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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/umis">Debian Med / umis</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/umis/-/commit/dd42ef2b3ba77febd0afbda28f8e0139f95d662c">dd42ef2b</a></strong>
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<span>by Andreas Tille</span>
<i>at 2021-10-12T09:00:16+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.0.8</pre>
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<h4>3 changed files:</h4>
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<a href="#d30b04166486087de34ff05cf278d3dd2ddd2360">
HISTORY.md
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<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<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/dd42ef2b3ba77febd0afbda28f8e0139f95d662c#d30b04166486087de34ff05cf278d3dd2ddd2360"><strong>HISTORY.md</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 1.0.8</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"><span class="p">-</span> Add support for dual UMI indexes. Thanks @lbeltrame!</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 1.0.7</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"><span class="p">-</span> Ensure headers are not written when writing out a Series, to make us compatible with pandas > 0.24.</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"><span class="p">-</span> Fix for deprecated .ix call, .loc is the new replacement. Thanks to @naumenko-sa.</span>
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<li id="8e2edce0d507e1297474f25c00cae94258db38d8">
<a href="https://salsa.debian.org/med-team/umis/-/commit/dd42ef2b3ba77febd0afbda28f8e0139f95d662c#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<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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<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">7</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">8</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"> <span class="n" style="color: #333;">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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<li id="993a5ccc8a9a226410ec4fb8767ac9f1a99859c7">
<a href="https://salsa.debian.org/med-team/umis/-/commit/dd42ef2b3ba77febd0afbda28f8e0139f95d662c#993a5ccc8a9a226410ec4fb8767ac9f1a99859c7"><strong>umis/umis.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -102,7 +102,7 @@ def write_fastq(filename):</td>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">filename</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">filename</span><span class="p">.</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="LC105" 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="p">.</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;">'w<span class="idiff left right">b</span>'</span><span class="p">)</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" 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="p">.</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;">'w<span class="idiff left right">t</span>'</span><span class="p">)</span></span>
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106
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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107
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">filename_fh</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;">'w'</span><span class="p">)</span></span>
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108
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -190,7 +190,7 @@ def fastqtransform(transform, fastq1, fastq2, fastq3, fastq4, keep_fastq_tags,</td>
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190
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">options</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_infer_transform_options</span><span class="p">(</span><span class="n" style="color: #333;">transform</span><span class="p">)</span></span>
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191
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="python"> <span class="n" style="color: #333;">read_template</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'{name}'</span></span>
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192
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Transforming %s."</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">fastq1</span><span class="p">)</span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">dual_index</span><span class="p">:</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">dual_index</span><span class="idiff left"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">options</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">CB</span></span><span class="p">:</span></span>
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194
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Detected dual cellular indexes."</span><span class="p">)</span></span>
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195
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">separate_cb</span><span class="p">:</span></span>
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196
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="python"> <span class="n" style="color: #333;">read_template</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">':CELL_{CB1}-{CB2}'</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="205" style="width: 35px; color: rgba(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="205" style="width: 35px; color: rgba(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">@@ -205,9 +205,12 @@ def fastqtransform(transform, fastq1, fastq2, fastq3, fastq4, keep_fastq_tags,</td>
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205
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">CB</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">demuxed_cb</span><span class="p">:</span></span>
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206
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206
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Detected cellular barcodes."</span><span class="p">)</span></span>
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207
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207
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">read_template</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">':CELL_{CB}'</span></span>
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208
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">MB</span><span class="p">:</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">MB</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">dual_index</span><span class="p">:</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Detected dual UMI."</span><span class="p">)</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">read_template</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">':UMI_{MB1}-{MB2}'</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">MB</span><span class="p">:</span></span>
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209
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212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Detected UMI."</span><span class="p">)</span></span>
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210
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">read_template</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;"><span class="idiff left">'</span>:UMI_{MB}<span class="idiff right">'</span></span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"> <span class="n" style="color: #333;">read_template</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;"><span class="idiff left">"</span>:UMI_{MB}<span class="idiff right">"</span></span></span>
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211
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214
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">SB</span><span class="p">:</span></span>
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212
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215
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Detected sample."</span><span class="p">)</span></span>
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213
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216
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="python"> <span class="n" style="color: #333;">read_template</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">':SAMPLE_{SB}'</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -251,7 +254,7 @@ def fastqtransform(transform, fastq1, fastq2, fastq3, fastq4, keep_fastq_tags,</td>
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251
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254
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">chunk</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="n" style="color: #333;">transform</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">bigchunk</span><span class="p">)):</span></span>
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252
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255
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">paired</span><span class="p">:</span></span>
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253
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256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">read1_dict</span><span class="p">,</span> <span class="n" style="color: #333;">read2_dict</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tz</span><span class="p">.</span><span class="n" style="color: #333;">partition</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">chunk</span><span class="p">):</span></span>
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254
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">dual_index</span><span class="p">:</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">dual_index</span><span class="idiff left"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">options</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">CB</span></span><span class="p">:</span></span>
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255
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258
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">separate_cb</span><span class="p">:</span></span>
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256
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259
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="python"> <span class="n" style="color: #333;">read1_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'CB'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read1_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'CB1'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">read1_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'CB2'</span><span class="p">]</span></span>
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257
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260
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="python"> <span class="n" style="color: #333;">read2_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'CB'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read2_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'CB1'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">read2_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'CB2'</span><span class="p">]</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="259" style="width: 35px; color: rgba(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="262" style="width: 35px; color: rgba(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">@@ -259,6 +262,8 @@ def fastqtransform(transform, fastq1, fastq2, fastq3, fastq4, keep_fastq_tags,</td>
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259
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262
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">demuxed_cb</span><span class="p">:</span></span>
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260
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263
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="python"> <span class="n" style="color: #333;">read1_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'CB'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">demuxed_cb</span></span>
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261
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="python"> <span class="n" style="color: #333;">read2_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'CB'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">demuxed_cb</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">dual_index</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">MB</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="python"> <span class="n" style="color: #333;">read1_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'MB'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read1_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'MB1'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">read2_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'MB2'</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="python"></span>
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268
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Deal with spaces in read names</span></span>
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269
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">keep_fastq_tags</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">@@ -282,13 +287,16 @@ def fastqtransform(transform, fastq1, fastq2, fastq3, fastq4, keep_fastq_tags,</td>
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282
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287
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="python"> <span class="n" style="color: #333;">fastq2out_fh</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">read_template</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">read2_dict</span><span class="p">))</span></span>
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283
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288
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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284
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289
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">read1_dict</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">chunk</span><span class="p">:</span></span>
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285
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">dual_index</span><span class="p">:</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">dual_index</span><span class="idiff left"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">options</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">CB</span></span><span class="p">:</span></span>
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291
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">separate_cb</span><span class="p">:</span></span>
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292
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="python"> <span class="n" style="color: #333;">read1_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'CB'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read1_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'CB1'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">read1_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'CB2'</span><span class="p">]</span></span>
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293
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">demuxed_cb</span><span class="p">:</span></span>
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290
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295
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="python"> <span class="n" style="color: #333;">read1_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'CB'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">demuxed_cb</span></span>
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296
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">dual_index</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">MB</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="python"> <span class="n" style="color: #333;">read1_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'MB'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read1_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'MB1'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">read1_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'MB2'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Deal with spaces in read names</span></span>
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">keep_fastq_tags</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">tag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read1_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">].</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">' '</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">@@ -326,6 +334,8 @@ def _infer_transform_options(transform):</td>
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="python"> <span class="n" style="color: #333;">triple_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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327
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335
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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328
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336
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="python"> <span class="n" style="color: #333;">dual_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"MB1"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rx</span><span class="p">:</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="python"> <span class="n" style="color: #333;">dual_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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329
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339
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"SB"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rx</span><span class="p">:</span></span>
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330
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340
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="python"> <span class="n" style="color: #333;">SB</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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341
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"CB"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rx</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="353" style="width: 35px; color: rgba(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="363" style="width: 35px; color: rgba(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">@@ -353,7 +363,7 @@ def _extract_readnum(read_dict):</td>
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353
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363
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<pre style="margin: 0;"> <span id="LC363" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">transformer</span><span class="p">(</span><span class="n" style="color: #333;">chunk</span><span class="p">,</span> <span class="n" style="color: #333;">read1_regex</span><span class="p">,</span> <span class="n" style="color: #333;">read2_regex</span><span class="p">,</span> <span class="n" style="color: #333;">read3_regex</span><span class="p">,</span> <span class="n" style="color: #333;">read4_regex</span><span class="p">,</span></span>
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354
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364
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="python"> <span class="n" style="color: #333;">paired</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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365
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Parse the reads with the regexes</span></span>
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<pre style="margin: 0;">-<span id="LC356" class="line" lang="python"> <span class="n" style="color: #333;">update_keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"MB"</span><span class="p">,</span> <span class="s" style="color: #d14;">"CB"</span><span class="p">,</span> <span class="s" style="color: #d14;">"CB1"</span><span class="p">,</span> <span class="s" style="color: #d14;">"CB2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"SP"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="python"> <span class="n" style="color: #333;">update_keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"MB"</span><span class="p">,</span> <span class="s" style="color: #d14;">"CB"</span><span class="p">,</span> <span class="s" style="color: #d14;">"CB1"</span><span class="p">,</span> <span class="s" style="color: #d14;">"CB2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"SP"</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"MB1"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"MB2"</span></span><span class="p">)</span></span>
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357
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367
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="python"> <span class="n" style="color: #333;">reads</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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358
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368
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;">read3</span><span class="p">,</span> <span class="n" style="color: #333;">read4</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">chunk</span><span class="p">:</span></span>
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359
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369
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="python"> <span class="n" style="color: #333;">read1_match</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read1_regex</span><span class="p">.</span><span class="n" style="color: #333;">search</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="p">)</span></span>
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