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GitLab

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<h3>

Andreas Tille 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/de9edc7eabfa7879116d23be04a786ee8cf2964b">de9edc7e</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-03-01T22:49:43+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.16</pre>

</li>

</ul>

<h4>15 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#4990be809a537bf86e4be2fe2e8251c83d8bd129">

CHANGES.rst

</a>

</li>

<li class="file-stats">

<a href="#0398ccd0f49298b10a3d76a47800d2ebecd49859">

LICENSE

</a>

</li>

<li class="file-stats">

<a href="#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">

PKG-INFO

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</li>

<li class="file-stats">

<a href="#df0576cbb783bc50b36e1efa3cbe0564a26c8295">

doc/conf.py

</a>

</li>

<li class="file-stats">

<a href="#b4bd93cdaa5fb9911a25756bafa10455bb3abf8a">

doc/develop.rst

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<li class="file-stats">

<a href="#ee1d7278a009e2c5c652622fe43dc77e39af740d">

doc/guide.rst

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<li class="file-stats">

<a href="#8c91c0296909b5ea3c496fde69e9dc44a6c6ae5f">

setup.cfg

</a>

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<li class="file-stats">

<a href="#c58dd6a240caf4978db09a259f9ba4e79ead2c34">

src/cutadapt.egg-info/PKG-INFO

</a>

</li>

<li class="file-stats">

<a href="#babdfe5d368a4907abadce7f9b00dfab2489185a">

src/cutadapt/__main__.py

</a>

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<li class="file-stats">

<a href="#3fdf9aa7a8f7f494997913e3e527a05e6d95fa34">

src/cutadapt/_align.c

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<a href="#88bdbbd0e1c81d2dd33c1d7a01e9d2da37402cf8">

src/cutadapt/_qualtrim.c

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<a href="#47e98a86e535e5e4ae3467416d695ed228868764">

src/cutadapt/_seqio.c

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<li class="file-stats">

<a href="#4045e163dd270b4b21bcebce419a3b9ab8ffb64e">

src/cutadapt/_version.py

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<li class="file-stats">

<a href="#1b86cdea057b59b4d05ba7fde4aea9df4e8fe9e8">

src/cutadapt/pipeline.py

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<li class="file-stats">

<a href="#eeec058d84dee20221538717c0787f27d322dd31">

src/cutadapt/seqio.py

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</ul>

<h4>Changes:</h4>

<li id="4990be809a537bf86e4be2fe2e8251c83d8bd129">

<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/de9edc7eabfa7879116d23be04a786ee8cf2964b#4990be809a537bf86e4be2fe2e8251c83d8bd129"><strong>CHANGES.rst</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,6 +2,14 @@</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

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2

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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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<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

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<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

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

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

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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

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<td class="diff-line-num new_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

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

<pre style="margin: 0;"> <span id="LC4" class="line" lang="mosel"></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="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">

5

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

<pre style="margin: 0;">+<span id="LC5" class="line" lang="mosel"><span class="n" style="color: #333;">v1</span><span class="m" style="color: #099;">.16</span> <span class="p">(</span><span class="m" style="color: #099;">2018</span><span class="p">-</span><span class="m" style="color: #099;">02</span><span class="p">-</span><span class="m" style="color: #099;">21</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="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">

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="mosel"><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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7

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

<pre style="margin: 0;">+<span id="LC7" class="line" lang="mosel"></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="8" 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">

8

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

<pre style="margin: 0;">+<span id="LC8" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">Fix</span> <span class="p">:</span><span class="n" style="color: #333;">issue</span><span class="p">:`</span><span class="m" style="color: #099;">291</span><span class="p">`:</span> <span class="n" style="color: #333;">When</span> <span class="n" style="color: #333;">processing</span> <span class="n" style="color: #333;">paired</span><span class="p">-</span><span class="k" style="font-weight: 600;">end</span> <span class="n" style="color: #333;">reads</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">multiple</span> <span class="n" style="color: #333;">cores</span><span class="p">,</span> <span class="n" style="color: #333;">there</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">

9

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

<pre style="margin: 0;">+<span id="LC9" class="line" lang="mosel">  <span class="n" style="color: #333;">could</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">errors</span> <span class="n" style="color: #333;">about</span> <span class="n" style="color: #333;">incomplete</span> <span class="n" style="color: #333;">FASTQs</span> <span class="n" style="color: #333;">although</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">files</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">intact</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="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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">Fix</span> <span class="p">:</span><span class="n" style="color: #333;">issue</span><span class="p">:`</span><span class="m" style="color: #099;">280</span><span class="p">`:</span> <span class="n" style="color: #333;">Quality</span> <span class="n" style="color: #333;">trimming</span> <span class="n" style="color: #333;">statistics</span> <span class="n" style="color: #333;">incorrectly</span> <span class="n" style="color: #333;">show</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">same</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="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">

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

<pre style="margin: 0;">+<span id="LC11" class="line" lang="mosel">  <span class="n" style="color: #333;">values</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">R1</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">R2</span><span class="p">.</span></span>

</pre>

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

<pre style="margin: 0;">+<span id="LC12" class="line" lang="mosel"></span>

</pre>

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

<pre style="margin: 0;"> <span id="LC13" class="line" lang="mosel"><span class="n" style="color: #333;">v1</span><span class="m" style="color: #099;">.15</span> <span class="p">(</span><span class="m" style="color: #099;">2017</span><span class="p">-</span><span class="m" style="color: #099;">11</span><span class="p">-</span><span class="m" style="color: #099;">23</span><span class="p">)</span></span>

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6

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="mosel"><span class="p">------------------</span></span>

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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="mosel"></span>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,10 +23,9 @@ v1.15 (2017-11-23)</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">

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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="mosel"><span class="p">*</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">plan</span> <span class="n" style="color: #333;">is</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">make</span> <span class="n" style="color: #333;">multi</span><span class="p">-</span><span class="n" style="color: #333;">core</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">default</span> <span class="p">(</span><span class="n" style="color: #333;">automatically</span> <span class="n" style="color: #333;">using</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">many</span> <span class="n" style="color: #333;">cores</span> <span class="k" style="font-weight: 600;">as</span></span>

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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="24" style="width: 35px; color: rgba(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="LC24" class="line" lang="mosel">  <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">available</span><span class="p">)</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">future</span> <span class="n" style="color: #333;">releases</span><span class="p">,</span> <span class="n" style="color: #333;">so</span> <span class="n" style="color: #333;">please</span> <span class="n" style="color: #333;">test</span> <span class="n" style="color: #333;">it</span> <span class="k" style="font-weight: 600;">and</span> <span class="p">`</span><span class="n" style="color: #333;">report</span> <span class="n" style="color: #333;">an</span></span>

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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

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<td class="diff-line-num new_line" data-linenumber="25" style="width: 35px; color: rgba(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="LC25" class="line" lang="mosel">  <span class="n" style="color: #333;">issue</span> <span class="p"><</span><span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">marcelm</span><span class="p">/</span><span class="n" style="color: #333;">cutadapt</span><span class="p">/</span><span class="n" style="color: #333;">issues</span><span class="p">/>`</span><span class="n" style="color: #333;">_</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">find</span> <span class="n" style="color: #333;">problems</span><span class="c1" style="color: #998; font-style: italic;">!</span></span>

</pre>

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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">

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<td class="diff-line-num new_line old" data-linenumber="26" 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="LC18" class="line" lang="mosel"><span class="p">*</span> <span class="p"><span class="idiff left">`</span></span><span class="n" style="color: #333;"><span class="idiff">Issue</span></span><span class="idiff"> </span><span class="p"><span class="idiff">#</span></span><span class="m" style="color: #099;"><span class="idiff">256</span></span><span class="idiff"> </span><span class="p"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">https</span></span><span class="p"><span class="idiff">://</span></span><span class="n" style="color: #333;"><span class="idiff">github</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">com</span></span><span class="p"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">marcelm</span></span><span class="p"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">cutadapt</span></span><span class="p"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">issues</span></span><span class="p"><span class="idiff">/</span></span><span class="m" style="color: #099;"><span class="idiff">256</span></span><span class="p"><span class="idiff">>`</span></span><span class="n" style="color: #333;"><span class="idiff right">_</span></span><span class="p">:</span> <span class="p">``--</span><span class="n" style="color: #333;">discard</span><span class="p">-</span><span class="n" style="color: #333;">untrimmed</span><span class="p">``</span> <span class="n" style="color: #333;">did</span> <span class="k" style="font-weight: 600;">not</span></span>

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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">

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<td class="diff-line-num new new_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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<pre style="margin: 0;">+<span id="LC26" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;"><span class="idiff left">Issue</span></span><span class="idiff"> </span><span class="p"><span class="idiff">:</span></span><span class="n" style="color: #333;"><span class="idiff">issue</span></span><span class="p"><span class="idiff">:`</span></span><span class="m" style="color: #099;"><span class="idiff">256</span></span><span class="p"><span class="idiff right">`</span>:</span> <span class="p">``--</span><span class="n" style="color: #333;">discard</span><span class="p">-</span><span class="n" style="color: #333;">untrimmed</span><span class="p">``</span> <span class="n" style="color: #333;">did</span> <span class="k" style="font-weight: 600;">not</span></span>

</pre>

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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">

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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="mosel">  <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">effect</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">non</span><span class="p">-</span><span class="n" style="color: #333;">anchored</span> <span class="n" style="color: #333;">linked</span> <span class="n" style="color: #333;">adapters</span><span class="p">.</span></span>

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<td class="diff-line-num old old_line" data-linenumber="20" 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="28" 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="LC20" 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;">118</span> <span class="p"><</span><span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">marcelm</span><span class="p">/</span><span class="n" style="color: #333;">cutadapt</span><span class="p">/</span><span class="n" style="color: #333;">issues</span><span class="p">/</span><span class="m" style="color: #099;">118</span><span class="p">>`</span><span class="n" style="color: #333;">_</span><span class="p">:</span></span>

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<td class="diff-line-num old old_line" data-linenumber="21" 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="28" 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="LC21" class="line" lang="mosel">  <span class="n" style="color: #333;">Added</span> <span class="n" style="color: #333;">support</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">demultiplexing</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">paired</span><span class="p">-</span><span class="k" style="font-weight: 600;">end</span> <span class="n" style="color: #333;">data</span><span class="p">.</span></span>

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<td class="diff-line-num new old_line" data-linenumber="22" 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="28" 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="LC28" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">Issue</span> <span class="p">:</span><span class="n" style="color: #333;">issue</span><span class="p">:`</span><span class="m" style="color: #099;">118</span><span class="p">`:</span> <span class="n" style="color: #333;">Added</span> <span class="n" style="color: #333;">support</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">demultiplexing</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">paired</span><span class="p">-</span><span class="k" style="font-weight: 600;">end</span> <span class="n" style="color: #333;">data</span><span class="p">.</span></span>

</pre>

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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="29" style="width: 35px; color: rgba(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="LC29" class="line" lang="mosel"></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="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC30" class="line" lang="mosel"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="24" style="width: 35px; color: rgba(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="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC31" class="line" lang="mosel"><span class="n" style="color: #333;">v1</span><span class="m" style="color: #099;">.14</span> <span class="p">(</span><span class="m" style="color: #099;">2017</span><span class="p">-</span><span class="m" style="color: #099;">06</span><span class="p">-</span><span class="m" style="color: #099;">16</span><span class="p">)</span></span>

</pre>

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<li id="0398ccd0f49298b10a3d76a47800d2ebecd49859">

<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/de9edc7eabfa7879116d23be04a786ee8cf2964b#0398ccd0f49298b10a3d76a47800d2ebecd49859"><strong>LICENSE</strong></a>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Copyright (c) 2010-201<span class="idiff left right">7</span> Marcel Martin <marcel.martin@scilifelab.se></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2" 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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1

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

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Copyright (c) 2010-201<span class="idiff left right">8</span> Marcel Martin <marcel.martin@scilifelab.se></span>

</pre>

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2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Permission is hereby granted, free of charge, to any person obtaining a copy</span>

</pre>

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<td class="diff-line-num new_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

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

<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">of this software and associated documentation files (the "Software"), to deal</span>

</pre>

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<br>

</li>

<li id="7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">

<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/de9edc7eabfa7879116d23be04a786ee8cf2964b#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf"><strong>PKG-INFO</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 12px;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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1

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1

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

<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Metadata-Version: 1.1</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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Name: cutadapt</span>

</pre>

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<td class="diff-line-num old old_line" 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">

3

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Version: 1.1<span class="idiff left right">5</span></span>

</pre>

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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">

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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="plaintext">Version: 1.1<span class="idiff left right">6</span></span>

</pre>

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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

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<td class="diff-line-num new_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

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

<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Summary: trim adapters from high-throughput sequencing reads</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">

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Home-page: https://cutadapt.readthedocs.io/</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">

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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">

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Author: Marcel Martin</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="df0576cbb783bc50b36e1efa3cbe0564a26c8295">

<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/de9edc7eabfa7879116d23be04a786ee8cf2964b#df0576cbb783bc50b36e1efa3cbe0564a26c8295"><strong>doc/conf.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="30" style="width: 35px; color: rgba(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="30" style="width: 35px; color: rgba(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">@@ -30,6 +30,7 @@ sys.path.insert(0, os.path.abspath(os.path.join(os.pardir, 'src')))</td>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># ones.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"><span class="n" style="color: #333;">extensions</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python">        <span class="s" style="color: #d14;">'sphinx.ext.autodoc'</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python">        <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="LC34" class="line" lang="python"><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># Add any paths that contain templates here, relative to this directory.</span></span>

</pre>

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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="c" 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'cutadapt'</span></span>

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<pre style="margin: 0;">-<span id="LC49" 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'2010-201<span class="idiff left right">7</span>, Marcel Martin'</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'2010-201<span class="idiff left right">8</span>, 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="c" 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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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># |version| and |release|, also used in various other places throughout the</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">@@ -66,6 +67,8 @@ if version.endswith('.dirty') and os.environ.get('READTHEDOCS') == 'True':</td>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># The full version, including alpha/beta/rc tags.</span></span>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"><span class="n" style="color: #333;">release</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">version</span></span>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"><span class="n" style="color: #333;">issues_uri</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'https://github.com/marcelm/cutadapt/issues/{issue}'</span></span>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"><span class="n" style="color: #333;">suppress_warnings</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'image.nonlocal_uri'</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># The language for content autogenerated by Sphinx. Refer to documentation</span></span>

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<li id="b4bd93cdaa5fb9911a25756bafa10455bb3abf8a">

<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/de9edc7eabfa7879116d23be04a786ee8cf2964b#b4bd93cdaa5fb9911a25756bafa10455bb3abf8a"><strong>doc/develop.rst</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">@@ -17,7 +17,7 @@ using a virtualenv. This sequence of commands should work::</td>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">     git clone https://github.com/marcelm/cutadapt.git  # or clone your own fork</span>

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18

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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="plaintext">     cd cutadapt</span>

</pre>

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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

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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="plaintext">     virtualenv -p python3 venv  # or omit the "-p python3" for Python 2</span>

</pre>

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

20

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<td class="diff-line-num new_line old" data-linenumber="20" 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="LC20" class="line" lang="plaintext">     venv/bin/pip3 install Cython nose tox  # pip3 becomes just pip for Python 2</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="21" 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="20" 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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">     venv/bin/pip3 install Cython <span class="idiff left right">pytest </span>nose tox  # pip3 becomes just pip for Python 2</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

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<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">

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

<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">     venv/bin/pip3 install -e .</span>

</pre>

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

<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></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="plaintext">Then you can run Cutadapt like this (or activate the virtualenv and omit the</span>

</pre>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -27,7 +27,7 @@ Then you can run Cutadapt like this (or activate the virtualenv and omit the</td>

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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">

27

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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="plaintext"></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">

28

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

<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">The tests can then be run like this::</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="29" style="width: 35px; color: rgba(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="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

29

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

<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="30" 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">

30

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<td class="diff-line-num new_line old" data-linenumber="30" 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="LC30" class="line" lang="plaintext">     venv/bin/<span class="idiff left right">nosetests</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="31" 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="30" 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">

30

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">     venv/bin/<span class="idiff left right">pytest</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

31

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<td class="diff-line-num new_line" data-linenumber="31" style="width: 35px; color: rgba(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="LC31" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="32" style="width: 35px; color: rgba(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="32" style="width: 35px; color: rgba(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="LC32" class="line" lang="plaintext">Or with tox (but then you will need to have binaries for all tested Python</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="33" style="width: 35px; color: rgba(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="33" style="width: 35px; color: rgba(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="LC33" class="line" lang="plaintext">versions installed)::</span>

</pre>

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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">@@ -38,13 +38,14 @@ versions installed)::</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">

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">Development installation (without virtualenv)</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">

39

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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">

39

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

</pre>

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<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">

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<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">

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

</pre>

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<td class="diff-line-num old old_line" data-linenumber="41" 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="41" 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="LC41" class="line" lang="plaintext">Alternatively, if you do not want to use virtualenv, <span class="idiff left right">you can do the following</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="41" 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="LC42" class="line" lang="plaintext">from within the cloned repository::</span>

</pre>

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<td class="diff-line-num new old_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">

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<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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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">Alternatively, if you do not want to use virtualenv, <span class="idiff left right">running the following may</span></span>

</pre>

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<td class="diff-line-num new old_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">

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

<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"><span class="idiff left right">work </span>from within the cloned repository::</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">

43

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

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

</pre>

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<td class="diff-line-num old_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">

44

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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">

44

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

<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext">     python3 setup.py build_ext -i  # omit the "3" for Python 2</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="45" 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">

45

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<td class="diff-line-num new_line old" data-linenumber="45" 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="LC45" class="line" lang="plaintext">     <span class="idiff left right">nosetests</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">     <span class="idiff left right">pytest</span></span>

</pre>

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<td class="diff-line-num 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">

46

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<td class="diff-line-num 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">

46

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

<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="47" 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">

47

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<td class="diff-line-num new_line old" data-linenumber="47" 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="LC47" class="line" lang="plaintext">This requires Cython and nose to be installed.</span>

</pre>

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<td class="diff-line-num new old_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">

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<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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">This requires Cython and pytest to be installed. Avoid this method and use a</span>

</pre>

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<td class="diff-line-num new old_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">

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<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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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">virtualenv instead if you can.</span>

</pre>

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48

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<td class="diff-line-num new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

49

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

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

49

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<td class="diff-line-num new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

50

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="50" style="width: 35px; color: rgba(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="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">

51

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

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

</pre>

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<br>

</li>

<li id="ee1d7278a009e2c5c652622fe43dc77e39af740d">

<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/de9edc7eabfa7879116d23be04a786ee8cf2964b#ee1d7278a009e2c5c652622fe43dc77e39af740d"><strong>doc/guide.rst</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 12px;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -143,6 +143,10 @@ There are some limitations:</td>

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<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">

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<pre style="margin: 0;"> <span id="LC143" class="line" lang="plaintext">      - ``--untrimmed-output``, ``--untrimmed-paired-output``</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="144" style="width: 35px; color: rgba(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="LC144" class="line" lang="plaintext">      - ``--too-short-output``, ``--too-short-paired-output``</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="145" style="width: 35px; color: rgba(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="145" style="width: 35px; color: rgba(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="LC145" class="line" lang="plaintext">      - ``--too-long-output``, ``--too-long-paired-output``</span>

</pre>

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<td class="diff-line-num new old_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">

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<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">

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

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="147" 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="LC147" class="line" lang="plaintext">* Additionally, the following command-line arguments are not compatible with</span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_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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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext">  multi-core:</span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="plaintext">      - ``--format``</span>

</pre>

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="plaintext">      - ``--colorspace``</span>

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<pre style="margin: 0;"> <span id="LC152" class="line" lang="plaintext"></span>

</pre>

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<li id="8c91c0296909b5ea3c496fde69e9dc44a6c6ae5f">

<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/de9edc7eabfa7879116d23be04a786ee8cf2964b#8c91c0296909b5ea3c496fde69e9dc44a6c6ae5f"><strong>setup.cfg</strong></a>

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

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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">@@ -8,6 +8,6 @@ parentdir_prefix = cutadapt-</td>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">[egg_info]</span>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">tag_build = </span>

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

11

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">tag_svn_revision = 0</span>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">tag_date = 0</span>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">tag_svn_revision = 0</span>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span></pre>

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<li id="c58dd6a240caf4978db09a259f9ba4e79ead2c34">

<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/de9edc7eabfa7879116d23be04a786ee8cf2964b#c58dd6a240caf4978db09a259f9ba4e79ead2c34"><strong>src/cutadapt.egg-info/PKG-INFO</strong></a>

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Metadata-Version: 1.1</span>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Name: cutadapt</span>

</pre>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Version: 1.1<span class="idiff left right">5</span></span>

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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Version: 1.1<span class="idiff left right">6</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Summary: trim adapters from high-throughput sequencing reads</span>

</pre>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Home-page: https://cutadapt.readthedocs.io/</span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Author: Marcel Martin</span>

</pre>

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</li>

<li id="babdfe5d368a4907abadce7f9b00dfab2489185a">

<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/de9edc7eabfa7879116d23be04a786ee8cf2964b#babdfe5d368a4907abadce7f9b00dfab2489185a"><strong>src/cutadapt/__main__.py</strong></a>

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<td class="diff-line-num unfold js-unfold new_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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -707,7 +707,12 @@ def main(cmdlineargs=None, default_outfile=sys.stdout):</td>

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<pre style="margin: 0;"> <span id="LC707" 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;">'Running in parallel is not supported on Python 2'</span><span class="p">)</span></span>

</pre>

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708

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<td class="diff-line-num 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">

708

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<pre style="margin: 0;"> <span id="LC708" 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 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

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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">

709

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<pre style="margin: 0;"> <span id="LC709" 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;">'Running in parallel is currently not supported for '</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="710" 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">

710

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<td class="diff-line-num new_line old" data-linenumber="710" 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="LC710" class="line" lang="python">                                       <span class="s" style="color: #d14;">'the given combination of command-line parameters.'</span><span class="p">)</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="710" 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">

710

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<pre style="margin: 0;">+<span id="LC710" 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>

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<td class="diff-line-num new old_line" data-linenumber="711" 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="711" 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">

711

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<pre style="margin: 0;">+<span id="LC711" class="line" lang="python">                                       <span class="s" style="color: #d14;">'options are not supported: --info-file, --rest-file, '</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="711" 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="712" 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">

712

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<pre style="margin: 0;">+<span id="LC712" class="line" lang="python">                                       <span class="s" style="color: #d14;">'--wildcard-file, --untrimmed-output, '</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="713" 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="LC713" class="line" lang="python">                                       <span class="s" style="color: #d14;">'--untrimmed-paired-output, --too-short-output, '</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="714" 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">

714

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<pre style="margin: 0;">+<span id="LC714" class="line" lang="python">                                       <span class="s" style="color: #d14;">'--too-short-paired-output, --too-long-output, '</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="715" 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">

715

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<pre style="margin: 0;">+<span id="LC715" class="line" lang="python">                                       <span class="s" style="color: #d14;">'--too-long-paired-output, --format, --colorspace'</span><span class="p">)</span></span>

</pre>

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711

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<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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<pre style="margin: 0;"> <span id="LC716" class="line" lang="python">                       <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</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="LC717" class="line" lang="python">       <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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718

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<pre style="margin: 0;"> <span id="LC718" class="line" lang="python">               <span class="n" style="color: #333;">runner</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pipeline</span></span>

</pre>

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<br>

</li>

<li id="3fdf9aa7a8f7f494997913e3e527a05e6d95fa34">

<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/de9edc7eabfa7879116d23be04a786ee8cf2964b#3fdf9aa7a8f7f494997913e3e527a05e6d95fa34"><strong>src/cutadapt/_align.c</strong></a>

The diff for this file was not included because it is too large.

<br>

</li>

<li id="88bdbbd0e1c81d2dd33c1d7a01e9d2da37402cf8">

<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/de9edc7eabfa7879116d23be04a786ee8cf2964b#88bdbbd0e1c81d2dd33c1d7a01e9d2da37402cf8"><strong>src/cutadapt/_qualtrim.c</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold new_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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -705,7 +705,7 @@ static const char __pyx_k_Quality_trimming[] = "\nQuality trimming.\n";</td>

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705

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC705" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">__pyx_k_cutadapt__qualtrim</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"cutadapt._qualtrim"</span><span class="p">;</span></span>

</pre>

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<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

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<td class="diff-line-num new_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

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<pre style="margin: 0;"> <span id="LC706" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">__pyx_k_nextseq_trim_index</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"nextseq_trim_index"</span><span class="p">;</span></span>

</pre>

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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

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<td class="diff-line-num new_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

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<pre style="margin: 0;"> <span id="LC707" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">__pyx_k_quality_trim_index</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"quality_trim_index"</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC708" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">__pyx_k_home_marcel_scm_cutadapt_<span class="idiff left">cutada</span></span><span class="p"><span class="idiff">[]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"/home/marcel/scm/cutadapt</span>/cutadapt/src/cutadapt/_qualtrim.pyx"</span><span class="p">;</span></span>

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<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">

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<td class="diff-line-num new new_line" data-linenumber="708" 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">

708

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

<pre style="margin: 0;">+<span id="LC708" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">__pyx_k_home_marcel_scm_cutadapt_<span class="idiff left">src_cu</span></span><span class="p"><span class="idiff">[]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"/home/marcel/scm</span>/cutadapt/src/cutadapt/_qualtrim.pyx"</span><span class="p">;</span></span>

</pre>

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<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

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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">

709

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

<pre style="margin: 0;"> <span id="LC709" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">PyObject</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">__pyx_n_s_G</span><span class="p">;</span></span>

</pre>

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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

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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">

710

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

<pre style="margin: 0;"> <span id="LC710" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">PyObject</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">__pyx_n_s_base</span><span class="p">;</span></span>

</pre>

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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="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

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

<pre style="margin: 0;"> <span id="LC711" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">PyObject</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">__pyx_n_s_bases</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="713" style="width: 35px; color: rgba(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="713" style="width: 35px; color: rgba(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">@@ -713,7 +713,7 @@ static PyObject *__pyx_n_s_cutadapt__qualtrim;</td>

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<td class="diff-line-num old_line" data-linenumber="713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

713

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<td class="diff-line-num new_line" data-linenumber="713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

713

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<pre style="margin: 0;"> <span id="LC713" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">PyObject</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">__pyx_n_s_cutoff</span><span class="p">;</span></span>

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<td class="diff-line-num old_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

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<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

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

<pre style="margin: 0;"> <span id="LC714" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">PyObject</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">__pyx_n_s_cutoff_back</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_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

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<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

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

<pre style="margin: 0;"> <span id="LC715" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">PyObject</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">__pyx_n_s_cutoff_front</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="716" 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">

716

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<td class="diff-line-num new_line old" data-linenumber="716" 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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC716" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">PyObject</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">__pyx_kp_s_home_marcel_scm_cutadapt_<span class="idiff left right">cutada</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="717" 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="716" 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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC716" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">PyObject</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">__pyx_kp_s_home_marcel_scm_cutadapt_<span class="idiff left right">src_cu</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_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

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<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

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

<pre style="margin: 0;"> <span id="LC717" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">PyObject</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">__pyx_n_s_i</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_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

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<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

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

<pre style="margin: 0;"> <span id="LC718" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">PyObject</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">__pyx_n_s_main</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_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="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

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

<pre style="margin: 0;"> <span id="LC719" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">PyObject</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">__pyx_n_s_max_i</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1162" style="width: 35px; color: rgba(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="1162" style="width: 35px; color: rgba(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">@@ -1162,7 +1162,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {</td>

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<td class="diff-line-num old_line" data-linenumber="1162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1162

</td>

<td class="diff-line-num new_line" data-linenumber="1162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1162

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

<pre style="margin: 0;"> <span id="LC1162" class="line" lang="c">  <span class="p">{</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">__pyx_n_s_cutoff</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_k_cutoff</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">__pyx_k_cutoff</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 class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">},</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1163

</td>

<td class="diff-line-num new_line" data-linenumber="1163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1163

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

<pre style="margin: 0;"> <span id="LC1163" class="line" lang="c">  <span class="p">{</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">__pyx_n_s_cutoff_back</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_k_cutoff_back</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">__pyx_k_cutoff_back</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 class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">},</span></span>

</pre>

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

<td class="diff-line-num old_line" data-linenumber="1164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1164

</td>

<td class="diff-line-num new_line" data-linenumber="1164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1164

</td>

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

<pre style="margin: 0;"> <span id="LC1164" class="line" lang="c">  <span class="p">{</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">__pyx_n_s_cutoff_front</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_k_cutoff_front</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">__pyx_k_cutoff_front</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 class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</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="1165" 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">

1165

</td>

<td class="diff-line-num new_line old" data-linenumber="1165" 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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1165" class="line" lang="c">  <span class="p">{</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">__pyx_kp_s_home_marcel_scm_cutadapt_<span class="idiff left">cutada</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">__pyx_k_home_marcel_scm_cutadapt_cutada</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">sizeof</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">__pyx_k_home_marcel_scm_cutadapt_cutada</span></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 class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">},</span></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="1166" 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="1165" 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">

1165

</td>

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

<pre style="margin: 0;">+<span id="LC1165" class="line" lang="c">  <span class="p">{</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">__pyx_kp_s_home_marcel_scm_cutadapt_<span class="idiff left">src_cu</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">__pyx_k_home_marcel_scm_cutadapt_src_cu</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">sizeof</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">__pyx_k_home_marcel_scm_cutadapt_src_cu</span></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 class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</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="1166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1166

</td>

<td class="diff-line-num new_line" data-linenumber="1166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1166

</td>

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

<pre style="margin: 0;"> <span id="LC1166" class="line" lang="c">  <span class="p">{</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">__pyx_n_s_i</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_k_i</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">__pyx_k_i</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 class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</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="1167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1167

</td>

<td class="diff-line-num new_line" data-linenumber="1167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1167

</td>

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

<pre style="margin: 0;"> <span id="LC1167" class="line" lang="c">  <span class="p">{</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">__pyx_n_s_main</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_k_main</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">__pyx_k_main</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 class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</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="1168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1168

</td>

<td class="diff-line-num new_line" data-linenumber="1168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1168

</td>

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

<pre style="margin: 0;"> <span id="LC1168" class="line" lang="c">  <span class="p">{</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">__pyx_n_s_max_i</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_k_max_i</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">__pyx_k_max_i</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 class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">},</span></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="1201" style="width: 35px; color: rgba(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="1201" style="width: 35px; color: rgba(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">@@ -1201,12 +1201,12 @@ static int __Pyx_InitCachedConstants(void) {</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1201

</td>

<td class="diff-line-num new_line" data-linenumber="1201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1201

</td>

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

<pre style="margin: 0;"> <span id="LC1201" class="line" lang="c">  <span class="n" style="color: #333;">__pyx_tuple_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PyTuple_Pack</span><span class="p">(</span><span class="mi" style="color: #099;">9</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_qualities</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_cutoff_front</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_cutoff_back</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_base</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_s</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_max_qual</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_stop</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_start</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_i</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">__pyx_tuple_</span><span class="p">))</span> <span class="n" style="color: #333;">__PYX_ERR</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">7</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_L1_error</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="1202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1202

</td>

<td class="diff-line-num new_line" data-linenumber="1202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1202

</td>

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

<pre style="margin: 0;"> <span id="LC1202" class="line" lang="c">  <span class="n" style="color: #333;">__Pyx_GOTREF</span><span class="p">(</span><span class="n" style="color: #333;">__pyx_tuple_</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="1203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1203

</td>

<td class="diff-line-num new_line" data-linenumber="1203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1203

</td>

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

<pre style="margin: 0;"> <span id="LC1203" class="line" lang="c">  <span class="n" style="color: #333;">__Pyx_GIVEREF</span><span class="p">(</span><span class="n" style="color: #333;">__pyx_tuple_</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="1204" 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">

1204

</td>

<td class="diff-line-num new_line old" data-linenumber="1204" 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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1204" class="line" lang="c">  <span class="n" style="color: #333;">__pyx_codeobj__2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">PyObject</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">__Pyx_PyCode_New</span><span class="p">(</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">9</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 class="n" style="color: #333;">__pyx_empty_bytes</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_tuple_</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_kp_s_home_marcel_scm_cutadapt_<span class="idiff left right">cutada</span></span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_quality_trim_index</span><span class="p">,</span> <span class="mi" style="color: #099;">7</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_bytes</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">__pyx_codeobj__2</span><span class="p">))</span> <span class="n" style="color: #333;">__PYX_ERR</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">7</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_L1_error</span><span class="p">)</span></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="1205" 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="1204" 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">

1204

</td>

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

<pre style="margin: 0;">+<span id="LC1204" class="line" lang="c">  <span class="n" style="color: #333;">__pyx_codeobj__2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">PyObject</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">__Pyx_PyCode_New</span><span class="p">(</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">9</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 class="n" style="color: #333;">__pyx_empty_bytes</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_tuple_</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_kp_s_home_marcel_scm_cutadapt_<span class="idiff left right">src_cu</span></span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_quality_trim_index</span><span class="p">,</span> <span class="mi" style="color: #099;">7</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_bytes</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">__pyx_codeobj__2</span><span class="p">))</span> <span class="n" style="color: #333;">__PYX_ERR</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">7</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_L1_error</span><span class="p">)</span></span>

</pre>

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

<td class="diff-line-num old_line" data-linenumber="1205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1205

</td>

<td class="diff-line-num new_line" data-linenumber="1205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1205

</td>

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

<pre style="margin: 0;"> <span id="LC1205" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1206

</td>

<td class="diff-line-num new_line" data-linenumber="1206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1206

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

<pre style="margin: 0;"> <span id="LC1206" class="line" lang="c">  <span class="n" style="color: #333;">__pyx_tuple__3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PyTuple_Pack</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_sequence</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_cutoff</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_base</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_bases</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_qualities</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_s</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_max_qual</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_max_i</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_i</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_q</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">__pyx_tuple__3</span><span class="p">))</span> <span class="n" style="color: #333;">__PYX_ERR</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">52</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_L1_error</span><span class="p">)</span></span>

</pre>

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

<td class="diff-line-num old_line" data-linenumber="1207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1207

</td>

<td class="diff-line-num new_line" data-linenumber="1207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1207

</td>

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

<pre style="margin: 0;"> <span id="LC1207" class="line" lang="c">  <span class="n" style="color: #333;">__Pyx_GOTREF</span><span class="p">(</span><span class="n" style="color: #333;">__pyx_tuple__3</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="1208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1208

</td>

<td class="diff-line-num new_line" data-linenumber="1208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1208

</td>

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

<pre style="margin: 0;"> <span id="LC1208" class="line" lang="c">  <span class="n" style="color: #333;">__Pyx_GIVEREF</span><span class="p">(</span><span class="n" style="color: #333;">__pyx_tuple__3</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="1209" 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">

1209

</td>

<td class="diff-line-num new_line old" data-linenumber="1209" 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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1209" class="line" lang="c">  <span class="n" style="color: #333;">__pyx_codeobj__4</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">PyObject</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">__Pyx_PyCode_New</span><span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">10</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 class="n" style="color: #333;">__pyx_empty_bytes</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_tuple__3</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_kp_s_home_marcel_scm_cutadapt_<span class="idiff left right">cutada</span></span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_nextseq_trim_index</span><span class="p">,</span> <span class="mi" style="color: #099;">52</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_bytes</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">__pyx_codeobj__4</span><span class="p">))</span> <span class="n" style="color: #333;">__PYX_ERR</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">52</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_L1_error</span><span class="p">)</span></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="1210" 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="1209" 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">

1209

</td>

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

<pre style="margin: 0;">+<span id="LC1209" class="line" lang="c">  <span class="n" style="color: #333;">__pyx_codeobj__4</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">PyObject</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">__Pyx_PyCode_New</span><span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">10</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 class="n" style="color: #333;">__pyx_empty_bytes</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_tuple__3</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_kp_s_home_marcel_scm_cutadapt_<span class="idiff left right">src_cu</span></span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_nextseq_trim_index</span><span class="p">,</span> <span class="mi" style="color: #099;">52</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_bytes</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">__pyx_codeobj__4</span><span class="p">))</span> <span class="n" style="color: #333;">__PYX_ERR</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">52</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_L1_error</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="1210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1210

</td>

<td class="diff-line-num new_line" data-linenumber="1210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1210

</td>

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

<pre style="margin: 0;"> <span id="LC1210" class="line" lang="c">  <span class="n" style="color: #333;">__Pyx_RefNannyFinishContext</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="1211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1211

</td>

<td class="diff-line-num new_line" data-linenumber="1211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1211

</td>

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

<pre style="margin: 0;"> <span id="LC1211" class="line" lang="c">  <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</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="1212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1212

</td>

<td class="diff-line-num new_line" data-linenumber="1212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1212

</td>

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

<pre style="margin: 0;"> <span id="LC1212" class="line" lang="c">  <span class="nl">__pyx_L1_error:</span><span class="p">;</span></span>

</pre>

</td>

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</table>

<br>

</li>

<li id="47e98a86e535e5e4ae3467416d695ed228868764">

<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/de9edc7eabfa7879116d23be04a786ee8cf2964b#47e98a86e535e5e4ae3467416d695ed228868764"><strong>src/cutadapt/_seqio.c</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 12px;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1137" style="width: 35px; color: rgba(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="1137" style="width: 35px; color: rgba(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">@@ -1137,7 +1137,7 @@ static const char __pyx_k_Expected_at_least_d_arguments[] = "Expected at least %</td>

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<td class="diff-line-num new_line" data-linenumber="1137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1137

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

<pre style="margin: 0;"> <span id="LC1137" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">__pyx_k_Sequence_name_0_r_sequence_1_r</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<Sequence(name={0!r}, sequence={1!r}{2})>"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1138

</td>

<td class="diff-line-num new_line" data-linenumber="1138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1138

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

<pre style="margin: 0;"> <span id="LC1138" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">__pyx_k_At_line_0_Sequence_descriptions</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"At line {0}: Sequence descriptions in the FASTQ file don't match ({1!r} != {2!r}).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">The second sequence description must be either empty or equal to the first description."</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1139

</td>

<td class="diff-line-num new_line" data-linenumber="1139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1139

</td>

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

<pre style="margin: 0;"> <span id="LC1139" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">__pyx_k_Reader_for_FASTQ_files_Does_not</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;">Reader for FASTQ files. Does not support multi-line FASTQ files.</span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1140" 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">

1140

</td>

<td class="diff-line-num new_line old" data-linenumber="1140" 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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1140" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">__pyx_k_home_marcel_scm_cutadapt_<span class="idiff left">cutada</span></span><span class="p"><span class="idiff">[]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"/home/marcel/scm/cutadapt</span>/cutadapt/src/cutadapt/_seqio.pyx"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1141" 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="1140" 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">

1140

</td>

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

<pre style="margin: 0;">+<span id="LC1140" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">__pyx_k_home_marcel_scm_cutadapt_<span class="idiff left">src_cu</span></span><span class="p"><span class="idiff">[]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"/home/marcel/scm</span>/cutadapt/src/cutadapt/_seqio.pyx"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1141

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<td class="diff-line-num new_line" data-linenumber="1141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1141

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

<pre style="margin: 0;"> <span id="LC1141" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">__pyx_k_Function_call_with_ambiguous_arg</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Function call with ambiguous argument types"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1142

</td>

<td class="diff-line-num new_line" data-linenumber="1142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1142

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

<pre style="margin: 0;"> <span id="LC1142" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">__pyx_k_In_read_named_0_r_length_of_qual</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"In read named {0!r}: length of quality sequence ({1}) and length of read ({2}) do not match"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1143

</td>

<td class="diff-line-num new_line" data-linenumber="1143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1143

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

<pre style="margin: 0;"> <span id="LC1143" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">__pyx_k_Line_0_in_FASTQ_file_is_expected</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Line {0} in FASTQ file is expected to start with '@', but found {1!r}"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1189" style="width: 35px; color: rgba(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="1189" style="width: 35px; color: rgba(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">@@ -1189,7 +1189,7 @@ static PyObject *__pyx_n_s_file;</td>

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<td class="diff-line-num old_line" data-linenumber="1189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1189

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<td class="diff-line-num new_line" data-linenumber="1189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1189

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

<pre style="margin: 0;"> <span id="LC1189" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">PyObject</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">__pyx_n_s_file_2</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1190

</td>

<td class="diff-line-num new_line" data-linenumber="1190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1190

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

<pre style="margin: 0;"> <span id="LC1190" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">PyObject</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">__pyx_n_s_format</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1191

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<td class="diff-line-num new_line" data-linenumber="1191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1191

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

<pre style="margin: 0;"> <span id="LC1191" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">PyObject</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">__pyx_n_s_head</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1192" 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">

1192

</td>

<td class="diff-line-num new_line old" data-linenumber="1192" 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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1192" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">PyObject</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">__pyx_kp_s_home_marcel_scm_cutadapt_<span class="idiff left right">cutada</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1193" 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="1192" 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">

1192

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

<pre style="margin: 0;">+<span id="LC1192" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">PyObject</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">__pyx_kp_s_home_marcel_scm_cutadapt_<span class="idiff left right">src_cu</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1193

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<td class="diff-line-num new_line" data-linenumber="1193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1193

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

<pre style="margin: 0;"> <span id="LC1193" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">PyObject</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">__pyx_n_s_i</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1194

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<td class="diff-line-num new_line" data-linenumber="1194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1194

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

<pre style="margin: 0;"> <span id="LC1194" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">PyObject</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">__pyx_n_s_import</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1195

</td>

<td class="diff-line-num new_line" data-linenumber="1195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1195

</td>

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

<pre style="margin: 0;"> <span id="LC1195" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">PyObject</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">__pyx_n_s_init</span><span class="p">;</span></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="6254" style="width: 35px; color: rgba(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="6254" style="width: 35px; color: rgba(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">@@ -6254,7 +6254,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {</td>

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

<td class="diff-line-num old_line" data-linenumber="6254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6254

</td>

<td class="diff-line-num new_line" data-linenumber="6254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6254

</td>

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

<pre style="margin: 0;"> <span id="LC6254" class="line" lang="c">  <span class="p">{</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">__pyx_n_s_file_2</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_k_file_2</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">__pyx_k_file_2</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 class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</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="6255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6255

</td>

<td class="diff-line-num new_line" data-linenumber="6255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6255

</td>

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

<pre style="margin: 0;"> <span id="LC6255" class="line" lang="c">  <span class="p">{</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">__pyx_n_s_format</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_k_format</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">__pyx_k_format</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 class="mi" style="color: #099;">1</span><span class="p">,</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="6256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6256

</td>

<td class="diff-line-num new_line" data-linenumber="6256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6256

</td>

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

<pre style="margin: 0;"> <span id="LC6256" class="line" lang="c">  <span class="p">{</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">__pyx_n_s_head</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_k_head</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">__pyx_k_head</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 class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</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="6257" 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">

6257

</td>

<td class="diff-line-num new_line old" data-linenumber="6257" 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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC6257" class="line" lang="c">  <span class="p">{</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">__pyx_kp_s_home_marcel_scm_cutadapt_<span class="idiff left">cutada</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">__pyx_k_home_marcel_scm_cutadapt_cutada</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">sizeof</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">__pyx_k_home_marcel_scm_cutadapt_cutada</span></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 class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">},</span></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="6258" 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="6257" 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">

6257

</td>

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

<pre style="margin: 0;">+<span id="LC6257" class="line" lang="c">  <span class="p">{</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">__pyx_kp_s_home_marcel_scm_cutadapt_<span class="idiff left">src_cu</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">__pyx_k_home_marcel_scm_cutadapt_src_cu</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">sizeof</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">__pyx_k_home_marcel_scm_cutadapt_src_cu</span></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 class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</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="6258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6258

</td>

<td class="diff-line-num new_line" data-linenumber="6258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6258

</td>

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

<pre style="margin: 0;"> <span id="LC6258" class="line" lang="c">  <span class="p">{</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">__pyx_n_s_i</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_k_i</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">__pyx_k_i</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 class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</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="6259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6259

</td>

<td class="diff-line-num new_line" data-linenumber="6259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6259

</td>

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

<pre style="margin: 0;"> <span id="LC6259" class="line" lang="c">  <span class="p">{</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">__pyx_n_s_import</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_k_import</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">__pyx_k_import</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 class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</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="6260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6260

</td>

<td class="diff-line-num new_line" data-linenumber="6260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6260

</td>

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

<pre style="margin: 0;"> <span id="LC6260" class="line" lang="c">  <span class="p">{</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">__pyx_n_s_init</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_k_init</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">__pyx_k_init</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 class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">},</span></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="6366" style="width: 35px; color: rgba(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="6366" style="width: 35px; color: rgba(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">@@ -6366,27 +6366,27 @@ static int __Pyx_InitCachedConstants(void) {</td>

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<td class="diff-line-num old_line" data-linenumber="6366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6366

</td>

<td class="diff-line-num new_line" data-linenumber="6366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6366

</td>

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

<pre style="margin: 0;"> <span id="LC6366" class="line" lang="c">  <span class="n" style="color: #333;">__pyx_tuple__23</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PyTuple_Pack</span><span class="p">(</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_buf</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_lines</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_pos</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_linebreaks_seen</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_length</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_data</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">__pyx_tuple__23</span><span class="p">))</span> <span class="n" style="color: #333;">__PYX_ERR</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_L1_error</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="6367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6367

</td>

<td class="diff-line-num new_line" data-linenumber="6367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6367

</td>

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

<pre style="margin: 0;"> <span id="LC6367" class="line" lang="c">  <span class="n" style="color: #333;">__Pyx_GOTREF</span><span class="p">(</span><span class="n" style="color: #333;">__pyx_tuple__23</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="6368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6368

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<td class="diff-line-num new_line" data-linenumber="6368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6368

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

<pre style="margin: 0;"> <span id="LC6368" class="line" lang="c">  <span class="n" style="color: #333;">__Pyx_GIVEREF</span><span class="p">(</span><span class="n" style="color: #333;">__pyx_tuple__23</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="6369" 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">

6369

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<td class="diff-line-num new_line old" data-linenumber="6369" 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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC6369" class="line" lang="c">  <span class="n" style="color: #333;">__pyx_codeobj__24</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">PyObject</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">__Pyx_PyCode_New</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">6</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 class="n" style="color: #333;">__pyx_empty_bytes</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_tuple__23</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_kp_s_home_marcel_scm_cutadapt_<span class="idiff left right">cutada</span></span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_head</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_bytes</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">__pyx_codeobj__24</span><span class="p">))</span> <span class="n" style="color: #333;">__PYX_ERR</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_L1_error</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="6370" 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="6369" 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">

6369

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

<pre style="margin: 0;">+<span id="LC6369" class="line" lang="c">  <span class="n" style="color: #333;">__pyx_codeobj__24</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">PyObject</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">__Pyx_PyCode_New</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">6</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 class="n" style="color: #333;">__pyx_empty_bytes</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_tuple__23</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_kp_s_home_marcel_scm_cutadapt_<span class="idiff left right">src_cu</span></span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_head</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_bytes</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">__pyx_codeobj__24</span><span class="p">))</span> <span class="n" style="color: #333;">__PYX_ERR</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_L1_error</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="6370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6370

</td>

<td class="diff-line-num new_line" data-linenumber="6370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6370

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

<pre style="margin: 0;"> <span id="LC6370" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="6371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6371

</td>

<td class="diff-line-num new_line" data-linenumber="6371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6371

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

<pre style="margin: 0;"> <span id="LC6371" class="line" lang="c">  <span class="n" style="color: #333;">__pyx_tuple__25</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PyTuple_Pack</span><span class="p">(</span><span class="mi" style="color: #099;">7</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_buf</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_end</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_pos</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_linebreaks</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_length</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_data</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_record_start</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">__pyx_tuple__25</span><span class="p">))</span> <span class="n" style="color: #333;">__PYX_ERR</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">38</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_L1_error</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="6372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6372

</td>

<td class="diff-line-num new_line" data-linenumber="6372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6372

</td>

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

<pre style="margin: 0;"> <span id="LC6372" class="line" lang="c">  <span class="n" style="color: #333;">__Pyx_GOTREF</span><span class="p">(</span><span class="n" style="color: #333;">__pyx_tuple__25</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="6373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6373

</td>

<td class="diff-line-num new_line" data-linenumber="6373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6373

</td>

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

<pre style="margin: 0;"> <span id="LC6373" class="line" lang="c">  <span class="n" style="color: #333;">__Pyx_GIVEREF</span><span class="p">(</span><span class="n" style="color: #333;">__pyx_tuple__25</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="6374" 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">

6374

</td>

<td class="diff-line-num new_line old" data-linenumber="6374" 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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC6374" class="line" lang="c">  <span class="n" style="color: #333;">__pyx_codeobj__26</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">PyObject</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">__Pyx_PyCode_New</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">7</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 class="n" style="color: #333;">__pyx_empty_bytes</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_tuple__25</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_kp_s_home_marcel_scm_cutadapt_<span class="idiff left right">cutada</span></span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_fastq_head</span><span class="p">,</span> <span class="mi" style="color: #099;">38</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_bytes</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">__pyx_codeobj__26</span><span class="p">))</span> <span class="n" style="color: #333;">__PYX_ERR</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">38</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_L1_error</span><span class="p">)</span></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="6375" 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="6374" 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">

6374

</td>

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

<pre style="margin: 0;">+<span id="LC6374" class="line" lang="c">  <span class="n" style="color: #333;">__pyx_codeobj__26</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">PyObject</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">__Pyx_PyCode_New</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">7</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 class="n" style="color: #333;">__pyx_empty_bytes</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_tuple__25</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_kp_s_home_marcel_scm_cutadapt_<span class="idiff left right">src_cu</span></span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_fastq_head</span><span class="p">,</span> <span class="mi" style="color: #099;">38</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_bytes</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">__pyx_codeobj__26</span><span class="p">))</span> <span class="n" style="color: #333;">__PYX_ERR</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">38</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_L1_error</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="6375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6375

</td>

<td class="diff-line-num new_line" data-linenumber="6375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6375

</td>

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

<pre style="margin: 0;"> <span id="LC6375" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="6376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6376

</td>

<td class="diff-line-num new_line" data-linenumber="6376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6376

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

<pre style="margin: 0;"> <span id="LC6376" class="line" lang="c">  <span class="n" style="color: #333;">__pyx_tuple__27</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PyTuple_Pack</span><span class="p">(</span><span class="mi" style="color: #099;">11</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_buf1</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_buf2</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_end1</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_end2</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_pos1</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_pos2</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_linebreaks</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_data1</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_data2</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_record_start1</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_record_start2</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">__pyx_tuple__27</span><span class="p">))</span> <span class="n" style="color: #333;">__PYX_ERR</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">69</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_L1_error</span><span class="p">)</span></span>

</pre>

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

<td class="diff-line-num old_line" data-linenumber="6377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6377

</td>

<td class="diff-line-num new_line" data-linenumber="6377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6377

</td>

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

<pre style="margin: 0;"> <span id="LC6377" class="line" lang="c">  <span class="n" style="color: #333;">__Pyx_GOTREF</span><span class="p">(</span><span class="n" style="color: #333;">__pyx_tuple__27</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="6378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6378

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<td class="diff-line-num new_line" data-linenumber="6378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6378

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

<pre style="margin: 0;"> <span id="LC6378" class="line" lang="c">  <span class="n" style="color: #333;">__Pyx_GIVEREF</span><span class="p">(</span><span class="n" style="color: #333;">__pyx_tuple__27</span><span class="p">);</span></span>

</pre>

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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="6379" 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">

6379

</td>

<td class="diff-line-num new_line old" data-linenumber="6379" 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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC6379" class="line" lang="c">  <span class="n" style="color: #333;">__pyx_codeobj__28</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">PyObject</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">__Pyx_PyCode_New</span><span class="p">(</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">11</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 class="n" style="color: #333;">__pyx_empty_bytes</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_tuple__27</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_kp_s_home_marcel_scm_cutadapt_<span class="idiff left right">cutada</span></span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_two_fastq_heads</span><span class="p">,</span> <span class="mi" style="color: #099;">69</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_bytes</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">__pyx_codeobj__28</span><span class="p">))</span> <span class="n" style="color: #333;">__PYX_ERR</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">69</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_L1_error</span><span class="p">)</span></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="6380" 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="6379" 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">

6379

</td>

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

<pre style="margin: 0;">+<span id="LC6379" class="line" lang="c">  <span class="n" style="color: #333;">__pyx_codeobj__28</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">PyObject</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">__Pyx_PyCode_New</span><span class="p">(</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">11</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 class="n" style="color: #333;">__pyx_empty_bytes</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_tuple__27</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_kp_s_home_marcel_scm_cutadapt_<span class="idiff left right">src_cu</span></span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_two_fastq_heads</span><span class="p">,</span> <span class="mi" style="color: #099;">69</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_bytes</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">__pyx_codeobj__28</span><span class="p">))</span> <span class="n" style="color: #333;">__PYX_ERR</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">69</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_L1_error</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="6380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6380

</td>

<td class="diff-line-num new_line" data-linenumber="6380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6380

</td>

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

<pre style="margin: 0;"> <span id="LC6380" class="line" lang="c"></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="6381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6381

</td>

<td class="diff-line-num new_line" data-linenumber="6381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6381

</td>

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

<pre style="margin: 0;"> <span id="LC6381" class="line" lang="c">  <span class="n" style="color: #333;">__pyx_tuple__29</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PyTuple_Pack</span><span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_self</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_file</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_sequence_class</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">__pyx_tuple__29</span><span class="p">))</span> <span class="n" style="color: #333;">__PYX_ERR</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">175</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_L1_error</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="6382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6382

</td>

<td class="diff-line-num new_line" data-linenumber="6382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6382

</td>

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

<pre style="margin: 0;"> <span id="LC6382" class="line" lang="c">  <span class="n" style="color: #333;">__Pyx_GOTREF</span><span class="p">(</span><span class="n" style="color: #333;">__pyx_tuple__29</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="6383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6383

</td>

<td class="diff-line-num new_line" data-linenumber="6383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6383

</td>

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

<pre style="margin: 0;"> <span id="LC6383" class="line" lang="c">  <span class="n" style="color: #333;">__Pyx_GIVEREF</span><span class="p">(</span><span class="n" style="color: #333;">__pyx_tuple__29</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="6384" 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">

6384

</td>

<td class="diff-line-num new_line old" data-linenumber="6384" 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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC6384" class="line" lang="c">  <span class="n" style="color: #333;">__pyx_codeobj__30</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">PyObject</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">__Pyx_PyCode_New</span><span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">3</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 class="n" style="color: #333;">__pyx_empty_bytes</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_tuple__29</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_kp_s_home_marcel_scm_cutadapt_<span class="idiff left right">cutada</span></span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_init</span><span class="p">,</span> <span class="mi" style="color: #099;">175</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_bytes</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">__pyx_codeobj__30</span><span class="p">))</span> <span class="n" style="color: #333;">__PYX_ERR</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">175</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_L1_error</span><span class="p">)</span></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="6385" 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="6384" 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">

6384

</td>

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

<pre style="margin: 0;">+<span id="LC6384" class="line" lang="c">  <span class="n" style="color: #333;">__pyx_codeobj__30</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">PyObject</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">__Pyx_PyCode_New</span><span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">3</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 class="n" style="color: #333;">__pyx_empty_bytes</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_tuple__29</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_kp_s_home_marcel_scm_cutadapt_<span class="idiff left right">src_cu</span></span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_init</span><span class="p">,</span> <span class="mi" style="color: #099;">175</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_bytes</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">__pyx_codeobj__30</span><span class="p">))</span> <span class="n" style="color: #333;">__PYX_ERR</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">175</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_L1_error</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="6385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6385

</td>

<td class="diff-line-num new_line" data-linenumber="6385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6385

</td>

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

<pre style="margin: 0;"> <span id="LC6385" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="6386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6386

</td>

<td class="diff-line-num new_line" data-linenumber="6386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6386

</td>

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

<pre style="margin: 0;"> <span id="LC6386" class="line" lang="c">  <span class="n" style="color: #333;">__pyx_tuple__31</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PyTuple_Pack</span><span class="p">(</span><span class="mi" style="color: #099;">11</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_self</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_i</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_strip</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_line</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_name</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_qualities</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_sequence</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_name2</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_sequence_class</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_it</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_second_header</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">__pyx_tuple__31</span><span class="p">))</span> <span class="n" style="color: #333;">__PYX_ERR</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">184</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_L1_error</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="6387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6387

</td>

<td class="diff-line-num new_line" data-linenumber="6387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6387

</td>

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

<pre style="margin: 0;"> <span id="LC6387" class="line" lang="c">  <span class="n" style="color: #333;">__Pyx_GOTREF</span><span class="p">(</span><span class="n" style="color: #333;">__pyx_tuple__31</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="6388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6388

</td>

<td class="diff-line-num new_line" data-linenumber="6388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6388

</td>

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

<pre style="margin: 0;"> <span id="LC6388" class="line" lang="c">  <span class="n" style="color: #333;">__Pyx_GIVEREF</span><span class="p">(</span><span class="n" style="color: #333;">__pyx_tuple__31</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="6389" 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">

6389

</td>

<td class="diff-line-num new_line old" data-linenumber="6389" 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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC6389" class="line" lang="c">  <span class="n" style="color: #333;">__pyx_codeobj__32</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">PyObject</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">__Pyx_PyCode_New</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">11</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 class="n" style="color: #333;">__pyx_empty_bytes</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_tuple__31</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_kp_s_home_marcel_scm_cutadapt_<span class="idiff left right">cutada</span></span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_iter</span><span class="p">,</span> <span class="mi" style="color: #099;">184</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_bytes</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">__pyx_codeobj__32</span><span class="p">))</span> <span class="n" style="color: #333;">__PYX_ERR</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">184</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_L1_error</span><span class="p">)</span></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="6390" 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="6389" 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">

6389

</td>

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

<pre style="margin: 0;">+<span id="LC6389" class="line" lang="c">  <span class="n" style="color: #333;">__pyx_codeobj__32</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">PyObject</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">__Pyx_PyCode_New</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">11</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 class="n" style="color: #333;">__pyx_empty_bytes</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_tuple__31</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_tuple</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_kp_s_home_marcel_scm_cutadapt_<span class="idiff left right">src_cu</span></span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_n_s_iter</span><span class="p">,</span> <span class="mi" style="color: #099;">184</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_empty_bytes</span><span class="p">);</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">__pyx_codeobj__32</span><span class="p">))</span> <span class="n" style="color: #333;">__PYX_ERR</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">184</span><span class="p">,</span> <span class="n" style="color: #333;">__pyx_L1_error</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="6390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6390

</td>

<td class="diff-line-num new_line" data-linenumber="6390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6390

</td>

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

<pre style="margin: 0;"> <span id="LC6390" class="line" lang="c">  <span class="n" style="color: #333;">__Pyx_RefNannyFinishContext</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="6391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6391

</td>

<td class="diff-line-num new_line" data-linenumber="6391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6391

</td>

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

<pre style="margin: 0;"> <span id="LC6391" class="line" lang="c">  <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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6392

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<td class="diff-line-num new_line" data-linenumber="6392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6392

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

<pre style="margin: 0;"> <span id="LC6392" class="line" lang="c">  <span class="nl">__pyx_L1_error:</span><span class="p">;</span></span>

</pre>

</td>

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</table>

<br>

</li>

<li id="4045e163dd270b4b21bcebce419a3b9ab8ffb64e">

<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/de9edc7eabfa7879116d23be04a786ee8cf2964b#4045e163dd270b4b21bcebce419a3b9ab8ffb64e"><strong>src/cutadapt/_version.py</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 12px;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,8 +11,8 @@ version_json = '''</td>

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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="python"><span class="s" style="color: #d14;">{</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">

12

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12

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="s" style="color: #d14;"> "dirty": false,</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

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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">

13

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="s" style="color: #d14;"> "error": null,</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

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<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="python"><span class="s" style="color: #d14;"> "full-revisionid": "<span class="idiff left right">8d0b61222e77973592bd2fb9e2ce57445fccf8dd</span>",</span></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">

15

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<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="LC15" class="line" lang="python"><span class="s" style="color: #d14;"> "version": "1.1<span class="idiff left right">5</span>"</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="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="python"><span class="s" style="color: #d14;"> "full-revisionid": "<span class="idiff left right">77ade52bc2a7fe2d278fdb4256c5b46936011c2c</span>",</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="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">

15

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="s" style="color: #d14;"> "version": "1.1<span class="idiff left right">6</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">

16

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16

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<pre style="margin: 0;"> <span id="LC16" 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="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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17

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="s" style="color: #d14;">'''</span>  <span class="c" style="color: #998; font-style: italic;"># END VERSION_JSON</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">

18

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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">

18

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"></span>

</pre>

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<br>

</li>

<li id="1b86cdea057b59b4d05ba7fde4aea9df4e8fe9e8">

<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/de9edc7eabfa7879116d23be04a786ee8cf2964b#1b86cdea057b59b4d05ba7fde4aea9df4e8fe9e8"><strong>src/cutadapt/pipeline.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold new_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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,6 +4,7 @@ import io</td>

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4

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<td class="diff-line-num new_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

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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;">os</span></span>

</pre>

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5

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<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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<td class="line_content noteable_line" 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;">re</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="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<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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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">copy</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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<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;">logging</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">

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

<pre style="margin: 0;"> <span id="LC9" 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="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;">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>

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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">@@ -262,7 +263,8 @@ class PairedEndPipeline(Pipeline):</td>

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<pre style="margin: 0;"> <span id="LC263" class="line" lang="python"><span class="s" style="color: #d14;">                """</span></span>

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<pre style="margin: 0;"> <span id="LC264" 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="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">modifier</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC265" class="line" lang="python">               <span class="k" style="font-weight: 600;">if</span> <span class="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;">_modify_first_read_only</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;">_modifiers2</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;">modifier</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC266" class="line" lang="python">                       <span class="n" style="color: #333;">modifier2</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="n" style="color: #333;">modifier</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC267" 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;">_modifiers2</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;">modifier2</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC268" 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="LC269" 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;">_should_warn_legacy</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="LC270" class="line" lang="python"></span>

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<br>

</li>

<li id="eeec058d84dee20221538717c0787f27d322dd31">

<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/de9edc7eabfa7879116d23be04a786ee8cf2964b#eeec058d84dee20221538717c0787f27d322dd31"><strong>src/cutadapt/seqio.py</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="882" style="width: 35px; color: rgba(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">@@ -882,7 +882,7 @@ def read_paired_chunks(f, f2, buffer_size=4*1024**2):</td>

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<pre style="margin: 0;"> <span id="LC882" class="line" lang="python">       <span class="n" style="color: #333;">buf1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">bytearray</span><span class="p">(</span><span class="n" style="color: #333;">buffer_size</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC883" class="line" lang="python">       <span class="n" style="color: #333;">buf2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">bytearray</span><span class="p">(</span><span class="n" style="color: #333;">buffer_size</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC884" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC885" class="line" lang="python">       <span class="c" style="color: #998; font-style: italic;"># Read one byte to make sure are processing FASTQ</span></span>

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<pre style="margin: 0;">+<span id="LC885" class="line" lang="python">       <span class="c" style="color: #998; font-style: italic;"># Read one byte to make sure <span class="idiff left right">we </span>are processing FASTQ</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC886" class="line" lang="python">       <span class="n" style="color: #333;">start1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">readinto</span><span class="p">(</span><span class="n" style="color: #333;">memoryview</span><span class="p">(</span><span class="n" style="color: #333;">buf1</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>

</pre>

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887

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<pre style="margin: 0;"> <span id="LC887" class="line" lang="python">       <span class="n" style="color: #333;">start2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">readinto</span><span class="p">(</span><span class="n" style="color: #333;">memoryview</span><span class="p">(</span><span class="n" style="color: #333;">buf2</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

888

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<td class="diff-line-num new_line" data-linenumber="888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

888

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<pre style="margin: 0;"> <span id="LC888" class="line" lang="python">       <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">start1</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">buf1</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">:</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;">b</span><span class="s" style="color: #d14;">'@'</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="n" style="color: #333;">start2</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">buf2</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">:</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;">b</span><span class="s" style="color: #d14;">'@'</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="890" style="width: 35px; color: rgba(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="890" style="width: 35px; color: rgba(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">@@ -890,10 +890,8 @@ def read_paired_chunks(f, f2, buffer_size=4*1024**2):</td>

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<td class="diff-line-num old_line" data-linenumber="890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

890

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<td class="diff-line-num new_line" data-linenumber="890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

890

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

<pre style="margin: 0;"> <span id="LC890" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

891

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<td class="diff-line-num new_line" data-linenumber="891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

891

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<pre style="margin: 0;"> <span id="LC891" class="line" lang="python">       <span class="k" style="font-weight: 600;">while</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

892

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<td class="diff-line-num new_line" data-linenumber="892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

892

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<pre style="margin: 0;"> <span id="LC892" class="line" lang="python">               <span class="n" style="color: #333;">bufend1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">readinto</span><span class="p">(</span><span class="n" style="color: #333;">memoryview</span><span class="p">(</span><span class="n" style="color: #333;">buf1</span><span class="p">)[</span><span class="n" style="color: #333;">start1</span><span class="p">:])</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start1</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="893" 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">

893

</td>

<td class="diff-line-num new_line old" data-linenumber="893" 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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC893" class="line" lang="python">               <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">start1</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bufend1</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="894" 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">

894

</td>

<td class="diff-line-num new_line old" data-linenumber="893" 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="LC894" class="line" lang="python">                       <span class="k" style="font-weight: 600;">break</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

895

</td>

<td class="diff-line-num new_line" data-linenumber="893" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

893

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<pre style="margin: 0;"> <span id="LC893" class="line" lang="python">               <span class="n" style="color: #333;">bufend2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">readinto</span><span class="p">(</span><span class="n" style="color: #333;">memoryview</span><span class="p">(</span><span class="n" style="color: #333;">buf2</span><span class="p">)[</span><span class="n" style="color: #333;">start2</span><span class="p">:])</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start2</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="896" 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">

896

</td>

<td class="diff-line-num new_line old" data-linenumber="894" 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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC896" class="line" lang="python">               <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">start2</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bufend2</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="897" 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="894" 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">

894

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

<pre style="margin: 0;">+<span id="LC894" class="line" lang="python">               <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">start<span class="idiff left">1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bufend1</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">start</span>2</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bufend2</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

897

</td>

<td class="diff-line-num new_line" data-linenumber="895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

895

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

<pre style="margin: 0;"> <span id="LC895" class="line" lang="python">                       <span class="k" style="font-weight: 600;">break</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="898" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

898

</td>

<td class="diff-line-num new_line" data-linenumber="896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

896

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

<pre style="margin: 0;"> <span id="LC896" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

899

</td>

<td class="diff-line-num new_line" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

897

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

<pre style="margin: 0;"> <span id="LC897" class="line" lang="python">               <span class="n" style="color: #333;">end1</span><span class="p">,</span> <span class="n" style="color: #333;">end2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">two_fastq_heads</span><span class="p">(</span><span class="n" style="color: #333;">buf1</span><span class="p">,</span> <span class="n" style="color: #333;">buf2</span><span class="p">,</span> <span class="n" style="color: #333;">bufend1</span><span class="p">,</span> <span class="n" style="color: #333;">bufend2</span><span class="p">)</span></span>

</pre>

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