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GitLab

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<h3>

Steffen Möller pushed to branch upstream

at <a href="https://salsa.debian.org/med-team/python-cutadapt">Debian Med / python-cutadapt</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/python-cutadapt/commit/31e5476ee9dc8503e7d2a812af0957c982687b8b">31e5476e</a></strong>

<div>

<span>by Steffen Moeller</span>

<i>at 2019-11-25T13:17:52Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.7</pre>

</li>

</ul>

<h4>14 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">

.travis.yml

</a>

</li>

<li class="file-stats">

<a href="#4990be809a537bf86e4be2fe2e8251c83d8bd129">

CHANGES.rst

</a>

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<li class="file-stats">

<a href="#f75f54159d8ca95918e0cdbdcbc2012a7f8d47ed">

buildwheels.sh

</a>

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<li class="file-stats">

<a href="#df0576cbb783bc50b36e1efa3cbe0564a26c8295">

doc/conf.py

</a>

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<li class="file-stats">

<a href="#ee1d7278a009e2c5c652622fe43dc77e39af740d">

doc/guide.rst

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<li class="file-stats">

<a href="#6677207c6fa30ac9cec19ad036ae842582159ecb">

doc/installation.rst

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<li class="file-stats">

<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">

setup.py

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<li class="file-stats">

<a href="#babdfe5d368a4907abadce7f9b00dfab2489185a">

src/cutadapt/__main__.py

</a>

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<li class="file-stats">

<a href="#8fb347891ec0a40b16ef2bdbe361f823e12aa016">

src/cutadapt/adapters.py

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<li class="file-stats">

<a href="#6ed465db6839a69141086c2acf1dc01a8b17a981">

src/cutadapt/filters.py

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<a href="#12b6e14dcfabba52d86396a9e2818f75b0c0c8d5">

src/cutadapt/parser.py

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<a href="#1b86cdea057b59b4d05ba7fde4aea9df4e8fe9e8">

src/cutadapt/pipeline.py

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<a href="#af95dfcb30a51908f338d0fd6a196b9e4c108046">

src/cutadapt/utils.py

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<li class="file-stats">

<a href="#83ff0d8e113228f36b352922cbbb938d0aa9384b">

tests/test_commandline.py

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<h4>Changes:</h4>

<li id="dea01dd89a3b602828e630677fde5d77c06441c8">

<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/31e5476ee9dc8503e7d2a812af0957c982687b8b#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10" 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>

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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">@@ -10,7 +10,7 @@ python:</td>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="yaml">  <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.5"</span></span>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="yaml">  <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.6"</span></span>

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<td class="diff-line-num old_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="yaml">  <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.7"</span></span>

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<td class="diff-line-num old old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC13" class="line" lang="yaml">  <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.8<span class="idiff left right">-dev</span>"</span></span>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml">  <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.8"</span></span>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="yaml">  <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">nightly"</span></span>

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

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC16" class="line" lang="yaml"><span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>

</pre>

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<br>

</li>

<li id="4990be809a537bf86e4be2fe2e8251c83d8bd129">

<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/31e5476ee9dc8503e7d2a812af0957c982687b8b#4990be809a537bf86e4be2fe2e8251c83d8bd129"><strong>CHANGES.rst</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2" 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>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="mosel"><span class="n" style="color: #333;">Changes</span></span>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="mosel"><span class="p">=======</span></span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="mosel"><span class="n" style="color: #333;">v2</span><span class="m" style="color: #099;">.7</span> <span class="p">(</span><span class="m" style="color: #099;">2019</span><span class="p">-</span><span class="m" style="color: #099;">11</span><span class="p">-</span><span class="m" style="color: #099;">22</span><span class="p">)</span></span>

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

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="mosel"></span>

</pre>

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8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="mosel"><span class="p">*</span> <span class="p">:</span><span class="n" style="color: #333;">issue</span><span class="p">:`</span><span class="m" style="color: #099;">427</span><span class="p">`:</span> <span class="n" style="color: #333;">Multicore</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">supported</span> <span class="n" style="color: #333;">even</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">using</span> <span class="p">``--</span><span class="n" style="color: #333;">info</span><span class="p">-</span><span class="n" style="color: #333;">file</span><span class="p">``,</span></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">

9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="mosel">  <span class="p">``--</span><span class="n" style="color: #333;">rest</span><span class="p">-</span><span class="n" style="color: #333;">file</span><span class="p">``</span> <span class="k" style="font-weight: 600;">or</span> <span class="p">``--</span><span class="n" style="color: #333;">wildcard</span><span class="p">-</span><span class="n" style="color: #333;">file</span><span class="p">``.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">remaining</span> <span class="n" style="color: #333;">feature</span> <span class="n" style="color: #333;">that</span></span>

</pre>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="10" 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">

10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="mosel">  <span class="n" style="color: #333;">still</span> <span class="n" style="color: #333;">does</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">work</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">multicore</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">demultiplexing</span><span class="p">.</span></span>

</pre>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="11" 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">

11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="mosel"><span class="p">*</span> <span class="p">:</span><span class="n" style="color: #333;">issue</span><span class="p">:`</span><span class="m" style="color: #099;">290</span><span class="p">`:</span> <span class="n" style="color: #333;">When</span> <span class="n" style="color: #333;">running</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">single</span> <span class="n" style="color: #333;">core</span><span class="p">,</span> <span class="n" style="color: #333;">Cutadapt</span> <span class="n" style="color: #333;">no</span> <span class="n" style="color: #333;">longer</span> <span class="n" style="color: #333;">spawns</span></span>

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<td class="diff-line-num new new_line" data-linenumber="12" 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">

12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="mosel">  <span class="n" style="color: #333;">external</span> <span class="p">``</span><span class="n" style="color: #333;">pigz</span><span class="p">``</span> <span class="n" style="color: #333;">processes</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">writing</span> <span class="n" style="color: #333;">gzip</span><span class="p">-</span><span class="n" style="color: #333;">compressed</span> <span class="n" style="color: #333;">files</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">first</span></span>

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<td class="diff-line-num new new_line" data-linenumber="13" 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">

13

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="mosel">  <span class="n" style="color: #333;">step</span> <span class="n" style="color: #333;">towards</span> <span class="n" style="color: #333;">ensuring</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">using</span> <span class="p">``--</span><span class="n" style="color: #333;">cores</span><span class="p">=</span><span class="n" style="color: #333;">n</span><span class="p">``</span> <span class="k" style="font-weight: 600;">uses</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">most</span> <span class="p">*</span><span class="n" style="color: #333;">n</span><span class="p">*</span> <span class="n" style="color: #333;">CPU</span></span>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="14" 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">

14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="mosel">  <span class="n" style="color: #333;">cores</span><span class="p">.</span></span>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="15" 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="LC15" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">release</span> <span class="n" style="color: #333;">adds</span> <span class="n" style="color: #333;">support</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">Python</span> <span class="m" style="color: #099;">3.8</span><span class="p">.</span></span>

</pre>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="16" 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">

16

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

</pre>

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5

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

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="mosel"><span class="n" style="color: #333;">v2</span><span class="m" style="color: #099;">.6</span> <span class="p">(</span><span class="m" style="color: #099;">2019</span><span class="p">-</span><span class="m" style="color: #099;">10</span><span class="p">-</span><span class="m" style="color: #099;">26</span><span class="p">)</span></span>

</pre>

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6

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<td class="diff-line-num new_line" data-linenumber="18" 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="LC18" class="line" lang="mosel"><span class="p">-----------------</span></span>

</pre>

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7

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<td class="diff-line-num new_line" data-linenumber="19" 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">

19

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

</pre>

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<br>

</li>

<li id="f75f54159d8ca95918e0cdbdcbc2012a7f8d47ed">

<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/31e5476ee9dc8503e7d2a812af0957c982687b8b#f75f54159d8ca95918e0cdbdcbc2012a7f8d47ed"><strong>buildwheels.sh</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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1

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<td class="diff-line-num new_line" data-linenumber="1" 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">

1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="2" 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">

2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>

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<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Build manylinux<span class="idiff left right">1 wheels for cutadapt</span>. Based on the example at</span></span>

</pre>

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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">

3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Build manylinux<span class="idiff left right"> wheels</span>. Based on the example at</span></span>

</pre>

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4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <https://github.com/pypa/python-manylinux-demo></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5" 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">

5

</td>

<td class="diff-line-num new_line" data-linenumber="5" 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">

5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="6" 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">

6

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<td class="diff-line-num new_line" data-linenumber="6" 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">

6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># It is best to run this in a fresh clone of the repository!</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="7" 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">

7

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<td class="diff-line-num new_line" data-linenumber="7" 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">

7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>

</pre>

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<td class="diff-line-num 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">

8

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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Run this within the repository root:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

9

</td>

<td class="diff-line-num new_line old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#   <span class="idiff left right">docker run --rm -v $(pwd):/io quay.io/pypa/manylinux1_x86_64 /io</span>/buildwheels.sh</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="10" 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">

</td>

<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">

9

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#   <span class="idiff left right">.</span>/buildwheels.sh</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="10" 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">

10

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<td class="diff-line-num new_line" data-linenumber="10" 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">

10

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="11" 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">

11

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<td class="diff-line-num new_line" data-linenumber="11" 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">

11

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># The wheels will be put into the wheelhouse/ subdirectory.</span></span>

</pre>

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<td class="diff-line-num old_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">

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">

12

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>

</pre>

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<td class="diff-line-num old_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">

13

</td>

<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">

13

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># For interactive tests:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

14

</td>

<td class="diff-line-num new_line old" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#   docker run -it -v $(pwd):/io quay.io/pypa/manylinux<span class="idiff left right">1</span>_x86_64 /bin/bash</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="15" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="14" 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">

14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#   docker run -it -v $(pwd):/io quay.io/pypa/manylinux<span class="idiff left right">2010</span>_x86_64 /bin/bash</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="15" 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">

15

</td>

<td class="diff-line-num new_line" data-linenumber="15" 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">

15

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

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

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="16" 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">

16

</td>

<td class="diff-line-num new_line" data-linenumber="16" 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">

16

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-xeuo</span> pipefail</span>

</pre>

</td>

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

17

</td>

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

17

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

18

</td>

<td class="diff-line-num new_line old" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell"><span class="nv" style="color: #008080;"><span class="idiff left right">MANYLINUX</span></span><span class="o" style="font-weight: 600;">=</span>quay.io/pypa/manylinux2010_x86_64</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="19" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="18" 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">

18

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="nv" style="color: #008080;"><span class="idiff left right">manylinux</span></span><span class="o" style="font-weight: 600;">=</span>quay.io/pypa/manylinux2010_x86_64</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="19" 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">

19

</td>

<td class="diff-line-num new_line" data-linenumber="19" 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">

19

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

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

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="20" 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">

20

</td>

<td class="diff-line-num new_line" data-linenumber="20" 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">

20

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># For convenience, if this script is called from outside of a docker container,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="21" 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">

21

</td>

<td class="diff-line-num new_line" data-linenumber="21" 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">

21

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># it starts a container and runs itself inside of it.</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="22" 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="LC22" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">!</span> <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-q</span> docker /proc/1/cgroup<span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="23" 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">

23

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<td class="diff-line-num new_line" data-linenumber="23" 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="LC23" class="line" lang="shell">  <span class="c" style="color: #998; font-style: italic;"># We are not inside a container</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="shell">  docker pull <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;"><span class="idiff left right">MANYLINUX</span></span><span class="k" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="shell">  <span class="nb" style="color: #0086b3;">exec </span>docker run <span class="nt" style="color: #000080;">--rm</span> <span class="nt" style="color: #000080;">-v</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">pwd</span><span class="si" style="color: #d14;">)</span>:/io <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;"><span class="idiff left right">MANYLINUX</span></span><span class="k" style="font-weight: 600;">}</span> /io/<span class="nv" style="color: #008080;">$0</span></span>

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<td class="diff-line-num new old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell">  docker pull <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;"><span class="idiff left right">manylinux</span></span><span class="k" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell">  <span class="nb" style="color: #0086b3;">exec </span>docker run <span class="nt" style="color: #000080;">--rm</span> <span class="nt" style="color: #000080;">-v</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">pwd</span><span class="si" style="color: #d14;">)</span>:/io <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;"><span class="idiff left right">manylinux</span></span><span class="k" style="font-weight: 600;">}</span> /io/<span class="nv" style="color: #008080;">$0</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="26" 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="LC26" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="27" 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="LC27" class="line" lang="shell"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="28" 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="LC28" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Strip binaries (copied from multibuild)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="37" 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="37" 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">@@ -37,11 +37,12 @@ PYBINS="/opt/python/*/bin"</td>

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<td class="diff-line-num old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="37" 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="LC37" class="line" lang="shell"><span class="nv" style="color: #008080;">HAS_CYTHON</span><span class="o" style="font-weight: 600;">=</span>0</span>

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

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

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>PYBIN <span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">PYBINS</span><span class="k" style="font-weight: 600;">}</span><span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#    ${PYBIN}/pip install -r /io/requirements.txt</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="shell">    <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">PYBIN</span><span class="k" style="font-weight: 600;">}</span>/pip wheel /io/ <span class="nt" style="color: #000080;">-w</span> wheelhouse/</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="40" 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="LC40" class="line" lang="shell">    <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">PYBIN</span><span class="k" style="font-weight: 600;">}</span>/pip wheel <span class="nt" style="color: #000080;"><span class="idiff left">--no-deps</span></span><span class="idiff right"> </span>/io/ <span class="nt" style="color: #000080;">-w</span> wheelhouse/</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="41" 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">

41

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<td class="diff-line-num new_line" data-linenumber="41" 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="LC41" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="42" 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">

42

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"><span class="nb" style="color: #0086b3;">ls </span>wheelhouse/</span>

</pre>

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

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

43

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="shell"></span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="44" 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="LC44" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Bundle external shared libraries into the wheels</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>whl <span class="k" style="font-weight: 600;">in </span>wheelhouse/<span class="idiff left right">cutadapt-</span><span class="k" style="font-weight: 600;">*</span>.whl<span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>whl <span class="k" style="font-weight: 600;">in </span>wheelhouse/<span class="k" style="font-weight: 600;">*</span>.whl<span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="shell"><span class="k" style="font-weight: 600;">    </span>auditwheel repair <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$whl</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: #000080;">--plat</span> manylinux1_x86_64 <span class="nt" style="color: #000080;">-w</span> repaired/</span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="shell"></span>

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<li id="df0576cbb783bc50b36e1efa3cbe0564a26c8295">

<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/31e5476ee9dc8503e7d2a812af0957c982687b8b#df0576cbb783bc50b36e1efa3cbe0564a26c8295"><strong>doc/conf.py</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="46" 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>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"><span class="n" style="color: #333;">master_doc</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'index'</span></span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># General information about the project.</span></span>

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"><span class="n" style="color: #333;">project</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">u'<span class="idiff left right">c</span>utadapt'</span></span>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"><span class="n" style="color: #333;">project</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">u'<span class="idiff left right">C</span>utadapt'</span></span>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"><span class="n" style="color: #333;">copyright</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">u'2010-2019, Marcel Martin'</span></span>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The version info for the project you're documenting, acts as replacement for</span></span>

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<li id="ee1d7278a009e2c5c652622fe43dc77e39af740d">

<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/31e5476ee9dc8503e7d2a812af0957c982687b8b#ee1d7278a009e2c5c652622fe43dc77e39af740d"><strong>doc/guide.rst</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="129" 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">@@ -129,22 +129,9 @@ Make also sure that you have ``pigz`` (parallel gzip) installed if you use</td>

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<pre style="margin: 0;"> <span id="LC129" class="line" lang="plaintext">multiple cores and write to a ``.gz`` output file. Otherwise, compression of</span>

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="plaintext">the output will be done in a single thread and therefore be a bottleneck.</span>

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC132" class="line" lang="plaintext">There are some limitations at the moment:</span>

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<pre style="margin: 0;">-<span id="LC133" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

134

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<td class="diff-line-num new_line old" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC134" class="line" lang="plaintext">* The following command-line arguments are not compatible with</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

135

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<td class="diff-line-num new_line old" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC135" class="line" lang="plaintext">  multi-core:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

136

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<td class="diff-line-num new_line old" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC136" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

137

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<td class="diff-line-num new_line old" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC137" class="line" lang="plaintext">      - ``--info-file``</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

138

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<td class="diff-line-num new_line old" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC138" class="line" lang="plaintext">      - ``--rest-file``</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

139

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<td class="diff-line-num new_line old" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC139" class="line" lang="plaintext">      - ``--wildcard-file``</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

140

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<td class="diff-line-num new_line old" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC140" class="line" lang="plaintext">      - ``--format``</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

141

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<td class="diff-line-num new_line old" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC141" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

142

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<td class="diff-line-num new_line old" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC142" class="line" lang="plaintext">* Multi-core is not available when you use Cutadapt for demultiplexing.</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

143

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<td class="diff-line-num new_line old" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC143" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

144

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<td class="diff-line-num new_line old" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC144" class="line" lang="plaintext">If you try to use multiple cores with an incompatible commandline option, you</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC145" class="line" lang="plaintext">will get an error message.</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC146" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC147" class="line" lang="plaintext">Some of these limitations will be lifted in the future, as time allows.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="132" 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="LC132" class="line" lang="plaintext">Currently, multi-core support is not available when demultiplexing. You</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="148" 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">

</td>

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

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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">will get an error message if you try to use it. This limitations may be</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">lifted in the future.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="135" 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">

135

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC135" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="136" 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">

136

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="plaintext">.. versionadded:: 1.15</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="137" 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="LC137" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="154" 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="141" 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">@@ -154,6 +141,9 @@ Some of these limitations will be lifted in the future, as time allows.</td>

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<td class="diff-line-num old_line" data-linenumber="154" 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">

154

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<td class="diff-line-num new_line" data-linenumber="141" 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">

141

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="plaintext">.. versionadded:: 2.5</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="155" 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">

155

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<td class="diff-line-num new_line" data-linenumber="142" 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">

142

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="plaintext">    Multicore works with ``--untrimmed/too-short/too-long-(paired)-output``</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="156" 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">

156

</td>

<td class="diff-line-num new_line" data-linenumber="143" 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">

143

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC143" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="157" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="144" 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">

144

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext">.. versionadded:: 2.7</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="157" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="145" 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">

145

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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext">    Muticore works with ``--info-file``, ``--rest-file``, ``--wildcard-file``</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="157" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="146" 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">

146

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="157" 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">

157

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<td class="diff-line-num new_line" data-linenumber="147" 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">

147

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC147" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="158" 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">

158

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<td class="diff-line-num new_line" data-linenumber="148" 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">

148

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="plaintext">Speed-up tricks</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="159" 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">

159

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<td class="diff-line-num new_line" data-linenumber="149" 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">

149

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="plaintext">---------------</span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1037" 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="1027" 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">@@ -1037,7 +1027,7 @@ each read. Steps not requested on the command-line are skipped.</td>

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<td class="diff-line-num old_line" data-linenumber="1037" 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">

1037

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<td class="diff-line-num new_line" data-linenumber="1027" 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">

1027

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<pre style="margin: 0;"> <span id="LC1027" class="line" lang="plaintext">Filtering reads</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1038" 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">

1038

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<td class="diff-line-num new_line" data-linenumber="1028" 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">

1028

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1028" class="line" lang="plaintext">===============</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1039" 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">

1039

</td>

<td class="diff-line-num new_line" data-linenumber="1029" 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">

1029

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1029" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1040

</td>

<td class="diff-line-num new_line old" data-linenumber="1030" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1040" class="line" lang="plaintext">By default, all processed reads, no matter whether they were trimmed <span class="idiff left right">are</span> not,</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1041" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1030" 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">

1030

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1030" class="line" lang="plaintext">By default, all processed reads, no matter whether they were trimmed <span class="idiff left right">or</span> not,</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1041" 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">

1041

</td>

<td class="diff-line-num new_line" data-linenumber="1031" 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">

1031

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1031" class="line" lang="plaintext">are written to the output file specified by the ``-o`` option (or to standard</span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1042" 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">

1042

</td>

<td class="diff-line-num new_line" data-linenumber="1032" 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">

1032

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1032" class="line" lang="plaintext">output if ``-o`` was not provided). For paired-end reads, the second read in a</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1043" 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">

1043

</td>

<td class="diff-line-num new_line" data-linenumber="1033" 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">

1033

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1033" class="line" lang="plaintext">pair is always written to the file specified by the ``-p`` option.</span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1047" 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="1037" 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">@@ -1047,23 +1037,22 @@ them entirely or by redirecting them to other files. When redirecting reads,</td>

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<td class="diff-line-num old_line" data-linenumber="1047" 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">

1047

</td>

<td class="diff-line-num new_line" data-linenumber="1037" 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">

1037

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<pre style="margin: 0;"> <span id="LC1037" class="line" lang="plaintext">the basic rule is that *each read is written to at most one file*. You cannot</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1048" 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">

1048

</td>

<td class="diff-line-num new_line" data-linenumber="1038" 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">

1038

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1038" class="line" lang="plaintext">write reads to more than one output file.</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1049" 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">

1049

</td>

<td class="diff-line-num new_line" data-linenumber="1039" 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">

1039

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1039" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1050

</td>

<td class="diff-line-num new_line old" data-linenumber="1040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1050" class="line" lang="plaintext">In the following, the term "processed read" refers to a read to which all</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1051

</td>

<td class="diff-line-num new_line old" data-linenumber="1040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1051" class="line" lang="plaintext">modifications have been applied (adapter removal, quality trimming etc.). A</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1052" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1052

</td>

<td class="diff-line-num new_line old" data-linenumber="1040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1052" class="line" lang="plaintext">processed read can be identical to the input read if no modifications were done.</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1053" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1053

</td>

<td class="diff-line-num new_line old" data-linenumber="1040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1053" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1054" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1040" 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">

1040

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1040" class="line" lang="plaintext">Filters are applied to *all* processed reads, no matter whether they have been</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1054" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1041" 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">

1041

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1041" class="line" lang="plaintext">modified by adapter- or quality trimming.</span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num 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">

1054

</td>

<td class="diff-line-num new_line" data-linenumber="1042" 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">

1042

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1042" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1055" 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">

1055

</td>

<td class="diff-line-num new_line" data-linenumber="1043" 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">

1043

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1043" class="line" lang="plaintext">``--minimum-length LENGTH`` or ``-m LENGTH``</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1056

</td>

<td class="diff-line-num new_line old" data-linenumber="1044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC1056" class="line" lang="plaintext">    Discard processed reads that are shorter than LENGTH. Reads that are too</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1057" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1057

</td>

<td class="diff-line-num new_line old" data-linenumber="1044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1057" class="line" lang="plaintext">    short even before adapter removal are also discarded. Without this option,</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1058" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1058

</td>

<td class="diff-line-num new_line old" data-linenumber="1044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1058" class="line" lang="plaintext">    reads that have a length of zero (empty reads) are kept in the output.</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1059" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1044" 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">

1044

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1044" class="line" lang="plaintext">    Discard processed reads that are shorter than LENGTH.</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1059" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1045" 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">

1045

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1045" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1059" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1046" 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">

1046

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1046" class="line" lang="plaintext">    If you do not use this option, reads that have a length of zero (empty</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1059" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1047" 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">

1047

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1047" class="line" lang="plaintext">    reads) are kept in the output. Some downstream tools may have problems</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1059" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1048" 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">

1048

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1048" class="line" lang="plaintext">    with zero-length sequences. In that case, specify at least ``-m 1``.</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1059" 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">

1059

</td>

<td class="diff-line-num new_line" data-linenumber="1049" 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">

1049

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1049" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1060" 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">

1060

</td>

<td class="diff-line-num new_line" data-linenumber="1050" 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">

1050

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1050" class="line" lang="plaintext">``--too-short-output FILE``</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1061" 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">

1061

</td>

<td class="diff-line-num new_line" data-linenumber="1051" 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">

1051

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1051" class="line" lang="plaintext">    Instead of discarding the reads that are too short according to ``-m``,</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1062" 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">

1062

</td>

<td class="diff-line-num new_line" data-linenumber="1052" 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">

1052

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1052" class="line" lang="plaintext">    write them to *FILE* (in FASTA/FASTQ format).</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1063" 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">

1063

</td>

<td class="diff-line-num new_line" data-linenumber="1053" 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">

1053

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1053" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1064" 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">

1064

</td>

<td class="diff-line-num new_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">

1054

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1054" class="line" lang="plaintext">``--maximum-length LENGTH`` or ``-M LENGTH``</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1065

</td>

<td class="diff-line-num new_line old" data-linenumber="1055" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1065" class="line" lang="plaintext">    Discard processed reads that are longer than LENGTH. Reads that are too</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1066

</td>

<td class="diff-line-num new_line old" data-linenumber="1055" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1066" class="line" lang="plaintext">    long even before adapter removal are also discarded.</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1067" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1055" 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">

1055

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1055" class="line" lang="plaintext">    Discard processed reads that are longer than LENGTH.</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1067" 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">

1067

</td>

<td class="diff-line-num new_line" data-linenumber="1056" 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">

1056

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1056" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1068" 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">

1068

</td>

<td class="diff-line-num 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">

1057

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1057" class="line" lang="plaintext">``--too-long-output FILE``</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1069" 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">

1069

</td>

<td class="diff-line-num new_line" data-linenumber="1058" 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">

1058

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1058" class="line" lang="plaintext">    Instead of discarding reads that are too long (according to ``-M``),</span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1074" 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="1063" 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">@@ -1074,11 +1063,11 @@ processed read can be identical to the input read if no modifications were done.</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1074" 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">

1074

</td>

<td class="diff-line-num new_line" data-linenumber="1063" 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">

1063

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1063" class="line" lang="plaintext">    of writing them to the regular output file.</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1075" 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">

1075

</td>

<td class="diff-line-num new_line" data-linenumber="1064" 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">

1064

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1064" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1076" 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">

1076

</td>

<td class="diff-line-num new_line" data-linenumber="1065" 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">

1065

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1065" class="line" lang="plaintext">``--discard-trimmed``</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1077

</td>

<td class="diff-line-num new_line old" data-linenumber="1066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1077" class="line" lang="plaintext">   Discard reads in which an adapter was found.</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1078" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1066" 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">

1066

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1066" class="line" lang="plaintext">   <span class="idiff left right"> </span>Discard reads in which an adapter was found.</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1078" 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">

1078

</td>

<td class="diff-line-num new_line" data-linenumber="1067" 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">

1067

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1067" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1079" 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">

1079

</td>

<td class="diff-line-num new_line" data-linenumber="1068" 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">

1068

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1068" class="line" lang="plaintext">``--discard-untrimmed``</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1080" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1080

</td>

<td class="diff-line-num new_line old" data-linenumber="1069" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1080" class="line" lang="plaintext">   Discard reads in which *no* adapter was found. This has the same effect as</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1081

</td>

<td class="diff-line-num new_line old" data-linenumber="1069" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1081" class="line" lang="plaintext">   specifying ``--untrimmed-output /dev/null``.</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1082" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1069" 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">

1069

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1069" class="line" lang="plaintext">   <span class="idiff left right"> </span>Discard reads in which *no* adapter was found. This has the same effect as</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1082" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1070" 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">

1070

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1070" class="line" lang="plaintext">   <span class="idiff left right"> </span>specifying ``--untrimmed-output /dev/null``.</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1082" 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">

1082

</td>

<td class="diff-line-num new_line" data-linenumber="1071" 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">

1071

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1071" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1083" 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">

1083

</td>

<td class="diff-line-num new_line" data-linenumber="1072" 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">

1072

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1072" class="line" lang="plaintext">The options ``--too-short-output`` and ``--too-long-output`` are applied first.</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1084" 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">

1084

</td>

<td class="diff-line-num new_line" data-linenumber="1073" 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">

1073

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1073" class="line" lang="plaintext">This means, for example, that a read that is too long will never end up in the</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1089" 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="1078" 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">@@ -1089,11 +1078,11 @@ The options ``--untrimmed-output``, ``--discard-trimmed`` and ``-discard-untrimm</td>

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1089

</td>

<td class="diff-line-num new_line" data-linenumber="1078" 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">

1078

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<pre style="margin: 0;"> <span id="LC1078" class="line" lang="plaintext">are mutually exclusive.</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1090" 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">

1090

</td>

<td class="diff-line-num new_line" data-linenumber="1079" 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">

1079

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1079" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1091" 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">

1091

</td>

<td class="diff-line-num new_line" data-linenumber="1080" 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">

1080

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<pre style="margin: 0;"> <span id="LC1080" class="line" lang="plaintext">The following filtering options do not have a corresponding option for redirecting</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1092

</td>

<td class="diff-line-num new_line old" data-linenumber="1081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1092" class="line" lang="plaintext">reads. They always discard reads for which the filtering criterion applies.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1093" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="1081" 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">

1081

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<pre style="margin: 0;">+<span id="LC1081" class="line" lang="plaintext">reads. They always discard <span class="idiff left right">those </span>reads for which the filtering criterion applies.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1093" 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">

1093

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<td class="diff-line-num new_line" data-linenumber="1082" 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">

1082

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1082" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1094" 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">

1094

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<td class="diff-line-num new_line" data-linenumber="1083" 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">

1083

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<pre style="margin: 0;"> <span id="LC1083" class="line" lang="plaintext">``--max-n COUNT_or_FRACTION``</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1095" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1095

</td>

<td class="diff-line-num new_line old" data-linenumber="1084" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1095" class="line" lang="plaintext">    Discard reads with more than COUNT ``N`` bases. If ``COUNT_or_FRACTION`` is<span class="idiff left right"> an</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1096" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1096

</td>

<td class="diff-line-num new_line old" data-linenumber="1084" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1096" class="line" lang="plaintext">    number between 0 and 1, it is interpreted as a fraction of the read length</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1097" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1084" 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">

1084

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<pre style="margin: 0;">+<span id="LC1084" class="line" lang="plaintext">    Discard reads with more than COUNT ``N`` bases. If ``COUNT_or_FRACTION`` is</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1097" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1085" 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">

1085

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<pre style="margin: 0;">+<span id="LC1085" class="line" lang="plaintext">    <span class="idiff left right">a </span>number between 0 and 1, it is interpreted as a fraction of the read length</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1097" 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">

1097

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<td class="diff-line-num new_line" data-linenumber="1086" 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">

1086

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1086" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1098" 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">

1098

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<td class="diff-line-num new_line" data-linenumber="1087" 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">

1087

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<pre style="margin: 0;"> <span id="LC1087" class="line" lang="plaintext">``--discard-casava``</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1099" 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">

1099

</td>

<td class="diff-line-num new_line" data-linenumber="1088" 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">

1088

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<pre style="margin: 0;"> <span id="LC1088" class="line" lang="plaintext">    Discard reads that did not pass CASAVA filtering. Illumina’s CASAVA pipeline in</span>

</pre>

</td>

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<br>

</li>

<li id="6677207c6fa30ac9cec19ad036ae842582159ecb">

<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/31e5476ee9dc8503e7d2a812af0957c982687b8b#6677207c6fa30ac9cec19ad036ae842582159ecb"><strong>doc/installation.rst</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -38,6 +38,24 @@ Then install Cutadapt like this::</td>

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

38

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

38

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">If neither ``pip`` nor ``conda`` installation works, keep reading.</span>

</pre>

</td>

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

39

</td>

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

39

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="40" 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">

40

</td>

<td class="diff-line-num new_line" data-linenumber="40" 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">

40

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

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

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="41" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="41" 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">

41

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">Installation on a Debian-based Linux distribution</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="41" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="42" 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">

42

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">-------------------------------------------------</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="43" 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">

43

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="41" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="44" 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">

44

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">Cutadapt is also included in Debian-based Linux distributions, such as Ubuntu.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="41" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="45" 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">

45

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">Simply use your favorite package manager to install Cutadapt. On the</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="41" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="46" 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">

46

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">command-line, this should work ::</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="41" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="47" 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">

47

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="41" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="48" 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">

48

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">    sudo apt install cutadapt</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="41" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="49" 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">

49

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="41" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="50" 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">

50

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">or possibly ::</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="51" 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">

51

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="41" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="52" 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">

52

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">    sudo apt install python3-cutadapt</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="53" 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">

53

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="41" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">Please be aware that this will likely give you an old version of Cutadapt. If</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="41" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="55" 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">

55

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">you encounter unexpected behavior, please use one of the other installation</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="41" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="56" 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">

56

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">methods to get an up-to-date version before reporting bugs.</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="41" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="57" 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">

57

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="41" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="58" 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">

58

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="41" 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">

41

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<td class="diff-line-num new_line" data-linenumber="59" 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">

59

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext">.. _dependencies:</span>

</pre>

</td>

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

42

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<td class="diff-line-num new_line" data-linenumber="60" 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">

60

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext"></span>

</pre>

</td>

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

43

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<td class="diff-line-num new_line" data-linenumber="61" 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">

61

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext">Dependencies</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="8e2edce0d507e1297474f25c00cae94258db38d8">

<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/31e5476ee9dc8503e7d2a812af0957c982687b8b#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="103" 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="103" 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">@@ -103,11 +103,11 @@ setup(</td>

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<td class="diff-line-num old_line" data-linenumber="103" 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">

103

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<pre style="margin: 0;"> <span id="LC103" 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 class="s" style="color: #d14;">'src'</span><span class="p">),</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python">    <span class="n" style="color: #333;">entry_points</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'console_scripts'</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">'cutadapt = cutadapt.__main__:main'</span><span class="p">]},</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="105" 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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105

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<pre style="margin: 0;"> <span id="LC105" 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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC106" class="line" lang="python">        <span class="s" style="color: #d14;">'dnaio~=0.4.<span class="idiff left right">0</span>'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python">        <span class="s" style="color: #d14;">'dnaio~=0.4.<span class="idiff left right">1</span>'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="107" 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">

107

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<td class="diff-line-num new_line" data-linenumber="107" 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="LC107" class="line" lang="python">        <span class="s" style="color: #d14;">'xopen~=0.8.4'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="108" 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="LC108" class="line" lang="python">    <span class="p">],</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="109" 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="LC109" class="line" lang="python">    <span class="n" style="color: #333;">extras_require</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python">        <span class="s" style="color: #d14;">'dev'</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">'Cython'</span><span class="p">,</span> <span class="s" style="color: #d14;">'pytest'</span><span class="p">,</span> <span class="s" style="color: #d14;">'pytest-timeout'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sphinx'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sphinx_issues'</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="110" 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="LC110" class="line" lang="python">        <span class="s" style="color: #d14;">'dev'</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">'Cython'</span><span class="p">,</span> <span class="s" style="color: #d14;">'pytest'</span><span class="p">,</span> <span class="s" style="color: #d14;">'pytest-timeout'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left">pytest-mock'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'</span>sphinx'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sphinx_issues'</span><span class="p">],</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python">    <span class="p">},</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="112" 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="LC112" class="line" lang="python">    <span class="n" style="color: #333;">python_requires</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'>=3.5'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="113" 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="LC113" class="line" lang="python">    <span class="n" style="color: #333;">classifiers</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span></span>

</pre>

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<br>

</li>

<li id="babdfe5d368a4907abadce7f9b00dfab2489185a">

<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/31e5476ee9dc8503e7d2a812af0957c982687b8b#babdfe5d368a4907abadce7f9b00dfab2489185a"><strong>src/cutadapt/__main__.py</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="60" 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="60" 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">@@ -60,7 +60,6 @@ import logging</td>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">platform</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="61" 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="LC61" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">argparse</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ArgumentParser</span><span class="p">,</span> <span class="n" style="color: #333;">SUPPRESS</span><span class="p">,</span> <span class="n" style="color: #333;">HelpFormatter</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="62" 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="LC62" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">xopen</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">xopen</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="63" 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="LC63" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">dnaio</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="65" 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="LC64" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cutadapt</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">__version__</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="72" 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="71" 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">@@ -72,7 +71,7 @@ from cutadapt.modifiers import (LengthTagModifier, SuffixRemover, PrefixSuffixAd</td>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cutadapt.report</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">full_report</span><span class="p">,</span> <span class="n" style="color: #333;">minimal_report</span></span>

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cutadapt.pipeline</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span><span class="n" style="color: #333;">SingleEndPipeline</span><span class="p">,</span> <span class="n" style="color: #333;">PairedEndPipeline</span><span class="p">,</span> <span class="n" style="color: #333;">InputFiles</span><span class="p">,</span> <span class="n" style="color: #333;">OutputFiles</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python">    <span class="n" style="color: #333;">SerialPipelineRunner</span><span class="p">,</span> <span class="n" style="color: #333;">ParallelPipelineRunner</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cutadapt.utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">available_cpu_count</span><span class="p">,</span> <span class="n" style="color: #333;">Progress</span><span class="p">,</span> <span class="n" style="color: #333;">DummyProgress</span></span>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cutadapt.utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">available_cpu_count</span><span class="p">,</span> <span class="n" style="color: #333;">Progress</span><span class="p">,</span> <span class="n" style="color: #333;">DummyProgress</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">FileOpener</span></span></span>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cutadapt.log</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">setup_logging</span><span class="p">,</span> <span class="n" style="color: #333;">REPORT</span></span>

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC77" 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>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="184" 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">@@ -185,7 +184,7 @@ def get_argument_parser():</td>

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<pre style="margin: 0;"> <span id="LC184" class="line" lang="python">            <span class="s" style="color: #d14;">"mask: replace with 'N' characters; "</span></span>

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<pre style="margin: 0;"> <span id="LC185" class="line" lang="python">            <span class="s" style="color: #d14;">"lowercase: convert to lowercase; "</span></span>

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<pre style="margin: 0;"> <span id="LC186" class="line" lang="python">            <span class="s" style="color: #d14;">"none: leave unchanged (useful with "</span></span>

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<pre style="margin: 0;">-<span id="LC188" class="line" lang="python">            <span class="s" style="color: #d14;">"--discard-untrimmed). Default: <span class="idiff left right">trim</span>"</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python">            <span class="s" style="color: #d14;">"--discard-untrimmed). Default: </span><span class="si" style="color: #d14;"><span class="idiff left">%(default)</span></span><span class="s" style="color: #d14;"><span class="idiff right">s</span>"</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC188" class="line" lang="python">    <span class="n" style="color: #333;">group</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--no-trim"</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'action'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_const'</span><span class="p">,</span> <span class="n" style="color: #333;">const</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'none'</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC189" class="line" lang="python">        <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">SUPPRESS</span><span class="p">)</span>  <span class="c1" style="color: #998; font-style: italic;"># Deprecated, use --action=none</span></span>

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<pre style="margin: 0;"> <span id="LC190" class="line" lang="python">    <span class="n" style="color: #333;">group</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--mask-adapter"</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'action'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_const'</span><span class="p">,</span> <span class="n" style="color: #333;">const</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'mask'</span><span class="p">,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="381" 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>

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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">@@ -381,25 +380,24 @@ def parse_lengths(s):</td>

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<pre style="margin: 0;"> <span id="LC380" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="n" style="color: #333;">values</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC381" class="line" lang="python"></span>

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<td class="diff-line-num new_line" data-linenumber="382" 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="LC382" class="line" lang="python"></span>

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<td class="diff-line-num new_line old" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC384" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">open_output_files</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">default_outfile</span><span class="p">,</span> <span class="n" style="color: #333;">interleaved</span><span class="p">):</span></span>

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<td class="diff-line-num new old_line" data-linenumber="385" 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="LC383" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">open_output_files</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">default_outfile</span><span class="p">,</span> <span class="n" style="color: #333;">interleaved</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">file_opener</span></span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="384" 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="LC384" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

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<td class="diff-line-num old_line" data-linenumber="386" 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="LC385" class="line" lang="python"><span class="s" style="color: #d14;">    Return an OutputFiles instance. If demultiplex is True, the untrimmed, untrimmed2, out and out2</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="387" 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="LC386" class="line" lang="python"><span class="s" style="color: #d14;">    attributes are not opened files, but paths (out and out2 with the '{name}' template).</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="388" 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="LC387" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<pre style="margin: 0;">-<span id="LC389" class="line" lang="python">    <span class="n" style="color: #333;">compression_level</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">compression_level</span></span>

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<td class="diff-line-num new_line" data-linenumber="388" 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="LC388" class="line" lang="python"></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC389" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">open1</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">):</span></span>

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<td class="diff-line-num old_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC390" class="line" lang="python">        <span class="s" style="color: #d14;">"""Return opened file (or None if path is None)"""</span></span>

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

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<pre style="margin: 0;"> <span id="LC391" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">path</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="392" 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="LC392" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>

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<td class="diff-line-num old old_line" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC395" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left">xopen</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">path</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"w"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">compresslevel</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff right">compression_level</span></span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC393" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left">file_opener</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">xopen</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">path</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"wb"</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

394

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<pre style="margin: 0;"> <span id="LC394" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<pre style="margin: 0;"> <span id="LC395" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">open2</span><span class="p">(</span><span class="n" style="color: #333;">path1</span><span class="p">,</span> <span class="n" style="color: #333;">path2</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="398" 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">

398

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<td class="diff-line-num new_line" data-linenumber="396" 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="LC396" class="line" lang="python">        <span class="n" style="color: #333;">file1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file2</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="399" 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">

399

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<td class="diff-line-num new_line" data-linenumber="397" 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="LC397" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">path1</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC400" class="line" lang="python">            <span class="n" style="color: #333;">file1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">xopen</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">path1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'wb'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">compresslevel</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff right">compression_level</span></span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC398" class="line" lang="python">            <span class="n" style="color: #333;">file1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">file_opener</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">xopen</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">path1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"wb"</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="401" 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">

401

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<td class="diff-line-num new_line" data-linenumber="399" 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="LC399" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">path2</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

402

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<td class="diff-line-num new_line old" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC402" class="line" lang="python">                <span class="n" style="color: #333;">file2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">xopen</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">path2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'wb'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">compresslevel</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff right">compression_level</span></span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC400" class="line" lang="python">                <span class="n" style="color: #333;">file2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">file_opener</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">xopen</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">path2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"wb"</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="401" 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="LC401" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">file1</span><span class="p">,</span> <span class="n" style="color: #333;">file2</span></span>

</pre>

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404

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<td class="diff-line-num new_line" data-linenumber="402" 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="LC402" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC403" class="line" lang="python">    <span class="n" style="color: #333;">rest_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">open1</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rest_file</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="599" 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="597" 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">@@ -599,7 +597,7 @@ def check_arguments(args, paired, is_interleaved_output):</td>

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<td class="diff-line-num old_line" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="597" 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="LC597" class="line" lang="python">        <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">CommandLineError</span><span class="p">(</span><span class="s" style="color: #d14;">"--pair-adapters cannot be used with --times"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="598" 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="LC598" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="599" 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="LC599" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC602" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">pipeline_from_parsed_args</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">paired</span><span class="p">,</span> <span class="n" style="color: #333;">is_interleaved_output</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC600" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">pipeline_from_parsed_args</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">paired</span><span class="p">,</span> <span class="n" style="color: #333;">is_interleaved_output</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">file_opener</span></span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC601" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

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<td class="diff-line-num old_line" data-linenumber="604" 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="LC602" class="line" lang="python"><span class="s" style="color: #d14;">    Setup a processing pipeline from parsed command-line arguments.</span></span>

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<pre style="margin: 0;"> <span id="LC603" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="632" 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="630" 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">@@ -632,9 +630,9 @@ def pipeline_from_parsed_args(args, paired, is_interleaved_output):</td>

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<pre style="margin: 0;"> <span id="LC630" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Create the processing pipeline</span></span>

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<pre style="margin: 0;"> <span id="LC631" 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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<pre style="margin: 0;"> <span id="LC632" class="line" lang="python">        <span class="n" style="color: #333;">pair_filter_mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'any'</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pair_filter</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pair_filter</span></span>

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<pre style="margin: 0;">-<span id="LC635" class="line" lang="python">        <span class="n" style="color: #333;">pipeline</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PairedEndPipeline</span><span class="p">(</span><span class="n" style="color: #333;">pair_filter_mode</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC633" class="line" lang="python">        <span class="n" style="color: #333;">pipeline</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PairedEndPipeline</span><span class="p">(</span><span class="n" style="color: #333;">pair_filter_mode</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">file_opener</span></span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC634" 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="LC637" class="line" lang="python">        <span class="n" style="color: #333;">pipeline</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SingleEndPipeline</span><span class="p">()</span></span>

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<td class="diff-line-num new old_line" data-linenumber="638" 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="LC635" class="line" lang="python">        <span class="n" style="color: #333;">pipeline</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SingleEndPipeline</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">file_opener</span></span><span class="p">)</span></span>

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<td class="diff-line-num old_line" data-linenumber="638" 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="LC636" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC637" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># When adapters are being trimmed only in R1 or R2, override the pair filter mode</span></span>

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<pre style="margin: 0;"> <span id="LC638" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># as using the default of 'any' would regard all read pairs as untrimmed.</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">@@ -780,30 +778,30 @@ def main(cmdlineargs=None, default_outfile=sys.stdout.buffer):</td>

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<pre style="margin: 0;"> <span id="LC778" class="line" lang="python"></span>

</pre>

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781

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<td class="diff-line-num new_line" data-linenumber="779" 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="LC779" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Print the header now because some of the functions below create logging output</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="782" 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">

782

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<td class="diff-line-num new_line" data-linenumber="780" 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="LC780" class="line" lang="python">    <span class="n" style="color: #333;">log_header</span><span class="p">(</span><span class="n" style="color: #333;">cmdlineargs</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="783" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="781" 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">

781

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<pre style="margin: 0;">+<span id="LC781" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cores</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="783" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="782" 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">

782

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<pre style="margin: 0;">+<span id="LC782" class="line" lang="python">        <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">'Value for --cores cannot be negative'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="783" 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">

783

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<pre style="margin: 0;">+<span id="LC783" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="783" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="784" 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">

784

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<pre style="margin: 0;">+<span id="LC784" class="line" lang="python">    <span class="n" style="color: #333;">cores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">available_cpu_count</span><span class="p">()</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cores</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cores</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="785" 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">

785

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<pre style="margin: 0;">+<span id="LC785" class="line" lang="python">    <span class="n" style="color: #333;">file_opener</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FileOpener</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="786" 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">

786

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<pre style="margin: 0;">+<span id="LC786" class="line" lang="python">        <span class="n" style="color: #333;">compression_level</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">compression_level</span><span class="p">,</span> <span class="n" style="color: #333;">threads</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cores</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="783" 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">

783

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<td class="diff-line-num new_line" data-linenumber="787" 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="LC787" class="line" lang="python">    <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="788" 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">

788

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<pre style="margin: 0;"> <span id="LC788" class="line" lang="python">        <span class="n" style="color: #333;">is_interleaved_input</span><span class="p">,</span> <span class="n" style="color: #333;">is_interleaved_output</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">determine_interleaved</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">)</span></span>

</pre>

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785

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<td class="diff-line-num new_line" data-linenumber="789" 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">

789

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<pre style="margin: 0;"> <span id="LC789" class="line" lang="python">        <span class="n" style="color: #333;">input_filename</span><span class="p">,</span> <span class="n" style="color: #333;">input_paired_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">input_files_from_parsed_args</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">inputs</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="790" 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">

790

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<pre style="margin: 0;"> <span id="LC790" class="line" lang="python">            <span class="n" style="color: #333;">paired</span><span class="p">,</span> <span class="n" style="color: #333;">is_interleaved_input</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

787

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<td class="diff-line-num new_line old" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC787" class="line" lang="python">        <span class="n" style="color: #333;">pipeline</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pipeline_from_parsed_args</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">paired</span><span class="p">,</span> <span class="n" style="color: #333;">is_interleaved_output</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

788

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<td class="diff-line-num new_line old" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC788" class="line" lang="python">        <span class="n" style="color: #333;">outfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">open_output_files</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">default_outfile</span><span class="p">,</span> <span class="n" style="color: #333;">is_interleaved_output</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="789" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="791" 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">

791

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<pre style="margin: 0;">+<span id="LC791" class="line" lang="python">        <span class="n" style="color: #333;">pipeline</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pipeline_from_parsed_args</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">paired</span><span class="p">,</span> <span class="n" style="color: #333;">is_interleaved_output</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">file_opener</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="789" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="792" 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">

792

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC792" class="line" lang="python">        <span class="n" style="color: #333;">outfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">open_output_files</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">default_outfile</span><span class="p">,</span> <span class="n" style="color: #333;">is_interleaved_output</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">file_opener</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="789" 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">

789

</td>

<td class="diff-line-num new_line" data-linenumber="793" 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">

793

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC793" class="line" lang="python">    <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">CommandLineError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="790" 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">

790

</td>

<td class="diff-line-num new_line" data-linenumber="794" 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">

794

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC794" class="line" lang="python">        <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">))</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="791" 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">

791

</td>

<td class="diff-line-num new_line" data-linenumber="795" 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">

795

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC795" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span>  <span class="c1" style="color: #998; font-style: italic;"># avoid IDE warnings below</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="792" 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">

792

</td>

<td class="diff-line-num new_line" data-linenumber="796" 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">

796

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC796" class="line" lang="python"></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

793

</td>

<td class="diff-line-num new_line old" data-linenumber="797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC793" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cores</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

794

</td>

<td class="diff-line-num new_line old" data-linenumber="797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC794" class="line" lang="python">        <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">'Value for --cores cannot be negative'</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

795

</td>

<td class="diff-line-num new_line old" data-linenumber="797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC795" class="line" lang="python">    <span class="n" style="color: #333;">cores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">available_cpu_count</span><span class="p">()</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cores</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cores</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="796" 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">

796

</td>

<td class="diff-line-num new_line" data-linenumber="797" 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">

797

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC797" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cores</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="797" 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">

797

</td>

<td class="diff-line-num new_line" data-linenumber="798" 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">

798

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC798" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ParallelPipelineRunner</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">can_output_to</span><span class="p">(</span><span class="n" style="color: #333;">outfiles</span><span class="p">):</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="798" 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">

798

</td>

<td class="diff-line-num new_line" data-linenumber="799" 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">

799

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC799" class="line" lang="python">            <span class="n" style="color: #333;">runner_class</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ParallelPipelineRunner</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="799" 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">

799

</td>

<td class="diff-line-num new_line" data-linenumber="800" 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">

800

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC800" class="line" lang="python">            <span class="n" style="color: #333;">runner_kwargs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">n_workers</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cores</span><span class="p">,</span> <span class="n" style="color: #333;">buffer_size</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">buffer_size</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="800" 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">

800

</td>

<td class="diff-line-num new_line" data-linenumber="801" 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">

801

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC801" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

801

</td>

<td class="diff-line-num new_line old" data-linenumber="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC801" class="line" lang="python">            <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">'Running in parallel is currently not supported for '</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

802

</td>

<td class="diff-line-num new_line old" data-linenumber="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC802" class="line" lang="python">                <span class="s" style="color: #d14;">'the given combination of command-line parameters.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">These '</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

803

</td>

<td class="diff-line-num new_line old" data-linenumber="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC803" class="line" lang="python">                <span class="s" style="color: #d14;">'options are not supported: --info-file, --rest-file, '</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

804

</td>

<td class="diff-line-num new_line old" data-linenumber="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC804" class="line" lang="python">                <span class="s" style="color: #d14;">'--wildcard-file, --format</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

805

</td>

<td class="diff-line-num new_line old" data-linenumber="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC805" class="line" lang="python">                <span class="s" style="color: #d14;">'Also, demultiplexing is not supported.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

806

</td>

<td class="diff-line-num new_line old" data-linenumber="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC806" class="line" lang="python">                <span class="s" style="color: #d14;">'Omit --cores/-j to continue.'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="802" 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="LC802" class="line" lang="python">            <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"Running in parallel is currently not supported "</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="803" 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="LC803" class="line" lang="python">                <span class="s" style="color: #d14;">"when using --format or when demultiplexing.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<pre style="margin: 0;">+<span id="LC804" class="line" lang="python">                <span class="s" style="color: #d14;">"Omit --cores/-j to continue."</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC805" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span>  <span class="c1" style="color: #998; font-style: italic;"># avoid IDE warnings below</span></span>

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<pre style="margin: 0;"> <span id="LC806" 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="LC807" class="line" lang="python">        <span class="n" style="color: #333;">runner_class</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SerialPipelineRunner</span></span>

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<br>

</li>

<li id="8fb347891ec0a40b16ef2bdbe361f823e12aa016">

<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/31e5476ee9dc8503e7d2a812af0957c982687b8b#8fb347891ec0a40b16ef2bdbe361f823e12aa016"><strong>src/cutadapt/adapters.py</strong></a>

<hr>

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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">@@ -73,6 +73,15 @@ class EndStatistics:</td>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_remove</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">adapter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span></span>

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">adjacent_bases</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'A'</span><span class="p">:</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">:</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">'G'</span><span class="p">:</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">'T'</span><span class="p">:</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">''</span><span class="p">:</span> <span class="mi" style="color: #099;">0</span><span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__repr__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<td class="diff-line-num new new_line" data-linenumber="77" 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="LC77" class="line" lang="python">        <span class="n" style="color: #333;">errors</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">k</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">errors</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">()}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"EndStatistics(where={}, max_error_rate={}, errors={}, adjacent_bases={})"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>

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<td class="diff-line-num new old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">where</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">max_error_rate</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python">            <span class="n" style="color: #333;">errors</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">adjacent_bases</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python">        <span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__iadd__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">other</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">other</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__class__</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Cannot compare"</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">@@ -140,6 +149,14 @@ class AdapterStatistics:</td>

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<pre style="margin: 0;"> <span id="LC149" 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="LC150" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">back</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">EndStatistics</span><span class="p">(</span><span class="n" style="color: #333;">adapter2</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__repr__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"AdapterStatistics(name={}, where={}, front={}, back={})"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>

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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">where</span><span class="p">,</span></span>

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<td class="diff-line-num new old_line" data-linenumber="143" 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="LC156" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">front</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">back</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python">        <span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__iadd__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">other</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">where</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">other</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">where</span><span class="p">:</span>  <span class="c1" style="color: #998; font-style: italic;"># TODO self.name != other.name or</span></span>

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">'incompatible objects'</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">@@ -297,7 +314,7 @@ class Adapter:</td>

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<pre style="margin: 0;"> <span id="LC314" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_generate_adapter_name</span><span class="p">()</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">name</span></span>

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<pre style="margin: 0;"> <span id="LC315" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">upper</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'U'</span><span class="p">,</span> <span class="s" style="color: #d14;">'T'</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC316" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC300" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">'Sequence is empty'</span></span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC317" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">"Adapter sequence is empty"</span></span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC318" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">where</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">where</span></span>

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<pre style="margin: 0;"> <span id="LC319" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">remove</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="s" style="color: #d14;">'prefix'</span><span class="p">,</span> <span class="s" style="color: #d14;">'suffix'</span><span class="p">,</span> <span class="s" style="color: #d14;">'auto'</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC320" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">'remove parameter must be "prefix", "suffix", "auto" or None'</span><span class="p">)</span></span>

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<br>

</li>

<li id="6ed465db6839a69141086c2acf1dc01a8b17a981">

<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/31e5476ee9dc8503e7d2a812af0957c982687b8b#6ed465db6839a69141086c2acf1dc01a8b17a981"><strong>src/cutadapt/filters.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">@@ -14,11 +14,6 @@ The read is then assumed to have been "consumed", that is, either written</td>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="s" style="color: #d14;">somewhere or filtered (should be discarded).</span></span>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">abc</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ABC</span><span class="p">,</span> <span class="n" style="color: #333;">abstractmethod</span></span>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">errno</span></span>

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">dnaio</span></span>

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">raise_open_files_limit</span></span>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Constants used when returning from a Filter’s __call__ method to improve</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">@@ -230,29 +225,13 @@ class CasavaFilter(SingleEndFilter):</td>

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<pre style="margin: 0;"> <span id="LC225" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">right</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">':Y:'</span>  <span class="c1" style="color: #998; font-style: italic;"># discard if :Y: found</span></span>

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<pre style="margin: 0;"> <span id="LC226" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC227" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC233" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_open_raise_limit</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">qualities</span><span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC234" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;">-<span id="LC235" class="line" lang="python"><span class="s" style="color: #d14;">    Open a FASTA/FASTQ file for writing. If it fails because the number of open files</span></span>

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<pre style="margin: 0;">-<span id="LC236" class="line" lang="python"><span class="s" style="color: #d14;">    would be exceeded, try to raise the soft limit and re-try.</span></span>

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<pre style="margin: 0;">-<span id="LC237" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<pre style="margin: 0;">-<span id="LC238" class="line" lang="python">    <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC239" class="line" lang="python">        <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dnaio</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;">path</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 class="n" style="color: #333;">qualities</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">qualities</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC240" class="line" lang="python">    <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">OSError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC241" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">errno</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">errno</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">EMFILE</span><span class="p">:</span>  <span class="c1" style="color: #998; font-style: italic;"># Too many open files</span></span>

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<pre style="margin: 0;">-<span id="LC242" class="line" lang="python">            <span class="n" style="color: #333;">raise_open_files_limit</span><span class="p">(</span><span class="mi" style="color: #099;">8</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC243" class="line" lang="python">            <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dnaio</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;">path</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 class="n" style="color: #333;">qualities</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">qualities</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC244" 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="LC245" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span></span>

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<pre style="margin: 0;">-<span id="LC246" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">f</span></span>

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<pre style="margin: 0;">-<span id="LC247" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC248" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC228" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Demultiplexer</span><span class="p">(</span><span class="n" style="color: #333;">SingleEndFilter</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC229" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;"> <span id="LC230" class="line" lang="python"><span class="s" style="color: #d14;">    Demultiplex trimmed reads. Reads are written to different output files</span></span>

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<pre style="margin: 0;"> <span id="LC231" class="line" lang="python"><span class="s" style="color: #d14;">    depending on which adapter matches. Files are created when the first read</span></span>

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<pre style="margin: 0;"> <span id="LC232" class="line" lang="python"><span class="s" style="color: #d14;">    is written to them.</span></span>

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<pre style="margin: 0;">-<span id="LC255" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">path_template</span><span class="p">,</span> <span class="n" style="color: #333;">untrimmed_path</span><span class="p">,</span> <span class="n" style="color: #333;">qualities</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC234" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">path_template</span><span class="p">,</span> <span class="n" style="color: #333;">untrimmed_path</span><span class="p">,</span> <span class="n" style="color: #333;">qualities</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">file_opener</span></span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC235" class="line" lang="python">        <span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;"> <span id="LC236" class="line" lang="python"><span class="s" style="color: #d14;">        path_template must contain the string '{name}', which will be replaced</span></span>

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<pre style="margin: 0;"> <span id="LC237" class="line" lang="python"><span class="s" style="color: #d14;">        with the name of the adapter to form the final output path.</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="267" 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>

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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">@@ -267,6 +246,7 @@ class Demultiplexer(SingleEndFilter):</td>

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<pre style="margin: 0;"> <span id="LC246" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

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<pre style="margin: 0;"> <span id="LC247" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written_bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC248" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qualities</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qualities</span></span>

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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">file_opener</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file_opener</span></span>

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<pre style="margin: 0;"> <span id="LC250" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC251" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;">matches</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC252" class="line" lang="python">        <span class="s" style="color: #d14;">"""</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">@@ -275,14 +255,14 @@ class Demultiplexer(SingleEndFilter):</td>

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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;">matches</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC256" class="line" lang="python">            <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matches</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">adapter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>

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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;">name</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">writers</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC278" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">writers</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_open_raise_limit</span><span class="p">(</span></span>

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<pre style="margin: 0;">+<span id="LC258" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">writers</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">file_opener</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">dnaio</span>_open_raise_limit</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC259" class="line" lang="python">                    <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">template</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'{name}'</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">),</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qualities</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC260" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

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<pre style="margin: 0;"> <span id="LC261" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written_bp</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC262" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">writers</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC263" 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="LC264" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">untrimmed_writer</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">untrimmed_path</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC285" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">untrimmed_writer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_open_raise_limit</span><span class="p">(</span></span>

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<pre style="margin: 0;">+<span id="LC265" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">untrimmed_writer</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">file_opener</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">dnaio</span>_open_raise_limit</span><span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC266" class="line" lang="python">                    <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">untrimmed_path</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qualities</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC267" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">untrimmed_writer</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC268" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</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">@@ -303,16 +283,16 @@ class PairedDemultiplexer(PairedEndFilter):</td>

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<pre style="margin: 0;"> <span id="LC283" class="line" lang="python"><span class="s" style="color: #d14;">    depending on which adapter (in read 1) matches.</span></span>

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<pre style="margin: 0;"> <span id="LC284" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<pre style="margin: 0;"> <span id="LC285" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">path_template</span><span class="p">,</span> <span class="n" style="color: #333;">path_paired_template</span><span class="p">,</span> <span class="n" style="color: #333;">untrimmed_path</span><span class="p">,</span> <span class="n" style="color: #333;">untrimmed_paired_path</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC306" class="line" lang="python">            <span class="n" style="color: #333;">qualities</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC286" class="line" lang="python">            <span class="n" style="color: #333;">qualities</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">file_opener</span></span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC287" class="line" lang="python">        <span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;"> <span id="LC288" class="line" lang="python"><span class="s" style="color: #d14;">        The path templates must contain the string '{name}', which will be replaced</span></span>

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<pre style="margin: 0;"> <span id="LC289" class="line" lang="python"><span class="s" style="color: #d14;">        with the name of the adapter to form the final output path.</span></span>

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<pre style="margin: 0;"> <span id="LC290" class="line" lang="python"><span class="s" style="color: #d14;">        Read pairs without an adapter match are written to the files named by</span></span>

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<pre style="margin: 0;"> <span id="LC291" class="line" lang="python"><span class="s" style="color: #d14;">        untrimmed_path.</span></span>

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<pre style="margin: 0;"> <span id="LC292" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC313" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_demultiplexer1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Demultiplexer</span><span class="p">(</span><span class="n" style="color: #333;">path_template</span><span class="p">,</span> <span class="n" style="color: #333;">untrimmed_path</span><span class="p">,</span> <span class="n" style="color: #333;">qualities</span><span class="p">)</span></span>

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<td class="diff-line-num new old_line" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="293" 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="LC293" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_demultiplexer1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Demultiplexer</span><span class="p">(</span><span class="n" style="color: #333;">path_template</span><span class="p">,</span> <span class="n" style="color: #333;">untrimmed_path</span><span class="p">,</span> <span class="n" style="color: #333;">qualities</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">file_opener</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="294" 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="LC294" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_demultiplexer2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Demultiplexer</span><span class="p">(</span><span class="n" style="color: #333;">path_paired_template</span><span class="p">,</span> <span class="n" style="color: #333;">untrimmed_paired_path</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC315" class="line" lang="python">            <span class="n" style="color: #333;">qualities</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="316" 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="LC295" class="line" lang="python">            <span class="n" style="color: #333;">qualities</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">file_opener</span></span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC296" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="317" 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="LC297" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</span></span>

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<td class="diff-line-num new_line" data-linenumber="298" 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="LC298" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">written</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="337" 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="317" 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">@@ -337,7 +317,7 @@ class CombinatorialDemultiplexer(PairedEndFilter):</td>

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<td class="diff-line-num old_line" data-linenumber="337" 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="LC317" class="line" lang="python"><span class="s" style="color: #d14;">    Demultiplex reads depending on which adapter matches, taking into account both matches</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC318" class="line" lang="python"><span class="s" style="color: #d14;">    on R1 and R2.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC319" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC340" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">path_template</span><span class="p">,</span> <span class="n" style="color: #333;">path_paired_template</span><span class="p">,</span> <span class="n" style="color: #333;">untrimmed_name</span><span class="p">,</span> <span class="n" style="color: #333;">qualities</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="341" 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="LC320" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">path_template</span><span class="p">,</span> <span class="n" style="color: #333;">path_paired_template</span><span class="p">,</span> <span class="n" style="color: #333;">untrimmed_name</span><span class="p">,</span> <span class="n" style="color: #333;">qualities</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">file_opener</span></span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="321" 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="LC321" class="line" lang="python">        <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="322" 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="LC322" class="line" lang="python"><span class="s" style="color: #d14;">        path_template must contain the string '{name1}' and '{name2}', which will be replaced</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="323" 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="LC323" class="line" lang="python"><span class="s" style="color: #d14;">        with the name of the adapters found on R1 and R2, respectively to form the final output</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="355" 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="335" 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">@@ -355,6 +335,7 @@ class CombinatorialDemultiplexer(PairedEndFilter):</td>

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<pre style="margin: 0;"> <span id="LC335" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

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<pre style="margin: 0;"> <span id="LC336" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written_bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC337" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qualities</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qualities</span></span>

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<td class="diff-line-num new new_line" data-linenumber="338" 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="LC338" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">file_opener</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file_opener</span></span>

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<pre style="margin: 0;"> <span id="LC339" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC340" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>

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<pre style="margin: 0;"> <span id="LC341" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_make_path</span><span class="p">(</span><span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">name1</span><span class="p">,</span> <span class="n" style="color: #333;">name2</span><span class="p">):</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="379" 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>

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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">@@ -379,8 +360,8 @@ class CombinatorialDemultiplexer(PairedEndFilter):</td>

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<pre style="margin: 0;"> <span id="LC360" class="line" lang="python">            <span class="n" style="color: #333;">path1</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_make_path</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">name1</span><span class="p">,</span> <span class="n" style="color: #333;">name2</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC361" class="line" lang="python">            <span class="n" style="color: #333;">path2</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_make_path</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">paired_template</span><span class="p">,</span> <span class="n" style="color: #333;">name1</span><span class="p">,</span> <span class="n" style="color: #333;">name2</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC362" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">writers</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>

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<pre style="margin: 0;">-<span id="LC382" class="line" lang="python">                <span class="n" style="color: #333;">_open_raise_limit</span><span class="p">(</span><span class="n" style="color: #333;">path1</span><span class="p">,</span> <span class="n" style="color: #333;">qualities</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qualities</span><span class="p">),</span></span>

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<pre style="margin: 0;">-<span id="LC383" class="line" lang="python">                <span class="n" style="color: #333;">_open_raise_limit</span><span class="p">(</span><span class="n" style="color: #333;">path2</span><span class="p">,</span> <span class="n" style="color: #333;">qualities</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qualities</span><span class="p">),</span></span>

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<pre style="margin: 0;">+<span id="LC363" class="line" lang="python">                <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">file_opener</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">dnaio</span>_open_raise_limit</span><span class="p">(</span><span class="n" style="color: #333;">path1</span><span class="p">,</span> <span class="n" style="color: #333;">qualities</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qualities</span><span class="p">),</span></span>

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<td class="diff-line-num new old_line" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="364" 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="LC364" class="line" lang="python">                <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">file_opener</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">dnaio</span>_open_raise_limit</span><span class="p">(</span><span class="n" style="color: #333;">path2</span><span class="p">,</span> <span class="n" style="color: #333;">qualities</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qualities</span><span class="p">),</span></span>

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<pre style="margin: 0;"> <span id="LC365" class="line" lang="python">            <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;">writer1</span><span class="p">,</span> <span class="n" style="color: #333;">writer2</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">writers</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC367" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<br>

</li>

<li id="12b6e14dcfabba52d86396a9e2818f75b0c0c8d5">

<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/31e5476ee9dc8503e7d2a812af0957c982687b8b#12b6e14dcfabba52d86396a9e2818f75b0c0c8d5"><strong>src/cutadapt/parser.py</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,6 +3,7 @@ Parse adapter specifications</td>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">re</span></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">logging</span></span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">xopen</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">xopen</span></span>

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6

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">dnaio.readers</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">FastaReader</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.adapters</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Where</span><span class="p">,</span> <span class="n" style="color: #333;">WHERE_TO_REMOVE_MAP</span><span class="p">,</span> <span class="n" style="color: #333;">Adapter</span><span class="p">,</span> <span class="n" style="color: #333;">BackOrFrontAdapter</span><span class="p">,</span> <span class="n" style="color: #333;">LinkedAdapter</span></span>

</pre>

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8

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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">

9

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

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="397" 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="398" 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">@@ -397,7 +398,8 @@ class AdapterParser:</td>

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<pre style="margin: 0;"> <span id="LC398" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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<td class="diff-line-num new_line" data-linenumber="399" 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="LC399" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'file:'</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="400" 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="LC400" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># read adapter sequences from a file</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC400" class="line" lang="python">            <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">FastaReader</span><span class="p">(</span><span class="n" style="color: #333;">spec</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">:])</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fasta</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC401" class="line" lang="python">            <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">xopen</span><span class="p">(</span><span class="n" style="color: #333;">spec</span><span class="p">[</span><span class="mi" style="color: #099;">5</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;">"rb"</span><span class="p">,</span> <span class="n" style="color: #333;">threads</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="402" 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="LC402" class="line" lang="python">                <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FastaReader</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC403" class="line" lang="python">                <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fasta</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC404" class="line" lang="python">                    <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">record</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC405" class="line" lang="python">                    <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">name</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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<br>

</li>

<li id="1b86cdea057b59b4d05ba7fde4aea9df4e8fe9e8">

<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/31e5476ee9dc8503e7d2a812af0957c982687b8b#1b86cdea057b59b4d05ba7fde4aea9df4e8fe9e8"><strong>src/cutadapt/pipeline.py</strong></a>

<hr>

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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">@@ -6,13 +6,14 @@ import logging</td>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">functools</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="7" 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="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">abc</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ABC</span><span class="p">,</span> <span class="n" style="color: #333;">abstractmethod</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">multiprocessing</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Process</span><span class="p">,</span> <span class="n" style="color: #333;">Pipe</span><span class="p">,</span> <span class="n" style="color: #333;">Queue</span></span>

</pre>

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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="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pathlib</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Path</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="10" 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="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">multiprocessing.connection</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="11" 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="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">traceback</span></span>

</pre>

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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>

</pre>

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<td class="diff-line-num old_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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<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="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">xopen</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">xopen</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="14" 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="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">dnaio</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="15" 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="LC15" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Progress</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="16" 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="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Progress</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">FileOpener</span></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.modifiers</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">PairedModifier</span></span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="18" 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="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.report</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Statistics</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="19" 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="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.filters</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span><span class="n" style="color: #333;">Redirector</span><span class="p">,</span> <span class="n" style="color: #333;">PairedRedirector</span><span class="p">,</span> <span class="n" style="color: #333;">NoFilter</span><span class="p">,</span> <span class="n" style="color: #333;">PairedNoFilter</span><span class="p">,</span> <span class="n" style="color: #333;">InfoFileWriter</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="93" 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="94" 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">@@ -93,13 +94,14 @@ class Pipeline(ABC):</td>

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<td class="diff-line-num old_line" data-linenumber="94" 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="LC95" class="line" lang="python">    <span class="n" style="color: #333;">n_adapters</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 new_line" data-linenumber="96" 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="LC96" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">file_opener</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">FileOpener</span></span><span class="p">):</span></span>

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<td class="diff-line-num old_line" data-linenumber="97" 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="LC98" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_close_files</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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<td class="diff-line-num new_line" data-linenumber="99" 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="LC99" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

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<td class="diff-line-num old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="100" 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="LC100" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_filters</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

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<td class="diff-line-num old_line" data-linenumber="100" 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="LC101" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_modifiers</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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<td class="diff-line-num old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="102" 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="LC102" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_outfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

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<td class="diff-line-num old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="103" 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="LC103" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_demultiplexer</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

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<td class="diff-line-num new old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="104" 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="LC104" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_textiowrappers</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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<td class="diff-line-num new_line" data-linenumber="105" 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="LC105" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="106" 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="LC106" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Filter settings</span></span>

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<td class="diff-line-num old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="107" 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="LC107" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_minimum_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="108" 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="110" 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">@@ -108,6 +110,7 @@ class Pipeline(ABC):</td>

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<td class="diff-line-num old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="110" 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="LC110" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">discard_casava</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

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<td class="diff-line-num old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="111" 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="LC111" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">discard_trimmed</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">discard_untrimmed</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">file_opener</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file_opener</span></span>

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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">connect_io</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">infiles</span><span class="p">:</span> <span class="n" style="color: #333;">InputFiles</span><span class="p">,</span> <span class="n" style="color: #333;">outfiles</span><span class="p">:</span> <span class="n" style="color: #333;">OutputFiles</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dnaio</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;">infiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">file1</span><span class="p">,</span> <span class="n" style="color: #333;">file2</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">infiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">file2</span><span class="p">,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="119" 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>

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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">@@ -119,6 +122,10 @@ class Pipeline(ABC):</td>

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># for all outputs</span></span>

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">force_fasta</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python">            <span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">'fileformat'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'fasta'</span></span>

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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># file and file2 must already be file-like objects because we don’t want to</span></span>

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># take care of threads and compression levels here.</span></span>

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">file</span><span class="p">,</span> <span class="n" style="color: #333;">file2</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python">            <span class="k" style="font-weight: 600;">assert</span> <span class="ow" style="font-weight: 600;">not</span> <span class="p">(</span><span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">bytes</span><span class="p">,</span> <span class="n" style="color: #333;">Path</span><span class="p">)))</span></span>

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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">dnaio</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="nb" style="color: #0086b3;">file</span><span class="p">,</span> <span class="n" style="color: #333;">file2</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">file2</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 class="n" style="color: #333;">qualities</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">uses_qualities</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python">            <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -133,7 +140,9 @@ class Pipeline(ABC):</td>

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<td class="diff-line-num new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

140

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python">            <span class="p">(</span><span class="n" style="color: #333;">WildcardFileWriter</span><span class="p">,</span> <span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">wildcard</span><span class="p">),</span></span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="141" 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">

141

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python">        <span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="135" 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">

135

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<td class="diff-line-num new_line" data-linenumber="142" 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="LC142" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">outfile</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

136

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<td class="diff-line-num new_line old" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC136" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_filters</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;">filter_wrapper</span><span class="p">(</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">filter_class</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">),</span> <span class="bp" style="color: #999;">None</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="143" 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="LC143" class="line" lang="python">                <span class="n" style="color: #333;">textiowrapper</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">io</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">TextIOWrapper</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="144" 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="LC144" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_textiowrappers</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;">textiowrapper</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="145" 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="LC145" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_filters</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;">filter_wrapper</span><span class="p">(</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">filter_class</span><span class="p">(</span><span class="n" style="color: #333;">textiowrapper</span><span class="p">),</span> <span class="bp" style="color: #999;">None</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="146" 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="LC146" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="147" 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="LC147" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># minimum length and maximum length</span></span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="148" 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="LC148" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">lengths</span><span class="p">,</span> <span class="n" style="color: #333;">file1</span><span class="p">,</span> <span class="n" style="color: #333;">file2</span><span class="p">,</span> <span class="n" style="color: #333;">filter_class</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="184" 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="193" 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">@@ -184,7 +193,16 @@ class Pipeline(ABC):</td>

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<td class="diff-line-num old_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="193" 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="LC193" class="line" lang="python">                    <span class="n" style="color: #333;">untrimmed_filter_wrapper</span><span class="p">(</span><span class="n" style="color: #333;">untrimmed_writer</span><span class="p">,</span> <span class="n" style="color: #333;">DiscardUntrimmedFilter</span><span class="p">(),</span> <span class="n" style="color: #333;">DiscardUntrimmedFilter</span><span class="p">()))</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="194" 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="LC194" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_filters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_final_filter</span><span class="p">(</span><span class="n" style="color: #333;">outfiles</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="195" 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="LC195" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="196" 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="LC196" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">flush</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="197" 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="LC197" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_textiowrappers</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="198" 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="LC198" class="line" lang="python">            <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">flush</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="199" 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="LC199" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_outfiles</span><span class="p">:</span></span>

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<td class="diff-line-num new new_line" data-linenumber="200" 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="LC200" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

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<td class="diff-line-num new old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="201" 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="LC201" class="line" lang="python">                <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">flush</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="202" 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="LC202" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="203" 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="LC203" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">close</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<td class="diff-line-num new old_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="204" 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="LC204" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_textiowrappers</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="205" 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="LC205" class="line" lang="python">            <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span>  <span class="c1" style="color: #998; font-style: italic;"># This also closes the underlying files; a second close occurs below</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="206" 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="LC206" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_outfiles</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="207" 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="LC207" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># TODO do not use hasattr</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="208" 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="LC208" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</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 class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdout</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="s" style="color: #d14;">'close'</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="223" 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="241" 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">@@ -223,8 +241,8 @@ class SingleEndPipeline(Pipeline):</td>

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<pre style="margin: 0;"> <span id="LC241" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<pre style="margin: 0;"> <span id="LC242" 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>

</pre>

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<pre style="margin: 0;"> <span id="LC243" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC226" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC227" class="line" lang="python">        <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="244" 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="LC244" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">file_opener</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">FileOpener</span></span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="245" 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="LC245" class="line" lang="python">        <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">file_opener</span></span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC246" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_modifiers</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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<pre style="margin: 0;"> <span id="LC247" class="line" lang="python"></span>

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<td class="diff-line-num new_line" data-linenumber="248" 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="LC248" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">modifier</span><span class="p">):</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="261" 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="279" 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">@@ -261,7 +279,8 @@ class SingleEndPipeline(Pipeline):</td>

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<pre style="margin: 0;"> <span id="LC279" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">NoFilter</span><span class="p">(</span><span class="n" style="color: #333;">writer</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC280" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC281" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_create_demultiplexer</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">outfiles</span><span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC264" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Demultiplexer</span><span class="p">(</span><span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">untrimmed</span><span class="p">,</span> <span class="n" style="color: #333;">qualities</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">uses_qualities</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC282" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Demultiplexer</span><span class="p">(</span><span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">untrimmed</span><span class="p">,</span> <span class="n" style="color: #333;">qualities</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">uses_qualities</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC283" class="line" lang="python">            <span class="n" style="color: #333;">file_opener</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">file_opener</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC284" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC285" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</span></span>

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<pre style="margin: 0;"> <span id="LC286" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">minimum_length</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="288" 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="307" 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">@@ -288,8 +307,8 @@ class PairedEndPipeline(Pipeline):</td>

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<pre style="margin: 0;"> <span id="LC307" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<pre style="margin: 0;"> <span id="LC308" 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;">True</span></span>

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<pre style="margin: 0;"> <span id="LC309" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC291" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">pair_filter_mode</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC292" class="line" lang="python">        <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">()</span></span>

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<pre style="margin: 0;">+<span id="LC310" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">pair_filter_mode</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">file_opener</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">FileOpener</span></span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC311" class="line" lang="python">        <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">file_opener</span></span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC312" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_pair_filter_mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pair_filter_mode</span></span>

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<pre style="margin: 0;"> <span id="LC313" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_reader</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="LC314" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Whether to ignore pair_filter mode for discard-untrimmed filter</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="359" 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>

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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">@@ -359,10 +378,11 @@ class PairedEndPipeline(Pipeline):</td>

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<pre style="margin: 0;"> <span id="LC378" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_create_demultiplexer</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">outfiles</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC379" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'{name1}'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">out</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">'{name2}'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">out</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC380" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">CombinatorialDemultiplexer</span><span class="p">(</span><span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">out2</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC362" class="line" lang="python">                <span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">untrimmed</span><span class="p">,</span> <span class="n" style="color: #333;">qualities</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">uses_qualities</span><span class="p">)</span></span>

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<td class="diff-line-num new new_line" data-linenumber="381" 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="LC381" class="line" lang="python">                <span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">untrimmed</span><span class="p">,</span> <span class="n" style="color: #333;">qualities</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">uses_qualities</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">file_opener</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">file_opener</span></span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC382" 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 new_line" data-linenumber="383" 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="LC383" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">PairedDemultiplexer</span><span class="p">(</span><span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">out2</span><span class="p">,</span></span>

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<td class="diff-line-num new_line old" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC365" class="line" lang="python">            <span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">untrimmed</span><span class="p">,</span> <span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">untrimmed2</span><span class="p">,</span> <span class="n" style="color: #333;">qualities</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">uses_qualities</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC384" class="line" lang="python">                <span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">untrimmed</span><span class="p">,</span> <span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">untrimmed2</span><span class="p">,</span> <span class="n" style="color: #333;">qualities</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">uses_qualities</span><span class="p">,</span></span>

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<td class="diff-line-num new new_line" data-linenumber="385" 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="LC385" class="line" lang="python">                <span class="n" style="color: #333;">file_opener</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">file_opener</span><span class="p">)</span></span>

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<td class="diff-line-num new_line" data-linenumber="386" 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="LC386" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="387" 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="LC387" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</span></span>

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<td class="diff-line-num new_line" data-linenumber="388" 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="LC388" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">minimum_length</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="472" 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="492" 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">@@ -472,6 +492,7 @@ class WorkerProcess(Process):</td>

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<td class="diff-line-num old_line" data-linenumber="472" 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="LC492" class="line" lang="python">                <span class="n" style="color: #333;">outfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_make_output_files</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC493" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_pipeline</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">connect_io</span><span class="p">(</span><span class="n" style="color: #333;">infiles</span><span class="p">,</span> <span class="n" style="color: #333;">outfiles</span><span class="p">)</span></span>

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<td class="diff-line-num new_line" data-linenumber="494" 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="LC494" class="line" lang="python">                <span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">bp1</span><span class="p">,</span> <span class="n" style="color: #333;">bp2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_pipeline</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">process_reads</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="475" 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="LC495" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_pipeline</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">flush</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="496" 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="LC496" class="line" lang="python">                <span class="n" style="color: #333;">cur_stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Statistics</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">collect</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">bp1</span><span class="p">,</span> <span class="n" style="color: #333;">bp2</span><span class="p">,</span> <span class="p">[],</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_pipeline</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_filters</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="497" 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="LC497" class="line" lang="python">                <span class="n" style="color: #333;">stats</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">cur_stats</span></span>

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<td class="diff-line-num new_line" data-linenumber="498" 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="LC498" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_send_outfiles</span><span class="p">(</span><span class="n" style="color: #333;">outfiles</span><span class="p">,</span> <span class="n" style="color: #333;">chunk_index</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="502" 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="523" 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">@@ -502,7 +523,6 @@ class WorkerProcess(Process):</td>

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<td class="diff-line-num old_line" data-linenumber="502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="523" 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="LC523" class="line" lang="python"><span class="s" style="color: #d14;">        that has BytesIO instances for each non-None output file</span></span>

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<td class="diff-line-num new_line" data-linenumber="524" 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="LC524" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="525" 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="LC525" class="line" lang="python">        <span class="n" style="color: #333;">output_files</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">copy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copy</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_orig_outfiles</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC505" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># TODO info, rest, wildcard need to be StringIO()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="526" 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="LC526" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">attr</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC527" class="line" lang="python">            <span class="s" style="color: #d14;">"out"</span><span class="p">,</span> <span class="s" style="color: #d14;">"out2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"untrimmed"</span><span class="p">,</span> <span class="s" style="color: #d14;">"untrimmed2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"too_short"</span><span class="p">,</span> <span class="s" style="color: #d14;">"too_short2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"too_long"</span><span class="p">,</span></span>

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<td class="diff-line-num old_line" data-linenumber="508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="528" 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="LC528" class="line" lang="python">            <span class="s" style="color: #d14;">"too_long2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"info"</span><span class="p">,</span> <span class="s" style="color: #d14;">"rest"</span><span class="p">,</span> <span class="s" style="color: #d14;">"wildcard"</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="632" 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="652" 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">@@ -632,13 +652,7 @@ class ParallelPipelineRunner(PipelineRunner):</td>

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<pre style="margin: 0;"> <span id="LC652" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC653" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>

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<pre style="margin: 0;"> <span id="LC654" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">can_output_to</span><span class="p">(</span><span class="n" style="color: #333;">outfiles</span><span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC635" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span></span>

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<td class="diff-line-num old old_line" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC636" class="line" lang="python">            <span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">out</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span></span>

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<pre style="margin: 0;">-<span id="LC637" class="line" lang="python">            <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rest</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span></span>

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<pre style="margin: 0;">-<span id="LC638" class="line" lang="python">            <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span></span>

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<td class="diff-line-num new_line old" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC639" class="line" lang="python">            <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">wildcard</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span></span>

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<td class="diff-line-num old old_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

640

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<td class="diff-line-num new_line old" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC640" class="line" lang="python">            <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">demultiplex</span></span>

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<td class="diff-line-num old old_line" data-linenumber="641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC641" class="line" lang="python">        <span class="p">)</span></span>

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<td class="diff-line-num new old_line" data-linenumber="642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="655" 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="LC655" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">out</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">demultiplex</span></span>

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<td class="diff-line-num old_line" data-linenumber="642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="656" 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="LC656" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="657" 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="LC657" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_assign_output</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">outfiles</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="658" 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="LC658" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">can_output_to</span><span class="p">(</span><span class="n" style="color: #333;">outfiles</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="682" 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="696" 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">@@ -682,8 +696,7 @@ class ParallelPipelineRunner(PipelineRunner):</td>

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<pre style="margin: 0;"> <span id="LC696" class="line" lang="python">                        <span class="c1" style="color: #998; font-style: italic;"># this happens only when there is an exception sending</span></span>

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<pre style="margin: 0;"> <span id="LC697" class="line" lang="python">                        <span class="c1" style="color: #998; font-style: italic;"># the statistics)</span></span>

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<pre style="margin: 0;"> <span id="LC698" class="line" lang="python">                        <span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="n" style="color: #333;">tb_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">connection</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">recv</span><span class="p">()</span></span>

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<pre style="margin: 0;">-<span id="LC685" class="line" lang="python">                        <span class="c1" style="color: #998; font-style: italic;"># TODO traceback should only be printed in development</span></span>

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<pre style="margin: 0;">-<span id="LC686" 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;">debug</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</span><span class="p">,</span> <span class="n" style="color: #333;">tb_str</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="687" 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="LC699" 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;">error</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</span><span class="p">,</span> <span class="n" style="color: #333;">tb_str</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC700" class="line" lang="python">                        <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">e</span></span>

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<pre style="margin: 0;"> <span id="LC701" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">stats</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC702" class="line" lang="python">                        <span class="n" style="color: #333;">stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_stats</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="695" 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="708" 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">@@ -695,17 +708,16 @@ class ParallelPipelineRunner(PipelineRunner):</td>

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<td class="diff-line-num old_line" data-linenumber="695" 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="LC708" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># An exception has occurred in the worker</span></span>

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<td class="diff-line-num new_line" data-linenumber="709" 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="LC709" class="line" lang="python">                    <span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="n" style="color: #333;">tb_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">connection</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">recv</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="710" 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="LC710" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC698" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># TODO traceback should only be printed in development</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="711" 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="LC711" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># We should use the worker's actual traceback object</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="712" 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="LC712" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># here, but traceback objects are not picklable.</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC701" 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;"><span class="idiff left right">debug</span></span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</span><span class="p">,</span> <span class="n" style="color: #333;">tb_str</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC713" 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;"><span class="idiff left right">error</span></span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</span><span class="p">,</span> <span class="n" style="color: #333;">tb_str</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="702" 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">

702

</td>

<td class="diff-line-num new_line" data-linenumber="714" 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">

714

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC714" class="line" lang="python">                    <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">e</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="703" 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">

703

</td>

<td class="diff-line-num new_line" data-linenumber="715" 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">

715

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC715" class="line" lang="python"></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="704" 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">

704

</td>

<td class="diff-line-num new_line" data-linenumber="716" 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">

716

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC716" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># No. of reads processed in this chunk</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="705" 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">

705

</td>

<td class="diff-line-num new_line" data-linenumber="717" 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">

717

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC717" class="line" lang="python">                <span class="n" style="color: #333;">chunk_n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">connection</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">recv</span><span class="p">()</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="706" 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">

706

</td>

<td class="diff-line-num new_line" data-linenumber="718" 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">

718

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC718" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">chunk_n</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="707" 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">

707

</td>

<td class="diff-line-num new_line" data-linenumber="719" 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">

719

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC719" class="line" lang="python">                    <span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="n" style="color: #333;">tb_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">connection</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">recv</span><span class="p">()</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

708

</td>

<td class="diff-line-num new_line old" data-linenumber="720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC708" 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;"><span class="idiff left right">debug</span></span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</span><span class="p">,</span> <span class="n" style="color: #333;">tb_str</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="709" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="720" 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">

720

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC720" 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;"><span class="idiff left right">error</span></span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</span><span class="p">,</span> <span class="n" style="color: #333;">tb_str</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="709" 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">

709

</td>

<td class="diff-line-num new_line" data-linenumber="721" 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">

721

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC721" class="line" lang="python">                    <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">e</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="710" 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">

710

</td>

<td class="diff-line-num new_line" data-linenumber="722" 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">

722

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC722" class="line" lang="python">                <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">chunk_n</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="711" 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">

711

</td>

<td class="diff-line-num new_line" data-linenumber="723" 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">

723

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC723" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_progress</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">)</span></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="af95dfcb30a51908f338d0fd6a196b9e4c108046">

<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/31e5476ee9dc8503e7d2a812af0957c982687b8b#af95dfcb30a51908f338d0fd6a196b9e4c108046"><strong>src/cutadapt/utils.py</strong></a>

<hr>

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<td class="diff-line-num old_line" data-linenumber="1" 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">

1

</td>

<td class="diff-line-num new_line" data-linenumber="1" 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">

1

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">re</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2" 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">

2

</td>

<td class="diff-line-num new_line" data-linenumber="2" 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">

2

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

</td>

<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">time</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_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">

</td>

<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">

4

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">errno</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old_line" data-linenumber="4" 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">

4

</td>

<td class="diff-line-num new_line" data-linenumber="5" 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">

5

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">multiprocessing</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="5" 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">

5

</td>

<td class="diff-line-num new_line" data-linenumber="6" 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">

6

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

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

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="6" 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">

</td>

<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">

7

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">xopen</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">xopen</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">dnaio</span></span>

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

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

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -142,3 +144,31 @@ def reverse_complemented_sequence(sequence: dnaio.Sequence):</td>

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<pre style="margin: 0;"> <span id="LC144" 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="LC145" class="line" lang="python">        <span class="n" style="color: #333;">qualities</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qualities</span><span class="p">[::</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

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<td class="diff-line-num new_line" data-linenumber="146" 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="LC146" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">dnaio</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Sequence</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">reverse_complement</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span><span class="p">),</span> <span class="n" style="color: #333;">qualities</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">FileOpener</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">compression_level</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">int</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="n" style="color: #333;">threads</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">int</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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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">compression_level</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">compression_level</span></span>

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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">threads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">threads</span></span>

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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"></span>

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<td class="diff-line-num new new_line" data-linenumber="154" 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="LC154" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">xopen</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="p">):</span></span>

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<td class="diff-line-num new new_line" data-linenumber="155" 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="LC155" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">xopen</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="p">,</span> <span class="n" style="color: #333;">compresslevel</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">compression_level</span><span class="p">,</span> <span class="n" style="color: #333;">threads</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">threads</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">dnaio_open</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="158" 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="LC158" class="line" lang="python">        <span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">"opener"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">xopen</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="159" 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="LC159" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">dnaio</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="160" 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="LC160" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="161" 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="LC161" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">dnaio_open_raise_limit</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">qualities</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="162" 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="LC162" class="line" lang="python">        <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="163" 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="LC163" class="line" lang="python"><span class="s" style="color: #d14;">        Open a FASTA/FASTQ file for writing. If it fails because the number of open files</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="164" 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="LC164" class="line" lang="python"><span class="s" style="color: #d14;">        would be exceeded, try to raise the soft limit and re-try.</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="165" 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="LC165" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="166" 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="LC166" class="line" lang="python">        <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="167" 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="LC167" class="line" lang="python">            <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dnaio_open</span><span class="p">(</span><span class="n" style="color: #333;">path</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 class="n" style="color: #333;">qualities</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">qualities</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="168" 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="LC168" class="line" lang="python">        <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">OSError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="169" 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="LC169" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">errno</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">errno</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">EMFILE</span><span class="p">:</span>  <span class="c1" style="color: #998; font-style: italic;"># Too many open files</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="170" 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="LC170" class="line" lang="python">                <span class="n" style="color: #333;">raise_open_files_limit</span><span class="p">(</span><span class="mi" style="color: #099;">8</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="171" 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="LC171" class="line" lang="python">                <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dnaio_open</span><span class="p">(</span><span class="n" style="color: #333;">path</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 class="n" style="color: #333;">qualities</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">qualities</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="172" 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="LC172" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="173" 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="LC173" class="line" lang="python">                <span class="k" style="font-weight: 600;">raise</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">f</span></span></pre>

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<br>

</li>

<li id="83ff0d8e113228f36b352922cbbb938d0aa9384b">

<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/31e5476ee9dc8503e7d2a812af0957c982687b8b#83ff0d8e113228f36b352922cbbb938d0aa9384b"><strong>tests/test_commandline.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="46" 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="46" 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">@@ -46,10 +46,10 @@ def test_lowercase(run):</td>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python">    <span class="n" style="color: #333;">run</span><span class="p">(</span><span class="s" style="color: #d14;">'-a ttagacatatctccgtcg'</span><span class="p">,</span> <span class="s" style="color: #d14;">'lowercase.fastq'</span><span class="p">,</span> <span class="s" style="color: #d14;">'small.fastq'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"></span>

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<td class="diff-line-num old old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_rest</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">,</span> <span class="n" style="color: #333;">tmpdir</span><span class="p">):</span></span>

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<td class="diff-line-num new old_line" data-linenumber="50" 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="LC49" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_rest</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">,</span> <span class="n" style="color: #333;">tmpdir</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">cores</span></span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python">    <span class="s" style="color: #d14;">"""-r/--rest-file"""</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="51" 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="LC51" class="line" lang="python">    <span class="n" style="color: #333;">rest</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"rest.tmp"</span><span class="p">))</span></span>

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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python">    <span class="n" style="color: #333;">run</span><span class="p">([</span><span class="s" style="color: #d14;">'-b'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ADAPTER'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-N'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-r'</span><span class="p">,</span> <span class="n" style="color: #333;">rest</span><span class="p">],</span> <span class="s" style="color: #d14;">"rest.fa"</span><span class="p">,</span> <span class="s" style="color: #d14;">"rest.fa"</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python">    <span class="n" style="color: #333;">run</span><span class="p">([</span><span class="s" style="color: #d14;">'-<span class="idiff left">-cores'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">cores</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'-</span>b'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ADAPTER'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-N'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-r'</span><span class="p">,</span> <span class="n" style="color: #333;">rest</span><span class="p">],</span> <span class="s" style="color: #d14;">"rest.fa"</span><span class="p">,</span> <span class="s" style="color: #d14;">"rest.fa"</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python">    <span class="n" style="color: #333;">assert_files_equal</span><span class="p">(</span><span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">'rest.txt'</span><span class="p">),</span> <span class="n" style="color: #333;">rest</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="228" 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="228" 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">@@ -228,11 +228,14 @@ def test_read_wildcard(run):</td>

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<pre style="margin: 0;"> <span id="LC228" class="line" lang="python">    <span class="p">(</span><span class="s" style="color: #d14;">"-a"</span><span class="p">,</span> <span class="s" style="color: #d14;">"wildcard_adapter.fa"</span><span class="p">),</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC229" class="line" lang="python">    <span class="p">(</span><span class="s" style="color: #d14;">"-b"</span><span class="p">,</span> <span class="s" style="color: #d14;">"wildcard_adapter_anywhere.fa"</span><span class="p">),</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC230" class="line" lang="python"><span class="p">])</span></span>

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<pre style="margin: 0;">-<span id="LC231" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_adapter_wildcard</span><span class="p">(</span><span class="n" style="color: #333;">adapter_type</span><span class="p">,</span> <span class="n" style="color: #333;">expected</span><span class="p">,</span> <span class="n" style="color: #333;">run</span><span class="p">,</span> <span class="n" style="color: #333;">tmpdir</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC231" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_adapter_wildcard</span><span class="p">(</span><span class="n" style="color: #333;">adapter_type</span><span class="p">,</span> <span class="n" style="color: #333;">expected</span><span class="p">,</span> <span class="n" style="color: #333;">run</span><span class="p">,</span> <span class="n" style="color: #333;">tmpdir</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">cores</span></span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC232" class="line" lang="python">    <span class="s" style="color: #d14;">"""wildcards in adapter"""</span></span>

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="python">    <span class="n" style="color: #333;">wildcard_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"wildcards.txt"</span><span class="p">))</span></span>

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<td class="diff-line-num old old_line" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC234" class="line" lang="python">    <span class="n" style="color: #333;">run</span><span class="p">(</span><span class="s" style="color: #d14;">"--wildcard-file {} {} ACGTNNNACGT"</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;">wildcard_path</span><span class="p">,</span> <span class="n" style="color: #333;">adapter_type</span><span class="p">),</span></span>

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<pre style="margin: 0;">-<span id="LC235" class="line" lang="python">        <span class="n" style="color: #333;">expected</span><span class="p">,</span> <span class="s" style="color: #d14;">"wildcard_adapter.fa"</span><span class="p">)</span></span>

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<td class="diff-line-num new old_line" data-linenumber="236" 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="LC234" class="line" lang="python">    <span class="n" style="color: #333;">run</span><span class="p">([</span></span>

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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python">            <span class="s" style="color: #d14;">"--cores"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">cores</span><span class="p">),</span></span>

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<td class="diff-line-num new old_line" data-linenumber="236" 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="LC236" class="line" lang="python">            <span class="s" style="color: #d14;">"--wildcard-file"</span><span class="p">,</span> <span class="n" style="color: #333;">wildcard_path</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python">            <span class="n" style="color: #333;">adapter_type</span><span class="p">,</span> <span class="s" style="color: #d14;">"ACGTNNNACGT"</span></span>

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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python">        <span class="p">],</span>  <span class="n" style="color: #333;">expected</span><span class="p">,</span> <span class="s" style="color: #d14;">"wildcard_adapter.fa"</span><span class="p">)</span></span>

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<td class="diff-line-num new_line" data-linenumber="239" 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="LC239" class="line" lang="python">    <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">wildcard_path</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">wct</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC240" class="line" lang="python">        <span class="n" style="color: #333;">lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">wct</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">readlines</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC241" class="line" lang="python">    <span class="n" style="color: #333;">lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">line</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;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">lines</span><span class="p">]</span></span>

</pre>

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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">@@ -309,26 +312,26 @@ def test_strip_suffix(run):</td>

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<pre style="margin: 0;"> <span id="LC312" class="line" lang="python">    <span class="n" style="color: #333;">run</span><span class="p">(</span><span class="s" style="color: #d14;">"--strip-suffix _sequence -a XXXXXXX"</span><span class="p">,</span> <span class="s" style="color: #d14;">"stripped.fasta"</span><span class="p">,</span> <span class="s" style="color: #d14;">"simple.fasta"</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC313" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC314" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC312" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_info_file</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">,</span> <span class="n" style="color: #333;">tmpdir</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="315" 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="LC315" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_info_file</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">,</span> <span class="n" style="color: #333;">tmpdir</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">cores</span></span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="316" 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="LC316" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># The true adapter sequence in the illumina.fastq.gz data set is</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="317" 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="LC317" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># GCCTAACTTCTTAGACTGCCTTAAGGACGT (fourth base is different from the sequence shown here)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="318" 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="LC318" class="line" lang="python">    <span class="n" style="color: #333;">info_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"info.txt"</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC316" class="line" lang="python">    <span class="n" style="color: #333;">run</span><span class="p">([</span><span class="s" style="color: #d14;">"--info-file"</span><span class="p">,</span> <span class="n" style="color: #333;">info_path</span><span class="p">,</span> <span class="s" style="color: #d14;">"-a"</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapt=GCCGAACTTCTTAGACTGCCTTAAGGACGT"</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="319" 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="LC319" class="line" lang="python">    <span class="n" style="color: #333;">run</span><span class="p">([</span><span class="s" style="color: #d14;">"--<span class="idiff left">cores"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">cores</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"--</span>info-file"</span><span class="p">,</span> <span class="n" style="color: #333;">info_path</span><span class="p">,</span> <span class="s" style="color: #d14;">"-a"</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapt=GCCGAACTTCTTAGACTGCCTTAAGGACGT"</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="320" 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="LC320" class="line" lang="python">        <span class="s" style="color: #d14;">"illumina.fastq"</span><span class="p">,</span> <span class="s" style="color: #d14;">"illumina.fastq.gz"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="321" 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="LC321" class="line" lang="python">    <span class="n" style="color: #333;">assert_files_equal</span><span class="p">(</span><span class="n" style="color: #333;">cutpath</span><span class="p">(</span><span class="s" style="color: #d14;">"illumina.info.txt"</span><span class="p">),</span> <span class="n" style="color: #333;">info_path</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="322" 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="LC322" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="323" 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="LC323" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC321" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_info_file_times</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">,</span> <span class="n" style="color: #333;">tmpdir</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="324" 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="LC324" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_info_file_times</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">,</span> <span class="n" style="color: #333;">tmpdir</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">cores</span></span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC325" class="line" lang="python">    <span class="n" style="color: #333;">info_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"info.txt"</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC323" class="line" lang="python">    <span class="n" style="color: #333;">run</span><span class="p">([</span><span class="s" style="color: #d14;">"--info-file"</span><span class="p">,</span> <span class="n" style="color: #333;">info_path</span><span class="p">,</span> <span class="s" style="color: #d14;">"--times"</span><span class="p">,</span> <span class="s" style="color: #d14;">"2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-a"</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapt=GCCGAACTTCTTA"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="326" 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="LC326" class="line" lang="python">    <span class="n" style="color: #333;">run</span><span class="p">([</span><span class="s" style="color: #d14;">"--<span class="idiff left">cores"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">cores</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"--</span>info-file"</span><span class="p">,</span> <span class="n" style="color: #333;">info_path</span><span class="p">,</span> <span class="s" style="color: #d14;">"--times"</span><span class="p">,</span> <span class="s" style="color: #d14;">"2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-a"</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapt=GCCGAACTTCTTA"</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC327" class="line" lang="python">        <span class="s" style="color: #d14;">"-a"</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapt2=GACTGCCTTAAGGACGT"</span><span class="p">],</span> <span class="s" style="color: #d14;">"illumina5.fastq"</span><span class="p">,</span> <span class="s" style="color: #d14;">"illumina5.fastq"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

325

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<td class="diff-line-num new_line" data-linenumber="328" 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="LC328" class="line" lang="python">    <span class="n" style="color: #333;">assert_files_equal</span><span class="p">(</span><span class="n" style="color: #333;">cutpath</span><span class="p">(</span><span class="s" style="color: #d14;">'illumina5.info.txt'</span><span class="p">),</span> <span class="n" style="color: #333;">info_path</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="329" 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">

329

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<pre style="margin: 0;"> <span id="LC329" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC330" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC328" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_info_file_fasta</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">,</span> <span class="n" style="color: #333;">tmpdir</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="329" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="331" 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="LC331" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_info_file_fasta</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">,</span> <span class="n" style="color: #333;">tmpdir</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">cores</span></span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC332" class="line" lang="python">    <span class="n" style="color: #333;">info_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"info.txt"</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="333" 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="LC333" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Just make sure that it runs</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC331" class="line" lang="python">    <span class="n" style="color: #333;">run</span><span class="p">([</span><span class="s" style="color: #d14;">"--info-file"</span><span class="p">,</span> <span class="n" style="color: #333;">info_path</span><span class="p">,</span> <span class="s" style="color: #d14;">"-a"</span><span class="p">,</span> <span class="s" style="color: #d14;">"TTAGACATAT"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-g"</span><span class="p">,</span> <span class="s" style="color: #d14;">"GAGATTGCCA"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--no-indels"</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="334" 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="LC334" class="line" lang="python">    <span class="n" style="color: #333;">run</span><span class="p">([</span><span class="s" style="color: #d14;">"--<span class="idiff left">cores"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">cores</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"--</span>info-file"</span><span class="p">,</span> <span class="n" style="color: #333;">info_path</span><span class="p">,</span> <span class="s" style="color: #d14;">"-a"</span><span class="p">,</span> <span class="s" style="color: #d14;">"TTAGACATAT"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-g"</span><span class="p">,</span> <span class="s" style="color: #d14;">"GAGATTGCCA"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--no-indels"</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="335" 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="LC335" class="line" lang="python">        <span class="s" style="color: #d14;">"no_indels.fasta"</span><span class="p">,</span> <span class="s" style="color: #d14;">"no_indels.fasta"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="333" 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">

333

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<td class="diff-line-num new_line" data-linenumber="336" 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="LC336" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="337" 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="LC337" class="line" lang="python"></span>

</pre>

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