493" class="line" lang="python"> <span class="n" style="color: #333;">cb_hist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cb_hist</span><span class="p">[</span><span class="n" style="color: #333;">cb_hist</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">cb_cutoff</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC494" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">'Keeping {} out of {} cellular barcodes.'</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">cb_hist</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">shape</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">total_num_cbs</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">@@ -712,9 +715,9 @@ def tagcount(sam, out, genemap, output_evidence_table, positional, minevidence,</td>
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<pre style="margin: 0;"> <span id="LC715" class="line" lang="python"> <span class="s" style="color: #d14;">'read gene mapping information in stead of the mapping '</span></span>
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713
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<pre style="margin: 0;"> <span id="LC716" class="line" lang="python"> <span class="s" style="color: #d14;">'target nane. Useful if e.g. reads have been mapped to '</span></span>
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717
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<pre style="margin: 0;"> <span id="LC717" class="line" lang="python"> <span class="s" style="color: #d14;">'genome in stead of transcriptome.'</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC715" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'--umi_matrix'</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span><span class="idiff left right"> </span></span>
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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'--umi_matrix'</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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719
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<pre style="margin: 0;"> <span id="LC719" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'Save a sparse matrix of counts without UMI deduping to this file.'</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC717" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fasttagcount</span><span class="p">(</span><span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">genemap</span><span class="p">,</span> <span class="n" style="color: #333;">positional</span><span class="p">,</span> <span class="n" style="color: #333;">minevidence</span><span class="p">,</span> <span class="n" style="color: #333;">cb_histogram</span><span class="p">,</span><span class="idiff left right"> </span></span>
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720
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fasttagcount</span><span class="p">(</span><span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">genemap</span><span class="p">,</span> <span class="n" style="color: #333;">positional</span><span class="p">,</span> <span class="n" style="color: #333;">minevidence</span><span class="p">,</span> <span class="n" style="color: #333;">cb_histogram</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC721" class="line" lang="python"> <span class="n" style="color: #333;">cb_cutoff</span><span class="p">,</span> <span class="n" style="color: #333;">subsample</span><span class="p">,</span> <span class="n" style="color: #333;">parse_tags</span><span class="p">,</span> <span class="n" style="color: #333;">gene_tags</span><span class="p">,</span> <span class="n" style="color: #333;">umi_matrix</span><span class="p">):</span></span>
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722
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<pre style="margin: 0;"> <span id="LC722" class="line" lang="python"> <span class="s" style="color: #d14;">''' Count up evidence for tagged molecules, this implementation assumes the</span></span>
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723
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<pre style="margin: 0;"> <span id="LC723" class="line" lang="python"><span class="s" style="color: #d14;"> alignment file is coordinate sorted</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">@@ -758,7 +761,7 @@ def fasttagcount(sam, out, genemap, positional, minevidence, cb_histogram,</td>
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758
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761
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<pre style="margin: 0;"> <span id="LC761" class="line" lang="python"> <span class="n" style="color: #333;">cb_hist</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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759
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762
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<pre style="margin: 0;"> <span id="LC762" class="line" lang="python"> <span class="n" style="color: #333;">filter_cb</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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760
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763
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<pre style="margin: 0;"> <span id="LC763" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cb_histogram</span><span class="p">:</span></span>
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761
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<pre style="margin: 0;">-<span id="LC761" class="line" lang="python"> <span class="n" style="color: #333;">cb_hist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read_csv</span><span class="p">(</span><span class="n" style="color: #333;">cb_histogram</span><span class="p">,</span> <span class="n" style="color: #333;">index_col</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">=<span class="idiff left">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">,</span> <span class="n" style="color: #333;">squeeze</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="python"> <span class="n" style="color: #333;">cb_hist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read_csv</span><span class="p">(</span><span class="n" style="color: #333;">cb_histogram</span><span class="p">,</span> <span class="n" style="color: #333;">index_col</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;"><span class="idiff left right">None</span></span><span class="p">,</span> <span class="n" style="color: #333;">squeeze</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC765" class="line" lang="python"> <span class="n" style="color: #333;">total_num_cbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cb_hist</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">shape</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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763
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766
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<pre style="margin: 0;"> <span id="LC766" class="line" lang="python"> <span class="n" style="color: #333;">cb_hist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cb_hist</span><span class="p">[</span><span class="n" style="color: #333;">cb_hist</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">cb_cutoff</span><span class="p">]</span></span>
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764
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767
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<pre style="margin: 0;"> <span id="LC767" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">'Keeping {} out of {} cellular barcodes.'</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">cb_hist</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">shape</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">total_num_cbs</span><span class="p">))</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="974" style="width: 35px; color: rgba(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">@@ -971,9 +974,9 @@ def cb_histogram(fastq, umi_histogram):</td>
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971
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974
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<pre style="margin: 0;"> <span id="LC974" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">read</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">read_fastq</span><span class="p">(</span><span class="n" style="color: #333;">fastq</span><span class="p">):</span></span>
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972
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975
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<pre style="margin: 0;"> <span id="LC975" class="line" lang="python"> <span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser_re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">search</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">groupdict</span><span class="p">()</span></span>
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973
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976
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<pre style="margin: 0;"> <span id="LC976" class="line" lang="python"> <span class="n" style="color: #333;">cb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">match</span><span class="p">[</span><span class="s" style="color: #d14;">'CB'</span><span class="p">]</span></span>
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974
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<pre style="margin: 0;">-<span id="LC974" class="line" lang="python"> <span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">match</span><span class="p">[</span><span class="s" style="color: #d14;">'MB'</span><span class="p">]</span></span>
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975
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977
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<pre style="margin: 0;"> <span id="LC977" class="line" lang="python"> <span class="n" style="color: #333;">cb_counter</span><span class="p">[</span><span class="n" style="color: #333;">cb</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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976
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978
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<pre style="margin: 0;"> <span id="LC978" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">umi_histogram</span><span class="p">:</span></span>
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979
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<pre style="margin: 0;">+<span id="LC979" class="line" lang="python"> <span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">match</span><span class="p">[</span><span class="s" style="color: #d14;">'MB'</span><span class="p">]</span></span>
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977
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980
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<pre style="margin: 0;"> <span id="LC980" class="line" lang="python"> <span class="n" style="color: #333;">umi_counter</span><span class="p">[(</span><span class="n" style="color: #333;">cb</span><span class="p">,</span> <span class="n" style="color: #333;">umi</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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978
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981
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<pre style="margin: 0;"> <span id="LC981" class="line" lang="python"></span>
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979
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982
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<pre style="margin: 0;"> <span id="LC982" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">bc</span><span class="p">,</span> <span class="n" style="color: #333;">count</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">cb_counter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">most_common</span><span class="p">():</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1054" style="width: 35px; color: rgba(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="1057" style="width: 35px; color: rgba(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">@@ -1054,9 +1057,9 @@ def cb_filter(fastq, bc1, bc2, bc3, cores, nedit):</td>
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1054
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1057
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<pre style="margin: 0;"> <span id="LC1057" class="line" lang="python"> <span class="s" style="color: #d14;">''' Filters reads with non-matching barcodes</span></span>
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1055
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1058
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<pre style="margin: 0;"> <span id="LC1058" class="line" lang="python"><span class="s" style="color: #d14;"> Expects formatted fastq files.</span></span>
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1056
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1059
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<pre style="margin: 0;"> <span id="LC1059" class="line" lang="python"><span class="s" style="color: #d14;"> '''</span></span>
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1057
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<pre style="margin: 0;">-<span id="LC1057" class="line" lang="python"></span>
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1058
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1060
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<pre style="margin: 0;"> <span id="LC1060" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">open_gzipsafe</span><span class="p">(</span><span class="n" style="color: #333;">bc1</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">bc1_fh</span><span class="p">:</span></span>
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1059
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1061
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<pre style="margin: 0;"> <span id="LC1061" class="line" lang="python"> <span class="n" style="color: #333;">bc1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">cb</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">cb</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">bc1_fh</span><span class="p">)</span></span>
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1062
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<pre style="margin: 0;">+<span id="LC1062" class="line" lang="python"></span>
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1060
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1063
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<pre style="margin: 0;"> <span id="LC1063" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">bc2</span><span class="p">:</span></span>
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1061
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1064
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<pre style="margin: 0;"> <span id="LC1064" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">open_gzipsafe</span><span class="p">(</span><span class="n" style="color: #333;">bc2</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">bc2_fh</span><span class="p">:</span></span>
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1062
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1065
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<pre style="margin: 0;"> <span id="LC1065" class="line" lang="python"> <span class="n" style="color: #333;">bc2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">cb</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">cb</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">bc2_fh</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1312" style="width: 35px; color: rgba(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="1315" style="width: 35px; color: rgba(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">@@ -1312,7 +1315,10 @@ def is_python3():</td>
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1312
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1315
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<pre style="margin: 0;"> <span id="LC1315" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'--out_dir'</span><span class="p">,</span> <span class="n" style="color: #333;">default</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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1313
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1316
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<pre style="margin: 0;"> <span id="LC1316" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'--readnumber'</span><span class="p">,</span> <span class="n" style="color: #333;">default</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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1314
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1317
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<pre style="margin: 0;"> <span id="LC1317" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'--prefix'</span><span class="p">,</span> <span class="n" style="color: #333;">default</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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1315
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<pre style="margin: 0;">-<span id="LC1315" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">demultiplex_cells</span><span class="p">(</span><span class="n" style="color: #333;">fastq</span><span class="p">,</span> <span class="n" style="color: #333;">out_dir</span><span class="p">,</span> <span class="n" style="color: #333;">readnumber</span><span class="p">,</span> <span class="n" style="color: #333;">prefix</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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1318
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<pre style="margin: 0;">+<span id="LC1318" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'--cb_histogram'</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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1319
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<pre style="margin: 0;">+<span id="LC1319" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'--cb_cutoff'</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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1320
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<pre style="margin: 0;">+<span id="LC1320" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">demultiplex_cells</span><span class="p">(</span><span class="n" style="color: #333;">fastq</span><span class="p">,</span> <span class="n" style="color: #333;">out_dir</span><span class="p">,</span> <span class="n" style="color: #333;">readnumber</span><span class="p">,</span> <span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="n" style="color: #333;">cb_histogram</span><span class="p">,</span></span>
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1321
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<pre style="margin: 0;">+<span id="LC1321" class="line" lang="python"> <span class="n" style="color: #333;">cb_cutoff</span><span class="p">):</span></span>
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1316
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1322
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<pre style="margin: 0;"> <span id="LC1322" class="line" lang="python"> <span class="s" style="color: #d14;">''' Demultiplex a fastqtransformed FASTQ file into a FASTQ file for</span></span>
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1317
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1323
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<pre style="margin: 0;"> <span id="LC1323" class="line" lang="python"><span class="s" style="color: #d14;"> each cell.</span></span>
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1318
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1324
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<pre style="margin: 0;"> <span id="LC1324" class="line" lang="python"><span class="s" style="color: #d14;"> '''</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1327" style="width: 35px; color: rgba(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">@@ -1321,7 +1327,9 @@ def demultiplex_cells(fastq, out_dir, readnumber, prefix=""):</td>
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1321
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1327
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<pre style="margin: 0;"> <span id="LC1327" class="line" lang="python"> <span class="n" style="color: #333;">parser_re</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="n" style="color: #333;">re_string</span><span class="p">)</span></span>
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1322
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1328
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<pre style="margin: 0;"> <span id="LC1328" class="line" lang="python"> <span class="n" style="color: #333;">readstring</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">readnumber</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"_R{}"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">readnumber</span><span class="p">)</span></span>
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1323
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1329
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<pre style="margin: 0;"> <span id="LC1329" class="line" lang="python"> <span class="n" style="color: #333;">filestring</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"{prefix}{sample}{readstring}.fq"</span></span>
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1324
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<pre style="margin: 0;">-<span id="LC1324" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC1330" class="line" lang="python"> <span class="n" style="color: #333;">cb_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>
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1331
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<pre style="margin: 0;">+<span id="LC1331" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cb_histogram</span><span class="p">:</span></span>
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1332
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<pre style="margin: 0;">+<span id="LC1332" class="line" lang="python"> <span class="n" style="color: #333;">cb_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_cb_depth_set</span><span class="p">(</span><span class="n" style="color: #333;">cb_histogram</span><span class="p">,</span> <span class="n" style="color: #333;">cb_cutoff</span><span class="p">)</span></span>
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1325
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1333
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<pre style="margin: 0;"> <span id="LC1333" class="line" lang="python"> <span class="n" style="color: #333;">sample_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>
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<td class="diff-line-num old_line" data-linenumber="1326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1326
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<td class="diff-line-num new_line" data-linenumber="1334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1334
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<pre style="margin: 0;"> <span id="LC1334" class="line" lang="python"> <span class="n" style="color: #333;">batch</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">collections</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">defaultdict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="1327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1327
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1335
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<pre style="margin: 0;"> <span id="LC1335" class="line" lang="python"> <span class="n" style="color: #333;">parsed</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1330" style="width: 35px; color: rgba(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="1338" style="width: 35px; color: rgba(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">@@ -1330,6 +1338,8 @@ def demultiplex_cells(fastq, out_dir, readnumber, prefix=""):</td>
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1330
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<pre style="margin: 0;"> <span id="LC1338" class="line" lang="python"> <span class="n" style="color: #333;">parsed</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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1331
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<td class="diff-line-num new_line" data-linenumber="1339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1339
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<pre style="margin: 0;"> <span id="LC1339" class="line" lang="python"> <span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser_re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">search</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">groupdict</span><span class="p">()</span></span>
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1332
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1340
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<pre style="margin: 0;"> <span id="LC1340" class="line" lang="python"> <span class="n" style="color: #333;">sample</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">match</span><span class="p">[</span><span class="s" style="color: #d14;">'CB'</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1341
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<pre style="margin: 0;">+<span id="LC1341" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cb_set</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">sample</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">cb_set</span><span class="p">:</span></span>
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1342
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<pre style="margin: 0;">+<span id="LC1342" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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1333
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1343
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<pre style="margin: 0;"> <span id="LC1343" class="line" lang="python"> <span class="n" style="color: #333;">sample_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">sample</span><span class="p">)</span></span>
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1334
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<td class="diff-line-num new_line" data-linenumber="1344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1344
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<pre style="margin: 0;"> <span id="LC1344" class="line" lang="python"> <span class="n" style="color: #333;">batch</span><span class="p">[</span><span class="n" style="color: #333;">sample</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">)</span></span>
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1335
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1345
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<pre style="margin: 0;"> <span id="LC1345" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># write in batches to avoid opening up file handles repeatedly</span></span>
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